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Contrib: Added function CalcLigRMSD to calculate RMSD between pre-aligned molecules (#3812)

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* added function and examples

* suggested changes from review

* Add files via upload

Co-authored-by: greg landrum <greg.landrum@gmail.com>
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2021-02-17 20:30:59 +01:00
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#
# Copyright (C) 2021 Carmen Esposito
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import Chem
from rdkit.Chem import rdFMCS
import numpy as np
def CalcLigRMSD(lig1, lig2, rename_lig2 = True, output_filename="tmp.pdb"):
"""
Calculate the Root-mean-square deviation (RMSD) between two prealigned ligands,
even when atom names between the two ligands are not matching.
The symmetry of the molecules is taken into consideration (e.g. tri-methyl groups).
Moreover, if one ligand structure has missing atoms (e.g. undefined electron density in the crystal structure),
the RMSD is calculated for the maximum common substructure (MCS).
Parameters
----------
lig1 : RDKit molecule
lig2 : RDKit molecule
rename_lig2 : bool, optional
True to rename the atoms of lig2 according to the atom names of lig1
output_filename : str, optional
If rename_lig2 is set to True, a PDB file with the renamed lig2 atoms is written as output.
This may be useful to check that the RMSD has been "properly" calculated,
i.e. that the atoms have been properly matched for the calculation of the RMSD.
Returns
-------
rmsd : float
Root-mean-square deviation between the two input molecules
"""
# Exclude hydrogen atoms from the RMSD calculation
lig1 = Chem.RemoveHs(lig1)
lig2 = Chem.RemoveHs(lig2)
# Extract coordinates
coordinates_lig2 = lig2.GetConformer().GetPositions()
coordinates_lig1 = lig1.GetConformer().GetPositions()
# Calculate the RMSD between the MCS of lig1 and lig2 (useful if e.g. the crystal structures has missing atoms)
res=rdFMCS.FindMCS([lig1,lig2])
ref_mol = Chem.MolFromSmarts(res.smartsString)
# Match the ligands to the MCS
# For lig2, the molecular symmetry is considered:
# If 2 atoms are symmetric (3 and 4), two indeces combinations are printed out
# ((0,1,2,3,4), (0,1,2,4,3)) and stored in mas2_list
mas1 = list(lig1.GetSubstructMatch(ref_mol)) # match lig1 to MCS
mas2_list = lig2.GetSubstructMatches(ref_mol, uniquify =False)
# Reorder the coordinates of the ligands and calculate the RMSD between all possible symmetrical atom matches
coordinates_lig1 = coordinates_lig1[mas1]
list_rmsd = []
for match1 in mas2_list:
coordinates_lig2_tmp = coordinates_lig2[list(match1)]
diff = coordinates_lig2_tmp - coordinates_lig1
list_rmsd.append(np.sqrt((diff * diff).sum() / len(coordinates_lig2_tmp))) # rmsd
# Return the minimum RMSD
lig_rmsd = min(list_rmsd)
# Write out a PDB file with matched atom names
if rename_lig2:
mas2 = mas2_list[np.argmin(list_rmsd)]
correspondence_key2_item1 = dict(zip(mas2, mas1))
atom_names_lig1 = [atom1.GetPDBResidueInfo().GetName() for atom1 in lig1.GetAtoms()]
lig1_ResName = lig1.GetAtoms()[0].GetPDBResidueInfo().GetResidueName()
for i, atom1 in enumerate(lig2.GetAtoms()):
atom1.GetPDBResidueInfo().SetResidueName(lig1_ResName)
if i in correspondence_key2_item1.keys():
atom1.GetPDBResidueInfo().SetName(atom_names_lig1[correspondence_key2_item1[i]])
Chem.MolToPDBFile(lig2, output_filename)
return lig_rmsd

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Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb Normal file
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from CalcLigRMSD import *"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# CalcLigRMSD"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"CalcLigRMSD calculates the Root-mean-square deviation (RMSD) between two prealigned molecules. \n",
"\n",
"This jupyter notebook shows examples of how to use the CalcLigRMSD function. \n",
"This function is particularly useful in 2 cases:\n",
"\n",
"1. when the atom names in the compared structures do not match, i.e. when the same atoms present different names in the coordinate files. \n",
"2. when one or both structures have missing atoms. This occurs, for example, in crystallographic structures when some atoms are not well defined in the electron density map.\n",
"\n",
"Below, there are also examples of how to align protein structures and extract ligand coordinates using a python/pymol function. The code below may be used both when the protein structures have multiple chains/domains and when protein structures present multiple copies of the ligand of interest, either in the binding pocket or on the surface."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### How to use the CalcLigRMSD function:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Help on function CalcLigRMSD in module CalcLigRMSD:\n",
"\n",
"CalcLigRMSD(lig1, lig2, rename_lig2=True, output_filename='tmp.pdb')\n",
" Calculate the Root-mean-square deviation (RMSD) between two prealigned ligands, \n",
" even when atom names between the two ligands are not matching.\n",
" The symmetry of the molecules is taken into consideration (e.g. tri-methyl groups). \n",
" Moreover, if one ligand structure has missing atoms (e.g. undefined electron density in the crystal structure), \n",
" the RMSD is calculated for the maximum common substructure (MCS).\n",
" \n",
" Parameters\n",
" ----------\n",
" lig1 : RDKit molecule\n",
" lig2 : RDKit molecule\n",
" rename_lig2 : bool, optional\n",
" True to rename the atoms of lig2 according to the atom names of lig1\n",
" output_filename : str, optional\n",
" If rename_lig2 is set to True, a PDB file with the renamed lig2 atoms is written as output.\n",
" This may be useful to check that the RMSD has been \"properly\" calculated, \n",
" i.e. that the atoms have been properly matched for the calculation of the RMSD.\n",
" \n",
" Returns\n",
" -------\n",
" rmsd : float\n",
" Root-mean-square deviation between the two input molecules\n",
"\n"
]
}
],
"source": [
"help(CalcLigRMSD)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# RMSD between Pre-aligned Ligands with not Matching Atom Names "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Basic Example"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Complex between the kinase protein AURKA and the JVE ligand\n",
"\n",
"Comparison between the crystal structure of JVE (pink, PDB code: 4UZH) and the docked pose of JVE (yellow).\n",
"JVE was docked into the the AURKA structure 2C6E using AutodockVina. "
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 1.66\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/docked_2c6e_JVE_pH74_netcharge1.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/4uzh_JVE.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/JVE_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The atom names in the docked structure and in the crystal structure are different. However, the function is able to match the atoms and calculate the RMSD.\n",
"\n",
"<img src=\"./figures/JVE.png\" width=600>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Examples where symmetry needs to be considered"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Complex between the kinase protein AURKA and the N15 ligand"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 1.49\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/docked_2c6e_N15_pH74_netcharge1.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/3w2c_N15.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/N15_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The N15 ligand contains two symmetric groups (highlighted in the Figure below). The algorithm takes symmetry into consideration: it calculates the RMSD between all possible \"symmetrical\" combinations and returns the minimum RMSD. The structures with matched atom names corresponding to the lowest RMSD are reported in the figure below.\n",
"\n",
"<img src=\"./figures/N15.png\" width=800>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Complex between the kinase protein AURKA and the AKI ligand"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 4.55\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/docked_2c6e_AKI_pH74_netcharge1.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/3m11_AKI.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/AKI_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The AKI ligand contains four symmetric groups (highlighted in the Figure below). Again, the code takes symmetry into consideration!\n",
"\n",
"<img src=\"./figures/AKI.png\" width=800>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Example for a very symmetrical molecule\n",
"\n",
"<img src=\"./figures/BEG.png\" width=300>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"BEG is a very symmetrical molecule (see [this ref](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0362-7)). Not only it does it contain two benzene groups but the entire molecule is symmetrical. We have downloaded the crystal structure 1D4I and extracted the coordinates of the BEG molecule (1d4i_BEG.pdb). In a copy (BEG_test.pdb), we have then renamed the atoms randomly. If the alghoritm is able to correctly match the atoms, then it will return an RMSD of zero. And indeed:"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 0.00\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/BEG_test.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/1d4i_BEG.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = False, output_filename = 'data/AKI_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example where there are missing atoms in the crystal structure"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Two crystal structures are available for the EGFR/1C9 complex. However, the electron density of the 1C9 is not well defined in any of the structures (see figure below). In such cases, one can calculate the RMSD between the docked and crystal structures by excluding the atoms which are not defined in the crystal structure.\n",
"\n",
"This is achived by calculating the RMSD for the maximum common substructure."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 6.47\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/docked_3w2p_1C9_pH74_netcharge1.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/4i23_1C9.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/1C9_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 7.71\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(\"data/docked_3w2p_1C9_pH74_netcharge1.pdb\")\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/4i24_1C9.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/1C9_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<img src=\"./figures/1C9.png\" width=800>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"In this figure, the missing groups are highlighted in green in the docked pose while the truncation point in the crystal structure is highlighted in red."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Align docking and crystal structures prior to the RMSD calculation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The function above takes as input pre-aligned ligand structures. In this section, we show how one could align crystallographic protein-ligand structure to the docked structure and extract the ligand coordinates from the crystal structure using Pymol. "
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"from pymol import cmd"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 1. Load the crystallographic and docked protein-ligand structures in pymol\n",
"\n",
"Docking programs often return as output only the coordinates of the docked ligand.\n",
"Therefore, in order to be able to perform the protein alignment,\n",
"we first need to load both the protein structure used for docking and the docked ligand structure in pymol\n",
"and merge the coordinates in a temporary PDB file, complex.pdb\n",
"\n",
"\n",
"Input files:\n",
"- `docked_lig_file` : name of file containing the coordinates of the docked ligand\n",
"- `protein_file` : name of file containing the the protein structure used for docking\n",
"- `crystal_file`: name of file containing the crystal structure of the complex"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# Function to merge the ligand and protein PDB files in a unique PDB file \n",
"def merge_prot_lig_pdbs(protein_file, docked_lig_file, output_file = 'complex.pdb'):\n",
" cmd.reinitialize()\n",
" cmd.load(protein_file, 'protein')\n",
" cmd.load(docked_lig_file, 'docked_lig')\n",
" cmd.save(output_file, \"protein or docked_lig\")\n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" PyMOL not running, entering library mode (experimental)\n"
]
}
],
"source": [
"docked_lig_file = \"data/docked_2c6e_SKE_pH74_netcharge1.pdb\"\n",
"protein_file = \"data/aurka_protein_2c6e.pdb\"\n",
"crystal_file = \"data/5dt0.pdb\"\n",
"\n",
"merge_prot_lig_pdbs(protein_file, docked_lig_file)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can reinitialize Pymol and load both the docked and crystal complexes in Pymol. The step above can be skipped if the docked complex is directly available."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"# load both the docked and crystallographic protein-ligand structures \n",
"cmd.reinitialize()\n",
"cmd.load(\"complex.pdb\", \"docked\")\n",
"cmd.load(crystal_file, \"crystal\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 2. Proteins Alignment"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Simple Example"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Align the proteins on the backbone alpha carbons and extract the coordinates of the ligand from the crystal structure:\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"# align the protein structures on the CA \n",
"cmd.align(\"crystal and name CA\", \"docked and name CA\")\n",
"\n",
"# save the coordinates of the ligand in a PDB file\n",
"cmd.save(\"data/lig_crystal_aligned.pdb\", \"crystal and resn SKE\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now, you can calculate the RMSD:"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 8.21\n"
]
}
],
"source": [
"docked_ligand = Chem.MolFromPDBFile(docked_lig_file)\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/lig_crystal_aligned.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/1C9_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Alignment for Structures with Multiple Chains/Domains and Different/Multiple Ligands"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The structure alignment and ligand extraction becomes more complicated for crystal structures that contain dimers, or higher oligomers, multi-protein complexes, multiple and different ligands!\n",
"In these case, the code below can be used. It reads as input the crystallographic and docked structures.\n",
"The function does the following:\n",
"\n",
" - check for the presence of organic molecules in the crystal structure.\n",
" - check for the presence of organic molecules in each of the chains\n",
" - if a chain contains an organic molecule, then that chain is aligned to the docked structure based on the C-alpha backbone atoms.\n",
" - calculate the distance between the organic molecule in the aligned crystal structure and the organic molecule in the aligned docked structure.\n",
" - if the distance is lower than a given threshold (max_dist), the coordinates of the organic molecule from the aligned crystal structure are stored in a PDB file.\n"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"from pymol import stored\n",
"import numpy as np \n",
"\n",
"def find_organic_ligs(obj_name):\n",
" cmd.select(f\"ligs\", f\"{obj_name} and organic\")\n",
" stored.residues = set()\n",
" cmd.iterate(f\"ligs\", 'stored.residues.add(resn)')\n",
" ligs_resname = list(stored.residues)\n",
" return list(set(ligs_resname) - set(['ACE', 'NME']))\n",
"\n",
"\n",
"def extract_lig_from_aligned_crystal(crystal_file, docked_file, max_dist = 7):\n",
" count = 0\n",
" # load structures\n",
" cmd.reinitialize()\n",
" cmd.load(docked_file, \"docked\")\n",
" cmd.load(crystal_file, \"crystal\")\n",
" # identify organic molecules in both the docked and crystal structures\n",
" lig_docked_name = find_organic_ligs('docked')[0]\n",
" lig_crystal_names = find_organic_ligs('crystal')\n",
" # check the number of chains in the crystal structure\n",
" chains = cmd.get_chains(\"crystal\")\n",
" print(f\"The crystal structure {crystal_file} contains {len(chains)} chains and {len(lig_crystal_names)} ligands {lig_crystal_names}\")\n",
" # loop over the organic molecules\n",
" for lig_crystal_name in lig_crystal_names:\n",
" print(f\"\\n{lig_crystal_name}\")\n",
" # loop over the chains\n",
" for chain in chains:\n",
" sel = cmd.select(f\"ligs{chain}\", f\"crystal and chain {chain} and resn {lig_crystal_name}\")\n",
" if sel == 0:\n",
" continue\n",
" else:\n",
" cmd.align(f\"crystal and chain {chain} and name CA\", \"docked and name CA\")\n",
" cmd.save(\"data/crystal_aligned.pdb\", \"crystal\")\n",
" cmd.select(f\"ligs{chain}\", f\"crystal and chain {chain} and resn {lig_crystal_name}\")\n",
" stored.residues = set()\n",
" cmd.iterate(f\"ligs{chain}\", 'stored.residues.add(resv)')\n",
" lig_res = list(stored.residues)\n",
" # measure the distance between the center of mass of the ligands in docked and crystal structures.\n",
" center2 = cmd.centerofmass(f\"docked and resn {lig_docked_name}\")\n",
" # there may be multiple ligand copies in the crystal structure. Loop over them.\n",
" for lig1 in lig_res:\n",
" center1 = cmd.centerofmass(f\"crystal and chain {chain} and resi {lig1}\")\n",
" # calculate distance\n",
" dist = np.linalg.norm(np.array(center1)-np.array(center2)) \n",
" # if the distance is lower than the threshold, the ligand is in the binding pocket.\n",
" # Therefore, the coordinates of this crystal ligand are written out in a PDB file\n",
" if dist < max_dist:\n",
" count += 1\n",
" cmd.save(f\"data/{lig_crystal_name}_crystal_aligned_{count}.pdb\", f\"crystal and chain {chain} and resi {lig1}\")\n",
" print(f\"The coordinates of {lig_crystal_name} extracted from the crystal structure and chain {chain} are stored in data/{lig_crystal_name}_crystal_aligned_{count}.pdb\")\n",
" else:\n",
" print(f\"PDB {crystal_file} cmpd {lig_crystal_name} res {lig1} is out of the binding pocket\")\n",
" \n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Example where the crystal structure contains multiple chains\n",
"\n",
"The PDB structure 6C83 contains four protein chains, two of the target of interest AURKA and two of another protein.\n",
"The two monomers of AURKA, both contain the compound of interest in the binding pocket. The other two proteins do not contain any organic molecule.\n",
"\n",
"In this case, we can use the function described above to perform the protein alignment and extract the coordinates of the ligand. As both monomers contain the ligand, two PDB files will be outputted.\n",
"\n",
"<img src=\"./figures/6c83_complex.png\" width=400>"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"# merge protein and docked ligand\n",
"docked_lig_file = \"data/docked_2c6e_ACP_pH74_netcharge1.pdb\"\n",
"protein_file = \"data/aurka_protein_2c6e.pdb\"\n",
"crystal_file = \"data/6c83.pdb\"\n",
"\n",
"merge_prot_lig_pdbs(protein_file, docked_lig_file)\n"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The crystal structure data/6c83.pdb contains 4 chains and 1 ligands ['ACP']\n",
"\n",
"ACP\n",
"The coordinates of ACP extracted from the crystal structure and chain A are stored in data/ACP_crystal_aligned_1.pdb\n",
"The coordinates of ACP extracted from the crystal structure and chain B are stored in data/ACP_crystal_aligned_2.pdb\n"
]
}
],
"source": [
"# extract the coordinated of the ligand from the crystal structure\n",
"extract_lig_from_aligned_crystal(crystal_file, \"complex.pdb\", max_dist = 7)\n"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 3.82\n"
]
}
],
"source": [
"# Calculate RMSD for ACP extracted from chain A:\n",
"docked_ligand = Chem.MolFromPDBFile(docked_lig_file)\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/ACP_crystal_aligned_1.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/ACP_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 3.02\n"
]
}
],
"source": [
"# Calculate RMSD for ACP extracted from chain B:\n",
"docked_ligand = Chem.MolFromPDBFile(docked_lig_file)\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/ACP_crystal_aligned_2.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/ACP_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Example where the crystal structure contains different ligands\n",
"\n",
"The PDB structure 5DPV of AURKA contains two different ligands, 5DN and SKE. Tthe figure below shows that SKE (blue) is located in the binding pocket while 5DN (orange) lies on the surface of the protein. \n",
"\n",
"It occurs very often that a crystal structure contains different ligands or multiple copies of the same ligand. It is important to extract only the coordinates of the ligand located in the binding pocket, corresponding to the ligand of interest.\n",
"\n",
"The function described above checks the location of the ligand before extracting the coordinates. And this is achived by measuring the distance between the center of mass of the ligand in the docked structure (assuming that it is located in the binding pocket) and that of the ligand in the crystal structure. \n",
"\n",
"<img src=\"./figures/5dpv_complex.png\" width=300>"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"docked_lig_file = \"data/docked_2c6e_SKE_pH74_netcharge1.pdb\"\n",
"protein_file = \"data/aurka_protein_2c6e.pdb\"\n",
"crystal_file = \"data/5dpv.pdb\"\n",
"\n",
"merge_prot_lig_pdbs(protein_file, docked_lig_file)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The crystal structure data/5dpv.pdb contains 1 chains and 2 ligands ['SKE', '5DN']\n",
"\n",
"SKE\n",
"The coordinates of SKE extracted from the crystal structure and chain A are stored in data/SKE_crystal_aligned_1.pdb\n",
"\n",
"5DN\n",
"PDB data/5dpv.pdb cmpd 5DN res 401 is out of the binding pocket\n"
]
}
],
"source": [
"extract_lig_from_aligned_crystal(crystal_file, \"complex.pdb\", max_dist = 7)"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RMSD: 8.17\n"
]
}
],
"source": [
"# Calculare RMSD:\n",
"docked_ligand = Chem.MolFromPDBFile(docked_lig_file)\n",
"crystal_ligand = Chem.MolFromPDBFile(\"data/SKE_crystal_aligned_1.pdb\")\n",
"rmsd2 = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/SKE_renamed.pdb')\n",
"print(f\"RMSD: {rmsd2:.2f}\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

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# CalcLigRMSD: Calculate RMSD between prealigned molecules
`CalcLigRMSD` calculates the Root-mean-square deviation (RMSD) between two prealigned molecules.
To evaluate the goodness of docking programs, docked protein-ligand structures are compared to the corresponding crystallographic complexes.
First, the protein structure is aligned based on the backbone atoms. Then, the RMSD between the docked and crystal ligands is calculated.
However, two problems may arise in the RMSD calculation, which are dealt with the `CalcLigRMSD` function:
1. the atom names in the compared structures do not match, i.e. the same atoms present different names in the two coordinate files. In this case, we cannot rely on the atom names for the RMSD caculation and we need to first identify equivalent atoms. This "matching" problem is particularly challenging when the molecule of interest contains symmetrical chemical groups or when the entire molecule is symmetrical. In this case, the symmetry of the mocule needs to be taked into account. For example for a tri-methyl group, there are 6 possible symmetrical combinations:
(C1, C2, C3), (C1, C3, C2), (C2, C1, C3), (C2, C3, C1), (C3, C1, C2), (C3, C2, C1). The `CalcLigRMSD` function takes symmetry into consideration (using rdkit functions) by calculating the RMSD with all possible "symmetrical" combinations and returns the minimum RMSD. You can see examples in the attached jupyter notebook Examples_CalcLigRMSD.ipynb.
2. one or both structures have missing atoms. This occurs, for example, in crystallographic structures when some atoms are not well defined in the electron density map. In this case, the `CalcLigRMSD` returns the RMSD for the maximum common substructure (MCS). You can see examples in the attached jupyter notebook Examples_CalcLigRMSD.ipynb.
### Dependencies
- rdkit
- numpy
### Usage
```
CalcLigRMSD(lig1, lig2, rename_lig2=True, output_filename='tmp.pdb')
Parameters
----------
lig1 : RDKit molecule
lig2 : RDKit molecule
rename_lig2 : bool, optional
True to rename the atoms of lig2 according to the atom names of lig1
output_filename : str, optional
If rename_lig2 is set to True, a PDB file with the renamed lig2 atoms is written as output.
This may be useful to check that the RMSD has been "properly" calculated,
i.e. that the atoms have been properly matched for the calculation of the RMSD.
Returns
-------
rmsd : float
Root-mean-square deviation between the two input molecules
```
### Example
```
from CalcLigRMSD import *
# load ligand pre-aligned coordinates
docked_ligand = Chem.rdmolfiles.MolFromPDBFile("data/docked_2c6e_JVE_pH74_netcharge1.pdb")
crystal_ligand = Chem.rdmolfiles.MolFromPDBFile("data/4uzh_JVE.pdb")
# calculate RMSD
ligs_rmsd = CalcLigRMSD(docked_ligand, crystal_ligand, rename_lig2 = True, output_filename = 'data/JVE_renamed.pdb')
print(f"RMSD: {ligs_rmsd:.2f}")
>> RMSD: 1.66
```
### Examples_CalcLigRMSD.ipynb
This jupyter notebook shows examples of how to use the `CalcLigRMSD` function.
In addition, it contains a python/pymol function that can be used to align protein structures and extract (pre-aligned) ligand coordinates.
### Acknowledgements
This work was conducted by Carmen Esposito as a member of the [Riniker lab](https://github.com/rinikerlab) at ETH Zurich.
### References
1. Velázquez-Libera, José Luis, et al. "LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking." Bioinformatics 36.9 (2020): 2912-2914. [Link](https://academic.oup.com/bioinformatics/article/36/9/2912/5700716?login=true)
2. Bell, Eric W., and Yang Zhang. "DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism." Journal of cheminformatics 11.1 (2019): 1-9. [Link](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0362-7)

48
Contrib/CalcLigRMSD/data/1C9_renamed.pdb Normal file
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HETATM 1 C7 LIG A 401 1.488 7.044 32.935 1.00 46.39 C
HETATM 2 N5 LIG A 401 2.835 7.154 33.072 1.00 41.54 N
HETATM 3 O2 LIG A 401 -6.931 4.694 29.366 1.00 63.10 O
HETATM 4 C8 LIG A 401 -0.389 6.180 32.539 1.00 46.08 C
HETATM 5 N1 LIG A 401 0.887 5.836 32.854 1.00 44.73 N
HETATM 6 O1 LIG A 401 -7.233 6.869 29.971 1.00 55.97 O
HETATM 7 C9 LIG A 401 -2.661 5.392 31.980 1.00 49.24 C
HETATM 8 N3 LIG A 401 -1.398 5.261 32.491 1.00 50.33 N
HETATM 9 O LIG A 401 2.003 9.847 32.711 1.00 57.98 O
HETATM 10 C14 LIG A 401 -3.390 4.210 31.742 1.00 48.24 C
HETATM 11 N4 LIG A 401 -7.888 5.165 31.608 1.00 63.28 N
HETATM 12 C13 LIG A 401 -4.712 4.290 31.271 1.00 46.59 C
HETATM 13 N2 LIG A 401 -0.598 7.496 32.384 1.00 46.80 N
HETATM 14 C12 LIG A 401 -5.342 5.536 31.046 1.00 53.17 C
HETATM 15 N LIG A 401 0.699 8.008 32.456 1.00 49.69 N
HETATM 16 C11 LIG A 401 -4.594 6.711 31.255 1.00 51.47 C
HETATM 17 C10 LIG A 401 -3.281 6.638 31.735 1.00 48.76 C
HETATM 18 C6 LIG A 401 0.892 9.376 32.550 1.00 52.86 C
HETATM 19 C3 LIG A 401 -0.295 10.306 32.501 1.00 51.73 C
HETATM 20 C4 LIG A 401 -1.140 10.319 31.383 1.00 50.46 C
HETATM 21 C5 LIG A 401 -2.272 11.129 31.323 1.00 50.35 C
HETATM 22 C LIG A 401 -2.544 11.971 32.406 1.00 52.34 C
HETATM 23 C1 LIG A 401 -1.735 11.942 33.550 1.00 51.66 C
HETATM 24 C2 LIG A 401 -0.594 11.130 33.596 1.00 53.33 C
HETATM 25 F LIG A 401 -0.852 9.565 30.327 1.00 51.73 F
HETATM 26 F1 LIG A 401 0.181 11.144 34.710 1.00 51.81 F
HETATM 27 S LIG A 401 -6.870 5.596 30.471 1.00 59.71 S
CONECT 1 2 5 15
CONECT 3 27
CONECT 4 5 8 13
CONECT 6 27
CONECT 7 8 10 17
CONECT 9 18
CONECT 10 12
CONECT 11 27
CONECT 12 14
CONECT 13 15
CONECT 14 16 27
CONECT 15 18
CONECT 16 17
CONECT 18 19
CONECT 19 20 24
CONECT 20 21 25
CONECT 21 22
CONECT 22 23
CONECT 23 24
CONECT 24 26
END

49
Contrib/CalcLigRMSD/data/1d4i_BEG.pdb Normal file
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HETATM 1519 C01 BEG A 501 9.764 24.084 2.234 1.00 16.71 C
HETATM 1520 C02 BEG A 501 9.044 25.251 1.867 1.00 17.16 C
HETATM 1521 C03 BEG A 501 7.641 25.363 2.003 1.00 18.56 C
HETATM 1522 C04 BEG A 501 6.904 24.272 2.523 1.00 17.81 C
HETATM 1523 C05 BEG A 501 7.585 23.088 2.893 1.00 17.98 C
HETATM 1524 C06 BEG A 501 8.994 22.996 2.747 1.00 17.88 C
HETATM 1525 C07 BEG A 501 16.298 22.149 8.773 1.00 19.56 C
HETATM 1526 C08 BEG A 501 15.570 21.130 9.459 1.00 20.75 C
HETATM 1527 C09 BEG A 501 16.175 19.934 9.922 1.00 20.57 C
HETATM 1528 C10 BEG A 501 17.561 19.729 9.711 1.00 20.37 C
HETATM 1529 C11 BEG A 501 18.315 20.725 9.045 1.00 20.47 C
HETATM 1530 C12 BEG A 501 17.690 21.914 8.586 1.00 20.23 C
HETATM 1531 C13 BEG A 501 15.560 23.358 8.195 1.00 19.50 C
HETATM 1532 O14 BEG A 501 14.526 23.015 7.272 1.00 18.69 O
HETATM 1533 C23 BEG A 501 11.287 24.077 2.148 1.00 17.57 C
HETATM 1534 O22 BEG A 501 11.920 23.554 3.313 1.00 17.43 O
HETATM 1535 C15 BEG A 501 15.031 22.699 5.968 1.00 16.68 C
HETATM 1536 C16 BEG A 501 13.991 23.019 4.924 1.00 17.37 C
HETATM 1537 C17 BEG A 501 13.502 24.425 5.006 1.00 17.54 C
HETATM 1538 O24 BEG A 501 14.483 25.178 4.305 1.00 17.08 O
HETATM 1539 C18 BEG A 501 12.117 24.538 4.353 1.00 16.43 C
HETATM 1540 C19 BEG A 501 10.944 24.485 5.324 1.00 15.74 C
HETATM 1541 O20 BEG A 501 10.696 23.492 6.004 1.00 15.85 O
HETATM 1542 N21 BEG A 501 10.140 25.606 5.373 1.00 13.93 N
HETATM 1543 C25 BEG A 501 15.140 21.202 5.836 1.00 15.73 C
HETATM 1544 O26 BEG A 501 14.193 20.464 6.087 1.00 16.50 O
HETATM 1545 N27 BEG A 501 16.358 20.692 5.436 1.00 13.98 N
HETATM 1546 C28 BEG A 501 16.620 19.277 5.261 1.00 13.60 C
HETATM 1547 C29 BEG A 501 16.571 18.847 3.820 1.00 14.30 C
HETATM 1548 C30 BEG A 501 17.534 17.849 3.551 1.00 14.91 C
HETATM 1549 C31 BEG A 501 15.732 19.314 2.777 1.00 14.61 C
HETATM 1550 C32 BEG A 501 15.863 18.764 1.468 1.00 15.46 C
HETATM 1551 C33 BEG A 501 16.833 17.755 1.212 1.00 15.55 C
HETATM 1552 C34 BEG A 501 18.018 18.781 5.673 1.00 13.85 C
HETATM 1553 O35 BEG A 501 18.937 19.823 5.379 1.00 13.10 O
HETATM 1554 C36 BEG A 501 17.679 17.289 2.256 1.00 15.32 C
HETATM 1555 C37 BEG A 501 18.309 17.538 4.794 1.00 14.18 C
HETATM 1556 C38 BEG A 501 8.968 25.778 6.216 1.00 14.18 C
HETATM 1557 C39 BEG A 501 9.256 26.507 7.503 1.00 14.71 C
HETATM 1558 C40 BEG A 501 8.181 27.361 7.860 1.00 15.26 C
HETATM 1559 C41 BEG A 501 10.408 26.446 8.332 1.00 15.21 C
HETATM 1560 C42 BEG A 501 10.467 27.240 9.518 1.00 16.49 C
HETATM 1561 C43 BEG A 501 9.377 28.089 9.863 1.00 16.60 C
HETATM 1562 C44 BEG A 501 7.849 26.663 5.625 1.00 14.38 C
HETATM 1563 O45 BEG A 501 8.482 27.684 4.868 1.00 12.28 O
HETATM 1564 C46 BEG A 501 8.224 28.156 9.035 1.00 16.17 C
HETATM 1565 C47 BEG A 501 7.093 27.273 6.832 1.00 14.54 C
END

81
Contrib/CalcLigRMSD/data/3m11_AKI.pdb Normal file
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HETATM 1 CAA AKI A 1 -4.318 10.286 31.606 1.00 49.28 C
HETATM 2 CAB AKI A 1 -3.574 9.160 31.940 1.00 50.62 C
HETATM 3 CAC AKI A 1 -2.383 8.892 31.275 1.00 50.85 C
HETATM 4 CAD AKI A 1 -1.936 9.749 30.277 1.00 50.53 C
HETATM 5 CAE AKI A 1 -2.681 10.875 29.942 1.00 48.75 C
HETATM 6 CAF AKI A 1 -3.872 11.143 30.608 1.00 48.39 C
HETATM 7 CAG AKI A 1 -1.639 7.766 31.609 1.00 51.06 C
HETATM 8 CAH AKI A 1 -2.089 6.458 31.592 1.00 50.47 C
HETATM 9 CAL AKI A 1 -3.368 6.048 31.236 1.00 50.37 C
HETATM 10 CAM AKI A 1 -4.245 6.945 30.639 1.00 48.95 C
HETATM 11 CAN AKI A 1 -5.525 6.533 30.284 1.00 47.24 C
HETATM 12 CAO AKI A 1 -5.926 5.226 30.526 1.00 46.94 C
HETATM 13 CAP AKI A 1 -5.049 4.328 31.122 1.00 44.98 C
HETATM 14 CAQ AKI A 1 -3.770 4.738 31.478 1.00 48.36 C
HETATM 15 CAV AKI A 1 1.373 11.051 32.209 1.00 53.10 C
HETATM 16 CAW AKI A 1 1.352 11.519 33.665 1.00 57.01 C
HETATM 17 CAX AKI A 1 2.362 12.646 33.894 1.00 59.68 C
HETATM 18 CAY AKI A 1 3.724 12.394 33.777 1.00 61.91 C
HETATM 19 CAZ AKI A 1 4.640 13.418 33.985 1.00 63.98 C
HETATM 20 OAI AKI A 1 -1.069 5.636 31.982 1.00 51.79 O
HETATM 21 CBA AKI A 1 4.196 14.693 34.309 1.00 64.22 C
HETATM 22 CBB AKI A 1 2.834 14.946 34.426 1.00 63.53 C
HETATM 23 CBC AKI A 1 1.917 13.923 34.219 1.00 61.40 C
HETATM 24 CBE AKI A 1 5.096 16.723 33.691 1.00 69.52 C
HETATM 25 CBG AKI A 1 6.081 18.740 33.178 1.00 74.91 C
HETATM 26 CBH AKI A 1 6.497 19.953 33.717 1.00 75.89 C
HETATM 27 CBI AKI A 1 6.582 21.080 32.908 1.00 75.73 C
HETATM 28 CBJ AKI A 1 6.251 20.995 31.560 1.00 75.71 C
HETATM 29 CBK AKI A 1 5.836 19.783 31.021 1.00 76.87 C
HETATM 30 CBL AKI A 1 5.752 18.656 31.831 1.00 76.42 C
HETATM 31 NBD AKI A 1 5.073 15.674 34.508 1.00 67.56 N
HETATM 32 NBF AKI A 1 6.000 17.663 33.953 1.00 72.60 N
HETATM 33 NBN AKI A 1 0.345 10.019 32.010 1.00 52.09 N
HETATM 34 OBM AKI A 1 4.319 16.820 32.742 1.00 69.50 O
HETATM 35 N1 AKI A 1 1.270 6.142 32.655 1.00 50.81 N
HETATM 36 C2 AKI A 1 2.158 7.106 32.839 1.00 50.39 C
HETATM 37 N3 AKI A 1 1.863 8.379 32.630 1.00 51.12 N
HETATM 38 C4 AKI A 1 0.639 8.739 32.220 1.00 51.03 C
HETATM 39 C5 AKI A 1 -0.315 7.754 32.017 1.00 51.11 C
HETATM 40 C6 AKI A 1 0.026 6.427 32.246 1.00 51.70 C
CONECT 1 2 6
CONECT 2 1 3
CONECT 3 2 4 7
CONECT 4 3 5
CONECT 5 4 6
CONECT 6 1 5
CONECT 7 3 8 39
CONECT 8 7 9 20
CONECT 9 8 10 14
CONECT 10 9 11
CONECT 11 10 12
CONECT 12 11 13
CONECT 13 12 14
CONECT 14 9 13
CONECT 15 16 33
CONECT 16 15 17
CONECT 17 16 18 23
CONECT 18 17 19
CONECT 19 18 21
CONECT 20 8 40
CONECT 21 19 22 31
CONECT 22 21 23
CONECT 23 17 22
CONECT 24 32 34 31
CONECT 25 26 30 32
CONECT 26 25 27
CONECT 27 26 28
CONECT 28 27 29
CONECT 29 28 30
CONECT 30 25 29
CONECT 31 21 24
CONECT 32 24 25
CONECT 33 15 38
CONECT 34 24
CONECT 35 36 40
CONECT 36 35 37
CONECT 37 36 38
CONECT 38 37 33 39
CONECT 39 38 7 40
CONECT 40 35 39 20
END

65
Contrib/CalcLigRMSD/data/3w2c_N15.pdb Normal file
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HETATM 1 N N15 A 401 4.149 12.998 33.333 1.00 44.90 N
HETATM 2 CA N15 A 401 4.977 14.161 33.415 1.00 46.23 C
HETATM 3 CAA N15 A 401 9.897 15.441 36.239 1.00 57.65 C
HETATM 4 CAB N15 A 401 11.551 15.449 34.421 1.00 56.31 C
HETATM 5 CAD N15 A 401 -5.532 5.836 30.671 1.00 30.00 C
HETATM 6 CAE N15 A 401 -5.169 4.490 30.897 1.00 30.51 C
HETATM 7 CAF N15 A 401 0.760 10.526 32.426 1.00 35.13 C
HETATM 8 CAG N15 A 401 -4.585 6.842 30.899 1.00 29.52 C
HETATM 9 CAH N15 A 401 -3.857 4.231 31.373 1.00 29.13 C
HETATM 10 CAI N15 A 401 -0.057 9.397 32.229 1.00 35.80 C
HETATM 11 CAJ N15 A 401 3.751 11.145 34.170 1.00 44.29 C
HETATM 12 CAK N15 A 401 2.490 8.972 33.044 1.00 36.35 C
HETATM 13 CAL N15 A 401 3.187 12.473 32.549 1.00 44.30 C
HETATM 14 CAM N15 A 401 8.487 13.062 34.480 1.00 48.16 C
HETATM 15 CAN N15 A 401 9.344 14.265 34.066 1.00 51.39 C
HETATM 16 CAW N15 A 401 2.076 10.294 32.827 1.00 38.41 C
HETATM 17 CAX N15 A 401 2.953 11.272 33.104 1.00 43.16 C
HETATM 18 CAY N15 A 401 -1.309 6.516 31.994 1.00 33.89 C
HETATM 19 CAZ N15 A 401 -0.079 6.916 32.360 1.00 35.12 C
HETATM 20 C N15 A 401 6.428 13.629 33.325 1.00 47.33 C
HETATM 21 O N15 A 401 6.907 13.243 32.250 1.00 47.93 O
HETATM 22 NAP N15 A 401 4.486 12.239 34.251 1.00 44.60 N
HETATM 23 NAQ N15 A 401 0.881 6.050 32.700 1.00 36.09 N
HETATM 24 NAR N15 A 401 -2.310 7.298 31.617 1.00 33.12 N
HETATM 25 NAS N15 A 401 7.088 13.512 34.474 1.00 47.03 N
HETATM 26 NAT N15 A 401 1.830 6.629 32.963 1.00 36.82 N
HETATM 27 NAU N15 A 401 -1.734 5.250 31.988 1.00 31.71 N
HETATM 28 CBA N15 A 401 -3.356 6.513 31.341 1.00 29.45 C
HETATM 29 CBB N15 A 401 -3.001 5.246 31.567 1.00 27.92 C
HETATM 30 CBC N15 A 401 1.656 7.950 32.843 1.00 35.69 C
HETATM 31 CBD N15 A 401 0.408 8.153 32.437 1.00 34.80 C
HETATM 32 CBE N15 A 401 10.447 14.608 35.084 1.00 54.34 C
CONECT 1 13 22 2
CONECT 2 1 20
CONECT 3 32
CONECT 4 32
CONECT 5 8 6
CONECT 6 5 9
CONECT 7 10 16
CONECT 8 5 28
CONECT 9 6 29
CONECT 10 7 31
CONECT 11 17 22
CONECT 12 30 16
CONECT 13 1 17
CONECT 14 25 15
CONECT 15 14 32
CONECT 16 7 12 17
CONECT 17 11 13 16
CONECT 18 24 27 19
CONECT 19 18 23 31
CONECT 20 2 21 25
CONECT 21 20
CONECT 22 1 11
CONECT 23 19 26
CONECT 24 18 28
CONECT 25 14 20
CONECT 26 23 30
CONECT 27 18 29
CONECT 28 8 24 29
CONECT 29 27 9 28
CONECT 30 12 26 31
CONECT 31 10 19 30
CONECT 32 3 4 15
END

45
Contrib/CalcLigRMSD/data/4i23_1C9.pdb Normal file
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@@ -0,0 +1,45 @@
HETATM 1 CL 1C9 A9001 6.542 10.953 31.718 1.00 89.26 CL
HETATM 2 C1 1C9 A9001 -2.403 9.519 31.631 1.00 83.47 C
HETATM 3 C2 1C9 A9001 -2.596 8.098 31.626 1.00 83.68 C
HETATM 4 C3 1C9 A9001 -1.546 7.233 32.079 1.00 82.47 C
HETATM 5 C4 1C9 A9001 -0.315 7.723 32.536 1.00 82.50 C
HETATM 6 C5 1C9 A9001 -0.097 9.152 32.546 1.00 84.12 C
HETATM 7 C6 1C9 A9001 -1.155 10.030 32.089 1.00 83.53 C
HETATM 8 N7 1C9 A9001 0.621 6.826 32.948 1.00 81.78 N
HETATM 9 C8 1C9 A9001 1.804 7.322 33.390 1.00 83.59 C
HETATM 10 N9 1C9 A9001 2.140 8.633 33.454 1.00 84.30 N
HETATM 11 C10 1C9 A9001 1.194 9.562 33.033 1.00 85.59 C
HETATM 12 O11 1C9 A9001 -3.838 7.668 31.167 1.00 85.44 O
HETATM 13 C12 1C9 A9001 -3.908 6.408 30.489 1.00 84.41 C
HETATM 14 N13 1C9 A9001 -3.415 10.406 31.194 1.00 82.67 N
HETATM 15 N14 1C9 A9001 1.519 10.964 33.085 1.00 86.44 N
HETATM 16 C15 1C9 A9001 2.816 11.531 33.228 1.00 87.38 C
HETATM 17 C16 1C9 A9001 3.937 11.034 32.486 1.00 88.13 C
HETATM 18 C17 1C9 A9001 5.225 11.597 32.638 1.00 88.88 C
HETATM 19 C18 1C9 A9001 5.412 12.674 33.545 1.00 88.55 C
HETATM 20 C19 1C9 A9001 4.318 13.192 34.295 1.00 87.62 C
HETATM 21 C20 1C9 A9001 3.024 12.621 34.139 1.00 87.82 C
HETATM 22 F21 1C9 A9001 6.630 13.219 33.704 1.00 88.92 F
CONECT 1 18
CONECT 2 3 7 14
CONECT 3 2 4 12
CONECT 4 3 5
CONECT 5 4 6 8
CONECT 6 5 7 11
CONECT 7 2 6
CONECT 8 5 9
CONECT 9 8 10
CONECT 10 9 11
CONECT 11 6 10 15
CONECT 12 3 13
CONECT 13 12
CONECT 14 2
CONECT 15 11 16
CONECT 16 15 17 21
CONECT 17 16 18
CONECT 18 17 1 19
CONECT 19 18 20 22
CONECT 20 19 21
CONECT 21 16 20
CONECT 22 19
END

57
Contrib/CalcLigRMSD/data/4i24_1C9.pdb Normal file
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@@ -0,0 +1,57 @@
HETATM 1 CL 1C9 A9001 6.080 12.253 31.916 1.00 31.70 CL
HETATM 2 C1 1C9 A9001 -2.554 10.289 32.410 1.00 30.38 C
HETATM 3 C2 1C9 A9001 -2.668 8.915 32.008 1.00 29.65 C
HETATM 4 C3 1C9 A9001 -1.523 8.063 32.126 1.00 28.21 C
HETATM 5 C4 1C9 A9001 -0.290 8.534 32.621 1.00 27.21 C
HETATM 6 C5 1C9 A9001 -0.172 9.918 33.010 1.00 26.27 C
HETATM 7 C6 1C9 A9001 -1.310 10.774 32.899 1.00 29.22 C
HETATM 8 N7 1C9 A9001 0.742 7.659 32.710 1.00 25.99 N
HETATM 9 C8 1C9 A9001 1.910 8.139 33.185 1.00 24.59 C
HETATM 10 N9 1C9 A9001 2.147 9.411 33.572 1.00 25.70 N
HETATM 11 C10 1C9 A9001 1.108 10.315 33.488 1.00 27.48 C
HETATM 12 O11 1C9 A9001 -3.920 8.539 31.531 1.00 31.09 O
HETATM 13 C12 1C9 A9001 -4.145 7.197 31.091 1.00 29.66 C
HETATM 14 N13 1C9 A9001 -3.715 11.107 32.316 1.00 34.61 N
HETATM 15 N14 1C9 A9001 1.327 11.672 33.885 1.00 23.22 N
HETATM 16 C15 1C9 A9001 2.565 12.364 33.899 1.00 24.25 C
HETATM 17 C16 1C9 A9001 3.627 12.030 32.998 1.00 25.06 C
HETATM 18 C17 1C9 A9001 4.850 12.718 33.028 1.00 28.28 C
HETATM 19 C18 1C9 A9001 5.049 13.763 33.961 1.00 25.55 C
HETATM 20 C19 1C9 A9001 4.018 14.120 34.867 1.00 24.70 C
HETATM 21 C20 1C9 A9001 2.779 13.421 34.834 1.00 24.32 C
HETATM 22 C23 1C9 A9001 -6.017 13.373 34.295 1.00 34.93 C
HETATM 23 C24 1C9 A9001 -5.468 12.600 33.084 1.00 35.38 C
HETATM 24 C25 1C9 A9001 -7.140 14.307 33.829 1.00 37.23 C
HETATM 25 C26 1C9 A9001 -4.195 11.839 33.416 1.00 36.24 C
HETATM 26 O27 1C9 A9001 -3.693 11.867 34.540 1.00 39.97 O
HETATM 27 N33 1C9 A9001 -7.462 15.332 34.888 1.00 41.10 N
HETATM 28 F21 1C9 A9001 6.211 14.431 34.009 1.00 27.22 F
CONECT 1 18
CONECT 2 3 7 14
CONECT 3 2 4 12
CONECT 4 3 5
CONECT 5 4 6 8
CONECT 6 5 7 11
CONECT 7 2 6
CONECT 8 5 9
CONECT 9 8 10
CONECT 10 9 11
CONECT 11 6 10 15
CONECT 12 3 13
CONECT 13 12
CONECT 14 2 25
CONECT 15 11 16
CONECT 16 15 17 21
CONECT 17 16 18
CONECT 18 17 1 19
CONECT 19 18 20 28
CONECT 20 19 21
CONECT 21 16 20
CONECT 22 24 23
CONECT 23 22 25
CONECT 24 22 27
CONECT 25 14 23 26
CONECT 26 25
CONECT 27 24
CONECT 28 19
END

43
Contrib/CalcLigRMSD/data/4uzh_JVE.pdb Normal file
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@@ -0,0 +1,43 @@
HETATM 1 C8 JVE A1392 -3.535 8.248 31.088 1.00 26.07 C
HETATM 2 N9 JVE A1392 -4.119 9.607 31.118 1.00 26.91 N
HETATM 3 C10 JVE A1392 -3.456 10.558 30.202 1.00 26.19 C
HETATM 4 C11 JVE A1392 -1.943 10.648 30.468 1.00 26.33 C
HETATM 5 C12 JVE A1392 -2.034 8.300 31.362 1.00 25.00 C
HETATM 6 C13 JVE A1392 -1.258 9.423 31.082 1.00 25.38 C
HETATM 7 C14 JVE A1392 0.288 9.475 31.371 1.00 24.48 C
HETATM 8 O15 JVE A1392 -1.336 11.641 30.198 1.00 28.67 O
HETATM 9 C16 JVE A1392 0.732 10.635 32.309 1.00 25.61 C
HETATM 10 C17 JVE A1392 2.002 11.275 32.168 1.00 26.63 C
HETATM 11 C18 JVE A1392 -0.118 11.111 33.361 1.00 26.90 C
HETATM 12 C19 JVE A1392 2.418 12.329 33.015 1.00 27.56 C
HETATM 13 C21 JVE A1392 0.286 12.169 34.217 1.00 26.88 C
HETATM 14 C22 JVE A1392 1.553 12.775 34.044 1.00 27.37 C
HETATM 15 C23 JVE A1392 -0.096 7.045 32.215 1.00 22.71 C
HETATM 16 C24 JVE A1392 0.804 8.150 31.974 1.00 23.08 C
HETATM 17 N25 JVE A1392 0.548 6.007 32.730 1.00 20.54 N
HETATM 18 N26 JVE A1392 -1.414 7.076 31.948 1.00 24.00 N
HETATM 19 C27 JVE A1392 2.016 7.723 32.371 1.00 21.34 C
HETATM 20 N28 JVE A1392 1.940 6.331 32.879 1.00 19.89 N
HETATM 21 F20 JVE A1392 2.858 10.887 31.207 1.00 29.36 F
CONECT 1 2 5
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 6 8
CONECT 5 1 6 18
CONECT 6 4 5 7
CONECT 7 6 9 16
CONECT 8 4
CONECT 9 7 10 11
CONECT 10 9 12 21
CONECT 11 9 13
CONECT 12 10 14
CONECT 13 11 14
CONECT 14 12 13
CONECT 15 16 17 18
CONECT 16 7 15 19
CONECT 17 15 20
CONECT 18 5 15
CONECT 19 16 20
CONECT 20 17 19
CONECT 21 10
END

2705
Contrib/CalcLigRMSD/data/5dpv.pdb Normal file
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File diff suppressed because it is too large Load Diff

4895
Contrib/CalcLigRMSD/data/5dt0.pdb Normal file
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File diff suppressed because it is too large Load Diff

10539
Contrib/CalcLigRMSD/data/6c83.pdb Normal file
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File diff suppressed because it is too large Load Diff

63
Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb Normal file
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@@ -0,0 +1,63 @@
HETATM 1 PA ACP A 501 -1.185 13.784 29.849 0.75114.22 P
HETATM 2 PB ACP A 501 -2.243 16.269 31.018 0.75127.40 P
HETATM 3 PG ACP A 501 -5.113 15.367 30.520 0.75136.16 P
HETATM 4 C5' ACP A 501 -2.030 11.688 28.413 0.75 99.38 C
HETATM 5 O5' ACP A 501 -2.373 12.930 28.990 0.75107.18 O
HETATM 6 C4' ACP A 501 -3.223 10.673 28.618 0.75 93.18 C
HETATM 7 O4' ACP A 501 -2.727 9.227 28.357 0.75 88.42 O
HETATM 8 C3' ACP A 501 -3.622 10.715 29.824 0.75 93.45 C
HETATM 9 O3' ACP A 501 -4.957 11.260 29.879 0.75 95.79 O
HETATM 10 C2' ACP A 501 -3.621 9.169 30.406 0.75 89.70 C
HETATM 11 O2' ACP A 501 -4.940 8.561 30.216 0.75 86.98 O
HETATM 12 C1' ACP A 501 -2.750 8.535 29.734 0.75 86.09 C
HETATM 13 N1 ACP A 501 0.400 5.318 31.815 0.75 74.02 N
HETATM 14 O1A ACP A 501 -0.444 14.713 28.901 0.75113.39 O1-
HETATM 15 O1B ACP A 501 -1.350 16.980 31.985 0.75128.13 O
HETATM 16 O1G ACP A 501 -4.974 15.667 29.044 0.75134.88 O
HETATM 17 C2 ACP A 501 -0.817 5.138 31.233 0.75 74.12 C
HETATM 18 O2A ACP A 501 -0.191 12.813 30.459 0.75113.21 O1-
HETATM 19 O2B ACP A 501 -2.023 16.819 29.640 0.75127.80 O
HETATM 20 O2G ACP A 501 -6.536 15.556 30.932 0.75137.10 O
HETATM 21 C3B ACP A 501 -4.018 16.532 31.502 0.75131.82 C
HETATM 22 N3 ACP A 501 -1.491 6.199 30.729 0.75 73.41 N
HETATM 23 O3A ACP A 501 -1.917 14.647 31.055 0.75121.40 O
HETATM 24 O3G ACP A 501 -4.698 13.933 30.786 0.75136.87 O
HETATM 25 C4 ACP A 501 -0.957 7.437 30.803 0.75 76.01 C
HETATM 26 C5 ACP A 501 0.240 7.616 31.374 0.75 76.95 C
HETATM 27 C6 ACP A 501 0.927 6.533 31.888 0.75 74.17 C
HETATM 28 N6 ACP A 501 2.186 6.222 32.566 0.75 75.62 N
HETATM 29 N7 ACP A 501 0.536 8.930 31.317 0.75 76.65 N
HETATM 30 C8 ACP A 501 -0.474 9.555 30.713 0.75 76.76 C
HETATM 31 N9 ACP A 501 -1.401 8.634 30.393 0.75 77.41 N
CONECT 1 5 14 18 23
CONECT 2 15 19 21 23
CONECT 3 16 20 21 24
CONECT 4 6 5
CONECT 5 1 4
CONECT 6 4 7 8
CONECT 7 6 12
CONECT 8 6 9 10
CONECT 9 8
CONECT 10 8 11 12
CONECT 11 10
CONECT 12 7 10 31
CONECT 13 17 27
CONECT 14 1
CONECT 15 2
CONECT 16 3
CONECT 17 13 22
CONECT 18 1
CONECT 19 2
CONECT 20 3
CONECT 21 2 3
CONECT 22 17 25
CONECT 23 1 2
CONECT 24 3
CONECT 25 22 26 31
CONECT 26 25 27 29
CONECT 27 26 13 28
CONECT 28 27
CONECT 29 26 30
CONECT 30 29 31
CONECT 31 12 25 30
END

63
Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb Normal file
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HETATM 1 PA ACP B 501 -1.917 14.672 30.124 0.61 99.60 P
HETATM 2 PB ACP B 501 -1.351 17.171 31.552 0.61112.78 P
HETATM 3 PG ACP B 501 -4.103 17.610 30.303 0.61121.54 P
HETATM 4 C5' ACP B 501 -1.993 12.428 31.528 0.61 84.76 C
HETATM 5 O5' ACP B 501 -1.293 13.155 30.543 0.61 92.56 O
HETATM 6 C4' ACP B 501 -3.113 11.543 30.851 0.61 78.56 C
HETATM 7 O4' ACP B 501 -2.508 10.582 29.796 0.61 73.80 O
HETATM 8 C3' ACP B 501 -3.660 10.810 31.728 0.61 78.83 C
HETATM 9 O3' ACP B 501 -5.090 10.984 31.665 0.61 81.17 O
HETATM 10 C2' ACP B 501 -3.268 9.235 31.410 0.61 75.08 C
HETATM 11 O2' ACP B 501 -4.448 8.538 30.896 0.61 72.36 O
HETATM 12 C1' ACP B 501 -2.355 9.229 30.520 0.61 71.47 C
HETATM 13 N1 ACP B 501 0.623 5.609 32.304 0.61 59.40 N
HETATM 14 O1A ACP B 501 -3.330 14.485 29.601 0.61 98.77 O1-
HETATM 15 O1B ACP B 501 -0.684 17.392 32.873 0.61113.51 O
HETATM 16 O1G ACP B 501 -4.693 16.435 31.012 0.61122.48 O
HETATM 17 C2 ACP B 501 -0.640 5.554 31.800 0.61 59.50 C
HETATM 18 O2A ACP B 501 -1.049 15.302 29.049 0.61 98.59 O1-
HETATM 19 O2B ACP B 501 -0.355 17.393 30.452 0.61113.18 O
HETATM 20 O2G ACP B 501 -5.185 18.632 30.040 0.61120.26 O
HETATM 21 C3B ACP B 501 -2.760 18.370 31.369 0.61117.20 C
HETATM 22 N3 ACP B 501 -1.252 6.684 31.372 0.61 58.79 N
HETATM 23 O3A ACP B 501 -1.925 15.623 31.480 0.61106.78 O
HETATM 24 O3G ACP B 501 -3.502 17.172 28.980 0.61122.25 O
HETATM 25 C4 ACP B 501 -0.613 7.875 31.444 0.61 61.39 C
HETATM 26 C5 ACP B 501 0.630 7.925 31.942 0.61 62.33 C
HETATM 27 C6 ACP B 501 1.253 6.773 32.377 0.61 59.55 C
HETATM 28 N6 ACP B 501 2.523 6.345 32.962 0.61 61.00 N
HETATM 29 N7 ACP B 501 1.048 9.202 31.911 0.61 62.03 N
HETATM 30 C8 ACP B 501 0.069 9.937 31.395 0.61 62.14 C
HETATM 31 N9 ACP B 501 -0.970 9.128 31.107 0.61 62.79 N
CONECT 1 5 14 18 23
CONECT 2 15 19 21 23
CONECT 3 16 20 21 24
CONECT 4 6 5
CONECT 5 1 4
CONECT 6 4 7 8
CONECT 7 6 12
CONECT 8 6 9 10
CONECT 9 8
CONECT 10 8 11 12
CONECT 11 10
CONECT 12 7 10 31
CONECT 13 17 27
CONECT 14 1
CONECT 15 2
CONECT 16 3
CONECT 17 13 22
CONECT 18 1
CONECT 19 2
CONECT 20 3
CONECT 21 2 3
CONECT 22 17 25
CONECT 23 1 2
CONECT 24 3
CONECT 25 22 26 31
CONECT 26 25 27 29
CONECT 27 26 13 28
CONECT 28 27
CONECT 29 26 30
CONECT 30 29 31
CONECT 31 12 25 30
END

49
Contrib/CalcLigRMSD/data/ACP_renamed.pdb Normal file
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@@ -0,0 +1,49 @@
HETATM 1 P LIG B 501 -1.917 14.672 30.124 0.61 99.60 P
HETATM 2 P1 LIG B 501 -1.351 17.171 31.552 0.61112.78 P
HETATM 3 P2 LIG B 501 -4.103 17.610 30.303 0.61121.54 P
HETATM 4 C9 LIG B 501 -1.993 12.428 31.528 0.61 84.76 C
HETATM 5 O1 LIG B 501 -1.293 13.155 30.543 0.61 92.56 O
HETATM 6 C8 LIG B 501 -3.113 11.543 30.851 0.61 78.56 C
HETATM 7 O LIG B 501 -2.508 10.582 29.796 0.61 73.80 O
HETATM 8 C7 LIG B 501 -3.660 10.810 31.728 0.61 78.83 C
HETATM 9 O10 LIG B 501 -5.090 10.984 31.665 0.61 81.17 O
HETATM 10 C6 LIG B 501 -3.268 9.235 31.410 0.61 75.08 C
HETATM 11 O11 LIG B 501 -4.448 8.538 30.896 0.61 72.36 O
HETATM 12 C5 LIG B 501 -2.355 9.229 30.520 0.61 71.47 C
HETATM 13 N LIG B 501 0.623 5.609 32.304 0.61 59.40 N
HETATM 14 O3 LIG B 501 -3.330 14.485 29.601 0.61 98.77 O1-
HETATM 15 O9 LIG B 501 -0.684 17.392 32.873 0.61113.51 O
HETATM 16 O7 LIG B 501 -4.693 16.435 31.012 0.61122.48 O
HETATM 17 C LIG B 501 -0.640 5.554 31.800 0.61 59.50 C
HETATM 18 O2 LIG B 501 -1.049 15.302 29.049 0.61 98.59 O1-
HETATM 19 O5 LIG B 501 -0.355 17.393 30.452 0.61113.18 O
HETATM 20 O6 LIG B 501 -5.185 18.632 30.040 0.61120.26 O
HETATM 21 C10 LIG B 501 -2.760 18.370 31.369 0.61117.20 C
HETATM 22 N1 LIG B 501 -1.252 6.684 31.372 0.61 58.79 N
HETATM 23 O4 LIG B 501 -1.925 15.623 31.480 0.61106.78 O
HETATM 24 O8 LIG B 501 -3.502 17.172 28.980 0.61122.25 O
HETATM 25 C3 LIG B 501 -0.613 7.875 31.444 0.61 61.39 C
HETATM 26 C2 LIG B 501 0.630 7.925 31.942 0.61 62.33 C
HETATM 27 C1 LIG B 501 1.253 6.773 32.377 0.61 59.55 C
HETATM 28 N4 LIG B 501 2.523 6.345 32.962 0.61 61.00 N
HETATM 29 N3 LIG B 501 1.048 9.202 31.911 0.61 62.03 N
HETATM 30 C4 LIG B 501 0.069 9.937 31.395 0.61 62.14 C
HETATM 31 N2 LIG B 501 -0.970 9.128 31.107 0.61 62.79 N
CONECT 1 5 14 18 23
CONECT 2 15 19 21 23
CONECT 3 16 20 21 24
CONECT 4 5 6
CONECT 6 7 8
CONECT 7 12
CONECT 8 9 10
CONECT 10 11 12
CONECT 12 31
CONECT 13 17 27
CONECT 17 22
CONECT 22 25
CONECT 25 26 31
CONECT 26 27 29
CONECT 27 28
CONECT 29 30
CONECT 30 31
END

73
Contrib/CalcLigRMSD/data/AKI_renamed.pdb Normal file
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@@ -0,0 +1,73 @@
HETATM 1 C1 LIG A 1 -4.318 10.286 31.606 1.00 49.28 C
HETATM 2 C2 LIG A 1 -3.574 9.160 31.940 1.00 50.62 C
HETATM 3 C3 LIG A 1 -2.383 8.892 31.275 1.00 50.85 C
HETATM 4 C4 LIG A 1 -1.936 9.749 30.277 1.00 50.53 C
HETATM 5 C5 LIG A 1 -2.681 10.875 29.942 1.00 48.75 C
HETATM 6 C LIG A 1 -3.872 11.143 30.608 1.00 48.39 C
HETATM 7 C6 LIG A 1 -1.639 7.766 31.609 1.00 51.06 C
HETATM 8 C11 LIG A 1 -2.089 6.458 31.592 1.00 50.47 C
HETATM 9 C12 LIG A 1 -3.368 6.048 31.236 1.00 50.37 C
HETATM 10 C17 LIG A 1 -4.245 6.945 30.639 1.00 48.95 C
HETATM 11 C16 LIG A 1 -5.525 6.533 30.284 1.00 47.24 C
HETATM 12 C15 LIG A 1 -5.926 5.226 30.526 1.00 46.94 C
HETATM 13 C14 LIG A 1 -5.049 4.328 31.122 1.00 44.98 C
HETATM 14 C13 LIG A 1 -3.770 4.738 31.478 1.00 48.36 C
HETATM 15 C18 LIG A 1 1.373 11.051 32.209 1.00 53.10 C
HETATM 16 C19 LIG A 1 1.352 11.519 33.665 1.00 57.01 C
HETATM 17 C20 LIG A 1 2.362 12.646 33.894 1.00 59.68 C
HETATM 18 C21 LIG A 1 3.724 12.394 33.777 1.00 61.91 C
HETATM 19 C22 LIG A 1 4.640 13.418 33.985 1.00 63.98 C
HETATM 20 O LIG A 1 -1.069 5.636 31.982 1.00 51.79 O
HETATM 21 C23 LIG A 1 4.196 14.693 34.309 1.00 64.22 C
HETATM 22 C24 LIG A 1 2.834 14.946 34.426 1.00 63.53 C
HETATM 23 C25 LIG A 1 1.917 13.923 34.219 1.00 61.40 C
HETATM 24 C26 LIG A 1 5.096 16.723 33.691 1.00 69.52 C
HETATM 25 C27 LIG A 1 6.081 18.740 33.178 1.00 74.91 C
HETATM 26 C28 LIG A 1 6.497 19.953 33.717 1.00 75.89 C
HETATM 27 C29 LIG A 1 6.582 21.080 32.908 1.00 75.73 C
HETATM 28 C30 LIG A 1 6.251 20.995 31.560 1.00 75.71 C
HETATM 29 C31 LIG A 1 5.836 19.783 31.021 1.00 76.87 C
HETATM 30 C32 LIG A 1 5.752 18.656 31.831 1.00 76.42 C
HETATM 31 N3 LIG A 1 5.073 15.674 34.508 1.00 67.56 N
HETATM 32 N4 LIG A 1 6.000 17.663 33.953 1.00 72.60 N
HETATM 33 N2 LIG A 1 0.345 10.019 32.010 1.00 52.09 N
HETATM 34 O1 LIG A 1 4.319 16.820 32.742 1.00 69.50 O
HETATM 35 N1 LIG A 1 1.270 6.142 32.655 1.00 50.81 N
HETATM 36 C9 LIG A 1 2.158 7.106 32.839 1.00 50.39 C
HETATM 37 N LIG A 1 1.863 8.379 32.630 1.00 51.12 N
HETATM 38 C8 LIG A 1 0.639 8.739 32.220 1.00 51.03 C
HETATM 39 C7 LIG A 1 -0.315 7.754 32.017 1.00 51.11 C
HETATM 40 C10 LIG A 1 0.026 6.427 32.246 1.00 51.70 C
CONECT 1 2 6
CONECT 2 3
CONECT 3 4 7
CONECT 4 5
CONECT 5 6
CONECT 7 8 39
CONECT 8 9 20
CONECT 9 10 14
CONECT 10 11
CONECT 11 12
CONECT 12 13
CONECT 13 14
CONECT 15 16 33
CONECT 16 17
CONECT 17 18 23
CONECT 18 19
CONECT 19 21
CONECT 20 40
CONECT 21 22 31
CONECT 22 23
CONECT 24 31 32 34
CONECT 25 26 30 32
CONECT 26 27
CONECT 27 28
CONECT 28 29
CONECT 29 30
CONECT 33 38
CONECT 35 36 40
CONECT 36 37
CONECT 37 38
CONECT 38 39
CONECT 39 40
END

48
Contrib/CalcLigRMSD/data/BEG_test.pdb Normal file
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HETATM 1519 C1 BEG A 501 9.764 24.084 2.234 1.00 16.71 C
HETATM 1520 C2 BEG A 501 9.044 25.251 1.867 1.00 17.16 C
HETATM 1521 C3 BEG A 501 7.641 25.363 2.003 1.00 18.56 C
HETATM 1522 C4 BEG A 501 6.904 24.272 2.523 1.00 17.81 C
HETATM 1523 C5 BEG A 501 7.585 23.088 2.893 1.00 17.98 C
HETATM 1524 C6 BEG A 501 8.994 22.996 2.747 1.00 17.88 C
HETATM 1525 C7 BEG A 501 16.298 22.149 8.773 1.00 19.56 C
HETATM 1526 C8 BEG A 501 15.570 21.130 9.459 1.00 20.75 C
HETATM 1527 C9 BEG A 501 16.175 19.934 9.922 1.00 20.57 C
HETATM 1528 CA0 BEG A 501 17.561 19.729 9.711 1.00 20.37 C
HETATM 1529 CA1 BEG A 501 18.315 20.725 9.045 1.00 20.47 C
HETATM 1530 CA2 BEG A 501 17.690 21.914 8.586 1.00 20.23 C
HETATM 1531 CA3 BEG A 501 15.560 23.358 8.195 1.00 19.50 C
HETATM 1532 OA4 BEG A 501 14.526 23.015 7.272 1.00 18.69 O
HETATM 1533 CA3 BEG A 501 11.287 24.077 2.148 1.00 17.57 C
HETATM 1534 OA2 BEG A 501 11.920 23.554 3.313 1.00 17.43 O
HETATM 1535 CA5 BEG A 501 15.031 22.699 5.968 1.00 16.68 C
HETATM 1536 CA6 BEG A 501 13.991 23.019 4.924 1.00 17.37 C
HETATM 1537 CA7 BEG A 501 13.502 24.425 5.006 1.00 17.54 C
HETATM 1538 OA4 BEG A 501 14.483 25.178 4.305 1.00 17.08 O
HETATM 1539 CA8 BEG A 501 12.117 24.538 4.353 1.00 16.43 C
HETATM 1540 CA9 BEG A 501 10.944 24.485 5.324 1.00 15.74 C
HETATM 1541 OA0 BEG A 501 10.696 23.492 6.004 1.00 15.85 O
HETATM 1542 NB1 BEG A 501 10.140 25.606 5.373 1.00 13.93 N
HETATM 1543 CB5 BEG A 501 15.140 21.202 5.836 1.00 15.73 C
HETATM 1544 OB6 BEG A 501 14.193 20.464 6.087 1.00 16.50 O
HETATM 1545 NB7 BEG A 501 16.358 20.692 5.436 1.00 13.98 N
HETATM 1546 CB8 BEG A 501 16.620 19.277 5.261 1.00 13.60 C
HETATM 1547 CB9 BEG A 501 16.571 18.847 3.820 1.00 14.30 C
HETATM 1548 CC0 BEG A 501 17.534 17.849 3.551 1.00 14.91 C
HETATM 1549 CC1 BEG A 501 15.732 19.314 2.777 1.00 14.61 C
HETATM 1550 CC2 BEG A 501 15.863 18.764 1.468 1.00 15.46 C
HETATM 1551 CC3 BEG A 501 16.833 17.755 1.212 1.00 15.55 C
HETATM 1552 CC4 BEG A 501 18.018 18.781 5.673 1.00 13.85 C
HETATM 1553 OC5 BEG A 501 18.937 19.823 5.379 1.00 13.10 O
HETATM 1554 CC6 BEG A 501 17.679 17.289 2.256 1.00 15.32 C
HETATM 1555 CC7 BEG A 501 18.309 17.538 4.794 1.00 14.18 C
HETATM 1556 CC8 BEG A 501 8.968 25.778 6.216 1.00 14.18 C
HETATM 1557 CC9 BEG A 501 9.256 26.507 7.503 1.00 14.71 C
HETATM 1558 CD0 BEG A 501 8.181 27.361 7.860 1.00 15.26 C
HETATM 1559 CD1 BEG A 501 10.408 26.446 8.332 1.00 15.21 C
HETATM 1560 CD2 BEG A 501 10.467 27.240 9.518 1.00 16.49 C
HETATM 1561 CD3 BEG A 501 9.377 28.089 9.863 1.00 16.60 C
HETATM 1562 CD4 BEG A 501 7.849 26.663 5.625 1.00 14.38 C
HETATM 1563 OD5 BEG A 501 8.482 27.684 4.868 1.00 12.28 O
HETATM 1564 CD6 BEG A 501 8.224 28.156 9.035 1.00 16.17 C
HETATM 1565 CD7 BEG A 501 7.093 27.273 6.832 1.00 14.54 C
END

38
Contrib/CalcLigRMSD/data/JVE_renamed.pdb Normal file
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HETATM 1 C14 LIG A1392 -3.535 8.248 31.088 1.00 26.07 C
HETATM 2 N3 LIG A1392 -4.119 9.607 31.118 1.00 26.91 N
HETATM 3 C13 LIG A1392 -3.456 10.558 30.202 1.00 26.19 C
HETATM 4 C12 LIG A1392 -1.943 10.648 30.468 1.00 26.33 C
HETATM 5 C10 LIG A1392 -2.034 8.300 31.362 1.00 25.00 C
HETATM 6 C11 LIG A1392 -1.258 9.423 31.082 1.00 25.38 C
HETATM 7 C6 LIG A1392 0.288 9.475 31.371 1.00 24.48 C
HETATM 8 O LIG A1392 -1.336 11.641 30.198 1.00 28.67 O
HETATM 9 C4 LIG A1392 0.732 10.635 32.309 1.00 25.61 C
HETATM 10 C3 LIG A1392 2.002 11.275 32.168 1.00 26.63 C
HETATM 11 C5 LIG A1392 -0.118 11.111 33.361 1.00 26.90 C
HETATM 12 C2 LIG A1392 2.418 12.329 33.015 1.00 27.56 C
HETATM 13 C LIG A1392 0.286 12.169 34.217 1.00 26.88 C
HETATM 14 C1 LIG A1392 1.553 12.775 34.044 1.00 27.37 C
HETATM 15 C9 LIG A1392 -0.096 7.045 32.215 1.00 22.71 C
HETATM 16 C7 LIG A1392 0.804 8.150 31.974 1.00 23.08 C
HETATM 17 N1 LIG A1392 0.548 6.007 32.730 1.00 20.54 N
HETATM 18 N2 LIG A1392 -1.414 7.076 31.948 1.00 24.00 N
HETATM 19 C8 LIG A1392 2.016 7.723 32.371 1.00 21.34 C
HETATM 20 N LIG A1392 1.940 6.331 32.879 1.00 19.89 N
HETATM 21 F LIG A1392 2.858 10.887 31.207 1.00 29.36 F
CONECT 1 2 5
CONECT 2 3
CONECT 3 4
CONECT 4 6 8
CONECT 5 6 18
CONECT 6 7
CONECT 7 9 16
CONECT 9 10 11
CONECT 10 12 21
CONECT 11 13
CONECT 12 14
CONECT 13 14
CONECT 15 16 17 18
CONECT 16 19
CONECT 17 20
CONECT 19 20
END

58
Contrib/CalcLigRMSD/data/N15_renamed.pdb Normal file
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HETATM 1 N1 LIG A 401 4.149 12.998 33.333 1.00 44.90 N
HETATM 2 C6 LIG A 401 4.977 14.161 33.415 1.00 46.23 C
HETATM 3 C LIG A 401 9.897 15.441 36.239 1.00 57.65 C
HETATM 4 C2 LIG A 401 11.551 15.449 34.421 1.00 56.31 C
HETATM 5 C21 LIG A 401 -5.532 5.836 30.671 1.00 30.00 C
HETATM 6 C20 LIG A 401 -5.169 4.490 30.897 1.00 30.51 C
HETATM 7 C11 LIG A 401 0.760 10.526 32.426 1.00 35.13 C
HETATM 8 C22 LIG A 401 -4.585 6.842 30.899 1.00 29.52 C
HETATM 9 C19 LIG A 401 -3.857 4.231 31.373 1.00 29.13 C
HETATM 10 C12 LIG A 401 -0.057 9.397 32.229 1.00 35.80 C
HETATM 11 C9 LIG A 401 3.751 11.145 34.170 1.00 44.29 C
HETATM 12 C15 LIG A 401 2.490 8.972 33.044 1.00 36.35 C
HETATM 13 C7 LIG A 401 3.187 12.473 32.549 1.00 44.30 C
HETATM 14 C4 LIG A 401 8.487 13.062 34.480 1.00 48.16 C
HETATM 15 C3 LIG A 401 9.344 14.265 34.066 1.00 51.39 C
HETATM 16 C10 LIG A 401 2.076 10.294 32.827 1.00 38.41 C
HETATM 17 C8 LIG A 401 2.953 11.272 33.104 1.00 43.16 C
HETATM 18 C17 LIG A 401 -1.309 6.516 31.994 1.00 33.89 C
HETATM 19 C16 LIG A 401 -0.079 6.916 32.360 1.00 35.12 C
HETATM 20 C5 LIG A 401 6.428 13.629 33.325 1.00 47.33 C
HETATM 21 O LIG A 401 6.907 13.243 32.250 1.00 47.93 O
HETATM 22 N2 LIG A 401 4.486 12.239 34.251 1.00 44.60 N
HETATM 23 N4 LIG A 401 0.881 6.050 32.700 1.00 36.09 N
HETATM 24 N6 LIG A 401 -2.310 7.298 31.617 1.00 33.12 N
HETATM 25 N LIG A 401 7.088 13.512 34.474 1.00 47.03 N
HETATM 26 N3 LIG A 401 1.830 6.629 32.963 1.00 36.82 N
HETATM 27 N5 LIG A 401 -1.734 5.250 31.988 1.00 31.71 N
HETATM 28 C23 LIG A 401 -3.356 6.513 31.341 1.00 29.45 C
HETATM 29 C18 LIG A 401 -3.001 5.246 31.567 1.00 27.92 C
HETATM 30 C14 LIG A 401 1.656 7.950 32.843 1.00 35.69 C
HETATM 31 C13 LIG A 401 0.408 8.153 32.437 1.00 34.80 C
HETATM 32 C1 LIG A 401 10.447 14.608 35.084 1.00 54.34 C
CONECT 1 2 13 22
CONECT 2 20
CONECT 3 32
CONECT 4 32
CONECT 5 6 8
CONECT 6 9
CONECT 7 10 16
CONECT 8 28
CONECT 9 29
CONECT 10 31
CONECT 11 17 22
CONECT 12 16 30
CONECT 13 17
CONECT 14 15 25
CONECT 15 32
CONECT 16 17
CONECT 18 19 24 27
CONECT 19 23 31
CONECT 20 21 25
CONECT 23 26
CONECT 24 28
CONECT 26 30
CONECT 27 29
CONECT 28 29
CONECT 30 31
END

55
Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb Normal file
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HETATM 1 C1 SKE A 402 1.219 6.910 32.590 1.00 64.62 C
HETATM 2 N1 SKE A 402 2.530 7.232 32.715 1.00 61.03 N
HETATM 3 O1 SKE A 402 -6.607 4.886 28.742 1.00 76.51 O
HETATM 4 C2 SKE A 402 -0.594 5.871 32.485 1.00 66.29 C
HETATM 5 N2 SKE A 402 0.735 5.655 32.672 1.00 63.60 N
HETATM 6 O2 SKE A 402 -6.896 6.912 29.887 1.00 71.93 O
HETATM 7 C3 SKE A 402 -2.692 5.010 31.911 1.00 66.41 C
HETATM 8 N3 SKE A 402 -1.483 4.855 32.490 1.00 66.66 N
HETATM 9 O3 SKE A 402 1.579 9.585 32.191 1.00 59.12 O
HETATM 10 C4 SKE A 402 -3.171 6.285 31.633 1.00 64.98 C
HETATM 11 N4 SKE A 402 -7.734 4.833 30.951 1.00 74.68 N
HETATM 12 C5 SKE A 402 -4.417 6.444 31.037 1.00 66.32 C
HETATM 13 N5 SKE A 402 -0.988 7.158 32.292 1.00 66.64 N
HETATM 14 C6 SKE A 402 -5.183 5.329 30.718 1.00 68.38 C
HETATM 15 N6 SKE A 402 0.253 7.792 32.374 1.00 66.43 N
HETATM 16 C7 SKE A 402 -4.703 4.055 30.996 1.00 61.22 C
HETATM 17 C8 SKE A 402 -3.458 3.895 31.593 1.00 64.03 C
HETATM 18 C9 SKE A 402 0.446 9.137 32.247 1.00 63.94 C
HETATM 19 C10 SKE A 402 -0.736 10.058 32.176 1.00 64.53 C
HETATM 20 C11 SKE A 402 -1.525 10.085 31.039 1.00 65.96 C
HETATM 21 C12 SKE A 402 -2.621 10.936 30.971 1.00 66.61 C
HETATM 22 C13 SKE A 402 -2.925 11.762 32.047 1.00 67.29 C
HETATM 23 C14 SKE A 402 -2.132 11.732 33.188 1.00 68.03 C
HETATM 24 C15 SKE A 402 -1.036 10.879 33.250 1.00 66.18 C
HETATM 25 F1 SKE A 402 -1.230 9.285 29.998 1.00 66.27 F
HETATM 26 F2 SKE A 402 -0.268 10.850 34.353 1.00 68.15 F
HETATM 27 S SKE A 402 -6.612 5.512 30.034 1.00 73.69 S
CONECT 1 2 5 15
CONECT 2 1
CONECT 3 27
CONECT 4 5 8 13
CONECT 5 1 4
CONECT 6 27
CONECT 7 8 10 17
CONECT 8 4 7
CONECT 9 18
CONECT 10 7 12
CONECT 11 27
CONECT 12 10 14
CONECT 13 4 15
CONECT 14 12 16 27
CONECT 15 1 13 18
CONECT 16 14 17
CONECT 17 7 16
CONECT 18 9 15 19
CONECT 19 18 20 24
CONECT 20 19 21 25
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 22 24
CONECT 24 19 23 26
CONECT 25 20
CONECT 26 24
CONECT 27 3 6 11 14
END

48
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HETATM 1 C7 LIG A 402 1.219 6.910 32.590 1.00 64.62 C
HETATM 2 N5 LIG A 402 2.530 7.232 32.715 1.00 61.03 N
HETATM 3 O2 LIG A 402 -6.607 4.886 28.742 1.00 76.51 O
HETATM 4 C8 LIG A 402 -0.594 5.871 32.485 1.00 66.29 C
HETATM 5 N1 LIG A 402 0.735 5.655 32.672 1.00 63.60 N
HETATM 6 O1 LIG A 402 -6.896 6.912 29.887 1.00 71.93 O
HETATM 7 C9 LIG A 402 -2.692 5.010 31.911 1.00 66.41 C
HETATM 8 N3 LIG A 402 -1.483 4.855 32.490 1.00 66.66 N
HETATM 9 O LIG A 402 1.579 9.585 32.191 1.00 59.12 O
HETATM 10 C10 LIG A 402 -3.171 6.285 31.633 1.00 64.98 C
HETATM 11 N4 LIG A 402 -7.734 4.833 30.951 1.00 74.68 N
HETATM 12 C11 LIG A 402 -4.417 6.444 31.037 1.00 66.32 C
HETATM 13 N2 LIG A 402 -0.988 7.158 32.292 1.00 66.64 N
HETATM 14 C12 LIG A 402 -5.183 5.329 30.718 1.00 68.38 C
HETATM 15 N LIG A 402 0.253 7.792 32.374 1.00 66.43 N
HETATM 16 C13 LIG A 402 -4.703 4.055 30.996 1.00 61.22 C
HETATM 17 C14 LIG A 402 -3.458 3.895 31.593 1.00 64.03 C
HETATM 18 C6 LIG A 402 0.446 9.137 32.247 1.00 63.94 C
HETATM 19 C3 LIG A 402 -0.736 10.058 32.176 1.00 64.53 C
HETATM 20 C4 LIG A 402 -1.525 10.085 31.039 1.00 65.96 C
HETATM 21 C5 LIG A 402 -2.621 10.936 30.971 1.00 66.61 C
HETATM 22 C LIG A 402 -2.925 11.762 32.047 1.00 67.29 C
HETATM 23 C1 LIG A 402 -2.132 11.732 33.188 1.00 68.03 C
HETATM 24 C2 LIG A 402 -1.036 10.879 33.250 1.00 66.18 C
HETATM 25 F LIG A 402 -1.230 9.285 29.998 1.00 66.27 F
HETATM 26 F1 LIG A 402 -0.268 10.850 34.353 1.00 68.15 F
HETATM 27 S LIG A 402 -6.612 5.512 30.034 1.00 73.69 S
CONECT 1 2 5 15
CONECT 3 27
CONECT 4 5 8 13
CONECT 6 27
CONECT 7 8 10 17
CONECT 9 18
CONECT 10 12
CONECT 11 27
CONECT 12 14
CONECT 13 15
CONECT 14 16 27
CONECT 15 18
CONECT 16 17
CONECT 18 19
CONECT 19 20 24
CONECT 20 21 25
CONECT 21 22
CONECT 22 23
CONECT 23 24
CONECT 24 26
END

4336
Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb Normal file
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2264
Contrib/CalcLigRMSD/data/crystal_aligned.pdb Normal file
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95
Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb Normal file
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MODEL 1
REMARK VINA RESULT: -7.4 0.000 0.000
REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C1_3 and N4_31
REMARK 2 A between atoms: N2_7 and C5_10
REMARK 3 A between atoms: C6_11 and O11_30
REMARK 4 A between atoms: C7_12 and O10_29
REMARK 5 A between atoms: C8_13 and C9_15
REMARK 6 A between atoms: C9_15 and O1_16
REMARK 7 A between atoms: O1_16 and P_17
REMARK 8 A between atoms: P_17 and O4_20
REMARK 9 A between atoms: O4_20 and P1_21
REMARK 10 A between atoms: P1_21 and C10_23
REMARK 11 A between atoms: C10_23 and P2_24
REMARK 12 A between atoms: P2_24 and O7_26
COMPND docked_2c6e_ACP_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C5 LIG d 1 -2.025 9.898 30.324 1.00 0.00 C
ATOM 2 C6 LIG d 1 -3.064 10.342 31.364 1.00 0.00 C
ATOM 3 C7 LIG d 1 -2.974 11.859 31.321 1.00 0.00 C
ATOM 4 C8 LIG d 1 -2.542 12.128 29.885 1.00 0.00 C
ATOM 5 O LIG d 1 -1.696 11.034 29.498 1.00 0.00 O
ATOM 6 C9 LIG d 1 -1.791 13.449 29.738 1.00 0.00 C
ATOM 7 O1 LIG d 1 -2.727 14.498 29.512 1.00 0.00 O
ATOM 8 P LIG d 1 -2.585 15.829 30.390 1.00 0.00 P
ATOM 9 O2 LIG d 1 -3.548 16.932 30.108 1.00 0.00 O
ATOM 10 O3 LIG d 1 -2.784 15.270 31.880 1.00 0.00 O
ATOM 11 O4 LIG d 1 -1.050 16.235 30.373 1.00 0.00 O
ATOM 12 P1 LIG d 1 -0.448 17.703 30.233 1.00 0.00 P
ATOM 13 O5 LIG d 1 -1.299 18.617 29.412 1.00 0.00 O
ATOM 14 O9 LIG d 1 -0.446 18.164 31.775 1.00 0.00 O
ATOM 15 C10 LIG d 1 1.260 17.534 29.797 1.00 0.00 C
ATOM 16 P2 LIG d 1 2.313 18.955 29.785 1.00 0.00 P
ATOM 17 O6 LIG d 1 1.953 20.141 28.961 1.00 0.00 O
ATOM 18 O8 LIG d 1 3.793 18.431 29.473 1.00 0.00 O
ATOM 19 O7 LIG d 1 2.486 19.364 31.328 1.00 0.00 O
ATOM 20 H10 LIG d 1 1.660 19.755 31.653 1.00 0.00 H
ATOM 21 O10 LIG d 1 -4.216 12.476 31.655 1.00 0.00 O
ATOM 22 H11 LIG d 1 -4.535 12.989 30.897 1.00 0.00 H
ATOM 23 O11 LIG d 1 -4.388 9.943 30.952 1.00 0.00 O
ATOM 24 H12 LIG d 1 -5.049 10.421 31.475 1.00 0.00 H
ATOM 25 N2 LIG d 1 -0.790 9.342 30.834 1.00 0.00 N
ATOM 26 C3 LIG d 1 -0.532 8.052 31.209 1.00 0.00 C
ATOM 27 C2 LIG d 1 0.797 8.054 31.606 1.00 0.00 C
ATOM 28 N1 LIG d 1 -1.366 7.000 31.188 1.00 0.00 N
ATOM 29 C1 LIG d 1 1.329 6.831 32.044 1.00 0.00 C
ATOM 30 N3 LIG d 1 1.353 9.309 31.460 1.00 0.00 N
ATOM 31 N LIG d 1 0.534 5.737 32.030 1.00 0.00 N
ATOM 32 C LIG d 1 -0.745 5.883 31.623 1.00 0.00 C
ATOM 33 C4 LIG d 1 0.365 10.060 31.023 1.00 0.00 C
ATOM 34 N4 LIG d 1 2.643 6.680 32.466 1.00 0.00 N
ATOM 35 H13 LIG d 1 3.268 6.127 31.944 1.00 0.00 H
ATOM 36 H14 LIG d 1 2.949 7.125 33.288 1.00 0.00 H
CONECT 1 5 25 2
CONECT 2 1 23 3
CONECT 3 4 2 21
CONECT 4 5 6 3
CONECT 5 4 1
CONECT 6 7 4
CONECT 7 6 8
CONECT 8 7 9 11 10
CONECT 8
CONECT 9 8
CONECT 10 8
CONECT 11 12 8
CONECT 12 13 15 11 14
CONECT 12
CONECT 13 12
CONECT 14 12
CONECT 15 16 12
CONECT 16 17 18 15 19
CONECT 16
CONECT 17 16
CONECT 18 16
CONECT 19 16 20
CONECT 20 19
CONECT 21 22 3
CONECT 22 21
CONECT 23 2 24
CONECT 24 23
CONECT 25 1 33 26
CONECT 26 25 28 27
CONECT 27 26 30 29
CONECT 28 26 32
CONECT 29 27 31 34
CONECT 30 33 27
CONECT 31 32 29
CONECT 32 28 31
CONECT 33 25 30
CONECT 34 35 29 36
CONECT 35 34
CONECT 36 34
MASTER 0 0 0 0 0 0 0 0 36 0 36 0
END

104
Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb Normal file
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MODEL 1
REMARK VINA RESULT: -11.2 0.000 0.000
REMARK 8 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C3_4 and C6_7
REMARK 2 A between atoms: C8_9 and N2_22
REMARK 3 A between atoms: C11_15 and C12_16
REMARK 4 A between atoms: N2_22 and C18_23
REMARK 5 A between atoms: C18_23 and C19_24
REMARK 6 A between atoms: C19_24 and C20_25
REMARK 7 A between atoms: C23_28 and N3_31
REMARK I between atoms: N3_31 and C26_32
REMARK I between atoms: C26_32 and N4_34
REMARK 8 A between atoms: N4_34 and C27_35
COMPND docked_2c6e_AKI_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 N2 LIG d 1 -1.503 10.887 31.482 1.00 0.00 N
ATOM 2 H11 LIG d 1 -1.316 10.677 32.426 1.00 0.00 H
ATOM 3 C8 LIG d 1 -2.792 10.823 30.944 1.00 0.00 C
ATOM 4 C7 LIG d 1 -3.434 9.602 30.671 1.00 0.00 C
ATOM 5 C6 LIG d 1 -3.147 8.205 30.786 1.00 0.00 C
ATOM 6 C10 LIG d 1 -4.706 9.684 30.127 1.00 0.00 C
ATOM 7 C11 LIG d 1 -4.261 7.530 30.303 1.00 0.00 C
ATOM 8 O LIG d 1 -5.199 8.440 29.898 1.00 0.00 O
ATOM 9 N1 LIG d 1 -5.400 10.793 29.839 1.00 0.00 N
ATOM 10 C9 LIG d 1 -4.708 11.892 30.153 1.00 0.00 C
ATOM 11 N LIG d 1 -3.472 11.966 30.679 1.00 0.00 N
ATOM 12 C3 LIG d 1 -1.948 7.557 31.282 1.00 0.00 C
ATOM 13 C2 LIG d 1 -1.971 6.887 32.511 1.00 0.00 C
ATOM 14 C1 LIG d 1 -0.825 6.240 32.978 1.00 0.00 C
ATOM 15 C LIG d 1 0.348 6.267 32.224 1.00 0.00 C
ATOM 16 C5 LIG d 1 0.380 6.944 31.005 1.00 0.00 C
ATOM 17 C4 LIG d 1 -0.764 7.590 30.535 1.00 0.00 C
ATOM 18 C12 LIG d 1 -4.665 6.133 30.138 1.00 0.00 C
ATOM 19 C13 LIG d 1 -3.769 5.157 29.680 1.00 0.00 C
ATOM 20 C14 LIG d 1 -4.174 3.828 29.518 1.00 0.00 C
ATOM 21 C15 LIG d 1 -5.481 3.455 29.820 1.00 0.00 C
ATOM 22 C16 LIG d 1 -6.382 4.407 30.289 1.00 0.00 C
ATOM 23 C17 LIG d 1 -5.975 5.734 30.447 1.00 0.00 C
ATOM 24 C18 LIG d 1 -0.452 11.288 30.549 1.00 0.00 C
ATOM 25 C19 LIG d 1 0.777 10.378 30.688 1.00 0.00 C
ATOM 26 C20 LIG d 1 1.864 10.975 31.551 1.00 0.00 C
ATOM 27 C21 LIG d 1 2.150 10.428 32.808 1.00 0.00 C
ATOM 28 C22 LIG d 1 3.144 10.984 33.621 1.00 0.00 C
ATOM 29 C23 LIG d 1 3.869 12.096 33.192 1.00 0.00 C
ATOM 30 C24 LIG d 1 3.577 12.650 31.940 1.00 0.00 C
ATOM 31 C25 LIG d 1 2.588 12.092 31.123 1.00 0.00 C
ATOM 32 N3 LIG d 1 4.873 12.722 33.960 1.00 0.00 N
ATOM 33 C26 LIG d 1 6.102 13.191 33.518 1.00 0.00 C
ATOM 34 O1 LIG d 1 6.466 13.224 32.352 1.00 0.00 O
ATOM 35 N4 LIG d 1 6.862 13.614 34.601 1.00 0.00 N
ATOM 36 H21 LIG d 1 6.497 13.423 35.495 1.00 0.00 H
ATOM 37 H20 LIG d 1 4.679 12.840 34.918 1.00 0.00 H
ATOM 38 C27 LIG d 1 8.101 14.288 34.559 1.00 0.00 C
ATOM 39 C28 LIG d 1 9.304 13.722 34.986 1.00 0.00 C
ATOM 40 C29 LIG d 1 10.498 14.443 34.895 1.00 0.00 C
ATOM 41 C30 LIG d 1 10.500 15.735 34.372 1.00 0.00 C
ATOM 42 C31 LIG d 1 9.307 16.306 33.937 1.00 0.00 C
ATOM 43 C32 LIG d 1 8.114 15.583 34.024 1.00 0.00 C
CONECT 1 24 3 2
CONECT 2 1
CONECT 3 4 11 1
CONECT 4 6 5 3
CONECT 5 7 4 12
CONECT 6 9 8 4
CONECT 7 8 18 5
CONECT 8 6 7
CONECT 9 6 10
CONECT 10 9 11
CONECT 11 10 3
CONECT 12 17 5 13
CONECT 13 12 14
CONECT 14 15 13
CONECT 15 16 14
CONECT 16 17 15
CONECT 17 16 12
CONECT 18 19 7 23
CONECT 19 20 18
CONECT 20 19 21
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 18 22
CONECT 24 25 1
CONECT 25 24 26
CONECT 26 25 31 27
CONECT 27 26 28
CONECT 28 27 29
CONECT 29 30 28 32
CONECT 30 31 29
CONECT 31 26 30
CONECT 32 29 33 37
CONECT 33 34 32 35
CONECT 34 33
CONECT 35 33 38 36
CONECT 36 35
CONECT 37 32
CONECT 38 43 35 39
CONECT 39 38 40
CONECT 40 41 39
CONECT 41 42 40
CONECT 42 43 41
CONECT 43 42 38
MASTER 0 0 0 0 0 0 0 0 43 0 43 0
END

57
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MODEL 1
REMARK VINA RESULT: -7.7 0.000 0.000
REMARK 1 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C4_5 and C6_7
COMPND docked_2c6e_JVE_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C6 LIG d 1 1.552 9.699 31.177 1.00 0.00 C
ATOM 2 C7 LIG d 1 1.858 8.313 31.672 1.00 0.00 C
ATOM 3 C8 LIG d 1 3.024 7.586 31.789 1.00 0.00 C
ATOM 4 N LIG d 1 2.655 6.381 32.314 1.00 0.00 N
ATOM 5 N1 LIG d 1 1.329 6.255 32.512 1.00 0.00 N
ATOM 6 C9 LIG d 1 0.847 7.432 32.126 1.00 0.00 C
ATOM 7 N2 LIG d 1 -0.441 7.828 32.111 1.00 0.00 N
ATOM 8 C10 LIG d 1 -0.848 9.071 31.633 1.00 0.00 C
ATOM 9 C11 LIG d 1 0.060 9.966 31.176 1.00 0.00 C
ATOM 10 C12 LIG d 1 -0.430 11.225 30.555 1.00 0.00 C
ATOM 11 O LIG d 1 0.353 11.976 29.972 1.00 0.00 O
ATOM 12 C13 LIG d 1 -1.931 11.491 30.552 1.00 0.00 C
ATOM 13 N3 LIG d 1 -2.602 10.817 31.668 1.00 0.00 N
ATOM 14 C14 LIG d 1 -2.328 9.382 31.658 1.00 0.00 C
ATOM 15 H6 LIG d 1 3.300 5.668 32.528 1.00 0.00 H
ATOM 16 H7 LIG d 1 -1.126 7.210 32.454 1.00 0.00 H
ATOM 17 H10 LIG d 1 -3.609 10.963 31.590 1.00 0.00 H
ATOM 18 C4 LIG d 1 2.363 10.634 32.060 1.00 0.00 C
ATOM 19 C3 LIG d 1 3.226 11.607 31.539 1.00 0.00 C
ATOM 20 C2 LIG d 1 3.958 12.454 32.370 1.00 0.00 C
ATOM 21 F LIG d 1 3.371 11.752 30.214 1.00 0.00 F
ATOM 22 C1 LIG d 1 3.843 12.338 33.753 1.00 0.00 C
ATOM 23 C LIG d 1 2.997 11.374 34.297 1.00 0.00 C
ATOM 24 C5 LIG d 1 2.264 10.529 33.459 1.00 0.00 C
CONECT 1 9 2 18
CONECT 2 1 3 6
CONECT 3 2 4
CONECT 4 3 5 15
CONECT 5 6 4
CONECT 6 2 7 5
CONECT 7 8 6 16
CONECT 8 9 14 7
CONECT 9 10 1 8
CONECT 10 11 12 9
CONECT 11 10
CONECT 12 10 13
CONECT 13 12 17 14
CONECT 14 8 13
CONECT 15 4
CONECT 16 7
CONECT 17 13
CONECT 18 1 19 24
CONECT 19 21 18 20
CONECT 20 19 22
CONECT 21 19
CONECT 22 20 23
CONECT 23 24 22
CONECT 24 18 23
MASTER 0 0 0 0 0 0 0 0 24 0 24 0
END

86
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MODEL 1
REMARK VINA RESULT: -10.7 0.000 0.000
REMARK 7 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C1_2 and C3_4
REMARK 2 A between atoms: C3_4 and C4_5
REMARK 3 A between atoms: C4_5 and N_6
REMARK I between atoms: N_6 and C5_7
REMARK 4 A between atoms: C5_7 and C6_9
REMARK 5 A between atoms: C6_9 and N1_10
REMARK 6 A between atoms: C8_12 and C10_15
REMARK 7 A between atoms: C16_23 and C17_24
COMPND docked_2c6e_N15_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C10 LIG d 1 1.907 9.877 31.884 1.00 0.00 C
ATOM 2 C11 LIG d 1 0.629 10.091 31.344 1.00 0.00 C
ATOM 3 C12 LIG d 1 -0.264 9.029 31.136 1.00 0.00 C
ATOM 4 C13 LIG d 1 0.134 7.726 31.483 1.00 0.00 C
ATOM 5 C14 LIG d 1 1.402 7.531 32.017 1.00 0.00 C
ATOM 6 C15 LIG d 1 2.312 8.575 32.229 1.00 0.00 C
ATOM 7 N3 LIG d 1 1.492 6.185 32.251 1.00 0.00 N
ATOM 8 N4 LIG d 1 0.391 5.487 31.918 1.00 0.00 N
ATOM 9 C16 LIG d 1 -0.439 6.430 31.444 1.00 0.00 C
ATOM 10 H19 LIG d 1 2.296 5.762 32.631 1.00 0.00 H
ATOM 11 C8 LIG d 1 2.796 11.008 32.097 1.00 0.00 C
ATOM 12 C7 LIG d 1 3.205 11.482 33.327 1.00 0.00 C
ATOM 13 N1 LIG d 1 4.057 12.524 33.083 1.00 0.00 N
ATOM 14 N2 LIG d 1 4.190 12.793 31.766 1.00 0.00 N
ATOM 15 C9 LIG d 1 3.447 11.856 31.174 1.00 0.00 C
ATOM 16 C6 LIG d 1 4.706 13.420 34.027 1.00 0.00 C
ATOM 17 C5 LIG d 1 5.949 12.863 34.685 1.00 0.00 C
ATOM 18 N LIG d 1 7.120 13.504 34.318 1.00 0.00 N
ATOM 19 H11 LIG d 1 7.071 14.297 33.737 1.00 0.00 H
ATOM 20 O LIG d 1 5.935 11.909 35.459 1.00 0.00 O
ATOM 21 C4 LIG d 1 8.417 13.037 34.769 1.00 0.00 C
ATOM 22 C3 LIG d 1 9.550 13.422 33.815 1.00 0.00 C
ATOM 23 C1 LIG d 1 10.237 14.768 34.126 1.00 0.00 C
ATOM 24 C LIG d 1 10.269 14.992 35.640 1.00 0.00 C
ATOM 25 C2 LIG d 1 9.545 15.948 33.443 1.00 0.00 C
ATOM 26 C17 LIG d 1 -1.864 6.062 30.927 1.00 0.00 C
ATOM 27 N5 LIG d 1 -2.432 4.837 31.159 1.00 0.00 N
ATOM 28 C18 LIG d 1 -3.674 4.820 30.582 1.00 0.00 C
ATOM 29 H20 LIG d 1 -2.018 4.095 31.656 1.00 0.00 H
ATOM 30 C19 LIG d 1 -4.669 3.844 30.512 1.00 0.00 C
ATOM 31 C23 LIG d 1 -3.796 6.082 30.010 1.00 0.00 C
ATOM 32 C20 LIG d 1 -5.836 4.189 29.819 1.00 0.00 C
ATOM 33 C21 LIG d 1 -5.989 5.449 29.232 1.00 0.00 C
ATOM 34 C22 LIG d 1 -4.973 6.410 29.320 1.00 0.00 C
ATOM 35 N6 LIG d 1 -2.671 6.840 30.233 1.00 0.00 N
CONECT 1 2 11 6
CONECT 2 3 1
CONECT 3 2 4
CONECT 4 3 9 5
CONECT 5 4 6 7
CONECT 6 1 5
CONECT 7 8 5 10
CONECT 8 9 7
CONECT 9 26 4 8
CONECT 10 7
CONECT 11 15 1 12
CONECT 12 11 13
CONECT 13 14 12 16
CONECT 14 15 13
CONECT 15 14 11
CONECT 16 13 17
CONECT 17 16 18 20
CONECT 18 19 17 21
CONECT 19 18
CONECT 20 17
CONECT 21 22 18
CONECT 22 23 21
CONECT 23 25 22 24
CONECT 24 23
CONECT 25 23
CONECT 26 35 27 9
CONECT 27 28 26 29
CONECT 28 31 30 27
CONECT 29 27
CONECT 30 32 28
CONECT 31 34 35 28
CONECT 32 33 30
CONECT 33 34 32
CONECT 34 33 31
CONECT 35 31 26
MASTER 0 0 0 0 0 0 0 0 35 0 35 0
END

80
Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb Normal file
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MODEL 1
REMARK VINA RESULT: -8.2 0.000 0.000
REMARK 6 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C3_4 and C6_8
REMARK I between atoms: C6_8 and N_10
REMARK 2 A between atoms: C7_11 and N5_26
REMARK 3 A between atoms: C8_13 and N3_15
REMARK 4 A between atoms: N3_15 and C9_16
REMARK 5 A between atoms: C12_19 and S_22
REMARK 6 A between atoms: S_22 and N4_25
COMPND docked_2c6e_SKE_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C6 LIG d 1 -3.234 11.414 30.466 1.00 0.00 C
ATOM 2 O LIG d 1 -4.311 11.082 29.972 1.00 0.00 O
ATOM 3 N LIG d 1 -2.244 10.441 30.645 1.00 0.00 N
ATOM 4 C7 LIG d 1 -2.273 9.090 30.344 1.00 0.00 C
ATOM 5 N1 LIG d 1 -1.113 8.561 30.634 1.00 0.00 N
ATOM 6 C8 LIG d 1 -0.389 9.599 31.144 1.00 0.00 C
ATOM 7 N2 LIG d 1 -1.041 10.763 31.192 1.00 0.00 N
ATOM 8 N3 LIG d 1 0.875 9.459 31.585 1.00 0.00 N
ATOM 9 H3 LIG d 1 1.156 8.520 31.678 1.00 0.00 H
ATOM 10 C9 LIG d 1 1.876 10.382 31.942 1.00 0.00 C
ATOM 11 C10 LIG d 1 2.428 11.316 31.054 1.00 0.00 C
ATOM 12 C11 LIG d 1 3.440 12.194 31.458 1.00 0.00 C
ATOM 13 C12 LIG d 1 3.925 12.131 32.763 1.00 0.00 C
ATOM 14 C13 LIG d 1 3.393 11.217 33.671 1.00 0.00 C
ATOM 15 C14 LIG d 1 2.380 10.348 33.255 1.00 0.00 C
ATOM 16 S LIG d 1 5.210 13.235 33.282 1.00 0.00 S
ATOM 17 O1 LIG d 1 5.393 13.092 34.708 1.00 0.00 O
ATOM 18 O2 LIG d 1 6.304 13.142 32.345 1.00 0.00 O
ATOM 19 N4 LIG d 1 4.470 14.733 33.066 1.00 0.00 N
ATOM 20 H8 LIG d 1 5.185 15.454 32.966 1.00 0.00 H
ATOM 21 H9 LIG d 1 3.886 14.943 33.875 1.00 0.00 H
ATOM 22 N5 LIG d 1 -3.344 8.449 29.836 1.00 0.00 N
ATOM 23 H10 LIG d 1 -3.667 7.620 30.257 1.00 0.00 H
ATOM 24 H11 LIG d 1 -3.802 8.809 29.042 1.00 0.00 H
ATOM 25 C3 LIG d 1 -3.033 12.817 30.827 1.00 0.00 C
ATOM 26 C2 LIG d 1 -3.589 13.318 31.996 1.00 0.00 C
ATOM 27 C1 LIG d 1 -3.406 14.655 32.345 1.00 0.00 C
ATOM 28 F1 LIG d 1 -4.289 12.524 32.816 1.00 0.00 F
ATOM 29 C LIG d 1 -2.662 15.494 31.511 1.00 0.00 C
ATOM 30 C5 LIG d 1 -2.104 14.990 30.333 1.00 0.00 C
ATOM 31 C4 LIG d 1 -2.294 13.652 29.997 1.00 0.00 C
ATOM 32 F LIG d 1 -1.769 13.185 28.856 1.00 0.00 F
CONECT 1 2 3 25
CONECT 2 1
CONECT 3 4 1 7
CONECT 4 22 5 3
CONECT 5 4 6
CONECT 6 5 7 8
CONECT 7 3 6
CONECT 8 6 9 10
CONECT 9 8
CONECT 10 11 8 15
CONECT 11 12 10
CONECT 12 11 13
CONECT 13 12 16 14
CONECT 14 13 15
CONECT 15 10 14
CONECT 16 18 13 19 17
CONECT 16
CONECT 17 16
CONECT 18 16
CONECT 19 20 16 21
CONECT 20 19
CONECT 21 19
CONECT 22 24 23 4
CONECT 23 22
CONECT 24 22
CONECT 25 31 1 26
CONECT 26 25 27 28
CONECT 27 29 26
CONECT 28 26
CONECT 29 30 27
CONECT 30 31 29
CONECT 31 32 30 25
CONECT 32 31
MASTER 0 0 0 0 0 0 0 0 32 0 32 0
END

89
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MODEL 1
REMARK VINA RESULT: -7.3 0.000 0.000
REMARK 7 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_2 and C1_3
REMARK 2 A between atoms: C6_8 and N_9
REMARK I between atoms: N_9 and C7_10
REMARK 3 A between atoms: C7_10 and C8_12
REMARK 4 A between atoms: C9_13 and C10_14
REMARK 5 A between atoms: C10_14 and N1_15
REMARK 6 A between atoms: C16_21 and N4_25
REMARK 7 A between atoms: N4_25 and C18_26
COMPND docked_3w2p_1C9_pH74_netcharge.pdbqt
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C1 LIG d 1 2.459 8.907 32.684 1.00 0.00 C
ATOM 2 C2 LIG d 1 1.527 7.870 32.783 1.00 0.00 C
ATOM 3 C3 LIG d 1 0.412 7.804 31.953 1.00 0.00 C
ATOM 4 C4 LIG d 1 0.224 8.799 30.986 1.00 0.00 C
ATOM 5 C5 LIG d 1 1.173 9.845 30.874 1.00 0.00 C
ATOM 6 C6 LIG d 1 2.277 9.913 31.723 1.00 0.00 C
ATOM 7 C16 LIG d 1 -0.931 8.661 30.183 1.00 0.00 C
ATOM 8 N2 LIG d 1 -1.781 7.631 30.339 1.00 0.00 N
ATOM 9 C17 LIG d 1 -1.492 6.747 31.298 1.00 0.00 C
ATOM 10 N3 LIG d 1 -0.434 6.786 32.116 1.00 0.00 N
ATOM 11 N LIG d 1 3.233 10.952 31.680 1.00 0.00 N
ATOM 12 C7 LIG d 1 4.169 11.203 30.706 1.00 0.00 C
ATOM 13 O1 LIG d 1 4.392 10.531 29.705 1.00 0.00 O
ATOM 14 H5 LIG d 1 3.228 11.572 32.444 1.00 0.00 H
ATOM 15 C8 LIG d 1 5.001 12.413 30.948 1.00 0.00 C
ATOM 16 C9 LIG d 1 4.871 13.240 32.001 1.00 0.00 C
ATOM 17 C10 LIG d 1 5.654 14.507 32.237 1.00 0.00 C
ATOM 18 N1 LIG d 1 5.172 15.341 33.342 1.00 0.00 N
ATOM 19 C11 LIG d 1 4.160 14.621 34.131 1.00 0.00 C
ATOM 20 C12 LIG d 1 3.343 15.558 35.018 1.00 0.00 C
ATOM 21 C13 LIG d 1 2.564 16.579 34.187 1.00 0.00 C
ATOM 22 C14 LIG d 1 3.202 16.821 32.823 1.00 0.00 C
ATOM 23 C15 LIG d 1 4.720 16.670 32.889 1.00 0.00 C
ATOM 24 H10 LIG d 1 5.959 15.528 33.963 1.00 0.00 H
ATOM 25 O LIG d 1 3.577 9.043 33.477 1.00 0.00 O
ATOM 26 C LIG d 1 3.637 8.242 34.648 1.00 0.00 C
ATOM 27 N4 LIG d 1 -1.189 9.631 29.177 1.00 0.00 N
ATOM 28 H22 LIG d 1 -0.888 9.387 28.273 1.00 0.00 H
ATOM 29 C18 LIG d 1 -1.812 10.893 29.282 1.00 0.00 C
ATOM 30 C19 LIG d 1 -2.632 11.149 30.396 1.00 0.00 C
ATOM 31 C20 LIG d 1 -3.224 12.400 30.587 1.00 0.00 C
ATOM 32 C21 LIG d 1 -2.981 13.419 29.675 1.00 0.00 C
ATOM 33 C22 LIG d 1 -2.145 13.202 28.584 1.00 0.00 C
ATOM 34 F LIG d 1 -3.556 14.615 29.874 1.00 0.00 F
ATOM 35 C23 LIG d 1 -1.554 11.949 28.396 1.00 0.00 C
ATOM 36 Cl LIG d 1 -1.819 14.472 27.463 1.00 0.00 Cl
CONECT 1 6 2 25
CONECT 2 3 1
CONECT 3 4 10 2
CONECT 4 7 5 3
CONECT 5 4 6
CONECT 6 5 11 1
CONECT 7 27 8 4
CONECT 8 7 9
CONECT 9 8 10
CONECT 10 9 3
CONECT 11 12 6 14
CONECT 12 13 15 11
CONECT 13 12
CONECT 14 11
CONECT 15 12 16
CONECT 16 15 17
CONECT 17 16 18
CONECT 18 17 23 24 19
CONECT 18
CONECT 19 18 20
CONECT 20 19 21
CONECT 21 22 20
CONECT 22 23 21
CONECT 23 22 18
CONECT 24 18
CONECT 25 1 26
CONECT 26 25
CONECT 27 28 29 7
CONECT 28 27
CONECT 29 35 27 30
CONECT 30 29 31
CONECT 31 32 30
CONECT 32 33 34 31
CONECT 33 36 35 32
CONECT 34 32
CONECT 35 33 29
CONECT 36 33
MASTER 0 0 0 0 0 0 0 0 36 0 36 0
END

55
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HETATM 1 C1 SKE A 401 1.488 7.044 32.935 1.00 46.39 C
HETATM 2 N1 SKE A 401 2.835 7.154 33.072 1.00 41.54 N
HETATM 3 O1 SKE A 401 -6.931 4.694 29.366 1.00 63.10 O
HETATM 4 C2 SKE A 401 -0.389 6.180 32.539 1.00 46.08 C
HETATM 5 N2 SKE A 401 0.887 5.836 32.854 1.00 44.73 N
HETATM 6 O2 SKE A 401 -7.233 6.869 29.971 1.00 55.97 O
HETATM 7 C3 SKE A 401 -2.661 5.392 31.980 1.00 49.24 C
HETATM 8 N3 SKE A 401 -1.398 5.261 32.491 1.00 50.33 N
HETATM 9 O3 SKE A 401 2.003 9.847 32.711 1.00 57.98 O
HETATM 10 C4 SKE A 401 -3.390 4.210 31.742 1.00 48.24 C
HETATM 11 N4 SKE A 401 -7.888 5.165 31.608 1.00 63.28 N
HETATM 12 C5 SKE A 401 -4.712 4.290 31.271 1.00 46.59 C
HETATM 13 N5 SKE A 401 -0.598 7.496 32.384 1.00 46.80 N
HETATM 14 C6 SKE A 401 -5.342 5.536 31.046 1.00 53.17 C
HETATM 15 N6 SKE A 401 0.699 8.008 32.456 1.00 49.69 N
HETATM 16 C7 SKE A 401 -4.594 6.711 31.255 1.00 51.47 C
HETATM 17 C8 SKE A 401 -3.281 6.638 31.735 1.00 48.76 C
HETATM 18 C9 SKE A 401 0.892 9.376 32.550 1.00 52.86 C
HETATM 19 C10 SKE A 401 -0.295 10.306 32.501 1.00 51.73 C
HETATM 20 C11 SKE A 401 -1.140 10.319 31.383 1.00 50.46 C
HETATM 21 C12 SKE A 401 -2.272 11.129 31.323 1.00 50.35 C
HETATM 22 C13 SKE A 401 -2.544 11.971 32.406 1.00 52.34 C
HETATM 23 C14 SKE A 401 -1.735 11.942 33.550 1.00 51.66 C
HETATM 24 C15 SKE A 401 -0.594 11.130 33.596 1.00 53.33 C
HETATM 25 F1 SKE A 401 -0.852 9.565 30.327 1.00 51.73 F
HETATM 26 F2 SKE A 401 0.181 11.144 34.710 1.00 51.81 F
HETATM 27 S SKE A 401 -6.870 5.596 30.471 1.00 59.71 S
CONECT 1 2 5 15
CONECT 2 1
CONECT 3 27
CONECT 4 5 8 13
CONECT 5 1 4
CONECT 6 27
CONECT 7 8 10 17
CONECT 8 4 7
CONECT 9 18
CONECT 10 7 12
CONECT 11 27
CONECT 12 10 14
CONECT 13 4 15
CONECT 14 12 16 27
CONECT 15 1 13 18
CONECT 16 14 17
CONECT 17 7 16
CONECT 18 9 15 19
CONECT 19 18 20 24
CONECT 20 19 21 25
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 22 24
CONECT 24 19 23 26
CONECT 25 20
CONECT 26 24
CONECT 27 3 6 11 14
END

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