# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:25:10 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-5-nitro[1,1'-biphenyl]-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@H]1Oc2ccccc2c3cc(cc(c3)[N+]([O-])=O)C(O)=O
#
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
 JCD  JCD  '2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-5-nitro[1,1'-biphenyl]-3-carboxylic acid'  ligand  54  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JCD
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
 JCD  N    N  N      1   0.331  -2.4974  -2.0459  -2.0116
 JCD  C    C  CH2    0  -0.167   5.5693   0.9716  -0.7363
 JCD  O    O  OH1    0  -0.664   5.4988   2.3743  -0.6434
 JCD  C1   C  CH1    0  -0.014   4.4549   0.3793   0.0951
 JCD  C10  C  CR16   0  -0.337  -2.8403   1.1069   0.7155
 JCD  C11  C  CR6    0  -0.077  -3.7731   0.0777   0.7555
 JCD  C12  C  C      0   0.417  -4.8925   0.0780   1.7932
 JCD  C13  C  CR16   0  -0.332  -3.6593  -0.9654  -0.1511
 JCD  C14  C  CR6    0   0.291  -2.6270  -0.9429  -1.0741
 JCD  C15  C  CR16   0  -0.314  -1.7073   0.0907  -1.1347
 JCD  C16  C  CH1    0  -0.147   2.0311  -1.1016   0.4806
 JCD  C18  C  CH3    0  -0.783  -1.1414  -2.5137   1.9707
 JCD  C19  C  CH1    0   0.050   3.3469  -1.6023   1.0795
 JCD  C2   C  CH1    0   0.319   2.1182   0.4139   0.2769
 JCD  C20  C  CH1    0  -0.026   4.5316  -1.1420   0.2254
 JCD  C3   C  CR6    0   0.319   0.5280   2.0895  -0.2729
 JCD  C4   C  CR16   0  -0.336   1.3894   3.1803  -0.2018
 JCD  C5   C  CR16   0  -0.254   0.8720   4.4619  -0.0787
 JCD  C6   C  CR16   0  -0.257  -0.4992   4.6646  -0.0376
 JCD  C7   C  CR16   0  -0.299  -1.3496   3.5725  -0.1100
 JCD  C8   C  CR6    0  -0.032  -0.8604   2.2714  -0.2204
 JCD  C9   C  CR6    0   0.128  -1.8057   1.1334  -0.2198
 JCD  N1   N  NH1    0  -0.628   0.9060  -1.4392   1.3063
 JCD  O1   O  O2     0  -0.489   3.2252   0.7407  -0.5047
 JCD  O2   O  O2     0  -0.490   0.9743   0.8126  -0.4029
 JCD  O3   O  OC    -1  -0.585  -5.6999  -0.8666   1.7337
 JCD  O4   O  O      0  -0.586  -4.8930   1.0224   2.6031
 JCD  O5   O  O     -1  -0.385  -1.7251  -1.9274  -2.9338
 JCD  O6   O  O      0  -0.386  -3.1748  -3.0307  -1.8288
 JCD  O7   O  O      0  -0.497  -0.1543  -2.7621  -0.1928
 JCD  O8   O  OH1    0  -0.657   3.2638  -2.9936   1.1996
 JCD  O9   O  OH1    0  -0.670   4.4642  -1.7843  -1.0232
 JCD  H6   H  HCH2   0   0.205   5.4759   0.6303  -1.7742
 JCD  H7   H  HCH2   0   0.207   6.5212   0.5837  -0.3504
 JCD  H5   H  HOH1   0   0.458   6.1474   2.7464  -1.2476
 JCD  H    H  HCH1   0   0.226   4.5246   0.8042   1.1101
 JCD  H12  H  HCR6   0   0.258  -2.9173   1.9001   1.4479
 JCD  H14  H  HCR6   0   0.282  -4.3702  -1.7779  -0.1231
 JCD  H15  H  HCR6   0   0.281  -0.9260   0.0835  -1.8781
 JCD  H2   H  HCH1   0   0.278   1.8754  -1.5657  -0.4953
 JCD  H17  H  HCH3   0   0.270  -0.8881  -3.4322   2.5036
 JCD  H18  H  HCH3   0   0.248  -1.2244  -1.7121   2.7028
 JCD  H19  H  HCH3   0   0.262  -2.1111  -2.6602   1.5023
 JCD  H3   H  HCH1   0   0.217   3.4743  -1.1299   2.0666
 JCD  H1   H  HCH1   0   0.203   2.1777   0.9286   1.2533
 JCD  H4   H  HCH1   0   0.245   5.4595  -1.3963   0.7571
 JCD  H8   H  HCR6   0   0.282   2.4608   3.0401  -0.2588
 JCD  H9   H  HCR6   0   0.263   1.5511   5.3025  -0.0264
 JCD  H10  H  HCR6   0   0.257  -0.9054   5.6636   0.0463
 JCD  H11  H  HCR6   0   0.261  -2.4211   3.7267  -0.0826
 JCD  H16  H  HNH1   0   0.397   0.8933  -1.0904   2.2521
 JCD  H20  H  HOH1   0   0.454   3.9922  -3.2959   1.7510
 JCD  H21  H  HOH1   0   0.459   5.3500  -1.8571  -1.3880
 JCD  C17  C  C      0   0.543  -0.0981  -2.2493   0.9149

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
 JCD  C5   C6   aromatic  1.387  0.020  1.387
 JCD  C5   C4   aromatic  1.388  0.020  1.388
 JCD  C6   C7   aromatic  1.386  0.020  1.386
 JCD  C4   C3   aromatic  1.392  0.020  1.392
 JCD  C    C1   single    1.511  0.020  1.511
 JCD  C    O    single    1.408  0.020  1.408
 JCD  C1   O1   single    1.415  0.020  1.415
 JCD  C1   C20  single    1.529  0.020  1.529
 JCD  O1   C2   single    1.394  0.020  1.394
 JCD  C7   C8   aromatic  1.394  0.020  1.394
 JCD  C3   C8   aromatic  1.401  0.020  1.401
 JCD  C3   O2   single    1.359  0.020  1.359
 JCD  C2   O2   single    1.389  0.020  1.389
 JCD  C2   C16  single    1.532  0.020  1.532
 JCD  C20  C19  single    1.531  0.020  1.531
 JCD  C20  O9   single    1.406  0.020  1.406
 JCD  C8   C9   single    1.479  0.020  1.479
 JCD  C19  C16  single    1.530  0.020  1.530
 JCD  C19  O8   single    1.399  0.020  1.399
 JCD  C16  N1   single    1.436  0.020  1.436
 JCD  N1   C17  single    1.348  0.020  1.348
 JCD  C9   C10  aromatic  1.395  0.020  1.395
 JCD  C9   C15  aromatic  1.391  0.020  1.391
 JCD  C10  C11  aromatic  1.390  0.020  1.390
 JCD  C15  C14  aromatic  1.385  0.020  1.385
 JCD  C17  C18  single    1.508  0.020  1.508
 JCD  C17  O7   double    1.222  0.020  1.222
 JCD  O4   C12  deloc     1.244  0.020  1.244
 JCD  C11  C12  single    1.526  0.020  1.526
 JCD  C11  C13  aromatic  1.387  0.020  1.387
 JCD  C12  O3   deloc     1.244  0.020  1.244
 JCD  C14  C13  aromatic  1.385  0.020  1.385
 JCD  C14  N    single    1.453  0.020  1.453
 JCD  O5   N    single    1.209  0.020  1.209
 JCD  N    O6   double    1.209  0.020  1.209
 JCD  C    H6   single    0.970  0.020  1.090
 JCD  C    H7   single    0.970  0.020  1.090
 JCD  O    H5   single    0.850  0.020  0.980
 JCD  C1   H    single    0.970  0.020  1.090
 JCD  C10  H12  single    0.930  0.020  1.080
 JCD  C13  H14  single    0.930  0.020  1.080
 JCD  C15  H15  single    0.930  0.020  1.080
 JCD  C16  H2   single    0.970  0.020  1.090
 JCD  C18  H17  single    0.970  0.020  1.090
 JCD  C18  H18  single    0.970  0.020  1.090
 JCD  C18  H19  single    0.970  0.020  1.090
 JCD  C19  H3   single    0.970  0.020  1.090
 JCD  C2   H1   single    0.970  0.020  1.090
 JCD  C20  H4   single    0.970  0.020  1.090
 JCD  C4   H8   single    0.930  0.020  1.080
 JCD  C5   H9   single    0.930  0.020  1.080
 JCD  C6   H10  single    0.930  0.020  1.080
 JCD  C7   H11  single    0.930  0.020  1.080
 JCD  N1   H16  single    0.860  0.020  1.020
 JCD  O8   H20  single    0.850  0.020  0.980
 JCD  O9   H21  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
 JCD  O6   N    O5   123.58  3.000
 JCD  O6   N    C14  118.08  3.000
 JCD  O5   N    C14  118.34  3.000
 JCD  H7   C    H6   107.25  3.000
 JCD  H7   C    C1   107.91  3.000
 JCD  H6   C    C1   109.63  3.000
 JCD  H7   C    O    111.86  3.000
 JCD  H6   C    O    111.61  3.000
 JCD  C1   C    O    108.50  3.000
 JCD  H5   O    C    108.09  3.000
 JCD  H    C1   O1   110.29  3.000
 JCD  H    C1   C20  107.57  3.000
 JCD  O1   C1   C20  109.50  3.000
 JCD  H    C1   C    107.98  3.000
 JCD  C20  C1   C    113.57  3.000
 JCD  O1   C1   C    107.91  3.000
 JCD  H12  C10  C9   119.50  3.000
 JCD  H12  C10  C11  118.40  3.000
 JCD  C9   C10  C11  122.09  3.000
 JCD  C13  C11  C12  120.32  3.000
 JCD  C13  C11  C10  118.89  3.000
 JCD  C12  C11  C10  120.78  3.000
 JCD  O4   C12  O3   127.39  3.000
 JCD  O3   C12  C11  116.31  3.000
 JCD  O4   C12  C11  116.30  3.000
 JCD  H14  C13  C14  121.35  3.000
 JCD  H14  C13  C11  119.67  3.000
 JCD  C14  C13  C11  118.99  3.000
 JCD  C15  C14  C13  122.44  3.000
 JCD  C13  C14  N    118.95  3.000
 JCD  C15  C14  N    118.62  3.000
 JCD  H15  C15  C9   120.65  3.000
 JCD  H15  C15  C14  120.42  3.000
 JCD  C9   C15  C14  118.94  3.000
 JCD  H2   C16  N1   107.60  3.000
 JCD  H2   C16  C2   108.05  3.000
 JCD  N1   C16  C2   110.71  3.000
 JCD  H2   C16  C19  109.48  3.000
 JCD  N1   C16  C19  111.83  3.000
 JCD  C2   C16  C19  109.08  3.000
 JCD  H19  C18  H18  108.72  3.000
 JCD  H19  C18  H17  107.70  3.000
 JCD  H18  C18  H17  107.99  3.000
 JCD  H19  C18  C17  109.83  3.000
 JCD  H18  C18  C17  113.23  3.000
 JCD  H17  C18  C17  109.20  3.000
 JCD  H3   C19  O8   110.88  3.000
 JCD  H3   C19  C20  106.34  3.000
 JCD  O8   C19  C20  113.13  3.000
 JCD  H3   C19  C16  108.05  3.000
 JCD  O8   C19  C16  107.94  3.000
 JCD  C20  C19  C16  110.40  3.000
 JCD  H1   C2   O2   110.06  3.000
 JCD  H1   C2   O1   110.08  3.000
 JCD  O2   C2   O1   108.20  3.000
 JCD  H1   C2   C16  110.26  3.000
 JCD  O2   C2   C16  107.59  3.000
 JCD  O1   C2   C16  110.59  3.000
 JCD  H4   C20  O9   111.37  3.000
 JCD  H4   C20  C19  108.28  3.000
 JCD  O9   C20  C19  108.72  3.000
 JCD  H4   C20  C1   108.29  3.000
 JCD  O9   C20  C1   112.12  3.000
 JCD  C19  C20  C1   107.93  3.000
 JCD  O2   C3   C8   116.81  3.000
 JCD  O2   C3   C4   122.56  3.000
 JCD  C8   C3   C4   120.64  3.000
 JCD  H8   C4   C5   119.58  3.000
 JCD  H8   C4   C3   120.57  3.000
 JCD  C5   C4   C3   119.84  3.000
 JCD  H9   C5   C6   120.38  3.000
 JCD  H9   C5   C4   119.20  3.000
 JCD  C6   C5   C4   120.42  3.000
 JCD  H10  C6   C7   120.09  3.000
 JCD  H10  C6   C5   120.57  3.000
 JCD  C7   C6   C5   119.34  3.000
 JCD  H11  C7   C8   118.82  3.000
 JCD  H11  C7   C6   119.58  3.000
 JCD  C8   C7   C6   121.61  3.000
 JCD  C9   C8   C7   119.57  3.000
 JCD  C9   C8   C3   122.23  3.000
 JCD  C7   C8   C3   118.14  3.000
 JCD  C8   C9   C15  122.09  3.000
 JCD  C15  C9   C10  118.64  3.000
 JCD  C8   C9   C10  119.27  3.000
 JCD  H16  N1   C17  118.09  3.000
 JCD  H16  N1   C16  117.90  3.000
 JCD  C17  N1   C16  123.92  3.000
 JCD  C2   O1   C1   113.12  3.000
 JCD  C3   O2   C2   119.56  3.000
 JCD  H20  O8   C19  108.46  3.000
 JCD  H21  O9   C20  109.12  3.000
 JCD  O7   C17  N1   123.34  3.000
 JCD  O7   C17  C18  121.96  3.000
 JCD  N1   C17  C18  114.68  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
 JCD  CONST_03  C14  C15  C9   C10    0.00   0.0  0
 JCD  CONST_04  C14  C13  C11  C10    0.00   0.0  0
 JCD  CONST_05  C8   C9   C10  C11  180.00   0.0  0
 JCD  CONST_06  C15  C9   C10  C11    0.00   0.0  0
 JCD  CONST_07  C15  C14  C13  C11    0.00   0.0  0
 JCD  CONST_08  C9   C10  C11  C13    0.00   0.0  0
 JCD  CONST_09  C9   C15  C14  C13    0.00   0.0  0
 JCD  CONST_10  C8   C9   C15  C14  180.00   0.0  0
 JCD  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 JCD  CONST_14  C6   C7   C8   C3     0.00   0.0  0
 JCD  CONST_15  C7   C6   C5   C4     0.00   0.0  0
 JCD  CONST_16  C7   C8   C3   C4     0.00   0.0  0
 JCD  CONST_17  C9   C8   C3   C4   180.00   0.0  0
 JCD  CONST_18  C8   C7   C6   C5     0.00   0.0  0
 JCD  CONST_19  C8   C3   C4   C5     0.00   0.0  0
 JCD  CONST_20  C9   C8   C7   C6   180.00   0.0  0
 JCD  CONST_21  C9   C15  C14  N    180.00   0.0  0
 JCD  CONST_22  C11  C13  C14  N    180.00   0.0  0
 JCD  CONST_23  C9   C10  C11  C12  180.00   0.0  0
 JCD  CONST_24  C14  C13  C11  C12  180.00   0.0  0
 JCD  CONST_25  O2   C3   C4   C5   180.00   0.0  0
 JCD  CONST_26  O2   C3   C8   C7   180.00   0.0  0
 JCD  CONST_27  O2   C3   C8   C9     0.00   0.0  0
 JCD  CONST_28  H15  C15  C9   C10  180.00   0.0  0
 JCD  CONST_29  H14  C13  C11  C10  180.00   0.0  0
 JCD  CONST_30  H12  C10  C11  C13  180.00   0.0  0
 JCD  CONST_31  H9   C5   C4   C3   180.00   0.0  0
 JCD  CONST_32  H11  C7   C8   C3   180.00   0.0  0
 JCD  CONST_33  H10  C6   C5   C4   180.00   0.0  0
 JCD  CONST_34  H8   C4   C5   C6   180.00   0.0  0
 JCD  CONST_35  O5   N    C14  C13  180.00   0.0  0
 JCD  CONST_36  O6   N    C14  C13    0.00   0.0  0
 JCD  CONST_37  O5   N    C14  C15    0.00   0.0  0
 JCD  CONST_38  O6   N    C14  C15  180.00   0.0  0
 JCD  CONST_39  C18  C17  N1   C16  180.00   0.0  0
 JCD  CONST_40  O7   C17  N1   C16    0.00   0.0  0
 JCD  CONST_41  H16  N1   C17  C18    0.00   0.0  0
 JCD  Var_01    C4   C3   O2   C2    38.32  30.0  2
 JCD  Var_02    O4   C12  C11  C10   -1.72  30.0  2
 JCD  Var_03    H17  C18  C17  N1   -93.59  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
 JCD  chir_01  C1   C   O1   C20  negativ
 JCD  chir_02  C16  N1  C2   C19  negativ
 JCD  chir_03  C19  O8  C16  C20  positiv
 JCD  chir_04  C2   O2  O1   C16  positiv
 JCD  chir_05  C20  O9  C1   C19  negativ

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
 JCD  plan-1  C3   0.020
 JCD  plan-1  C4   0.020
 JCD  plan-1  C5   0.020
 JCD  plan-1  C6   0.020
 JCD  plan-1  C7   0.020
 JCD  plan-1  C8   0.020
 JCD  plan-1  C9   0.020
 JCD  plan-1  O2   0.020
 JCD  plan-1  H8   0.020
 JCD  plan-1  H9   0.020
 JCD  plan-1  H10  0.020
 JCD  plan-1  H11  0.020
 JCD  plan-2  N    0.020
 JCD  plan-2  C10  0.020
 JCD  plan-2  C11  0.020
 JCD  plan-2  C12  0.020
 JCD  plan-2  C13  0.020
 JCD  plan-2  C14  0.020
 JCD  plan-2  C15  0.020
 JCD  plan-2  C8   0.020
 JCD  plan-2  C9   0.020
 JCD  plan-2  H12  0.020
 JCD  plan-2  H14  0.020
 JCD  plan-2  H15  0.020
 JCD  plan-3  N    0.020
 JCD  plan-3  C14  0.020
 JCD  plan-3  O5   0.020
 JCD  plan-3  O6   0.020
 JCD  plan-4  C16  0.020
 JCD  plan-4  C18  0.020
 JCD  plan-4  N1   0.020
 JCD  plan-4  O7   0.020
 JCD  plan-4  H16  0.020
 JCD  plan-4  C17  0.020
 JCD  plan-5  C11  0.020
 JCD  plan-5  C12  0.020
 JCD  plan-5  O3   0.020
 JCD  plan-5  O4   0.020

