# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 13:18:25 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (3R,4R)-3-(naphthalen-2-ylmethoxy)-4-phenylpiperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H]([C@H](CN1)OCc2ccc3ccccc3c2)c4ccccc4
#
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
 0LR  0LR  (3R,4R)-3-(naphthalen-2-ylmethoxy)-4-phenylpiperidine  ligand  47  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0LR
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
 0LR  C1   C  CR16  0  -0.246  -0.7614  -2.9164  -1.3422
 0LR  C2   C  CR16  0  -0.328  -1.5385  -1.7760  -1.5052
 0LR  C3   C  CR6   0   0.196  -2.0713  -1.1068  -0.4078
 0LR  C4   C  CR16  0  -0.311  -1.8081  -1.6110   0.8654
 0LR  C5   C  CR16  0  -0.241  -1.0269  -2.7450   1.0352
 0LR  C6   C  CR16  0  -0.275  -0.5001  -3.4039  -0.0692
 0LR  C7   C  CH1   0  -0.394  -2.9003   0.1374  -0.5957
 0LR  C8   C  CH1   0   0.102  -2.2534   1.3528   0.0673
 0LR  C9   C  CH2   0  -0.294  -5.1228   1.2607  -0.2401
 0LR  C10  C  CH2   0  -0.413  -4.3342  -0.0292  -0.0805
 0LR  N11  N  NH1   0  -0.601  -4.4374   2.3370   0.4514
 0LR  C12  C  CH2   0  -0.312  -3.1297   2.5890  -0.1188
 0LR  O13  O  O2    0  -0.494  -0.9780   1.5210  -0.5057
 0LR  C14  C  CH2   0  -0.182  -0.0610   2.2825   0.2325
 0LR  C15  C  CR6   0   0.042   1.2974   1.6314   0.2370
 0LR  C16  C  CR16  0  -0.293   2.4244   2.4272   0.5556
 0LR  C17  C  CR16  0  -0.300   3.6784   1.8877   0.6067
 0LR  C18  C  CR16  0  -0.383   1.4730   0.2987  -0.0262
 0LR  C19  C  CR66  0   0.138   2.7601  -0.2888   0.0160
 0LR  C20  C  CR66  0   0.100   3.8846   0.5141   0.3360
 0LR  C21  C  CR16  0  -0.311   5.1681  -0.0790   0.3698
 0LR  C22  C  CR16  0  -0.261   5.3282  -1.4114   0.0997
 0LR  C23  C  CR16  0  -0.262   4.2096  -2.2124  -0.2142
 0LR  C24  C  CR16  0  -0.317   2.9564  -1.6636  -0.2549
 0LR  H1   H  HCR6  0   0.253  -0.3553  -3.4195  -2.2107
 0LR  H2   H  HCR6  0   0.246  -1.7305  -1.3982  -2.5028
 0LR  H3   H  HCR6  0   0.247  -2.2114  -1.1121   1.7394
 0LR  H4   H  HCR6  0   0.251  -0.8288  -3.1160   2.0328
 0LR  H5   H  HCR6  0   0.255   0.1103  -4.2881   0.0628
 0LR  H6   H  HCH1  0   0.242  -2.9568   0.3480  -1.6713
 0LR  H7   H  HCH1  0   0.205  -2.1608   1.1627   1.1477
 0LR  H8   H  HCH2  0   0.191  -5.2567   1.4678  -1.3150
 0LR  H9   H  HCH2  0   0.236  -6.1201   1.1416   0.1875
 0LR  H10  H  HCH2  0   0.240  -4.8251  -0.8375  -0.6264
 0LR  H11  H  HCH2  0   0.224  -4.3211  -0.3179   0.9746
 0LR  H12  H  HNH1  0   0.357  -4.9929   3.1810   0.4181
 0LR  H14  H  HCH2  0   0.238  -2.6809   3.4456   0.3914
 0LR  H15  H  HCH2  0   0.193  -3.1652   2.8341  -1.1940
 0LR  H16  H  HCH2  0   0.231   0.0252   3.2967  -0.1780
 0LR  H17  H  HCH2  0   0.228  -0.3931   2.4034   1.2732
 0LR  H18  H  HCR6  0   0.251   2.2869   3.4838   0.7551
 0LR  H19  H  HCR6  0   0.253   4.5311   2.5117   0.8467
 0LR  H20  H  HCR6  0   0.276   0.6248  -0.3307  -0.2672
 0LR  H21  H  HCR6  0   0.253   6.0262   0.5367   0.6124
 0LR  H22  H  HCR6  0   0.256   6.3146  -1.8560   0.1267
 0LR  H23  H  HCR6  0   0.256   4.3483  -3.2657  -0.4212
 0LR  H24  H  HCR6  0   0.259   2.0935  -2.2759  -0.4899

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
 0LR  C9   N11  single    1.451  0.020  1.451
 0LR  C9   C10  single    1.520  0.020  1.520
 0LR  C12  N11  single    1.449  0.020  1.449
 0LR  C12  C8   single    1.527  0.020  1.527
 0LR  C23  C24  aromatic  1.369  0.020  1.369
 0LR  C23  C22  aromatic  1.411  0.020  1.411
 0LR  C24  C19  aromatic  1.415  0.020  1.415
 0LR  C22  C21  aromatic  1.369  0.020  1.369
 0LR  C19  C18  aromatic  1.415  0.020  1.415
 0LR  C19  C20  aromatic  1.418  0.020  1.418
 0LR  C10  C7   single    1.533  0.020  1.533
 0LR  O13  C8   single    1.408  0.020  1.408
 0LR  O13  C14  single    1.402  0.020  1.402
 0LR  C7   C8   single    1.528  0.020  1.528
 0LR  C7   C3   single    1.507  0.020  1.507
 0LR  C21  C20  aromatic  1.414  0.020  1.414
 0LR  C18  C15  aromatic  1.370  0.020  1.370
 0LR  C20  C17  aromatic  1.415  0.020  1.415
 0LR  C4   C3   aromatic  1.395  0.020  1.395
 0LR  C4   C5   aromatic  1.387  0.020  1.387
 0LR  C15  C14  single    1.506  0.020  1.506
 0LR  C15  C16  aromatic  1.416  0.020  1.416
 0LR  C17  C16  aromatic  1.366  0.020  1.366
 0LR  C3   C2   aromatic  1.391  0.020  1.391
 0LR  C5   C6   aromatic  1.390  0.020  1.390
 0LR  C2   C1   aromatic  1.390  0.020  1.390
 0LR  C6   C1   aromatic  1.388  0.020  1.388
 0LR  C1   H1   single    0.930  0.020  1.080
 0LR  C2   H2   single    0.930  0.020  1.080
 0LR  C4   H3   single    0.930  0.020  1.080
 0LR  C5   H4   single    0.930  0.020  1.080
 0LR  C6   H5   single    0.930  0.020  1.080
 0LR  C7   H6   single    0.970  0.020  1.090
 0LR  C8   H7   single    0.970  0.020  1.090
 0LR  C9   H8   single    0.970  0.020  1.090
 0LR  C9   H9   single    0.970  0.020  1.090
 0LR  C10  H10  single    0.970  0.020  1.090
 0LR  C10  H11  single    0.970  0.020  1.090
 0LR  N11  H12  single    0.890  0.020  1.040
 0LR  C12  H14  single    0.970  0.020  1.090
 0LR  C12  H15  single    0.970  0.020  1.090
 0LR  C14  H16  single    0.970  0.020  1.090
 0LR  C14  H17  single    0.970  0.020  1.090
 0LR  C16  H18  single    0.930  0.020  1.080
 0LR  C17  H19  single    0.930  0.020  1.080
 0LR  C18  H20  single    0.930  0.020  1.080
 0LR  C21  H21  single    0.930  0.020  1.080
 0LR  C22  H22  single    0.930  0.020  1.080
 0LR  C23  H23  single    0.930  0.020  1.080
 0LR  C24  H24  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
 0LR  H1   C1   C6   120.13  3.000
 0LR  H1   C1   C2   119.80  3.000
 0LR  C6   C1   C2   120.07  3.000
 0LR  H2   C2   C3   119.37  3.000
 0LR  H2   C2   C1   119.55  3.000
 0LR  C3   C2   C1   121.09  3.000
 0LR  C7   C3   C4   121.08  3.000
 0LR  C4   C3   C2   118.29  3.000
 0LR  C7   C3   C2   120.62  3.000
 0LR  H3   C4   C5   119.14  3.000
 0LR  H3   C4   C3   119.96  3.000
 0LR  C5   C4   C3   120.90  3.000
 0LR  H4   C5   C6   120.03  3.000
 0LR  H4   C5   C4   119.72  3.000
 0LR  C6   C5   C4   120.24  3.000
 0LR  H5   C6   C5   120.27  3.000
 0LR  H5   C6   C1   120.32  3.000
 0LR  C5   C6   C1   119.41  3.000
 0LR  H6   C7   C10  107.58  3.000
 0LR  H6   C7   C8   107.12  3.000
 0LR  C10  C7   C8   109.67  3.000
 0LR  H6   C7   C3   108.00  3.000
 0LR  C8   C7   C3   111.70  3.000
 0LR  C10  C7   C3   112.52  3.000
 0LR  H7   C8   O13  110.10  3.000
 0LR  H7   C8   C12  107.92  3.000
 0LR  O13  C8   C12  111.93  3.000
 0LR  H7   C8   C7   108.91  3.000
 0LR  O13  C8   C7   107.56  3.000
 0LR  C12  C8   C7   110.38  3.000
 0LR  H9   C9   H8   106.94  3.000
 0LR  H9   C9   N11  109.01  3.000
 0LR  H8   C9   N11  112.49  3.000
 0LR  H9   C9   C10  109.89  3.000
 0LR  H8   C9   C10  108.94  3.000
 0LR  N11  C9   C10  109.53  3.000
 0LR  H11  C10  H10  106.99  3.000
 0LR  H11  C10  C9   109.35  3.000
 0LR  H10  C10  C9   110.03  3.000
 0LR  H11  C10  C7   109.97  3.000
 0LR  H10  C10  C7   109.45  3.000
 0LR  C9   C10  C7   110.97  3.000
 0LR  H12  N11  C12  109.74  3.000
 0LR  H12  N11  C9   110.12  3.000
 0LR  C12  N11  C9   111.58  3.000
 0LR  H15  C12  H14  107.09  3.000
 0LR  H15  C12  N11  113.15  3.000
 0LR  H14  C12  N11  108.85  3.000
 0LR  H15  C12  C8   108.49  3.000
 0LR  H14  C12  C8   109.99  3.000
 0LR  N11  C12  C8   109.22  3.000
 0LR  C14  O13  C8   116.29  3.000
 0LR  H17  C14  H16  106.04  3.000
 0LR  H17  C14  C15  108.49  3.000
 0LR  H16  C14  C15  109.25  3.000
 0LR  H17  C14  O13  111.14  3.000
 0LR  H16  C14  O13  110.87  3.000
 0LR  C15  C14  O13  110.89  3.000
 0LR  C18  C15  C16  119.21  3.000
 0LR  C16  C15  C14  118.39  3.000
 0LR  C18  C15  C14  122.39  3.000
 0LR  H18  C16  C17  119.64  3.000
 0LR  H18  C16  C15  119.22  3.000
 0LR  C17  C16  C15  121.14  3.000
 0LR  H19  C17  C20  119.13  3.000
 0LR  H19  C17  C16  120.21  3.000
 0LR  C20  C17  C16  120.66  3.000
 0LR  H20  C18  C19  118.52  3.000
 0LR  H20  C18  C15  120.50  3.000
 0LR  C19  C18  C15  120.98  3.000
 0LR  C24  C19  C20  118.90  3.000
 0LR  C20  C19  C18  119.52  3.000
 0LR  C24  C19  C18  121.58  3.000
 0LR  C21  C20  C19  119.18  3.000
 0LR  C21  C20  C17  122.33  3.000
 0LR  C19  C20  C17  118.50  3.000
 0LR  H21  C21  C22  120.31  3.000
 0LR  H21  C21  C20  119.05  3.000
 0LR  C22  C21  C20  120.64  3.000
 0LR  H22  C22  C23  119.65  3.000
 0LR  H22  C22  C21  120.10  3.000
 0LR  C23  C22  C21  120.25  3.000
 0LR  H23  C23  C24  120.12  3.000
 0LR  H23  C23  C22  119.56  3.000
 0LR  C24  C23  C22  120.32  3.000
 0LR  H24  C24  C23  120.60  3.000
 0LR  H24  C24  C19  118.68  3.000
 0LR  C23  C24  C19  120.72  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
 0LR  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 0LR  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 0LR  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 0LR  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 0LR  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 0LR  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 0LR  CONST_07  C24  C19  C18  C15  180.00   0.0  0
 0LR  CONST_08  C20  C19  C18  C15    0.00   0.0  0
 0LR  CONST_09  C20  C17  C16  C15    0.00   0.0  0
 0LR  CONST_10  C19  C18  C15  C16    0.00   0.0  0
 0LR  CONST_11  C19  C20  C17  C16    0.00   0.0  0
 0LR  CONST_12  C21  C20  C17  C16  180.00   0.0  0
 0LR  CONST_13  C24  C19  C20  C17  180.00   0.0  0
 0LR  CONST_14  C18  C19  C20  C17    0.00   0.0  0
 0LR  CONST_15  C22  C21  C20  C17  180.00   0.0  0
 0LR  CONST_16  C18  C15  C16  C17    0.00   0.0  0
 0LR  CONST_17  C23  C24  C19  C18  180.00   0.0  0
 0LR  CONST_18  C21  C20  C19  C18  180.00   0.0  0
 0LR  CONST_19  C22  C23  C24  C19    0.00   0.0  0
 0LR  CONST_20  C22  C21  C20  C19    0.00   0.0  0
 0LR  CONST_21  C23  C24  C19  C20    0.00   0.0  0
 0LR  CONST_22  C23  C22  C21  C20    0.00   0.0  0
 0LR  CONST_23  C24  C23  C22  C21    0.00   0.0  0
 0LR  CONST_24  C24  C19  C20  C21    0.00   0.0  0
 0LR  CONST_25  C7   C3   C2   C1   180.00   0.0  0
 0LR  CONST_26  C7   C3   C4   C5   180.00   0.0  0
 0LR  CONST_27  C19  C18  C15  C14  180.00   0.0  0
 0LR  CONST_28  C17  C16  C15  C14  180.00   0.0  0
 0LR  CONST_29  H4   C5   C6   C1   180.00   0.0  0
 0LR  CONST_30  H3   C4   C3   C2   180.00   0.0  0
 0LR  CONST_31  H5   C6   C1   C2   180.00   0.0  0
 0LR  CONST_32  H1   C1   C2   C3   180.00   0.0  0
 0LR  CONST_33  H2   C2   C3   C4   180.00   0.0  0
 0LR  CONST_34  H19  C17  C16  C15  180.00   0.0  0
 0LR  CONST_35  H20  C18  C15  C16  180.00   0.0  0
 0LR  CONST_36  H21  C21  C20  C17    0.00   0.0  0
 0LR  CONST_37  H24  C24  C19  C18    0.00   0.0  0
 0LR  CONST_38  H18  C16  C15  C18  180.00   0.0  0
 0LR  CONST_39  H23  C23  C24  C19  180.00   0.0  0
 0LR  CONST_40  H22  C22  C21  C20  180.00   0.0  0
 0LR  Var_01    N11  C9   C10  C7   -56.81  30.0  1
 0LR  Var_02    C9   N11  C12  C8   -63.46  30.0  1
 0LR  Var_03    C12  N11  C9   C10   62.68  30.0  1
 0LR  Var_04    C15  C14  O13  C8   136.33  30.0  3
 0LR  Var_05    C18  C15  C14  O13  -20.96  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
 0LR  chir_01  C7  C10  C8  C3   negativ
 0LR  chir_02  C8  O13  C7  C12  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
 0LR  plan-1  C1   0.020
 0LR  plan-1  C2   0.020
 0LR  plan-1  C3   0.020
 0LR  plan-1  C4   0.020
 0LR  plan-1  C5   0.020
 0LR  plan-1  C6   0.020
 0LR  plan-1  C7   0.020
 0LR  plan-1  H1   0.020
 0LR  plan-1  H2   0.020
 0LR  plan-1  H3   0.020
 0LR  plan-1  H4   0.020
 0LR  plan-1  H5   0.020
 0LR  plan-2  C14  0.020
 0LR  plan-2  C15  0.020
 0LR  plan-2  C16  0.020
 0LR  plan-2  C17  0.020
 0LR  plan-2  C18  0.020
 0LR  plan-2  C19  0.020
 0LR  plan-2  C20  0.020
 0LR  plan-2  C21  0.020
 0LR  plan-2  C22  0.020
 0LR  plan-2  C23  0.020
 0LR  plan-2  C24  0.020
 0LR  plan-2  H18  0.020
 0LR  plan-2  H19  0.020
 0LR  plan-2  H20  0.020
 0LR  plan-2  H21  0.020
 0LR  plan-2  H22  0.020
 0LR  plan-2  H23  0.020
 0LR  plan-2  H24  0.020

