# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:16:02 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl tetradecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO
#
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
 GYM  GYM  '(2R)-2,3-dihydroxypropyl tetradecanoate'  ligand  55  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYM
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
 GYM  O21  O  OH1   0  -0.667   10.1082  -0.6516   0.7524
 GYM  C20  C  CH2   0  -0.165    9.1342   0.2586   0.3052
 GYM  C18  C  CH1   0  -0.049    7.7812  -0.4360   0.3026
 GYM  O19  O  OH1   0  -0.656    7.7575  -1.5732  -0.5247
 GYM  C17  C  CH2   0  -0.185    6.7033   0.5666  -0.0719
 GYM  O2   O  O2    0  -0.460    5.4411  -0.0885   0.0491
 GYM  C1   C  C     0   0.607    4.3466   0.6264  -0.1910
 GYM  O1   O  O     0  -0.454    4.3746   1.7899  -0.5068
 GYM  C2   C  CH2   0  -0.584    3.1000  -0.1988  -0.0219
 GYM  C3   C  CH2   0  -0.417    1.8156   0.5976  -0.1843
 GYM  C4   C  CH2   0  -0.416    0.5767  -0.2709  -0.0080
 GYM  C5   C  CH2   0  -0.412   -0.7186   0.5168  -0.1557
 GYM  C6   C  CH2   0  -0.412   -1.9677  -0.3369   0.0206
 GYM  C7   C  CH2   0  -0.412   -3.2601   0.4568  -0.1216
 GYM  C8   C  CH2   0  -0.412   -4.5134  -0.3914   0.0525
 GYM  C9   C  CH2   0  -0.411   -5.8031   0.4073  -0.0870
 GYM  C10  C  CH2   0  -0.411   -7.0591  -0.4373   0.0859
 GYM  C11  C  CH2   0  -0.411   -8.3468   0.3655  -0.0484
 GYM  C12  C  CH2   0  -0.406   -9.6039  -0.4771   0.1250
 GYM  C13  C  CH2   0  -0.418  -10.8924   0.3261  -0.0028
 GYM  C14  C  CH3   0  -0.662  -12.1408  -0.5274   0.1711
 GYM  H21  H  HOH1  0   0.457   10.9626  -0.2126   0.7179
 GYM  H17  H  HCH2  0   0.239    6.7435   1.4315   0.5947
 GYM  H71  H  HCH2  0   0.236    6.8471   0.9238  -1.0967
 GYM  H18  H  HCH1  0   0.240    7.5788  -0.7985   1.3160
 GYM  H19  H  HOH1  0   0.445    8.0117  -1.3113  -1.4167
 GYM  H20  H  HCH2  0   0.204    9.0753   1.1421   0.9540
 GYM  H22  H  HCH2  0   0.199    9.3553   0.6246  -0.7085
 GYM  H23  H  HCH2  0   0.275    3.1372  -1.0181  -0.7479
 GYM  H24  H  HCH2  0   0.271    3.1339  -0.6793   0.9608
 GYM  H33  H  HCH2  0   0.224    1.7931   1.4129   0.5442
 GYM  H34  H  HCH2  0   0.224    1.7926   1.0661  -1.1718
 GYM  H43  H  HCH2  0   0.212    0.5929  -1.0856  -0.7404
 GYM  H44  H  HCH2  0   0.212    0.6002  -0.7488   0.9776
 GYM  H53  H  HCH2  0   0.208   -0.7306   1.3321   0.5763
 GYM  H54  H  HCH2  0   0.208   -0.7411   0.9953  -1.1412
 GYM  H63  H  HCH2  0   0.207   -1.9587  -1.1509  -0.7130
 GYM  H64  H  HCH2  0   0.207   -1.9438  -0.8173   1.0052
 GYM  H73  H  HCH2  0   0.206   -3.2680   1.2694   0.6137
 GYM  H74  H  HCH2  0   0.206   -3.2822   0.9400  -1.1050
 GYM  H83  H  HCH2  0   0.206   -4.5079  -1.2037  -0.6832
 GYM  H84  H  HCH2  0   0.206   -4.4912  -0.8749   1.0357
 GYM  H93  H  HCH2  0   0.206   -5.8077   1.2183   0.6501
 GYM  H94  H  HCH2  0   0.206   -5.8240   0.8929  -1.0693
 GYM  HA1  H  HCH2  0   0.206   -7.0571  -1.2467  -0.6529
 GYM  HA2  H  HCH2  0   0.206   -7.0366  -0.9245   1.0673
 GYM  HA3  H  HCH2  0   0.206   -8.3478   1.1742   0.6912
 GYM  HA4  H  HCH2  0   0.206   -8.3691   0.8538  -1.0293
 GYM  HA5  H  HCH2  0   0.205   -9.6062  -1.2845  -0.6162
 GYM  HA6  H  HCH2  0   0.205   -9.5805  -0.9681   1.1047
 GYM  HA7  H  HCH2  0   0.209  -10.8924   1.1302   0.7399
 GYM  HA8  H  HCH2  0   0.209  -10.9161   0.8184  -0.9804
 GYM  H40  H  HCH3  0   0.215  -12.1932  -1.3104  -0.5878
 GYM  H41  H  HCH3  0   0.215  -12.1498  -1.0166   1.1472
 GYM  H42  H  HCH3  0   0.225  -13.0509   0.0689   0.0938

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
 GYM  O21  C20  single  1.406  0.020  1.406
 GYM  C20  C18  single  1.521  0.020  1.521
 GYM  C18  O19  single  1.407  0.020  1.407
 GYM  C18  C17  single  1.519  0.020  1.519
 GYM  C17  O2   single  1.427  0.020  1.427
 GYM  O2   C1   single  1.329  0.020  1.329
 GYM  C1   O1   double  1.206  0.020  1.206
 GYM  C1   C2   single  1.505  0.020  1.505
 GYM  C2   C3   single  1.520  0.020  1.520
 GYM  C3   C4   single  1.523  0.020  1.523
 GYM  C4   C5   single  1.523  0.020  1.523
 GYM  C5   C6   single  1.523  0.020  1.523
 GYM  C6   C7   single  1.523  0.020  1.523
 GYM  C7   C8   single  1.523  0.020  1.523
 GYM  C8   C9   single  1.523  0.020  1.523
 GYM  C9   C10  single  1.523  0.020  1.523
 GYM  C10  C11  single  1.523  0.020  1.523
 GYM  C11  C12  single  1.523  0.020  1.523
 GYM  C12  C13  single  1.524  0.020  1.524
 GYM  C13  C14  single  1.522  0.020  1.522
 GYM  O21  H21  single  0.850  0.020  0.980
 GYM  C18  H18  single  0.970  0.020  1.090
 GYM  C17  H17  single  0.970  0.020  1.090
 GYM  C17  H71  single  0.970  0.020  1.090
 GYM  C20  H20  single  0.970  0.020  1.090
 GYM  C20  H22  single  0.970  0.020  1.090
 GYM  O19  H19  single  0.850  0.020  0.980
 GYM  C2   H23  single  0.970  0.020  1.090
 GYM  C2   H24  single  0.970  0.020  1.090
 GYM  C3   H33  single  0.970  0.020  1.090
 GYM  C3   H34  single  0.970  0.020  1.090
 GYM  C4   H43  single  0.970  0.020  1.090
 GYM  C4   H44  single  0.970  0.020  1.090
 GYM  C5   H53  single  0.970  0.020  1.090
 GYM  C5   H54  single  0.970  0.020  1.090
 GYM  C6   H63  single  0.970  0.020  1.090
 GYM  C6   H64  single  0.970  0.020  1.090
 GYM  C7   H73  single  0.970  0.020  1.090
 GYM  C7   H74  single  0.970  0.020  1.090
 GYM  C8   H83  single  0.970  0.020  1.090
 GYM  C8   H84  single  0.970  0.020  1.090
 GYM  C9   H93  single  0.970  0.020  1.090
 GYM  C9   H94  single  0.970  0.020  1.090
 GYM  C10  HA1  single  0.970  0.020  1.090
 GYM  C10  HA2  single  0.970  0.020  1.090
 GYM  C11  HA3  single  0.970  0.020  1.090
 GYM  C11  HA4  single  0.970  0.020  1.090
 GYM  C12  HA5  single  0.970  0.020  1.090
 GYM  C12  HA6  single  0.970  0.020  1.090
 GYM  C13  HA7  single  0.970  0.020  1.090
 GYM  C13  HA8  single  0.970  0.020  1.090
 GYM  C14  H40  single  0.970  0.020  1.090
 GYM  C14  H41  single  0.970  0.020  1.090
 GYM  C14  H42  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
 GYM  H21  O21  C20  107.98  3.000
 GYM  H22  C20  H20  106.71  3.000
 GYM  H22  C20  C18  109.22  3.000
 GYM  H20  C20  C18  108.71  3.000
 GYM  H22  C20  O21  111.67  3.000
 GYM  H20  C20  O21  111.72  3.000
 GYM  C18  C20  O21  108.74  3.000
 GYM  H18  C18  C17  108.39  3.000
 GYM  H18  C18  O19  105.87  3.000
 GYM  C17  C18  O19  112.13  3.000
 GYM  H18  C18  C20  108.30  3.000
 GYM  C17  C18  C20  109.29  3.000
 GYM  O19  C18  C20  112.66  3.000
 GYM  H19  O19  C18  108.68  3.000
 GYM  H71  C17  H17  107.93  3.000
 GYM  H71  C17  O2   110.20  3.000
 GYM  H17  C17  O2   110.13  3.000
 GYM  H71  C17  C18  110.66  3.000
 GYM  H17  C17  C18  110.24  3.000
 GYM  O2   C17  C18  107.68  3.000
 GYM  C1   O2   C17  117.78  3.000
 GYM  C2   C1   O1   125.30  3.000
 GYM  C2   C1   O2   111.53  3.000
 GYM  O1   C1   O2   123.17  3.000
 GYM  H24  C2   H23  105.41  3.000
 GYM  H24  C2   C3   110.62  3.000
 GYM  H23  C2   C3   110.48  3.000
 GYM  H24  C2   C1   108.42  3.000
 GYM  H23  C2   C1   107.91  3.000
 GYM  C3   C2   C1   113.62  3.000
 GYM  H34  C3   H33  106.37  3.000
 GYM  H34  C3   C4   109.37  3.000
 GYM  H33  C3   C4   109.34  3.000
 GYM  H34  C3   C2   109.80  3.000
 GYM  H33  C3   C2   109.69  3.000
 GYM  C4   C3   C2   112.09  3.000
 GYM  H44  C4   H43  106.06  3.000
 GYM  H44  C4   C5   109.33  3.000
 GYM  H43  C4   C5   109.41  3.000
 GYM  H44  C4   C3   109.60  3.000
 GYM  H43  C4   C3   109.55  3.000
 GYM  C5   C4   C3   112.68  3.000
 GYM  H54  C5   H53  106.01  3.000
 GYM  H54  C5   C6   109.39  3.000
 GYM  H53  C5   C6   109.31  3.000
 GYM  H54  C5   C4   109.30  3.000
 GYM  H53  C5   C4   109.23  3.000
 GYM  C6   C5   C4   113.34  3.000
 GYM  H64  C6   H63  106.00  3.000
 GYM  H64  C6   C7   109.31  3.000
 GYM  H63  C6   C7   109.36  3.000
 GYM  H64  C6   C5   109.38  3.000
 GYM  H63  C6   C5   109.40  3.000
 GYM  C7   C6   C5   113.13  3.000
 GYM  H74  C7   H73  105.96  3.000
 GYM  H74  C7   C8   109.36  3.000
 GYM  H73  C7   C8   109.29  3.000
 GYM  H74  C7   C6   109.30  3.000
 GYM  H73  C7   C6   109.26  3.000
 GYM  C8   C7   C6   113.40  3.000
 GYM  H84  C8   H83  105.97  3.000
 GYM  H84  C8   C9   109.31  3.000
 GYM  H83  C8   C9   109.36  3.000
 GYM  H84  C8   C7   109.36  3.000
 GYM  H83  C8   C7   109.38  3.000
 GYM  C9   C8   C7   113.21  3.000
 GYM  H94  C9   H93  105.95  3.000
 GYM  H94  C9   C10  109.37  3.000
 GYM  H93  C9   C10  109.30  3.000
 GYM  H94  C9   C8   109.30  3.000
 GYM  H93  C9   C8   109.27  3.000
 GYM  C10  C9   C8   113.38  3.000
 GYM  HA2  C10  HA1  105.98  3.000
 GYM  HA2  C10  C11  109.30  3.000
 GYM  HA1  C10  C11  109.35  3.000
 GYM  HA2  C10  C9   109.34  3.000
 GYM  HA1  C10  C9   109.36  3.000
 GYM  C11  C10  C9   113.25  3.000
 GYM  HA4  C11  HA3  105.97  3.000
 GYM  HA4  C11  C12  109.37  3.000
 GYM  HA3  C11  C12  109.31  3.000
 GYM  HA4  C11  C10  109.32  3.000
 GYM  HA3  C11  C10  109.28  3.000
 GYM  C12  C11  C10  113.33  3.000
 GYM  HA6  C12  HA5  105.94  3.000
 GYM  HA6  C12  C13  109.22  3.000
 GYM  HA5  C12  C13  109.26  3.000
 GYM  HA6  C12  C11  109.38  3.000
 GYM  HA5  C12  C11  109.40  3.000
 GYM  C13  C12  C11  113.37  3.000
 GYM  HA8  C13  HA7  106.00  3.000
 GYM  HA8  C13  C14  109.66  3.000
 GYM  HA7  C13  C14  109.53  3.000
 GYM  HA8  C13  C12  109.28  3.000
 GYM  HA7  C13  C12  109.29  3.000
 GYM  C14  C13  C12  112.85  3.000
 GYM  H42  C14  H41  107.54  3.000
 GYM  H42  C14  H40  107.62  3.000
 GYM  H41  C14  H40  107.44  3.000
 GYM  H42  C14  C13  111.69  3.000
 GYM  H41  C14  C13  111.11  3.000
 GYM  H40  C14  C13  111.23  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
 GYM  Var_01  O1   C1   O2   C17     0.23  30.0  3
 GYM  Var_02  C3   C2   C1   O2    175.71  30.0  3
 GYM  Var_03  C4   C3   C2   C1    179.94  30.0  3
 GYM  Var_04  C5   C4   C3   C2    179.49  30.0  3
 GYM  Var_05  C6   C5   C4   C3   -179.89  30.0  3
 GYM  Var_06  C7   C6   C5   C4    179.73  30.0  3
 GYM  Var_07  C8   C7   C6   C5    179.95  30.0  3
 GYM  Var_08  C9   C8   C7   C6    179.86  30.0  3
 GYM  Var_09  C10  C9   C8   C7    179.98  30.0  3
 GYM  Var_10  C11  C10  C9   C8    179.76  30.0  3
 GYM  Var_11  C12  C11  C10  C9   -179.96  30.0  3
 GYM  Var_12  C13  C12  C11  C10   179.74  30.0  3
 GYM  Var_13  C14  C13  C12  C11   179.95  30.0  3
 GYM  Var_14  H17  C17  O2   C1     57.56  30.0  1
 GYM  Var_15  H40  C14  C13  C12   -60.74  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
 GYM  chir_01  C18  C20  O19  C17  positiv

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
 GYM  plan-1  O2  0.020
 GYM  plan-1  C1  0.020
 GYM  plan-1  O1  0.020
 GYM  plan-1  C2  0.020

