# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:11:55 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-[3-(1-{[5-(2-phenylethyl)pyridin-3-yl]carbonyl}piperidin-4-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)C2CCN(CC2)C(=O)c3cncc(CCc4ccccc4)c3
#
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
 PM2  PM2  1-[3-(1-{[5-(2-phenylethyl)pyridin-3-yl]carbonyl}piperidin-4-yl)phenyl]methanamine  ligand  59  30  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PM2
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
 PM2  C1    C  CR6   0   0.223   0.1945  -0.1131   4.7877
 PM2  C2    C  CR16  0  -0.384   1.0764   0.1830   5.8227
 PM2  C3    C  CR16  0  -0.339  -0.8500  -1.0036   5.0342
 PM2  C4    C  CR6   0   0.104   0.9415  -0.3868   7.0867
 PM2  C5    C  CR16  0  -0.225  -0.9930  -1.5854   6.2851
 PM2  C6    C  CR16  0  -0.328  -0.0998  -1.2835   7.3046
 PM2  C7    C  CH2   0  -0.333   1.8742  -0.0217   8.2151
 PM2  N8    N  NH2   0  -0.794   3.2153   0.2874   7.7514
 PM2  C9    C  CH2   0  -0.407   0.4219  -0.4652   2.2907
 PM2  C10   C  CH2   0  -0.330   0.5438   0.2349   0.9414
 PM2  C11   C  C     0   0.514  -1.6485   0.9399   0.0223
 PM2  O12   O  O     0  -0.482  -2.7042   1.5434   0.1626
 PM2  C13   C  CH1   0  -0.355   0.3567   0.5439   3.4402
 PM2  N14   N  NT    0  -0.438  -0.5478   1.1825   0.7617
 PM2  C15   C  CH2   0  -0.327  -0.5845   2.2013   1.8000
 PM2  C16   C  CH2   0  -0.413  -0.7521   1.5691   3.1752
 PM2  C17   C  CR6   0  -0.154  -1.5483  -0.0888  -1.0591
 PM2  C18   C  CR16  0  -0.194  -0.6125  -0.0034  -2.0809
 PM2  C19   C  CR16  0  -0.073  -2.4934  -1.1067  -1.1206
 PM2  C20   C  CR6   0   0.044  -0.6418  -0.9245  -3.1204
 PM2  N21   N  N     0  -0.398  -2.5209  -2.0083  -2.0907
 PM2  C22   C  CH2   0  -0.512   0.3048  -0.8275  -4.2792
 PM2  C23   C  CR16  0  -0.099  -1.6214  -1.9107  -3.0619
 PM2  C24   C  CH2   0  -0.510  -0.1802   0.1976  -5.3155
 PM2  C25   C  CR6   0   0.132   0.7725   0.3164  -6.4718
 PM2  C26   C  CR16  0  -0.308   0.6778  -0.5464  -7.5620
 PM2  C27   C  CR16  0  -0.311   1.7950   1.2625  -6.4603
 PM2  C28   C  CR16  0  -0.240   1.5779  -0.4644  -8.6160
 PM2  C29   C  CR16  0  -0.240   2.6980   1.3486  -7.5120
 PM2  C30   C  CR16  0  -0.273   2.5921   0.4847  -8.5942
 PM2  H2    H  HCR6  0   0.238   1.8912   0.8743   5.6426
 PM2  H3    H  HCR6  0   0.243  -1.5554  -1.2496   4.2489
 PM2  H5    H  HCR6  0   0.250  -1.8016  -2.2826   6.4653
 PM2  H6    H  HCR6  0   0.243  -0.2134  -1.7510   8.2763
 PM2  H7C1  H  HCH2  0   0.214   1.8370  -0.8200   8.9685
 PM2  H7C2  H  HCH2  0   0.240   1.4813   0.8712   8.7113
 PM2  H8N1  H  HNH2  0   0.354   3.7675   0.6209   8.5308
 PM2  H8N2  H  HNH2  0   0.343   3.6674  -0.5602   7.4320
 PM2  H9C1  H  HCH2  0   0.250   1.2764  -1.1327   2.4229
 PM2  H9C2  H  HCH2  0   0.227  -0.4742  -1.0925   2.2814
 PM2  H101  H  HCH2  0   0.250   1.4884   0.7833   0.8848
 PM2  H102  H  HCH2  0   0.277   0.5516  -0.5016   0.1431
 PM2  H13   H  HCH1  0   0.242   1.3074   1.0912   3.4475
 PM2  H151  H  HCH2  0   0.249   0.3589   2.7542   1.7570
 PM2  H152  H  HCH2  0   0.267  -1.3844   2.9073   1.5932
 PM2  H161  H  HCH2  0   0.232  -1.7352   1.0926   3.2352
 PM2  H162  H  HCH2  0   0.247  -0.7288   2.3512   3.9373
 PM2  H18   H  HCR6  0   0.275   0.1352   0.7825  -2.0750
 PM2  H19   H  HCR6  0   0.269  -3.2460  -1.2025  -0.3453
 PM2  H221  H  HCH2  0   0.259   1.2973  -0.5401  -3.9236
 PM2  H222  H  HCH2  0   0.258   0.4113  -1.8038  -4.7576
 PM2  H23   H  HCR6  0   0.262  -1.6771  -2.6600  -3.8457
 PM2  H241  H  HCH2  0   0.254  -1.1692  -0.0981  -5.6743
 PM2  H242  H  HCH2  0   0.254  -0.3005   1.1690  -4.8295
 PM2  H26   H  HCR6  0   0.247  -0.1126  -1.2879  -7.5889
 PM2  H27   H  HCR6  0   0.246   1.8832   1.9444  -5.6222
 PM2  H28   H  HCR6  0   0.253   1.4846  -1.1395  -9.4571
 PM2  H29   H  HCR6  0   0.254   3.4830   2.0934  -7.4871
 PM2  H30   H  HCR6  0   0.254   3.2919   0.5535  -9.4169

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
 PM2  C1   C2    aromatic  1.392  0.020  1.392
 PM2  C1   C3    aromatic  1.395  0.020  1.395
 PM2  C1   C13   single    1.508  0.020  1.508
 PM2  C2   C4    aromatic  1.393  0.020  1.393
 PM2  C2   H2    single    0.930  0.020  1.080
 PM2  C3   C5    aromatic  1.387  0.020  1.387
 PM2  C3   H3    single    0.930  0.020  1.080
 PM2  C4   C6    aromatic  1.391  0.020  1.391
 PM2  C4   C7    single    1.509  0.020  1.509
 PM2  C5   C6    aromatic  1.389  0.020  1.389
 PM2  C5   H5    single    0.930  0.020  1.080
 PM2  C6   H6    single    0.930  0.020  1.080
 PM2  C7   N8    single    1.452  0.020  1.452
 PM2  C7   H7C1  single    0.970  0.020  1.090
 PM2  C7   H7C2  single    0.970  0.020  1.090
 PM2  N8   H8N1  single    0.890  0.020  1.040
 PM2  N8   H8N2  single    0.890  0.020  1.040
 PM2  C9   C10   single    1.525  0.020  1.525
 PM2  C9   C13   single    1.531  0.020  1.531
 PM2  C9   H9C1  single    0.970  0.020  1.090
 PM2  C9   H9C2  single    0.970  0.020  1.090
 PM2  C10  N14   single    1.457  0.020  1.457
 PM2  C10  H101  single    0.970  0.020  1.090
 PM2  C10  H102  single    0.970  0.020  1.090
 PM2  C11  O12   double    1.224  0.020  1.224
 PM2  C11  N14   single    1.348  0.020  1.348
 PM2  C11  C17   single    1.496  0.020  1.496
 PM2  C13  C16   single    1.533  0.020  1.533
 PM2  C13  H13   single    0.970  0.020  1.090
 PM2  N14  C15   single    1.455  0.020  1.455
 PM2  C15  C16   single    1.523  0.020  1.523
 PM2  C15  H151  single    0.970  0.020  1.090
 PM2  C15  H152  single    0.970  0.020  1.090
 PM2  C16  H161  single    0.970  0.020  1.090
 PM2  C16  H162  single    0.970  0.020  1.090
 PM2  C17  C18   aromatic  1.388  0.020  1.388
 PM2  C17  C19   aromatic  1.390  0.020  1.390
 PM2  C18  C20   aromatic  1.389  0.020  1.389
 PM2  C18  H18   single    0.930  0.020  1.080
 PM2  C19  N21   aromatic  1.325  0.020  1.325
 PM2  C19  H19   single    0.930  0.020  1.080
 PM2  C20  C22   single    1.499  0.020  1.499
 PM2  C20  C23   aromatic  1.391  0.020  1.391
 PM2  N21  C23   aromatic  1.327  0.020  1.327
 PM2  C22  C24   single    1.536  0.020  1.536
 PM2  C22  H221  single    0.970  0.020  1.090
 PM2  C22  H222  single    0.970  0.020  1.090
 PM2  C23  H23   single    0.930  0.020  1.080
 PM2  C24  C25   single    1.503  0.020  1.503
 PM2  C24  H241  single    0.970  0.020  1.090
 PM2  C24  H242  single    0.970  0.020  1.090
 PM2  C25  C26   aromatic  1.394  0.020  1.394
 PM2  C25  C27   aromatic  1.393  0.020  1.393
 PM2  C26  C28   aromatic  1.388  0.020  1.388
 PM2  C26  H26   single    0.930  0.020  1.080
 PM2  C27  C29   aromatic  1.389  0.020  1.389
 PM2  C27  H27   single    0.930  0.020  1.080
 PM2  C28  C30   aromatic  1.389  0.020  1.389
 PM2  C28  H28   single    0.930  0.020  1.080
 PM2  C29  C30   aromatic  1.389  0.020  1.389
 PM2  C29  H29   single    0.930  0.020  1.080
 PM2  C30  H30   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
 PM2  C13   C1   C3    121.11  3.000
 PM2  C13   C1   C2    120.25  3.000
 PM2  C3    C1   C2    118.63  3.000
 PM2  H2    C2   C4    118.98  3.000
 PM2  H2    C2   C1    119.25  3.000
 PM2  C4    C2   C1    121.76  3.000
 PM2  H3    C3   C5    119.42  3.000
 PM2  H3    C3   C1    120.29  3.000
 PM2  C5    C3   C1    120.30  3.000
 PM2  C7    C4   C6    120.09  3.000
 PM2  C7    C4   C2    121.32  3.000
 PM2  C6    C4   C2    118.57  3.000
 PM2  H5    C5   C6    119.87  3.000
 PM2  H5    C5   C3    119.82  3.000
 PM2  C6    C5   C3    120.31  3.000
 PM2  H6    C6   C5    119.79  3.000
 PM2  H6    C6   C4    119.78  3.000
 PM2  C5    C6   C4    120.43  3.000
 PM2  H7C2  C7   H7C1  105.65  3.000
 PM2  H7C2  C7   N8    107.61  3.000
 PM2  H7C1  C7   N8    113.89  3.000
 PM2  H7C2  C7   C4    108.34  3.000
 PM2  H7C1  C7   C4    108.44  3.000
 PM2  N8    C7   C4    112.55  3.000
 PM2  H8N2  N8   H8N1  105.98  3.000
 PM2  H8N2  N8   C7    109.56  3.000
 PM2  H8N1  N8   C7    109.16  3.000
 PM2  H9C2  C9   H9C1  106.94  3.000
 PM2  H9C2  C9   C13   110.45  3.000
 PM2  H9C1  C9   C13   110.20  3.000
 PM2  H9C2  C9   C10   108.73  3.000
 PM2  H9C1  C9   C10   108.97  3.000
 PM2  C13   C9   C10   111.42  3.000
 PM2  H102  C10  H101  107.20  3.000
 PM2  H102  C10  N14   110.84  3.000
 PM2  H101  C10  N14   108.34  3.000
 PM2  H102  C10  C9    109.85  3.000
 PM2  H101  C10  C9    110.18  3.000
 PM2  N14   C10  C9    110.36  3.000
 PM2  C17   C11  N14   117.75  3.000
 PM2  C17   C11  O12   118.66  3.000
 PM2  N14   C11  O12   123.55  3.000
 PM2  H13   C13  C16   107.11  3.000
 PM2  H13   C13  C9    107.27  3.000
 PM2  C16   C13  C9    109.98  3.000
 PM2  H13   C13  C1    107.74  3.000
 PM2  C16   C13  C1    111.60  3.000
 PM2  C9    C13  C1    112.86  3.000
 PM2  C15   N14  C11   119.79  3.000
 PM2  C15   N14  C10   112.72  3.000
 PM2  C11   N14  C10   124.23  3.000
 PM2  H152  C15  H151  107.39  3.000
 PM2  H152  C15  C16   111.14  3.000
 PM2  H151  C15  C16   109.88  3.000
 PM2  H152  C15  N14   109.73  3.000
 PM2  H151  C15  N14   107.70  3.000
 PM2  C16   C15  N14   110.88  3.000
 PM2  H162  C16  H161  107.02  3.000
 PM2  H162  C16  C15   109.30  3.000
 PM2  H161  C16  C15   109.22  3.000
 PM2  H162  C16  C13   110.05  3.000
 PM2  H161  C16  C13   110.43  3.000
 PM2  C15   C16  C13   110.74  3.000
 PM2  C19   C17  C18   118.08  3.000
 PM2  C19   C17  C11   119.33  3.000
 PM2  C18   C17  C11   122.35  3.000
 PM2  H18   C18  C20   119.93  3.000
 PM2  H18   C18  C17   120.35  3.000
 PM2  C20   C18  C17   119.72  3.000
 PM2  H19   C19  N21   116.68  3.000
 PM2  H19   C19  C17   120.31  3.000
 PM2  N21   C19  C17   123.01  3.000
 PM2  C23   C20  C22   121.53  3.000
 PM2  C23   C20  C18   116.96  3.000
 PM2  C22   C20  C18   121.47  3.000
 PM2  C23   N21  C19   118.15  3.000
 PM2  H222  C22  H221  106.80  3.000
 PM2  H222  C22  C24   109.37  3.000
 PM2  H221  C22  C24   109.32  3.000
 PM2  H222  C22  C20   110.01  3.000
 PM2  H221  C22  C20   109.81  3.000
 PM2  C24   C22  C20   111.42  3.000
 PM2  H23   C23  N21   116.28  3.000
 PM2  H23   C23  C20   119.67  3.000
 PM2  N21   C23  C20   124.06  3.000
 PM2  H242  C24  H241  106.67  3.000
 PM2  H242  C24  C25   109.98  3.000
 PM2  H241  C24  C25   110.03  3.000
 PM2  H242  C24  C22   109.14  3.000
 PM2  H241  C24  C22   109.06  3.000
 PM2  C25   C24  C22   111.82  3.000
 PM2  C27   C25  C26   118.48  3.000
 PM2  C27   C25  C24   120.83  3.000
 PM2  C26   C25  C24   120.66  3.000
 PM2  H26   C26  C28   119.62  3.000
 PM2  H26   C26  C25   119.50  3.000
 PM2  C28   C26  C25   120.88  3.000
 PM2  H27   C27  C29   119.57  3.000
 PM2  H27   C27  C25   119.56  3.000
 PM2  C29   C27  C25   120.87  3.000
 PM2  H28   C28  C30   120.08  3.000
 PM2  H28   C28  C26   119.81  3.000
 PM2  C30   C28  C26   120.11  3.000
 PM2  H29   C29  C30   120.08  3.000
 PM2  H29   C29  C27   119.79  3.000
 PM2  C30   C29  C27   120.13  3.000
 PM2  H30   C30  C29   120.23  3.000
 PM2  H30   C30  C28   120.23  3.000
 PM2  C29   C30  C28   119.53  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
 PM2  CONST_01  C6    C4   C2   C1     0.00   0.0  0
 PM2  CONST_02  C6    C5   C3   C1     0.00   0.0  0
 PM2  CONST_03  C5    C3   C1   C2     0.00   0.0  0
 PM2  CONST_04  C5    C6   C4   C2     0.00   0.0  0
 PM2  CONST_05  C4    C2   C1   C3     0.00   0.0  0
 PM2  CONST_06  C4    C6   C5   C3     0.00   0.0  0
 PM2  CONST_07  C23   C20  C18  C17    0.00   0.0  0
 PM2  CONST_08  C23   N21  C19  C17    0.00   0.0  0
 PM2  CONST_09  N21   C19  C17  C18    0.00   0.0  0
 PM2  CONST_10  N21   C23  C20  C18    0.00   0.0  0
 PM2  CONST_11  C20   C18  C17  C19    0.00   0.0  0
 PM2  CONST_12  C20   C23  N21  C19    0.00   0.0  0
 PM2  CONST_13  C30   C28  C26  C25    0.00   0.0  0
 PM2  CONST_14  C30   C29  C27  C25    0.00   0.0  0
 PM2  CONST_15  C29   C27  C25  C26    0.00   0.0  0
 PM2  CONST_16  C29   C30  C28  C26    0.00   0.0  0
 PM2  CONST_17  C28   C26  C25  C27    0.00   0.0  0
 PM2  CONST_18  C28   C30  C29  C27    0.00   0.0  0
 PM2  CONST_19  C13   C1   C2   C4   180.00   0.0  0
 PM2  CONST_20  C13   C1   C3   C5   180.00   0.0  0
 PM2  CONST_21  C7    C4   C2   C1   180.00   0.0  0
 PM2  CONST_22  C7    C4   C6   C5   180.00   0.0  0
 PM2  CONST_23  C20   C18  C17  C11  180.00   0.0  0
 PM2  CONST_24  N21   C19  C17  C11  180.00   0.0  0
 PM2  CONST_25  C22   C20  C18  C17  180.00   0.0  0
 PM2  CONST_26  C22   C20  C23  N21  180.00   0.0  0
 PM2  CONST_27  C28   C26  C25  C24  180.00   0.0  0
 PM2  CONST_28  C29   C27  C25  C24  180.00   0.0  0
 PM2  CONST_30  C17   C11  N14  C15  180.00   0.0  0
 PM2  CONST_31  H5    C5   C3   C1   180.00   0.0  0
 PM2  CONST_32  H3    C3   C1   C2   180.00   0.0  0
 PM2  CONST_33  H6    C6   C4   C2   180.00   0.0  0
 PM2  CONST_34  H2    C2   C1   C3   180.00   0.0  0
 PM2  CONST_35  H19   C19  C17  C18  180.00   0.0  0
 PM2  CONST_36  H23   C23  C20  C18  180.00   0.0  0
 PM2  CONST_37  H18   C18  C17  C19  180.00   0.0  0
 PM2  CONST_38  H28   C28  C26  C25  180.00   0.0  0
 PM2  CONST_39  H29   C29  C27  C25  180.00   0.0  0
 PM2  CONST_40  H27   C27  C25  C26  180.00   0.0  0
 PM2  CONST_41  H30   C30  C28  C26  180.00   0.0  0
 PM2  CONST_42  H26   C26  C25  C27  180.00   0.0  0
 PM2  CONST_44  C15   N14  C11  O12    0.00   0.0  0
 PM2  Var_01    C15   N14  C10  C9    58.92  30.0  1
 PM2  Var_02    C16   C15  N14  C10  -59.55  30.0  1
 PM2  Var_03    N14   C10  C9   C13  -55.44  30.0  1
 PM2  Var_04    N14   C15  C16  C13   55.94  30.0  1
 PM2  Var_05    C18   C17  C11  N14  -57.04  30.0  2
 PM2  Var_06    N8    C7   C4   C2   -32.48  30.0  2
 PM2  Var_07    C24   C22  C20  C18  -81.19  30.0  2
 PM2  Var_08    C25   C24  C22  C20  179.18  30.0  3
 PM2  Var_09    C26   C25  C24  C22   86.16  30.0  2
 PM2  Var_10    H8N1  N8   C7   C4   173.89  30.0  3

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
 PM2  chir_01  C13  C1  C9  C16  negativ

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
 PM2  plan-1  C1   0.020
 PM2  plan-1  C2   0.020
 PM2  plan-1  C3   0.020
 PM2  plan-1  C4   0.020
 PM2  plan-1  C5   0.020
 PM2  plan-1  C6   0.020
 PM2  plan-1  C7   0.020
 PM2  plan-1  C13  0.020
 PM2  plan-1  H2   0.020
 PM2  plan-1  H3   0.020
 PM2  plan-1  H5   0.020
 PM2  plan-1  H6   0.020
 PM2  plan-2  C11  0.020
 PM2  plan-2  C17  0.020
 PM2  plan-2  C18  0.020
 PM2  plan-2  C19  0.020
 PM2  plan-2  C20  0.020
 PM2  plan-2  N21  0.020
 PM2  plan-2  C22  0.020
 PM2  plan-2  C23  0.020
 PM2  plan-2  H18  0.020
 PM2  plan-2  H19  0.020
 PM2  plan-2  H23  0.020
 PM2  plan-3  C24  0.020
 PM2  plan-3  C25  0.020
 PM2  plan-3  C26  0.020
 PM2  plan-3  C27  0.020
 PM2  plan-3  C28  0.020
 PM2  plan-3  C29  0.020
 PM2  plan-3  C30  0.020
 PM2  plan-3  H26  0.020
 PM2  plan-3  H27  0.020
 PM2  plan-3  H28  0.020
 PM2  plan-3  H29  0.020
 PM2  plan-3  H30  0.020
 PM2  plan-4  C10  0.020
 PM2  plan-4  C11  0.020
 PM2  plan-4  O12  0.020
 PM2  plan-4  N14  0.020
 PM2  plan-4  C15  0.020
 PM2  plan-4  C17  0.020

