# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 10:59:00 2021
#   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  55  33  .  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_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   0.335  31.8107   6.6651  -22.8975
 JCD  C    C  CH2    0  -0.174  30.2930   0.6834  -29.6223
 JCD  O    O  OH1    0  -0.659  29.0991   0.5482  -28.8975
 JCD  C1   C  CH1    0  -0.012  31.3959   1.2819  -28.7751
 JCD  C10  C  CR16   0  -0.293  28.7028   6.5289  -25.7069
 JCD  C11  C  CR6    0  -0.063  28.4014   6.5547  -24.3480
 JCD  C12  C  C      0   0.553  26.9694   6.5532  -23.9469
 JCD  C13  C  CR16   0  -0.299  29.4261   6.5724  -23.4111
 JCD  C14  C  CR6    0   0.302  30.7311   6.5980  -23.8703
 JCD  C15  C  CR16   0  -0.275  31.0460   6.5821  -25.2171
 JCD  C16  C  CH1    0  -0.161  32.6003   2.5692  -26.5222
 JCD  C18  C  CH3    0  -0.783  34.9066   4.7759  -24.4878
 JCD  C19  C  CH1    0   0.015  33.0712   1.1806  -26.9704
 JCD  C2   C  CH1    0   0.304  31.9916   3.2905  -27.7251
 JCD  C20  C  CH1    0   0.017  31.9240   0.4198  -27.6337
 JCD  C3   C  CR6    0   0.369  31.0230   5.4209  -28.1572
 JCD  C4   C  CR16   0  -0.351  31.2514   5.3726  -29.5282
 JCD  C5   C  CR16   0  -0.248  30.7839   6.3967  -30.3409
 JCD  C6   C  CR16   0  -0.267  30.0745   7.4604  -29.8061
 JCD  C7   C  CR16   0  -0.273  29.8373   7.4951  -28.4399
 JCD  C8   C  CR6    0  -0.059  30.3075   6.4895  -27.6031
 JCD  C9   C  CR6    0   0.104  30.0189   6.5293  -26.1525
 JCD  N1   N  NH1    0  -0.648  33.7019   3.3098  -25.9654
 JCD  O1   O  O2     0  -0.486  30.9626   2.5394  -28.2902
 JCD  O2   O  O2     0  -0.485  31.4416   4.4822  -27.2726
 JCD  O3   O  OH1    0  -0.590  26.8031   6.5778  -22.6352
 JCD  O4   O  O      0  -0.429  26.0599   6.5332  -24.7387
 JCD  O5   O  O     -1  -0.370  32.8677   7.1204  -23.2608
 JCD  O6   O  O      0  -0.376  31.5841   6.2798  -21.7760
 JCD  O7   O  O      0  -0.482  32.6842   3.9879  -24.0597
 JCD  O8   O  OH1    0  -0.665  33.5350   0.4138  -25.8913
 JCD  O9   O  OH1    0  -0.658  30.9032   0.1330  -26.7165
 JCD  H6   H  HCH2   0   0.217  30.1604   1.3337  -30.4960
 JCD  H7   H  HCH2   0   0.201  30.6626  -0.2783  -30.0038
 JCD  H5   H  HOH1   0   0.456  28.4014   0.3422  -29.5257
 JCD  H    H  HCH1   0   0.237  32.2441   1.4181  -29.4661
 JCD  H12  H  HCR6   0   0.280  27.8997   6.4953  -26.4314
 JCD  H14  H  HCR6   0   0.303  29.2184   6.5860  -22.3513
 JCD  H15  H  HCR6   0   0.291  32.0751   6.6104  -25.5445
 JCD  H2   H  HCH1   0   0.280  31.8335   2.4632  -25.7526
 JCD  H17  H  HCH3   0   0.263  35.0594   4.8237  -23.4125
 JCD  H18  H  HCH3   0   0.253  35.7939   4.3528  -24.9553
 JCD  H19  H  HCH3   0   0.272  34.7940   5.7979  -24.8521
 JCD  H3   H  HCH1   0   0.219  33.8604   1.3119  -27.7274
 JCD  H1   H  HCH1   0   0.206  32.7841   3.4782  -28.4717
 JCD  H4   H  HCH1   0   0.233  32.3366  -0.4985  -28.0795
 JCD  H8   H  HCR6   0   0.282  31.7801   4.5491  -29.9867
 JCD  H9   H  HCR6   0   0.266  30.9736   6.3487  -31.4052
 JCD  H10  H  HCR6   0   0.259  29.7074   8.2539  -30.4425
 JCD  H11  H  HCR6   0   0.261  29.2863   8.3211  -28.0074
 JCD  H16  H  HNH1   0   0.405  34.5276   3.4097  -26.5373
 JCD  H13  H  HOH1   0   0.493  25.8587   6.5767  -22.4170
 JCD  H20  H  HOH1   0   0.456  34.2004   0.9201  -25.4124
 JCD  H21  H  HOH1   0   0.449  31.3114  -0.2850  -25.9501
 JCD  C17  C  C      0   0.527  33.6556   3.9940  -24.7978

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  1.386  0.020  1.386
 JCD  C5   C4   aromatic  1.389  0.020  1.389
 JCD  C6   C7   aromatic  1.387  0.020  1.387
 JCD  C4   C3   aromatic  1.391  0.020  1.391
 JCD  C    C1   single    1.514  0.020  1.514
 JCD  C    O    single    1.403  0.020  1.403
 JCD  C1   O1   single    1.416  0.020  1.416
 JCD  C1   C20  single    1.525  0.020  1.525
 JCD  O1   C2   single    1.394  0.020  1.394
 JCD  C7   C8   aromatic  1.390  0.020  1.390
 JCD  C3   C8   aromatic  1.400  0.020  1.400
 JCD  C3   O2   single    1.356  0.020  1.356
 JCD  C2   O2   single    1.388  0.020  1.388
 JCD  C2   C16  single    1.529  0.020  1.529
 JCD  C20  C19  single    1.528  0.020  1.528
 JCD  C20  O9   single    1.402  0.020  1.402
 JCD  C8   C9   single    1.480  0.020  1.480
 JCD  C19  C16  single    1.533  0.020  1.533
 JCD  C19  O8   single    1.403  0.020  1.403
 JCD  C16  N1   single    1.439  0.020  1.439
 JCD  N1   C17  single    1.354  0.020  1.354
 JCD  C9   C10  aromatic  1.389  0.020  1.389
 JCD  C9   C15  aromatic  1.390  0.020  1.390
 JCD  C10  C11  aromatic  1.392  0.020  1.392
 JCD  C15  C14  aromatic  1.383  0.020  1.383
 JCD  C17  C18  single    1.508  0.020  1.508
 JCD  C17  O7   double    1.220  0.020  1.220
 JCD  O4   C12  double    1.206  0.020  1.206
 JCD  C11  C12  single    1.487  0.020  1.487
 JCD  C11  C13  aromatic  1.389  0.020  1.389
 JCD  C12  O3   single    1.322  0.020  1.322
 JCD  C14  C13  aromatic  1.384  0.020  1.384
 JCD  C14  N    single    1.455  0.020  1.455
 JCD  O5   N    single    1.207  0.020  1.207
 JCD  N    O6   double    1.207  0.020  1.207
 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  O3   H13  single    0.850  0.020  0.980
 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   124.36  3.000
 JCD  O6   N    C14  117.85  3.000
 JCD  O5   N    C14  117.78  3.000
 JCD  H7   C    H6   106.44  3.000
 JCD  H7   C    C1   107.18  3.000
 JCD  H6   C    C1   107.42  3.000
 JCD  H7   C    O    112.41  3.000
 JCD  H6   C    O    111.44  3.000
 JCD  C1   C    O    111.64  3.000
 JCD  H5   O    C    107.50  3.000
 JCD  H    C1   O1   109.90  3.000
 JCD  H    C1   C20  105.82  3.000
 JCD  O1   C1   C20  110.60  3.000
 JCD  H    C1   C    104.98  3.000
 JCD  C20  C1   C    116.59  3.000
 JCD  O1   C1   C    108.65  3.000
 JCD  H12  C10  C9   119.23  3.000
 JCD  H12  C10  C11  119.56  3.000
 JCD  C9   C10  C11  121.21  3.000
 JCD  C13  C11  C12  121.91  3.000
 JCD  C13  C11  C10  119.94  3.000
 JCD  C12  C11  C10  118.15  3.000
 JCD  O4   C12  O3   123.83  3.000
 JCD  O3   C12  C11  112.87  3.000
 JCD  O4   C12  C11  123.30  3.000
 JCD  H14  C13  C14  120.45  3.000
 JCD  H14  C13  C11  121.35  3.000
 JCD  C14  C13  C11  118.19  3.000
 JCD  C15  C14  C13  122.52  3.000
 JCD  C13  C14  N    118.61  3.000
 JCD  C15  C14  N    118.86  3.000
 JCD  H15  C15  C9   120.06  3.000
 JCD  H15  C15  C14  120.77  3.000
 JCD  C9   C15  C14  119.17  3.000
 JCD  H2   C16  N1   108.35  3.000
 JCD  H2   C16  C2   108.71  3.000
 JCD  N1   C16  C2   111.49  3.000
 JCD  H2   C16  C19  109.51  3.000
 JCD  N1   C16  C19  110.12  3.000
 JCD  C2   C16  C19  108.64  3.000
 JCD  H19  C18  H18  107.76  3.000
 JCD  H19  C18  H17  107.68  3.000
 JCD  H18  C18  H17  109.10  3.000
 JCD  H19  C18  C17  109.37  3.000
 JCD  H18  C18  C17  112.74  3.000
 JCD  H17  C18  C17  110.05  3.000
 JCD  H3   C19  O8   110.91  3.000
 JCD  H3   C19  C20  107.39  3.000
 JCD  O8   C19  C20  108.06  3.000
 JCD  H3   C19  C16  108.24  3.000
 JCD  O8   C19  C16  111.83  3.000
 JCD  C20  C19  C16  110.32  3.000
 JCD  H1   C2   O2   111.01  3.000
 JCD  H1   C2   O1   110.31  3.000
 JCD  O2   C2   O1   107.59  3.000
 JCD  H1   C2   C16  109.04  3.000
 JCD  O2   C2   C16  107.84  3.000
 JCD  O1   C2   C16  111.02  3.000
 JCD  H4   C20  O9   111.54  3.000
 JCD  H4   C20  C19  108.04  3.000
 JCD  O9   C20  C19  111.38  3.000
 JCD  H4   C20  C1   107.35  3.000
 JCD  O9   C20  C1   110.68  3.000
 JCD  C19  C20  C1   107.66  3.000
 JCD  O2   C3   C8   115.33  3.000
 JCD  O2   C3   C4   124.63  3.000
 JCD  C8   C3   C4   120.03  3.000
 JCD  H8   C4   C5   118.58  3.000
 JCD  H8   C4   C3   121.68  3.000
 JCD  C5   C4   C3   119.74  3.000
 JCD  H9   C5   C6   120.22  3.000
 JCD  H9   C5   C4   118.94  3.000
 JCD  C6   C5   C4   120.83  3.000
 JCD  H10  C6   C7   120.21  3.000
 JCD  H10  C6   C5   120.65  3.000
 JCD  C7   C6   C5   119.13  3.000
 JCD  H11  C7   C8   118.91  3.000
 JCD  H11  C7   C6   119.96  3.000
 JCD  C8   C7   C6   121.13  3.000
 JCD  C9   C8   C7   120.31  3.000
 JCD  C9   C8   C3   120.54  3.000
 JCD  C7   C8   C3   119.12  3.000
 JCD  C8   C9   C15  121.10  3.000
 JCD  C15  C9   C10  118.95  3.000
 JCD  C8   C9   C10  119.95  3.000
 JCD  H16  N1   C17  117.81  3.000
 JCD  H16  N1   C16  117.24  3.000
 JCD  C17  N1   C16  124.57  3.000
 JCD  C2   O1   C1   113.05  3.000
 JCD  C3   O2   C2   120.26  3.000
 JCD  H13  O3   C12  110.23  3.000
 JCD  H20  O8   C19  108.87  3.000
 JCD  H21  O9   C20  107.49  3.000
 JCD  O7   C17  N1   123.12  3.000
 JCD  O7   C17  C18  122.61  3.000
 JCD  N1   C17  C18  114.27  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_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  H13  O3   C12  C11   180.00   0.0  0
 JCD  CONST_42  H16  N1   C17  C18     0.00   0.0  0
 JCD  Var_01    C4   C3   O2   C2     -8.69  30.0  1
 JCD  Var_02    O4   C12  C11  C10    -0.13  30.0  2
 JCD  Var_03    H17  C18  C17  N1   -148.39  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
 JCD  plan-5  H13  0.020

