# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:26:18 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: N-(3,3-diphenylpropyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCC(c1ccccc1)c2ccccc2)c3cccnc3
#
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
 33N  33N  N-(3,3-diphenylpropyl)pyridine-3-carboxamide  ligand  44  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_33N
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
 33N  C4    C  CH2   0  -0.441   0.4901  -0.5997   0.3765
 33N  C5    C  CR16  0  -0.309   2.9784   2.1339   0.9316
 33N  C6    C  CR16  0  -0.318   1.8629   1.6373  -1.1251
 33N  C7    C  CR16  0  -0.325   3.9673  -1.5038   1.1685
 33N  C8    C  CR16  0  -0.320   2.9846  -1.6712  -1.0061
 33N  C10   C  CR16  0  -0.239   3.3371   3.3827   0.4423
 33N  C13   C  CR16  0  -0.237   3.9776  -2.5635  -1.3859
 33N  C15   C  CR16  0  -0.273   2.9583   3.7635  -0.8381
 33N  C17   C  C     0   0.526  -2.8538   0.5620   0.1296
 33N  C20   C  CR16  0  -0.152  -5.3275   0.5961  -0.1463
 33N  C21   C  CR16  0  -0.077  -4.2400  -1.5157  -0.3263
 33N  C22   C  CR16  0  -0.318  -6.5241  -0.0589  -0.3744
 33N  C24   C  CR16  0  -0.056  -6.4988  -1.4323  -0.5737
 33N  O19   O  O     0  -0.484  -2.7124   1.7257  -0.2194
 33N  C18   C  CR6   0  -0.135  -4.1511  -0.1449  -0.1007
 33N  N23   N  N     0  -0.399  -5.3816  -2.1487  -0.5603
 33N  N14   N  NH1   0  -0.647  -1.8997  -0.1624   0.7341
 33N  C9    C  CH2   0  -0.264  -0.5602   0.3088   1.0035
 33N  C1    C  CH1   0  -0.433   1.9092  -0.1318   0.7084
 33N  C3    C  CR6   0   0.203   2.9656  -1.1284   0.2772
 33N  C16   C  CR16  0  -0.274   4.9735  -2.9286  -0.4885
 33N  C12   C  CR16  0  -0.237   4.9637  -2.3956   0.7929
 33N  C2    C  CR6   0   0.176   2.2405   1.2423   0.1568
 33N  C11   C  CR16  0  -0.238   2.2182   2.8856  -1.6189
 33N  H4    H  HCH2  0   0.251   0.3647  -1.6175   0.7565
 33N  H4A   H  HCH2  0   0.238   0.3266  -0.6513  -0.7026
 33N  H5    H  HCR6  0   0.246   3.2773   1.8478   1.9336
 33N  H6    H  HCR6  0   0.249   1.2748   0.9783  -1.7519
 33N  H7    H  HCR6  0   0.247   3.9656  -1.0977   2.1735
 33N  H8    H  HCR6  0   0.246   2.2194  -1.4048  -1.7247
 33N  H10   H  HCR6  0   0.255   3.9086   4.0596   1.0643
 33N  H13   H  HCR6  0   0.254   3.9724  -2.9754  -2.3870
 33N  H15   H  HCR6  0   0.254   3.2313   4.7386  -1.2204
 33N  H21   H  HCR6  0   0.265  -3.3475  -2.1329  -0.3449
 33N  H22   H  HCR6  0   0.278  -7.4607   0.4800  -0.4020
 33N  H24   H  HCR6  0   0.274  -7.4196  -1.9741  -0.7579
 33N  HN14  H  HNH1  0   0.407  -2.1376  -1.0729   1.0938
 33N  H9    H  HCH2  0   0.246  -0.4037   0.3646   2.0849
 33N  H9A   H  HCH2  0   0.254  -0.4713   1.3227   0.6182
 33N  H1    H  HCH1  0   0.265   1.9727  -0.0584   1.7993
 33N  H16   H  HCR6  0   0.254   5.7477  -3.6246  -0.7845
 33N  H12   H  HCR6  0   0.254   5.7299  -2.6754   1.5046
 33N  H11   H  HCR6  0   0.255   1.9106   3.1720  -2.6164
 33N  H20   H  HCR6  0   0.278  -5.3063   1.6673   0.0045

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
 33N  C4   C9    single    1.524  0.020  1.524
 33N  C4   C1    single    1.531  0.020  1.531
 33N  C5   C10   aromatic  1.388  0.020  1.388
 33N  C5   C2    aromatic  1.393  0.020  1.393
 33N  C6   C2    aromatic  1.394  0.020  1.394
 33N  C6   C11   aromatic  1.389  0.020  1.389
 33N  C7   C3    aromatic  1.392  0.020  1.392
 33N  C7   C12   aromatic  1.389  0.020  1.389
 33N  C8   C13   aromatic  1.388  0.020  1.388
 33N  C8   C3    aromatic  1.393  0.020  1.393
 33N  C10  C15   aromatic  1.388  0.020  1.388
 33N  C13  C16   aromatic  1.389  0.020  1.389
 33N  C15  C11   aromatic  1.389  0.020  1.389
 33N  C17  O19   double    1.223  0.020  1.223
 33N  C17  C18   single    1.495  0.020  1.495
 33N  C17  N14   single    1.342  0.020  1.342
 33N  C20  C22   aromatic  1.383  0.020  1.383
 33N  C20  C18   aromatic  1.391  0.020  1.391
 33N  C21  C18   aromatic  1.392  0.020  1.392
 33N  C21  N23   aromatic  1.326  0.020  1.326
 33N  C22  C24   aromatic  1.388  0.020  1.388
 33N  C24  N23   aromatic  1.327  0.020  1.327
 33N  N14  C9    single    1.445  0.020  1.445
 33N  C1   C3    single    1.515  0.020  1.515
 33N  C1   C2    single    1.517  0.020  1.517
 33N  C16  C12   aromatic  1.388  0.020  1.388
 33N  C4   H4    single    0.970  0.020  1.090
 33N  C4   H4A   single    0.970  0.020  1.090
 33N  C5   H5    single    0.930  0.020  1.080
 33N  C6   H6    single    0.930  0.020  1.080
 33N  C7   H7    single    0.930  0.020  1.080
 33N  C8   H8    single    0.930  0.020  1.080
 33N  C10  H10   single    0.930  0.020  1.080
 33N  C13  H13   single    0.930  0.020  1.080
 33N  C15  H15   single    0.930  0.020  1.080
 33N  C20  H20   single    0.930  0.020  1.080
 33N  C21  H21   single    0.930  0.020  1.080
 33N  C22  H22   single    0.930  0.020  1.080
 33N  C24  H24   single    0.930  0.020  1.080
 33N  N14  HN14  single    0.860  0.020  1.020
 33N  C9   H9    single    0.970  0.020  1.090
 33N  C9   H9A   single    0.970  0.020  1.090
 33N  C1   H1    single    0.970  0.020  1.090
 33N  C16  H16   single    0.930  0.020  1.080
 33N  C12  H12   single    0.930  0.020  1.080
 33N  C11  H11   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
 33N  H4A   C4   H4   106.39  3.000
 33N  H4A   C4   C1   111.55  3.000
 33N  H4    C4   C1   108.39  3.000
 33N  H4A   C4   C9   109.36  3.000
 33N  H4    C4   C9   109.45  3.000
 33N  C1    C4   C9   111.56  3.000
 33N  H5    C5   C2   119.43  3.000
 33N  H5    C5   C10  119.46  3.000
 33N  C2    C5   C10  121.11  3.000
 33N  H6    C6   C11  118.70  3.000
 33N  H6    C6   C2   120.46  3.000
 33N  C11   C6   C2   120.84  3.000
 33N  H7    C7   C12  119.50  3.000
 33N  H7    C7   C3   119.43  3.000
 33N  C12   C7   C3   121.07  3.000
 33N  H8    C8   C3   120.38  3.000
 33N  H8    C8   C13  118.82  3.000
 33N  C3    C8   C13  120.81  3.000
 33N  H10   C10  C15  120.16  3.000
 33N  H10   C10  C5   119.76  3.000
 33N  C15   C10  C5   120.08  3.000
 33N  H13   C13  C16  120.05  3.000
 33N  H13   C13  C8   119.62  3.000
 33N  C16   C13  C8   120.33  3.000
 33N  H15   C15  C11  120.35  3.000
 33N  H15   C15  C10  120.27  3.000
 33N  C11   C15  C10  119.38  3.000
 33N  N14   C17  C18  115.54  3.000
 33N  N14   C17  O19  124.05  3.000
 33N  C18   C17  O19  120.41  3.000
 33N  H20   C20  C18  120.42  3.000
 33N  H20   C20  C22  120.58  3.000
 33N  C18   C20  C22  119.00  3.000
 33N  H21   C21  N23  115.69  3.000
 33N  H21   C21  C18  120.68  3.000
 33N  N23   C21  C18  123.61  3.000
 33N  H22   C22  C24  120.36  3.000
 33N  H22   C22  C20  121.18  3.000
 33N  C24   C22  C20  118.46  3.000
 33N  H24   C24  N23  116.54  3.000
 33N  H24   C24  C22  120.23  3.000
 33N  N23   C24  C22  123.23  3.000
 33N  C21   C18  C20  117.73  3.000
 33N  C21   C18  C17  123.08  3.000
 33N  C20   C18  C17  119.14  3.000
 33N  C24   N23  C21  117.95  3.000
 33N  HN14  N14  C9   116.55  3.000
 33N  HN14  N14  C17  118.74  3.000
 33N  C9    N14  C17  124.54  3.000
 33N  H9A   C9   H9   106.90  3.000
 33N  H9A   C9   N14  108.27  3.000
 33N  H9    C9   N14  109.48  3.000
 33N  H9A   C9   C4   110.70  3.000
 33N  H9    C9   C4   109.79  3.000
 33N  N14   C9   C4   111.57  3.000
 33N  H1    C1   C2   106.78  3.000
 33N  H1    C1   C3   106.68  3.000
 33N  C2    C1   C3   109.88  3.000
 33N  H1    C1   C4   106.88  3.000
 33N  C2    C1   C4   113.61  3.000
 33N  C3    C1   C4   112.56  3.000
 33N  C1    C3   C8   121.86  3.000
 33N  C1    C3   C7   119.79  3.000
 33N  C8    C3   C7   118.34  3.000
 33N  H16   C16  C12  120.30  3.000
 33N  H16   C16  C13  120.33  3.000
 33N  C12   C16  C13  119.37  3.000
 33N  H12   C12  C16  120.19  3.000
 33N  H12   C12  C7   119.73  3.000
 33N  C16   C12  C7   120.09  3.000
 33N  C1    C2   C6   122.14  3.000
 33N  C1    C2   C5   119.55  3.000
 33N  C6    C2   C5   118.29  3.000
 33N  H11   C11  C15  120.16  3.000
 33N  H11   C11  C6   119.52  3.000
 33N  C15   C11  C6   120.31  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
 33N  CONST_01  C11   C15  C10  C5      0.00   0.0  0
 33N  CONST_02  C11   C6   C2   C5      0.00   0.0  0
 33N  CONST_03  C10   C5   C2   C6      0.00   0.0  0
 33N  CONST_04  C10   C15  C11  C6      0.00   0.0  0
 33N  CONST_05  C13   C8   C3   C7      0.00   0.0  0
 33N  CONST_06  C13   C16  C12  C7      0.00   0.0  0
 33N  CONST_07  C12   C16  C13  C8      0.00   0.0  0
 33N  CONST_08  C12   C7   C3   C8      0.00   0.0  0
 33N  CONST_09  C2    C5   C10  C15     0.00   0.0  0
 33N  CONST_10  C2    C6   C11  C15     0.00   0.0  0
 33N  CONST_11  N23   C24  C22  C20     0.00   0.0  0
 33N  CONST_12  N23   C21  C18  C20     0.00   0.0  0
 33N  CONST_13  C22   C20  C18  C21     0.00   0.0  0
 33N  CONST_14  C22   C24  N23  C21     0.00   0.0  0
 33N  CONST_15  C18   C20  C22  C24     0.00   0.0  0
 33N  CONST_16  C18   C21  N23  C24     0.00   0.0  0
 33N  CONST_17  C16   C12  C7   C3      0.00   0.0  0
 33N  CONST_18  C16   C13  C8   C3      0.00   0.0  0
 33N  CONST_19  C1    C2   C5   C10   180.00   0.0  0
 33N  CONST_20  C1    C3   C8   C13   180.00   0.0  0
 33N  CONST_21  C22   C20  C18  C17   180.00   0.0  0
 33N  CONST_22  N23   C21  C18  C17   180.00   0.0  0
 33N  CONST_23  C12   C7   C3   C1    180.00   0.0  0
 33N  CONST_24  C11   C6   C2   C1    180.00   0.0  0
 33N  CONST_25  H15   C15  C10  C5    180.00   0.0  0
 33N  CONST_26  H6    C6   C2   C5    180.00   0.0  0
 33N  CONST_27  H5    C5   C2   C6    180.00   0.0  0
 33N  CONST_28  H8    C8   C3   C7    180.00   0.0  0
 33N  CONST_29  H16   C16  C12  C7    180.00   0.0  0
 33N  CONST_30  H7    C7   C3   C8    180.00   0.0  0
 33N  CONST_31  H11   C11  C15  C10   180.00   0.0  0
 33N  CONST_32  H12   C12  C16  C13   180.00   0.0  0
 33N  CONST_33  H24   C24  C22  C20   180.00   0.0  0
 33N  CONST_34  H21   C21  C18  C20   180.00   0.0  0
 33N  CONST_35  H20   C20  C18  C21   180.00   0.0  0
 33N  CONST_36  H22   C22  C20  C18   180.00   0.0  0
 33N  CONST_37  H13   C13  C8   C3    180.00   0.0  0
 33N  CONST_38  H10   C10  C5   C2    180.00   0.0  0
 33N  CONST_39  C9    N14  C17  C18   180.00   0.0  0
 33N  CONST_40  HN14  N14  C17  C18     0.00   0.0  0
 33N  CONST_41  C9    N14  C17  O19     0.00   0.0  0
 33N  Var_01    C3    C1   C2   C5    -92.96  30.0  2
 33N  Var_02    C2    C1   C3   C7    100.65  30.0  3
 33N  Var_03    O19   C17  C18  C20   -28.03  30.0  3
 33N  Var_04    C17   N14  C9   C4   -123.09  30.0  2
 33N  Var_05    C1    C4   C9   N14  -177.75  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
 33N  plan-1  C5    0.020
 33N  plan-1  C6    0.020
 33N  plan-1  C10   0.020
 33N  plan-1  C15   0.020
 33N  plan-1  C1    0.020
 33N  plan-1  C2    0.020
 33N  plan-1  C11   0.020
 33N  plan-1  H5    0.020
 33N  plan-1  H6    0.020
 33N  plan-1  H10   0.020
 33N  plan-1  H15   0.020
 33N  plan-1  H11   0.020
 33N  plan-2  C7    0.020
 33N  plan-2  C8    0.020
 33N  plan-2  C13   0.020
 33N  plan-2  C1    0.020
 33N  plan-2  C3    0.020
 33N  plan-2  C16   0.020
 33N  plan-2  C12   0.020
 33N  plan-2  H7    0.020
 33N  plan-2  H8    0.020
 33N  plan-2  H13   0.020
 33N  plan-2  H16   0.020
 33N  plan-2  H12   0.020
 33N  plan-3  C17   0.020
 33N  plan-3  C20   0.020
 33N  plan-3  C21   0.020
 33N  plan-3  C22   0.020
 33N  plan-3  C24   0.020
 33N  plan-3  C18   0.020
 33N  plan-3  N23   0.020
 33N  plan-3  H21   0.020
 33N  plan-3  H22   0.020
 33N  plan-3  H24   0.020
 33N  plan-3  H20   0.020
 33N  plan-4  C17   0.020
 33N  plan-4  O19   0.020
 33N  plan-4  C18   0.020
 33N  plan-4  N14   0.020
 33N  plan-4  C9    0.020
 33N  plan-4  HN14  0.020

