# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:43:24 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C)c1CNC(=O)c2cnn(Cc3ccc(Cn4cccn4)cc3)c2
#
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
 7SD  7SD  N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide  ligand  56  31  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7SD
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
 7SD  C01   C  CH3   0  -0.750  -4.8060   2.4006  -1.7850
 7SD  C02   C  CR6   0   0.211  -5.7064   1.6430  -0.8549
 7SD  C04   C  CR6   0   0.454  -7.5262   1.5912   0.7089
 7SD  N05   N  NH2   0  -0.838  -8.4796   2.2217   1.4523
 7SD  C07   C  CR6   0   0.229  -6.4475  -0.3721   0.2115
 7SD  C09   C  CR6   0  -0.119  -5.5759   0.2559  -0.6769
 7SD  C10   C  CH2   0  -0.353  -4.5089  -0.5256  -1.3885
 7SD  C12   C  C     0   0.507  -2.2400  -1.3328  -0.9198
 7SD  C14   C  CR5   0  -0.292  -1.1121  -1.3281   0.0232
 7SD  C15   C  CR15  0  -0.065  -0.9191  -0.6555   1.2473
 7SD  C19   C  CR6   0   0.127   3.1905  -1.1907   0.8251
 7SD  C20   C  CR16  0  -0.277   3.6588  -1.0475  -0.4784
 7SD  C22   C  CR6   0   0.130   5.0269   0.8242   0.1855
 7SD  C23   C  CH2   0  -0.400   6.0290   1.8932  -0.1610
 7SD  C26   C  CR15  0  -0.518   9.1195   0.5326  -1.4055
 7SD  C27   C  CR15  0  -0.049   9.1493   0.3478  -0.0138
 7SD  C29   C  CR16  0  -0.289   4.5619   0.6791   1.4861
 7SD  C31   C  CR15  0   0.097   0.0536  -2.0489  -0.1459
 7SD  C03   C  CR16  0  -0.451  -6.6918   2.3116  -0.1565
 7SD  N06   N  N     0  -0.490  -7.3969   0.2785   0.8809
 7SD  C08   C  CH3   0  -0.748  -6.3624  -1.8504   0.4652
 7SD  N11   N  NH1   0  -0.656  -3.3151  -0.6126  -0.5620
 7SD  O13   O  O     0  -0.505  -2.1905  -1.9621  -1.9718
 7SD  N16   N  N     0  -0.266   0.2534  -0.9427   1.7703
 7SD  N17   N  NR5   0  -0.262   0.8235  -1.7925   0.9161
 7SD  C21   C  CR16  0  -0.274   4.5652  -0.0497  -0.7956
 7SD  N24   N  NR5   0  -0.254   7.3383   1.3382  -0.4313
 7SD  C25   C  CR15  0   0.048   7.9247   1.1759  -1.6320
 7SD  N28   N  N     0  -0.283   8.0645   0.8354   0.5613
 7SD  C30   C  CR16  0  -0.277   3.6482  -0.3175   1.8034
 7SD  H011  H  HCH3  0   0.257  -4.9591   2.0920  -2.8207
 7SD  H013  H  HCH3  0   0.257  -4.9938   3.4712  -1.7267
 7SD  H012  H  HCH3  0   0.250  -3.7539   2.2307  -1.5538
 7SD  H052  H  HNH2  0   0.381  -9.2096   1.6414   1.8313
 7SD  H051  H  HNH2  0   0.389  -8.7879   3.1296   1.1474
 7SD  H101  H  HCH2  0   0.260  -4.8623  -1.5314  -1.6238
 7SD  H102  H  HCH2  0   0.262  -4.2627  -0.0591  -2.3446
 7SD  H151  H  HCR5  0   0.266  -1.5851   0.0190   1.7654
 7SD  H181  H  HCH2  0   0.290   2.3323  -3.1408   0.5399
 7SD  H182  H  HCH2  0   0.293   2.2507  -2.5583   2.1973
 7SD  H201  H  HCR6  0   0.256   3.3139  -1.7216  -1.2537
 7SD  H232  H  HCH2  0   0.284   5.7185   2.4388  -1.0517
 7SD  H231  H  HCH2  0   0.285   6.1209   2.6160   0.6494
 7SD  H271  H  HCR5  0   0.259   9.9209  -0.1137   0.5838
 7SD  H291  H  HCR6  0   0.258   4.9132   1.3496   2.2612
 7SD  H311  H  HCR5  0   0.302   0.3635  -2.7141  -0.9357
 7SD  H031  H  HCR6  0   0.256  -6.8214   3.3807  -0.2739
 7SD  H083  H  HCH3  0   0.245  -5.3490  -2.1593   0.7238
 7SD  H082  H  HCH3  0   0.254  -7.0256  -2.1315   1.2803
 7SD  H081  H  HCH3  0   0.253  -6.6549  -2.4226  -0.4179
 7SD  H111  H  HNH1  0   0.404  -3.3219  -0.1205   0.3163
 7SD  H211  H  HCR6  0   0.256   4.9159   0.0451  -1.8169
 7SD  H251  H  HCR5  0   0.292   7.4642   1.5287  -2.5404
 7SD  H301  H  HCR6  0   0.258   3.2952  -0.4158   2.8227
 7SD  C18   C  CH2   0  -0.414   2.1781  -2.2543   1.1539
 7SD  H261  H  HCR5  0   0.261   9.8600   0.2470  -2.1334

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
 7SD  N05  C04   single    1.363  0.020  1.363
 7SD  C04  N06   aromatic  1.330  0.020  1.330
 7SD  C04  C03   aromatic  1.401  0.020  1.401
 7SD  N06  C07   aromatic  1.331  0.020  1.331
 7SD  C03  C02   aromatic  1.381  0.020  1.381
 7SD  C07  C08   single    1.502  0.020  1.502
 7SD  C07  C09   aromatic  1.394  0.020  1.394
 7SD  C02  C09   aromatic  1.405  0.020  1.405
 7SD  C02  C01   single    1.500  0.020  1.500
 7SD  C09  C10   single    1.502  0.020  1.502
 7SD  C10  N11   single    1.455  0.020  1.455
 7SD  O13  C12   double    1.227  0.020  1.227
 7SD  N11  C12   single    1.343  0.020  1.343
 7SD  C12  C14   single    1.470  0.020  1.470
 7SD  C14  C15   aromatic  1.410  0.020  1.410
 7SD  C14  C31   aromatic  1.381  0.020  1.381
 7SD  C15  N16   aromatic  1.316  0.020  1.316
 7SD  C31  N17   aromatic  1.337  0.020  1.337
 7SD  N16  N17   aromatic  1.333  0.020  1.333
 7SD  N17  C18   single    1.451  0.020  1.451
 7SD  C18  C19   single    1.505  0.020  1.505
 7SD  C20  C19   aromatic  1.392  0.020  1.392
 7SD  C20  C21   aromatic  1.385  0.020  1.385
 7SD  C19  C30   aromatic  1.389  0.020  1.389
 7SD  C21  C22   aromatic  1.393  0.020  1.393
 7SD  C30  C29   aromatic  1.389  0.020  1.389
 7SD  C22  C29   aromatic  1.389  0.020  1.389
 7SD  C22  C23   single    1.506  0.020  1.506
 7SD  C23  N24   single    1.448  0.020  1.448
 7SD  C25  N24   aromatic  1.346  0.020  1.346
 7SD  C25  C26   aromatic  1.376  0.020  1.376
 7SD  N24  N28   aromatic  1.329  0.020  1.329
 7SD  C26  C27   aromatic  1.404  0.020  1.404
 7SD  N28  C27   aromatic  1.321  0.020  1.321
 7SD  C01  H011  single    0.970  0.020  1.090
 7SD  C01  H013  single    0.970  0.020  1.090
 7SD  C01  H012  single    0.970  0.020  1.090
 7SD  N05  H052  single    0.890  0.020  1.040
 7SD  N05  H051  single    0.890  0.020  1.040
 7SD  C10  H101  single    0.970  0.020  1.090
 7SD  C10  H102  single    0.970  0.020  1.090
 7SD  C15  H151  single    0.930  0.020  1.080
 7SD  C18  H181  single    0.970  0.020  1.090
 7SD  C18  H182  single    0.970  0.020  1.090
 7SD  C20  H201  single    0.930  0.020  1.080
 7SD  C23  H232  single    0.970  0.020  1.090
 7SD  C23  H231  single    0.970  0.020  1.090
 7SD  C26  H261  single    0.930  0.020  1.080
 7SD  C27  H271  single    0.930  0.020  1.080
 7SD  C29  H291  single    0.930  0.020  1.080
 7SD  C31  H311  single    0.930  0.020  1.080
 7SD  C03  H031  single    0.930  0.020  1.080
 7SD  C08  H083  single    0.970  0.020  1.090
 7SD  C08  H082  single    0.970  0.020  1.090
 7SD  C08  H081  single    0.970  0.020  1.090
 7SD  N11  H111  single    0.860  0.020  1.020
 7SD  C21  H211  single    0.930  0.020  1.080
 7SD  C25  H251  single    0.930  0.020  1.080
 7SD  C30  H301  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
 7SD  H012  C01  H013  107.96  3.000
 7SD  H012  C01  H011  107.00  3.000
 7SD  H013  C01  H011  107.74  3.000
 7SD  H012  C01  C02   111.66  3.000
 7SD  H013  C01  C02   111.10  3.000
 7SD  H011  C01  C02   111.18  3.000
 7SD  C03   C02  C09   118.72  3.000
 7SD  C09   C02  C01   121.44  3.000
 7SD  C03   C02  C01   119.84  3.000
 7SD  N06   C04  C03   121.96  3.000
 7SD  C03   C04  N05   121.01  3.000
 7SD  N06   C04  N05   116.99  3.000
 7SD  H051  N05  H052  114.33  3.000
 7SD  H051  N05  C04   117.80  3.000
 7SD  H052  N05  C04   116.47  3.000
 7SD  C08   C07  N06   115.87  3.000
 7SD  C08   C07  C09   121.03  3.000
 7SD  N06   C07  C09   123.10  3.000
 7SD  C10   C09  C07   120.78  3.000
 7SD  C10   C09  C02   121.32  3.000
 7SD  C07   C09  C02   117.87  3.000
 7SD  H102  C10  H101  106.13  3.000
 7SD  H102  C10  N11   109.75  3.000
 7SD  H101  C10  N11   109.45  3.000
 7SD  H102  C10  C09   110.66  3.000
 7SD  H101  C10  C09   110.58  3.000
 7SD  N11   C10  C09   110.18  3.000
 7SD  O13   C12  N11   122.41  3.000
 7SD  N11   C12  C14   116.21  3.000
 7SD  O13   C12  C14   121.38  3.000
 7SD  C31   C14  C15   103.88  3.000
 7SD  C31   C14  C12   124.56  3.000
 7SD  C15   C14  C12   131.56  3.000
 7SD  H151  C15  N16   119.68  3.000
 7SD  H151  C15  C14   129.04  3.000
 7SD  N16   C15  C14   111.28  3.000
 7SD  C30   C19  C20   118.94  3.000
 7SD  C30   C19  C18   120.81  3.000
 7SD  C20   C19  C18   120.24  3.000
 7SD  H201  C20  C21   119.51  3.000
 7SD  H201  C20  C19   119.91  3.000
 7SD  C21   C20  C19   120.58  3.000
 7SD  C21   C22  C29   118.90  3.000
 7SD  C29   C22  C23   120.83  3.000
 7SD  C21   C22  C23   120.27  3.000
 7SD  H231  C23  H232  107.45  3.000
 7SD  H231  C23  N24   108.47  3.000
 7SD  H232  C23  N24   107.28  3.000
 7SD  H231  C23  C22   110.84  3.000
 7SD  H232  C23  C22   110.73  3.000
 7SD  N24   C23  C22   111.88  3.000
 7SD  H261  C26  C25   127.59  3.000
 7SD  H261  C26  C27   128.34  3.000
 7SD  C25   C26  C27   104.07  3.000
 7SD  H271  C27  N28   120.25  3.000
 7SD  H271  C27  C26   128.32  3.000
 7SD  N28   C27  C26   111.44  3.000
 7SD  H291  C29  C30   119.60  3.000
 7SD  H291  C29  C22   119.79  3.000
 7SD  C30   C29  C22   120.61  3.000
 7SD  H311  C31  N17   122.34  3.000
 7SD  H311  C31  C14   130.88  3.000
 7SD  N17   C31  C14   106.78  3.000
 7SD  H031  C03  C04   120.20  3.000
 7SD  H031  C03  C02   120.56  3.000
 7SD  C04   C03  C02   119.24  3.000
 7SD  C07   N06  C04   119.11  3.000
 7SD  H081  C08  H082  107.90  3.000
 7SD  H081  C08  H083  106.99  3.000
 7SD  H082  C08  H083  108.40  3.000
 7SD  H081  C08  C07   111.34  3.000
 7SD  H082  C08  C07   110.26  3.000
 7SD  H083  C08  C07   111.80  3.000
 7SD  H111  N11  C12   120.01  3.000
 7SD  H111  N11  C10   117.44  3.000
 7SD  C12   N11  C10   122.54  3.000
 7SD  N17   N16  C15   105.40  3.000
 7SD  N16   N17  C31   112.66  3.000
 7SD  N16   N17  C18   119.82  3.000
 7SD  C31   N17  C18   127.37  3.000
 7SD  H211  C21  C22   120.10  3.000
 7SD  H211  C21  C20   119.38  3.000
 7SD  C22   C21  C20   120.51  3.000
 7SD  N28   N24  C25   112.50  3.000
 7SD  N28   N24  C23   120.00  3.000
 7SD  C25   N24  C23   127.36  3.000
 7SD  H251  C25  N24   121.75  3.000
 7SD  H251  C25  C26   131.51  3.000
 7SD  N24   C25  C26   106.73  3.000
 7SD  N24   N28  C27   105.26  3.000
 7SD  H301  C30  C29   119.64  3.000
 7SD  H301  C30  C19   119.90  3.000
 7SD  C29   C30  C19   120.46  3.000
 7SD  H182  C18  H181  107.66  3.000
 7SD  H182  C18  N17   107.94  3.000
 7SD  H181  C18  N17   107.39  3.000
 7SD  H182  C18  C19   111.21  3.000
 7SD  H181  C18  C19   110.91  3.000
 7SD  N17   C18  C19   111.56  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
 7SD  CONST_01  N06   C04  C03  C02    0.00   0.0  0
 7SD  CONST_02  N06   C07  C09  C02    0.00   0.0  0
 7SD  CONST_03  C09   C07  N06  C04    0.00   0.0  0
 7SD  CONST_04  C09   C02  C03  C04    0.00   0.0  0
 7SD  CONST_05  C03   C04  N06  C07    0.00   0.0  0
 7SD  CONST_06  C03   C02  C09  C07    0.00   0.0  0
 7SD  CONST_07  N17   N16  C15  C14    0.00   0.0  0
 7SD  CONST_08  N16   N17  C31  C14    0.00   0.0  0
 7SD  CONST_09  N17   C31  C14  C15    0.00   0.0  0
 7SD  CONST_10  C31   N17  N16  C15    0.00   0.0  0
 7SD  CONST_11  C22   C21  C20  C19    0.00   0.0  0
 7SD  CONST_12  C22   C29  C30  C19    0.00   0.0  0
 7SD  CONST_13  C29   C30  C19  C20    0.00   0.0  0
 7SD  CONST_14  C29   C22  C21  C20    0.00   0.0  0
 7SD  CONST_15  N28   N24  C25  C26    0.00   0.0  0
 7SD  CONST_16  N24   N28  C27  C26    0.00   0.0  0
 7SD  CONST_17  N24   C25  C26  C27    0.00   0.0  0
 7SD  CONST_18  C25   N24  N28  C27    0.00   0.0  0
 7SD  CONST_19  N16   C15  C14  C31    0.00   0.0  0
 7SD  CONST_20  C30   C19  C20  C21    0.00   0.0  0
 7SD  CONST_21  C30   C29  C22  C21    0.00   0.0  0
 7SD  CONST_22  N28   C27  C26  C25    0.00   0.0  0
 7SD  CONST_23  C04   C03  C02  C01  180.00   0.0  0
 7SD  CONST_24  C07   C09  C02  C01  180.00   0.0  0
 7SD  CONST_25  N05   C04  C03  C02  180.00   0.0  0
 7SD  CONST_26  C08   C07  C09  C02  180.00   0.0  0
 7SD  CONST_27  C08   C07  N06  C04  180.00   0.0  0
 7SD  CONST_28  C07   N06  C04  N05  180.00   0.0  0
 7SD  CONST_29  N06   C07  C09  C10  180.00   0.0  0
 7SD  CONST_30  C03   C02  C09  C10  180.00   0.0  0
 7SD  CONST_31  N16   C15  C14  C12  180.00   0.0  0
 7SD  CONST_32  N17   C31  C14  C12  180.00   0.0  0
 7SD  CONST_33  C18   N17  C31  C14  180.00   0.0  0
 7SD  CONST_34  C18   N17  N16  C15  180.00   0.0  0
 7SD  CONST_35  C21   C20  C19  C18  180.00   0.0  0
 7SD  CONST_36  C29   C30  C19  C18  180.00   0.0  0
 7SD  CONST_37  C23   C22  C21  C20  180.00   0.0  0
 7SD  CONST_38  C30   C29  C22  C23  180.00   0.0  0
 7SD  CONST_39  C26   C25  N24  C23  180.00   0.0  0
 7SD  CONST_40  C27   N28  N24  C23  180.00   0.0  0
 7SD  CONST_41  H031  C03  C02  C09  180.00   0.0  0
 7SD  CONST_42  H311  C31  C14  C15  180.00   0.0  0
 7SD  CONST_43  H211  C21  C20  C19  180.00   0.0  0
 7SD  CONST_44  H291  C29  C30  C19  180.00   0.0  0
 7SD  CONST_45  H301  C30  C19  C20  180.00   0.0  0
 7SD  CONST_46  H201  C20  C21  C22  180.00   0.0  0
 7SD  CONST_47  H251  C25  C26  C27  180.00   0.0  0
 7SD  CONST_48  H151  C15  C14  C31  180.00   0.0  0
 7SD  CONST_49  H261  C26  C25  N24  180.00   0.0  0
 7SD  CONST_50  H271  C27  N28  N24  180.00   0.0  0
 7SD  CONST_53  C14   C12  N11  C10  180.00   0.0  0
 7SD  CONST_54  H111  N11  C12  C14    0.00   0.0  0
 7SD  CONST_55  O13   C12  N11  C10    0.00   0.0  0
 7SD  Var_01    C31   N17  C18  C19   99.85  30.0  1
 7SD  Var_02    N17   C18  C19  C20  -85.92  30.0  2
 7SD  Var_03    C25   N24  C23  C22  104.40  30.0  2
 7SD  Var_04    N24   C23  C22  C29  108.03  30.0  2
 7SD  Var_05    N11   C10  C09  C02   92.00  30.0  2
 7SD  Var_06    O13   C12  C14  C15  177.40  30.0  2
 7SD  Var_07    H083  C08  C07  C09   51.64  30.0  2
 7SD  Var_08    H011  C01  C02  C09   65.14  30.0  2
 7SD  Var_09    C12   N11  C10  C09  175.42  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
 7SD  plan-1  C12   0.020
 7SD  plan-1  C14   0.020
 7SD  plan-1  C15   0.020
 7SD  plan-1  C31   0.020
 7SD  plan-1  N16   0.020
 7SD  plan-1  N17   0.020
 7SD  plan-1  H151  0.020
 7SD  plan-1  H311  0.020
 7SD  plan-1  C18   0.020
 7SD  plan-2  C23   0.020
 7SD  plan-2  C26   0.020
 7SD  plan-2  C27   0.020
 7SD  plan-2  N24   0.020
 7SD  plan-2  C25   0.020
 7SD  plan-2  N28   0.020
 7SD  plan-2  H271  0.020
 7SD  plan-2  H251  0.020
 7SD  plan-2  H261  0.020
 7SD  plan-3  C01   0.020
 7SD  plan-3  C02   0.020
 7SD  plan-3  C04   0.020
 7SD  plan-3  N05   0.020
 7SD  plan-3  C07   0.020
 7SD  plan-3  C09   0.020
 7SD  plan-3  C10   0.020
 7SD  plan-3  C03   0.020
 7SD  plan-3  N06   0.020
 7SD  plan-3  C08   0.020
 7SD  plan-3  H031  0.020
 7SD  plan-4  C19   0.020
 7SD  plan-4  C20   0.020
 7SD  plan-4  C22   0.020
 7SD  plan-4  C23   0.020
 7SD  plan-4  C29   0.020
 7SD  plan-4  C21   0.020
 7SD  plan-4  C30   0.020
 7SD  plan-4  H201  0.020
 7SD  plan-4  H291  0.020
 7SD  plan-4  H211  0.020
 7SD  plan-4  H301  0.020
 7SD  plan-4  C18   0.020
 7SD  plan-5  C10   0.020
 7SD  plan-5  C12   0.020
 7SD  plan-5  C14   0.020
 7SD  plan-5  N11   0.020
 7SD  plan-5  O13   0.020
 7SD  plan-5  H111  0.020
 7SD  plan-6  C04   0.020
 7SD  plan-6  N05   0.020
 7SD  plan-6  H052  0.020
 7SD  plan-6  H051  0.020

