# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 02:16:38 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-(5-nitro-1H-indol-1-yl)phenyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2)n3ccc4cc(ccc34)[N+]([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
 3XN  3XN  '4-(5-nitro-1H-indol-1-yl)phenyl alpha-D-mannopyranoside'  ligand  50  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XN
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
 3XN  O3   O  OH1    0  -0.672  -6.5549  -2.1759  -0.7643
 3XN  C4   C  CH1    0  -0.017  -4.7428   1.0135  -0.1830
 3XN  C5   C  CH2    0  -0.160  -5.1848   2.4235   0.1455
 3XN  O4   O  OH1    0  -0.665  -5.4062  -1.8116   1.7454
 3XN  C6   C  CR6    0   0.387  -1.3253  -0.3572  -0.1739
 3XN  C7   C  CR16   0  -0.353  -0.9353   0.6189   0.7394
 3XN  C8   C  CR16   0  -0.267   0.3765   1.0716   0.7408
 3XN  C9   C  CR6    0   0.282   1.2938   0.5870  -0.1783
 3XN  O5   O  O2     0  -0.502  -2.5676  -0.8868  -0.2500
 3XN  C10  C  CR16   0  -0.273   0.8967  -0.3691  -1.1065
 3XN  O6   O  O      0  -0.390   7.7422  -2.3901   0.5380
 3XN  C11  C  CR16   0  -0.348  -0.4003  -0.8458  -1.0959
 3XN  C12  C  CR15   0  -0.020   2.9762   2.4022  -0.2912
 3XN  C13  C  CR15   0  -0.401   4.3276   2.5327  -0.2354
 3XN  O7   O  O     -1  -0.391   8.5665  -0.4401   0.2904
 3XN  C14  C  CR56   0   0.062   4.8563   1.2150  -0.0738
 3XN  C15  C  CR56   0   0.378   3.7542   0.3288  -0.0388
 3XN  C18  C  CR6    0   0.241   6.2910  -0.6533   0.2231
 3XN  C19  C  CR16   0  -0.372   6.1458   0.7124   0.0552
 3XN  C17  C  CR16   0  -0.297   5.1952  -1.5313   0.2717
 3XN  C16  C  CR16   0  -0.284   3.9153  -1.0451   0.1419
 3XN  N    N  NR5    0  -0.627   2.6210   1.0750  -0.1775
 3XN  C    C  CH1    0   0.204  -3.4687  -0.7333   0.8240
 3XN  O    O  O2     0  -0.489  -3.9728   0.5539   0.9183
 3XN  O1   O  OH1    0  -0.666  -4.0449   3.2377   0.2835
 3XN  C3   C  CH1    0   0.033  -5.9326   0.0828  -0.4205
 3XN  O2   O  OH1    0  -0.675  -6.5987   0.5260  -1.5779
 3XN  C2   C  CH1    0  -0.000  -5.4308  -1.3477  -0.5890
 3XN  C1   C  CH1    0  -0.023  -4.5824  -1.7649   0.6102
 3XN  HO3  H  HOH1   0   0.459  -6.2825  -2.9751  -1.2252
 3XN  H4   H  HCH1   0   0.232  -4.1297   1.0389  -1.0950
 3XN  H52  H  HCH2   0   0.214  -5.8383   2.7746  -0.6598
 3XN  H51  H  HCH2   0   0.195  -5.7870   2.4034   1.0651
 3XN  HO4  H  HOH1   0   0.459  -4.9430  -2.2868   2.4420
 3XN  H7   H  HCR6   0   0.292  -1.6283   1.0467   1.4485
 3XN  H8   H  HCR6   0   0.279   0.6771   1.8145   1.4687
 3XN  H10  H  HCR6   0   0.282   1.5975  -0.7454  -1.8407
 3XN  H11  H  HCR6   0   0.274  -0.7051  -1.5981  -1.8119
 3XN  H13  H  HCR5   0   0.262   4.8830   3.4534  -0.3092
 3XN  H19  H  HCR6   0   0.290   6.9985   1.3760   0.0297
 3XN  H17  H  HCR6   0   0.291   5.3466  -2.5912   0.4101
 3XN  H16  H  HCR6   0   0.283   3.0710  -1.7191   0.1805
 3XN  H    H  HCH1   0   0.266  -2.9511  -0.9242   1.7722
 3XN  HO1  H  HOH1   0   0.456  -4.3434   4.1463   0.3805
 3XN  H3   H  HCH1   0   0.215  -6.5951   0.1298   0.4566
 3XN  HO2  H  HOH1   0   0.453  -7.3027  -0.1027  -1.7693
 3XN  H2   H  HCH1   0   0.233  -4.7902  -1.3730  -1.4811
 3XN  H1   H  HCH1   0   0.242  -4.1238  -2.7428   0.4099
 3XN  H12  H  HCR5   0   0.301   2.2137   3.1537  -0.4204
 3XN  N1   N  N      1   0.328   7.6244  -1.1982   0.3596

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
 3XN  C13  C12  aromatic  1.359  0.020  1.359
 3XN  C13  C14  aromatic  1.429  0.020  1.429
 3XN  C12  N    aromatic  1.379  0.020  1.379
 3XN  C14  C19  aromatic  1.390  0.020  1.390
 3XN  C14  C15  aromatic  1.415  0.020  1.415
 3XN  N    C9   single    1.414  0.020  1.414
 3XN  N    C15  aromatic  1.364  0.020  1.364
 3XN  C19  C18  aromatic  1.384  0.020  1.384
 3XN  C8   C9   aromatic  1.386  0.020  1.386
 3XN  C8   C7   aromatic  1.388  0.020  1.388
 3XN  C9   C10  aromatic  1.391  0.020  1.391
 3XN  C15  C16  aromatic  1.395  0.020  1.395
 3XN  C7   C6   aromatic  1.392  0.020  1.392
 3XN  C10  C11  aromatic  1.382  0.020  1.382
 3XN  O7   N1   single    1.211  0.020  1.211
 3XN  C6   C11  aromatic  1.394  0.020  1.394
 3XN  C6   O5   single    1.353  0.020  1.353
 3XN  C18  N1   single    1.447  0.020  1.447
 3XN  C18  C17  aromatic  1.405  0.020  1.405
 3XN  O5   C    single    1.410  0.020  1.410
 3XN  C16  C17  aromatic  1.375  0.020  1.375
 3XN  C    C1   single    1.533  0.020  1.533
 3XN  C    O    single    1.386  0.020  1.386
 3XN  N1   O6   double    1.211  0.020  1.211
 3XN  C1   O4   single    1.403  0.020  1.403
 3XN  C1   C2   single    1.527  0.020  1.527
 3XN  O    C4   single    1.420  0.020  1.420
 3XN  C2   O3   single    1.407  0.020  1.407
 3XN  C2   C3   single    1.525  0.020  1.525
 3XN  C4   C3   single    1.529  0.020  1.529
 3XN  C4   C5   single    1.514  0.020  1.514
 3XN  C3   O2   single    1.407  0.020  1.407
 3XN  C5   O1   single    1.408  0.020  1.408
 3XN  O3   HO3  single    0.850  0.020  0.980
 3XN  C4   H4   single    0.970  0.020  1.090
 3XN  C5   H52  single    0.970  0.020  1.090
 3XN  C5   H51  single    0.970  0.020  1.090
 3XN  O4   HO4  single    0.850  0.020  0.980
 3XN  C7   H7   single    0.930  0.020  1.080
 3XN  C8   H8   single    0.930  0.020  1.080
 3XN  C10  H10  single    0.930  0.020  1.080
 3XN  C11  H11  single    0.930  0.020  1.080
 3XN  C12  H12  single    0.930  0.020  1.080
 3XN  C13  H13  single    0.930  0.020  1.080
 3XN  C19  H19  single    0.930  0.020  1.080
 3XN  C17  H17  single    0.930  0.020  1.080
 3XN  C16  H16  single    0.930  0.020  1.080
 3XN  C    H    single    0.970  0.020  1.090
 3XN  O1   HO1  single    0.850  0.020  0.980
 3XN  C3   H3   single    0.970  0.020  1.090
 3XN  O2   HO2  single    0.850  0.020  0.980
 3XN  C2   H2   single    0.970  0.020  1.090
 3XN  C1   H1   single    0.970  0.020  1.090

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
 3XN  HO3  O3   C2   108.81  3.000
 3XN  H4   C4   C3   108.62  3.000
 3XN  H4   C4   O    110.39  3.000
 3XN  C3   C4   O    110.20  3.000
 3XN  H4   C4   C5   108.75  3.000
 3XN  C3   C4   C5   111.93  3.000
 3XN  O    C4   C5   106.94  3.000
 3XN  H51  C5   H52  107.10  3.000
 3XN  H51  C5   O1   111.85  3.000
 3XN  H52  C5   O1   111.71  3.000
 3XN  H51  C5   C4   108.93  3.000
 3XN  H52  C5   C4   108.26  3.000
 3XN  O1   C5   C4   108.89  3.000
 3XN  HO4  O4   C1   108.64  3.000
 3XN  C11  C6   O5   115.78  3.000
 3XN  O5   C6   C7   124.65  3.000
 3XN  C11  C6   C7   119.57  3.000
 3XN  H7   C7   C8   118.47  3.000
 3XN  H7   C7   C6   121.91  3.000
 3XN  C8   C7   C6   119.61  3.000
 3XN  H8   C8   C9   120.13  3.000
 3XN  H8   C8   C7   119.15  3.000
 3XN  C9   C8   C7   120.72  3.000
 3XN  N    C9   C10  120.38  3.000
 3XN  C10  C9   C8   119.61  3.000
 3XN  N    C9   C8   120.01  3.000
 3XN  C    O5   C6   120.09  3.000
 3XN  H10  C10  C11  119.54  3.000
 3XN  H10  C10  C9   120.46  3.000
 3XN  C11  C10  C9   120.01  3.000
 3XN  H11  C11  C10  119.93  3.000
 3XN  H11  C11  C6   119.61  3.000
 3XN  C10  C11  C6   120.45  3.000
 3XN  H12  C12  N    119.91  3.000
 3XN  H12  C12  C13  129.88  3.000
 3XN  N    C12  C13  110.20  3.000
 3XN  H13  C13  C14  127.21  3.000
 3XN  H13  C13  C12  126.28  3.000
 3XN  C14  C13  C12  106.51  3.000
 3XN  C19  C14  C15  119.60  3.000
 3XN  C15  C14  C13  106.99  3.000
 3XN  C19  C14  C13  133.41  3.000
 3XN  N    C15  C16  130.38  3.000
 3XN  C16  C15  C14  122.02  3.000
 3XN  N    C15  C14  107.58  3.000
 3XN  C17  C18  C19  122.63  3.000
 3XN  C17  C18  N1   118.69  3.000
 3XN  C19  C18  N1   118.68  3.000
 3XN  H19  C19  C18  121.74  3.000
 3XN  H19  C19  C14  120.51  3.000
 3XN  C18  C19  C14  117.74  3.000
 3XN  H17  C17  C16  119.32  3.000
 3XN  H17  C17  C18  120.57  3.000
 3XN  C16  C17  C18  120.11  3.000
 3XN  H16  C16  C17  120.20  3.000
 3XN  H16  C16  C15  121.90  3.000
 3XN  C17  C16  C15  117.89  3.000
 3XN  C15  N    C12  108.72  3.000
 3XN  C15  N    C9   126.23  3.000
 3XN  C12  N    C9   125.03  3.000
 3XN  H    C    C1   110.26  3.000
 3XN  H    C    O    105.93  3.000
 3XN  C1   C    O    111.73  3.000
 3XN  H    C    O5   109.75  3.000
 3XN  O    C    O5   112.67  3.000
 3XN  C1   C    O5   106.54  3.000
 3XN  C    O    C4   116.43  3.000
 3XN  HO1  O1   C5   107.77  3.000
 3XN  H3   C3   C2   109.04  3.000
 3XN  H3   C3   O2   110.93  3.000
 3XN  C2   C3   O2   111.12  3.000
 3XN  H3   C3   C4   108.59  3.000
 3XN  O2   C3   C4   107.72  3.000
 3XN  C2   C3   C4   109.39  3.000
 3XN  HO2  O2   C3   107.69  3.000
 3XN  H2   C2   C1   107.91  3.000
 3XN  H2   C2   C3   107.65  3.000
 3XN  C1   C2   C3   110.63  3.000
 3XN  H2   C2   O3   110.55  3.000
 3XN  C3   C2   O3   107.63  3.000
 3XN  C1   C2   O3   112.38  3.000
 3XN  H1   C1   C2   109.39  3.000
 3XN  H1   C1   C    108.73  3.000
 3XN  C2   C1   C    109.22  3.000
 3XN  H1   C1   O4   111.28  3.000
 3XN  C2   C1   O4   108.56  3.000
 3XN  C    C1   O4   109.63  3.000
 3XN  C18  N1   O7   118.41  3.000
 3XN  C18  N1   O6   118.31  3.000
 3XN  O7   N1   O6   123.29  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
 3XN  CONST_01  C9   C8   C7   C6     0.00  0.0  0
 3XN  CONST_02  C9   C10  C11  C6     0.00  0.0  0
 3XN  CONST_03  N    C9   C8   C7   180.00  0.0  0
 3XN  CONST_04  C10  C9   C8   C7     0.00  0.0  0
 3XN  CONST_05  C10  C11  C6   C7     0.00  0.0  0
 3XN  CONST_08  C11  C10  C9   C8     0.00  0.0  0
 3XN  CONST_09  C11  C6   C7   C8     0.00  0.0  0
 3XN  CONST_10  C13  C12  N    C9   180.00  0.0  0
 3XN  CONST_11  C14  C15  N    C9   180.00  0.0  0
 3XN  CONST_12  C16  C15  N    C9     0.00  0.0  0
 3XN  CONST_15  N    C9   C10  C11  180.00  0.0  0
 3XN  CONST_16  C19  C14  C13  C12  180.00  0.0  0
 3XN  CONST_17  C15  C14  C13  C12    0.00  0.0  0
 3XN  CONST_18  C14  C15  N    C12    0.00  0.0  0
 3XN  CONST_19  C16  C15  N    C12  180.00  0.0  0
 3XN  CONST_20  C15  N    C12  C13    0.00  0.0  0
 3XN  CONST_21  C18  C19  C14  C13  180.00  0.0  0
 3XN  CONST_22  N    C15  C14  C13    0.00  0.0  0
 3XN  CONST_23  C16  C15  C14  C13  180.00  0.0  0
 3XN  CONST_24  N    C12  C13  C14    0.00  0.0  0
 3XN  CONST_25  C17  C18  C19  C14    0.00  0.0  0
 3XN  CONST_26  C17  C16  C15  C14    0.00  0.0  0
 3XN  CONST_27  C18  C19  C14  C15    0.00  0.0  0
 3XN  CONST_28  C18  C17  C16  C15    0.00  0.0  0
 3XN  CONST_29  N    C15  C14  C19  180.00  0.0  0
 3XN  CONST_30  C16  C15  C14  C19    0.00  0.0  0
 3XN  CONST_31  C16  C17  C18  C19    0.00  0.0  0
 3XN  CONST_32  N    C15  C16  C17  180.00  0.0  0
 3XN  CONST_33  C14  C19  C18  N1   180.00  0.0  0
 3XN  CONST_34  C16  C17  C18  N1   180.00  0.0  0
 3XN  CONST_35  O5   C6   C7   C8   180.00  0.0  0
 3XN  CONST_36  C10  C11  C6   O5   180.00  0.0  0
 3XN  CONST_37  H8   C8   C7   C6   180.00  0.0  0
 3XN  CONST_38  H10  C10  C11  C6   180.00  0.0  0
 3XN  CONST_39  H11  C11  C6   C7   180.00  0.0  0
 3XN  CONST_40  H12  C12  N    C9     0.00  0.0  0
 3XN  CONST_41  H7   C7   C8   C9   180.00  0.0  0
 3XN  CONST_42  H19  C19  C14  C13    0.00  0.0  0
 3XN  CONST_43  H16  C16  C15  C14  180.00  0.0  0
 3XN  CONST_44  H13  C13  C14  C15  180.00  0.0  0
 3XN  CONST_45  H17  C17  C16  C15  180.00  0.0  0
 3XN  CONST_46  C19  C18  N1   O6   180.00  0.0  0
 3XN  CONST_47  C17  C18  N1   O6     0.00  0.0  0
 3XN  CONST_48  C19  C18  N1   O7     0.00  0.0  0
 3XN  CONST_49  C17  C18  N1   O7   180.00  0.0  0

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
 3XN  chir_01  C4  O   C3  C5  negativ
 3XN  chir_02  C   O   O5  C1  positiv
 3XN  chir_03  C3  O2  C4  C2  positiv
 3XN  chir_04  C2  O3  C3  C1  negativ
 3XN  chir_05  C1  O4  C2  C   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
 3XN  plan-1  C6   0.020
 3XN  plan-1  C7   0.020
 3XN  plan-1  C8   0.020
 3XN  plan-1  C9   0.020
 3XN  plan-1  O5   0.020
 3XN  plan-1  C10  0.020
 3XN  plan-1  C11  0.020
 3XN  plan-1  N    0.020
 3XN  plan-1  H7   0.020
 3XN  plan-1  H8   0.020
 3XN  plan-1  H10  0.020
 3XN  plan-1  H11  0.020
 3XN  plan-2  C9   0.020
 3XN  plan-2  C12  0.020
 3XN  plan-2  C13  0.020
 3XN  plan-2  C14  0.020
 3XN  plan-2  C15  0.020
 3XN  plan-2  C18  0.020
 3XN  plan-2  C19  0.020
 3XN  plan-2  C17  0.020
 3XN  plan-2  C16  0.020
 3XN  plan-2  N    0.020
 3XN  plan-2  H13  0.020
 3XN  plan-2  H19  0.020
 3XN  plan-2  H17  0.020
 3XN  plan-2  H16  0.020
 3XN  plan-2  H12  0.020
 3XN  plan-2  N1   0.020
 3XN  plan-3  O6   0.020
 3XN  plan-3  O7   0.020
 3XN  plan-3  C18  0.020
 3XN  plan-3  N1   0.020

