# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:31:33 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 4-[(3S)-3-hydroxy-3-methoxypropyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](O)CCc1ccc(O)cc1
#
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
 5K3  5K3  4-[(3S)-3-hydroxy-3-methoxypropyl]phenol  ligand  27  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5K3
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
 5K3  O2    O  OH1   0  -0.662  -3.3086   1.2099   0.7101
 5K3  C1    C  CH1   0   0.304  -2.9208  -0.0468   0.2369
 5K3  O     O  O2    0  -0.497  -3.6779  -0.4552  -0.8652
 5K3  C     C  CH3   0  -0.410  -5.0373  -0.7020  -0.5811
 5K3  C2    C  CH2   0  -0.498  -1.4582  -0.0965  -0.1763
 5K3  C3    C  CH2   0  -0.506  -0.5115   0.2946   0.9593
 5K3  C4    C  CR6   0   0.121   0.9291   0.1452   0.5571
 5K3  C9    C  CR16  0  -0.302   1.5849   1.1574  -0.1398
 5K3  C8    C  CR16  0  -0.313   2.9030   1.0133  -0.5489
 5K3  C7    C  CR6   0   0.307   3.5943  -0.1599  -0.2683
 5K3  O1    O  OH1   0  -0.675   4.8813  -0.3256  -0.7070
 5K3  C6    C  CR16  0  -0.312   2.9545  -1.1796   0.4259
 5K3  C5    C  CR16  0  -0.308   1.6351  -1.0237   0.8283
 5K3  H2    H  HOH1  0   0.448  -3.0432   1.8806   0.0687
 5K3  H1    H  HCH1  0   0.196  -3.0927  -0.7299   1.0815
 5K3  H21C  H  HCH2  0   0.244  -1.2235  -1.1107  -0.5088
 5K3  H22C  H  HCH2  0   0.239  -1.2993   0.5637  -1.0368
 5K3  HC1   H  HCH3  0   0.206  -5.1579  -1.4483   0.2130
 5K3  HC2   H  HCH3  0   0.211  -5.5765   0.2013  -0.2840
 5K3  HC3   H  HCH3  0   0.234  -5.4969  -1.0912  -1.4884
 5K3  H31C  H  HCH2  0   0.244  -0.7041   1.3257   1.2625
 5K3  H32C  H  HCH2  0   0.242  -0.7160  -0.3320   1.8320
 5K3  H9    H  HCR6  0   0.248   1.0598   2.0784  -0.3668
 5K3  H5    H  HCR6  0   0.248   1.1482  -1.8277   1.3683
 5K3  H8    H  HCR6  0   0.261   3.3954   1.8110  -1.0916
 5K3  HA    H  HOH1  0   0.472   5.4984  -0.0127  -0.0365
 5K3  H6    H  HCR6  0   0.260   3.4864  -2.0971   0.6482

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
 5K3  O2  C1    single    1.398  0.020  1.398
 5K3  C1  O     single    1.398  0.020  1.398
 5K3  C1  C2    single    1.521  0.020  1.521
 5K3  O   C     single    1.411  0.020  1.411
 5K3  C2  C3    single    1.529  0.020  1.529
 5K3  C3  C4    single    1.503  0.020  1.503
 5K3  C4  C9    aromatic  1.393  0.020  1.393
 5K3  C4  C5    aromatic  1.392  0.020  1.392
 5K3  C9  C8    aromatic  1.388  0.020  1.388
 5K3  C8  C7    aromatic  1.390  0.020  1.390
 5K3  C7  O1    single    1.370  0.020  1.370
 5K3  C7  C6    aromatic  1.390  0.020  1.390
 5K3  C6  C5    aromatic  1.388  0.020  1.388
 5K3  O2  H2    single    0.850  0.020  0.980
 5K3  C1  H1    single    0.970  0.020  1.090
 5K3  C2  H21C  single    0.970  0.020  1.090
 5K3  C2  H22C  single    0.970  0.020  1.090
 5K3  C   HC1   single    0.970  0.020  1.090
 5K3  C   HC2   single    0.970  0.020  1.090
 5K3  C   HC3   single    0.970  0.020  1.090
 5K3  C3  H31C  single    0.970  0.020  1.090
 5K3  C3  H32C  single    0.970  0.020  1.090
 5K3  C9  H9    single    0.930  0.020  1.080
 5K3  C5  H5    single    0.930  0.020  1.080
 5K3  C8  H8    single    0.930  0.020  1.080
 5K3  O1  HA    single    0.850  0.020  0.980
 5K3  C6  H6    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
 5K3  H2    O2  C1    108.88  3.000
 5K3  H1    C1  C2    109.80  3.000
 5K3  H1    C1  O     109.83  3.000
 5K3  C2    C1  O     107.28  3.000
 5K3  H1    C1  O2    104.78  3.000
 5K3  C2    C1  O2    112.85  3.000
 5K3  O     C1  O2    112.29  3.000
 5K3  C     O   C1    114.47  3.000
 5K3  HC3   C   HC2   108.27  3.000
 5K3  HC3   C   HC1   108.29  3.000
 5K3  HC2   C   HC1   108.14  3.000
 5K3  HC3   C   O     107.55  3.000
 5K3  HC2   C   O     112.68  3.000
 5K3  HC1   C   O     111.78  3.000
 5K3  H22C  C2  H21C  106.80  3.000
 5K3  H22C  C2  C3    109.83  3.000
 5K3  H21C  C2  C3    109.29  3.000
 5K3  H22C  C2  C1    109.45  3.000
 5K3  H21C  C2  C1    108.64  3.000
 5K3  C3    C2  C1    112.66  3.000
 5K3  H32C  C3  H31C  106.65  3.000
 5K3  H32C  C3  C4    109.62  3.000
 5K3  H31C  C3  C4    109.71  3.000
 5K3  H32C  C3  C2    109.29  3.000
 5K3  H31C  C3  C2    109.79  3.000
 5K3  C4    C3  C2    111.66  3.000
 5K3  C5    C4  C9    117.96  3.000
 5K3  C5    C4  C3    121.15  3.000
 5K3  C9    C4  C3    120.86  3.000
 5K3  H9    C9  C8    119.11  3.000
 5K3  H9    C9  C4    119.60  3.000
 5K3  C8    C9  C4    121.28  3.000
 5K3  H8    C8  C7    119.77  3.000
 5K3  H8    C8  C9    120.20  3.000
 5K3  C7    C8  C9    120.03  3.000
 5K3  C6    C7  O1    120.25  3.000
 5K3  C6    C7  C8    119.41  3.000
 5K3  O1    C7  C8    120.31  3.000
 5K3  HA    O1  C7    109.85  3.000
 5K3  H6    C6  C5    120.14  3.000
 5K3  H6    C6  C7    119.86  3.000
 5K3  C5    C6  C7    120.00  3.000
 5K3  H5    C5  C6    119.21  3.000
 5K3  H5    C5  C4    119.47  3.000
 5K3  C6    C5  C4    121.32  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
 5K3  CONST_01  C7   C8  C9  C4    0.00   0.0  0
 5K3  CONST_02  C7   C6  C5  C4    0.00   0.0  0
 5K3  CONST_03  C6   C5  C4  C9    0.00   0.0  0
 5K3  CONST_04  C6   C7  C8  C9    0.00   0.0  0
 5K3  CONST_05  C5   C4  C9  C8    0.00   0.0  0
 5K3  CONST_06  C5   C6  C7  C8    0.00   0.0  0
 5K3  CONST_07  C8   C9  C4  C3  180.00   0.0  0
 5K3  CONST_08  C6   C5  C4  C3  180.00   0.0  0
 5K3  CONST_09  O1   C7  C8  C9  180.00   0.0  0
 5K3  CONST_10  C5   C6  C7  O1  180.00   0.0  0
 5K3  CONST_11  H8   C8  C9  C4  180.00   0.0  0
 5K3  CONST_12  H6   C6  C5  C4  180.00   0.0  0
 5K3  CONST_13  H5   C5  C4  C9  180.00   0.0  0
 5K3  CONST_14  H9   C9  C8  C7  180.00   0.0  0
 5K3  Var_01    C9   C4  C3  C2   83.99  30.0  2
 5K3  Var_02    C4   C3  C2  C1  176.00  30.0  3
 5K3  Var_03    HC1  C   O   C1  -56.52  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
 5K3  chir_01  C1  O2  O  C2  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
 5K3  plan-1  C3  0.020
 5K3  plan-1  C4  0.020
 5K3  plan-1  C9  0.020
 5K3  plan-1  C8  0.020
 5K3  plan-1  C7  0.020
 5K3  plan-1  O1  0.020
 5K3  plan-1  C6  0.020
 5K3  plan-1  C5  0.020
 5K3  plan-1  H9  0.020
 5K3  plan-1  H5  0.020
 5K3  plan-1  H8  0.020
 5K3  plan-1  H6  0.020

