# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:32:16 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc2ccccc2c(Cc3c(O)c(cc4ccccc34)C(O)=O)c1O
#
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
 JBR  JBR  "4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid"  ligand  43  29  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JBR
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
 JBR  C02  C  C      0   0.316  -10.1476  -28.7171  30.0605
 JBR  C03  C  C      0   0.008  -10.2068  -27.6678  29.1554
 JBR  C04  C  CR6    0   0.119   -9.4531  -27.7568  27.9532
 JBR  C05  C  CR16   0  -0.343   -9.3485  -26.6902  27.0231
 JBR  C06  C  CR16   0  -0.250   -8.6226  -26.8155  25.8685
 JBR  C07  C  CR16   0  -0.277   -7.9502  -28.0143  25.5600
 JBR  C08  C  CR16   0  -0.303   -8.0051  -29.0544  26.4454
 JBR  C09  C  CR6    0   0.097   -8.7366  -28.9493  27.6510
 JBR  C10  C  C1     0  -0.386   -8.7488  -30.0102  28.5773
 JBR  C11  C  C      0  -0.258   -9.4193  -29.9132  29.7625
 JBR  C12  C  C      0   0.496   -9.3976  -31.0578  30.7524
 JBR  C15  C  CH2    0  -0.663  -11.0318  -26.4403  29.4935
 JBR  C16  C  CR6    0   0.021  -12.1238  -26.0939  28.4973
 JBR  C17  C  CR66   0   0.092  -13.1718  -27.0311  28.2414
 JBR  C18  C  CR16   0  -0.351  -13.3465  -28.2162  28.9985
 JBR  C19  C  CR16   0  -0.257  -14.3556  -29.1010  28.7160
 JBR  C20  C  CR16   0  -0.272  -15.2496  -28.8603  27.6564
 JBR  C21  C  CR16   0  -0.312  -15.1234  -27.7135  26.9208
 JBR  C22  C  CR66   0   0.102  -14.1036  -26.7769  27.2015
 JBR  C23  C  CR16   0  -0.391  -13.9989  -25.5772  26.4640
 JBR  C24  C  CR6    0  -0.108  -13.0783  -24.6217  26.7797
 JBR  C25  C  C      0   0.367  -13.0814  -23.2984  26.0192
 JBR  C28  C  CR6    0   0.239  -12.1457  -24.8894  27.8194
 JBR  O01  O  OH1    0  -0.668  -10.7905  -28.6439  31.2239
 JBR  O13  O  O      0  -0.533   -8.7583  -32.0744  30.4838
 JBR  O14  O  OC    -1  -0.624  -10.0661  -30.8689  31.8189
 JBR  O26  O  O      0  -0.593  -12.9431  -23.3843  24.7857
 JBR  O27  O  OC    -1  -0.589  -13.2669  -22.2751  26.6991
 JBR  O29  O  OH1    0  -0.624  -11.2405  -23.9026  28.0134
 JBR  H1   H  HCR6   0   0.243   -9.8191  -25.7419  27.2269
 JBR  H2   H  HCR6   0   0.249   -8.5609  -25.9762  25.1873
 JBR  H3   H  HCR6   0   0.247   -7.3871  -28.1006  24.6400
 JBR  H4   H  HCR6   0   0.248   -7.4789  -29.9792  26.2393
 JBR  H5   H  H      0   0.246   -8.2046  -30.9173  28.3432
 JBR  H6   H  HCH2   0   0.253  -10.3377  -25.6066  29.6363
 JBR  H7   H  HCH2   0   0.286  -11.4784  -26.5762  30.4788
 JBR  H8   H  HCR6   0   0.267  -12.7013  -28.4234  29.8389
 JBR  H9   H  HCR6   0   0.246  -14.4679  -29.9914  29.3217
 JBR  H10  H  HCR6   0   0.246  -16.0364  -29.5706  27.4378
 JBR  H11  H  HCR6   0   0.246  -15.8159  -27.5002  26.1145
 JBR  H12  H  HCR6   0   0.242  -14.6973  -25.4084  25.6519
 JBR  H13  H  HOH1   0   0.460  -10.6025  -29.5666  31.6690
 JBR  H16  H  HOH1   0   0.467  -10.6858  -24.0775  28.7804

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
 JBR  O26  C25  deloc     1.244  0.020  1.244
 JBR  C07  C06  aromatic  1.409  0.020  1.409
 JBR  C07  C08  aromatic  1.367  0.020  1.367
 JBR  C06  C05  aromatic  1.370  0.020  1.370
 JBR  C25  O27  deloc     1.242  0.020  1.242
 JBR  C25  C24  single    1.526  0.020  1.526
 JBR  C08  C09  aromatic  1.414  0.020  1.414
 JBR  C23  C24  aromatic  1.364  0.020  1.364
 JBR  C23  C22  aromatic  1.412  0.020  1.412
 JBR  C21  C22  aromatic  1.413  0.020  1.413
 JBR  C21  C20  aromatic  1.368  0.020  1.368
 JBR  C24  C28  aromatic  1.422  0.020  1.422
 JBR  C05  C04  aromatic  1.419  0.020  1.419
 JBR  C22  C17  aromatic  1.419  0.020  1.419
 JBR  C20  C19  aromatic  1.407  0.020  1.407
 JBR  C09  C04  aromatic  1.424  0.020  1.424
 JBR  C09  C10  aromatic  1.408  0.020  1.408
 JBR  C28  O29  single    1.353  0.020  1.353
 JBR  C28  C16  aromatic  1.382  0.020  1.382
 JBR  C04  C03  aromatic  1.422  0.020  1.422
 JBR  C17  C16  aromatic  1.429  0.020  1.429
 JBR  C17  C18  aromatic  1.417  0.020  1.417
 JBR  C19  C18  aromatic  1.371  0.020  1.371
 JBR  C16  C15  single    1.518  0.020  1.518
 JBR  C10  C11  aromatic  1.365  0.020  1.365
 JBR  C03  C15  single    1.517  0.020  1.517
 JBR  C03  C02  aromatic  1.387  0.020  1.387
 JBR  C11  C02  aromatic  1.432  0.020  1.432
 JBR  C11  C12  single    1.513  0.020  1.513
 JBR  C02  O01  single    1.331  0.020  1.331
 JBR  O13  C12  deloc     1.231  0.020  1.231
 JBR  C12  O14  deloc     1.273  0.020  1.273
 JBR  C05  H1   single    0.930  0.020  1.080
 JBR  C06  H2   single    0.930  0.020  1.080
 JBR  C07  H3   single    0.930  0.020  1.080
 JBR  C08  H4   single    0.930  0.020  1.080
 JBR  C10  H5   single    0.930  0.020  1.080
 JBR  C15  H6   single    0.970  0.020  1.090
 JBR  C15  H7   single    0.970  0.020  1.090
 JBR  C18  H8   single    0.930  0.020  1.080
 JBR  C19  H9   single    0.930  0.020  1.080
 JBR  C20  H10  single    0.930  0.020  1.080
 JBR  C21  H11  single    0.930  0.020  1.080
 JBR  C23  H12  single    0.930  0.020  1.080
 JBR  O01  H13  single    0.850  0.020  0.980
 JBR  O29  H16  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
 JBR  O01  C02  C11  118.26  3.000
 JBR  O01  C02  C03  120.54  3.000
 JBR  C11  C02  C03  121.19  3.000
 JBR  C15  C03  C04  121.82  3.000
 JBR  C15  C03  C02  119.33  3.000
 JBR  C04  C03  C02  118.81  3.000
 JBR  C09  C04  C05  116.96  3.000
 JBR  C09  C04  C03  119.91  3.000
 JBR  C05  C04  C03  123.12  3.000
 JBR  H1   C05  C06  118.11  3.000
 JBR  H1   C05  C04  120.33  3.000
 JBR  C06  C05  C04  121.53  3.000
 JBR  H2   C06  C07  119.65  3.000
 JBR  H2   C06  C05  119.32  3.000
 JBR  C07  C06  C05  121.03  3.000
 JBR  H3   C07  C08  120.72  3.000
 JBR  H3   C07  C06  120.17  3.000
 JBR  C08  C07  C06  119.10  3.000
 JBR  H4   C08  C09  118.47  3.000
 JBR  H4   C08  C07  120.43  3.000
 JBR  C09  C08  C07  121.10  3.000
 JBR  C10  C09  C08  120.61  3.000
 JBR  C10  C09  C04  119.14  3.000
 JBR  C08  C09  C04  120.23  3.000
 JBR  H5   C10  C11  119.59  3.000
 JBR  H5   C10  C09  118.96  3.000
 JBR  C11  C10  C09  121.45  3.000
 JBR  C12  C11  C10  120.47  3.000
 JBR  C12  C11  C02  120.20  3.000
 JBR  C10  C11  C02  119.33  3.000
 JBR  O14  C12  O13  125.34  3.000
 JBR  O14  C12  C11  115.35  3.000
 JBR  O13  C12  C11  119.31  3.000
 JBR  H7   C15  H6   103.70  3.000
 JBR  H7   C15  C16  109.08  3.000
 JBR  H6   C15  C16  111.60  3.000
 JBR  H7   C15  C03  108.86  3.000
 JBR  H6   C15  C03  107.50  3.000
 JBR  C16  C15  C03  115.44  3.000
 JBR  C28  C16  C17  118.16  3.000
 JBR  C17  C16  C15  119.70  3.000
 JBR  C28  C16  C15  122.14  3.000
 JBR  C22  C17  C18  117.41  3.000
 JBR  C18  C17  C16  122.89  3.000
 JBR  C22  C17  C16  119.69  3.000
 JBR  H8   C18  C19  118.44  3.000
 JBR  H8   C18  C17  120.18  3.000
 JBR  C19  C18  C17  121.34  3.000
 JBR  H9   C19  C20  119.73  3.000
 JBR  H9   C19  C18  119.45  3.000
 JBR  C20  C19  C18  120.82  3.000
 JBR  H10  C20  C21  120.57  3.000
 JBR  H10  C20  C19  120.12  3.000
 JBR  C21  C20  C19  119.31  3.000
 JBR  H11  C21  C22  118.58  3.000
 JBR  H11  C21  C20  120.39  3.000
 JBR  C22  C21  C20  121.02  3.000
 JBR  C23  C22  C21  120.86  3.000
 JBR  C21  C22  C17  120.05  3.000
 JBR  C23  C22  C17  119.09  3.000
 JBR  H12  C23  C24  119.94  3.000
 JBR  H12  C23  C22  118.40  3.000
 JBR  C24  C23  C22  121.62  3.000
 JBR  C28  C24  C25  121.93  3.000
 JBR  C28  C24  C23  118.69  3.000
 JBR  C25  C24  C23  119.39  3.000
 JBR  O27  C25  O26  128.02  3.000
 JBR  O27  C25  C24  116.21  3.000
 JBR  O26  C25  C24  115.72  3.000
 JBR  O29  C28  C24  113.97  3.000
 JBR  O29  C28  C16  123.68  3.000
 JBR  C24  C28  C16  122.20  3.000
 JBR  H13  O01  C02  103.74  3.000
 JBR  H16  O29  C28  111.54  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
 JBR  CONST_01  C05  C04  C03  C02   180.00   0.0  0
 JBR  CONST_02  C09  C04  C03  C02     0.00   0.0  0
 JBR  CONST_03  C09  C10  C11  C02     0.00   0.0  0
 JBR  CONST_04  C06  C05  C04  C03   180.00   0.0  0
 JBR  CONST_05  C08  C09  C04  C03   180.00   0.0  0
 JBR  CONST_06  C10  C09  C04  C03     0.00   0.0  0
 JBR  CONST_07  C10  C11  C02  C03     0.00   0.0  0
 JBR  CONST_08  C07  C06  C05  C04     0.00   0.0  0
 JBR  CONST_09  C07  C08  C09  C04     0.00   0.0  0
 JBR  CONST_10  C11  C10  C09  C04     0.00   0.0  0
 JBR  CONST_11  C11  C02  C03  C04     0.00   0.0  0
 JBR  CONST_12  C08  C07  C06  C05     0.00   0.0  0
 JBR  CONST_13  C08  C09  C04  C05     0.00   0.0  0
 JBR  CONST_14  C10  C09  C04  C05   180.00   0.0  0
 JBR  CONST_15  C09  C08  C07  C06     0.00   0.0  0
 JBR  CONST_16  C09  C04  C05  C06     0.00   0.0  0
 JBR  CONST_17  C10  C09  C08  C07   180.00   0.0  0
 JBR  CONST_18  C11  C10  C09  C08   180.00   0.0  0
 JBR  CONST_19  C23  C24  C28  C16     0.00   0.0  0
 JBR  CONST_20  C23  C22  C17  C16     0.00   0.0  0
 JBR  CONST_21  C21  C22  C17  C16   180.00   0.0  0
 JBR  CONST_22  C19  C18  C17  C16   180.00   0.0  0
 JBR  CONST_23  C24  C23  C22  C17     0.00   0.0  0
 JBR  CONST_24  C20  C21  C22  C17     0.00   0.0  0
 JBR  CONST_25  C24  C28  C16  C17     0.00   0.0  0
 JBR  CONST_26  C20  C19  C18  C17     0.00   0.0  0
 JBR  CONST_27  C23  C22  C17  C18   180.00   0.0  0
 JBR  CONST_28  C21  C22  C17  C18     0.00   0.0  0
 JBR  CONST_29  C28  C16  C17  C18   180.00   0.0  0
 JBR  CONST_30  C21  C20  C19  C18     0.00   0.0  0
 JBR  CONST_31  C22  C21  C20  C19     0.00   0.0  0
 JBR  CONST_32  C22  C17  C18  C19     0.00   0.0  0
 JBR  CONST_33  C23  C22  C21  C20   180.00   0.0  0
 JBR  CONST_34  C24  C23  C22  C21   180.00   0.0  0
 JBR  CONST_35  C28  C24  C23  C22     0.00   0.0  0
 JBR  CONST_36  C28  C16  C17  C22     0.00   0.0  0
 JBR  CONST_37  C12  C11  C02  C03   180.00   0.0  0
 JBR  CONST_38  O01  C02  C03  C04   180.00   0.0  0
 JBR  CONST_39  C15  C03  C04  C05     0.00   0.0  0
 JBR  CONST_40  C15  C03  C04  C09   180.00   0.0  0
 JBR  CONST_41  C12  C11  C10  C09   180.00   0.0  0
 JBR  CONST_42  O01  C02  C11  C10   180.00   0.0  0
 JBR  CONST_43  C15  C03  C02  C11   180.00   0.0  0
 JBR  CONST_44  C24  C28  C16  C15   180.00   0.0  0
 JBR  CONST_45  C22  C17  C16  C15   180.00   0.0  0
 JBR  CONST_46  C18  C17  C16  C15     0.00   0.0  0
 JBR  CONST_47  C25  C24  C28  C16   180.00   0.0  0
 JBR  CONST_48  O29  C28  C16  C17   180.00   0.0  0
 JBR  CONST_49  C25  C24  C23  C22   180.00   0.0  0
 JBR  CONST_50  O29  C28  C24  C23   180.00   0.0  0
 JBR  CONST_51  H5   C10  C11  C02   180.00   0.0  0
 JBR  CONST_52  H1   C05  C04  C03     0.00   0.0  0
 JBR  CONST_53  H2   C06  C05  C04   180.00   0.0  0
 JBR  CONST_54  H4   C08  C09  C04   180.00   0.0  0
 JBR  CONST_55  H5   C10  C09  C04   180.00   0.0  0
 JBR  CONST_56  H3   C07  C06  C05   180.00   0.0  0
 JBR  CONST_57  H4   C08  C07  C06   180.00   0.0  0
 JBR  CONST_58  H1   C05  C06  C07   180.00   0.0  0
 JBR  CONST_59  H2   C06  C07  C08   180.00   0.0  0
 JBR  CONST_60  H5   C10  C09  C08     0.00   0.0  0
 JBR  CONST_61  H3   C07  C08  C09   180.00   0.0  0
 JBR  CONST_62  H1   C05  C04  C09   180.00   0.0  0
 JBR  CONST_63  H4   C08  C09  C10     0.00   0.0  0
 JBR  CONST_64  H8   C18  C17  C16     0.00   0.0  0
 JBR  CONST_65  H12  C23  C22  C17   180.00   0.0  0
 JBR  CONST_66  H11  C21  C22  C17   180.00   0.0  0
 JBR  CONST_67  H9   C19  C18  C17   180.00   0.0  0
 JBR  CONST_68  H10  C20  C19  C18   180.00   0.0  0
 JBR  CONST_69  H11  C21  C20  C19   180.00   0.0  0
 JBR  CONST_70  H8   C18  C19  C20   180.00   0.0  0
 JBR  CONST_71  H12  C23  C22  C21     0.00   0.0  0
 JBR  CONST_72  H9   C19  C20  C21   180.00   0.0  0
 JBR  CONST_73  H10  C20  C21  C22   180.00   0.0  0
 JBR  CONST_74  H8   C18  C17  C22   180.00   0.0  0
 JBR  CONST_75  H11  C21  C22  C23     0.00   0.0  0
 JBR  CONST_76  H12  C23  C24  C28   180.00   0.0  0
 JBR  Var_01    C16  C15  C03  C02  -122.33  30.0  2
 JBR  Var_02    C28  C16  C15  C03  -119.44  30.0  2
 JBR  Var_03    C17  C16  C15  C03    60.65  30.0  2
 JBR  Var_04    C16  C15  C03  C04    59.81  30.0  2
 JBR  Var_05    O13  C12  C11  C02  -179.47  30.0  2
 JBR  Var_06    O14  C12  C11  C02     0.55  30.0  2
 JBR  Var_07    O13  C12  C11  C10     0.67  30.0  2
 JBR  Var_08    O14  C12  C11  C10  -179.31  30.0  2
 JBR  Var_09    O26  C25  C24  C23   -58.02  30.0  2
 JBR  Var_10    O27  C25  C24  C23   119.60  30.0  2
 JBR  Var_11    O26  C25  C24  C28   122.38  30.0  2
 JBR  Var_12    O27  C25  C24  C28   -60.00  30.0  2
 JBR  Var_13    H6   C15  C03  C02   112.40  30.0  2
 JBR  Var_14    H7   C15  C03  C02     0.69  30.0  2
 JBR  Var_15    H6   C15  C03  C04   -65.45  30.0  2
 JBR  Var_16    H7   C15  C03  C04  -177.17  30.0  2
 JBR  Var_17    H6   C15  C16  C17  -176.23  30.0  2
 JBR  Var_18    H7   C15  C16  C17   -62.25  30.0  2
 JBR  Var_19    H6   C15  C16  C28     3.67  30.0  2
 JBR  Var_20    H7   C15  C16  C28   117.65  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
 JBR  plan-1  C02  0.020
 JBR  plan-1  C03  0.020
 JBR  plan-1  C04  0.020
 JBR  plan-1  C05  0.020
 JBR  plan-1  C06  0.020
 JBR  plan-1  C07  0.020
 JBR  plan-1  C08  0.020
 JBR  plan-1  C09  0.020
 JBR  plan-1  C10  0.020
 JBR  plan-1  C11  0.020
 JBR  plan-1  C12  0.020
 JBR  plan-1  C15  0.020
 JBR  plan-1  O01  0.020
 JBR  plan-1  H1   0.020
 JBR  plan-1  H2   0.020
 JBR  plan-1  H3   0.020
 JBR  plan-1  H4   0.020
 JBR  plan-1  H5   0.020
 JBR  plan-2  C15  0.020
 JBR  plan-2  C16  0.020
 JBR  plan-2  C17  0.020
 JBR  plan-2  C18  0.020
 JBR  plan-2  C19  0.020
 JBR  plan-2  C20  0.020
 JBR  plan-2  C21  0.020
 JBR  plan-2  C22  0.020
 JBR  plan-2  C23  0.020
 JBR  plan-2  C24  0.020
 JBR  plan-2  C25  0.020
 JBR  plan-2  C28  0.020
 JBR  plan-2  O29  0.020
 JBR  plan-2  H8   0.020
 JBR  plan-2  H9   0.020
 JBR  plan-2  H10  0.020
 JBR  plan-2  H11  0.020
 JBR  plan-2  H12  0.020
 JBR  plan-3  C11  0.020
 JBR  plan-3  C12  0.020
 JBR  plan-3  O13  0.020
 JBR  plan-3  O14  0.020
 JBR  plan-4  C24  0.020
 JBR  plan-4  C25  0.020
 JBR  plan-4  O26  0.020
 JBR  plan-4  O27  0.020

