# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:06:50 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: {[(2,7-dichloro-9H-fluoren-9-ylidene)amino]oxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CON=C1c2cc(Cl)ccc2c3ccc(Cl)cc13
#
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
 5JW  5JW  '{[(2,7-dichloro-9H-fluoren-9-ylidene)amino]oxy}acetic acid'  ligand  30  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5JW
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
 5JW  CL1  CL  CL    0  -0.117  -3.7041   3.0596  -0.0075
 5JW  C16  C   CR6   0  -0.042  -2.0417   2.5735  -0.0082
 5JW  C15  C   CR16  0  -0.247  -1.7440   1.2153  -0.0050
 5JW  C17  C   CR16  0  -0.198  -1.0544   3.5491  -0.0117
 5JW  C18  C   CR16  0  -0.349   0.2842   3.1756  -0.0116
 5JW  C12  C   CR56  0   0.102   0.6052   1.8310  -0.0084
 5JW  C02  C   CR56  0   0.128   1.9089   1.1680  -0.0083
 5JW  C01  C   CR16  0  -0.351   3.1945   1.6804  -0.0125
 5JW  C06  C   CR16  0  -0.202   4.2676   0.7978  -0.0124
 5JW  C13  C   CR56  0   0.033  -0.4060   0.8536  -0.0049
 5JW  C14  C   CR5   0   0.121   0.2508  -0.4654  -0.0013
 5JW  C03  C   CR56  0   0.021   1.6996  -0.2150  -0.0044
 5JW  C04  C   CR16  0  -0.249   2.7548  -1.1068  -0.0044
 5JW  C05  C   CR6   0  -0.048   4.0373  -0.5735  -0.0086
 5JW  CL2  CL  CL    0  -0.117   5.3927  -1.6519  -0.0104
 5JW  N14  N   N     0  -0.084  -0.2091  -1.6534   0.0023
 5JW  O29  O   O2    0  -0.380  -1.5543  -1.6974   0.0039
 5JW  CB5  C   CH2   0  -0.232  -2.0104  -3.0304   0.0054
 5JW  CA1  C   C     0   0.497  -3.5171  -2.9785  -0.0031
 5JW  OA2  O   OH1   0  -0.588  -4.0181  -4.2026   0.0208
 5JW  OA3  O   O     0  -0.421  -4.1690  -1.9697  -0.0304
 5JW  H1   H   HCR6  0   0.285  -2.5389   0.4849  -0.0026
 5JW  H2   H   HCR6  0   0.290  -1.3244   4.5963  -0.0131
 5JW  H3   H   HCR6  0   0.267   1.0524   3.9379  -0.0140
 5JW  H4   H   HCR6  0   0.264   3.3765   2.7471  -0.0156
 5JW  H5   H   HCR6  0   0.288   5.2807   1.1760  -0.0145
 5JW  H6   H   HCR6  0   0.280   2.5939  -2.1767  -0.0025
 5JW  H7   H   HCH2  0   0.280  -1.6589  -3.5738  -0.8777
 5JW  H8   H   HCH2  0   0.279  -1.6639  -3.5712   0.8919
 5JW  H9   H   HOH1  0   0.490  -4.9868  -4.1703   0.0079

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
 5JW  OA3  CA1  double    1.201  0.020  1.201
 5JW  OA2  CA1  single    1.323  0.020  1.323
 5JW  CA1  CB5  single    1.508  0.020  1.508
 5JW  CB5  O29  single    1.409  0.020  1.409
 5JW  O29  N14  single    1.346  0.020  1.346
 5JW  N14  C14  double    1.274  0.020  1.274
 5JW  C14  C03  single    1.470  0.020  1.470
 5JW  C14  C13  single    1.473  0.020  1.473
 5JW  C04  C03  aromatic  1.382  0.020  1.382
 5JW  C04  C05  aromatic  1.389  0.020  1.389
 5JW  C15  C13  aromatic  1.386  0.020  1.386
 5JW  C15  C16  aromatic  1.391  0.020  1.391
 5JW  C03  C02  aromatic  1.399  0.020  1.399
 5JW  C13  C12  aromatic  1.406  0.020  1.406
 5JW  CL1  C16  single    1.732  0.020  1.732
 5JW  CL2  C05  single    1.732  0.020  1.732
 5JW  C05  C06  aromatic  1.391  0.020  1.391
 5JW  C16  C17  aromatic  1.388  0.020  1.388
 5JW  C02  C12  aromatic  1.463  0.020  1.463
 5JW  C02  C01  aromatic  1.384  0.020  1.384
 5JW  C12  C18  aromatic  1.382  0.020  1.382
 5JW  C06  C01  aromatic  1.389  0.020  1.389
 5JW  C17  C18  aromatic  1.390  0.020  1.390
 5JW  C15  H1   single    0.930  0.020  1.080
 5JW  C17  H2   single    0.930  0.020  1.080
 5JW  C18  H3   single    0.930  0.020  1.080
 5JW  C01  H4   single    0.930  0.020  1.080
 5JW  C06  H5   single    0.930  0.020  1.080
 5JW  C04  H6   single    0.930  0.020  1.080
 5JW  CB5  H7   single    0.970  0.020  1.090
 5JW  CB5  H8   single    0.970  0.020  1.090
 5JW  OA2  H9   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
 5JW  C17  C16  C15  122.30  3.000
 5JW  C17  C16  CL1  119.04  3.000
 5JW  C15  C16  CL1  118.66  3.000
 5JW  H1   C15  C13  122.30  3.000
 5JW  H1   C15  C16  120.22  3.000
 5JW  C13  C15  C16  117.49  3.000
 5JW  H2   C17  C18  120.05  3.000
 5JW  H2   C17  C16  120.20  3.000
 5JW  C18  C17  C16  119.75  3.000
 5JW  H3   C18  C12  121.35  3.000
 5JW  H3   C18  C17  119.63  3.000
 5JW  C12  C18  C17  119.02  3.000
 5JW  C13  C12  C02  109.02  3.000
 5JW  C02  C12  C18  130.38  3.000
 5JW  C13  C12  C18  120.60  3.000
 5JW  C03  C02  C01  120.34  3.000
 5JW  C01  C02  C12  131.32  3.000
 5JW  C03  C02  C12  108.35  3.000
 5JW  H4   C01  C06  119.75  3.000
 5JW  H4   C01  C02  121.41  3.000
 5JW  C06  C01  C02  118.84  3.000
 5JW  H5   C06  C05  120.00  3.000
 5JW  H5   C06  C01  120.09  3.000
 5JW  C05  C06  C01  119.90  3.000
 5JW  C14  C13  C12  107.55  3.000
 5JW  C12  C13  C15  120.85  3.000
 5JW  C14  C13  C15  131.60  3.000
 5JW  N14  C14  C03  120.97  3.000
 5JW  C03  C14  C13  106.67  3.000
 5JW  N14  C14  C13  132.37  3.000
 5JW  C04  C03  C14  129.99  3.000
 5JW  C04  C03  C02  121.60  3.000
 5JW  C14  C03  C02  108.41  3.000
 5JW  H6   C04  C05  121.13  3.000
 5JW  H6   C04  C03  121.66  3.000
 5JW  C05  C04  C03  117.22  3.000
 5JW  CL2  C05  C04  118.92  3.000
 5JW  CL2  C05  C06  118.97  3.000
 5JW  C04  C05  C06  122.11  3.000
 5JW  O29  N14  C14  113.03  3.000
 5JW  CB5  O29  N14  110.76  3.000
 5JW  H8   CB5  H7   107.84  3.000
 5JW  H8   CB5  CA1  109.75  3.000
 5JW  H7   CB5  CA1  109.47  3.000
 5JW  H8   CB5  O29  111.46  3.000
 5JW  H7   CB5  O29  111.40  3.000
 5JW  CA1  CB5  O29  106.92  3.000
 5JW  OA3  CA1  OA2  124.88  3.000
 5JW  OA2  CA1  CB5  110.28  3.000
 5JW  OA3  CA1  CB5  124.84  3.000
 5JW  H9   OA2  CA1  110.33  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
 5JW  CONST_01  C12  C13  C15  C16     0.00   0.0  0
 5JW  CONST_02  C12  C18  C17  C16     0.00   0.0  0
 5JW  CONST_03  C02  C12  C13  C15   180.00   0.0  0
 5JW  CONST_04  C18  C12  C13  C15     0.00   0.0  0
 5JW  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 5JW  CONST_06  C13  C15  C16  C17     0.00   0.0  0
 5JW  CONST_07  C13  C12  C18  C17     0.00   0.0  0
 5JW  CONST_08  C02  C12  C18  C17   180.00   0.0  0
 5JW  CONST_09  C03  C02  C12  C18   180.00   0.0  0
 5JW  CONST_10  C01  C02  C12  C18     0.00   0.0  0
 5JW  CONST_11  C04  C03  C02  C12   180.00   0.0  0
 5JW  CONST_12  C06  C01  C02  C12   180.00   0.0  0
 5JW  CONST_13  C05  C04  C03  C02     0.00   0.0  0
 5JW  CONST_14  C05  C06  C01  C02     0.00   0.0  0
 5JW  CONST_15  C04  C03  C02  C01     0.00   0.0  0
 5JW  CONST_16  C13  C12  C02  C01   180.00   0.0  0
 5JW  CONST_17  C04  C05  C06  C01     0.00   0.0  0
 5JW  CONST_18  C03  C04  C05  C06     0.00   0.0  0
 5JW  CONST_19  C03  C02  C01  C06     0.00   0.0  0
 5JW  CONST_20  C03  C02  C12  C13     0.00   0.0  0
 5JW  CONST_21  C13  C15  C16  CL1   180.00   0.0  0
 5JW  CONST_22  C18  C17  C16  CL1   180.00   0.0  0
 5JW  CONST_23  CL2  C05  C06  C01   180.00   0.0  0
 5JW  CONST_24  CL2  C05  C04  C03   180.00   0.0  0
 5JW  CONST_25  H3   C18  C17  C16   180.00   0.0  0
 5JW  CONST_26  H2   C17  C16  C15   180.00   0.0  0
 5JW  CONST_27  H1   C15  C16  C17   180.00   0.0  0
 5JW  CONST_28  H4   C01  C02  C12     0.00   0.0  0
 5JW  CONST_29  H6   C04  C03  C02   180.00   0.0  0
 5JW  CONST_30  H5   C06  C01  C02   180.00   0.0  0
 5JW  CONST_31  H9   OA2  CA1  CB5   180.00   0.0  0
 5JW  Var_01    N14  C14  C13  C15     0.02  30.0  1
 5JW  Var_02    CA1  CB5  O29  N14  -179.59  30.0  2
 5JW  Var_03    OA3  CA1  CB5  O29     1.20  30.0  2

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
 5JW  plan-1  CB5  0.020
 5JW  plan-1  CA1  0.020
 5JW  plan-1  OA2  0.020
 5JW  plan-1  OA3  0.020
 5JW  plan-1  H9   0.020
 5JW  plan-2  CL1  0.020
 5JW  plan-2  C16  0.020
 5JW  plan-2  C15  0.020
 5JW  plan-2  C17  0.020
 5JW  plan-2  C18  0.020
 5JW  plan-2  C12  0.020
 5JW  plan-2  C02  0.020
 5JW  plan-2  C01  0.020
 5JW  plan-2  C06  0.020
 5JW  plan-2  C13  0.020
 5JW  plan-2  C14  0.020
 5JW  plan-2  C03  0.020
 5JW  plan-2  C04  0.020
 5JW  plan-2  C05  0.020
 5JW  plan-2  CL2  0.020
 5JW  plan-2  H1   0.020
 5JW  plan-2  H2   0.020
 5JW  plan-2  H3   0.020
 5JW  plan-2  H4   0.020
 5JW  plan-2  H5   0.020
 5JW  plan-2  H6   0.020

