# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 23:33:57 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (3R,4R,5R)-5-(hydroxymethyl)-1-(3-phenylpropyl)piperidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN(CCCc2ccccc2)C[C@@H](O)[C@@H]1O
#
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
 G27  G27  (3R,4R,5R)-5-(hydroxymethyl)-1-(3-phenylpropyl)piperidine-3,4-diol  ligand  42  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G27
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
 G27  C12   C  CR16  0  -0.315  -4.5669   1.1248   0.7897
 G27  C13   C  CR16  0  -0.239  -5.7487   0.6146   1.3117
 G27  C14   C  CR16  0  -0.275  -6.3380  -0.5049   0.7384
 G27  C15   C  CR16  0  -0.240  -5.7369  -1.1072  -0.3597
 G27  C16   C  CR16  0  -0.312  -4.5557  -0.5927  -0.8774
 G27  C11   C  CR6   0   0.138  -3.9541   0.5301  -0.3114
 G27  C10   C  CH2   0  -0.508  -2.6509   1.0539  -0.8453
 G27  C9    C  CH2   0  -0.442  -1.4485   0.3464  -0.2175
 G27  C8    C  CH2   0  -0.254  -0.1389   0.8811  -0.7797
 G27  N1    N  NT    0  -0.430   1.0439   0.3090  -0.1612
 G27  C7    C  CH2   0  -0.257   2.2314   1.0767  -0.4874
 G27  C2    C  CH2   0  -0.323   1.2365  -1.0853  -0.5029
 G27  C3    C  CH1   0   0.030   2.3961  -1.6705   0.2923
 G27  O3    O  OH1   0  -0.679   2.6362  -3.0179  -0.0563
 G27  C4    C  CH1   0   0.060   3.6747  -0.8964   0.0136
 G27  O4    O  OH1   0  -0.675   4.7435  -1.3574   0.8086
 G27  C5    C  CH1   0  -0.329   3.4557   0.5875   0.2834
 G27  C6    C  CH2   0  -0.131   4.6947   1.3900  -0.0876
 G27  O6    O  OH1   0  -0.674   4.4735   2.7507   0.2168
 G27  H12   H  HCR6  0   0.244  -4.1145   1.9997   1.2431
 G27  H13   H  HCR6  0   0.252  -6.2114   1.0949   2.1646
 G27  H14   H  HCR6  0   0.252  -7.2602  -0.9028   1.1420
 G27  H15   H  HCR6  0   0.252  -6.1908  -1.9774  -0.8168
 G27  H16   H  HCR6  0   0.244  -4.0948  -1.0696  -1.7354
 G27  H101  H  HCH2  0   0.240  -2.5769   2.1282  -0.6558
 G27  H102  H  HCH2  0   0.241  -2.6167   0.9250  -1.9309
 G27  H91   H  HCH2  0   0.233  -1.5435  -0.7281  -0.3957
 G27  H92   H  HCH2  0   0.228  -1.4618   0.4876   0.8670
 G27  H81   H  HCH2  0   0.229  -0.1120   1.9614  -0.6091
 G27  H82   H  HCH2  0   0.189  -0.1298   0.7446  -1.8757
 G27  H71   H  HCH2  0   0.245   2.0469   2.1229  -0.2410
 G27  H72   H  HCH2  0   0.183   2.4493   1.0404  -1.5718
 G27  H21   H  HCH2  0   0.244   0.3318  -1.6510  -0.2704
 G27  H22   H  HCH2  0   0.193   1.4296  -1.2205  -1.5833
 G27  H3    H  HCH1  0   0.205   2.1633  -1.5772   1.3628
 G27  HO3   H  HOH1  0   0.456   1.9401  -3.5618   0.3243
 G27  H4    H  HCH1  0   0.189   3.9100  -1.0180  -1.0586
 G27  HO4   H  HOH1  0   0.447   4.8374  -2.3036   0.6565
 G27  H5    H  HCH1  0   0.233   3.2585   0.7147   1.3552
 G27  H61   H  HCH2  0   0.187   4.9005   1.2483  -1.1585
 G27  H62   H  HCH2  0   0.211   5.5616   1.0014   0.4578
 G27  HO6   H  HOH1  0   0.454   5.2297   3.2524  -0.0997

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
 G27  C12  C13   aromatic  1.389  0.020  1.389
 G27  C12  C11   aromatic  1.393  0.020  1.393
 G27  C12  H12   single    0.930  0.020  1.080
 G27  C13  C14   aromatic  1.389  0.020  1.389
 G27  C13  H13   single    0.930  0.020  1.080
 G27  C14  C15   aromatic  1.389  0.020  1.389
 G27  C14  H14   single    0.930  0.020  1.080
 G27  C15  C16   aromatic  1.389  0.020  1.389
 G27  C15  H15   single    0.930  0.020  1.080
 G27  C16  C11   aromatic  1.394  0.020  1.394
 G27  C16  H16   single    0.930  0.020  1.080
 G27  C11  C10   single    1.503  0.020  1.503
 G27  C10  C9    single    1.530  0.020  1.530
 G27  C10  H101  single    0.970  0.020  1.090
 G27  C10  H102  single    0.970  0.020  1.090
 G27  C9   C8    single    1.522  0.020  1.522
 G27  C9   H91   single    0.970  0.020  1.090
 G27  C9   H92   single    0.970  0.020  1.090
 G27  C8   N1    single    1.452  0.020  1.452
 G27  C8   H81   single    0.970  0.020  1.090
 G27  C8   H82   single    0.970  0.020  1.090
 G27  N1   C7    single    1.451  0.020  1.451
 G27  N1   C2    single    1.448  0.020  1.448
 G27  C7   C5    single    1.527  0.020  1.527
 G27  C7   H71   single    0.970  0.020  1.090
 G27  C7   H72   single    0.970  0.020  1.090
 G27  C2   C3    single    1.523  0.020  1.523
 G27  C2   H21   single    0.970  0.020  1.090
 G27  C2   H22   single    0.970  0.020  1.090
 G27  C3   O3    single    1.412  0.020  1.412
 G27  C3   C4    single    1.520  0.020  1.520
 G27  C3   H3    single    0.970  0.020  1.090
 G27  O3   HO3   single    0.850  0.020  0.980
 G27  C4   O4    single    1.409  0.020  1.409
 G27  C4   C5    single    1.524  0.020  1.524
 G27  C4   H4    single    0.970  0.020  1.090
 G27  O4   HO4   single    0.850  0.020  0.980
 G27  C5   C6    single    1.522  0.020  1.522
 G27  C5   H5    single    0.970  0.020  1.090
 G27  C6   O6    single    1.412  0.020  1.412
 G27  C6   H61   single    0.970  0.020  1.090
 G27  C6   H62   single    0.970  0.020  1.090
 G27  O6   HO6   single    0.850  0.020  0.980

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
 G27  H12   C12  C11   119.43  3.000
 G27  H12   C12  C13   119.62  3.000
 G27  C11   C12  C13   120.95  3.000
 G27  H13   C13  C14   120.09  3.000
 G27  H13   C13  C12   119.78  3.000
 G27  C14   C13  C12   120.13  3.000
 G27  H14   C14  C15   120.26  3.000
 G27  H14   C14  C13   120.26  3.000
 G27  C15   C14  C13   119.48  3.000
 G27  H15   C15  C16   119.81  3.000
 G27  H15   C15  C14   120.05  3.000
 G27  C16   C15  C14   120.14  3.000
 G27  H16   C16  C11   119.48  3.000
 G27  H16   C16  C15   119.57  3.000
 G27  C11   C16  C15   120.95  3.000
 G27  C10   C11  C16   120.72  3.000
 G27  C10   C11  C12   120.89  3.000
 G27  C16   C11  C12   118.35  3.000
 G27  H102  C10  H101  106.61  3.000
 G27  H102  C10  C9    109.16  3.000
 G27  H101  C10  C9    109.28  3.000
 G27  H102  C10  C11   109.80  3.000
 G27  H101  C10  C11   109.85  3.000
 G27  C9    C10  C11   112.00  3.000
 G27  H92   C9   H91   106.70  3.000
 G27  H92   C9   C8    109.35  3.000
 G27  H91   C9   C8    111.08  3.000
 G27  H92   C9   C10   109.74  3.000
 G27  H91   C9   C10   108.63  3.000
 G27  C8    C9   C10   111.23  3.000
 G27  H82   C8   H81   106.06  3.000
 G27  H82   C8   N1    111.55  3.000
 G27  H81   C8   N1    107.61  3.000
 G27  H82   C8   C9    109.28  3.000
 G27  H81   C8   C9    108.08  3.000
 G27  N1    C8   C9    113.89  3.000
 G27  C2    N1   C7    110.33  3.000
 G27  C2    N1   C8    112.77  3.000
 G27  C7    N1   C8    111.24  3.000
 G27  H72   C7   H71   106.63  3.000
 G27  H72   C7   C5    109.04  3.000
 G27  H71   C7   C5    109.20  3.000
 G27  H72   C7   N1    111.34  3.000
 G27  H71   C7   N1    108.56  3.000
 G27  C5    C7   N1    111.91  3.000
 G27  H22   C2   H21   106.82  3.000
 G27  H22   C2   C3    109.27  3.000
 G27  H21   C2   C3    108.70  3.000
 G27  H22   C2   N1    111.80  3.000
 G27  H21   C2   N1    109.78  3.000
 G27  C3    C2   N1    110.36  3.000
 G27  H3    C3   C4    108.26  3.000
 G27  H3    C3   O3    110.93  3.000
 G27  C4    C3   O3    107.31  3.000
 G27  H3    C3   C2    108.33  3.000
 G27  C4    C3   C2    110.43  3.000
 G27  O3    C3   C2    111.54  3.000
 G27  HO3   O3   C3    108.58  3.000
 G27  H4    C4   C5    108.03  3.000
 G27  H4    C4   O4    110.49  3.000
 G27  C5    C4   O4    109.12  3.000
 G27  H4    C4   C3    107.52  3.000
 G27  C5    C4   C3    110.03  3.000
 G27  O4    C4   C3    111.58  3.000
 G27  HO4   O4   C4    107.83  3.000
 G27  H5    C5   C6    108.86  3.000
 G27  H5    C5   C4    108.15  3.000
 G27  C6    C5   C4    110.69  3.000
 G27  H5    C5   C7    108.16  3.000
 G27  C6    C5   C7    111.14  3.000
 G27  C4    C5   C7    109.74  3.000
 G27  H62   C6   H61   106.92  3.000
 G27  H62   C6   O6    111.01  3.000
 G27  H61   C6   O6    111.31  3.000
 G27  H62   C6   C5    109.62  3.000
 G27  H61   C6   C5    108.77  3.000
 G27  O6    C6   C5    109.15  3.000
 G27  HO6   O6   C6    107.99  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
 G27  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 G27  CONST_02  C15  C16  C11  C12     0.00   0.0  0
 G27  CONST_03  C16  C11  C12  C13     0.00   0.0  0
 G27  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 G27  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 G27  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 G27  CONST_07  C10  C11  C12  C13   180.00   0.0  0
 G27  CONST_08  C10  C11  C16  C15   180.00   0.0  0
 G27  CONST_09  H14  C14  C13  C12   180.00   0.0  0
 G27  CONST_10  H16  C16  C11  C12   180.00   0.0  0
 G27  CONST_11  H15  C15  C14  C13   180.00   0.0  0
 G27  CONST_12  H12  C12  C13  C14   180.00   0.0  0
 G27  CONST_13  H13  C13  C14  C15   180.00   0.0  0
 G27  Var_01    C3   C2   N1   C7     61.21  30.0  1
 G27  Var_02    C5   C7   N1   C2    -60.72  30.0  1
 G27  Var_03    C9   C10  C11  C12    91.90  30.0  2
 G27  Var_04    C7   N1   C8   C9   -165.79  30.0  3
 G27  Var_05    C8   C9   C10  C11   179.48  30.0  3
 G27  Var_06    N1   C8   C9   C10   176.28  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
 G27  chir_01  C3  C2  O3  C4  negativ
 G27  chir_02  C4  O4  C3  C5  negativ
 G27  chir_03  C5  C7  C4  C6  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
 G27  plan-1  C12  0.020
 G27  plan-1  C13  0.020
 G27  plan-1  C14  0.020
 G27  plan-1  C15  0.020
 G27  plan-1  C16  0.020
 G27  plan-1  C11  0.020
 G27  plan-1  C10  0.020
 G27  plan-1  H12  0.020
 G27  plan-1  H13  0.020
 G27  plan-1  H14  0.020
 G27  plan-1  H15  0.020
 G27  plan-1  H16  0.020

