# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:42:35 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-azanyl-6-(1~{H}-imidazol-2-ylmethylsulfanyl)-4-phenyl-pyridine-3,5-dicarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCc2[nH]ccn2)c(C#N)c(c3ccccc3)c1C#N
#
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
 RVZ  RVZ  2-azanyl-6-(1~{H}-imidazol-2-ylmethylsulfanyl)-4-phenyl-pyridine-3,5-dicarbonitrile  ligand  36  24  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RVZ
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
 RVZ  C10  C  CR16  0  -0.247  21.6543  178.6679  159.5741
 RVZ  C13  C  CR6   0  -0.093  22.6128  174.0085  157.7212
 RVZ  C21  C  CR15  0  -0.101  21.0961  170.6355  153.3851
 RVZ  C22  C  CR15  0  -0.222  20.5422  169.5883  154.0618
 RVZ  C02  C  CR6   0   0.550  20.3491  172.4850  158.0513
 RVZ  C03  C  CR6   0  -0.202  20.3481  173.8449  158.4696
 RVZ  C04  C  CSP   0  -0.004  19.1610  174.4098  158.9978
 RVZ  C06  C  CR6   0   0.363  21.4975  174.6099  158.3059
 RVZ  C07  C  CR6   0  -0.026  21.5410  176.0180  158.7415
 RVZ  C08  C  CR16  0  -0.268  21.7931  177.0304  157.8182
 RVZ  C09  C  CR16  0  -0.240  21.8443  178.3516  158.2353
 RVZ  C11  C  CR16  0  -0.240  21.4047  177.6603  160.4962
 RVZ  C12  C  CR16  0  -0.268  21.3431  176.3382  160.0829
 RVZ  C16  C  CR6   0   0.116  22.5156  172.6555  157.3327
 RVZ  C18  C  CH2   0  -0.666  23.3116  170.2458  156.2338
 RVZ  C19  C  CR5   0   0.491  22.2403  170.1922  155.2021
 RVZ  N01  N  NH2   0  -0.811  19.2856  171.7025  158.1813
 RVZ  N05  N  NS    0  -0.233  18.1676  174.8255  159.4115
 RVZ  N15  N  NS    0  -0.231  24.8352  175.2599  157.4063
 RVZ  N20  N  NR15  0  -0.593  22.1805  171.0058  154.1284
 RVZ  N23  N  N     0  -0.450  21.2619  169.3233  155.1940
 RVZ  N24  N  N     0  -0.467  21.4365  171.9377  157.4989
 RVZ  S17  S  S2    0   0.112  23.9193  171.9116  156.6016
 RVZ  H1   H  HCR6  0   0.265  21.7010  179.6992  159.8984
 RVZ  H3   H  HCR5  0   0.248  19.6643  169.0191  153.7982
 RVZ  H4   H  HCR6  0   0.270  21.9337  176.7892  156.7720
 RVZ  H5   H  HCR6  0   0.266  22.0340  179.1341  157.5126
 RVZ  H6   H  HCR6  0   0.266  21.2602  177.9016  161.5409
 RVZ  H7   H  HCR6  0   0.270  21.1608  175.5544  160.8077
 RVZ  H8   H  HCH2  0   0.316  22.9682  169.7606  157.1454
 RVZ  H9   H  HCH2  0   0.327  24.2099  169.7209  155.8977
 RVZ  H10  H  HNH2  0   0.418  19.3281  170.7561  157.8392
 RVZ  H11  H  HNH2  0   0.427  18.4149  172.0192  158.5737
 RVZ  H12  H  HNR5  0   0.417  22.8217  171.7529  153.9084
 RVZ  C14  C  CSP   0  -0.041  23.8301  174.7133  157.5526
 RVZ  H2   H  HCR5  0   0.283  20.8206  171.1406  152.4751

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
 RVZ  C21  C22  aromatic  1.364  0.020  1.364
 RVZ  C21  N20  aromatic  1.366  0.020  1.366
 RVZ  C22  N23  aromatic  1.368  0.020  1.368
 RVZ  N20  C19  aromatic  1.348  0.020  1.348
 RVZ  N23  C19  aromatic  1.308  0.020  1.308
 RVZ  C19  C18  single    1.488  0.020  1.488
 RVZ  C18  S17  single    1.811  0.020  1.811
 RVZ  S17  C16  single    1.749  0.020  1.749
 RVZ  N15  C14  triple    1.153  0.020  1.153
 RVZ  C14  C13  single    1.417  0.020  1.417
 RVZ  C16  C13  aromatic  1.411  0.020  1.411
 RVZ  C16  N24  aromatic  1.307  0.020  1.307
 RVZ  C08  C09  aromatic  1.386  0.020  1.386
 RVZ  C08  C07  aromatic  1.393  0.020  1.393
 RVZ  C13  C06  aromatic  1.395  0.020  1.395
 RVZ  N24  C02  aromatic  1.337  0.020  1.337
 RVZ  C09  C10  aromatic  1.389  0.020  1.389
 RVZ  C02  C03  aromatic  1.423  0.020  1.423
 RVZ  C02  N01  single    1.327  0.020  1.327
 RVZ  C06  C03  aromatic  1.390  0.020  1.390
 RVZ  C06  C07  single    1.475  0.020  1.475
 RVZ  C03  C04  single    1.417  0.020  1.417
 RVZ  C07  C12  aromatic  1.393  0.020  1.393
 RVZ  C10  C11  aromatic  1.389  0.020  1.389
 RVZ  C04  N05  triple    1.154  0.020  1.154
 RVZ  C12  C11  aromatic  1.387  0.020  1.387
 RVZ  C10  H1   single    0.930  0.020  1.080
 RVZ  C21  H2   single    0.930  0.020  1.080
 RVZ  C22  H3   single    0.930  0.020  1.080
 RVZ  C08  H4   single    0.930  0.020  1.080
 RVZ  C09  H5   single    0.930  0.020  1.080
 RVZ  C11  H6   single    0.930  0.020  1.080
 RVZ  C12  H7   single    0.930  0.020  1.080
 RVZ  C18  H8   single    0.970  0.020  1.090
 RVZ  C18  H9   single    0.970  0.020  1.090
 RVZ  N01  H10  single    0.860  0.020  1.020
 RVZ  N01  H11  single    0.860  0.020  1.020
 RVZ  N20  H12  single    0.860  0.020  1.020

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
 RVZ  H1   C10  C11  120.02  3.000
 RVZ  H1   C10  C09  120.01  3.000
 RVZ  C11  C10  C09  119.97  3.000
 RVZ  C16  C13  C14  120.22  3.000
 RVZ  C16  C13  C06  118.26  3.000
 RVZ  C14  C13  C06  121.48  3.000
 RVZ  H2   C21  N20  122.41  3.000
 RVZ  H2   C21  C22  132.49  3.000
 RVZ  N20  C21  C22  105.10  3.000
 RVZ  H3   C22  N23  121.89  3.000
 RVZ  H3   C22  C21  127.89  3.000
 RVZ  N23  C22  C21  110.22  3.000
 RVZ  N24  C02  N01  116.81  3.000
 RVZ  N01  C02  C03  122.30  3.000
 RVZ  N24  C02  C03  120.89  3.000
 RVZ  C06  C03  C04  121.14  3.000
 RVZ  C04  C03  C02  119.42  3.000
 RVZ  C06  C03  C02  119.39  3.000
 RVZ  N05  C04  C03  180.00  3.000
 RVZ  C07  C06  C03  121.00  3.000
 RVZ  C07  C06  C13  120.78  3.000
 RVZ  C03  C06  C13  118.23  3.000
 RVZ  C12  C07  C08  119.78  3.000
 RVZ  C12  C07  C06  119.99  3.000
 RVZ  C08  C07  C06  120.23  3.000
 RVZ  H4   C08  C09  119.87  3.000
 RVZ  H4   C08  C07  120.13  3.000
 RVZ  C09  C08  C07  119.99  3.000
 RVZ  H5   C09  C08  119.65  3.000
 RVZ  H5   C09  C10  120.21  3.000
 RVZ  C08  C09  C10  120.14  3.000
 RVZ  H6   C11  C12  119.65  3.000
 RVZ  H6   C11  C10  120.22  3.000
 RVZ  C12  C11  C10  120.13  3.000
 RVZ  H7   C12  C11  119.87  3.000
 RVZ  H7   C12  C07  120.12  3.000
 RVZ  C11  C12  C07  119.99  3.000
 RVZ  S17  C16  N24  118.84  3.000
 RVZ  N24  C16  C13  123.27  3.000
 RVZ  S17  C16  C13  117.88  3.000
 RVZ  H9   C18  H8   107.62  3.000
 RVZ  H9   C18  S17  103.19  3.000
 RVZ  H8   C18  S17  110.24  3.000
 RVZ  H9   C18  C19  111.16  3.000
 RVZ  H8   C18  C19  109.73  3.000
 RVZ  S17  C18  C19  114.55  3.000
 RVZ  N23  C19  N20  111.26  3.000
 RVZ  N23  C19  C18  124.50  3.000
 RVZ  N20  C19  C18  124.21  3.000
 RVZ  H11  N01  H10  117.69  3.000
 RVZ  H11  N01  C02  123.11  3.000
 RVZ  H10  N01  C02  119.15  3.000
 RVZ  H12  N20  C19  126.32  3.000
 RVZ  H12  N20  C21  125.92  3.000
 RVZ  C19  N20  C21  107.75  3.000
 RVZ  C19  N23  C22  105.66  3.000
 RVZ  C16  N24  C02  119.96  3.000
 RVZ  C18  S17  C16  101.94  3.000
 RVZ  N15  C14  C13  180.00  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
 RVZ  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 RVZ  CONST_02  C07  C12  C11  C10    0.00   0.0  0
 RVZ  CONST_03  C02  N24  C16  C13    0.00   0.0  0
 RVZ  CONST_04  C02  C03  C06  C13    0.00   0.0  0
 RVZ  CONST_07  C19  N23  C22  C21    0.00   0.0  0
 RVZ  CONST_08  N23  C19  N20  C21    0.00   0.0  0
 RVZ  CONST_09  C19  N20  C21  C22    0.00   0.0  0
 RVZ  CONST_10  N20  C19  N23  C22    0.00   0.0  0
 RVZ  CONST_11  C07  C06  C03  C02  180.00   0.0  0
 RVZ  CONST_12  C16  N24  C02  C03    0.00   0.0  0
 RVZ  CONST_13  C16  C13  C06  C03    0.00   0.0  0
 RVZ  CONST_16  N24  C16  C13  C06    0.00   0.0  0
 RVZ  CONST_17  N24  C02  C03  C06    0.00   0.0  0
 RVZ  CONST_18  C09  C08  C07  C06  180.00   0.0  0
 RVZ  CONST_19  C11  C12  C07  C06  180.00   0.0  0
 RVZ  CONST_20  C16  C13  C06  C07  180.00   0.0  0
 RVZ  CONST_21  C11  C10  C09  C08    0.00   0.0  0
 RVZ  CONST_22  C11  C12  C07  C08    0.00   0.0  0
 RVZ  CONST_23  C12  C07  C08  C09    0.00   0.0  0
 RVZ  CONST_24  C12  C11  C10  C09    0.00   0.0  0
 RVZ  CONST_25  N23  C22  C21  N20    0.00   0.0  0
 RVZ  CONST_26  C04  C03  C06  C13  180.00   0.0  0
 RVZ  CONST_27  C18  C19  N20  C21  180.00   0.0  0
 RVZ  CONST_28  C18  C19  N23  C22  180.00   0.0  0
 RVZ  CONST_29  S17  C16  N24  C02  180.00   0.0  0
 RVZ  CONST_30  C14  C13  C06  C03  180.00   0.0  0
 RVZ  CONST_31  N24  C02  C03  C04  180.00   0.0  0
 RVZ  CONST_32  C07  C06  C03  C04    0.00   0.0  0
 RVZ  CONST_33  S17  C16  C13  C06  180.00   0.0  0
 RVZ  CONST_34  N01  C02  C03  C06  180.00   0.0  0
 RVZ  CONST_35  C14  C13  C06  C07    0.00   0.0  0
 RVZ  CONST_36  N24  C16  C13  C14  180.00   0.0  0
 RVZ  CONST_37  N01  C02  N24  C16  180.00   0.0  0
 RVZ  CONST_38  H4   C08  C09  C10  180.00   0.0  0
 RVZ  CONST_39  H7   C12  C11  C10  180.00   0.0  0
 RVZ  CONST_40  H12  N20  C21  C22  180.00   0.0  0
 RVZ  CONST_41  H5   C09  C08  C07  180.00   0.0  0
 RVZ  CONST_42  H6   C11  C12  C07  180.00   0.0  0
 RVZ  CONST_43  H1   C10  C09  C08  180.00   0.0  0
 RVZ  CONST_44  H2   C21  N20  C19  180.00   0.0  0
 RVZ  CONST_45  H3   C22  N23  C19  180.00   0.0  0
 RVZ  CONST_46  H10  N01  C02  C03  180.00   0.0  0
 RVZ  CONST_47  H11  N01  C02  C03    0.00   0.0  0
 RVZ  Var_01    C19  C18  S17  C16   66.24  30.0  1
 RVZ  Var_02    N24  C16  S17  C18    2.17  30.0  2
 RVZ  Var_03    S17  C18  C19  N20   35.56  30.0  2

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
 RVZ  plan-1  C21  0.020
 RVZ  plan-1  C22  0.020
 RVZ  plan-1  C18  0.020
 RVZ  plan-1  C19  0.020
 RVZ  plan-1  N20  0.020
 RVZ  plan-1  N23  0.020
 RVZ  plan-1  H3   0.020
 RVZ  plan-1  H12  0.020
 RVZ  plan-1  H2   0.020
 RVZ  plan-2  C10  0.020
 RVZ  plan-2  C06  0.020
 RVZ  plan-2  C07  0.020
 RVZ  plan-2  C08  0.020
 RVZ  plan-2  C09  0.020
 RVZ  plan-2  C11  0.020
 RVZ  plan-2  C12  0.020
 RVZ  plan-2  H1   0.020
 RVZ  plan-2  H4   0.020
 RVZ  plan-2  H5   0.020
 RVZ  plan-2  H6   0.020
 RVZ  plan-2  H7   0.020
 RVZ  plan-3  C13  0.020
 RVZ  plan-3  C02  0.020
 RVZ  plan-3  C03  0.020
 RVZ  plan-3  C04  0.020
 RVZ  plan-3  C06  0.020
 RVZ  plan-3  C07  0.020
 RVZ  plan-3  C16  0.020
 RVZ  plan-3  N01  0.020
 RVZ  plan-3  N05  0.020
 RVZ  plan-3  N15  0.020
 RVZ  plan-3  N24  0.020
 RVZ  plan-3  S17  0.020
 RVZ  plan-3  C14  0.020
 RVZ  plan-4  C02  0.020
 RVZ  plan-4  N01  0.020
 RVZ  plan-4  H10  0.020
 RVZ  plan-4  H11  0.020

