# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:44 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: (1aR,8S,10Z,13S,14S,15aR)-5,13,14-trihydroxy-3-methoxy-8-methyl-8,9,13,14,15,15a-hexahydro-6H-oxireno[k][2]benzoxacyclotetradecine-6,12(1aH)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c2C(=O)O[C@@H](C)C\C=C/C(=O)[C@@H](O)[C@@H](O)C[C@H]3O[C@@H]3c2c1
#
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
 HMY  HMY  (1aR,8S,10Z,13S,14S,15aR)-5,13,14-trihydroxy-3-methoxy-8-methyl-8,9,13,14,15,15a-hexahydro-6H-oxireno[k][2]benzoxacyclotetradecine-6,12(1aH)-dione  ligand  49  27  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HMY
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
 HMY  O23   O  O     0  -0.415   0.6414   0.7404   1.1101
 HMY  C7    C  C     0   0.600  -0.1750   1.2168   0.3652
 HMY  O8    O  O2    0  -0.527   0.0565   2.3089  -0.3745
 HMY  C9    C  CH1   0   0.030   1.2585   3.1090  -0.2396
 HMY  C25   C  CH3   0  -0.714   1.2927   3.8357   1.0907
 HMY  C10   C  CH2   0  -0.558   2.5412   2.3603  -0.6188
 HMY  C11   C  C1    0  -0.135   3.3571   1.7676   0.4827
 HMY  C12   C  C1    0  -0.338   4.0435   0.6276   0.4734
 HMY  C2    C  CR6   0  -0.254  -1.5333   0.6845   0.1564
 HMY  C1    C  CR6   0   0.390  -2.6100   1.5185  -0.2071
 HMY  O20   O  OH1   0  -0.624  -2.4866   2.8189  -0.4914
 HMY  C6    C  CR16  0  -0.484  -3.9132   1.0256  -0.2618
 HMY  C5    C  CR6   0   0.435  -4.1514  -0.3108   0.0004
 HMY  O21   O  O2    0  -0.462  -5.3624  -0.8764  -0.0253
 HMY  C22   C  CH3   0  -0.441  -6.4898  -0.0691  -0.3147
 HMY  C4    C  CR16  0  -0.412  -3.0842  -1.1669   0.2975
 HMY  C3    C  CR6   0   0.071  -1.7967  -0.6850   0.3868
 HMY  C18   C  CH1   0  -0.074  -0.7308  -1.6995   0.6945
 HMY  O31   O  O2    0  -0.478  -1.0840  -3.0056   0.2801
 HMY  C17   C  CH1   0   0.020   0.0044  -2.3748  -0.3827
 HMY  C16   C  CH2   0  -0.521   1.3219  -3.0962  -0.2267
 HMY  C15   C  CH1   0   0.033   2.5767  -2.2681   0.0241
 HMY  O29   O  OH1   0  -0.645   2.6163  -1.7390   1.3252
 HMY  C14   C  CH1   0  -0.080   2.7413  -1.0924  -0.9472
 HMY  O28   O  OH1   0  -0.661   2.7530  -1.6288  -2.2383
 HMY  C13   C  C     0   0.329   4.0557  -0.3999  -0.5918
 HMY  O24   O  O     0  -0.395   5.0939  -0.7610  -1.1016
 HMY  H9    H  HCH1  0   0.269   1.0976   3.8492  -1.0224
 HMY  H25   H  HCH3  0   0.247   1.3971   3.1671   1.9429
 HMY  H25A  H  HCH3  0   0.252   2.1371   4.5260   1.0992
 HMY  H25B  H  HCH3  0   0.256   0.3861   4.4265   1.2227
 HMY  H10   H  HCH2  0   0.267   2.3322   1.6496  -1.4206
 HMY  H10A  H  HCH2  0   0.282   3.1800   3.1200  -1.0832
 HMY  H11   H  H     0   0.257   3.5102   2.4158   1.3390
 HMY  H12   H  H     0   0.273   4.7257   0.4305   1.2935
 HMY  HO20  H  HOH1  0   0.484  -1.5462   3.0459  -0.5687
 HMY  H6    H  HCR6  0   0.291  -4.7061   1.7148  -0.5200
 HMY  H22   H  HCH3  0   0.265  -7.3550  -0.7256  -0.2774
 HMY  H22A  H  HCH3  0   0.235  -6.6179   0.7270   0.4224
 HMY  H22B  H  HCH3  0   0.234  -6.4258   0.3746  -1.3107
 HMY  H4    H  HCR6  0   0.268  -3.2915  -2.2157   0.4570
 HMY  H18   H  HCH1  0   0.273  -0.2708  -1.6372   1.6766
 HMY  H17   H  HCH1  0   0.254  -0.2246  -2.0472  -1.3966
 HMY  H16   H  HCH2  0   0.258   1.2322  -3.8039   0.6032
 HMY  H16A  H  HCH2  0   0.255   1.4721  -3.7087  -1.1183
 HMY  H15   H  HCH1  0   0.225   3.4314  -2.9409  -0.1430
 HMY  HO29  H  HOH1  0   0.455   2.6581  -2.4769   1.9415
 HMY  H14   H  HCH1  0   0.251   1.9085  -0.3980  -0.7966
 HMY  HO28  H  HOH1  0   0.460   2.7170  -0.9097  -2.8761

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
 HMY  O23  C7    double    1.203  0.020  1.203
 HMY  C7   O8    single    1.339  0.020  1.339
 HMY  C7   C2    single    1.474  0.020  1.474
 HMY  O8   C9    single    1.450  0.020  1.450
 HMY  C9   C25   single    1.516  0.020  1.516
 HMY  C9   C10   single    1.533  0.020  1.533
 HMY  C10  C11   single    1.493  0.020  1.493
 HMY  C11  C12   double    1.331  0.020  1.331
 HMY  C12  C13   single    1.480  0.020  1.480
 HMY  C2   C1    single    1.410  0.020  1.410
 HMY  C2   C3    aromatic  1.414  0.020  1.414
 HMY  C1   O20   single    1.337  0.020  1.337
 HMY  C1   C6    aromatic  1.394  0.020  1.394
 HMY  C6   C5    aromatic  1.383  0.020  1.383
 HMY  C5   O21   single    1.337  0.020  1.337
 HMY  C5   C4    aromatic  1.400  0.020  1.400
 HMY  O21  C22   single    1.417  0.020  1.417
 HMY  C4   C3    single    1.378  0.020  1.378
 HMY  C3   C18   single    1.503  0.020  1.503
 HMY  C18  O31   single    1.415  0.020  1.415
 HMY  C18  C17   single    1.469  0.020  1.469
 HMY  O31  C17   single    1.422  0.020  1.422
 HMY  C17  C16   single    1.510  0.020  1.510
 HMY  C16  C15   single    1.524  0.020  1.524
 HMY  C15  O29   single    1.405  0.020  1.405
 HMY  C15  C14   single    1.534  0.020  1.534
 HMY  C14  O28   single    1.398  0.020  1.398
 HMY  C14  C13   single    1.528  0.020  1.528
 HMY  C13  O24   double    1.212  0.020  1.212
 HMY  C9   H9    single    0.970  0.020  1.090
 HMY  C25  H25   single    0.970  0.020  1.090
 HMY  C25  H25A  single    0.970  0.020  1.090
 HMY  C25  H25B  single    0.970  0.020  1.090
 HMY  C10  H10   single    0.970  0.020  1.090
 HMY  C10  H10A  single    0.970  0.020  1.090
 HMY  C11  H11   single    0.930  0.020  1.080
 HMY  C12  H12   single    0.930  0.020  1.080
 HMY  O20  HO20  single    0.850  0.020  0.980
 HMY  C6   H6    single    0.930  0.020  1.080
 HMY  C22  H22   single    0.970  0.020  1.090
 HMY  C22  H22A  single    0.970  0.020  1.090
 HMY  C22  H22B  single    0.970  0.020  1.090
 HMY  C4   H4    single    0.930  0.020  1.080
 HMY  C18  H18   single    0.970  0.020  1.090
 HMY  C17  H17   single    0.970  0.020  1.090
 HMY  C16  H16   single    0.970  0.020  1.090
 HMY  C16  H16A  single    0.970  0.020  1.090
 HMY  C15  H15   single    0.970  0.020  1.090
 HMY  O29  HO29  single    0.850  0.020  0.980
 HMY  C14  H14   single    0.970  0.020  1.090
 HMY  O28  HO28  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
 HMY  C2    C7   O8    112.06  3.000
 HMY  C2    C7   O23   124.75  3.000
 HMY  O8    C7   O23   123.18  3.000
 HMY  C9    O8   C7    122.81  3.000
 HMY  H9    C9   C10   106.12  3.000
 HMY  H9    C9   C25   107.94  3.000
 HMY  C10   C9   C25   115.61  3.000
 HMY  H9    C9   O8    100.70  3.000
 HMY  C10   C9   O8    113.65  3.000
 HMY  C25   C9   O8    111.39  3.000
 HMY  H25B  C25  H25A  107.46  3.000
 HMY  H25B  C25  H25   108.54  3.000
 HMY  H25A  C25  H25   107.97  3.000
 HMY  H25B  C25  C9    110.32  3.000
 HMY  H25A  C25  C9    109.12  3.000
 HMY  H25   C25  C9    113.25  3.000
 HMY  H10A  C10  H10   104.58  3.000
 HMY  H10A  C10  C11   105.62  3.000
 HMY  H10   C10  C11   112.83  3.000
 HMY  H10A  C10  C9    104.72  3.000
 HMY  H10   C10  C9    109.85  3.000
 HMY  C11   C10  C9    117.94  3.000
 HMY  H11   C11  C12   116.40  3.000
 HMY  H11   C11  C10   114.97  3.000
 HMY  C12   C11  C10   128.07  3.000
 HMY  H12   C12  C13   114.38  3.000
 HMY  H12   C12  C11   118.34  3.000
 HMY  C13   C12  C11   127.16  3.000
 HMY  C3    C2   C1    118.22  3.000
 HMY  C3    C2   C7    119.91  3.000
 HMY  C1    C2   C7    121.79  3.000
 HMY  C6    C1   O20   114.95  3.000
 HMY  C6    C1   C2    120.99  3.000
 HMY  O20   C1   C2    124.04  3.000
 HMY  HO20  O20  C1    109.51  3.000
 HMY  H6    C6   C5    122.33  3.000
 HMY  H6    C6   C1    117.98  3.000
 HMY  C5    C6   C1    119.68  3.000
 HMY  C4    C5   O21   115.84  3.000
 HMY  C4    C5   C6    120.00  3.000
 HMY  O21   C5   C6    124.15  3.000
 HMY  C22   O21  C5    118.94  3.000
 HMY  H22B  C22  H22A  109.04  3.000
 HMY  H22B  C22  H22   108.87  3.000
 HMY  H22A  C22  H22   108.89  3.000
 HMY  H22B  C22  O21   111.78  3.000
 HMY  H22A  C22  O21   111.76  3.000
 HMY  H22   C22  O21   106.40  3.000
 HMY  H4    C4   C3    120.60  3.000
 HMY  H4    C4   C5    118.59  3.000
 HMY  C3    C4   C5    120.81  3.000
 HMY  C18   C3   C4    116.09  3.000
 HMY  C18   C3   C2    123.71  3.000
 HMY  C4    C3   C2    120.17  3.000
 HMY  H18   C18  C17   118.52  3.000
 HMY  H18   C18  O31   115.05  3.000
 HMY  C17   C18  O31    59.05  3.000
 HMY  H18   C18  C3    116.53  3.000
 HMY  C17   C18  C3    121.01  3.000
 HMY  O31   C18  C3    112.71  3.000
 HMY  C17   O31  C18    62.35  3.000
 HMY  H17   C17  C16   115.03  3.000
 HMY  H17   C17  O31   113.96  3.000
 HMY  C16   C17  O31   114.06  3.000
 HMY  H17   C17  C18   116.03  3.000
 HMY  C16   C17  C18   125.49  3.000
 HMY  O31   C17  C18    58.59  3.000
 HMY  H16A  C16  H16   105.53  3.000
 HMY  H16A  C16  C15   109.01  3.000
 HMY  H16   C16  C15   107.10  3.000
 HMY  H16A  C16  C17   107.67  3.000
 HMY  H16   C16  C17   108.41  3.000
 HMY  C15   C16  C17   118.40  3.000
 HMY  H15   C15  C14   106.81  3.000
 HMY  H15   C15  O29   110.42  3.000
 HMY  C14   C15  O29   107.14  3.000
 HMY  H15   C15  C16   106.39  3.000
 HMY  C14   C15  C16   113.62  3.000
 HMY  O29   C15  C16   112.34  3.000
 HMY  HO29  O29  C15   107.79  3.000
 HMY  H14   C14  C13   109.57  3.000
 HMY  H14   C14  O28   112.13  3.000
 HMY  C13   C14  O28   112.43  3.000
 HMY  H14   C14  C15   108.51  3.000
 HMY  C13   C14  C15   107.01  3.000
 HMY  O28   C14  C15   106.96  3.000
 HMY  HO28  O28  C14   108.98  3.000
 HMY  O24   C13  C14   120.28  3.000
 HMY  O24   C13  C12   121.11  3.000
 HMY  C14   C13  C12   118.37  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
 HMY  CONST_01  C5   C6   C1   C2      0.00   0.0  0
 HMY  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 HMY  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 HMY  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 HMY  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 HMY  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 HMY  CONST_07  O20  C1   C2   C7      0.00   0.0  0
 HMY  CONST_08  O21  C5   C6   C1    180.00   0.0  0
 HMY  CONST_09  C3   C2   C1   O20   180.00   0.0  0
 HMY  CONST_10  C5   C6   C1   O20   180.00   0.0  0
 HMY  CONST_11  C3   C4   C5   O21   180.00   0.0  0
 HMY  CONST_12  H6   C6   C1   C2    180.00   0.0  0
 HMY  CONST_13  H4   C4   C3   C2    180.00   0.0  0
 HMY  Var_01    C13  C12  C11  C10    -6.59   0.0  0
 HMY  Var_02    C1   C2   C7   O8    -28.72  30.0  1
 HMY  Var_03    C2   C7   O8   C9    172.82  30.0  1
 HMY  Var_04    C12  C11  C10  C9    144.02  30.0  1
 HMY  Var_05    C14  C13  C12  C11   -60.93  30.0  1
 HMY  Var_06    O31  C18  C3   C2   -152.21  30.0  1
 HMY  Var_07    C15  C16  C17  C18   -70.89  30.0  1
 HMY  Var_08    H11  C11  C12  C13  -177.51   0.0  0
 HMY  Var_09    C4   C5   O21  C22   179.78  30.0  3
 HMY  Var_10    H22  C22  O21  C5   -179.71  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
 HMY  chir_01  C9   O8   C25  C10  negativ
 HMY  chir_04  C15  C16  O29  C14  positiv
 HMY  chir_05  C14  O28  C15  C13  negativ
 HMY  chir_06  C18  C3   O31  C17  both
 HMY  chir_07  C17  O31  C16  C18  both

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
 HMY  plan-1  C7   0.020
 HMY  plan-1  C2   0.020
 HMY  plan-1  C1   0.020
 HMY  plan-1  O20  0.020
 HMY  plan-1  C6   0.020
 HMY  plan-1  C5   0.020
 HMY  plan-1  O21  0.020
 HMY  plan-1  C4   0.020
 HMY  plan-1  C3   0.020
 HMY  plan-1  C18  0.020
 HMY  plan-1  H6   0.020
 HMY  plan-1  H4   0.020
 HMY  plan-2  O23  0.020
 HMY  plan-2  C7   0.020
 HMY  plan-2  O8   0.020
 HMY  plan-2  C2   0.020
 HMY  plan-3  C10  0.020
 HMY  plan-3  C11  0.020
 HMY  plan-3  C12  0.020
 HMY  plan-3  C13  0.020
 HMY  plan-3  H11  0.020
 HMY  plan-3  H12  0.020
 HMY  plan-4  C12  0.020
 HMY  plan-4  C14  0.020
 HMY  plan-4  C13  0.020
 HMY  plan-4  O24  0.020

