# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:15:08 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-[(3S,3aS,8bS)-7-chloro-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]2Oc3ccc(Cl)cc3[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
 F8D  F8D  1-[(3S,3aS,8bS)-7-chloro-3-(hydroxymethyl)-2,3,3a,8b-tetrahydro-1H-[1]benzofuro[3,2-b]pyrrol-1-yl]ethan-1-one  ligand  32  18  .  2021-08-09  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_F8D
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
 F8D  C13   C   CR16  0  -0.209  -3.0100   1.5044   0.7110
 F8D  C17   C   CR56  0   0.031  -0.7325   0.3632  -0.3562
 F8D  C01   C   CH3   0  -0.795   1.9406  -3.0426   1.0518
 F8D  C02   C   C     0   0.526   1.1612  -2.2142   0.0620
 F8D  O03   O   O     0  -0.503   0.3882  -2.7186  -0.7436
 F8D  N04   N   NT    0  -0.442   1.3581  -0.8820   0.1007
 F8D  C05   C   CH2   0  -0.298   2.2108  -0.1413   1.0145
 F8D  C06   C   CH1   0  -0.332   2.6369   1.0643   0.1808
 F8D  C07   C   CH2   0  -0.136   3.8083   0.7535  -0.7389
 F8D  O08   O   OH1   0  -0.669   4.9290   0.4459   0.0545
 F8D  C09   C   CR15  0   0.017   1.3914   1.3664  -0.6424
 F8D  O10   O   O     0  -0.490   0.5036   2.2342   0.0804
 F8D  C11   C   CR56  0   0.400  -0.7050   1.6474   0.1652
 F8D  C12   C   CR16  0  -0.358  -1.8312   2.2405   0.7087
 F8D  C14   C   CR6   0  -0.054  -3.0385   0.2221   0.1789
 F8D  CL15  CL  CL    0  -0.138  -4.5318  -0.6655   0.1895
 F8D  C16   C   CR16  0  -0.270  -1.9028  -0.3702  -0.3611
 F8D  C18   C   CR15  0  -0.199   0.6577   0.0147  -0.8085
 F8D  H131  H   HCR6  0   0.283  -3.9094   1.9393   1.1252
 F8D  H012  H   HCH3  0   0.267   1.7262  -2.7421   2.0780
 F8D  H013  H   HCH3  0   0.270   1.6785  -4.0908   0.9346
 F8D  H011  H   HCH3  0   0.266   3.0159  -2.9368   0.9015
 F8D  H051  H   HCH2  0   0.261   1.6568   0.1721   1.9051
 F8D  H052  H   HCH2  0   0.275   3.0602  -0.7328   1.3481
 F8D  H061  H   HCH1  0   0.282   2.8990   1.9169   0.8111
 F8D  H072  H   HCH2  0   0.205   3.5534  -0.0771  -1.4122
 F8D  H071  H   HCH2  0   0.214   3.9925   1.6294  -1.3751
 F8D  H081  H   HOH1  0   0.458   5.6401   0.1630  -0.5271
 F8D  H091  H   HCR5  0   0.284   1.6162   1.8399  -1.6011
 F8D  H121  H   HCR6  0   0.276  -1.8060   3.2414   1.1182
 F8D  H161  H   HCR6  0   0.280  -1.9335  -1.3707  -0.7687
 F8D  H181  H   HCR5  0   0.299   0.6946  -0.3652  -1.8295

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
 F8D  O08  C07   single    1.407  0.020  1.407
 F8D  C07  C06   single    1.521  0.020  1.521
 F8D  O03  C02   double    1.225  0.020  1.225
 F8D  C06  C05   single    1.526  0.020  1.526
 F8D  C06  C09   single    1.523  0.020  1.523
 F8D  C05  N04   single    1.453  0.020  1.453
 F8D  C02  N04   single    1.347  0.020  1.347
 F8D  C02  C01   single    1.508  0.020  1.508
 F8D  N04  C18   single    1.456  0.020  1.456
 F8D  C09  C18   single    1.547  0.020  1.547
 F8D  C09  O10   single    1.437  0.020  1.437
 F8D  C18  C17   single    1.503  0.020  1.503
 F8D  O10  C11   single    1.346  0.020  1.346
 F8D  C17  C11   aromatic  1.386  0.020  1.386
 F8D  C17  C16   aromatic  1.381  0.020  1.381
 F8D  C11  C12   aromatic  1.384  0.020  1.384
 F8D  C16  C14   aromatic  1.390  0.020  1.390
 F8D  C12  C13   aromatic  1.390  0.020  1.390
 F8D  C14  C13   aromatic  1.389  0.020  1.389
 F8D  C14  CL15  single    1.737  0.020  1.737
 F8D  C13  H131  single    0.930  0.020  1.080
 F8D  C01  H012  single    0.970  0.020  1.090
 F8D  C01  H013  single    0.970  0.020  1.090
 F8D  C01  H011  single    0.970  0.020  1.090
 F8D  C05  H051  single    0.970  0.020  1.090
 F8D  C05  H052  single    0.970  0.020  1.090
 F8D  C06  H061  single    0.970  0.020  1.090
 F8D  C07  H072  single    0.970  0.020  1.090
 F8D  C07  H071  single    0.970  0.020  1.090
 F8D  O08  H081  single    0.850  0.020  0.980
 F8D  C09  H091  single    0.970  0.020  1.090
 F8D  C12  H121  single    0.930  0.020  1.080
 F8D  C16  H161  single    0.930  0.020  1.080
 F8D  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
 F8D  H131  C13  C14   120.07  3.000
 F8D  H131  C13  C12   119.54  3.000
 F8D  C14   C13  C12   120.39  3.000
 F8D  C18   C17  C16   131.27  3.000
 F8D  C16   C17  C11   120.67  3.000
 F8D  C18   C17  C11   108.04  3.000
 F8D  H011  C01  H013  108.44  3.000
 F8D  H011  C01  H012  107.26  3.000
 F8D  H013  C01  H012  108.65  3.000
 F8D  H011  C01  C02   111.46  3.000
 F8D  H013  C01  C02   109.54  3.000
 F8D  H012  C01  C02   111.39  3.000
 F8D  N04   C02  O03   121.22  3.000
 F8D  N04   C02  C01   116.67  3.000
 F8D  O03   C02  C01   122.11  3.000
 F8D  C18   N04  C05   111.16  3.000
 F8D  C18   N04  C02   121.37  3.000
 F8D  C05   N04  C02   127.45  3.000
 F8D  H052  C05  H051  107.54  3.000
 F8D  H052  C05  C06   112.28  3.000
 F8D  H051  C05  C06   111.07  3.000
 F8D  H052  C05  N04   111.97  3.000
 F8D  H051  C05  N04   111.14  3.000
 F8D  C06   C05  N04   102.88  3.000
 F8D  H061  C06  C09   110.69  3.000
 F8D  H061  C06  C07   108.88  3.000
 F8D  C09   C06  C07   110.08  3.000
 F8D  H061  C06  C05   111.61  3.000
 F8D  C09   C06  C05   102.92  3.000
 F8D  C07   C06  C05   112.57  3.000
 F8D  H071  C07  H072  106.66  3.000
 F8D  H071  C07  O08   111.55  3.000
 F8D  H072  C07  O08   111.40  3.000
 F8D  H071  C07  C06   108.45  3.000
 F8D  H072  C07  C06   110.25  3.000
 F8D  O08   C07  C06   108.48  3.000
 F8D  H081  O08  C07   108.20  3.000
 F8D  H091  C09  C18   112.46  3.000
 F8D  H091  C09  O10   107.87  3.000
 F8D  C18   C09  O10   106.78  3.000
 F8D  H091  C09  C06   113.08  3.000
 F8D  O10   C09  C06   110.68  3.000
 F8D  C18   C09  C06   105.82  3.000
 F8D  C11   O10  C09   108.86  3.000
 F8D  C12   C11  O10   124.64  3.000
 F8D  C12   C11  C17   121.91  3.000
 F8D  O10   C11  C17   113.45  3.000
 F8D  H121  C12  C11   121.75  3.000
 F8D  H121  C12  C13   120.61  3.000
 F8D  C11   C12  C13   117.64  3.000
 F8D  C16   C14  CL15  119.14  3.000
 F8D  CL15  C14  C13   119.15  3.000
 F8D  C16   C14  C13   121.71  3.000
 F8D  H161  C16  C14   121.18  3.000
 F8D  H161  C16  C17   121.13  3.000
 F8D  C14   C16  C17   117.69  3.000
 F8D  H181  C18  C09   112.89  3.000
 F8D  H181  C18  N04   110.72  3.000
 F8D  C09   C18  N04   104.05  3.000
 F8D  H181  C18  C17   113.21  3.000
 F8D  C09   C18  C17   101.76  3.000
 F8D  N04   C18  C17   113.56  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
 F8D  CONST_01  C17   C11  C12  C13     0.00   0.0  0
 F8D  CONST_02  C17   C16  C14  C13     0.00   0.0  0
 F8D  CONST_03  C14   C16  C17  C11     0.00   0.0  0
 F8D  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 F8D  CONST_05  C16   C17  C11  C12     0.00   0.0  0
 F8D  CONST_06  C16   C14  C13  C12     0.00   0.0  0
 F8D  CONST_07  CL15  C14  C16  C17   180.00   0.0  0
 F8D  CONST_08  CL15  C14  C13  C12   180.00   0.0  0
 F8D  CONST_09  H161  C16  C14  C13   180.00   0.0  0
 F8D  CONST_10  H121  C12  C11  C17   180.00   0.0  0
 F8D  CONST_11  H131  C13  C12  C11   180.00   0.0  0
 F8D  CONST_12  C05   N04  C02  C01     0.00   0.0  0
 F8D  CONST_13  C18   N04  C02  C01   180.00   0.0  0
 F8D  CONST_14  C05   N04  C02  O03   180.00   0.0  0
 F8D  CONST_15  C18   N04  C02  O03     0.00   0.0  0
 F8D  Var_01    C18   N04  C05  C06   -31.70  30.0  1
 F8D  Var_02    C12   C11  O10  C09  -175.02  30.0  1
 F8D  Var_03    H012  C01  C02  N04    58.52  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
 F8D  chir_01  C06  C07  C05  C09  positiv
 F8D  chir_02  C09  O10  C06  C18  negativ
 F8D  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
 F8D  plan-1  C01   0.020
 F8D  plan-1  C02   0.020
 F8D  plan-1  O03   0.020
 F8D  plan-1  N04   0.020
 F8D  plan-1  C05   0.020
 F8D  plan-1  C18   0.020
 F8D  plan-2  C13   0.020
 F8D  plan-2  C17   0.020
 F8D  plan-2  O10   0.020
 F8D  plan-2  C11   0.020
 F8D  plan-2  C12   0.020
 F8D  plan-2  C14   0.020
 F8D  plan-2  CL15  0.020
 F8D  plan-2  C16   0.020
 F8D  plan-2  C18   0.020
 F8D  plan-2  H131  0.020
 F8D  plan-2  H121  0.020
 F8D  plan-2  H161  0.020

