# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 05:21:29 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 2'-(beta-D-galactopyranosyloxy)-5-nitro[1,1'-biphenyl]-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccccc2c3cc(cc(c3)[N+]([O-])=O)C(O)=O)[C@H](O)[C@@H](O)[C@H]1O
#
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
 JC4  JC4  '2'-(beta-D-galactopyranosyloxy)-5-nitro[1,1'-biphenyl]-3-carboxylic acid'  ligand  49  30  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JC4
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
 JC4  C10  C  CR16   0  -0.264  29.2741   7.7907  -30.1267
 JC4  C13  C  CR6    0   0.123  29.1864   6.7600  -26.5032
 JC4  C15  C  CR6    0  -0.046  29.9266   6.4048  -24.2226
 JC4  C20  C  CR6    0   0.308  27.7514   7.2594  -24.6457
 JC4  C24  C  CR16   0  -0.326  27.9633   7.2063  -26.0148
 JC4  O01  O  OH1    0  -0.660  29.1817   0.3241  -29.8689
 JC4  C02  C  CH2    0  -0.174  30.3960   0.7766  -30.4070
 JC4  C03  C  CH1    0  -0.013  31.2070   1.5470  -29.3868
 JC4  O04  O  O2     0  -0.491  30.4296   2.6314  -28.9148
 JC4  C05  C  CH1    0   0.270  31.1741   3.5556  -28.1802
 JC4  C07  C  CR6    0   0.352  29.9925   5.5885  -28.5744
 JC4  C08  C  CR16   0  -0.350  30.1836   5.5656  -29.9519
 JC4  C09  C  CR16   0  -0.247  29.8320   6.6683  -30.7182
 JC4  C11  C  CR16   0  -0.287  29.0715   7.8020  -28.7556
 JC4  C12  C  CR6    0  -0.030  29.4288   6.7168  -27.9596
 JC4  C14  C  CR16   0  -0.288  30.1633   6.3729  -25.5904
 JC4  C16  C  C      0   0.570  30.9908   5.8948  -23.3198
 JC4  O17  O  OH1    0  -0.580  30.8051   6.2303  -22.0598
 JC4  O18  O  O      0  -0.443  31.9249   5.2303  -23.7067
 JC4  C19  C  CR16   0  -0.305  28.7103   6.8624  -23.7317
 JC4  N21  N  N      1   0.328  26.4639   7.7340  -24.1516
 JC4  O22  O  O      0  -0.370  26.2856   7.7451  -22.9577
 JC4  O23  O  O     -1  -0.370  25.6447   8.0928  -24.9626
 JC4  C25  C  CH1    0  -0.035  31.7898   2.9066  -26.9395
 JC4  O26  O  OH1    0  -0.686  32.6497   3.8047  -26.2795
 JC4  C27  C  CH1    0  -0.007  32.6146   1.6959  -27.3737
 JC4  O28  O  OH1    0  -0.672  33.1053   0.9812  -26.2679
 JC4  C29  C  CH1    0   0.015  31.7724   0.7444  -28.2205
 JC4  O30  O  OH1    0  -0.659  30.7370   0.1674  -27.4696
 JC4  H1   H  HCR6   0   0.261  28.9980   8.6491  -30.7236
 JC4  H2   H  HCR6   0   0.305  27.1820   7.4954  -26.7038
 JC4  H3   H  HOH1   0   0.455  28.6449   0.0015  -30.5979
 JC4  H4   H  HCH2   0   0.216  30.2319   1.4389  -31.2666
 JC4  H5   H  HCH2   0   0.201  31.0266  -0.0478  -30.7665
 JC4  H7   H  HCH1   0   0.213  31.9780   3.9906  -28.8000
 JC4  H8   H  HCR6   0   0.287  30.5798   4.6904  -30.4467
 JC4  H9   H  HCR6   0   0.267  29.9899   6.6367  -31.7882
 JC4  H10  H  HCR6   0   0.265  28.6485   8.6811  -28.2857
 JC4  H11  H  HCR6   0   0.267  31.1319   6.0628  -25.9507
 JC4  H12  H  HOH1   0   0.498  31.5006   5.8521  -21.5000
 JC4  H13  H  HCR6   0   0.309  28.5123   6.8980  -22.6707
 JC4  H14  H  HCH1   0   0.241  30.9757   2.5677  -26.2869
 JC4  H15  H  HOH1   0   0.464  32.2292   4.1565  -25.4864
 JC4  H16  H  HCH1   0   0.217  33.4444   2.0556  -28.0026
 JC4  H17  H  HOH1   0   0.454  33.5400   1.6025  -25.6731
 JC4  H18  H  HCH1   0   0.228  32.4386  -0.0229  -28.6442
 JC4  H19  H  HOH1   0   0.448  31.1246  -0.1689  -26.6539
 JC4  O06  O  O2     0  -0.496  30.2972   4.5512  -27.7568
 JC4  H6   H  HCH1   0   0.236  32.0805   1.9248  -29.9425

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
 JC4  C09  C10  aromatic  1.386  0.020  1.386
 JC4  C09  C08  aromatic  1.388  0.020  1.388
 JC4  C10  C11  aromatic  1.386  0.020  1.386
 JC4  C02  C03  single    1.514  0.020  1.514
 JC4  C02  O01  single    1.403  0.020  1.403
 JC4  C08  C07  aromatic  1.391  0.020  1.391
 JC4  C03  O04  single    1.415  0.020  1.415
 JC4  C03  C29  single    1.525  0.020  1.525
 JC4  O04  C05  single    1.396  0.020  1.396
 JC4  C11  C12  aromatic  1.392  0.020  1.392
 JC4  C07  C12  aromatic  1.403  0.020  1.403
 JC4  C07  O06  single    1.355  0.020  1.355
 JC4  C05  O06  single    1.393  0.020  1.393
 JC4  C05  C25  single    1.530  0.020  1.530
 JC4  C29  C27  single    1.527  0.020  1.527
 JC4  C29  O30  single    1.403  0.020  1.403
 JC4  C12  C13  single    1.477  0.020  1.477
 JC4  C27  C25  single    1.528  0.020  1.528
 JC4  C27  O28  single    1.405  0.020  1.405
 JC4  C25  O26  single    1.408  0.020  1.408
 JC4  C13  C24  aromatic  1.391  0.020  1.391
 JC4  C13  C14  aromatic  1.392  0.020  1.392
 JC4  C24  C20  aromatic  1.386  0.020  1.386
 JC4  C14  C15  aromatic  1.389  0.020  1.389
 JC4  O23  N21  single    1.207  0.020  1.207
 JC4  C20  N21  single    1.458  0.020  1.458
 JC4  C20  C19  aromatic  1.383  0.020  1.383
 JC4  N21  O22  double    1.207  0.020  1.207
 JC4  C15  C19  aromatic  1.389  0.020  1.389
 JC4  C15  C16  single    1.486  0.020  1.486
 JC4  O18  C16  double    1.210  0.020  1.210
 JC4  C16  O17  single    1.317  0.020  1.317
 JC4  C10  H1   single    0.930  0.020  1.080
 JC4  C24  H2   single    0.930  0.020  1.080
 JC4  O01  H3   single    0.850  0.020  0.980
 JC4  C02  H4   single    0.970  0.020  1.090
 JC4  C02  H5   single    0.970  0.020  1.090
 JC4  C03  H6   single    0.970  0.020  1.090
 JC4  C05  H7   single    0.970  0.020  1.090
 JC4  C08  H8   single    0.930  0.020  1.080
 JC4  C09  H9   single    0.930  0.020  1.080
 JC4  C11  H10  single    0.930  0.020  1.080
 JC4  C14  H11  single    0.930  0.020  1.080
 JC4  O17  H12  single    0.850  0.020  0.980
 JC4  C19  H13  single    0.930  0.020  1.080
 JC4  C25  H14  single    0.970  0.020  1.090
 JC4  O26  H15  single    0.850  0.020  0.980
 JC4  C27  H16  single    0.970  0.020  1.090
 JC4  O28  H17  single    0.850  0.020  0.980
 JC4  C29  H18  single    0.970  0.020  1.090
 JC4  O30  H19  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
 JC4  H1   C10  C11  120.14  3.000
 JC4  H1   C10  C09  120.67  3.000
 JC4  C11  C10  C09  119.19  3.000
 JC4  C14  C13  C12  121.55  3.000
 JC4  C14  C13  C24  118.44  3.000
 JC4  C12  C13  C24  120.00  3.000
 JC4  C19  C15  C16  121.70  3.000
 JC4  C16  C15  C14  117.94  3.000
 JC4  C19  C15  C14  120.33  3.000
 JC4  N21  C20  C19  118.80  3.000
 JC4  C19  C20  C24  122.39  3.000
 JC4  N21  C20  C24  118.81  3.000
 JC4  H2   C24  C20  120.57  3.000
 JC4  H2   C24  C13  119.85  3.000
 JC4  C20  C24  C13  119.58  3.000
 JC4  H3   O01  C02  107.50  3.000
 JC4  H5   C02  H4   106.41  3.000
 JC4  H5   C02  C03  107.16  3.000
 JC4  H4   C02  C03  107.50  3.000
 JC4  H5   C02  O01  112.35  3.000
 JC4  H4   C02  O01  111.44  3.000
 JC4  C03  C02  O01  111.66  3.000
 JC4  H6   C03  C29  105.80  3.000
 JC4  H6   C03  O04  109.93  3.000
 JC4  C29  C03  O04  110.61  3.000
 JC4  H6   C03  C02  105.02  3.000
 JC4  C29  C03  C02  116.50  3.000
 JC4  O04  C03  C02  108.69  3.000
 JC4  C05  O04  C03  112.95  3.000
 JC4  H7   C05  C25  109.23  3.000
 JC4  H7   C05  O06  110.33  3.000
 JC4  C25  C05  O06  108.07  3.000
 JC4  H7   C05  O04  110.72  3.000
 JC4  C25  C05  O04  111.14  3.000
 JC4  O06  C05  O04  107.31  3.000
 JC4  C12  C07  C08  120.16  3.000
 JC4  C12  C07  O06  116.19  3.000
 JC4  C08  C07  O06  123.64  3.000
 JC4  H8   C08  C09  118.91  3.000
 JC4  H8   C08  C07  121.14  3.000
 JC4  C09  C08  C07  119.93  3.000
 JC4  H9   C09  C08  119.06  3.000
 JC4  H9   C09  C10  120.29  3.000
 JC4  C08  C09  C10  120.64  3.000
 JC4  H10  C11  C12  119.00  3.000
 JC4  H10  C11  C10  119.54  3.000
 JC4  C12  C11  C10  121.44  3.000
 JC4  C11  C12  C07  118.64  3.000
 JC4  C07  C12  C13  121.43  3.000
 JC4  C11  C12  C13  119.92  3.000
 JC4  H11  C14  C15  119.24  3.000
 JC4  H11  C14  C13  119.41  3.000
 JC4  C15  C14  C13  121.33  3.000
 JC4  O18  C16  O17  123.69  3.000
 JC4  O17  C16  C15  113.13  3.000
 JC4  O18  C16  C15  123.18  3.000
 JC4  H12  O17  C16  110.60  3.000
 JC4  H13  C19  C20  120.84  3.000
 JC4  H13  C19  C15  121.24  3.000
 JC4  C20  C19  C15  117.91  3.000
 JC4  O23  N21  O22  124.15  3.000
 JC4  O22  N21  C20  117.93  3.000
 JC4  O23  N21  C20  117.92  3.000
 JC4  H14  C25  C27  108.96  3.000
 JC4  H14  C25  O26  111.80  3.000
 JC4  C27  C25  O26  108.00  3.000
 JC4  H14  C25  C05  108.35  3.000
 JC4  O26  C25  C05  110.82  3.000
 JC4  C27  C25  C05  108.85  3.000
 JC4  H15  O26  C25  110.61  3.000
 JC4  H16  C27  C29  107.60  3.000
 JC4  H16  C27  O28  110.63  3.000
 JC4  C29  C27  O28  108.18  3.000
 JC4  H16  C27  C25  108.07  3.000
 JC4  O28  C27  C25  111.59  3.000
 JC4  C29  C27  C25  110.71  3.000
 JC4  H17  O28  C27  108.38  3.000
 JC4  H18  C29  O30  111.47  3.000
 JC4  H18  C29  C27  108.30  3.000
 JC4  O30  C29  C27  111.50  3.000
 JC4  H18  C29  C03  107.27  3.000
 JC4  O30  C29  C03  110.62  3.000
 JC4  C27  C29  C03  107.50  3.000
 JC4  H19  O30  C29  107.43  3.000
 JC4  C07  O06  C05  120.34  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
 JC4  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 JC4  CONST_02  C07  C12  C11  C10    0.00   0.0  0
 JC4  CONST_03  C13  C12  C11  C10  180.00   0.0  0
 JC4  CONST_04  C08  C07  C12  C13  180.00   0.0  0
 JC4  CONST_05  C19  C20  C24  C13    0.00   0.0  0
 JC4  CONST_06  C19  C15  C14  C13    0.00   0.0  0
 JC4  CONST_07  C12  C13  C14  C15  180.00   0.0  0
 JC4  CONST_08  C24  C13  C14  C15    0.00   0.0  0
 JC4  CONST_09  C24  C20  C19  C15    0.00   0.0  0
 JC4  CONST_10  C12  C13  C24  C20  180.00   0.0  0
 JC4  CONST_11  C14  C13  C24  C20    0.00   0.0  0
 JC4  CONST_12  C14  C15  C19  C20    0.00   0.0  0
 JC4  CONST_16  C11  C10  C09  C08    0.00   0.0  0
 JC4  CONST_17  C11  C12  C07  C08    0.00   0.0  0
 JC4  CONST_18  C12  C11  C10  C09    0.00   0.0  0
 JC4  CONST_19  C12  C07  C08  C09    0.00   0.0  0
 JC4  CONST_21  O06  C07  C12  C13    0.00   0.0  0
 JC4  CONST_22  N21  C20  C24  C13  180.00   0.0  0
 JC4  CONST_23  C16  C15  C14  C13  180.00   0.0  0
 JC4  CONST_24  N21  C20  C19  C15  180.00   0.0  0
 JC4  CONST_25  C16  C15  C19  C20  180.00   0.0  0
 JC4  CONST_26  C09  C08  C07  O06  180.00   0.0  0
 JC4  CONST_27  C11  C12  C07  O06  180.00   0.0  0
 JC4  CONST_28  H8   C08  C09  C10  180.00   0.0  0
 JC4  CONST_29  H10  C11  C12  C13    0.00   0.0  0
 JC4  CONST_30  H11  C14  C13  C24  180.00   0.0  0
 JC4  CONST_31  H13  C19  C20  C24  180.00   0.0  0
 JC4  CONST_32  H9   C09  C08  C07  180.00   0.0  0
 JC4  CONST_33  H1   C10  C09  C08  180.00   0.0  0
 JC4  CONST_34  H2   C24  C13  C12    0.00   0.0  0
 JC4  CONST_35  O23  N21  C20  C24    0.00   0.0  0
 JC4  CONST_36  O22  N21  C20  C24  180.00   0.0  0
 JC4  CONST_37  O23  N21  C20  C19  180.00   0.0  0
 JC4  CONST_38  O22  N21  C20  C19    0.00   0.0  0
 JC4  CONST_39  H12  O17  C16  C15  180.00   0.0  0
 JC4  Var_01    C08  C07  O06  C05   19.03  30.0  2
 JC4  Var_02    O18  C16  C15  C14  -14.56  30.0  2

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
 JC4  chir_01  C03  C02  O04  C29  negativ
 JC4  chir_02  C05  O04  O06  C25  negativ
 JC4  chir_03  C25  O26  C05  C27  negativ
 JC4  chir_04  C27  O28  C25  C29  positiv
 JC4  chir_05  C29  O30  C03  C27  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
 JC4  plan-1  C13  0.020
 JC4  plan-1  C15  0.020
 JC4  plan-1  C20  0.020
 JC4  plan-1  C24  0.020
 JC4  plan-1  C12  0.020
 JC4  plan-1  C14  0.020
 JC4  plan-1  C16  0.020
 JC4  plan-1  C19  0.020
 JC4  plan-1  N21  0.020
 JC4  plan-1  H2   0.020
 JC4  plan-1  H11  0.020
 JC4  plan-1  H13  0.020
 JC4  plan-2  C10  0.020
 JC4  plan-2  C13  0.020
 JC4  plan-2  C07  0.020
 JC4  plan-2  C08  0.020
 JC4  plan-2  C09  0.020
 JC4  plan-2  C11  0.020
 JC4  plan-2  C12  0.020
 JC4  plan-2  H1   0.020
 JC4  plan-2  H8   0.020
 JC4  plan-2  H9   0.020
 JC4  plan-2  H10  0.020
 JC4  plan-2  O06  0.020
 JC4  plan-3  C20  0.020
 JC4  plan-3  N21  0.020
 JC4  plan-3  O22  0.020
 JC4  plan-3  O23  0.020
 JC4  plan-4  C15  0.020
 JC4  plan-4  C16  0.020
 JC4  plan-4  O17  0.020
 JC4  plan-4  O18  0.020
 JC4  plan-4  H12  0.020

