# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:35:26 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-1-methyl-2-[(2S,4R)-2-methyl-4-phenylpentyl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C[C@@H](C)c1ccccc1)C[C@@H]2CCCCN2C
#
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
 L18  L18  (2S)-1-methyl-2-[(2S,4R)-2-methyl-4-phenylpentyl]piperidine  ligand  48  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L18
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
 L18  C8    C  CH1   0  -0.223  -29.7745  -30.3416  42.2601
 L18  C9    C  CH3   0  -0.680  -30.5472  -31.5805  42.7054
 L18  C10   C  CH2   0  -0.412  -28.3160  -30.3712  42.7446
 L18  C11   C  CH1   0  -0.330  -27.5219  -31.6668  42.5137
 L18  C12   C  CH3   0  -0.666  -27.3852  -32.0656  41.0443
 L18  C15   C  CR16  0  -0.335  -25.8929  -32.2504  44.3507
 L18  C16   C  CR16  0  -0.238  -24.6603  -32.1371  44.9828
 L18  C17   C  CR16  0  -0.276  -23.6768  -31.3164  44.4488
 L18  C18   C  CR16  0  -0.240  -23.9387  -30.6109  43.2805
 L18  C19   C  CR16  0  -0.312  -25.1718  -30.7279  42.6544
 L18  C13   C  CR6   0   0.184  -26.1691  -31.5506  43.1789
 L18  C1    C  CH2   0  -0.288  -31.7186  -27.8356  38.4152
 L18  C2    C  CH2   0  -0.430  -32.9113  -28.7906  38.3867
 L18  C3    C  CH2   0  -0.437  -32.9528  -29.6542  39.6554
 L18  C5    C  CH2   0  -0.487  -32.1987  -28.9541  40.7752
 L18  C6    C  CH1   0  -0.045  -30.7147  -28.8039  40.4217
 L18  C7    C  CH2   0  -0.438  -29.9173  -30.0722  40.7473
 L18  N1    N  NT    0  -0.428  -30.5566  -28.4801  38.9989
 L18  H8    H  HCH1  0   0.225  -30.2225  -29.4883  42.7843
 L18  H9C1  H  HCH3  0   0.221  -30.2015  -32.4820  42.1954
 L18  H9C2  H  HCH3  0   0.224  -30.4487  -31.7470  43.7802
 L18  H9C3  H  HCH3  0   0.232  -31.6112  -31.4805  42.4852
 L18  H101  H  HCH2  0   0.220  -27.7784  -29.5302  42.2920
 L18  H102  H  HCH2  0   0.227  -28.3133  -30.1800  43.8226
 L18  H7C1  H  HCH2  0   0.229  -28.9270  -29.9751  40.2985
 L18  H7C2  H  HCH2  0   0.222  -30.3860  -30.9240  40.2427
 L18  H11   H  HCH1  0   0.240  -28.0540  -32.4760  43.0238
 L18  H121  H  HCH3  0   0.217  -26.9446  -31.2686  40.4423
 L18  H122  H  HCH3  0   0.237  -26.7493  -32.9463  40.9442
 L18  H123  H  HCH3  0   0.237  -28.3534  -32.3069  40.6059
 L18  H15   H  HCR6  0   0.244  -26.6527  -32.8965  44.7757
 L18  H16   H  HCR6  0   0.251  -24.4697  -32.6922  45.8926
 L18  H17   H  HCR6  0   0.251  -22.7140  -31.2286  44.9357
 L18  H18   H  HCR6  0   0.251  -23.1796  -29.9674  42.8541
 L18  H19   H  HCR6  0   0.242  -25.3543  -30.1720  41.7422
 L18  H1C1  H  HCH2  0   0.232  -31.4673  -27.5339  37.3955
 L18  H1C2  H  HCH2  0   0.189  -31.9848  -26.9049  38.9447
 L18  H2C1  H  HCH2  0   0.219  -33.8276  -28.2032  38.2934
 L18  H2C2  H  HCH2  0   0.222  -32.8559  -29.4264  37.5008
 L18  H3C1  H  HCH2  0   0.231  -33.9833  -29.8553  39.9538
 L18  H3C2  H  HCH2  0   0.221  -32.4966  -30.6287  39.4639
 L18  H5C1  H  HCH2  0   0.230  -32.6420  -27.9698  40.9515
 L18  H5C2  H  HCH2  0   0.245  -32.2996  -29.4933  41.7186
 L18  H6    H  HCH1  0   0.200  -30.3058  -27.9841  41.0392
 L18  H141  H  HCH3  0   0.190  -29.3844  -26.7058  39.1731
 L18  H142  H  HCH3  0   0.228  -28.4840  -28.2250  39.1798
 L18  H143  H  HCH3  0   0.229  -29.1761  -27.6314  37.6776
 L18  C14   C  CH3   0  -0.525  -29.3518  -27.7229  38.7510

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
 L18  C8   C9    single    1.527  0.020  1.527
 L18  C8   C10   single    1.537  0.020  1.537
 L18  C8   C7    single    1.543  0.020  1.543
 L18  C10  C11   single    1.537  0.020  1.537
 L18  C11  C12   single    1.529  0.020  1.529
 L18  C11  C13   single    1.512  0.020  1.512
 L18  C15  C16   aromatic  1.390  0.020  1.390
 L18  C15  C13   aromatic  1.393  0.020  1.393
 L18  C16  C17   aromatic  1.388  0.020  1.388
 L18  C17  C18   aromatic  1.390  0.020  1.390
 L18  C18  C19   aromatic  1.388  0.020  1.388
 L18  C19  C13   aromatic  1.395  0.020  1.395
 L18  C1   C2    single    1.528  0.020  1.528
 L18  C1   N1    single    1.451  0.020  1.451
 L18  C2   C3    single    1.535  0.020  1.535
 L18  C3   C5    single    1.521  0.020  1.521
 L18  C5   C6    single    1.533  0.020  1.533
 L18  C6   C7    single    1.533  0.020  1.533
 L18  C6   N1    single    1.468  0.020  1.468
 L18  C14  N1    single    1.444  0.020  1.444
 L18  C8   H8    single    0.970  0.020  1.090
 L18  C9   H9C1  single    0.970  0.020  1.090
 L18  C9   H9C2  single    0.970  0.020  1.090
 L18  C9   H9C3  single    0.970  0.020  1.090
 L18  C10  H101  single    0.970  0.020  1.090
 L18  C10  H102  single    0.970  0.020  1.090
 L18  C7   H7C1  single    0.970  0.020  1.090
 L18  C7   H7C2  single    0.970  0.020  1.090
 L18  C11  H11   single    0.970  0.020  1.090
 L18  C12  H121  single    0.970  0.020  1.090
 L18  C12  H122  single    0.970  0.020  1.090
 L18  C12  H123  single    0.970  0.020  1.090
 L18  C15  H15   single    0.930  0.020  1.080
 L18  C16  H16   single    0.930  0.020  1.080
 L18  C17  H17   single    0.930  0.020  1.080
 L18  C18  H18   single    0.930  0.020  1.080
 L18  C19  H19   single    0.930  0.020  1.080
 L18  C1   H1C1  single    0.970  0.020  1.090
 L18  C1   H1C2  single    0.970  0.020  1.090
 L18  C2   H2C1  single    0.970  0.020  1.090
 L18  C2   H2C2  single    0.970  0.020  1.090
 L18  C3   H3C1  single    0.970  0.020  1.090
 L18  C3   H3C2  single    0.970  0.020  1.090
 L18  C5   H5C1  single    0.970  0.020  1.090
 L18  C5   H5C2  single    0.970  0.020  1.090
 L18  C6   H6    single    0.970  0.020  1.090
 L18  C14  H141  single    0.970  0.020  1.090
 L18  C14  H142  single    0.970  0.020  1.090
 L18  C14  H143  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
 L18  H8    C8   C7    107.15  3.000
 L18  H8    C8   C10   104.59  3.000
 L18  C7    C8   C10   113.59  3.000
 L18  H8    C8   C9    106.57  3.000
 L18  C7    C8   C9    112.38  3.000
 L18  C10   C8   C9    111.88  3.000
 L18  H9C3  C9   H9C2  107.50  3.000
 L18  H9C3  C9   H9C1  106.87  3.000
 L18  H9C2  C9   H9C1  107.77  3.000
 L18  H9C3  C9   C8    111.12  3.000
 L18  H9C2  C9   C8    111.42  3.000
 L18  H9C1  C9   C8    111.93  3.000
 L18  H102  C10  H101  105.75  3.000
 L18  H102  C10  C11   107.09  3.000
 L18  H101  C10  C11   109.34  3.000
 L18  H102  C10  C8    108.02  3.000
 L18  H101  C10  C8    108.69  3.000
 L18  C11   C10  C8    117.33  3.000
 L18  H11   C11  C13   106.66  3.000
 L18  H11   C11  C12   107.37  3.000
 L18  C13   C11  C12   111.28  3.000
 L18  H11   C11  C10   107.57  3.000
 L18  C13   C11  C10   109.35  3.000
 L18  C12   C11  C10   114.24  3.000
 L18  H123  C12  H122  107.59  3.000
 L18  H123  C12  H121  107.36  3.000
 L18  H122  C12  H121  107.67  3.000
 L18  H123  C12  C11   111.40  3.000
 L18  H122  C12  C11   110.54  3.000
 L18  H121  C12  C11   112.07  3.000
 L18  H15   C15  C13   119.37  3.000
 L18  H15   C15  C16   119.46  3.000
 L18  C13   C15  C16   121.17  3.000
 L18  H16   C16  C17   120.12  3.000
 L18  H16   C16  C15   119.77  3.000
 L18  C17   C16  C15   120.11  3.000
 L18  H17   C17  C18   120.30  3.000
 L18  H17   C17  C16   120.35  3.000
 L18  C18   C17  C16   119.35  3.000
 L18  H18   C18  C19   119.70  3.000
 L18  H18   C18  C17   120.05  3.000
 L18  C19   C18  C17   120.25  3.000
 L18  H19   C19  C13   119.90  3.000
 L18  H19   C19  C18   119.09  3.000
 L18  C13   C19  C18   121.01  3.000
 L18  C19   C13  C15   118.09  3.000
 L18  C19   C13  C11   121.30  3.000
 L18  C15   C13  C11   120.60  3.000
 L18  H1C2  C1   H1C1  105.69  3.000
 L18  H1C2  C1   N1    112.00  3.000
 L18  H1C1  C1   N1    108.29  3.000
 L18  H1C2  C1   C2    110.35  3.000
 L18  H1C1  C1   C2    109.55  3.000
 L18  N1    C1   C2    110.79  3.000
 L18  H2C2  C2   H2C1  106.64  3.000
 L18  H2C2  C2   C3    110.14  3.000
 L18  H2C1  C2   C3    110.51  3.000
 L18  H2C2  C2   C1    109.84  3.000
 L18  H2C1  C2   C1    108.68  3.000
 L18  C3    C2   C1    110.93  3.000
 L18  H3C2  C3   H3C1  106.13  3.000
 L18  H3C2  C3   C5    109.42  3.000
 L18  H3C1  C3   C5    110.59  3.000
 L18  H3C2  C3   C2    110.21  3.000
 L18  H3C1  C3   C2    110.80  3.000
 L18  C5    C3   C2    109.64  3.000
 L18  H5C2  C5   H5C1  105.54  3.000
 L18  H5C2  C5   C6    109.71  3.000
 L18  H5C1  C5   C6    109.96  3.000
 L18  H5C2  C5   C3    111.30  3.000
 L18  H5C1  C5   C3    109.39  3.000
 L18  C6    C5   C3    110.81  3.000
 L18  H6    C6   N1    109.77  3.000
 L18  H6    C6   C7    107.62  3.000
 L18  N1    C6   C7    109.41  3.000
 L18  H6    C6   C5    107.58  3.000
 L18  N1    C6   C5    110.45  3.000
 L18  C7    C6   C5    111.93  3.000
 L18  H7C2  C7   H7C1  105.54  3.000
 L18  H7C2  C7   C6    108.84  3.000
 L18  H7C1  C7   C6    108.12  3.000
 L18  H7C2  C7   C8    110.82  3.000
 L18  H7C1  C7   C8    109.55  3.000
 L18  C6    C7   C8    113.62  3.000
 L18  C14   N1   C6    111.83  3.000
 L18  C14   N1   C1    111.47  3.000
 L18  C6    N1   C1    113.68  3.000
 L18  H143  C14  H142  107.29  3.000
 L18  H143  C14  H141  107.71  3.000
 L18  H142  C14  H141  107.34  3.000
 L18  H143  C14  N1    110.30  3.000
 L18  H142  C14  N1    110.79  3.000
 L18  H141  C14  N1    113.18  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
 L18  CONST_01  C18   C17  C16  C15    0.00   0.0  0
 L18  CONST_02  C18   C19  C13  C15    0.00   0.0  0
 L18  CONST_03  C19   C13  C15  C16    0.00   0.0  0
 L18  CONST_04  C19   C18  C17  C16    0.00   0.0  0
 L18  CONST_05  C13   C15  C16  C17    0.00   0.0  0
 L18  CONST_06  C13   C19  C18  C17    0.00   0.0  0
 L18  CONST_07  C16   C15  C13  C11  180.00   0.0  0
 L18  CONST_08  C18   C19  C13  C11  180.00   0.0  0
 L18  CONST_09  H17   C17  C16  C15  180.00   0.0  0
 L18  CONST_10  H19   C19  C13  C15  180.00   0.0  0
 L18  CONST_11  H18   C18  C17  C16  180.00   0.0  0
 L18  CONST_12  H15   C15  C16  C17  180.00   0.0  0
 L18  CONST_13  H16   C16  C17  C18  180.00   0.0  0
 L18  Var_01    C5    C3   C2   C1    23.21  30.0  1
 L18  Var_02    C6    N1   C1   C2   -66.13  30.0  1
 L18  Var_03    C6    C5   C3   C2   -63.61  30.0  1
 L18  Var_04    N1    C1   C2   C3    38.09  30.0  1
 L18  Var_05    H141  C14  N1   C1    60.32  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
 L18  chir_01  C8   C9   C10  C7   negativ
 L18  chir_02  C11  C13  C12  C10  positiv
 L18  chir_03  C6   N1   C5   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
 L18  plan-1  C11  0.020
 L18  plan-1  C15  0.020
 L18  plan-1  C16  0.020
 L18  plan-1  C17  0.020
 L18  plan-1  C18  0.020
 L18  plan-1  C19  0.020
 L18  plan-1  C13  0.020
 L18  plan-1  H15  0.020
 L18  plan-1  H16  0.020
 L18  plan-1  H17  0.020
 L18  plan-1  H18  0.020
 L18  plan-1  H19  0.020

