# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 19:28:38 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-(1,2-dihydroacenaphthylen-5-ylsulfanyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ccc2CCc3cccc1c23
#
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
 U5B  U5B  "2-(1,2-dihydroacenaphthylen-5-ylsulfanyl)ethanoic acid"  ligand  28  17  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U5B
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
 U5B  C14  C  CH2    0  -0.715   6.5202  -4.2976  6.0578
 U5B  C11  C  CR56   0   0.066   2.0002  -7.1072  6.7326
 U5B  C10  C  CR16   0  -0.358   3.3087  -7.1804  7.1169
 U5B  C12  C  C      0   0.079   1.6071  -6.0214  5.9318
 U5B  C01  C  CH2    0  -0.510   0.8058  -7.9892  6.9920
 U5B  C02  C  CH2    0  -0.511  -0.3694  -7.2946  6.2487
 U5B  C03  C  CR56   0   0.081   0.2400  -6.0716  5.6113
 U5B  C04  C  CR16   0  -0.368  -0.2955  -5.0809  4.8328
 U5B  C05  C  CR16   0  -0.231   0.5536  -4.0439  4.3806
 U5B  C06  C  CR16   0  -0.372   1.8917  -3.9951  4.6957
 U5B  C07  C  CR66   0   0.212   2.4709  -5.0057  5.5001
 U5B  C08  C  CR6    0  -0.202   3.8343  -5.1006  5.9186
 U5B  C09  C  CR16   0  -0.273   4.2136  -6.1712  6.7037
 U5B  C15  C  C      0   0.444   7.5777  -3.2420  5.6568
 U5B  O16  O  O      0  -0.586   7.1732  -2.2604  5.0103
 U5B  O17  O  OC    -1  -0.597   8.7328  -3.4961  6.0353
 U5B  S13  S  S2     0   0.014   4.9160  -3.8139  5.3880
 U5B  H1   H  HCH2   0   0.271   6.8100  -5.2795  5.6768
 U5B  H2   H  HCH2   0   0.272   6.4691  -4.3717  7.1466
 U5B  H5   H  HCH2   0   0.259  -1.1733  -7.0224  6.9352
 U5B  H6   H  HCR6   0   0.247  -1.3432  -5.0746  4.5581
 U5B  H7   H  HCR6   0   0.253   0.1333  -3.2601  3.7631
 U5B  H8   H  HCR6   0   0.248   2.4917  -3.1763  4.3188
 U5B  H9   H  HCR6   0   0.260   5.2403  -6.2621  7.0303
 U5B  H11  H  HCH2   0   0.257   0.9700  -9.0019  6.6190
 U5B  H12  H  HCH2   0   0.259  -0.8143  -7.9512  5.4989
 U5B  H3   H  HCR6   0   0.245   3.6786  -7.9906  7.7335
 U5B  H4   H  HCH2   0   0.257   0.6032  -8.0829  8.0604

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
 U5B  C05  C06  aromatic  1.376  0.020  1.376
 U5B  C05  C04  aromatic  1.414  0.020  1.414
 U5B  C06  C07  aromatic  1.416  0.020  1.416
 U5B  C04  C03  aromatic  1.369  0.020  1.369
 U5B  O16  C15  deloc     1.243  0.020  1.243
 U5B  C15  O17  deloc     1.242  0.020  1.242
 U5B  C15  C14  single    1.547  0.020  1.547
 U5B  C07  C12  aromatic  1.401  0.020  1.401
 U5B  C07  C08  aromatic  1.429  0.020  1.429
 U5B  C03  C12  aromatic  1.405  0.020  1.405
 U5B  C03  C02  single    1.508  0.020  1.508
 U5B  S13  C14  single    1.804  0.020  1.804
 U5B  S13  C08  single    1.763  0.020  1.763
 U5B  C12  C11  aromatic  1.405  0.020  1.405
 U5B  C08  C09  aromatic  1.381  0.020  1.381
 U5B  C02  C01  single    1.554  0.020  1.554
 U5B  C11  C01  single    1.507  0.020  1.507
 U5B  C11  C10  aromatic  1.366  0.020  1.366
 U5B  C09  C10  aromatic  1.417  0.020  1.417
 U5B  C14  H1   single    0.970  0.020  1.090
 U5B  C14  H2   single    0.970  0.020  1.090
 U5B  C10  H3   single    0.930  0.020  1.080
 U5B  C01  H4   single    0.970  0.020  1.090
 U5B  C02  H5   single    0.970  0.020  1.090
 U5B  C04  H6   single    0.930  0.020  1.080
 U5B  C05  H7   single    0.930  0.020  1.080
 U5B  C06  H8   single    0.930  0.020  1.080
 U5B  C09  H9   single    0.930  0.020  1.080
 U5B  C01  H11  single    0.970  0.020  1.090
 U5B  C02  H12  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
 U5B  H2   C14  H1   107.40  3.000
 U5B  H2   C14  S13  110.28  3.000
 U5B  H1   C14  S13  110.33  3.000
 U5B  H2   C14  C15  109.67  3.000
 U5B  H1   C14  C15  109.97  3.000
 U5B  S13  C14  C15  109.18  3.000
 U5B  C01  C11  C12  109.19  3.000
 U5B  C01  C11  C10  132.80  3.000
 U5B  C12  C11  C10  118.02  3.000
 U5B  H3   C10  C09  118.73  3.000
 U5B  H3   C10  C11  121.83  3.000
 U5B  C09  C10  C11  119.44  3.000
 U5B  C07  C12  C03  123.73  3.000
 U5B  C03  C12  C11  112.00  3.000
 U5B  C07  C12  C11  124.27  3.000
 U5B  H11  C01  H4   106.42  3.000
 U5B  H11  C01  C02  111.41  3.000
 U5B  H4   C01  C02  111.47  3.000
 U5B  H11  C01  C11  111.40  3.000
 U5B  H4   C01  C11  111.46  3.000
 U5B  C02  C01  C11  104.79  3.000
 U5B  H12  C02  H5   106.37  3.000
 U5B  H12  C02  C03  111.24  3.000
 U5B  H5   C02  C03  111.18  3.000
 U5B  H12  C02  C01  111.58  3.000
 U5B  H5   C02  C01  111.56  3.000
 U5B  C03  C02  C01  105.01  3.000
 U5B  C04  C03  C02  132.01  3.000
 U5B  C02  C03  C12  109.02  3.000
 U5B  C04  C03  C12  118.98  3.000
 U5B  H6   C04  C05  119.70  3.000
 U5B  H6   C04  C03  121.78  3.000
 U5B  C05  C04  C03  118.52  3.000
 U5B  H7   C05  C06  118.85  3.000
 U5B  H7   C05  C04  118.68  3.000
 U5B  C06  C05  C04  122.46  3.000
 U5B  H8   C06  C07  120.73  3.000
 U5B  H8   C06  C05  119.08  3.000
 U5B  C07  C06  C05  120.19  3.000
 U5B  C08  C07  C06  127.16  3.000
 U5B  C08  C07  C12  116.72  3.000
 U5B  C06  C07  C12  116.12  3.000
 U5B  S13  C08  C09  124.65  3.000
 U5B  C09  C08  C07  118.68  3.000
 U5B  S13  C08  C07  116.66  3.000
 U5B  H9   C09  C08  119.85  3.000
 U5B  H9   C09  C10  117.29  3.000
 U5B  C08  C09  C10  122.86  3.000
 U5B  O17  C15  O16  128.52  3.000
 U5B  O17  C15  C14  114.66  3.000
 U5B  O16  C15  C14  116.82  3.000
 U5B  C08  S13  C14  103.78  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
 U5B  CONST_01  C06  C07  C12  C11   180.00   0.0  0
 U5B  CONST_02  C08  C07  C12  C11     0.00   0.0  0
 U5B  CONST_03  C04  C03  C12  C11   180.00   0.0  0
 U5B  CONST_04  C03  C02  C01  C11     0.00   0.0  0
 U5B  CONST_05  C08  C09  C10  C11     0.00   0.0  0
 U5B  CONST_06  C07  C12  C11  C10     0.00   0.0  0
 U5B  CONST_07  C03  C12  C11  C10   180.00   0.0  0
 U5B  CONST_08  C07  C08  C09  C10     0.00   0.0  0
 U5B  CONST_09  C05  C06  C07  C12     0.00   0.0  0
 U5B  CONST_10  C09  C08  C07  C12     0.00   0.0  0
 U5B  CONST_11  C05  C04  C03  C12     0.00   0.0  0
 U5B  CONST_12  C09  C10  C11  C12     0.00   0.0  0
 U5B  CONST_13  C06  C05  C04  C03     0.00   0.0  0
 U5B  CONST_14  C06  C07  C12  C03     0.00   0.0  0
 U5B  CONST_15  C08  C07  C12  C03   180.00   0.0  0
 U5B  CONST_16  C07  C06  C05  C04     0.00   0.0  0
 U5B  CONST_17  C07  C12  C03  C04     0.00   0.0  0
 U5B  CONST_18  C08  C07  C06  C05   180.00   0.0  0
 U5B  CONST_19  C09  C08  C07  C06   180.00   0.0  0
 U5B  CONST_20  S13  C08  C09  C10   180.00   0.0  0
 U5B  CONST_21  S13  C08  C07  C12   180.00   0.0  0
 U5B  CONST_22  S13  C08  C07  C06     0.00   0.0  0
 U5B  CONST_23  H9   C09  C10  C11   180.00   0.0  0
 U5B  CONST_24  H8   C06  C07  C12   180.00   0.0  0
 U5B  CONST_25  H6   C04  C03  C12   180.00   0.0  0
 U5B  CONST_26  H3   C10  C11  C12   180.00   0.0  0
 U5B  CONST_27  H3   C10  C11  C01     0.00   0.0  0
 U5B  CONST_28  H6   C04  C03  C02     0.00   0.0  0
 U5B  CONST_29  H7   C05  C04  C03   180.00   0.0  0
 U5B  CONST_30  H8   C06  C05  C04   180.00   0.0  0
 U5B  CONST_31  H6   C04  C05  C06   180.00   0.0  0
 U5B  CONST_32  H7   C05  C06  C07   180.00   0.0  0
 U5B  CONST_33  H9   C09  C08  C07   180.00   0.0  0
 U5B  CONST_34  H8   C06  C07  C08     0.00   0.0  0
 U5B  CONST_35  H3   C10  C09  C08   180.00   0.0  0
 U5B  Var_01    H5   C02  C01  C11  -120.18  30.0  1
 U5B  Var_02    H12  C02  C01  C11   120.98  30.0  1
 U5B  Var_03    H4   C01  C11  C10    59.10  30.0  1
 U5B  Var_04    H11  C01  C11  C10   -59.61  30.0  1
 U5B  Var_05    H5   C02  C03  C12   120.43  30.0  1
 U5B  Var_06    H12  C02  C03  C12  -121.21  30.0  1
 U5B  Var_07    H4   C01  C11  C12  -120.95  30.0  1
 U5B  Var_08    H11  C01  C11  C12   120.35  30.0  1
 U5B  Var_09    H4   C01  C02  C03   121.06  30.0  1
 U5B  Var_10    H11  C01  C02  C03  -120.23  30.0  1
 U5B  Var_11    H5   C02  C03  C04   -59.41  30.0  1
 U5B  Var_12    H12  C02  C03  C04    58.95  30.0  1
 U5B  Var_13    C07  C08  S13  C14  -178.43  30.0  2
 U5B  Var_14    C09  C08  S13  C14     1.88  30.0  2
 U5B  Var_15    C15  C14  S13  C08   179.82  30.0  3
 U5B  Var_16    H1   C14  S13  C08    58.85  30.0  3
 U5B  Var_17    H2   C14  S13  C08   -59.62  30.0  3
 U5B  Var_18    S13  C14  C15  O16     2.14  30.0  3
 U5B  Var_19    S13  C14  C15  O17  -178.05  30.0  3
 U5B  Var_20    H1   C14  C15  O16   123.32  30.0  3
 U5B  Var_21    H2   C14  C15  O16  -118.80  30.0  3
 U5B  Var_22    H1   C14  C15  O17   -56.87  30.0  3
 U5B  Var_23    H2   C14  C15  O17    61.02  30.0  3

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
 U5B  plan-1  C14  0.020
 U5B  plan-1  C15  0.020
 U5B  plan-1  O16  0.020
 U5B  plan-1  O17  0.020
 U5B  plan-2  C11  0.020
 U5B  plan-2  C10  0.020
 U5B  plan-2  C12  0.020
 U5B  plan-2  C01  0.020
 U5B  plan-2  C02  0.020
 U5B  plan-2  C03  0.020
 U5B  plan-2  C04  0.020
 U5B  plan-2  C05  0.020
 U5B  plan-2  C06  0.020
 U5B  plan-2  C07  0.020
 U5B  plan-2  C08  0.020
 U5B  plan-2  C09  0.020
 U5B  plan-2  S13  0.020
 U5B  plan-2  H6   0.020
 U5B  plan-2  H7   0.020
 U5B  plan-2  H8   0.020
 U5B  plan-2  H9   0.020
 U5B  plan-2  H3   0.020

