# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 15:17:33 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[5-(1-methylpyrazol-4-yl)pyridin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cncc(c2)c3ccc(cc3)C(N)=O
#
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
 BV9  BV9  4-[5-(1-methylpyrazol-4-yl)pyridin-3-yl]benzamide  ligand  35  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BV9
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
 BV9  CAA  C  CR16  0  -0.252   3.2084   1.1309  -0.6347
 BV9  CAB  C  CR6   0  -0.049   4.1791   0.3209  -0.0504
 BV9  CAC  C  CR16  0  -0.265   3.8137  -0.9463   0.3977
 BV9  CAD  C  CR16  0  -0.292   2.5067  -1.3876   0.2743
 BV9  CAE  C  CR6   0   0.081   1.5290  -0.5727  -0.2955
 BV9  CAF  C  CR16  0  -0.296   1.9001   0.6953  -0.7456
 BV9  CAG  C  C     0   0.488   5.5805   0.8382   0.0311
 BV9  CAJ  C  CR6   0   0.018   0.1385  -1.0418  -0.4227
 BV9  CAK  C  CR16  0  -0.111  -0.1460  -2.3615  -0.7717
 BV9  CAM  C  CR16  0  -0.126  -2.3935  -2.0109  -0.6767
 BV9  CAN  C  CR6   0   0.026  -2.2426  -0.6699  -0.3182
 BV9  CAO  C  CR16  0  -0.275  -0.9402  -0.1944  -0.1950
 BV9  CAP  C  CR5   0  -0.148  -3.3970   0.1870  -0.0816
 BV9  CAQ  C  CR15  0  -0.095  -3.4690   1.5931  -0.1392
 BV9  CAT  C  CR15  0   0.022  -4.6851  -0.1894   0.2548
 BV9  NAH  N  NH2   0  -0.812   6.3680   0.2767   0.9604
 BV9  NAL  N  N     0  -0.388  -1.3784  -2.8324  -0.8938
 BV9  NAR  N  N     0  -0.275  -4.6834   2.0269   0.1329
 BV9  NAS  N  NR5   0  -0.265  -5.4038   0.9356   0.3727
 BV9  OAI  O  O     0  -0.480   5.9684   1.7211  -0.7221
 BV9  H1   H  HCR6  0   0.265   3.4765   2.1112  -1.0052
 BV9  H2   H  HCR6  0   0.263   4.5431  -1.6160   0.8350
 BV9  H3   H  HCR6  0   0.264   2.2467  -2.3712   0.6437
 BV9  H4   H  HCR6  0   0.262   1.1657   1.3418  -1.2099
 BV9  H5   H  HCR6  0   0.263   0.6591  -3.0581  -0.9804
 BV9  H6   H  HCR6  0   0.259  -3.3859  -2.4314  -0.8029
 BV9  H7   H  HCR6  0   0.265  -0.7639   0.8303   0.1101
 BV9  H8   H  HCR5  0   0.260  -2.6834   2.2936  -0.3813
 BV9  H9   H  HCR5  0   0.296  -5.1209  -1.1596   0.4323
 BV9  H10  H  HCH3  0   0.264  -6.9354   1.7119   1.5543
 BV9  H11  H  HCH3  0   0.262  -7.3642   1.4414  -0.1465
 BV9  H12  H  HCH3  0   0.260  -7.1896   0.0666   0.9545
 BV9  H13  H  HNH2  0   0.413   6.0127  -0.3364   1.6730
 BV9  H14  H  HNH2  0   0.406   7.3140   0.6034   1.0726
 BV9  CAU  C  CH3   0  -0.507  -6.8049   1.0499   0.7012

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
 BV9  OAI  CAG  double    1.224  0.020  1.224
 BV9  CAG  NAH  single    1.341  0.020  1.341
 BV9  CAG  CAB  single    1.496  0.020  1.496
 BV9  CAC  CAB  aromatic  1.393  0.020  1.393
 BV9  CAC  CAD  aromatic  1.385  0.020  1.385
 BV9  CAB  CAA  aromatic  1.393  0.020  1.393
 BV9  CAD  CAE  aromatic  1.394  0.020  1.394
 BV9  CAK  NAL  aromatic  1.325  0.020  1.325
 BV9  CAK  CAJ  aromatic  1.394  0.020  1.394
 BV9  CAA  CAF  aromatic  1.383  0.020  1.383
 BV9  CAE  CAJ  single    1.473  0.020  1.473
 BV9  CAE  CAF  aromatic  1.396  0.020  1.396
 BV9  NAL  CAM  aromatic  1.324  0.020  1.324
 BV9  CAJ  CAO  aromatic  1.391  0.020  1.391
 BV9  CAM  CAN  aromatic  1.396  0.020  1.396
 BV9  CAO  CAN  aromatic  1.392  0.020  1.392
 BV9  CAN  CAP  single    1.457  0.020  1.457
 BV9  CAP  CAT  aromatic  1.383  0.020  1.383
 BV9  CAP  CAQ  aromatic  1.409  0.020  1.409
 BV9  CAT  NAS  aromatic  1.340  0.020  1.340
 BV9  CAQ  NAR  aromatic  1.318  0.020  1.318
 BV9  NAS  NAR  aromatic  1.329  0.020  1.329
 BV9  NAS  CAU  single    1.444  0.020  1.444
 BV9  CAA  H1   single    0.930  0.020  1.080
 BV9  CAC  H2   single    0.930  0.020  1.080
 BV9  CAD  H3   single    0.930  0.020  1.080
 BV9  CAF  H4   single    0.930  0.020  1.080
 BV9  CAK  H5   single    0.930  0.020  1.080
 BV9  CAM  H6   single    0.930  0.020  1.080
 BV9  CAO  H7   single    0.930  0.020  1.080
 BV9  CAQ  H8   single    0.930  0.020  1.080
 BV9  CAT  H9   single    0.930  0.020  1.080
 BV9  CAU  H10  single    0.970  0.020  1.090
 BV9  CAU  H11  single    0.970  0.020  1.090
 BV9  CAU  H12  single    0.970  0.020  1.090
 BV9  NAH  H13  single    0.860  0.020  1.020
 BV9  NAH  H14  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
 BV9  H1   CAA  CAF  119.49  3.000
 BV9  H1   CAA  CAB  119.87  3.000
 BV9  CAF  CAA  CAB  120.64  3.000
 BV9  CAG  CAB  CAC  122.87  3.000
 BV9  CAC  CAB  CAA  118.77  3.000
 BV9  CAG  CAB  CAA  118.34  3.000
 BV9  H2   CAC  CAD  118.34  3.000
 BV9  H2   CAC  CAB  121.07  3.000
 BV9  CAD  CAC  CAB  120.58  3.000
 BV9  H3   CAD  CAE  120.13  3.000
 BV9  H3   CAD  CAC  119.07  3.000
 BV9  CAE  CAD  CAC  120.79  3.000
 BV9  CAJ  CAE  CAF  120.82  3.000
 BV9  CAF  CAE  CAD  118.44  3.000
 BV9  CAJ  CAE  CAD  120.74  3.000
 BV9  H4   CAF  CAE  120.02  3.000
 BV9  H4   CAF  CAA  119.19  3.000
 BV9  CAE  CAF  CAA  120.77  3.000
 BV9  OAI  CAG  NAH  122.84  3.000
 BV9  NAH  CAG  CAB  116.30  3.000
 BV9  OAI  CAG  CAB  120.86  3.000
 BV9  CAO  CAJ  CAK  117.35  3.000
 BV9  CAO  CAJ  CAE  121.61  3.000
 BV9  CAK  CAJ  CAE  121.04  3.000
 BV9  H5   CAK  NAL  116.38  3.000
 BV9  H5   CAK  CAJ  120.29  3.000
 BV9  NAL  CAK  CAJ  123.31  3.000
 BV9  H6   CAM  NAL  116.21  3.000
 BV9  H6   CAM  CAN  120.05  3.000
 BV9  NAL  CAM  CAN  123.73  3.000
 BV9  CAP  CAN  CAO  121.74  3.000
 BV9  CAP  CAN  CAM  121.39  3.000
 BV9  CAO  CAN  CAM  116.86  3.000
 BV9  H7   CAO  CAN  120.01  3.000
 BV9  H7   CAO  CAJ  119.75  3.000
 BV9  CAN  CAO  CAJ  120.21  3.000
 BV9  CAT  CAP  CAQ  103.53  3.000
 BV9  CAQ  CAP  CAN  128.36  3.000
 BV9  CAT  CAP  CAN  128.11  3.000
 BV9  H8   CAQ  NAR  120.20  3.000
 BV9  H8   CAQ  CAP  128.26  3.000
 BV9  NAR  CAQ  CAP  111.53  3.000
 BV9  H9   CAT  NAS  121.60  3.000
 BV9  H9   CAT  CAP  131.39  3.000
 BV9  NAS  CAT  CAP  106.99  3.000
 BV9  H14  NAH  H13  116.81  3.000
 BV9  H14  NAH  CAG  119.53  3.000
 BV9  H13  NAH  CAG  122.62  3.000
 BV9  CAM  NAL  CAK  118.53  3.000
 BV9  NAS  NAR  CAQ  105.44  3.000
 BV9  NAR  NAS  CAU  120.13  3.000
 BV9  CAU  NAS  CAT  127.37  3.000
 BV9  NAR  NAS  CAT  112.50  3.000
 BV9  H12  CAU  H11  108.99  3.000
 BV9  H12  CAU  H10  109.00  3.000
 BV9  H11  CAU  H10  109.28  3.000
 BV9  H12  CAU  NAS  108.98  3.000
 BV9  H11  CAU  NAS  110.49  3.000
 BV9  H10  CAU  NAS  110.07  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
 BV9  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 BV9  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 BV9  CONST_03  CAJ  CAE  CAF  CAA  180.00   0.0  0
 BV9  CONST_04  CAE  CAD  CAC  CAB    0.00   0.0  0
 BV9  CONST_05  CAE  CAF  CAA  CAB    0.00   0.0  0
 BV9  CONST_06  CAF  CAA  CAB  CAC    0.00   0.0  0
 BV9  CONST_07  CAJ  CAE  CAD  CAC  180.00   0.0  0
 BV9  CONST_08  CAF  CAE  CAD  CAC    0.00   0.0  0
 BV9  CONST_11  NAL  CAK  CAJ  CAE  180.00   0.0  0
 BV9  CONST_12  CAN  CAO  CAJ  CAE  180.00   0.0  0
 BV9  CONST_15  CAM  NAL  CAK  CAJ    0.00   0.0  0
 BV9  CONST_16  CAM  CAN  CAO  CAJ    0.00   0.0  0
 BV9  CONST_17  CAP  CAN  CAO  CAJ  180.00   0.0  0
 BV9  CONST_18  CAN  CAM  NAL  CAK    0.00   0.0  0
 BV9  CONST_19  CAN  CAO  CAJ  CAK    0.00   0.0  0
 BV9  CONST_22  NAS  CAT  CAP  CAN  180.00   0.0  0
 BV9  CONST_23  NAR  CAQ  CAP  CAN  180.00   0.0  0
 BV9  CONST_24  NAL  CAK  CAJ  CAO    0.00   0.0  0
 BV9  CONST_25  NAL  CAM  CAN  CAO    0.00   0.0  0
 BV9  CONST_28  NAL  CAM  CAN  CAP  180.00   0.0  0
 BV9  CONST_29  NAR  NAS  CAT  CAP    0.00   0.0  0
 BV9  CONST_30  NAS  NAR  CAQ  CAP    0.00   0.0  0
 BV9  CONST_31  NAS  CAT  CAP  CAQ    0.00   0.0  0
 BV9  CONST_32  CAT  NAS  NAR  CAQ    0.00   0.0  0
 BV9  CONST_33  NAR  CAQ  CAP  CAT    0.00   0.0  0
 BV9  CONST_34  CAG  CAB  CAC  CAD  180.00   0.0  0
 BV9  CONST_35  CAG  CAB  CAA  CAF  180.00   0.0  0
 BV9  CONST_36  CAU  NAS  CAT  CAP  180.00   0.0  0
 BV9  CONST_37  CAU  NAS  NAR  CAQ  180.00   0.0  0
 BV9  CONST_38  H2   CAC  CAB  CAA  180.00   0.0  0
 BV9  CONST_39  H3   CAD  CAC  CAB  180.00   0.0  0
 BV9  CONST_40  H4   CAF  CAA  CAB  180.00   0.0  0
 BV9  CONST_41  H1   CAA  CAB  CAC  180.00   0.0  0
 BV9  CONST_42  H5   CAK  CAJ  CAE    0.00   0.0  0
 BV9  CONST_43  H7   CAO  CAJ  CAE    0.00   0.0  0
 BV9  CONST_44  H6   CAM  NAL  CAK  180.00   0.0  0
 BV9  CONST_45  H9   CAT  CAP  CAN    0.00   0.0  0
 BV9  CONST_46  H8   CAQ  CAP  CAN    0.00   0.0  0
 BV9  CONST_47  H13  NAH  CAG  CAB    0.00   0.0  0
 BV9  CONST_48  H14  NAH  CAG  CAB  180.00   0.0  0
 BV9  Var_01    OAI  CAG  CAB  CAA  -22.04  30.0  2
 BV9  Var_02    H10  CAU  NAS  CAT  125.74  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
 BV9  plan-1  CAN  0.020
 BV9  plan-1  CAP  0.020
 BV9  plan-1  CAQ  0.020
 BV9  plan-1  CAT  0.020
 BV9  plan-1  NAR  0.020
 BV9  plan-1  NAS  0.020
 BV9  plan-1  H8   0.020
 BV9  plan-1  H9   0.020
 BV9  plan-1  CAU  0.020
 BV9  plan-2  CAA  0.020
 BV9  plan-2  CAB  0.020
 BV9  plan-2  CAC  0.020
 BV9  plan-2  CAD  0.020
 BV9  plan-2  CAE  0.020
 BV9  plan-2  CAF  0.020
 BV9  plan-2  CAG  0.020
 BV9  plan-2  CAJ  0.020
 BV9  plan-2  H1   0.020
 BV9  plan-2  H2   0.020
 BV9  plan-2  H3   0.020
 BV9  plan-2  H4   0.020
 BV9  plan-3  CAE  0.020
 BV9  plan-3  CAJ  0.020
 BV9  plan-3  CAK  0.020
 BV9  plan-3  CAM  0.020
 BV9  plan-3  CAN  0.020
 BV9  plan-3  CAO  0.020
 BV9  plan-3  CAP  0.020
 BV9  plan-3  NAL  0.020
 BV9  plan-3  H5   0.020
 BV9  plan-3  H6   0.020
 BV9  plan-3  H7   0.020
 BV9  plan-4  CAB  0.020
 BV9  plan-4  CAG  0.020
 BV9  plan-4  NAH  0.020
 BV9  plan-4  OAI  0.020
 BV9  plan-4  H13  0.020
 BV9  plan-4  H14  0.020

