# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 01:19:56 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3R)-3-[(3-methoxyphenyl)methyl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(C[C@H]2CCCNC2)c1
#
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
 7VY  7VY  (3R)-3-[(3-methoxyphenyl)methyl]piperidine  ligand  34  15  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7VY
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
 7VY  C1   C  CR16  0  -0.401   3.1054   1.0859  -0.0647
 7VY  C2   C  CR16  0  -0.229   2.1935   1.9914   0.4666
 7VY  C3   C  CR16  0  -0.336   0.9664   1.5727   0.9529
 7VY  C11  C  CH2   0  -0.314  -4.3571   0.2039  -0.8775
 7VY  C13  C  CH2   0  -0.288  -2.1089   0.9181  -0.3725
 7VY  C4   C  CR6   0   0.156   0.6220   0.2207   0.9076
 7VY  C5   C  CR16  0  -0.406   1.5308  -0.6853   0.3787
 7VY  C6   C  CR6   0   0.397   2.7713  -0.2659  -0.1045
 7VY  C7   C  CH2   0  -0.509  -0.7165  -0.2597   1.3958
 7VY  C8   C  CH1   0  -0.238  -1.7562  -0.4215   0.2806
 7VY  C9   C  CH2   0  -0.424  -3.0281  -1.0740   0.8218
 7VY  C10  C  CH2   0  -0.442  -4.1078  -1.1648  -0.2509
 7VY  N12  N  NH1   0  -0.579  -3.1517   0.8422  -1.3830
 7VY  O14  O  O2    0  -0.474   3.5787  -1.2344  -0.5829
 7VY  H1   H  HCR6  0   0.275   4.0555   1.4476  -0.4327
 7VY  H2   H  HCR6  0   0.255   2.4562   3.0413   0.4988
 7VY  H3   H  HCR6  0   0.243   0.2720   2.2925   1.3693
 7VY  H5   H  HCH2  0   0.210  -4.8038   0.8677  -0.1286
 7VY  H6   H  HCH2  0   0.204  -2.4447   1.6088   0.4120
 7VY  H7   H  HCH2  0   0.235  -1.2236   1.3696  -0.8248
 7VY  H8   H  HCH3  0   0.258   5.3614  -1.8020  -1.3261
 7VY  H9   H  HCH3  0   0.227   4.8428  -0.2043  -1.8858
 7VY  H10  H  HCH3  0   0.227   5.4627  -0.4120  -0.2328
 7VY  H11  H  HCR6  0   0.249   1.2835  -1.7413   0.3467
 7VY  H12  H  HCH2  0   0.244  -0.5950  -1.2232   1.8991
 7VY  H13  H  HCH2  0   0.236  -1.1077   0.4348   2.1464
 7VY  H14  H  HCH1  0   0.219  -1.3326  -1.0771  -0.4921
 7VY  H15  H  HCH2  0   0.229  -2.8007  -2.0660   1.2222
 7VY  H16  H  HCH2  0   0.209  -3.3995  -0.4774   1.6642
 7VY  H17  H  HCH2  0   0.224  -5.0358  -1.5592   0.1716
 7VY  H18  H  HCH2  0   0.212  -3.7947  -1.8663  -1.0319
 7VY  H19  H  HNH1  0   0.336  -2.8057   0.3062  -2.1711
 7VY  H4   H  HCH2  0   0.232  -5.0789   0.1259  -1.6935
 7VY  C15  C  CH3   0  -0.435   4.8722  -0.8785  -1.0258

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
 7VY  C10  C11  single    1.526  0.020  1.526
 7VY  C10  C9   single    1.525  0.020  1.525
 7VY  C11  N12  single    1.455  0.020  1.455
 7VY  C9   C8   single    1.529  0.020  1.529
 7VY  C15  O14  single    1.413  0.020  1.413
 7VY  O14  C6   single    1.349  0.020  1.349
 7VY  N12  C13  single    1.454  0.020  1.454
 7VY  C8   C13  single    1.531  0.020  1.531
 7VY  C8   C7   single    1.533  0.020  1.533
 7VY  C6   C5   aromatic  1.396  0.020  1.396
 7VY  C6   C1   aromatic  1.393  0.020  1.393
 7VY  C5   C4   aromatic  1.388  0.020  1.388
 7VY  C7   C4   single    1.504  0.020  1.504
 7VY  C1   C2   aromatic  1.391  0.020  1.391
 7VY  C4   C3   aromatic  1.396  0.020  1.396
 7VY  C2   C3   aromatic  1.385  0.020  1.385
 7VY  C1   H1   single    0.930  0.020  1.080
 7VY  C2   H2   single    0.930  0.020  1.080
 7VY  C3   H3   single    0.930  0.020  1.080
 7VY  C11  H4   single    0.970  0.020  1.090
 7VY  C11  H5   single    0.970  0.020  1.090
 7VY  C13  H6   single    0.970  0.020  1.090
 7VY  C13  H7   single    0.970  0.020  1.090
 7VY  C15  H8   single    0.970  0.020  1.090
 7VY  C15  H9   single    0.970  0.020  1.090
 7VY  C15  H10  single    0.970  0.020  1.090
 7VY  C5   H11  single    0.930  0.020  1.080
 7VY  C7   H12  single    0.970  0.020  1.090
 7VY  C7   H13  single    0.970  0.020  1.090
 7VY  C8   H14  single    0.970  0.020  1.090
 7VY  C9   H15  single    0.970  0.020  1.090
 7VY  C9   H16  single    0.970  0.020  1.090
 7VY  C10  H17  single    0.970  0.020  1.090
 7VY  C10  H18  single    0.970  0.020  1.090
 7VY  N12  H19  single    0.890  0.020  1.040

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
 7VY  H1   C1   C6   121.71  3.000
 7VY  H1   C1   C2   119.24  3.000
 7VY  C6   C1   C2   119.05  3.000
 7VY  H2   C2   C3   119.85  3.000
 7VY  H2   C2   C1   118.92  3.000
 7VY  C3   C2   C1   121.22  3.000
 7VY  H3   C3   C4   119.86  3.000
 7VY  H3   C3   C2   120.14  3.000
 7VY  C4   C3   C2   120.00  3.000
 7VY  H5   C11  H4   106.52  3.000
 7VY  H5   C11  N12  108.03  3.000
 7VY  H4   C11  N12  108.63  3.000
 7VY  H5   C11  C10  109.22  3.000
 7VY  H4   C11  C10  110.53  3.000
 7VY  N12  C11  C10  113.64  3.000
 7VY  H7   C13  H6   106.49  3.000
 7VY  H7   C13  N12  108.37  3.000
 7VY  H6   C13  N12  108.06  3.000
 7VY  H7   C13  C8   110.59  3.000
 7VY  H6   C13  C8   108.42  3.000
 7VY  N12  C13  C8   114.58  3.000
 7VY  C7   C4   C5   119.87  3.000
 7VY  C7   C4   C3   121.24  3.000
 7VY  C5   C4   C3   118.88  3.000
 7VY  H11  C5   C6   119.00  3.000
 7VY  H11  C5   C4   119.82  3.000
 7VY  C6   C5   C4   121.18  3.000
 7VY  O14  C6   C5   116.04  3.000
 7VY  C5   C6   C1   119.66  3.000
 7VY  O14  C6   C1   124.30  3.000
 7VY  H13  C7   H12  106.44  3.000
 7VY  H13  C7   C8   108.87  3.000
 7VY  H12  C7   C8   108.49  3.000
 7VY  H13  C7   C4   109.75  3.000
 7VY  H12  C7   C4   109.39  3.000
 7VY  C8   C7   C4   113.66  3.000
 7VY  H14  C8   C9   108.37  3.000
 7VY  H14  C8   C7   108.25  3.000
 7VY  C9   C8   C7   110.60  3.000
 7VY  H14  C8   C13  108.12  3.000
 7VY  C7   C8   C13  111.97  3.000
 7VY  C9   C8   C13  109.44  3.000
 7VY  H16  C9   H15  106.41  3.000
 7VY  H16  C9   C10  109.44  3.000
 7VY  H15  C9   C10  110.54  3.000
 7VY  H16  C9   C8   108.75  3.000
 7VY  H15  C9   C8   110.11  3.000
 7VY  C10  C9   C8   111.45  3.000
 7VY  H18  C10  H17  106.68  3.000
 7VY  H18  C10  C9   109.71  3.000
 7VY  H17  C10  C9   110.53  3.000
 7VY  H18  C10  C11  109.17  3.000
 7VY  H17  C10  C11  110.10  3.000
 7VY  C9   C10  C11  110.56  3.000
 7VY  H19  N12  C13  108.85  3.000
 7VY  H19  N12  C11  108.71  3.000
 7VY  C13  N12  C11  112.07  3.000
 7VY  C6   O14  C15  118.59  3.000
 7VY  H10  C15  H9   108.78  3.000
 7VY  H10  C15  H8   108.65  3.000
 7VY  H9   C15  H8   108.58  3.000
 7VY  H10  C15  O14  112.00  3.000
 7VY  H9   C15  O14  112.17  3.000
 7VY  H8   C15  O14  106.54  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
 7VY  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 7VY  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 7VY  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 7VY  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 7VY  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 7VY  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 7VY  CONST_07  O14  C6   C1   C2    180.00   0.0  0
 7VY  CONST_08  C7   C4   C3   C2    180.00   0.0  0
 7VY  CONST_09  O14  C6   C5   C4    180.00   0.0  0
 7VY  CONST_10  C7   C4   C5   C6    180.00   0.0  0
 7VY  CONST_11  H11  C5   C6   C1    180.00   0.0  0
 7VY  CONST_12  H3   C3   C2   C1    180.00   0.0  0
 7VY  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 7VY  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 7VY  Var_01    C8   C9   C10  C11   -53.30  30.0  1
 7VY  Var_02    C8   C13  N12  C11    53.83  30.0  1
 7VY  Var_03    C10  C11  N12  C13   -53.38  30.0  1
 7VY  Var_04    N12  C11  C10  C9     53.57  30.0  1
 7VY  Var_05    C8   C7   C4   C3     96.23  30.0  2
 7VY  Var_06    C5   C6   O14  C15  -176.99  30.0  2
 7VY  Var_07    H8   C15  O14  C6    177.64  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
 7VY  chir_01  C8  C9  C13  C7  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
 7VY  plan-1  C1   0.020
 7VY  plan-1  C2   0.020
 7VY  plan-1  C3   0.020
 7VY  plan-1  C4   0.020
 7VY  plan-1  C5   0.020
 7VY  plan-1  C6   0.020
 7VY  plan-1  C7   0.020
 7VY  plan-1  O14  0.020
 7VY  plan-1  H1   0.020
 7VY  plan-1  H2   0.020
 7VY  plan-1  H3   0.020
 7VY  plan-1  H11  0.020

