# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:22:30 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-[(3S,3aS,8bS)-5-fluoro-3-(hydroxymethyl)-2,3,3a,8b-tetrahydro-1H-[1]benzofuro[3,2-b]pyrrol-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1C[C@@H](CO)[C@@H]2Oc3c(F)cccc3[C@H]12
#
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
 JMY  JMY  1-[(3S,3aS,8bS)-5-fluoro-3-(hydroxymethyl)-2,3,3a,8b-tetrahydro-1H-[1]benzofuro[3,2-b]pyrrol-1-yl]ethan-1-one  ligand  32  18  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JMY
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
 JMY  C15   C  CR16  0  -0.261   3.2638   1.4575  -0.3142
 JMY  C17   C  CR56  0   0.043   1.1107   0.4752  -0.6079
 JMY  C01   C  CH3   0  -0.796  -2.4957   2.5978   1.2265
 JMY  C02   C  C     0   0.527  -1.5570   2.1454   0.1365
 JMY  O03   O  O     0  -0.503  -1.1239   2.9182  -0.7095
 JMY  N04   N  NT    0  -0.443  -1.2277   0.8395   0.1266
 JMY  C05   C  CH2   0  -0.298  -1.6654  -0.1871   1.0580
 JMY  C06   C  CH1   0  -0.335  -1.7056  -1.4403   0.1870
 JMY  C07   C  CH2   0  -0.137  -2.9871  -1.5436  -0.6284
 JMY  O08   O  OH1   0  -0.668  -4.0716  -1.6772   0.2575
 JMY  C09   C  CR15  0   0.017  -0.5176  -1.2433  -0.7441
 JMY  O10   O  O     0  -0.490   0.6926  -1.7307  -0.1367
 JMY  C11   C  CR56  0   0.248   1.5989  -0.7372  -0.1536
 JMY  C12   C  CR6   0   0.451   2.9225  -0.8568   0.2281
 JMY  F13   F  F     0  -0.311   3.3836  -2.0382   0.6657
 JMY  C14   C  CR16  0  -0.416   3.7574   0.2413   0.1503
 JMY  C16   C  CR16  0  -0.325   1.9326   1.5849  -0.6965
 JMY  C18   C  CR15  0  -0.198  -0.3534   0.2860  -0.8979
 JMY  H151  H  HCR6  0   0.265   3.9304   2.3066  -0.3751
 JMY  H012  H  HCH3  0   0.265  -2.1620   2.2815   2.2145
 JMY  H013  H  HCH3  0   0.269  -2.5705   3.6819   1.2136
 JMY  H011  H  HCH3  0   0.268  -3.4942   2.1846   1.0712
 JMY  H052  H  HCH2  0   0.262  -0.9521  -0.3015   1.8805
 JMY  H051  H  HCH2  0   0.276  -2.6352   0.0475   1.4912
 JMY  H061  H  HCH1  0   0.282  -1.5897  -2.3487   0.7828
 JMY  H072  H  HCH2  0   0.207  -3.0982  -0.6586  -1.2702
 JMY  H071  H  HCH2  0   0.214  -2.9031  -2.4093  -1.2981
 JMY  H081  H  HOH1  0   0.458  -4.8852  -1.6217  -0.2511
 JMY  H091  H  HCR5  0   0.284  -0.6351  -1.7509  -1.7049
 JMY  H141  H  HCR6  0   0.284   4.7939   0.1433   0.4468
 JMY  H161  H  HCR6  0   0.262   1.5481   2.5296  -1.0537
 JMY  H181  H  HCR5  0   0.299  -0.6434   0.6468  -1.8850

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
 JMY  O03  C02   double    1.225  0.020  1.225
 JMY  O08  C07   single    1.407  0.020  1.407
 JMY  C02  N04   single    1.347  0.020  1.347
 JMY  C02  C01   single    1.508  0.020  1.508
 JMY  C05  N04   single    1.454  0.020  1.454
 JMY  C05  C06   single    1.527  0.020  1.527
 JMY  C07  C06   single    1.522  0.020  1.522
 JMY  N04  C18   single    1.456  0.020  1.456
 JMY  C06  C09   single    1.522  0.020  1.522
 JMY  C18  C09   single    1.546  0.020  1.546
 JMY  C18  C17   single    1.505  0.020  1.505
 JMY  C09  O10   single    1.439  0.020  1.439
 JMY  C16  C17   aromatic  1.384  0.020  1.384
 JMY  C16  C15   aromatic  1.391  0.020  1.391
 JMY  C17  C11   aromatic  1.384  0.020  1.384
 JMY  C15  C14   aromatic  1.392  0.020  1.392
 JMY  C11  O10   single    1.345  0.020  1.345
 JMY  C11  C12   aromatic  1.383  0.020  1.383
 JMY  C14  C12   aromatic  1.382  0.020  1.382
 JMY  C12  F13   single    1.342  0.020  1.342
 JMY  C15  H151  single    0.930  0.020  1.080
 JMY  C01  H012  single    0.970  0.020  1.090
 JMY  C01  H013  single    0.970  0.020  1.090
 JMY  C01  H011  single    0.970  0.020  1.090
 JMY  C05  H052  single    0.970  0.020  1.090
 JMY  C05  H051  single    0.970  0.020  1.090
 JMY  C06  H061  single    0.970  0.020  1.090
 JMY  C07  H072  single    0.970  0.020  1.090
 JMY  C07  H071  single    0.970  0.020  1.090
 JMY  O08  H081  single    0.850  0.020  0.980
 JMY  C09  H091  single    0.970  0.020  1.090
 JMY  C14  H141  single    0.930  0.020  1.080
 JMY  C16  H161  single    0.930  0.020  1.080
 JMY  C18  H181  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
 JMY  H151  C15  C16   120.17  3.000
 JMY  H151  C15  C14   119.09  3.000
 JMY  C16   C15  C14   120.73  3.000
 JMY  C18   C17  C16   131.80  3.000
 JMY  C16   C17  C11   120.94  3.000
 JMY  C18   C17  C11   107.24  3.000
 JMY  H011  C01  H013  108.24  3.000
 JMY  H011  C01  H012  107.41  3.000
 JMY  H013  C01  H012  108.75  3.000
 JMY  H011  C01  C02   110.67  3.000
 JMY  H013  C01  C02   109.48  3.000
 JMY  H012  C01  C02   112.19  3.000
 JMY  N04   C02  O03   121.34  3.000
 JMY  N04   C02  C01   116.64  3.000
 JMY  O03   C02  C01   122.01  3.000
 JMY  C18   N04  C05   111.29  3.000
 JMY  C18   N04  C02   121.37  3.000
 JMY  C05   N04  C02   127.33  3.000
 JMY  H051  C05  H052  107.71  3.000
 JMY  H051  C05  C06   112.38  3.000
 JMY  H052  C05  C06   111.10  3.000
 JMY  H051  C05  N04   111.79  3.000
 JMY  H052  C05  N04   111.04  3.000
 JMY  C06   C05  N04   102.83  3.000
 JMY  H061  C06  C09   111.01  3.000
 JMY  H061  C06  C07   108.97  3.000
 JMY  C09   C06  C07   109.76  3.000
 JMY  H061  C06  C05   111.63  3.000
 JMY  C09   C06  C05   102.84  3.000
 JMY  C07   C06  C05   112.54  3.000
 JMY  H071  C07  H072  106.65  3.000
 JMY  H071  C07  O08   111.61  3.000
 JMY  H072  C07  O08   111.49  3.000
 JMY  H071  C07  C06   108.41  3.000
 JMY  H072  C07  C06   110.08  3.000
 JMY  O08   C07  C06   108.55  3.000
 JMY  H081  O08  C07   108.29  3.000
 JMY  H091  C09  C18   112.55  3.000
 JMY  H091  C09  O10   107.71  3.000
 JMY  C18   C09  O10   106.72  3.000
 JMY  H091  C09  C06   113.19  3.000
 JMY  O10   C09  C06   110.75  3.000
 JMY  C18   C09  C06   105.77  3.000
 JMY  C11   O10  C09   108.13  3.000
 JMY  C12   C11  O10   125.29  3.000
 JMY  C12   C11  C17   120.27  3.000
 JMY  O10   C11  C17   114.43  3.000
 JMY  C14   C12  F13   120.71  3.000
 JMY  F13   C12  C11   119.68  3.000
 JMY  C14   C12  C11   119.61  3.000
 JMY  H141  C14  C12   119.41  3.000
 JMY  H141  C14  C15   120.66  3.000
 JMY  C12   C14  C15   119.93  3.000
 JMY  H161  C16  C17   120.72  3.000
 JMY  H161  C16  C15   120.77  3.000
 JMY  C17   C16  C15   118.52  3.000
 JMY  H181  C18  C09   112.91  3.000
 JMY  H181  C18  N04   110.58  3.000
 JMY  C09   C18  N04   104.02  3.000
 JMY  H181  C18  C17   113.06  3.000
 JMY  C09   C18  C17   102.04  3.000
 JMY  N04   C18  C17   113.63  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
 JMY  CONST_01  C11   C17  C16  C15     0.00   0.0  0
 JMY  CONST_02  C11   C12  C14  C15     0.00   0.0  0
 JMY  CONST_03  C14   C15  C16  C17     0.00   0.0  0
 JMY  CONST_04  C14   C12  C11  C17     0.00   0.0  0
 JMY  CONST_05  C16   C17  C11  C12     0.00   0.0  0
 JMY  CONST_06  C16   C15  C14  C12     0.00   0.0  0
 JMY  CONST_07  F13   C12  C14  C15   180.00   0.0  0
 JMY  CONST_08  F13   C12  C11  C17   180.00   0.0  0
 JMY  CONST_09  F13   C12  C11  O10     0.00   0.0  0
 JMY  CONST_10  H151  C15  C16  C17   180.00   0.0  0
 JMY  CONST_11  H161  C16  C17  C11   180.00   0.0  0
 JMY  CONST_12  H141  C14  C12  C11   180.00   0.0  0
 JMY  CONST_13  C05   N04  C02  C01     0.00   0.0  0
 JMY  CONST_14  C18   N04  C02  C01   180.00   0.0  0
 JMY  CONST_15  C05   N04  C02  O03   180.00   0.0  0
 JMY  CONST_16  C18   N04  C02  O03     0.00   0.0  0
 JMY  Var_01    C18   N04  C05  C06   -31.05  30.0  1
 JMY  Var_02    C12   C11  O10  C09  -173.68  30.0  1
 JMY  Var_03    H012  C01  C02  N04    51.17  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
 JMY  chir_01  C06  C05  C07  C09  negativ
 JMY  chir_02  C09  O10  C06  C18  negativ
 JMY  chir_03  C18  N04  C09  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
 JMY  plan-1  C01   0.020
 JMY  plan-1  C02   0.020
 JMY  plan-1  O03   0.020
 JMY  plan-1  N04   0.020
 JMY  plan-1  C05   0.020
 JMY  plan-1  C18   0.020
 JMY  plan-2  C15   0.020
 JMY  plan-2  C17   0.020
 JMY  plan-2  O10   0.020
 JMY  plan-2  C11   0.020
 JMY  plan-2  C12   0.020
 JMY  plan-2  F13   0.020
 JMY  plan-2  C14   0.020
 JMY  plan-2  C16   0.020
 JMY  plan-2  C18   0.020
 JMY  plan-2  H151  0.020
 JMY  plan-2  H141  0.020
 JMY  plan-2  H161  0.020

