# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:03:22 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 5-(thiophen-2-yl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cncc(c1)c2sccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VM1  VM1  '5-(thiophen-2-yl)pyridine-3-carboxylic acid'  ligand  20  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VM1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VM1  O1A  O  O      0  -0.587   2.7914  -2.0793   0.4476
 VM1  C1B  C  C      0   0.408   3.1414  -0.9100   0.2053
 VM1  O1C  O  OC    -1  -0.588   4.3015  -0.4739   0.0983
 VM1  S1D  S  S2     0   0.215  -2.2818  -1.2518  -0.5352
 VM1  C1E  C  CR15   0  -0.468  -3.9209  -0.8474  -0.2469
 VM1  C1F  C  CR15   0  -0.171  -4.0492   0.4368   0.1860
 VM1  C1G  C  CR6    0  -0.176   2.0194   0.1066   0.0265
 VM1  C1H  C  CR16   0  -0.241   0.6880  -0.2802   0.0499
 VM1  C1I  C  CR6    0   0.072  -0.3219   0.6690  -0.0899
 VM1  C1J  C  CR5    0  -0.219  -1.7395   0.3205  -0.0683
 VM1  C1K  C  CR15   0  -0.246  -2.8022   1.1059   0.2887
 VM1  C1L  C  CR16   0  -0.094   2.2868   1.4609  -0.1437
 VM1  N1M  N  N      0  -0.396   1.3419   2.3861  -0.2781
 VM1  C1N  C  CR16   0  -0.114   0.0772   1.9975  -0.2540
 VM1  H1H  H  HCR6   0   0.254   0.4498  -1.3278   0.1938
 VM1  H1K  H  HCR5   0   0.265  -2.7021   2.1286   0.6268
 VM1  H1L  H  HCR6   0   0.257   3.3119   1.8117  -0.1677
 VM1  H1N  H  HCR6   0   0.259  -0.6694   2.7734  -0.3830
 VM1  H1E  H  HCR5   0   0.298  -4.6937  -1.5802  -0.4151
 VM1  H1F  H  HCR5   0   0.270  -4.9992   0.8930   0.4230

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VM1  C1B  O1A  deloc     1.244  0.020  1.244
 VM1  C1G  C1B  single    1.525  0.020  1.525
 VM1  C1B  O1C  deloc     1.244  0.020  1.244
 VM1  C1E  S1D  aromatic  1.713  0.020  1.713
 VM1  S1D  C1J  aromatic  1.728  0.020  1.728
 VM1  C1E  C1F  aromatic  1.361  0.020  1.361
 VM1  C1E  H1E  single    0.930  0.020  1.080
 VM1  C1F  C1K  aromatic  1.419  0.020  1.419
 VM1  C1F  H1F  single    0.930  0.020  1.080
 VM1  C1H  C1G  aromatic  1.387  0.020  1.387
 VM1  C1L  C1G  aromatic  1.391  0.020  1.391
 VM1  C1I  C1H  aromatic  1.393  0.020  1.393
 VM1  C1H  H1H  single    0.930  0.020  1.080
 VM1  C1J  C1I  single    1.460  0.020  1.460
 VM1  C1N  C1I  aromatic  1.397  0.020  1.397
 VM1  C1J  C1K  aromatic  1.369  0.020  1.369
 VM1  C1K  H1K  single    0.930  0.020  1.080
 VM1  N1M  C1L  aromatic  1.329  0.020  1.329
 VM1  C1L  H1L  single    0.930  0.020  1.080
 VM1  C1N  N1M  aromatic  1.323  0.020  1.323
 VM1  C1N  H1N  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VM1  C1G  C1B  O1C  116.26  3.000
 VM1  O1C  C1B  O1A  127.48  3.000
 VM1  C1G  C1B  O1A  116.26  3.000
 VM1  C1J  S1D  C1E   92.29  3.000
 VM1  H1E  C1E  C1F  128.55  3.000
 VM1  H1E  C1E  S1D  119.95  3.000
 VM1  C1F  C1E  S1D  111.50  3.000
 VM1  H1F  C1F  C1K  123.91  3.000
 VM1  H1F  C1F  C1E  123.44  3.000
 VM1  C1K  C1F  C1E  112.65  3.000
 VM1  C1L  C1G  C1H  117.28  3.000
 VM1  C1L  C1G  C1B  121.47  3.000
 VM1  C1H  C1G  C1B  121.24  3.000
 VM1  H1H  C1H  C1I  120.84  3.000
 VM1  H1H  C1H  C1G  118.87  3.000
 VM1  C1I  C1H  C1G  120.29  3.000
 VM1  C1N  C1I  C1J  120.41  3.000
 VM1  C1N  C1I  C1H  116.91  3.000
 VM1  C1J  C1I  C1H  122.67  3.000
 VM1  C1K  C1J  C1I  128.37  3.000
 VM1  C1K  C1J  S1D  110.43  3.000
 VM1  C1I  C1J  S1D  121.20  3.000
 VM1  H1K  C1K  C1J  123.51  3.000
 VM1  H1K  C1K  C1F  123.35  3.000
 VM1  C1J  C1K  C1F  113.13  3.000
 VM1  H1L  C1L  N1M  116.41  3.000
 VM1  H1L  C1L  C1G  119.98  3.000
 VM1  N1M  C1L  C1G  123.60  3.000
 VM1  C1N  N1M  C1L  118.23  3.000
 VM1  H1N  C1N  N1M  116.46  3.000
 VM1  H1N  C1N  C1I  119.85  3.000
 VM1  N1M  C1N  C1I  123.68  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VM1  CONST_01  C1K  C1F  C1E  S1D    0.00   0.0  0
 VM1  CONST_04  C1F  C1K  C1J  S1D    0.00   0.0  0
 VM1  CONST_05  C1I  C1J  S1D  C1E  180.00   0.0  0
 VM1  CONST_06  C1K  C1J  S1D  C1E    0.00   0.0  0
 VM1  CONST_07  C1J  C1K  C1F  C1E    0.00   0.0  0
 VM1  CONST_08  C1J  S1D  C1E  C1F    0.00   0.0  0
 VM1  CONST_09  C1I  C1J  C1K  C1F  180.00   0.0  0
 VM1  CONST_10  C1J  C1I  C1H  C1G  180.00   0.0  0
 VM1  CONST_11  C1N  C1I  C1H  C1G    0.00   0.0  0
 VM1  CONST_12  C1N  N1M  C1L  C1G    0.00   0.0  0
 VM1  CONST_13  N1M  C1L  C1G  C1H    0.00   0.0  0
 VM1  CONST_15  N1M  C1N  C1I  C1H    0.00   0.0  0
 VM1  CONST_16  C1L  C1G  C1H  C1I    0.00   0.0  0
 VM1  CONST_17  C1L  N1M  C1N  C1I    0.00   0.0  0
 VM1  CONST_18  N1M  C1N  C1I  C1J  180.00   0.0  0
 VM1  CONST_20  C1I  C1H  C1G  C1B  180.00   0.0  0
 VM1  CONST_21  N1M  C1L  C1G  C1B  180.00   0.0  0
 VM1  CONST_22  H1F  C1F  C1E  S1D  180.00   0.0  0
 VM1  CONST_23  H1K  C1K  C1J  S1D  180.00   0.0  0
 VM1  CONST_24  H1L  C1L  C1G  C1H  180.00   0.0  0
 VM1  CONST_25  H1N  C1N  C1I  C1H  180.00   0.0  0
 VM1  CONST_26  H1E  C1E  S1D  C1J  180.00   0.0  0
 VM1  CONST_27  H1H  C1H  C1I  C1J    0.00   0.0  0
 VM1  Var_01    C1H  C1G  C1B  O1A   -3.97  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VM1  plan-1  S1D  0.020
 VM1  plan-1  C1E  0.020
 VM1  plan-1  C1F  0.020
 VM1  plan-1  C1I  0.020
 VM1  plan-1  C1J  0.020
 VM1  plan-1  C1K  0.020
 VM1  plan-1  H1K  0.020
 VM1  plan-1  H1E  0.020
 VM1  plan-1  H1F  0.020
 VM1  plan-2  C1B  0.020
 VM1  plan-2  C1G  0.020
 VM1  plan-2  C1H  0.020
 VM1  plan-2  C1I  0.020
 VM1  plan-2  C1J  0.020
 VM1  plan-2  C1L  0.020
 VM1  plan-2  N1M  0.020
 VM1  plan-2  C1N  0.020
 VM1  plan-2  H1H  0.020
 VM1  plan-2  H1L  0.020
 VM1  plan-2  H1N  0.020
 VM1  plan-3  O1A  0.020
 VM1  plan-3  C1B  0.020
 VM1  plan-3  O1C  0.020
 VM1  plan-3  C1G  0.020

