# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:21:42 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-carbamimidoyl-N-phenyl-4-(pyrimidin-2-ylamino)naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2cc(cc(Nc3ncccn3)c2c1)C(=O)Nc4ccccc4
#
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
 J4X  J4X  6-carbamimidoyl-N-phenyl-4-(pyrimidin-2-ylamino)naphthalene-2-carboxamide  ligand  47  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J4X
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
 J4X  N1    N  NH2   0  -0.803  -6.7668   1.5397  -0.0119
 J4X  C2    C  C     0   0.334  -5.8321   0.6659   0.4562
 J4X  N3    N  N     0  -0.637  -6.1825  -0.4202   1.0305
 J4X  C4    C  CR6   0   0.017  -4.4200   1.1132   0.2834
 J4X  C5    C  CR16  0  -0.279  -4.0743   2.4771   0.4150
 J4X  C6    C  CR16  0  -0.296  -2.7702   2.8677   0.3129
 J4X  C7    C  CR66  0   0.119  -1.7453   1.9310   0.0464
 J4X  C8    C  CR16  0  -0.367  -0.3972   2.3349  -0.0254
 J4X  C9    C  CR6   0  -0.032   0.5845   1.4094  -0.2629
 J4X  C10   C  CR16  0  -0.353   0.2490   0.0601  -0.4988
 J4X  C11   C  CR6   0   0.360  -1.0542  -0.3689  -0.4381
 J4X  N12   N  NH1   0  -0.779  -1.4160  -1.6837  -0.7079
 J4X  C13   C  CR6   0   0.591  -0.7131  -2.8314  -0.4747
 J4X  N14   N  N     0  -0.454  -1.2964  -3.9408  -0.9360
 J4X  C15   C  CR16  0  -0.014  -0.6598  -5.0770  -0.7131
 J4X  C16   C  CR16  0  -0.379   0.5519  -5.1378  -0.0401
 J4X  C17   C  CR16  0  -0.000   1.0582  -3.9257   0.3929
 J4X  N18   N  N     0  -0.450   0.4386  -2.7725   0.1833
 J4X  C19   C  CR66  0   0.071  -2.0905   0.5653  -0.1278
 J4X  C20   C  CR16  0  -0.350  -3.4417   0.1862   0.0194
 J4X  C21   C  C     0   0.529   2.0038   1.8764  -0.3019
 J4X  O22   O  O     0  -0.458   2.2884   3.0140  -0.6330
 J4X  N23   N  NH1   0  -0.756   2.9123   0.9442   0.0810
 J4X  C24   C  CR6   0   0.384   4.3075   1.0342   0.1320
 J4X  C25   C  CR16  0  -0.316   5.0467   2.1318  -0.3118
 J4X  C26   C  CR16  0  -0.244   6.4329   2.1042  -0.2239
 J4X  C27   C  CR16  0  -0.271   7.1025   1.0079   0.2979
 J4X  C28   C  CR16  0  -0.243   6.3641  -0.0832   0.7383
 J4X  C29   C  CR16  0  -0.352   4.9829  -0.0716   0.6565
 J4X  HN1   H  HNH2  0   0.387  -7.7182   1.2069  -0.0233
 J4X  HN1A  H  HNH2  0   0.395  -6.5259   2.1235  -0.7958
 J4X  HN3   H  H     0   0.334  -5.3770  -0.9001   1.4143
 J4X  H5    H  HCR6  0   0.269  -4.8405   3.2105   0.6282
 J4X  H6    H  HCR6  0   0.266  -2.5045   3.9091   0.4437
 J4X  H8    H  HCR6  0   0.263  -0.1500   3.3769   0.1325
 J4X  H10   H  HCR6  0   0.276   1.0156  -0.6467  -0.7761
 J4X  HN12  H  HNH1  0   0.411  -2.3000  -1.8389  -1.1674
 J4X  H15   H  HCR6  0   0.278  -1.1345  -5.9780  -1.0857
 J4X  H16   H  HCR6  0   0.279   1.0658  -6.0708   0.1333
 J4X  H17   H  HCR6  0   0.275   1.9978  -3.8753   0.9316
 J4X  H20   H  HCR6  0   0.255  -3.7272  -0.8539  -0.0725
 J4X  HN23  H  HNH1  0   0.417   2.5403   0.0792   0.4432
 J4X  H25   H  HCR6  0   0.281   4.5609   3.0010  -0.7216
 J4X  H26   H  HCR6  0   0.259   6.9918   2.9629  -0.5733
 J4X  H27   H  HCR6  0   0.257   8.1824   1.0019   0.3610
 J4X  H28   H  HCR6  0   0.262   6.8620  -0.9511   1.1501
 J4X  H29   H  HCR6  0   0.266   4.4210  -0.9318   1.0022

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
 J4X  C2   N1    single    1.362  0.020  1.362
 J4X  N1   HN1   single    0.890  0.020  1.040
 J4X  N1   HN1A  single    0.890  0.020  1.040
 J4X  C4   C2    single    1.491  0.020  1.491
 J4X  C2   N3    double    1.278  0.020  1.278
 J4X  N3   HN3   single    0.890  0.020  1.040
 J4X  C20  C4    aromatic  1.373  0.020  1.373
 J4X  C4   C5    aromatic  1.413  0.020  1.413
 J4X  C6   C5    aromatic  1.365  0.020  1.365
 J4X  C5   H5    single    0.930  0.020  1.080
 J4X  C7   C6    aromatic  1.414  0.020  1.414
 J4X  C6   H6    single    0.930  0.020  1.080
 J4X  C8   C7    aromatic  1.409  0.020  1.409
 J4X  C19  C7    aromatic  1.419  0.020  1.419
 J4X  C9   C8    aromatic  1.370  0.020  1.370
 J4X  C8   H8    single    0.930  0.020  1.080
 J4X  C21  C9    single    1.495  0.020  1.495
 J4X  C10  C9    aromatic  1.410  0.020  1.410
 J4X  C10  C11   aromatic  1.373  0.020  1.373
 J4X  C10  H10   single    0.930  0.020  1.080
 J4X  N12  C11   single    1.390  0.020  1.390
 J4X  C11  C19   aromatic  1.429  0.020  1.429
 J4X  C13  N12   single    1.366  0.020  1.366
 J4X  N12  HN12  single    0.860  0.020  1.020
 J4X  N18  C13   aromatic  1.328  0.020  1.328
 J4X  C13  N14   aromatic  1.336  0.020  1.336
 J4X  C15  N14   aromatic  1.321  0.020  1.321
 J4X  C16  C15   aromatic  1.387  0.020  1.387
 J4X  C15  H15   single    0.930  0.020  1.080
 J4X  C17  C16   aromatic  1.383  0.020  1.383
 J4X  C16  H16   single    0.930  0.020  1.080
 J4X  C17  N18   aromatic  1.326  0.020  1.326
 J4X  C17  H17   single    0.930  0.020  1.080
 J4X  C19  C20   aromatic  1.411  0.020  1.411
 J4X  C20  H20   single    0.930  0.020  1.080
 J4X  O22  C21   double    1.219  0.020  1.219
 J4X  C21  N23   single    1.357  0.020  1.357
 J4X  C24  N23   single    1.399  0.020  1.399
 J4X  N23  HN23  single    0.860  0.020  1.020
 J4X  C29  C24   aromatic  1.398  0.020  1.398
 J4X  C25  C24   aromatic  1.396  0.020  1.396
 J4X  C26  C25   aromatic  1.389  0.020  1.389
 J4X  C25  H25   single    0.930  0.020  1.080
 J4X  C27  C26   aromatic  1.387  0.020  1.387
 J4X  C26  H26   single    0.930  0.020  1.080
 J4X  C27  C28   aromatic  1.389  0.020  1.389
 J4X  C27  H27   single    0.930  0.020  1.080
 J4X  C28  C29   aromatic  1.384  0.020  1.384
 J4X  C28  H28   single    0.930  0.020  1.080
 J4X  C29  H29   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
 J4X  HN1A  N1   HN1  114.12  3.000
 J4X  HN1A  N1   C2   118.37  3.000
 J4X  HN1   N1   C2   116.08  3.000
 J4X  C4    C2   N3   124.53  3.000
 J4X  N3    C2   N1   120.76  3.000
 J4X  C4    C2   N1   114.67  3.000
 J4X  HN3   N3   C2   110.79  3.000
 J4X  C20   C4   C5   119.68  3.000
 J4X  C5    C4   C2   120.68  3.000
 J4X  C20   C4   C2   119.63  3.000
 J4X  H5    C5   C6   119.83  3.000
 J4X  H5    C5   C4   119.96  3.000
 J4X  C6    C5   C4   120.19  3.000
 J4X  H6    C6   C7   118.82  3.000
 J4X  H6    C6   C5   120.04  3.000
 J4X  C7    C6   C5   121.14  3.000
 J4X  C19   C7   C8   120.15  3.000
 J4X  C19   C7   C6   118.96  3.000
 J4X  C8    C7   C6   120.88  3.000
 J4X  H8    C8   C9   120.80  3.000
 J4X  H8    C8   C7   119.14  3.000
 J4X  C9    C8   C7   120.05  3.000
 J4X  C21   C9   C10  121.37  3.000
 J4X  C10   C9   C8   120.33  3.000
 J4X  C21   C9   C8   118.28  3.000
 J4X  H10   C10  C11  118.75  3.000
 J4X  H10   C10  C9   120.05  3.000
 J4X  C11   C10  C9   121.15  3.000
 J4X  C19   C11  N12  118.14  3.000
 J4X  C19   C11  C10  119.57  3.000
 J4X  N12   C11  C10  122.27  3.000
 J4X  HN12  N12  C13  113.55  3.000
 J4X  HN12  N12  C11  117.53  3.000
 J4X  C13   N12  C11  128.88  3.000
 J4X  N18   C13  N14  125.93  3.000
 J4X  N14   C13  N12  114.47  3.000
 J4X  N18   C13  N12  119.58  3.000
 J4X  C15   N14  C13  116.46  3.000
 J4X  H15   C15  C16  120.84  3.000
 J4X  H15   C15  N14  116.46  3.000
 J4X  C16   C15  N14  122.70  3.000
 J4X  H16   C16  C17  122.21  3.000
 J4X  H16   C16  C15  122.12  3.000
 J4X  C17   C16  C15  115.67  3.000
 J4X  H17   C17  N18  116.30  3.000
 J4X  H17   C17  C16  120.90  3.000
 J4X  N18   C17  C16  122.80  3.000
 J4X  C17   N18  C13  116.43  3.000
 J4X  C20   C19  C11  122.77  3.000
 J4X  C20   C19  C7   118.60  3.000
 J4X  C11   C19  C7   118.63  3.000
 J4X  H20   C20  C19  120.12  3.000
 J4X  H20   C20  C4   118.49  3.000
 J4X  C19   C20  C4   121.39  3.000
 J4X  N23   C21  O22  124.17  3.000
 J4X  N23   C21  C9   114.45  3.000
 J4X  O22   C21  C9   121.37  3.000
 J4X  HN23  N23  C24  114.19  3.000
 J4X  HN23  N23  C21  116.33  3.000
 J4X  C24   N23  C21  129.34  3.000
 J4X  C29   C24  C25  119.04  3.000
 J4X  C25   C24  N23  124.55  3.000
 J4X  C29   C24  N23  116.40  3.000
 J4X  H25   C25  C26  119.36  3.000
 J4X  H25   C25  C24  121.12  3.000
 J4X  C26   C25  C24  119.52  3.000
 J4X  H26   C26  C27  119.96  3.000
 J4X  H26   C26  C25  118.62  3.000
 J4X  C27   C26  C25  121.42  3.000
 J4X  H27   C27  C28  120.52  3.000
 J4X  H27   C27  C26  120.56  3.000
 J4X  C28   C27  C26  118.92  3.000
 J4X  H28   C28  C29  119.25  3.000
 J4X  H28   C28  C27  120.40  3.000
 J4X  C29   C28  C27  120.35  3.000
 J4X  H29   C29  C28  119.46  3.000
 J4X  H29   C29  C24  119.80  3.000
 J4X  C28   C29  C24  120.74  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
 J4X  CONST_01  C7    C19  C20  C4      0.00   0.0  0
 J4X  CONST_02  C11   C19  C20  C4    180.00   0.0  0
 J4X  CONST_03  C7    C6   C5   C4      0.00   0.0  0
 J4X  CONST_04  C19   C20  C4   C5      0.00   0.0  0
 J4X  CONST_05  C8    C7   C6   C5    180.00   0.0  0
 J4X  CONST_06  C19   C7   C6   C5      0.00   0.0  0
 J4X  CONST_07  C20   C4   C5   C6      0.00   0.0  0
 J4X  CONST_08  C9    C8   C7   C6    180.00   0.0  0
 J4X  CONST_09  C11   C19  C7   C6    180.00   0.0  0
 J4X  CONST_10  C20   C19  C7   C6      0.00   0.0  0
 J4X  CONST_11  C10   C9   C8   C7      0.00   0.0  0
 J4X  CONST_12  C10   C11  C19  C7      0.00   0.0  0
 J4X  CONST_13  C11   C19  C7   C8      0.00   0.0  0
 J4X  CONST_14  C20   C19  C7   C8    180.00   0.0  0
 J4X  CONST_15  C11   C10  C9   C8      0.00   0.0  0
 J4X  CONST_16  C19   C7   C8   C9      0.00   0.0  0
 J4X  CONST_17  C19   C11  C10  C9      0.00   0.0  0
 J4X  CONST_18  C20   C19  C11  C10   180.00   0.0  0
 J4X  CONST_19  C16   C17  N18  C13     0.00   0.0  0
 J4X  CONST_20  C16   C15  N14  C13     0.00   0.0  0
 J4X  CONST_21  C17   N18  C13  N14     0.00   0.0  0
 J4X  CONST_22  C17   C16  C15  N14     0.00   0.0  0
 J4X  CONST_23  N18   C13  N14  C15     0.00   0.0  0
 J4X  CONST_24  N18   C17  C16  C15     0.00   0.0  0
 J4X  CONST_25  C27   C28  C29  C24     0.00   0.0  0
 J4X  CONST_26  C27   C26  C25  C24     0.00   0.0  0
 J4X  CONST_27  C28   C29  C24  C25     0.00   0.0  0
 J4X  CONST_28  C28   C27  C26  C25     0.00   0.0  0
 J4X  CONST_29  C29   C24  C25  C26     0.00   0.0  0
 J4X  CONST_30  C29   C28  C27  C26     0.00   0.0  0
 J4X  CONST_31  C19   C20  C4   C2    180.00   0.0  0
 J4X  CONST_32  C6    C5   C4   C2    180.00   0.0  0
 J4X  CONST_33  C21   C9   C8   C7    180.00   0.0  0
 J4X  CONST_34  N12   C11  C19  C7    180.00   0.0  0
 J4X  CONST_35  N12   C11  C10  C9    180.00   0.0  0
 J4X  CONST_36  C21   C9   C10  C11   180.00   0.0  0
 J4X  CONST_37  C20   C19  C11  N12     0.00   0.0  0
 J4X  CONST_38  C17   N18  C13  N12   180.00   0.0  0
 J4X  CONST_39  C15   N14  C13  N12   180.00   0.0  0
 J4X  CONST_40  C28   C29  C24  N23   180.00   0.0  0
 J4X  CONST_41  C26   C25  C24  N23   180.00   0.0  0
 J4X  CONST_42  H6    C6   C5   C4    180.00   0.0  0
 J4X  CONST_43  H20   C20  C4   C5    180.00   0.0  0
 J4X  CONST_44  H8    C8   C7   C6      0.00   0.0  0
 J4X  CONST_45  H5    C5   C6   C7    180.00   0.0  0
 J4X  CONST_46  H10   C10  C9   C8    180.00   0.0  0
 J4X  CONST_47  H17   C17  N18  C13   180.00   0.0  0
 J4X  CONST_48  H15   C15  N14  C13   180.00   0.0  0
 J4X  CONST_49  H16   C16  C15  N14   180.00   0.0  0
 J4X  CONST_50  H28   C28  C29  C24   180.00   0.0  0
 J4X  CONST_51  H26   C26  C25  C24   180.00   0.0  0
 J4X  CONST_52  H29   C29  C24  C25   180.00   0.0  0
 J4X  CONST_53  H27   C27  C26  C25   180.00   0.0  0
 J4X  CONST_54  H25   C25  C26  C27   180.00   0.0  0
 J4X  CONST_55  C24   N23  C21  C9    180.00   0.0  0
 J4X  CONST_56  C29   C24  N23  C21   180.00   0.0  0
 J4X  CONST_57  C25   C24  N23  C21     0.00   0.0  0
 J4X  CONST_58  HN23  N23  C24  C25   180.00   0.0  0
 J4X  CONST_59  C24   N23  C21  O22     0.00   0.0  0
 J4X  CONST_60  HN1   N1   C2   C4    180.00   0.0  0
 J4X  CONST_62  HN3   N3   C2   C4      0.00   0.0  0
 J4X  Var_01    C13   N12  C11  C10    32.78  30.0  2
 J4X  Var_02    N18   C13  N12  C11     5.57  30.0  2
 J4X  Var_03    C20   C4   C2   N1   -145.28  30.0  2
 J4X  Var_04    O22   C21  C9   C8    -28.15  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
 J4X  plan-1  N12   0.020
 J4X  plan-1  C13   0.020
 J4X  plan-1  N14   0.020
 J4X  plan-1  C15   0.020
 J4X  plan-1  C16   0.020
 J4X  plan-1  C17   0.020
 J4X  plan-1  N18   0.020
 J4X  plan-1  H15   0.020
 J4X  plan-1  H16   0.020
 J4X  plan-1  H17   0.020
 J4X  plan-2  N23   0.020
 J4X  plan-2  C24   0.020
 J4X  plan-2  C25   0.020
 J4X  plan-2  C26   0.020
 J4X  plan-2  C27   0.020
 J4X  plan-2  C28   0.020
 J4X  plan-2  C29   0.020
 J4X  plan-2  H25   0.020
 J4X  plan-2  H26   0.020
 J4X  plan-2  H27   0.020
 J4X  plan-2  H28   0.020
 J4X  plan-2  H29   0.020
 J4X  plan-3  C2    0.020
 J4X  plan-3  C4    0.020
 J4X  plan-3  C5    0.020
 J4X  plan-3  C6    0.020
 J4X  plan-3  C7    0.020
 J4X  plan-3  C8    0.020
 J4X  plan-3  C9    0.020
 J4X  plan-3  C10   0.020
 J4X  plan-3  C11   0.020
 J4X  plan-3  N12   0.020
 J4X  plan-3  C19   0.020
 J4X  plan-3  C20   0.020
 J4X  plan-3  C21   0.020
 J4X  plan-3  H5    0.020
 J4X  plan-3  H6    0.020
 J4X  plan-3  H8    0.020
 J4X  plan-3  H10   0.020
 J4X  plan-3  H20   0.020
 J4X  plan-4  C9    0.020
 J4X  plan-4  C21   0.020
 J4X  plan-4  O22   0.020
 J4X  plan-4  N23   0.020
 J4X  plan-4  C24   0.020
 J4X  plan-4  HN23  0.020
 J4X  plan-5  N1    0.020
 J4X  plan-5  C2    0.020
 J4X  plan-5  N3    0.020
 J4X  plan-5  C4    0.020
 J4X  plan-5  HN1   0.020
 J4X  plan-5  HN1A  0.020
 J4X  plan-5  HN3   0.020

