# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 17:18:40 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: pyridin-4-yl (5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-1-thio-beta-D-ribo-hept-5-enofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@H](O)[C@H](O[C@H]1Sc2ccncc2)\C=C\CNC(=O)c3cc(cc(O)c3O)[N+]([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
 611  611  'pyridin-4-yl (5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-1-thio-beta-D-ribo-hept-5-enofuranoside'  ligand  50  31  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_611
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
 611  C1    C  CH1    0  -0.005  -3.7816   2.8028   1.5726
 611  C2    C  CH1    0  -0.012  -3.0471   1.5339   1.9997
 611  C3    C  CH1    0  -0.124  -3.0155   0.7325   0.6784
 611  O4    O  O2     0  -0.467  -3.2335   1.6425  -0.3622
 611  C5    C  CH1    0  -0.043  -3.2306   2.9681   0.1624
 611  C6    C  C1     0  -0.284  -1.8457   3.5569   0.1731
 611  S7    S  S2     0   0.075  -1.4090  -0.1311   0.6049
 611  O8    O  OH1    0  -0.666  -5.1658   2.6023   1.4822
 611  O9    O  OH1    0  -0.655  -3.7083   0.8882   3.0427
 611  C10   C  C1     0  -0.182  -0.8592   3.1159  -0.5955
 611  C11   C  CR6    0  -0.006  -1.6641  -1.4174  -0.5576
 611  C12   C  CH2    0  -0.364   0.5662   3.5654  -0.5121
 611  N13   N  NH1    0  -0.616   1.4046   2.4073  -0.2535
 611  C14   C  C      0   0.541   1.8660   1.6268  -1.2493
 611  C15   C  CR6    0  -0.160   2.4814   0.3397  -0.7946
 611  C16   C  CR6    0   0.315   2.1536  -0.8487  -1.4481
 611  C17   C  CR6    0   0.300   2.7550  -2.0543  -1.0364
 611  C18   C  CR16   0  -0.401   3.6615  -2.0650  -0.0012
 611  C19   C  CR6    0   0.261   3.9749  -0.8655   0.6326
 611  C20   C  CR16   0  -0.312   3.3942   0.3293   0.2523
 611  N21   N  N      1   0.323   4.9336  -0.8761   1.7145
 611  O22   O  OH1    0  -0.586   1.2627  -0.8394  -2.4339
 611  O23   O  OH1    0  -0.637   2.3743  -3.1456  -1.7230
 611  O24   O  O      0  -0.470   1.8137   1.9311  -2.4287
 611  O25   O  O      0  -0.384   5.4145  -1.9380   2.0397
 611  O26   O  O     -1  -0.385   5.2092   0.1756   2.2458
 611  C27   C  CR16   0  -0.355  -0.8251  -2.5281  -0.4870
 611  C28   C  CR16   0  -0.057  -0.9812  -3.5411  -1.4166
 611  N29   N  N      0  -0.412  -1.8974  -3.5263  -2.3797
 611  C30   C  CR16   0  -0.059  -2.6940  -2.4661  -2.4374
 611  C31   C  CR16   0  -0.324  -2.6202  -1.3881  -1.5684
 611  H1    H  HCH1   0   0.251  -3.5292   3.6534   2.2177
 611  H2    H  HCH1   0   0.250  -2.0260   1.8192   2.2876
 611  H3    H  HCH1   0   0.295  -3.7951  -0.0338   0.6634
 611  H5    H  HCH1   0   0.282  -3.9044   3.5739  -0.4518
 611  H6    H  H      0   0.261  -1.6752   4.3699   0.8740
 611  HO8   H  HOH1   0   0.455  -5.4880   2.2880   2.3337
 611  HO9   H  HOH1   0   0.465  -3.1354   0.2070   3.4085
 611  H10   H  H      0   0.254  -1.0442   2.3094  -1.2976
 611  H12   H  HCH2   0   0.266   0.8966   4.0283  -1.4415
 611  H12A  H  HCH2   0   0.271   0.7102   4.2919   0.2876
 611  HN13  H  HNH1   0   0.405   1.3141   1.9934   0.6616
 611  H18   H  HCR6   0   0.317   4.1199  -2.9961   0.3046
 611  H20   H  HCR6   0   0.304   3.6548   1.2541   0.7468
 611  HO22  H  HOH1   0   0.486   1.0948  -1.7364  -2.7521
 611  HO23  H  HOH1   0   0.493   2.7802  -3.9482  -1.3748
 611  H27   H  HCR6   0   0.282  -0.0716  -2.6146   0.2852
 611  H28   H  HCR6   0   0.266  -0.3358  -4.4107  -1.3721
 611  H30   H  HCR6   0   0.269  -3.4369  -2.4589  -3.2271
 611  H31   H  HCR6   0   0.279  -3.2908  -0.5521  -1.7059

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
 611  C1   C2    single    1.527  0.020  1.527
 611  C1   C5    single    1.523  0.020  1.523
 611  C1   O8    single    1.402  0.020  1.402
 611  C2   C3    single    1.546  0.020  1.546
 611  C2   O9    single    1.394  0.020  1.394
 611  C3   O4    single    1.399  0.020  1.399
 611  C3   S7    single    1.825  0.020  1.825
 611  O4   C5    single    1.426  0.020  1.426
 611  C5   C6    single    1.505  0.020  1.505
 611  C6   C10   double    1.326  0.020  1.326
 611  S7   C11   single    1.752  0.020  1.752
 611  C10  C12   single    1.497  0.020  1.497
 611  C11  C27   aromatic  1.394  0.020  1.394
 611  C11  C31   aromatic  1.392  0.020  1.392
 611  C12  N13   single    1.453  0.020  1.453
 611  N13  C14   single    1.347  0.020  1.347
 611  C14  C15   single    1.497  0.020  1.497
 611  C14  O24   double    1.219  0.020  1.219
 611  C15  C16   aromatic  1.395  0.020  1.395
 611  C15  C20   aromatic  1.389  0.020  1.389
 611  C16  C17   aromatic  1.409  0.020  1.409
 611  C16  O22   single    1.329  0.020  1.329
 611  C17  C18   aromatic  1.376  0.020  1.376
 611  C17  O23   single    1.344  0.020  1.344
 611  C18  C19   aromatic  1.392  0.020  1.392
 611  C19  C20   aromatic  1.382  0.020  1.382
 611  C19  N21   single    1.446  0.020  1.446
 611  N21  O25   double    1.210  0.020  1.210
 611  N21  O26   single    1.210  0.020  1.210
 611  C27  C28   aromatic  1.384  0.020  1.384
 611  C28  N29   aromatic  1.329  0.020  1.329
 611  N29  C30   aromatic  1.327  0.020  1.327
 611  C30  C31   aromatic  1.387  0.020  1.387
 611  C1   H1    single    0.970  0.020  1.090
 611  C2   H2    single    0.970  0.020  1.090
 611  C3   H3    single    0.970  0.020  1.090
 611  C5   H5    single    0.970  0.020  1.090
 611  C6   H6    single    0.930  0.020  1.080
 611  O8   HO8   single    0.850  0.020  0.980
 611  O9   HO9   single    0.850  0.020  0.980
 611  C10  H10   single    0.930  0.020  1.080
 611  C12  H12   single    0.970  0.020  1.090
 611  C12  H12A  single    0.970  0.020  1.090
 611  N13  HN13  single    0.890  0.020  1.040
 611  C18  H18   single    0.930  0.020  1.080
 611  C20  H20   single    0.930  0.020  1.080
 611  O22  HO22  single    0.850  0.020  0.980
 611  O23  HO23  single    0.850  0.020  0.980
 611  C27  H27   single    0.930  0.020  1.080
 611  C28  H28   single    0.930  0.020  1.080
 611  C30  H30   single    0.930  0.020  1.080
 611  C31  H31   single    0.930  0.020  1.080

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
 611  H1    C1   O8   112.09  3.000
 611  H1    C1   C5   112.15  3.000
 611  O8    C1   C5   108.25  3.000
 611  H1    C1   C2   111.67  3.000
 611  O8    C1   C2   111.97  3.000
 611  C5    C1   C2   100.09  3.000
 611  H2    C2   O9   111.42  3.000
 611  H2    C2   C3   109.86  3.000
 611  O9    C2   C3   114.16  3.000
 611  H2    C2   C1   107.74  3.000
 611  O9    C2   C1   111.48  3.000
 611  C3    C2   C1   101.63  3.000
 611  H3    C3   S7   107.19  3.000
 611  H3    C3   O4   109.54  3.000
 611  S7    C3   O4   114.51  3.000
 611  H3    C3   C2   111.13  3.000
 611  S7    C3   C2   107.32  3.000
 611  O4    C3   C2   107.17  3.000
 611  C5    O4   C3   109.31  3.000
 611  H5    C5   C6   110.73  3.000
 611  H5    C5   O4   107.87  3.000
 611  C6    C5   O4   111.61  3.000
 611  H5    C5   C1   110.91  3.000
 611  C6    C5   C1   111.64  3.000
 611  O4    C5   C1   103.83  3.000
 611  H6    C6   C10  120.38  3.000
 611  H6    C6   C5   116.21  3.000
 611  C10   C6   C5   123.39  3.000
 611  C11   S7   C3   104.23  3.000
 611  HO8   O8   C1   108.67  3.000
 611  HO9   O9   C2   109.27  3.000
 611  H10   C10  C12  114.93  3.000
 611  H10   C10  C6   119.69  3.000
 611  C12   C10  C6   125.19  3.000
 611  C31   C11  C27  117.85  3.000
 611  C31   C11  S7   124.50  3.000
 611  C27   C11  S7   117.63  3.000
 611  H12A  C12  H12  107.61  3.000
 611  H12A  C12  N13  108.93  3.000
 611  H12   C12  N13  108.39  3.000
 611  H12A  C12  C10  111.52  3.000
 611  H12   C12  C10  111.65  3.000
 611  N13   C12  C10  108.67  3.000
 611  HN13  N13  C14  117.64  3.000
 611  HN13  N13  C12  115.90  3.000
 611  C14   N13  C12  121.88  3.000
 611  O24   C14  C15  121.74  3.000
 611  O24   C14  N13  123.77  3.000
 611  C15   C14  N13  114.48  3.000
 611  C20   C15  C16  120.07  3.000
 611  C20   C15  C14  120.36  3.000
 611  C16   C15  C14  119.56  3.000
 611  O22   C16  C17  120.60  3.000
 611  O22   C16  C15  119.94  3.000
 611  C17   C16  C15  119.45  3.000
 611  O23   C17  C18  124.37  3.000
 611  O23   C17  C16  115.12  3.000
 611  C18   C17  C16  120.51  3.000
 611  H18   C18  C19  121.16  3.000
 611  H18   C18  C17  119.89  3.000
 611  C19   C18  C17  118.95  3.000
 611  N21   C19  C20  119.41  3.000
 611  N21   C19  C18  118.92  3.000
 611  C20   C19  C18  121.67  3.000
 611  H20   C20  C19  120.84  3.000
 611  H20   C20  C15  119.80  3.000
 611  C19   C20  C15  119.35  3.000
 611  O26   N21  O25  123.65  3.000
 611  O26   N21  C19  118.25  3.000
 611  O25   N21  C19  118.10  3.000
 611  HO22  O22  C16  110.75  3.000
 611  HO23  O23  C17  111.83  3.000
 611  H27   C27  C28  119.96  3.000
 611  H27   C27  C11  121.26  3.000
 611  C28   C27  C11  118.78  3.000
 611  H28   C28  N29  116.69  3.000
 611  H28   C28  C27  119.51  3.000
 611  N29   C28  C27  123.80  3.000
 611  C30   N29  C28  117.00  3.000
 611  H30   C30  C31  119.20  3.000
 611  H30   C30  N29  116.62  3.000
 611  C31   C30  N29  124.18  3.000
 611  H31   C31  C30  119.25  3.000
 611  H31   C31  C11  122.35  3.000
 611  C30   C31  C11  118.39  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
 611  CONST_01  N29   C28  C27  C11     0.00   0.0  0
 611  CONST_02  N29   C30  C31  C11     0.00   0.0  0
 611  CONST_03  C18   C17  C16  C15     0.00   0.0  0
 611  CONST_04  C18   C19  C20  C15     0.00   0.0  0
 611  CONST_05  C19   C20  C15  C16     0.00   0.0  0
 611  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 611  CONST_07  C20   C15  C16  C17     0.00   0.0  0
 611  CONST_08  C20   C19  C18  C17     0.00   0.0  0
 611  CONST_09  C30   C31  C11  C27     0.00   0.0  0
 611  CONST_10  C30   N29  C28  C27     0.00   0.0  0
 611  CONST_11  C31   C11  C27  C28     0.00   0.0  0
 611  CONST_12  C31   C30  N29  C28     0.00   0.0  0
 611  CONST_13  C28   C27  C11  S7    180.00   0.0  0
 611  CONST_14  C30   C31  C11  S7    180.00   0.0  0
 611  CONST_15  C17   C16  C15  C14   180.00   0.0  0
 611  CONST_16  C19   C20  C15  C14   180.00   0.0  0
 611  CONST_17  O23   C17  C16  C15   180.00   0.0  0
 611  CONST_18  N21   C19  C20  C15   180.00   0.0  0
 611  CONST_19  N21   C19  C18  C17   180.00   0.0  0
 611  CONST_20  O22   C16  C17  C18   180.00   0.0  0
 611  CONST_21  O23   C17  C18  C19   180.00   0.0  0
 611  CONST_22  O22   C16  C15  C20   180.00   0.0  0
 611  CONST_23  H28   C28  C27  C11   180.00   0.0  0
 611  CONST_24  H30   C30  C31  C11   180.00   0.0  0
 611  CONST_25  H20   C20  C15  C16   180.00   0.0  0
 611  CONST_26  H18   C18  C17  C16   180.00   0.0  0
 611  CONST_27  H31   C31  C11  C27   180.00   0.0  0
 611  CONST_28  H27   C27  C28  N29   180.00   0.0  0
 611  CONST_29  O25   N21  C19  C18     0.00   0.0  0
 611  CONST_30  O26   N21  C19  C18   180.00   0.0  0
 611  CONST_31  O25   N21  C19  C20   180.00   0.0  0
 611  CONST_32  O26   N21  C19  C20     0.00   0.0  0
 611  CONST_33  C15   C14  N13  C12   180.00   0.0  0
 611  CONST_34  HN13  N13  C14  C15     0.00   0.0  0
 611  CONST_35  O24   C14  N13  C12     0.00   0.0  0
 611  Var_01    C27   C11  S7   C3   -157.04  30.0  2
 611  Var_02    C16   C15  C14  N13   134.51  30.0  2
 611  Var_03    C12   C10  C6   C5   -172.83   0.0  2
 611  Var_04    N13   C12  C10  C6    121.70  30.0  3
 611  Var_05    C14   N13  C12  C10    85.87  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
 611  chir_01  C1  C2  C5  O8  negativ
 611  chir_02  C2  O9  C3  C1  negativ
 611  chir_03  C3  S7  O4  C2  positiv
 611  chir_04  C5  O4  C1  C6  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
 611  plan-1  S7    0.020
 611  plan-1  C11   0.020
 611  plan-1  C27   0.020
 611  plan-1  C28   0.020
 611  plan-1  N29   0.020
 611  plan-1  C30   0.020
 611  plan-1  C31   0.020
 611  plan-1  H27   0.020
 611  plan-1  H28   0.020
 611  plan-1  H30   0.020
 611  plan-1  H31   0.020
 611  plan-2  C14   0.020
 611  plan-2  C15   0.020
 611  plan-2  C16   0.020
 611  plan-2  C17   0.020
 611  plan-2  C18   0.020
 611  plan-2  C19   0.020
 611  plan-2  C20   0.020
 611  plan-2  N21   0.020
 611  plan-2  O22   0.020
 611  plan-2  O23   0.020
 611  plan-2  H18   0.020
 611  plan-2  H20   0.020
 611  plan-3  C19   0.020
 611  plan-3  N21   0.020
 611  plan-3  O25   0.020
 611  plan-3  O26   0.020
 611  plan-4  C12   0.020
 611  plan-4  N13   0.020
 611  plan-4  C14   0.020
 611  plan-4  C15   0.020
 611  plan-4  O24   0.020
 611  plan-4  HN13  0.020
 611  plan-5  C5    0.020
 611  plan-5  C6    0.020
 611  plan-5  C10   0.020
 611  plan-5  C12   0.020
 611  plan-5  H6    0.020
 611  plan-5  H10   0.020

