# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 13:33:27 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1c(N)n(nc1c2ccc(Oc3ccc(F)cc3F)cc2)[C@@H]4CCCN(C4)C#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
 JVP  JVP  5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide  ligand  52  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JVP
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
 JVP  C4    C  CR16  0  -0.317   1.8022  -0.2927   2.1301
 JVP  C7    C  CR5   0   0.327  -1.3122   0.7435   0.2914
 JVP  C6    C  CR6   0  -0.017   0.0925   0.4057   0.5692
 JVP  C9    C  CR5   0   0.634  -3.2390   1.6222  -0.3821
 JVP  C13   C  CH2   0  -0.444  -4.7728  -0.7552   1.9379
 JVP  C8    C  CR5   0  -0.397  -1.8618   1.8692  -0.3816
 JVP  C18   C  CSP   0   0.275  -7.1088  -1.7594  -0.9113
 JVP  C26   C  CR16  0  -0.286   5.4111  -1.8019  -0.1441
 JVP  C1    C  CR16  0  -0.286   1.0387   0.3574  -0.4506
 JVP  C2    C  CR16  0  -0.326   2.3537  -0.0057  -0.1987
 JVP  C3    C  CR6   0   0.364   2.7335  -0.3274   1.0976
 JVP  C5    C  CR16  0  -0.269   0.4946   0.0677   1.8619
 JVP  N10   N  NR5   0  -0.361  -3.4177   0.4633   0.2770
 JVP  N11   N  N     0  -0.313  -2.2500  -0.0891   0.6698
 JVP  C12   C  CH1   0  -0.109  -4.6576  -0.2465   0.5031
 JVP  C14   C  CH2   0  -0.455  -6.0729  -1.5336   2.1224
 JVP  C15   C  CH2   0  -0.323  -6.1841  -2.6568   1.1037
 JVP  N16   N  NT    0  -0.439  -6.0276  -2.1370  -0.2594
 JVP  C17   C  CH2   0  -0.313  -4.7912  -1.4012  -0.4958
 JVP  N19   N  NS    0  -0.339  -8.0569  -1.4666  -1.5108
 JVP  N20   N  NH2   0  -0.858  -4.2590   2.3893  -0.8421
 JVP  O22   O  O     0  -0.513  -1.9428   3.8447  -1.6454
 JVP  N23   N  NH2   0  -0.819   0.0057   3.3628  -0.6344
 JVP  O24   O  O2    0  -0.500   3.9967  -0.7078   1.4441
 JVP  C25   C  CR6   0   0.146   4.9873  -0.6558   0.5066
 JVP  C27   C  CR16  0  -0.421   6.4582  -1.7509  -1.0535
 JVP  C28   C  CR6   0   0.545   7.0596  -0.5327  -1.2996
 JVP  C29   C  CR16  0  -0.564   6.6605   0.6336  -0.6723
 JVP  C30   C  CR6   0   0.524   5.6196   0.5488   0.2284
 JVP  F31   F  F     0  -0.294   5.1982   1.6511   0.8512
 JVP  F32   F  F     0  -0.307   8.0672  -0.4682  -2.1778
 JVP  HC4   H  HCR6  0   0.275   2.1058  -0.5440   3.1382
 JVP  H13A  H  HCH2  0   0.246  -3.9225  -1.4024   2.1647
 JVP  H13B  H  HCH2  0   0.263  -4.7318   0.0891   2.6280
 JVP  HC26  H  HCR6  0   0.297   4.9229  -2.7441   0.0678
 JVP  HC1   H  HCR6  0   0.269   0.7501   0.5920  -1.4671
 JVP  HC2   H  HCR6  0   0.283   3.0555  -0.0440  -1.0211
 JVP  HC5   H  HCR6  0   0.260  -0.2232   0.0971   2.6711
 JVP  HC12  H  HCH1  0   0.270  -5.4700   0.4658   0.3336
 JVP  H14B  H  HCH2  0   0.261  -6.1131  -1.9559   3.1278
 JVP  H14A  H  HCH2  0   0.241  -6.9332  -0.8653   2.0237
 JVP  H15A  H  HCH2  0   0.266  -5.3946  -3.3960   1.2568
 JVP  H15B  H  HCH2  0   0.283  -7.1384  -3.1761   1.1736
 JVP  H17B  H  HCH2  0   0.290  -4.7735  -1.0419  -1.5244
 JVP  H17A  H  HCH2  0   0.277  -3.9568  -2.0944  -0.3709
 JVP  H20A  H  HNH2  0   0.395  -5.0946   1.9253  -1.1597
 JVP  H20B  H  HNH2  0   0.403  -3.9536   3.1286  -1.4567
 JVP  H23B  H  HNH2  0   0.409   0.5328   2.8273   0.0325
 JVP  H23A  H  HNH2  0   0.401   0.4230   4.2121  -0.9778
 JVP  HC27  H  HCR6  0   0.294   6.7927  -2.6446  -1.5619
 JVP  HC29  H  HCR6  0   0.313   7.1436   1.5803  -0.8763
 JVP  C21   C  C     0   0.459  -1.2750   3.0887  -0.9348

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
 JVP  F32  C28   single    1.338  0.020  1.338
 JVP  C27  C28   aromatic  1.381  0.020  1.381
 JVP  C27  C26   aromatic  1.388  0.020  1.388
 JVP  C28  C29   aromatic  1.383  0.020  1.383
 JVP  C26  C25   aromatic  1.384  0.020  1.384
 JVP  N23  C21   single    1.344  0.020  1.344
 JVP  C29  C30   aromatic  1.379  0.020  1.379
 JVP  O22  C21   double    1.234  0.020  1.234
 JVP  C25  C30   aromatic  1.389  0.020  1.389
 JVP  C25  O24   single    1.365  0.020  1.365
 JVP  C30  F31   single    1.334  0.020  1.334
 JVP  C21  C8    single    1.462  0.020  1.462
 JVP  O24  C3    single    1.364  0.020  1.364
 JVP  C2   C3    aromatic  1.389  0.020  1.389
 JVP  C2   C1    aromatic  1.387  0.020  1.387
 JVP  C3   C4    aromatic  1.391  0.020  1.391
 JVP  C1   C6    aromatic  1.392  0.020  1.392
 JVP  C8   C7    aromatic  1.422  0.020  1.422
 JVP  C8   C9    aromatic  1.399  0.020  1.399
 JVP  C4   C5    aromatic  1.383  0.020  1.383
 JVP  C6   C5    aromatic  1.395  0.020  1.395
 JVP  C6   C7    single    1.471  0.020  1.471
 JVP  C7   N11   aromatic  1.310  0.020  1.310
 JVP  N20  C9    single    1.357  0.020  1.357
 JVP  C9   N10   aromatic  1.345  0.020  1.345
 JVP  N11  N10   aromatic  1.350  0.020  1.350
 JVP  N10  C12   single    1.446  0.020  1.446
 JVP  C12  C17   single    1.533  0.020  1.533
 JVP  C12  C13   single    1.527  0.020  1.527
 JVP  C17  N16   single    1.458  0.020  1.458
 JVP  C13  C14   single    1.526  0.020  1.526
 JVP  N16  C18   single    1.318  0.020  1.318
 JVP  N16  C15   single    1.467  0.020  1.467
 JVP  C14  C15   single    1.521  0.020  1.521
 JVP  C18  N19   triple    1.159  0.020  1.159
 JVP  C4   HC4   single    0.930  0.020  1.080
 JVP  C13  H13A  single    0.970  0.020  1.090
 JVP  C13  H13B  single    0.970  0.020  1.090
 JVP  C26  HC26  single    0.930  0.020  1.080
 JVP  C1   HC1   single    0.930  0.020  1.080
 JVP  C2   HC2   single    0.930  0.020  1.080
 JVP  C5   HC5   single    0.930  0.020  1.080
 JVP  C12  HC12  single    0.970  0.020  1.090
 JVP  C14  H14B  single    0.970  0.020  1.090
 JVP  C14  H14A  single    0.970  0.020  1.090
 JVP  C15  H15A  single    0.970  0.020  1.090
 JVP  C15  H15B  single    0.970  0.020  1.090
 JVP  C17  H17B  single    0.970  0.020  1.090
 JVP  C17  H17A  single    0.970  0.020  1.090
 JVP  N20  H20A  single    0.890  0.020  1.040
 JVP  N20  H20B  single    0.890  0.020  1.040
 JVP  N23  H23B  single    0.860  0.020  1.020
 JVP  N23  H23A  single    0.860  0.020  1.020
 JVP  C27  HC27  single    0.930  0.020  1.080
 JVP  C29  HC29  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
 JVP  HC4   C4   C5    120.43  3.000
 JVP  HC4   C4   C3    119.85  3.000
 JVP  C5    C4   C3    119.72  3.000
 JVP  N11   C7   C8    111.30  3.000
 JVP  N11   C7   C6    118.88  3.000
 JVP  C8    C7   C6    129.80  3.000
 JVP  C5    C6   C1    118.32  3.000
 JVP  C5    C6   C7    120.38  3.000
 JVP  C1    C6   C7    121.24  3.000
 JVP  N20   C9   N10   123.60  3.000
 JVP  N10   C9   C8    106.42  3.000
 JVP  N20   C9   C8    129.82  3.000
 JVP  H13B  C13  H13A  107.33  3.000
 JVP  H13B  C13  C14   110.49  3.000
 JVP  H13A  C13  C14   109.62  3.000
 JVP  H13B  C13  C12   109.49  3.000
 JVP  H13A  C13  C12   109.50  3.000
 JVP  C14   C13  C12   110.35  3.000
 JVP  C21   C8   C9    122.83  3.000
 JVP  C9    C8   C7    103.94  3.000
 JVP  C21   C8   C7    133.18  3.000
 JVP  N19   C18  N16   180.00  3.000
 JVP  HC26  C26  C27   120.05  3.000
 JVP  HC26  C26  C25   119.38  3.000
 JVP  C27   C26  C25   120.57  3.000
 JVP  HC1   C1   C2    118.68  3.000
 JVP  HC1   C1   C6    119.95  3.000
 JVP  C2    C1   C6    121.36  3.000
 JVP  HC2   C2   C3    121.60  3.000
 JVP  HC2   C2   C1    119.09  3.000
 JVP  C3    C2   C1    119.30  3.000
 JVP  O24   C3   C2    123.72  3.000
 JVP  C2    C3   C4    120.27  3.000
 JVP  O24   C3   C4    116.01  3.000
 JVP  HC5   C5   C6    119.68  3.000
 JVP  HC5   C5   C4    119.30  3.000
 JVP  C6    C5   C4    121.02  3.000
 JVP  C12   N10  N11   119.68  3.000
 JVP  C12   N10  C9    127.83  3.000
 JVP  N11   N10  C9    112.34  3.000
 JVP  N10   N11  C7    105.97  3.000
 JVP  HC12  C12  C17   108.96  3.000
 JVP  HC12  C12  N10   107.03  3.000
 JVP  C17   C12  N10   110.03  3.000
 JVP  HC12  C12  C13   107.85  3.000
 JVP  C17   C12  C13   110.79  3.000
 JVP  N10   C12  C13   112.03  3.000
 JVP  H14A  C14  H14B  106.89  3.000
 JVP  H14A  C14  C15   109.47  3.000
 JVP  H14B  C14  C15   109.19  3.000
 JVP  H14A  C14  C13   110.33  3.000
 JVP  H14B  C14  C13   109.88  3.000
 JVP  C15   C14  C13   110.98  3.000
 JVP  H15B  C15  H15A  107.57  3.000
 JVP  H15B  C15  N16   108.79  3.000
 JVP  H15A  C15  N16   107.03  3.000
 JVP  H15B  C15  C14   111.93  3.000
 JVP  H15A  C15  C14   110.67  3.000
 JVP  N16   C15  C14   110.67  3.000
 JVP  C17   N16  C15   114.82  3.000
 JVP  C15   N16  C18   118.27  3.000
 JVP  C17   N16  C18   118.10  3.000
 JVP  H17A  C17  H17B  107.75  3.000
 JVP  H17A  C17  N16   108.00  3.000
 JVP  H17B  C17  N16   109.46  3.000
 JVP  H17A  C17  C12   109.70  3.000
 JVP  H17B  C17  C12   111.43  3.000
 JVP  N16   C17  C12   110.40  3.000
 JVP  H20B  N20  H20A  113.37  3.000
 JVP  H20B  N20  C9    113.16  3.000
 JVP  H20A  N20  C9    118.05  3.000
 JVP  H23A  N23  H23B  117.30  3.000
 JVP  H23A  N23  C21   119.40  3.000
 JVP  H23B  N23  C21   122.67  3.000
 JVP  C25   O24  C3    119.15  3.000
 JVP  C30   C25  O24   120.08  3.000
 JVP  O24   C25  C26   120.90  3.000
 JVP  C30   C25  C26   118.99  3.000
 JVP  HC27  C27  C28   120.71  3.000
 JVP  HC27  C27  C26   120.75  3.000
 JVP  C28   C27  C26   118.55  3.000
 JVP  F32   C28  C29   118.31  3.000
 JVP  C29   C28  C27   122.51  3.000
 JVP  F32   C28  C27   119.18  3.000
 JVP  HC29  C29  C30   120.92  3.000
 JVP  HC29  C29  C28   121.56  3.000
 JVP  C30   C29  C28   117.53  3.000
 JVP  F31   C30  C29   119.50  3.000
 JVP  F31   C30  C25   118.64  3.000
 JVP  C29   C30  C25   121.86  3.000
 JVP  N23   C21  O22   121.31  3.000
 JVP  O22   C21  C8    120.78  3.000
 JVP  N23   C21  C8    117.91  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
 JVP  CONST_01  C1    C2   C3   C4     0.00   0.0  0
 JVP  CONST_02  C1    C6   C5   C4     0.00   0.0  0
 JVP  CONST_03  C7    C6   C5   C4   180.00   0.0  0
 JVP  CONST_04  N10   C9   C8   C7     0.00   0.0  0
 JVP  CONST_05  C2    C1   C6   C7   180.00   0.0  0
 JVP  CONST_06  C9    N10  N11  C7     0.00   0.0  0
 JVP  CONST_07  C3    C2   C1   C6     0.00   0.0  0
 JVP  CONST_08  C3    C4   C5   C6     0.00   0.0  0
 JVP  CONST_09  C9    C8   C7   C6   180.00   0.0  0
 JVP  CONST_10  N10   N11  C7   C6   180.00   0.0  0
 JVP  CONST_11  N11   C7   C8   C9     0.00   0.0  0
 JVP  CONST_14  N10   N11  C7   C8     0.00   0.0  0
 JVP  CONST_15  N11   N10  C9   C8     0.00   0.0  0
 JVP  CONST_16  C29   C28  C27  C26    0.00   0.0  0
 JVP  CONST_17  C29   C30  C25  C26    0.00   0.0  0
 JVP  CONST_19  C5    C4   C3   C2     0.00   0.0  0
 JVP  CONST_20  C5    C6   C1   C2     0.00   0.0  0
 JVP  CONST_22  C28   C27  C26  C25    0.00   0.0  0
 JVP  CONST_23  C28   C29  C30  C25    0.00   0.0  0
 JVP  CONST_24  C30   C29  C28  C27    0.00   0.0  0
 JVP  CONST_25  C30   C25  C26  C27    0.00   0.0  0
 JVP  CONST_26  C12   N10  N11  C7   180.00   0.0  0
 JVP  CONST_27  C12   N10  C9   C8   180.00   0.0  0
 JVP  CONST_28  N20   C9   C8   C7   180.00   0.0  0
 JVP  CONST_29  C21   C8   C7   C6     0.00   0.0  0
 JVP  CONST_30  N11   C7   C8   C21  180.00   0.0  0
 JVP  CONST_31  N10   C9   C8   C21  180.00   0.0  0
 JVP  CONST_32  F32   C28  C27  C26  180.00   0.0  0
 JVP  CONST_33  F31   C30  C25  C26  180.00   0.0  0
 JVP  CONST_34  O24   C3   C2   C1   180.00   0.0  0
 JVP  CONST_35  O24   C3   C4   C5   180.00   0.0  0
 JVP  CONST_36  N20   C9   N10  N11  180.00   0.0  0
 JVP  CONST_37  N20   C9   N10  C12    0.00   0.0  0
 JVP  CONST_38  C27   C26  C25  O24  180.00   0.0  0
 JVP  CONST_39  C29   C30  C25  O24  180.00   0.0  0
 JVP  CONST_40  F31   C30  C29  C28  180.00   0.0  0
 JVP  CONST_41  F32   C28  C29  C30  180.00   0.0  0
 JVP  CONST_42  HC2   C2   C3   C4   180.00   0.0  0
 JVP  CONST_43  HC1   C1   C6   C7     0.00   0.0  0
 JVP  CONST_44  HC5   C5   C6   C7     0.00   0.0  0
 JVP  CONST_45  HC4   C4   C5   C6   180.00   0.0  0
 JVP  CONST_46  HC27  C27  C26  C25  180.00   0.0  0
 JVP  CONST_47  HC29  C29  C30  C25  180.00   0.0  0
 JVP  CONST_48  HC26  C26  C27  C28  180.00   0.0  0
 JVP  CONST_51  H23B  N23  C21  C8     0.00   0.0  0
 JVP  CONST_52  H23A  N23  C21  C8   180.00   0.0  0
 JVP  Var_01    N16   C15  C14  C13  -54.27  30.0  1
 JVP  Var_02    C15   N16  C17  C12  -56.01  30.0  1
 JVP  Var_03    C15   C14  C13  C12   54.97  30.0  1
 JVP  Var_04    C17   N16  C15  C14   56.04  30.0  1
 JVP  Var_05    C30   C25  O24  C3    81.23  30.0  3
 JVP  Var_06    N23   C21  C8   C7   -10.82  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JVP  chir_01  C12  N10  C17  C13  negativ

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
 JVP  plan-1  C7    0.020
 JVP  plan-1  C6    0.020
 JVP  plan-1  C9    0.020
 JVP  plan-1  C8    0.020
 JVP  plan-1  N10   0.020
 JVP  plan-1  N11   0.020
 JVP  plan-1  C12   0.020
 JVP  plan-1  N20   0.020
 JVP  plan-1  C21   0.020
 JVP  plan-2  C4    0.020
 JVP  plan-2  C7    0.020
 JVP  plan-2  C6    0.020
 JVP  plan-2  C1    0.020
 JVP  plan-2  C2    0.020
 JVP  plan-2  C3    0.020
 JVP  plan-2  C5    0.020
 JVP  plan-2  O24   0.020
 JVP  plan-2  HC4   0.020
 JVP  plan-2  HC1   0.020
 JVP  plan-2  HC2   0.020
 JVP  plan-2  HC5   0.020
 JVP  plan-3  C26   0.020
 JVP  plan-3  O24   0.020
 JVP  plan-3  C25   0.020
 JVP  plan-3  C27   0.020
 JVP  plan-3  C28   0.020
 JVP  plan-3  C29   0.020
 JVP  plan-3  C30   0.020
 JVP  plan-3  F31   0.020
 JVP  plan-3  F32   0.020
 JVP  plan-3  HC26  0.020
 JVP  plan-3  HC27  0.020
 JVP  plan-3  HC29  0.020
 JVP  plan-4  C9    0.020
 JVP  plan-4  N20   0.020
 JVP  plan-4  H20A  0.020
 JVP  plan-4  H20B  0.020
 JVP  plan-5  C8    0.020
 JVP  plan-5  O22   0.020
 JVP  plan-5  N23   0.020
 JVP  plan-5  H23B  0.020
 JVP  plan-5  H23A  0.020
 JVP  plan-5  C21   0.020

