# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 04:54:04 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[4-(aminomethyl)phenyl]-6-carbamimidoyl-4-[(pyrimidin-2-yl)amino]naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(NC(=O)c2cc(Nc3ncccn3)c4cc(ccc4c2)C(N)=N)cc1
#
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
 UI1  UI1  N-[4-(aminomethyl)phenyl]-6-carbamimidoyl-4-[(pyrimidin-2-yl)amino]naphthalene-2-carboxamide  ligand  52  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UI1
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
 UI1  N1    N  NH2   0  -0.792  28.9512  11.4571  28.1239
 UI1  C2    C  CH2   0  -0.342  28.1059  10.8163  29.1173
 UI1  C3    C  CR6   0   0.083  27.2035  11.8078  29.8044
 UI1  C4    C  CR16  0  -0.273  26.5537  12.8099  29.0862
 UI1  C5    C  CR16  0  -0.332  25.7019  13.6992  29.7148
 UI1  C6    C  CR6   0   0.360  25.4693  13.6167  31.0895
 UI1  N7    N  NH1   0  -0.755  24.5708  14.5387  31.6432
 UI1  C8    C  C     0   0.526  24.4893  14.9549  32.9305
 UI1  O9    O  O     0  -0.458  25.2337  14.5791  33.8191
 UI1  C10   C  CR6   0  -0.038  23.4039  15.9467  33.2003
 UI1  C11   C  CR16  0  -0.320  23.6294  16.8853  34.2274
 UI1  C12   C  CR6   0   0.348  22.6774  17.8184  34.5531
 UI1  N13   N  NH1   0  -0.778  22.8979  18.8083  35.5082
 UI1  C14   C  CR6   0   0.587  23.6073  18.7257  36.6703
 UI1  N15   N  N     0  -0.454  23.7602  19.8851  37.3159
 UI1  C16   C  CR16  0  -0.016  24.4246  19.8396  38.4575
 UI1  C17   C  CR16  0  -0.378  24.9464  18.6633  38.9754
 UI1  C18   C  CR16  0  -0.003  24.7228  17.5258  38.2202
 UI1  N19   N  N     0  -0.447  24.0577  17.5433  37.0741
 UI1  C20   C  CR66  0   0.077  21.4211  17.8173  33.8708
 UI1  C21   C  CR16  0  -0.356  20.3740  18.7038  34.2005
 UI1  C22   C  CR6   0   0.020  19.1781  18.6817  33.5250
 UI1  C23   C  CR16  0  -0.282  18.9833  17.7502  32.4800
 UI1  C24   C  CR16  0  -0.296  19.9745  16.8718  32.1482
 UI1  C25   C  CR66  0   0.123  21.2103  16.8740  32.8336
 UI1  C26   C  CR16  0  -0.394  22.2185  15.9421  32.5117
 UI1  C27   C  C     0   0.335  18.0999  19.6403  33.9029
 UI1  N28   N  N     0  -0.637  18.2986  20.8418  34.2899
 UI1  N29   N  NH2   0  -0.805  16.8342  19.1573  33.7642
 UI1  C30   C  CR16  0  -0.290  26.1107  12.6190  31.8196
 UI1  C31   C  CR16  0  -0.305  26.9670  11.7377  31.1714
 UI1  HN11  H  HNH2  0   0.353  29.4746  10.7516  27.6221
 UI1  HN12  H  HNH2  0   0.343  29.6378  12.0381  28.5886
 UI1  H21A  H  HCH2  0   0.237  27.4852  10.0791  28.5987
 UI1  H22   H  HCH2  0   0.214  28.6606  10.2554  29.8816
 UI1  H4    H  HCR6  0   0.250  26.7259  12.9036  28.0218
 UI1  H5    H  HCR6  0   0.266  25.2116  14.4712  29.1328
 UI1  HN7   H  HNH1  0   0.420  24.0131  15.0430  30.9709
 UI1  H11   H  HCR6  0   0.273  24.5777  16.8785  34.7427
 UI1  H13   H  HNH1  0   0.408  22.5456  19.7318  35.3083
 UI1  H16   H  HCR6  0   0.277  24.5489  20.7808  38.9816
 UI1  H17   H  HCR6  0   0.277  25.4918  18.6379  39.9064
 UI1  H18   H  HCR6  0   0.275  25.0894  16.5593  38.5478
 UI1  H21   H  HCR6  0   0.258  20.4907  19.3900  35.0292
 UI1  H23   H  HCR6  0   0.269  18.0505  17.7386  31.9319
 UI1  H24   H  HCR6  0   0.267  19.8246  16.1588  31.3471
 UI1  H26   H  HCR6  0   0.269  22.0144  15.2120  31.7378
 UI1  H28   H  H     0   0.333  19.2812  21.0820  34.2352
 UI1  H291  H  HNH2  0   0.387  16.0939  19.7402  34.1211
 UI1  H292  H  HNH2  0   0.395  16.6792  18.1698  33.8801
 UI1  H30   H  HCR6  0   0.271  25.9542  12.5130  32.8811
 UI1  H31   H  HCR6  0   0.250  27.4603  10.9733  31.7602

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
 UI1  N1   C2    single    1.453  0.020  1.453
 UI1  N1   HN11  single    0.890  0.020  1.040
 UI1  N1   HN12  single    0.890  0.020  1.040
 UI1  C2   C3    single    1.507  0.020  1.507
 UI1  C2   H21A  single    0.970  0.020  1.090
 UI1  C2   H22   single    0.970  0.020  1.090
 UI1  C3   C4    aromatic  1.394  0.020  1.394
 UI1  C3   C31   aromatic  1.389  0.020  1.389
 UI1  C4   C5    aromatic  1.383  0.020  1.383
 UI1  C4   H4    single    0.930  0.020  1.080
 UI1  C5   C6    aromatic  1.397  0.020  1.397
 UI1  C5   H5    single    0.930  0.020  1.080
 UI1  C6   N7    single    1.401  0.020  1.401
 UI1  C6   C30   aromatic  1.393  0.020  1.393
 UI1  N7   C8    single    1.355  0.020  1.355
 UI1  N7   HN7   single    0.860  0.020  1.020
 UI1  C8   O9    double    1.219  0.020  1.219
 UI1  C8   C10   single    1.495  0.020  1.495
 UI1  C10  C11   aromatic  1.410  0.020  1.410
 UI1  C10  C26   aromatic  1.371  0.020  1.371
 UI1  C11  C12   aromatic  1.372  0.020  1.372
 UI1  C11  H11   single    0.930  0.020  1.080
 UI1  C12  N13   single    1.393  0.020  1.393
 UI1  C12  C20   aromatic  1.430  0.020  1.430
 UI1  N13  C14   single    1.364  0.020  1.364
 UI1  N13  H13   single    0.860  0.020  1.020
 UI1  C14  N15   aromatic  1.336  0.020  1.336
 UI1  C14  N19   aromatic  1.328  0.020  1.328
 UI1  N15  C16   aromatic  1.322  0.020  1.322
 UI1  C16  C17   aromatic  1.387  0.020  1.387
 UI1  C16  H16   single    0.930  0.020  1.080
 UI1  C17  C18   aromatic  1.384  0.020  1.384
 UI1  C17  H17   single    0.930  0.020  1.080
 UI1  C18  N19   aromatic  1.325  0.020  1.325
 UI1  C18  H18   single    0.930  0.020  1.080
 UI1  C20  C21   aromatic  1.411  0.020  1.411
 UI1  C20  C25   aromatic  1.418  0.020  1.418
 UI1  C21  C22   aromatic  1.374  0.020  1.374
 UI1  C21  H21   single    0.930  0.020  1.080
 UI1  C22  C23   aromatic  1.413  0.020  1.413
 UI1  C22  C27   single    1.491  0.020  1.491
 UI1  C23  C24   aromatic  1.365  0.020  1.365
 UI1  C23  H23   single    0.930  0.020  1.080
 UI1  C24  C25   aromatic  1.413  0.020  1.413
 UI1  C24  H24   single    0.930  0.020  1.080
 UI1  C25  C26   aromatic  1.410  0.020  1.410
 UI1  C26  H26   single    0.930  0.020  1.080
 UI1  C27  N28   double    1.278  0.020  1.278
 UI1  C27  N29   single    1.362  0.020  1.362
 UI1  N28  H28   single    0.890  0.020  1.040
 UI1  N29  H291  single    0.890  0.020  1.040
 UI1  N29  H292  single    0.890  0.020  1.040
 UI1  C30  C31   aromatic  1.389  0.020  1.389
 UI1  C30  H30   single    0.930  0.020  1.080
 UI1  C31  H31   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
 UI1  HN12  N1   HN11  106.07  3.000
 UI1  HN12  N1   C2    109.50  3.000
 UI1  HN11  N1   C2    109.42  3.000
 UI1  H22   C2   H21A  105.79  3.000
 UI1  H22   C2   C3    108.74  3.000
 UI1  H21A  C2   C3    108.65  3.000
 UI1  H22   C2   N1    114.03  3.000
 UI1  H21A  C2   N1    107.64  3.000
 UI1  C3    C2   N1    111.71  3.000
 UI1  C31   C3   C4    117.65  3.000
 UI1  C31   C3   C2    121.17  3.000
 UI1  C4    C3   C2    121.16  3.000
 UI1  H4    C4   C5    119.31  3.000
 UI1  H4    C4   C3    119.66  3.000
 UI1  C5    C4   C3    121.03  3.000
 UI1  H5    C5   C6    119.68  3.000
 UI1  H5    C5   C4    119.51  3.000
 UI1  C6    C5   C4    120.81  3.000
 UI1  C30   C6   N7    124.02  3.000
 UI1  C30   C6   C5    118.79  3.000
 UI1  N7    C6   C5    117.18  3.000
 UI1  HN7   N7   C8    116.51  3.000
 UI1  HN7   N7   C6    114.83  3.000
 UI1  C8    N7   C6    128.01  3.000
 UI1  C10   C8   O9    121.10  3.000
 UI1  C10   C8   N7    114.76  3.000
 UI1  O9    C8   N7    124.14  3.000
 UI1  C26   C10  C11   120.44  3.000
 UI1  C26   C10  C8    122.34  3.000
 UI1  C11   C10  C8    117.21  3.000
 UI1  H11   C11  C12   120.04  3.000
 UI1  H11   C11  C10   118.97  3.000
 UI1  C12   C11  C10   120.98  3.000
 UI1  C20   C12  N13   117.82  3.000
 UI1  C20   C12  C11   119.73  3.000
 UI1  N13   C12  C11   122.42  3.000
 UI1  H13   N13  C14   113.95  3.000
 UI1  H13   N13  C12   117.36  3.000
 UI1  C14   N13  C12   128.56  3.000
 UI1  N19   C14  N15   125.94  3.000
 UI1  N19   C14  N13   119.30  3.000
 UI1  N15   C14  N13   114.75  3.000
 UI1  C16   N15  C14   116.43  3.000
 UI1  H16   C16  C17   120.83  3.000
 UI1  H16   C16  N15   116.44  3.000
 UI1  C17   C16  N15   122.74  3.000
 UI1  H17   C17  C18   122.22  3.000
 UI1  H17   C17  C16   122.15  3.000
 UI1  C18   C17  C16   115.63  3.000
 UI1  H18   C18  N19   116.28  3.000
 UI1  H18   C18  C17   120.88  3.000
 UI1  N19   C18  C17   122.84  3.000
 UI1  C18   N19  C14   116.42  3.000
 UI1  C25   C20  C21   118.59  3.000
 UI1  C25   C20  C12   118.71  3.000
 UI1  C21   C20  C12   122.69  3.000
 UI1  H21   C21  C22   118.73  3.000
 UI1  H21   C21  C20   119.82  3.000
 UI1  C22   C21  C20   121.40  3.000
 UI1  C27   C22  C23   120.75  3.000
 UI1  C27   C22  C21   119.63  3.000
 UI1  C23   C22  C21   119.62  3.000
 UI1  H23   C23  C24   119.73  3.000
 UI1  H23   C23  C22   120.03  3.000
 UI1  C24   C23  C22   120.24  3.000
 UI1  H24   C24  C25   118.74  3.000
 UI1  H24   C24  C23   120.19  3.000
 UI1  C25   C24  C23   121.06  3.000
 UI1  C26   C25  C24   120.90  3.000
 UI1  C26   C25  C20   120.02  3.000
 UI1  C24   C25  C20   119.07  3.000
 UI1  H26   C26  C25   118.28  3.000
 UI1  H26   C26  C10   121.60  3.000
 UI1  C25   C26  C10   120.09  3.000
 UI1  N29   C27  N28   120.59  3.000
 UI1  N29   C27  C22   114.72  3.000
 UI1  N28   C27  C22   124.66  3.000
 UI1  H28   N28  C27   110.94  3.000
 UI1  H292  N29  H291  114.44  3.000
 UI1  H292  N29  C27   118.65  3.000
 UI1  H291  N29  C27   116.21  3.000
 UI1  H30   C30  C31   119.10  3.000
 UI1  H30   C30  C6    121.31  3.000
 UI1  C31   C30  C6    119.58  3.000
 UI1  H31   C31  C30   118.33  3.000
 UI1  H31   C31  C3    119.53  3.000
 UI1  C30   C31  C3    122.14  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
 UI1  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 UI1  CONST_02  C6    C30  C31  C3      0.00   0.0  0
 UI1  CONST_03  C30   C31  C3   C4      0.00   0.0  0
 UI1  CONST_04  C30   C6   C5   C4      0.00   0.0  0
 UI1  CONST_05  C31   C3   C4   C5      0.00   0.0  0
 UI1  CONST_06  C31   C30  C6   C5      0.00   0.0  0
 UI1  CONST_07  C20   C12  C11  C10     0.00   0.0  0
 UI1  CONST_08  C20   C25  C26  C10     0.00   0.0  0
 UI1  CONST_09  C24   C25  C26  C10   180.00   0.0  0
 UI1  CONST_10  C25   C26  C10  C11     0.00   0.0  0
 UI1  CONST_11  C21   C20  C12  C11   180.00   0.0  0
 UI1  CONST_12  C25   C20  C12  C11     0.00   0.0  0
 UI1  CONST_13  C26   C10  C11  C12     0.00   0.0  0
 UI1  CONST_14  C22   C21  C20  C12   180.00   0.0  0
 UI1  CONST_15  C24   C25  C20  C12   180.00   0.0  0
 UI1  CONST_16  C26   C25  C20  C12     0.00   0.0  0
 UI1  CONST_17  C17   C16  N15  C14     0.00   0.0  0
 UI1  CONST_18  C17   C18  N19  C14     0.00   0.0  0
 UI1  CONST_19  C18   N19  C14  N15     0.00   0.0  0
 UI1  CONST_20  C18   C17  C16  N15     0.00   0.0  0
 UI1  CONST_21  N19   C14  N15  C16     0.00   0.0  0
 UI1  CONST_22  N19   C18  C17  C16     0.00   0.0  0
 UI1  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 UI1  CONST_24  C23   C24  C25  C20     0.00   0.0  0
 UI1  CONST_25  C24   C25  C20  C21     0.00   0.0  0
 UI1  CONST_26  C26   C25  C20  C21   180.00   0.0  0
 UI1  CONST_27  C24   C23  C22  C21     0.00   0.0  0
 UI1  CONST_28  C25   C20  C21  C22     0.00   0.0  0
 UI1  CONST_29  C25   C24  C23  C22     0.00   0.0  0
 UI1  CONST_30  C26   C25  C24  C23   180.00   0.0  0
 UI1  CONST_31  C5    C4   C3   C2    180.00   0.0  0
 UI1  CONST_32  C30   C31  C3   C2    180.00   0.0  0
 UI1  CONST_33  N7    C6   C5   C4    180.00   0.0  0
 UI1  CONST_34  C31   C30  C6   N7    180.00   0.0  0
 UI1  CONST_35  C12   C11  C10  C8    180.00   0.0  0
 UI1  CONST_36  C25   C26  C10  C8    180.00   0.0  0
 UI1  CONST_37  N13   C12  C11  C10   180.00   0.0  0
 UI1  CONST_38  C21   C20  C12  N13     0.00   0.0  0
 UI1  CONST_39  C25   C20  C12  N13   180.00   0.0  0
 UI1  CONST_40  C16   N15  C14  N13   180.00   0.0  0
 UI1  CONST_41  C18   N19  C14  N13   180.00   0.0  0
 UI1  CONST_42  C27   C22  C21  C20   180.00   0.0  0
 UI1  CONST_43  C27   C22  C23  C24   180.00   0.0  0
 UI1  CONST_44  H5    C5   C4   C3    180.00   0.0  0
 UI1  CONST_45  H30   C30  C31  C3    180.00   0.0  0
 UI1  CONST_46  H31   C31  C3   C4    180.00   0.0  0
 UI1  CONST_47  H4    C4   C5   C6    180.00   0.0  0
 UI1  CONST_48  H26   C26  C10  C11   180.00   0.0  0
 UI1  CONST_49  H21   C21  C20  C12     0.00   0.0  0
 UI1  CONST_50  H16   C16  N15  C14   180.00   0.0  0
 UI1  CONST_51  H18   C18  N19  C14   180.00   0.0  0
 UI1  CONST_52  H17   C17  C16  N15   180.00   0.0  0
 UI1  CONST_53  H11   C11  C12  C20   180.00   0.0  0
 UI1  CONST_54  H24   C24  C25  C20   180.00   0.0  0
 UI1  CONST_55  H23   C23  C22  C21   180.00   0.0  0
 UI1  CONST_56  C10   C8   N7   C6    180.00   0.0  0
 UI1  CONST_59  HN7   N7   C6   C5      0.00   0.0  0
 UI1  CONST_60  O9    C8   N7   C6      0.00   0.0  0
 UI1  CONST_61  H28   N28  C27  C22     0.00   0.0  0
 UI1  CONST_62  H291  N29  C27  C22   180.00   0.0  0
 UI1  Var_01    C14   N13  C12  C11   -36.00  30.0  2
 UI1  Var_02    N15   C14  N13  C12   173.26  30.0  2
 UI1  Var_03    C4    C3   C2   N1     42.13  30.0  2
 UI1  Var_04    C11   C10  C8   N7   -149.45  30.0  2
 UI1  Var_05    N28   C27  C22  C21    35.70  30.0  2
 UI1  Var_06    HN11  N1   C2   C3   -174.46  30.0  3

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
 UI1  plan-1  C2    0.020
 UI1  plan-1  C3    0.020
 UI1  plan-1  C4    0.020
 UI1  plan-1  C5    0.020
 UI1  plan-1  C6    0.020
 UI1  plan-1  N7    0.020
 UI1  plan-1  C30   0.020
 UI1  plan-1  C31   0.020
 UI1  plan-1  H4    0.020
 UI1  plan-1  H5    0.020
 UI1  plan-1  H30   0.020
 UI1  plan-1  H31   0.020
 UI1  plan-2  N13   0.020
 UI1  plan-2  C14   0.020
 UI1  plan-2  N15   0.020
 UI1  plan-2  C16   0.020
 UI1  plan-2  C17   0.020
 UI1  plan-2  C18   0.020
 UI1  plan-2  N19   0.020
 UI1  plan-2  H16   0.020
 UI1  plan-2  H17   0.020
 UI1  plan-2  H18   0.020
 UI1  plan-3  C8    0.020
 UI1  plan-3  C10   0.020
 UI1  plan-3  C11   0.020
 UI1  plan-3  C12   0.020
 UI1  plan-3  N13   0.020
 UI1  plan-3  C20   0.020
 UI1  plan-3  C21   0.020
 UI1  plan-3  C22   0.020
 UI1  plan-3  C23   0.020
 UI1  plan-3  C24   0.020
 UI1  plan-3  C25   0.020
 UI1  plan-3  C26   0.020
 UI1  plan-3  C27   0.020
 UI1  plan-3  H11   0.020
 UI1  plan-3  H21   0.020
 UI1  plan-3  H23   0.020
 UI1  plan-3  H24   0.020
 UI1  plan-3  H26   0.020
 UI1  plan-4  C6    0.020
 UI1  plan-4  N7    0.020
 UI1  plan-4  C8    0.020
 UI1  plan-4  O9    0.020
 UI1  plan-4  C10   0.020
 UI1  plan-4  HN7   0.020
 UI1  plan-5  C22   0.020
 UI1  plan-5  C27   0.020
 UI1  plan-5  N28   0.020
 UI1  plan-5  N29   0.020
 UI1  plan-5  H28   0.020
 UI1  plan-5  H291  0.020
 UI1  plan-5  H292  0.020

