# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:29:09 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (3R,4R)-4-(4-bromophenyl)-3-(naphthalen-2-ylmethoxy)piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(cc1)[C@H]2CCNC[C@@H]2OCc3ccc4ccccc4c3
#
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
 RBP  RBP  (3R,4R)-4-(4-bromophenyl)-3-(naphthalen-2-ylmethoxy)piperidine  ligand  47  25  .  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_RBP
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
 RBP  N13   N   NH1   0  -0.602  -1.7435   5.3280   0.2810
 RBP  C12   C   CH2   0  -0.294  -2.6978   4.7516  -0.6492
 RBP  C11   C   CH2   0  -0.417  -2.7965   3.2509  -0.4208
 RBP  C3    C   CH1   0  -0.373  -1.4190   2.5973  -0.5684
 RBP  C4    C   CR6   0   0.205  -1.4278   1.1082  -0.3431
 RBP  C10   C   CR16  0  -0.317  -0.8813   0.2484  -1.2898
 RBP  C9    C   CR16  0  -0.209  -0.8590  -1.1265  -1.1002
 RBP  C7    C   CR6   0  -0.137  -1.3855  -1.6501   0.0693
 RBP  BR    BR  BR    0  -0.056  -1.3588  -3.5200   0.3516
 RBP  C6    C   CR16  0  -0.211  -1.9304  -0.8208   1.0389
 RBP  C5    C   CR16  0  -0.314  -1.9483   0.5496   0.8229
 RBP  C2    C   CH1   0   0.103  -0.4226   3.2958   0.3637
 RBP  O1    O   O2    0  -0.497   0.8641   2.7553   0.1609
 RBP  C15   C   CH2   0  -0.222   1.4300   2.0934   1.2736
 RBP  C16   C   CR6   0   0.092   2.4529   1.1213   0.7668
 RBP  C17   C   CR16  0  -0.288   3.7250   1.5819   0.3528
 RBP  C18   C   CR16  0  -0.304   4.6521   0.7177  -0.1588
 RBP  C19   C   CR66  0   0.101   4.3598  -0.6611  -0.2888
 RBP  C20   C   CR16  0  -0.311   5.2952  -1.5827  -0.8149
 RBP  C21   C   CR16  0  -0.259   4.9796  -2.9096  -0.9282
 RBP  C22   C   CR16  0  -0.260   3.7126  -3.3778  -0.5196
 RBP  C24   C   CR16  0  -0.310   2.7891  -2.5091  -0.0047
 RBP  C23   C   CR66  0   0.138   3.0868  -1.1318   0.1246
 RBP  C25   C   CR16  0  -0.359   2.1515  -0.2095   0.6479
 RBP  C14   C   CH2   0  -0.313  -0.4086   4.7941   0.0893
 RBP  H13   H   HNH1  0   0.357  -1.7244   6.3332   0.1734
 RBP  H121  H   HCH2  0   0.192  -2.4242   4.9322  -1.7017
 RBP  H122  H   HCH2  0   0.237  -3.6720   5.2169  -0.4875
 RBP  H111  H   HCH2  0   0.242  -3.4962   2.8096  -1.1336
 RBP  H112  H   HCH2  0   0.224  -3.1959   3.0646   0.5804
 RBP  H3    H   HCH1  0   0.243  -1.0744   2.7774  -1.5946
 RBP  H10   H   HCR6  0   0.257  -0.4627   0.6536  -2.2027
 RBP  H9    H   HCR6  0   0.275  -0.4251  -1.7669  -1.8567
 RBP  H6    H   HCR6  0   0.278  -2.3395  -1.2258   1.9547
 RBP  H5    H   HCR6  0   0.260  -2.3818   1.1816   1.5890
 RBP  H2    H   HCH1  0   0.209  -0.7499   3.1519   1.4032
 RBP  H151  H   HCH2  0   0.216   1.8953   2.8138   1.9591
 RBP  H152  H   HCH2  0   0.225   0.6636   1.5539   1.8396
 RBP  H17   H   HCR6  0   0.252   3.9648   2.6343   0.4492
 RBP  H18   H   HCR6  0   0.254   5.6237   1.0806  -0.4723
 RBP  H20   H   HCR6  0   0.255   6.2674  -1.2229  -1.1297
 RBP  H21   H   HCR6  0   0.258   5.7028  -3.6065  -1.3318
 RBP  H22   H   HCR6  0   0.258   3.4751  -4.4293  -0.6142
 RBP  H24   H   HCR6  0   0.244   1.8180  -2.8691   0.3141
 RBP  H25   H   HCR6  0   0.248   1.1763  -0.5713   0.9556
 RBP  H141  H   HCH2  0   0.193  -0.0184   4.9642  -0.9285
 RBP  H142  H   HCH2  0   0.238   0.2761   5.2849   0.7849

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
 RBP  N13  C12   single    1.452  0.020  1.452
 RBP  N13  C14   single    1.450  0.020  1.450
 RBP  N13  H13   single    0.890  0.020  1.040
 RBP  C12  C11   single    1.521  0.020  1.521
 RBP  C12  H121  single    0.970  0.020  1.090
 RBP  C12  H122  single    0.970  0.020  1.090
 RBP  C11  C3    single    1.532  0.020  1.532
 RBP  C11  H111  single    0.970  0.020  1.090
 RBP  C11  H112  single    0.970  0.020  1.090
 RBP  C3   C4    single    1.506  0.020  1.506
 RBP  C3   C2    single    1.533  0.020  1.533
 RBP  C3   H3    single    0.970  0.020  1.090
 RBP  C4   C10   aromatic  1.391  0.020  1.391
 RBP  C4   C5    aromatic  1.394  0.020  1.394
 RBP  C10  C9    aromatic  1.388  0.020  1.388
 RBP  C10  H10   single    0.930  0.020  1.080
 RBP  C9   C7    aromatic  1.385  0.020  1.385
 RBP  C9   H9    single    0.930  0.020  1.080
 RBP  C7   BR    single    1.891  0.020  1.891
 RBP  C7   C6    aromatic  1.387  0.020  1.387
 RBP  C6   C5    aromatic  1.387  0.020  1.387
 RBP  C6   H6    single    0.930  0.020  1.080
 RBP  C5   H5    single    0.930  0.020  1.080
 RBP  C2   O1    single    1.410  0.020  1.410
 RBP  C2   C14   single    1.523  0.020  1.523
 RBP  C2   H2    single    0.970  0.020  1.090
 RBP  O1   C15   single    1.413  0.020  1.413
 RBP  C15  C16   single    1.499  0.020  1.499
 RBP  C15  H151  single    0.970  0.020  1.090
 RBP  C15  H152  single    0.970  0.020  1.090
 RBP  C16  C17   aromatic  1.415  0.020  1.415
 RBP  C16  C25   aromatic  1.370  0.020  1.370
 RBP  C17  C18   aromatic  1.367  0.020  1.367
 RBP  C17  H17   single    0.930  0.020  1.080
 RBP  C18  C19   aromatic  1.415  0.020  1.415
 RBP  C18  H18   single    0.930  0.020  1.080
 RBP  C19  C20   aromatic  1.415  0.020  1.415
 RBP  C19  C23   aromatic  1.419  0.020  1.419
 RBP  C20  C21   aromatic  1.369  0.020  1.369
 RBP  C20  H20   single    0.930  0.020  1.080
 RBP  C21  C22   aromatic  1.411  0.020  1.411
 RBP  C21  H21   single    0.930  0.020  1.080
 RBP  C22  C24   aromatic  1.368  0.020  1.368
 RBP  C22  H22   single    0.930  0.020  1.080
 RBP  C24  C23   aromatic  1.415  0.020  1.415
 RBP  C24  H24   single    0.930  0.020  1.080
 RBP  C23  C25   aromatic  1.414  0.020  1.414
 RBP  C25  H25   single    0.930  0.020  1.080
 RBP  C14  H141  single    0.970  0.020  1.090
 RBP  C14  H142  single    0.970  0.020  1.090

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
 RBP  H13   N13  C14   109.54  3.000
 RBP  H13   N13  C12   109.81  3.000
 RBP  C14   N13  C12   111.97  3.000
 RBP  H122  C12  H121  107.04  3.000
 RBP  H122  C12  C11   109.90  3.000
 RBP  H121  C12  C11   108.73  3.000
 RBP  H122  C12  N13   108.81  3.000
 RBP  H121  C12  N13   112.55  3.000
 RBP  C11   C12  N13   109.76  3.000
 RBP  H112  C11  H111  107.14  3.000
 RBP  H112  C11  C3    110.11  3.000
 RBP  H111  C11  C3    109.93  3.000
 RBP  H112  C11  C12   109.21  3.000
 RBP  H111  C11  C12   110.01  3.000
 RBP  C3    C11  C12   110.37  3.000
 RBP  H3    C3   C2    106.84  3.000
 RBP  H3    C3   C4    107.70  3.000
 RBP  C2    C3   C4    111.30  3.000
 RBP  H3    C3   C11   107.61  3.000
 RBP  C2    C3   C11   109.36  3.000
 RBP  C4    C3   C11   113.71  3.000
 RBP  C5    C4   C10   117.93  3.000
 RBP  C5    C4   C3    121.58  3.000
 RBP  C10   C4   C3    120.47  3.000
 RBP  H10   C10  C9    118.65  3.000
 RBP  H10   C10  C4    119.63  3.000
 RBP  C9    C10  C4    121.71  3.000
 RBP  H9    C9   C7    121.26  3.000
 RBP  H9    C9   C10   119.81  3.000
 RBP  C7    C9   C10   118.92  3.000
 RBP  C6    C7   BR    119.49  3.000
 RBP  C6    C7   C9    120.88  3.000
 RBP  BR    C7   C9    119.63  3.000
 RBP  H6    C6   C5    119.78  3.000
 RBP  H6    C6   C7    121.10  3.000
 RBP  C5    C6   C7    119.12  3.000
 RBP  H5    C5   C6    118.11  3.000
 RBP  H5    C5   C4    120.47  3.000
 RBP  C6    C5   C4    121.42  3.000
 RBP  H2    C2   C14   107.57  3.000
 RBP  H2    C2   O1    110.95  3.000
 RBP  C14   C2   O1    110.04  3.000
 RBP  H2    C2   C3    108.78  3.000
 RBP  C14   C2   C3    110.16  3.000
 RBP  O1    C2   C3    109.33  3.000
 RBP  C15   O1   C2    115.57  3.000
 RBP  H152  C15  H151  107.29  3.000
 RBP  H152  C15  C16   109.44  3.000
 RBP  H151  C15  C16   110.32  3.000
 RBP  H152  C15  O1    110.96  3.000
 RBP  H151  C15  O1    110.74  3.000
 RBP  C16   C15  O1    108.11  3.000
 RBP  C25   C16  C17   119.26  3.000
 RBP  C25   C16  C15   120.61  3.000
 RBP  C17   C16  C15   120.08  3.000
 RBP  H17   C17  C18   119.82  3.000
 RBP  H17   C17  C16   119.28  3.000
 RBP  C18   C17  C16   120.90  3.000
 RBP  H18   C18  C19   119.00  3.000
 RBP  H18   C18  C17   120.32  3.000
 RBP  C19   C18  C17   120.68  3.000
 RBP  C23   C19  C20   119.05  3.000
 RBP  C23   C19  C18   118.80  3.000
 RBP  C20   C19  C18   122.16  3.000
 RBP  H20   C20  C21   120.32  3.000
 RBP  H20   C20  C19   119.02  3.000
 RBP  C21   C20  C19   120.66  3.000
 RBP  H21   C21  C22   119.61  3.000
 RBP  H21   C21  C20   120.08  3.000
 RBP  C22   C21  C20   120.31  3.000
 RBP  H22   C22  C24   120.11  3.000
 RBP  H22   C22  C21   119.61  3.000
 RBP  C24   C22  C21   120.28  3.000
 RBP  H24   C24  C23   119.01  3.000
 RBP  H24   C24  C22   120.30  3.000
 RBP  C23   C24  C22   120.69  3.000
 RBP  C25   C23  C24   121.98  3.000
 RBP  C25   C23  C19   119.01  3.000
 RBP  C24   C23  C19   119.01  3.000
 RBP  H25   C25  C23   118.82  3.000
 RBP  H25   C25  C16   119.82  3.000
 RBP  C23   C25  C16   121.35  3.000
 RBP  H142  C14  H141  107.25  3.000
 RBP  H142  C14  C2    109.45  3.000
 RBP  H141  C14  C2    108.73  3.000
 RBP  H142  C14  N13   109.11  3.000
 RBP  H141  C14  N13   113.00  3.000
 RBP  C2    C14  N13   109.25  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
 RBP  CONST_01  C7   C9   C10  C4     0.00   0.0  0
 RBP  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 RBP  CONST_03  C6   C5   C4   C10    0.00   0.0  0
 RBP  CONST_04  C6   C7   C9   C10    0.00   0.0  0
 RBP  CONST_05  C5   C4   C10  C9     0.00   0.0  0
 RBP  CONST_06  C5   C6   C7   C9     0.00   0.0  0
 RBP  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 RBP  CONST_08  C19  C23  C25  C16    0.00   0.0  0
 RBP  CONST_09  C24  C23  C25  C16  180.00   0.0  0
 RBP  CONST_10  C23  C25  C16  C17    0.00   0.0  0
 RBP  CONST_11  C20  C19  C18  C17  180.00   0.0  0
 RBP  CONST_12  C23  C19  C18  C17    0.00   0.0  0
 RBP  CONST_13  C25  C16  C17  C18    0.00   0.0  0
 RBP  CONST_14  C21  C20  C19  C18  180.00   0.0  0
 RBP  CONST_15  C24  C23  C19  C18  180.00   0.0  0
 RBP  CONST_16  C25  C23  C19  C18    0.00   0.0  0
 RBP  CONST_17  C22  C21  C20  C19    0.00   0.0  0
 RBP  CONST_18  C22  C24  C23  C19    0.00   0.0  0
 RBP  CONST_19  C24  C23  C19  C20    0.00   0.0  0
 RBP  CONST_20  C25  C23  C19  C20  180.00   0.0  0
 RBP  CONST_21  C24  C22  C21  C20    0.00   0.0  0
 RBP  CONST_22  C23  C19  C20  C21    0.00   0.0  0
 RBP  CONST_23  C23  C24  C22  C21    0.00   0.0  0
 RBP  CONST_24  C25  C23  C24  C22  180.00   0.0  0
 RBP  CONST_25  C9   C10  C4   C3   180.00   0.0  0
 RBP  CONST_26  C6   C5   C4   C3   180.00   0.0  0
 RBP  CONST_27  BR   C7   C9   C10  180.00   0.0  0
 RBP  CONST_28  C5   C6   C7   BR   180.00   0.0  0
 RBP  CONST_29  C18  C17  C16  C15  180.00   0.0  0
 RBP  CONST_30  C23  C25  C16  C15  180.00   0.0  0
 RBP  CONST_31  H10  C10  C4   C3     0.00   0.0  0
 RBP  CONST_32  H5   C5   C4   C3     0.00   0.0  0
 RBP  CONST_33  H9   C9   C10  C4   180.00   0.0  0
 RBP  CONST_34  H6   C6   C5   C4   180.00   0.0  0
 RBP  CONST_35  H18  C18  C17  C16  180.00   0.0  0
 RBP  CONST_36  H25  C25  C16  C17  180.00   0.0  0
 RBP  CONST_37  H20  C20  C19  C18    0.00   0.0  0
 RBP  CONST_38  H17  C17  C18  C19  180.00   0.0  0
 RBP  CONST_39  H21  C21  C20  C19  180.00   0.0  0
 RBP  CONST_40  H24  C24  C23  C19  180.00   0.0  0
 RBP  CONST_41  H22  C22  C21  C20  180.00   0.0  0
 RBP  Var_01    C3   C11  C12  N13  -57.22  30.0  1
 RBP  Var_02    C2   C14  N13  C12  -62.48  30.0  1
 RBP  Var_03    C14  N13  C12  C11   61.98  30.0  1
 RBP  Var_04    C16  C15  O1   C2   156.35  30.0  3
 RBP  Var_05    C17  C16  C15  O1    77.45  30.0  2

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
 RBP  chir_01  C3  C11  C4  C2   positiv
 RBP  chir_02  C2  O1   C3  C14  positiv

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
 RBP  plan-1  C3   0.020
 RBP  plan-1  C4   0.020
 RBP  plan-1  C10  0.020
 RBP  plan-1  C9   0.020
 RBP  plan-1  C7   0.020
 RBP  plan-1  BR   0.020
 RBP  plan-1  C6   0.020
 RBP  plan-1  C5   0.020
 RBP  plan-1  H10  0.020
 RBP  plan-1  H9   0.020
 RBP  plan-1  H6   0.020
 RBP  plan-1  H5   0.020
 RBP  plan-2  C15  0.020
 RBP  plan-2  C16  0.020
 RBP  plan-2  C17  0.020
 RBP  plan-2  C18  0.020
 RBP  plan-2  C19  0.020
 RBP  plan-2  C20  0.020
 RBP  plan-2  C21  0.020
 RBP  plan-2  C22  0.020
 RBP  plan-2  C24  0.020
 RBP  plan-2  C23  0.020
 RBP  plan-2  C25  0.020
 RBP  plan-2  H17  0.020
 RBP  plan-2  H18  0.020
 RBP  plan-2  H20  0.020
 RBP  plan-2  H21  0.020
 RBP  plan-2  H22  0.020
 RBP  plan-2  H24  0.020
 RBP  plan-2  H25  0.020

