# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:10:11 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (5R,6R)-5-ethyl-6-[(E,2R,3S,4R,5S)-4-methoxy-3,5-dimethyl-2-oxidanyl-non-7-enyl]oxan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]1CCC(=O)O[C@@H]1C[C@@H](O)[C@H](C)[C@H](OC)[C@@H](C)C/C=C/C
#
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
 X3H  X3H  (5R,6R)-5-ethyl-6-[(E,2R,3S,4R,5S)-4-methoxy-3,5-dimethyl-2-oxidanyl-non-7-enyl]oxan-2-one  ligand  57  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X3H
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
 X3H  C14   C  CH3   0  -0.707   8.3644   0.5121   0.5939
 X3H  C16   C  CH3   0  -0.667  -5.4650   2.5675   1.1155
 X3H  C19   C  CH3   0  -0.411   1.9436  -2.5025   0.1107
 X3H  C18   C  CH3   0  -0.665   3.5963   1.2079   1.2717
 X3H  C17   C  CH3   0  -0.718   1.2224   2.0182  -1.1994
 X3H  O01   O  O     0  -0.453  -3.8956  -2.6615   1.2016
 X3H  O07   O  OH1   0  -0.671  -0.3252  -0.3884  -2.0072
 X3H  C13   C  C1    0  -0.230   7.0143  -0.1275   0.6246
 X3H  C12   C  C1    0  -0.191   6.0295   0.1190  -0.2345
 X3H  C15   C  CH2   0  -0.437  -4.1923   1.7545   0.9193
 X3H  C11   C  CH2   0  -0.476   4.6793  -0.5251  -0.2072
 X3H  C02   C  CH2   0  -0.606  -5.3474  -1.0136   0.2728
 X3H  C06   C  CH2   0  -0.506  -1.5599   0.9008  -0.3488
 X3H  O09   O  O2    0  -0.505   1.9544  -1.1923   0.6193
 X3H  O06   O  O2    0  -0.452  -2.8973  -0.9722   0.2676
 X3H  C01   C  C     0   0.540  -4.0067  -1.6219   0.5982
 X3H  C10   C  CH1   0  -0.254   3.5367   0.4951  -0.0748
 X3H  C08   C  CH1   0  -0.273   0.9848   0.8000  -0.3073
 X3H  C07   C  CH1   0   0.038  -0.3194   0.0637  -0.6662
 X3H  C03   C  CH2   0  -0.458  -5.3097   0.1356  -0.7224
 X3H  C05   C  CH1   0   0.079  -2.8716   0.1825  -0.6039
 X3H  C04   C  CH1   0  -0.290  -4.1178   1.0419  -0.4351
 X3H  C09   C  CH1   0   0.100   2.1781  -0.1696  -0.3392
 X3H  H141  H  HCH3  0   0.233   9.1535  -0.2344   0.4778
 X3H  H142  H  HCH3  0   0.232   8.4559   1.2279  -0.2235
 X3H  H143  H  HCH3  0   0.233   8.5728   1.0384   1.5281
 X3H  H161  H  HCH3  0   0.235  -5.4148   3.1394   2.0423
 X3H  H162  H  HCH3  0   0.222  -5.6121   3.2769   0.2985
 X3H  H163  H  HCH3  0   0.223  -6.3558   1.9410   1.1732
 X3H  H191  H  HCH3  0   0.227   1.7304  -3.1777   0.9399
 X3H  H192  H  HCH3  0   0.206   1.1714  -2.6476  -0.6531
 X3H  H193  H  HCH3  0   0.208   2.9048  -2.7941  -0.3255
 X3H  H182  H  HCH3  0   0.233   4.5804   1.6498   1.4300
 X3H  H183  H  HCH3  0   0.227   2.8646   2.0139   1.3449
 X3H  H171  H  HCH3  0   0.247   2.0193   2.6482  -0.8066
 X3H  H172  H  HCH3  0   0.225   1.5067   1.7355  -2.2155
 X3H  H173  H  HCH3  0   0.246   0.3355   2.6490  -1.2634
 X3H  H071  H  HOH1  0   0.444  -0.3594   0.3787  -2.5892
 X3H  H13   H  H     0   0.225   6.8431  -0.8509   1.4187
 X3H  H12   H  H     0   0.224   6.1953   0.8461  -1.0286
 X3H  H151  H  HCH2  0   0.242  -3.3368   2.4286   1.0031
 X3H  H152  H  HCH2  0   0.221  -4.0867   1.0426   1.7438
 X3H  H111  H  HCH2  0   0.229   4.5406  -1.0865  -1.1393
 X3H  H112  H  HCH2  0   0.230   4.6326  -1.2512   0.6089
 X3H  H2    H  HCH2  0   0.291  -6.0037  -1.8172  -0.0645
 X3H  H021  H  HCH2  0   0.284  -5.7631  -0.6794   1.2292
 X3H  H061  H  HCH2  0   0.246  -1.5065   1.2347   0.6906
 X3H  H062  H  HCH2  0   0.241  -1.5735   1.8051  -0.9657
 X3H  H10   H  HCH1  0   0.228   3.6862   1.2364  -0.8673
 X3H  H08   H  HCH1  0   0.229   0.8652   1.1519   0.7243
 X3H  H07   H  HCH1  0   0.244  -0.3647  -0.8398  -0.0552
 X3H  H1    H  HCH2  0   0.250  -5.2216  -0.2556  -1.7393
 X3H  H031  H  HCH2  0   0.258  -6.2518   0.6831  -0.6905
 X3H  H05   H  HCH1  0   0.248  -2.8670  -0.1991  -1.6299
 X3H  H04   H  HCH1  0   0.254  -4.0697   1.8070  -1.2175
 X3H  H09   H  HCH1  0   0.210   2.2215  -0.6088  -1.3469
 X3H  H181  H  HCH3  0   0.219   3.4147   0.5120   2.0926

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
 X3H  C14  C13   single  1.494  0.020  1.494
 X3H  C13  C12   double  1.330  0.020  1.330
 X3H  C18  C10   single  1.525  0.020  1.525
 X3H  C12  C11   single  1.496  0.020  1.496
 X3H  C11  C10   single  1.537  0.020  1.537
 X3H  C10  C09   single  1.535  0.020  1.535
 X3H  O09  C09   single  1.419  0.020  1.419
 X3H  O09  C19   single  1.405  0.020  1.405
 X3H  C09  C08   single  1.538  0.020  1.538
 X3H  C08  C17   single  1.528  0.020  1.528
 X3H  C08  C07   single  1.540  0.020  1.540
 X3H  C07  C06   single  1.530  0.020  1.530
 X3H  C07  O07   single  1.415  0.020  1.415
 X3H  C06  C05   single  1.517  0.020  1.517
 X3H  C15  C16   single  1.523  0.020  1.523
 X3H  C15  C04   single  1.532  0.020  1.532
 X3H  O06  C05   single  1.447  0.020  1.447
 X3H  O06  C01   single  1.328  0.020  1.328
 X3H  O01  C01   double  1.207  0.020  1.207
 X3H  C05  C04   single  1.523  0.020  1.523
 X3H  C01  C02   single  1.508  0.020  1.508
 X3H  C04  C03   single  1.525  0.020  1.525
 X3H  C02  C03   single  1.521  0.020  1.521
 X3H  C16  H163  single  0.970  0.020  1.090
 X3H  C16  H161  single  0.970  0.020  1.090
 X3H  C16  H162  single  0.970  0.020  1.090
 X3H  C15  H151  single  0.970  0.020  1.090
 X3H  C15  H152  single  0.970  0.020  1.090
 X3H  C04  H04   single  0.970  0.020  1.090
 X3H  C03  H031  single  0.970  0.020  1.090
 X3H  C03  H1    single  0.970  0.020  1.090
 X3H  C02  H021  single  0.970  0.020  1.090
 X3H  C02  H2    single  0.970  0.020  1.090
 X3H  C05  H05   single  0.970  0.020  1.090
 X3H  C06  H061  single  0.970  0.020  1.090
 X3H  C06  H062  single  0.970  0.020  1.090
 X3H  C07  H07   single  0.970  0.020  1.090
 X3H  O07  H071  single  0.850  0.020  0.980
 X3H  C08  H08   single  0.970  0.020  1.090
 X3H  C17  H172  single  0.970  0.020  1.090
 X3H  C17  H173  single  0.970  0.020  1.090
 X3H  C17  H171  single  0.970  0.020  1.090
 X3H  C09  H09   single  0.970  0.020  1.090
 X3H  C19  H192  single  0.970  0.020  1.090
 X3H  C19  H191  single  0.970  0.020  1.090
 X3H  C19  H193  single  0.970  0.020  1.090
 X3H  C10  H10   single  0.970  0.020  1.090
 X3H  C18  H183  single  0.970  0.020  1.090
 X3H  C18  H181  single  0.970  0.020  1.090
 X3H  C18  H182  single  0.970  0.020  1.090
 X3H  C11  H111  single  0.970  0.020  1.090
 X3H  C11  H112  single  0.970  0.020  1.090
 X3H  C12  H12   single  0.930  0.020  1.080
 X3H  C13  H13   single  0.930  0.020  1.080
 X3H  C14  H143  single  0.970  0.020  1.090
 X3H  C14  H141  single  0.970  0.020  1.090
 X3H  C14  H142  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
 X3H  H143  C14  H142  107.98  3.000
 X3H  H142  C14  H141  107.96  3.000
 X3H  H143  C14  H141  106.40  3.000
 X3H  H142  C14  C13   111.85  3.000
 X3H  H141  C14  C13   111.25  3.000
 X3H  H143  C14  C13   111.16  3.000
 X3H  H163  C16  H162  107.62  3.000
 X3H  H162  C16  H161  107.55  3.000
 X3H  H163  C16  H161  107.09  3.000
 X3H  H162  C16  C15   111.29  3.000
 X3H  H161  C16  C15   110.56  3.000
 X3H  H163  C16  C15   112.51  3.000
 X3H  H193  C19  H192  107.80  3.000
 X3H  H193  C19  H191  108.04  3.000
 X3H  H192  C19  H191  108.08  3.000
 X3H  H193  C19  O09   112.68  3.000
 X3H  H191  C19  O09   107.67  3.000
 X3H  H192  C19  O09   112.40  3.000
 X3H  H183  C18  H182  107.23  3.000
 X3H  H182  C18  H181  107.42  3.000
 X3H  H183  C18  H181  108.00  3.000
 X3H  H182  C18  C10   110.67  3.000
 X3H  H181  C18  C10   111.08  3.000
 X3H  H183  C18  C10   112.24  3.000
 X3H  H173  C17  H172  107.87  3.000
 X3H  H173  C17  H171  106.36  3.000
 X3H  H172  C17  H171  107.14  3.000
 X3H  H171  C17  C08   111.36  3.000
 X3H  H173  C17  C08   111.65  3.000
 X3H  H172  C17  C08   112.16  3.000
 X3H  H071  O07  C07   108.55  3.000
 X3H  H13   C13  C12   118.57  3.000
 X3H  H13   C13  C14   116.22  3.000
 X3H  C12   C13  C14   125.20  3.000
 X3H  H12   C12  C11   115.98  3.000
 X3H  H12   C12  C13   118.81  3.000
 X3H  C11   C12  C13   125.21  3.000
 X3H  H152  C15  H151  105.55  3.000
 X3H  H152  C15  C04   111.03  3.000
 X3H  H151  C15  C04   108.46  3.000
 X3H  H152  C15  C16   109.32  3.000
 X3H  H151  C15  C16   108.37  3.000
 X3H  C04   C15  C16   113.75  3.000
 X3H  H112  C11  H111  106.80  3.000
 X3H  H112  C11  C10   110.16  3.000
 X3H  H111  C11  C10   108.59  3.000
 X3H  H112  C11  C12   109.76  3.000
 X3H  H111  C11  C12   108.60  3.000
 X3H  C10   C11  C12   112.74  3.000
 X3H  H021  C02  H2    105.45  3.000
 X3H  H2    C02  C03   111.66  3.000
 X3H  H021  C02  C03   110.51  3.000
 X3H  H2    C02  C01   107.72  3.000
 X3H  H021  C02  C01   105.80  3.000
 X3H  C03   C02  C01   115.10  3.000
 X3H  H062  C06  H061  106.51  3.000
 X3H  H062  C06  C05   106.59  3.000
 X3H  H061  C06  C05   110.29  3.000
 X3H  H062  C06  C07   110.19  3.000
 X3H  H061  C06  C07   108.96  3.000
 X3H  C05   C06  C07   114.03  3.000
 X3H  C09   O09  C19   115.37  3.000
 X3H  C05   O06  C01   123.74  3.000
 X3H  O06   C01  C02   119.46  3.000
 X3H  C02   C01  O01   122.49  3.000
 X3H  O06   C01  O01   117.98  3.000
 X3H  H10   C10  C09   106.81  3.000
 X3H  H10   C10  C11   106.58  3.000
 X3H  C09   C10  C11   110.82  3.000
 X3H  H10   C10  C18   108.49  3.000
 X3H  C09   C10  C18   112.89  3.000
 X3H  C11   C10  C18   110.93  3.000
 X3H  H08   C08  C09   107.85  3.000
 X3H  H08   C08  C07   106.28  3.000
 X3H  C09   C08  C07   110.54  3.000
 X3H  H08   C08  C17   108.08  3.000
 X3H  C07   C08  C17   112.13  3.000
 X3H  C09   C08  C17   111.70  3.000
 X3H  H07   C07  C08   107.48  3.000
 X3H  H07   C07  C06   107.64  3.000
 X3H  C08   C07  C06   112.13  3.000
 X3H  H07   C07  O07   105.42  3.000
 X3H  C06   C07  O07   111.60  3.000
 X3H  C08   C07  O07   112.15  3.000
 X3H  H031  C03  H1    106.06  3.000
 X3H  H1    C03  C04   108.97  3.000
 X3H  H031  C03  C04   111.81  3.000
 X3H  H1    C03  C02   109.90  3.000
 X3H  H031  C03  C02   109.82  3.000
 X3H  C04   C03  C02   110.20  3.000
 X3H  H05   C05  C04   107.70  3.000
 X3H  H05   C05  O06   106.64  3.000
 X3H  C04   C05  O06   111.65  3.000
 X3H  H05   C05  C06   108.60  3.000
 X3H  C04   C05  C06   114.94  3.000
 X3H  O06   C05  C06   106.97  3.000
 X3H  H04   C04  C05   106.20  3.000
 X3H  H04   C04  C03   108.36  3.000
 X3H  C05   C04  C03   106.46  3.000
 X3H  H04   C04  C15   107.98  3.000
 X3H  C03   C04  C15   113.89  3.000
 X3H  C05   C04  C15   113.58  3.000
 X3H  H09   C09  C08   107.54  3.000
 X3H  H09   C09  C10   107.19  3.000
 X3H  C08   C09  C10   114.21  3.000
 X3H  H09   C09  O09   109.70  3.000
 X3H  C08   C09  O09   108.54  3.000
 X3H  C10   C09  O09   109.58  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
 X3H  Var_01  C03   C02  C01  O06   14.84  30.0  1
 X3H  Var_02  C04   C03  C02  C01  -40.91  30.0  1
 X3H  Var_03  H163  C16  C15  C04   66.68  30.0  3
 X3H  Var_04  C11   C12  C13  C14  179.75   0.0  2
 X3H  Var_05  C10   C11  C12  C13  121.60  30.0  3
 X3H  Var_06  H143  C14  C13  C12  121.34  30.0  3
 X3H  Var_07  H192  C19  O09  C09  -59.22  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
 X3H  chir_01  C10  C18  C11  C09  negativ
 X3H  chir_02  C08  C07  C17  C09  positiv
 X3H  chir_03  C07  O07  C08  C06  negativ
 X3H  chir_04  C05  O06  C04  C06  negativ
 X3H  chir_05  C04  C03  C05  C15  positiv
 X3H  chir_06  C09  O09  C10  C08  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
 X3H  plan-1  O01  0.020
 X3H  plan-1  C02  0.020
 X3H  plan-1  O06  0.020
 X3H  plan-1  C01  0.020
 X3H  plan-2  C14  0.020
 X3H  plan-2  C13  0.020
 X3H  plan-2  C12  0.020
 X3H  plan-2  C11  0.020
 X3H  plan-2  H13  0.020
 X3H  plan-2  H12  0.020

