# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:44:21 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-(3-naphthalen-1-ylpropyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](CCCc2cccc3ccccc23)[C@H](O)[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
 Z47  Z47  (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-(3-naphthalen-1-ylpropyl)oxane-3,4,5-triol  ligand  48  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Z47
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
 Z47  C1    C  CH1   0  -0.019  -1.8889  -1.0475   0.5227
 Z47  C2    C  CH1   0   0.029  -3.1475  -1.7961   0.0919
 Z47  C3    C  CH1   0  -0.004  -4.0069  -0.9094  -0.8026
 Z47  C4    C  CH1   0   0.005  -4.2788   0.4300  -0.1294
 Z47  C5    C  CH1   0  -0.009  -2.9490   1.0739   0.2847
 Z47  C6    C  CH2   0  -0.158  -3.1613   2.3553   1.0618
 Z47  O2    O  OH1   0  -0.675  -3.8434  -2.1734   1.2579
 Z47  O3    O  OH1   0  -0.676  -5.1954  -1.6115  -1.0829
 Z47  O4    O  OH1   0  -0.676  -4.9803   1.2300  -1.0600
 Z47  O5    O  O2    0  -0.492  -2.2217   0.1930   1.1120
 Z47  O6    O  OH1   0  -0.667  -1.9139   2.9674   1.2877
 Z47  C7    C  CH2   0  -0.487  -0.8639  -0.9266  -0.6021
 Z47  C8    C  CH2   0  -0.413   0.4138  -0.2176  -0.1722
 Z47  C9    C  CH2   0  -0.540   1.3969  -0.0717  -1.3364
 Z47  C10   C  CR6   0   0.128   2.7144   0.5150  -0.9117
 Z47  C15   C  CR16  0  -0.340   2.9424   1.8598  -1.0671
 Z47  C14   C  CR16  0  -0.241   4.1443   2.4641  -0.6484
 Z47  C13   C  CR16  0  -0.338   5.1267   1.7105  -0.0715
 Z47  C12   C  CR66  0   0.117   4.9436   0.3194   0.1082
 Z47  C11   C  CR66  0   0.079   3.7287  -0.2895  -0.3116
 Z47  C16   C  CR16  0  -0.312   5.9532  -0.4777   0.6981
 Z47  C17   C  CR16  0  -0.262   5.7769  -1.8228   0.8701
 Z47  C18   C  CR16  0  -0.251   4.5751  -2.4315   0.4570
 Z47  C19   C  CR16  0  -0.339   3.5803  -1.6853  -0.1154
 Z47  H21   H  HCH1  0   0.248  -1.4222  -1.6258   1.3279
 Z47  H22   H  HCH1  0   0.225  -2.8413  -2.6837  -0.4821
 Z47  H23   H  HCH1  0   0.216  -3.4501  -0.7137  -1.7319
 Z47  H24   H  HCH1  0   0.221  -4.8845   0.2571   0.7704
 Z47  H71C  H  HCH2  0   0.243  -0.6185  -1.9406  -0.9318
 Z47  H72C  H  HCH2  0   0.233  -1.2798  -0.4230  -1.4803
 Z47  H2    H  HOH1  0   0.448  -4.7042  -2.5149   0.9927
 Z47  H3    H  HOH1  0   0.453  -5.7934  -1.0181  -1.5503
 Z47  H5    H  HCH1  0   0.215  -2.3842   1.3191  -0.6294
 Z47  H4    H  HOH1  0   0.460  -5.5895   1.8040  -0.5882
 Z47  H61C  H  HCH2  0   0.197  -3.8252   3.0079   0.4826
 Z47  H62C  H  HCH2  0   0.197  -3.6790   2.1209   2.0026
 Z47  H6    H  HOH1  0   0.455  -2.0695   3.7867   1.7659
 Z47  H81C  H  HCH2  0   0.238   0.1817   0.7753   0.2211
 Z47  H82C  H  HCH2  0   0.229   0.8807  -0.7735   0.6467
 Z47  H91C  H  HCH2  0   0.239   1.5404  -1.0401  -1.8233
 Z47  H92C  H  HCH2  0   0.252   0.9491   0.5788  -2.0918
 Z47  H15   H  HCR6  0   0.247   2.1766   2.4749  -1.5252
 Z47  H14   H  HCR6  0   0.255   4.2840   3.5279  -0.7912
 Z47  H13   H  HCR6  0   0.253   6.0545   2.1658   0.2539
 Z47  H16   H  HCR6  0   0.254   6.8738  -0.0021   1.0145
 Z47  H19   H  HCR6  0   0.248   2.6687  -2.1793  -0.4249
 Z47  H17   H  HCR6  0   0.257   6.5574  -2.4216   1.3211
 Z47  H18   H  HCR6  0   0.257   4.4381  -3.4962   0.5947

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
 Z47  C1   C2    single    1.526  0.020  1.526
 Z47  C1   O5    single    1.413  0.020  1.413
 Z47  C1   C7    single    1.527  0.020  1.527
 Z47  C2   C3    single    1.525  0.020  1.525
 Z47  C2   O2    single    1.409  0.020  1.409
 Z47  C3   C4    single    1.524  0.020  1.524
 Z47  C3   O3    single    1.409  0.020  1.409
 Z47  C4   C5    single    1.534  0.020  1.534
 Z47  C4   O4    single    1.414  0.020  1.414
 Z47  C5   C6    single    1.514  0.020  1.514
 Z47  C5   O5    single    1.410  0.020  1.410
 Z47  C6   O6    single    1.408  0.020  1.408
 Z47  C7   C8    single    1.523  0.020  1.523
 Z47  C8   C9    single    1.531  0.020  1.531
 Z47  C9   C10   single    1.503  0.020  1.503
 Z47  C10  C15   aromatic  1.373  0.020  1.373
 Z47  C10  C11   aromatic  1.427  0.020  1.427
 Z47  C15  C14   aromatic  1.409  0.020  1.409
 Z47  C14  C13   aromatic  1.366  0.020  1.366
 Z47  C13  C12   aromatic  1.415  0.020  1.415
 Z47  C12  C11   aromatic  1.422  0.020  1.422
 Z47  C12  C16   aromatic  1.415  0.020  1.415
 Z47  C11  C19   aromatic  1.417  0.020  1.417
 Z47  C16  C17   aromatic  1.367  0.020  1.367
 Z47  C17  C18   aromatic  1.409  0.020  1.409
 Z47  C18  C19   aromatic  1.369  0.020  1.369
 Z47  C1   H21   single    0.970  0.020  1.090
 Z47  C2   H22   single    0.970  0.020  1.090
 Z47  C3   H23   single    0.970  0.020  1.090
 Z47  C4   H24   single    0.970  0.020  1.090
 Z47  C7   H71C  single    0.970  0.020  1.090
 Z47  C7   H72C  single    0.970  0.020  1.090
 Z47  O2   H2    single    0.850  0.020  0.980
 Z47  O3   H3    single    0.850  0.020  0.980
 Z47  C5   H5    single    0.970  0.020  1.090
 Z47  O4   H4    single    0.850  0.020  0.980
 Z47  C6   H61C  single    0.970  0.020  1.090
 Z47  C6   H62C  single    0.970  0.020  1.090
 Z47  O6   H6    single    0.850  0.020  0.980
 Z47  C8   H81C  single    0.970  0.020  1.090
 Z47  C8   H82C  single    0.970  0.020  1.090
 Z47  C9   H91C  single    0.970  0.020  1.090
 Z47  C9   H92C  single    0.970  0.020  1.090
 Z47  C15  H15   single    0.930  0.020  1.080
 Z47  C14  H14   single    0.930  0.020  1.080
 Z47  C13  H13   single    0.930  0.020  1.080
 Z47  C16  H16   single    0.930  0.020  1.080
 Z47  C19  H19   single    0.930  0.020  1.080
 Z47  C17  H17   single    0.930  0.020  1.080
 Z47  C18  H18   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
 Z47  H21   C1   C7    107.29  3.000
 Z47  H21   C1   O5    104.90  3.000
 Z47  C7    C1   O5    113.32  3.000
 Z47  H21   C1   C2    107.45  3.000
 Z47  C7    C1   C2    112.62  3.000
 Z47  O5    C1   C2    110.73  3.000
 Z47  H22   C2   O2    110.67  3.000
 Z47  H22   C2   C3    108.65  3.000
 Z47  O2    C2   C3    111.27  3.000
 Z47  H22   C2   C1    108.26  3.000
 Z47  O2    C2   C1    107.76  3.000
 Z47  C3    C2   C1    110.19  3.000
 Z47  H23   C3   O3    110.33  3.000
 Z47  H23   C3   C4    107.88  3.000
 Z47  O3    C3   C4    112.05  3.000
 Z47  H23   C3   C2    108.28  3.000
 Z47  O3    C3   C2    107.61  3.000
 Z47  C4    C3   C2    110.64  3.000
 Z47  H24   C4   O4    110.78  3.000
 Z47  H24   C4   C5    108.84  3.000
 Z47  O4    C4   C5    111.73  3.000
 Z47  H24   C4   C3    108.79  3.000
 Z47  O4    C4   C3    107.17  3.000
 Z47  C5    C4   C3    109.48  3.000
 Z47  H5    C5   O5    111.17  3.000
 Z47  H5    C5   C6    108.02  3.000
 Z47  O5    C5   C6    107.46  3.000
 Z47  H5    C5   C4    108.28  3.000
 Z47  O5    C5   C4    110.07  3.000
 Z47  C6    C5   C4    111.85  3.000
 Z47  H62C  C6   H61C  107.09  3.000
 Z47  H62C  C6   O6    111.89  3.000
 Z47  H61C  C6   O6    111.26  3.000
 Z47  H62C  C6   C5    108.96  3.000
 Z47  H61C  C6   C5    108.52  3.000
 Z47  O6    C6   C5    109.04  3.000
 Z47  H2    O2   C2    107.97  3.000
 Z47  H3    O3   C3    108.26  3.000
 Z47  H4    O4   C4    109.24  3.000
 Z47  C5    O5   C1    115.16  3.000
 Z47  H6    O6   C6    107.88  3.000
 Z47  H72C  C7   H71C  105.66  3.000
 Z47  H72C  C7   C8    109.33  3.000
 Z47  H71C  C7   C8    109.17  3.000
 Z47  H72C  C7   C1    111.87  3.000
 Z47  H71C  C7   C1    107.41  3.000
 Z47  C8    C7   C1    113.09  3.000
 Z47  H82C  C8   H81C  106.43  3.000
 Z47  H82C  C8   C9    110.09  3.000
 Z47  H81C  C8   C9    108.87  3.000
 Z47  H82C  C8   C7    109.43  3.000
 Z47  H81C  C8   C7    110.27  3.000
 Z47  C9    C8   C7    111.62  3.000
 Z47  H92C  C9   H91C  105.85  3.000
 Z47  H92C  C9   C10   108.79  3.000
 Z47  H91C  C9   C10   110.88  3.000
 Z47  H92C  C9   C8    108.62  3.000
 Z47  H91C  C9   C8    109.79  3.000
 Z47  C10   C9   C8    112.65  3.000
 Z47  C11   C10  C15   118.80  3.000
 Z47  C11   C10  C9    121.45  3.000
 Z47  C15   C10  C9    119.72  3.000
 Z47  H15   C15  C14   119.01  3.000
 Z47  H15   C15  C10   119.10  3.000
 Z47  C14   C15  C10   121.89  3.000
 Z47  H14   C14  C13   120.34  3.000
 Z47  H14   C14  C15   119.50  3.000
 Z47  C13   C14  C15   120.16  3.000
 Z47  H13   C13  C12   119.07  3.000
 Z47  H13   C13  C14   120.72  3.000
 Z47  C12   C13  C14   120.21  3.000
 Z47  C16   C12  C11   119.42  3.000
 Z47  C16   C12  C13   120.97  3.000
 Z47  C11   C12  C13   119.61  3.000
 Z47  C19   C11  C12   118.05  3.000
 Z47  C19   C11  C10   122.61  3.000
 Z47  C12   C11  C10   119.34  3.000
 Z47  H16   C16  C17   120.31  3.000
 Z47  H16   C16  C12   118.72  3.000
 Z47  C17   C16  C12   120.97  3.000
 Z47  H17   C17  C18   119.89  3.000
 Z47  H17   C17  C16   120.24  3.000
 Z47  C18   C17  C16   119.87  3.000
 Z47  H18   C18  C19   119.83  3.000
 Z47  H18   C18  C17   119.71  3.000
 Z47  C19   C18  C17   120.46  3.000
 Z47  H19   C19  C18   118.88  3.000
 Z47  H19   C19  C11   119.88  3.000
 Z47  C18   C19  C11   121.24  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
 Z47  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 Z47  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 Z47  CONST_03  C16  C12  C11  C10   180.00   0.0  0
 Z47  CONST_04  C18  C19  C11  C10   180.00   0.0  0
 Z47  CONST_05  C12  C11  C10  C15     0.00   0.0  0
 Z47  CONST_06  C19  C11  C10  C15   180.00   0.0  0
 Z47  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 Z47  CONST_08  C11  C10  C15  C14     0.00   0.0  0
 Z47  CONST_09  C11  C12  C13  C14     0.00   0.0  0
 Z47  CONST_10  C16  C12  C13  C14   180.00   0.0  0
 Z47  CONST_11  C19  C11  C12  C13   180.00   0.0  0
 Z47  CONST_12  C17  C16  C12  C13   180.00   0.0  0
 Z47  CONST_13  C18  C19  C11  C12     0.00   0.0  0
 Z47  CONST_14  C18  C17  C16  C12     0.00   0.0  0
 Z47  CONST_15  C17  C16  C12  C11     0.00   0.0  0
 Z47  CONST_16  C17  C18  C19  C11     0.00   0.0  0
 Z47  CONST_17  C19  C11  C12  C16     0.00   0.0  0
 Z47  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 Z47  CONST_19  C14  C15  C10  C9    180.00   0.0  0
 Z47  CONST_20  C12  C11  C10  C9    180.00   0.0  0
 Z47  CONST_21  C19  C11  C10  C9      0.00   0.0  0
 Z47  CONST_22  H14  C14  C15  C10   180.00   0.0  0
 Z47  CONST_23  H19  C19  C11  C10     0.00   0.0  0
 Z47  CONST_24  H13  C13  C14  C15   180.00   0.0  0
 Z47  CONST_25  H15  C15  C14  C13   180.00   0.0  0
 Z47  CONST_26  H16  C16  C12  C13     0.00   0.0  0
 Z47  CONST_27  H17  C17  C16  C12   180.00   0.0  0
 Z47  CONST_28  H18  C18  C19  C11   180.00   0.0  0
 Z47  Var_01    C15  C10  C9   C8    -96.82  30.0  2
 Z47  Var_02    C9   C8   C7   C1   -178.02  30.0  3
 Z47  Var_03    C10  C9   C8   C7   -174.91  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
 Z47  chir_01  C1  C2  O5  C7  positiv
 Z47  chir_02  C2  O2  C1  C3  positiv
 Z47  chir_03  C3  O3  C2  C4  positiv
 Z47  chir_04  C4  O4  C5  C3  positiv
 Z47  chir_05  C5  O5  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
 Z47  plan-1  C9   0.020
 Z47  plan-1  C10  0.020
 Z47  plan-1  C15  0.020
 Z47  plan-1  C14  0.020
 Z47  plan-1  C13  0.020
 Z47  plan-1  C12  0.020
 Z47  plan-1  C11  0.020
 Z47  plan-1  C16  0.020
 Z47  plan-1  C17  0.020
 Z47  plan-1  C18  0.020
 Z47  plan-1  C19  0.020
 Z47  plan-1  H15  0.020
 Z47  plan-1  H14  0.020
 Z47  plan-1  H13  0.020
 Z47  plan-1  H16  0.020
 Z47  plan-1  H19  0.020
 Z47  plan-1  H17  0.020
 Z47  plan-1  H18  0.020

