# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:25:29 2022
#   Inital geometry file: a 158 line input string
#   Ligand name: 4-(2-{4-[(11R)-3,10-dibromo-8-chloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl]piperidin-1-yl}-2-oxoethyl)piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)N1CCC(CC1)CC(=O)N2CCC(CC2)[C@H]3c4ncc(Br)cc4CCc5cc(Cl)cc(Br)c35
#
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
 336  336  4-(2-{4-[(11R)-3,10-dibromo-8-chloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl]piperidin-1-yl}-2-oxoethyl)piperidine-1-carboxamide  ligand  67  36  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_336
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
 336  C1    C   CH2   0  -0.313  -1.8877  -1.5792   0.3277
 336  C4    C   CH1   0  -0.207  -1.0563   0.2469  -1.1883
 336  C6    C   CH2   0  -0.409  -1.0042   1.1517   0.0442
 336  C9    C   CH2   0  -0.333  -2.0274   0.7045   1.0815
 336  N12   N   NT    0  -0.451  -1.7904  -0.6770   1.4593
 336  C13   C   CH2   0  -0.440  -0.8869  -1.2093  -0.7648
 336  C17   C   CR16  0  -0.152   3.6931   0.4193  -2.0720
 336  C19   C   CR6   0  -0.039  -1.5714  -1.0060  -6.0458
 336  C20   C   CR16  0  -0.266  -0.5793  -1.6468  -5.3311
 336  C22   C   CH2   0  -0.566   1.0195  -1.8311  -3.4612
 336  C25   C   CH2   0  -0.507   2.3238  -1.0566  -3.4811
 336  C28   C   CR6   0  -0.193  -1.6039   0.7283  -4.4219
 336  C29   C   CR6   0  -0.190   3.8851   1.4784  -1.2130
 336  C30   C   CR16  0  -0.056   2.7768   2.2077  -0.8109
 336  N32   N   N     0  -0.404   1.5688   1.8963  -1.2274
 336  C33   C   CH1   0  -0.445  -0.1471   0.7487  -2.3566
 336  C35   C   CR16  0  -0.187  -2.0988   0.1897  -5.6012
 336  BR38  BR  BR    0  -0.034  -2.4259   2.3575  -3.8949
 336  C39   C   CR6   0   0.281   1.3415   0.8565  -2.0371
 336  C40   C   CR6   0   0.219  -0.5895   0.1249  -3.6648
 336  C41   C   CR6   0   0.017   2.4100   0.0851  -2.5095
 336  C42   C   CR6   0   0.072  -0.0925  -1.0953  -4.1511
 336  C43   C   CH2   0  -0.413   0.0327   0.5664   5.8851
 336  C46   C   CH2   0  -0.353   0.4444   0.0484   7.2575
 336  C49   C   CH1   0  -0.228  -0.5271  -0.5713   5.0260
 336  C51   C   CH2   0  -0.420  -1.6346  -1.3050   5.7864
 336  N54   N   NT    0  -0.454  -0.6723  -0.5945   7.9265
 336  C55   C   C     0   0.657  -1.4987   0.0319   8.8142
 336  N56   N   NH2   0  -0.846  -1.1030   1.2538   9.2755
 336  O57   O   O     0  -0.548  -2.5185  -0.5015   9.2450
 336  C58   C   CH2   0  -0.318  -1.1723  -1.7333   7.1755
 336  C61   C   CH2   0  -0.604  -1.0122  -0.0249   3.6893
 336  O64   O   O     0  -0.502  -0.8866  -2.2453   2.8005
 336  C65   C   C     0   0.575  -1.2227  -1.0811   2.6191
 336  H11   H   HCH2  0   0.242  -2.9045  -1.5170  -0.0745
 336  H12   H   HCH2  0   0.264  -1.7306  -2.6015   0.6594
 336  H4    H   HCH1  0   0.234  -2.0776   0.3354  -1.5826
 336  H61   H   HCH2  0   0.235  -1.2058   2.1872  -0.2389
 336  H62   H   HCH2  0   0.236  -0.0144   1.1362   0.5037
 336  H91   H   HCH2  0   0.245  -3.0395   0.7795   0.6704
 336  H92   H   HCH2  0   0.273  -1.9961   1.3579   1.9484
 336  H131  H   HCH2  0   0.230   0.1294  -1.3912  -0.3991
 336  H132  H   HCH2  0   0.245  -1.0643  -1.8841  -1.6039
 336  H17   H   HCR6  0   0.287   4.5339  -0.1678  -2.4205
 336  H20   H   HCR6  0   0.280  -0.1752  -2.5850  -5.6873
 336  H221  H   HCH2  0   0.275   0.7618  -2.0820  -2.4335
 336  H222  H   HCH2  0   0.279   1.1769  -2.7825  -3.9698
 336  H251  H   HCH2  0   0.269   2.5124  -0.6827  -4.4922
 336  H252  H   HCH2  0   0.268   3.1408  -1.7479  -3.2656
 336  H30   H   HCR6  0   0.279   2.8686   3.0636  -0.1514
 336  H33   H   HCH1  0   0.283  -0.4061   1.8054  -2.4284
 336  H35   H   HCR6  0   0.299  -2.8764   0.6873  -6.1636
 336  H432  H   HCH2  0   0.239   0.8975   1.0179   5.3919
 336  H461  H   HCH2  0   0.257   0.8779   0.8326   7.8750
 336  H462  H   HCH2  0   0.251   1.2311  -0.7028   7.1379
 336  H49   H   HCH1  0   0.226   0.2883  -1.2813   4.8482
 336  H511  H   HCH2  0   0.216  -2.5079  -0.6494   5.8825
 336  H512  H   HCH2  0   0.241  -1.9588  -2.1859   5.2300
 336  H561  H   HNH2  0   0.394  -1.7827   1.7413   9.8342
 336  H562  H   HNH2  0   0.400  -0.5051   1.8547   8.7364
 336  H581  H   HCH2  0   0.234  -0.3595  -2.4606   7.0838
 336  H582  H   HCH2  0   0.260  -1.9746  -2.2153   7.7266
 336  H611  H   HCH2  0   0.274  -0.2858   0.7007   3.3048
 336  H612  H   HCH2  0   0.264  -1.9354   0.5399   3.8508
 336  BR37  BR  BR    0  -0.027   5.6030   1.9435  -0.6080
 336  CL16  CL  CL    0  -0.117  -2.1640  -1.7040  -7.5126
 336  H431  H   HCH2  0   0.222  -0.7174   1.3565   6.0017

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
 336  C1    N12   single    1.451  0.020  1.451
 336  C1    C13   single    1.527  0.020  1.527
 336  C1    H11   single    0.970  0.020  1.090
 336  C1    H12   single    0.970  0.020  1.090
 336  C4    C6    single    1.530  0.020  1.530
 336  C4    C13   single    1.526  0.020  1.526
 336  C4    C33   single    1.563  0.020  1.563
 336  C4    H4    single    0.970  0.020  1.090
 336  C6    C9    single    1.524  0.020  1.524
 336  C6    H61   single    0.970  0.020  1.090
 336  C6    H62   single    0.970  0.020  1.090
 336  C9    N12   single    1.452  0.020  1.452
 336  C9    H91   single    0.970  0.020  1.090
 336  C9    H92   single    0.970  0.020  1.090
 336  N12   C65   single    1.353  0.020  1.353
 336  C13   H131  single    0.970  0.020  1.090
 336  C13   H132  single    0.970  0.020  1.090
 336  CL16  C19   single    1.729  0.020  1.729
 336  C17   C29   aromatic  1.377  0.020  1.377
 336  C17   C41   aromatic  1.396  0.020  1.396
 336  C17   H17   single    0.930  0.020  1.080
 336  C19   C20   aromatic  1.380  0.020  1.380
 336  C19   C35   aromatic  1.380  0.020  1.380
 336  C20   C42   aromatic  1.391  0.020  1.391
 336  C20   H20   single    0.930  0.020  1.080
 336  C22   C25   single    1.517  0.020  1.517
 336  C22   C42   single    1.501  0.020  1.501
 336  C22   H221  single    0.970  0.020  1.090
 336  C22   H222  single    0.970  0.020  1.090
 336  C25   C41   single    1.502  0.020  1.502
 336  C25   H251  single    0.970  0.020  1.090
 336  C25   H252  single    0.970  0.020  1.090
 336  C28   C35   aromatic  1.388  0.020  1.388
 336  C28   BR38  single    1.899  0.020  1.899
 336  C28   C40   aromatic  1.402  0.020  1.402
 336  C29   C30   aromatic  1.386  0.020  1.386
 336  C29   BR37  single    1.880  0.020  1.880
 336  C30   N32   aromatic  1.315  0.020  1.315
 336  C30   H30   single    0.930  0.020  1.080
 336  N32   C39   aromatic  1.337  0.020  1.337
 336  C33   C39   single    1.526  0.020  1.526
 336  C33   C40   single    1.515  0.020  1.515
 336  C33   H33   single    0.970  0.020  1.090
 336  C35   H35   single    0.930  0.020  1.080
 336  C39   C41   aromatic  1.400  0.020  1.400
 336  C40   C42   aromatic  1.404  0.020  1.404
 336  C43   C46   single    1.524  0.020  1.524
 336  C43   C49   single    1.532  0.020  1.532
 336  C43   H431  single    0.970  0.020  1.090
 336  C43   H432  single    0.970  0.020  1.090
 336  C46   N54   single    1.452  0.020  1.452
 336  C46   H461  single    0.970  0.020  1.090
 336  C46   H462  single    0.970  0.020  1.090
 336  C49   C51   single    1.531  0.020  1.531
 336  C49   C61   single    1.523  0.020  1.523
 336  C49   H49   single    0.970  0.020  1.090
 336  C51   C58   single    1.525  0.020  1.525
 336  C51   H511  single    0.970  0.020  1.090
 336  C51   H512  single    0.970  0.020  1.090
 336  N54   C55   single    1.365  0.020  1.365
 336  N54   C58   single    1.453  0.020  1.453
 336  C55   N56   single    1.365  0.020  1.365
 336  C55   O57   double    1.229  0.020  1.229
 336  N56   H561  single    0.890  0.020  1.040
 336  N56   H562  single    0.890  0.020  1.040
 336  C58   H581  single    0.970  0.020  1.090
 336  C58   H582  single    0.970  0.020  1.090
 336  C61   C65   single    1.518  0.020  1.518
 336  C61   H611  single    0.970  0.020  1.090
 336  C61   H612  single    0.970  0.020  1.090
 336  O64   C65   double    1.225  0.020  1.225

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
 336  H12   C1   H11   107.45  3.000
 336  H12   C1   C13   110.59  3.000
 336  H11   C1   C13   109.39  3.000
 336  H12   C1   N12   109.73  3.000
 336  H11   C1   N12   108.26  3.000
 336  C13   C1   N12   111.32  3.000
 336  H4    C4   C33   104.28  3.000
 336  H4    C4   C13   106.25  3.000
 336  C33   C4   C13   116.70  3.000
 336  H4    C4   C6    105.85  3.000
 336  C33   C4   C6    113.11  3.000
 336  C13   C4   C6    109.69  3.000
 336  H62   C6   H61   106.86  3.000
 336  H62   C6   C9    108.55  3.000
 336  H61   C6   C9    109.31  3.000
 336  H62   C6   C4    111.20  3.000
 336  H61   C6   C4    110.22  3.000
 336  C9    C6   C4    110.60  3.000
 336  H92   C9   H91   106.56  3.000
 336  H92   C9   N12   111.10  3.000
 336  H91   C9   N12   108.29  3.000
 336  H92   C9   C6    110.33  3.000
 336  H91   C9   C6    110.18  3.000
 336  N12   C9   C6    110.29  3.000
 336  C65   N12  C9    125.16  3.000
 336  C65   N12  C1    120.74  3.000
 336  C9    N12  C1    112.20  3.000
 336  H132  C13  H131  107.75  3.000
 336  H132  C13  C4    111.01  3.000
 336  H131  C13  C4    110.74  3.000
 336  H132  C13  C1    107.09  3.000
 336  H131  C13  C1    109.21  3.000
 336  C4    C13  C1    110.91  3.000
 336  H17   C17  C41   118.87  3.000
 336  H17   C17  C29   120.62  3.000
 336  C41   C17  C29   120.51  3.000
 336  C35   C19  C20   120.65  3.000
 336  C35   C19  CL16  119.47  3.000
 336  C20   C19  CL16  119.88  3.000
 336  H20   C20  C42   119.51  3.000
 336  H20   C20  C19   120.03  3.000
 336  C42   C20  C19   120.46  3.000
 336  H222  C22  H221  105.87  3.000
 336  H222  C22  C42   108.68  3.000
 336  H221  C22  C42   111.80  3.000
 336  H222  C22  C25   108.38  3.000
 336  H221  C22  C25   109.48  3.000
 336  C42   C22  C25   112.37  3.000
 336  H252  C25  H251  105.65  3.000
 336  H252  C25  C41   108.11  3.000
 336  H251  C25  C41   109.16  3.000
 336  H252  C25  C22   108.51  3.000
 336  H251  C25  C22   109.55  3.000
 336  C41   C25  C22   115.40  3.000
 336  C40   C28  BR38  122.17  3.000
 336  C40   C28  C35   123.36  3.000
 336  BR38  C28  C35   114.48  3.000
 336  BR37  C29  C30   120.47  3.000
 336  BR37  C29  C17   121.23  3.000
 336  C30   C29  C17   118.29  3.000
 336  H30   C30  N32   117.20  3.000
 336  H30   C30  C29   121.60  3.000
 336  N32   C30  C29   121.19  3.000
 336  C39   N32  C30   122.13  3.000
 336  H33   C33  C40   105.83  3.000
 336  H33   C33  C39   100.19  3.000
 336  C40   C33  C39   119.64  3.000
 336  H33   C33  C4    102.84  3.000
 336  C40   C33  C4    110.08  3.000
 336  C39   C33  C4    115.69  3.000
 336  H35   C35  C28   121.34  3.000
 336  H35   C35  C19   120.39  3.000
 336  C28   C35  C19   118.27  3.000
 336  C41   C39  C33   129.41  3.000
 336  C41   C39  N32   120.20  3.000
 336  C33   C39  N32   110.33  3.000
 336  C42   C40  C33   123.59  3.000
 336  C42   C40  C28   116.29  3.000
 336  C33   C40  C28   120.01  3.000
 336  C39   C41  C25   126.40  3.000
 336  C39   C41  C17   117.63  3.000
 336  C25   C41  C17   115.94  3.000
 336  C40   C42  C22   121.93  3.000
 336  C40   C42  C20   120.96  3.000
 336  C22   C42  C20   117.06  3.000
 336  H432  C43  H431  106.96  3.000
 336  H432  C43  C49   110.05  3.000
 336  H431  C43  C49   110.19  3.000
 336  H432  C43  C46   109.46  3.000
 336  H431  C43  C46   109.53  3.000
 336  C49   C43  C46   110.58  3.000
 336  H462  C46  H461  105.68  3.000
 336  H462  C46  N54   107.42  3.000
 336  H461  C46  N54   111.35  3.000
 336  H462  C46  C43   109.22  3.000
 336  H461  C46  C43   111.95  3.000
 336  N54   C46  C43   110.96  3.000
 336  H49   C49  C61   109.08  3.000
 336  H49   C49  C51   107.97  3.000
 336  C61   C49  C51   112.17  3.000
 336  H49   C49  C43   107.48  3.000
 336  C61   C49  C43   110.01  3.000
 336  C51   C49  C43   109.99  3.000
 336  H512  C51  H511  106.91  3.000
 336  H512  C51  C58   109.13  3.000
 336  H511  C51  C58   109.24  3.000
 336  H512  C51  C49   110.40  3.000
 336  H511  C51  C49   109.47  3.000
 336  C58   C51  C49   111.57  3.000
 336  C58   N54  C55   119.18  3.000
 336  C58   N54  C46   111.94  3.000
 336  C55   N54  C46   124.20  3.000
 336  O57   C55  N56   120.71  3.000
 336  O57   C55  N54   122.08  3.000
 336  N56   C55  N54   117.08  3.000
 336  H562  N56  H561  114.23  3.000
 336  H562  N56  C55   121.78  3.000
 336  H561  N56  C55   115.20  3.000
 336  H582  C58  H581  107.23  3.000
 336  H582  C58  N54   109.86  3.000
 336  H581  C58  N54   107.98  3.000
 336  H582  C58  C51   111.27  3.000
 336  H581  C58  C51   109.59  3.000
 336  N54   C58  C51   110.79  3.000
 336  H612  C61  H611  105.62  3.000
 336  H612  C61  C65   110.25  3.000
 336  H611  C61  C65   107.76  3.000
 336  H612  C61  C49   108.93  3.000
 336  H611  C61  C49   109.52  3.000
 336  C65   C61  C49   114.40  3.000
 336  O64   C65  C61   121.24  3.000
 336  O64   C65  N12   121.72  3.000
 336  C61   C65  N12   117.04  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
 336  CONST_01  N32   C30  C29  C17     0.00   0.0  0
 336  CONST_02  C40   C28  C35  C19     0.00   0.0  0
 336  CONST_03  C28   C35  C19  C20     0.00   0.0  0
 336  CONST_04  C39   N32  C30  C29     0.00   0.0  0
 336  CONST_05  C41   C17  C29  C30     0.00   0.0  0
 336  CONST_06  C42   C20  C19  C35     0.00   0.0  0
 336  CONST_07  C42   C20  C19  CL16  180.00   0.0  0
 336  CONST_08  C28   C35  C19  CL16  180.00   0.0  0
 336  CONST_09  BR38  C28  C35  C19   180.00   0.0  0
 336  CONST_10  BR37  C29  C30  N32   180.00   0.0  0
 336  CONST_11  C41   C17  C29  BR37  180.00   0.0  0
 336  CONST_12  H30   C30  C29  C17   180.00   0.0  0
 336  CONST_13  H35   C35  C19  C20   180.00   0.0  0
 336  CONST_14  H17   C17  C29  C30   180.00   0.0  0
 336  CONST_15  H20   C20  C19  C35   180.00   0.0  0
 336  CONST_16  C61   C65  N12  C1    180.00   0.0  0
 336  CONST_17  O64   C65  N12  C1      0.00   0.0  0
 336  CONST_18  C61   C65  N12  C9      0.00   0.0  0
 336  CONST_19  O64   C65  N12  C9    180.00   0.0  0
 336  CONST_20  O57   C55  N54  C46   180.00   0.0  0
 336  CONST_22  N56   C55  N54  C46     0.00   0.0  0
 336  CONST_23  C58   N54  C55  N56   180.00   0.0  0
 336  CONST_24  H561  N56  C55  N54   180.00   0.0  0
 336  Var_01    C6    C9   N12  C1    -59.98  30.0  1
 336  Var_02    N12   C9   C6   C4     57.66  30.0  1
 336  Var_03    N12   C1   C13  C4    -54.98  30.0  1
 336  Var_04    C13   C1   N12  C9     58.77  30.0  1
 336  Var_05    C58   N54  C46  C43    60.56  30.0  1
 336  Var_06    C51   C58  N54  C46   -59.25  30.0  1
 336  Var_07    N54   C46  C43  C49   -56.90  30.0  1
 336  Var_08    N54   C58  C51  C49    55.02  30.0  1
 336  Var_09    C49   C61  C65  N12   172.99  30.0  1

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
 336  chir_01  C4   C6   C13  C33  positiv
 336  chir_02  C33  C4   C39  C40  negativ
 336  chir_03  C49  C43  C51  C61  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
 336  plan-1  C17   0.020
 336  plan-1  C25   0.020
 336  plan-1  C29   0.020
 336  plan-1  C30   0.020
 336  plan-1  N32   0.020
 336  plan-1  C33   0.020
 336  plan-1  C39   0.020
 336  plan-1  C41   0.020
 336  plan-1  H17   0.020
 336  plan-1  H30   0.020
 336  plan-1  BR37  0.020
 336  plan-2  C19   0.020
 336  plan-2  C20   0.020
 336  plan-2  C22   0.020
 336  plan-2  C28   0.020
 336  plan-2  C33   0.020
 336  plan-2  C35   0.020
 336  plan-2  BR38  0.020
 336  plan-2  C40   0.020
 336  plan-2  C42   0.020
 336  plan-2  H20   0.020
 336  plan-2  H35   0.020
 336  plan-2  CL16  0.020
 336  plan-3  C46   0.020
 336  plan-3  N54   0.020
 336  plan-3  C55   0.020
 336  plan-3  N56   0.020
 336  plan-3  O57   0.020
 336  plan-3  C58   0.020
 336  plan-3  H561  0.020
 336  plan-3  H562  0.020
 336  plan-4  C1    0.020
 336  plan-4  C9    0.020
 336  plan-4  N12   0.020
 336  plan-4  C61   0.020
 336  plan-4  O64   0.020
 336  plan-4  C65   0.020

