# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 13:08:00 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N-(5-cyclopropyl-1H-pyrazol-3-yl)benzene-1,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(cc1)C(=O)Nc2cc([nH]n2)C3CC3
#
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
 03K  03K  N-(5-cyclopropyl-1H-pyrazol-3-yl)benzene-1,4-dicarboxamide  ligand  34  20  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_03K
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
 03K  N1L   N  NH1   0  -0.734  -0.7225  -0.3342  -0.2526
 03K  N2A   N  NH2   0  -0.809   6.2968  -1.3308   0.5056
 03K  N3K   N  NR15  0  -0.519  -4.0458  -1.0742  -0.4660
 03K  N4M   N  N     0  -0.319  -2.7547  -1.3803  -0.6165
 03K  OAB   O  O     0  -0.477   6.4929   0.4007  -0.9254
 03K  OAC   O  O     0  -0.460  -0.2781   1.8105   0.3262
 03K  CAD   C  CR16  0  -0.255   3.8137   1.1590  -0.4073
 03K  CAE   C  CR16  0  -0.265   3.4350  -1.1360   0.1831
 03K  CAF   C  CR16  0  -0.254   2.4540   1.4022  -0.3395
 03K  CAG   C  CR16  0  -0.276   2.0698  -0.9003   0.2229
 03K  CAH   C  CR15  0  -0.539  -2.9943   0.7149   0.1939
 03K  CAI   C  CH2   0  -0.475  -6.6959  -0.0748   0.8344
 03K  CAJ   C  CH2   0  -0.477  -6.7615   0.4104  -0.5745
 03K  CAO   C  C     0   0.526   0.1092   0.6923   0.0340
 03K  CAP   C  CR6   0  -0.036   4.3197  -0.1089  -0.1309
 03K  CAQ   C  CR6   0  -0.040   1.5670   0.3709  -0.0383
 03K  CAR   C  CR5   0   0.468  -2.1112  -0.3014  -0.2182
 03K  CAS   C  CR5   0   0.489  -4.2481   0.1637   0.0149
 03K  CAT   C  CH1   0  -0.371  -5.5676   0.7523   0.2766
 03K  HN1L  H  HNH1  0   0.417  -0.3298  -1.2013  -0.5875
 03K  HN2A  H  HNH2  0   0.408   7.2871  -1.5147   0.4942
 03K  HN2B  H  HNH2  0   0.415   5.7490  -1.8302   1.1843
 03K  HAD   H  HCR6  0   0.269   4.4872   1.9657  -0.6632
 03K  HAE   H  HCR6  0   0.270   3.7900  -2.1381   0.3849
 03K  HAF   H  HCR6  0   0.268   2.0791   2.3975  -0.5369
 03K  HAG   H  HCR6  0   0.271   1.4140  -1.7210   0.4838
 03K  HAH   H  HCR5  0   0.271  -2.7689   1.6968   0.5666
 03K  HAI   H  HCH2  0   0.266  -7.3349   0.3933   1.5716
 03K  HAIA  H  HCH2  0   0.258  -6.5158  -1.1287   1.0077
 03K  HAJ   H  HCH2  0   0.257  -6.6289  -0.3093  -1.3727
 03K  HAJA  H  HCH2  0   0.267  -7.4458   1.2143  -0.8117
 03K  HAT   H  HCH1  0   0.278  -5.5075   1.7750   0.6272
 03K  HN3K  H  HNR5  0   0.419  -4.7387  -1.7611  -0.7168
 03K  CAN   C  C     0   0.490   5.8005  -0.3197  -0.2204

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
 03K  CAO  N1L   single    1.352  0.020  1.352
 03K  CAR  N1L   single    1.389  0.020  1.389
 03K  N1L  HN1L  single    0.860  0.020  1.020
 03K  N2A  CAN   single    1.340  0.020  1.340
 03K  N2A  HN2A  single    0.860  0.020  1.020
 03K  N2A  HN2B  single    0.860  0.020  1.020
 03K  CAS  N3K   aromatic  1.343  0.020  1.343
 03K  N3K  N4M   aromatic  1.335  0.020  1.335
 03K  CAR  N4M   aromatic  1.318  0.020  1.318
 03K  CAN  OAB   double    1.223  0.020  1.223
 03K  OAC  CAO   double    1.219  0.020  1.219
 03K  CAF  CAD   aromatic  1.383  0.020  1.383
 03K  CAD  CAP   aromatic  1.393  0.020  1.393
 03K  CAD  HAD   single    0.930  0.020  1.080
 03K  CAP  CAE   aromatic  1.391  0.020  1.391
 03K  CAG  CAE   aromatic  1.386  0.020  1.386
 03K  CAE  HAE   single    0.930  0.020  1.080
 03K  CAF  CAQ   aromatic  1.393  0.020  1.393
 03K  CAF  HAF   single    0.930  0.020  1.080
 03K  CAQ  CAG   aromatic  1.392  0.020  1.392
 03K  CAG  HAG   single    0.930  0.020  1.080
 03K  CAS  CAH   aromatic  1.381  0.020  1.381
 03K  CAH  CAR   aromatic  1.408  0.020  1.408
 03K  CAH  HAH   single    0.930  0.020  1.080
 03K  CAI  CAJ   single    1.491  0.020  1.491
 03K  CAI  CAT   single    1.506  0.020  1.506
 03K  CAI  HAI   single    0.970  0.020  1.090
 03K  CAI  HAIA  single    0.970  0.020  1.090
 03K  CAJ  CAT   single    1.505  0.020  1.505
 03K  CAJ  HAJ   single    0.970  0.020  1.090
 03K  CAJ  HAJA  single    0.970  0.020  1.090
 03K  CAP  CAN   single    1.498  0.020  1.498
 03K  CAO  CAQ   single    1.495  0.020  1.495
 03K  CAT  CAS   single    1.468  0.020  1.468
 03K  CAT  HAT   single    0.970  0.020  1.090
 03K  N3K  HN3K  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
 03K  HN1L  N1L  CAR   114.68  3.000
 03K  HN1L  N1L  CAO   118.91  3.000
 03K  CAR   N1L  CAO   126.28  3.000
 03K  HN2B  N2A  HN2A  116.93  3.000
 03K  HN2B  N2A  CAN   122.61  3.000
 03K  HN2A  N2A  CAN   119.72  3.000
 03K  HN3K  N3K  CAS   127.87  3.000
 03K  HN3K  N3K  N4M   118.73  3.000
 03K  CAS   N3K  N4M   113.40  3.000
 03K  CAR   N4M  N3K   104.51  3.000
 03K  HAD   CAD  CAP   119.98  3.000
 03K  HAD   CAD  CAF   119.51  3.000
 03K  CAP   CAD  CAF   120.50  3.000
 03K  HAE   CAE  CAP   121.13  3.000
 03K  HAE   CAE  CAG   118.38  3.000
 03K  CAP   CAE  CAG   120.48  3.000
 03K  HAF   CAF  CAQ   119.99  3.000
 03K  HAF   CAF  CAD   119.58  3.000
 03K  CAQ   CAF  CAD   120.42  3.000
 03K  HAG   CAG  CAQ   121.26  3.000
 03K  HAG   CAG  CAE   118.34  3.000
 03K  CAQ   CAG  CAE   120.39  3.000
 03K  HAH   CAH  CAS   126.89  3.000
 03K  HAH   CAH  CAR   129.03  3.000
 03K  CAS   CAH  CAR   104.08  3.000
 03K  HAIA  CAI  HAI   114.21  3.000
 03K  HAIA  CAI  CAT   117.98  3.000
 03K  HAI   CAI  CAT   117.20  3.000
 03K  HAIA  CAI  CAJ   118.36  3.000
 03K  HAI   CAI  CAJ   118.48  3.000
 03K  CAT   CAI  CAJ    60.30  3.000
 03K  HAJA  CAJ  HAJ   114.17  3.000
 03K  HAJA  CAJ  CAT   117.18  3.000
 03K  HAJ   CAJ  CAT   118.07  3.000
 03K  HAJA  CAJ  CAI   118.47  3.000
 03K  HAJ   CAJ  CAI   118.34  3.000
 03K  CAT   CAJ  CAI    60.33  3.000
 03K  CAQ   CAO  OAC   121.25  3.000
 03K  CAQ   CAO  N1L   115.25  3.000
 03K  OAC   CAO  N1L   123.50  3.000
 03K  CAN   CAP  CAE   122.55  3.000
 03K  CAN   CAP  CAD   118.37  3.000
 03K  CAE   CAP  CAD   119.06  3.000
 03K  CAO   CAQ  CAG   122.66  3.000
 03K  CAO   CAQ  CAF   118.18  3.000
 03K  CAG   CAQ  CAF   119.12  3.000
 03K  CAH   CAR  N4M   111.90  3.000
 03K  CAH   CAR  N1L   130.63  3.000
 03K  N4M   CAR  N1L   117.47  3.000
 03K  CAT   CAS  CAH   129.24  3.000
 03K  CAT   CAS  N3K   124.65  3.000
 03K  CAH   CAS  N3K   106.11  3.000
 03K  HAT   CAT  CAS   112.73  3.000
 03K  HAT   CAT  CAJ   116.21  3.000
 03K  CAS   CAT  CAJ   121.39  3.000
 03K  HAT   CAT  CAI   116.13  3.000
 03K  CAS   CAT  CAI   121.27  3.000
 03K  CAJ   CAT  CAI    59.37  3.000
 03K  CAP   CAN  OAB   120.74  3.000
 03K  CAP   CAN  N2A   116.09  3.000
 03K  OAB   CAN  N2A   123.17  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
 03K  CONST_01  CAR   CAH  CAS  N3K    0.00   0.0  0
 03K  CONST_02  CAH   CAR  N4M  N3K    0.00   0.0  0
 03K  CONST_03  CAH   CAS  N3K  N4M    0.00   0.0  0
 03K  CONST_04  CAS   CAH  CAR  N4M    0.00   0.0  0
 03K  CONST_05  CAG   CAQ  CAF  CAD    0.00   0.0  0
 03K  CONST_06  CAG   CAE  CAP  CAD    0.00   0.0  0
 03K  CONST_07  CAF   CAD  CAP  CAE    0.00   0.0  0
 03K  CONST_08  CAF   CAQ  CAG  CAE    0.00   0.0  0
 03K  CONST_09  CAQ   CAF  CAD  CAP    0.00   0.0  0
 03K  CONST_10  CAQ   CAG  CAE  CAP    0.00   0.0  0
 03K  CONST_11  CAS   N3K  N4M  CAR    0.00   0.0  0
 03K  CONST_12  CAT   CAS  N3K  N4M  180.00   0.0  0
 03K  CONST_13  CAT   CAS  CAH  CAR  180.00   0.0  0
 03K  CONST_14  N3K   N4M  CAR  N1L  180.00   0.0  0
 03K  CONST_15  CAS   CAH  CAR  N1L  180.00   0.0  0
 03K  CONST_16  CAO   CAQ  CAF  CAD  180.00   0.0  0
 03K  CONST_17  CAO   CAQ  CAG  CAE  180.00   0.0  0
 03K  CONST_18  CAN   CAP  CAD  CAF  180.00   0.0  0
 03K  CONST_19  CAN   CAP  CAE  CAG  180.00   0.0  0
 03K  CONST_20  HAH   CAH  CAS  N3K  180.00   0.0  0
 03K  CONST_21  HAE   CAE  CAP  CAD  180.00   0.0  0
 03K  CONST_22  HAD   CAD  CAP  CAE  180.00   0.0  0
 03K  CONST_23  HAG   CAG  CAQ  CAF  180.00   0.0  0
 03K  CONST_24  HAF   CAF  CAQ  CAG  180.00   0.0  0
 03K  CONST_25  HN3K  N3K  CAS  CAH  180.00   0.0  0
 03K  CONST_26  CAR   N1L  CAO  CAQ  180.00   0.0  0
 03K  CONST_27  CAO   N1L  CAR  N4M  180.00   0.0  0
 03K  CONST_28  CAO   N1L  CAR  CAH    0.00   0.0  0
 03K  CONST_29  HN1L  N1L  CAR  N4M    0.00   0.0  0
 03K  CONST_30  CAR   N1L  CAO  OAC    0.00   0.0  0
 03K  CONST_31  HN2A  N2A  CAN  CAP  180.00   0.0  0
 03K  CONST_32  HN2B  N2A  CAN  CAP    0.00   0.0  0
 03K  Var_01    CAI   CAT  CAS  N3K   37.77  30.0  2
 03K  Var_02    CAS   CAT  CAJ  CAI  110.21  30.0  1
 03K  Var_03    CAF   CAQ  CAO  N1L  152.39  30.0  2
 03K  Var_04    CAD   CAP  CAN  N2A  155.65  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
 03K  chir_01  CAT  CAI  CAJ  CAS  both

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
 03K  plan-1  N1L   0.020
 03K  plan-1  N3K   0.020
 03K  plan-1  N4M   0.020
 03K  plan-1  CAH   0.020
 03K  plan-1  CAR   0.020
 03K  plan-1  CAS   0.020
 03K  plan-1  CAT   0.020
 03K  plan-1  HAH   0.020
 03K  plan-1  HN3K  0.020
 03K  plan-2  CAD   0.020
 03K  plan-2  CAE   0.020
 03K  plan-2  CAF   0.020
 03K  plan-2  CAG   0.020
 03K  plan-2  CAO   0.020
 03K  plan-2  CAP   0.020
 03K  plan-2  CAQ   0.020
 03K  plan-2  HAD   0.020
 03K  plan-2  HAE   0.020
 03K  plan-2  HAF   0.020
 03K  plan-2  HAG   0.020
 03K  plan-2  CAN   0.020
 03K  plan-3  N2A   0.020
 03K  plan-3  OAB   0.020
 03K  plan-3  CAP   0.020
 03K  plan-3  HN2A  0.020
 03K  plan-3  HN2B  0.020
 03K  plan-3  CAN   0.020
 03K  plan-4  N1L   0.020
 03K  plan-4  OAC   0.020
 03K  plan-4  CAO   0.020
 03K  plan-4  CAQ   0.020
 03K  plan-4  CAR   0.020
 03K  plan-4  HN1L  0.020

