# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 11:18:24 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 9-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1\C=C\CNC(=O)c2cc(cc(O)c2O)[N+]([O-])=O)n3cnc4cncnc34
#
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
 610  610  9-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}-9H-purine  ligand  51  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_610
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
 610  C1    C  CH1    0  -0.042  -3.0174   2.4826   1.1154
 610  C2    C  CH1    0  -0.038  -4.0164   1.5732   0.3939
 610  C3    C  CH1    0   0.164  -3.1829   1.1409  -0.8097
 610  O4    O  O2     0  -0.492  -2.3448   2.2103  -1.1202
 610  C5    C  CH1    0   0.016  -2.3150   3.1667  -0.0649
 610  C6    C  C1     0  -0.245  -0.9227   3.5906   0.2647
 610  N7    N  NR5    0  -0.543  -2.3773  -0.0406  -0.4945
 610  O8    O  OH1    0  -0.654  -3.6071   3.4455   1.9378
 610  O9    O  OH1    0  -0.662  -5.1081   2.3031  -0.0892
 610  C10   C  C1     0  -0.240   0.1623   3.3224  -0.4510
 610  C11   C  CR15   0   0.140  -1.0367  -0.1260  -0.2305
 610  N12   N  N      0  -0.441  -0.6201  -1.3311   0.0221
 610  C13   C  CH2    0  -0.368   1.5570   3.6280   0.0070
 610  N14   N  NH1    0  -0.648   2.2173   2.3714   0.3285
 610  C15   C  C      0   0.636   2.9356   1.6644  -0.5466
 610  C16   C  CR6    0  -0.168   3.1970   0.2325  -0.2428
 610  C17   C  CR6    0   0.315   4.1291  -0.4495  -1.0414
 610  C18   C  CR6    0   0.310   4.3645  -1.8249  -0.8176
 610  C19   C  CR16   0  -0.409   3.6299  -2.5048   0.1250
 610  C20   C  CR6    0   0.280   2.6847  -1.8134   0.8834
 610  C21   C  CR16   0  -0.342   2.4723  -0.4652   0.7201
 610  N22   N  N      1   0.328   1.8791  -2.5381   1.8370
 610  O23   O  OH1    0  -0.602   4.8122   0.1259  -2.0137
 610  O24   O  OH1    0  -0.617   5.3011  -2.3908  -1.5931
 610  O25   O  O      0  -0.526   3.3667   2.1591  -1.5962
 610  O26   O  O      0  -0.389   1.8844  -3.7482   1.7799
 610  O27   O  O     -1  -0.381   1.2391  -1.9073   2.6456
 610  C28   C  CR56   0   0.494  -2.8521  -1.3146  -0.4056
 610  C29   C  CR56   0   0.080  -1.7441  -2.1073  -0.0784
 610  C30   C  CR16   0  -0.063  -1.9962  -3.4603   0.0716
 610  N31   N  N      0  -0.411  -3.2288  -3.9211  -0.1025
 610  C32   C  CR16   0   0.039  -4.1969  -3.0599  -0.4178
 610  N33   N  N      0  -0.419  -4.0851  -1.7495  -0.5821
 610  H1    H  HCH1   0   0.253  -2.3002   1.8635   1.6698
 610  H2    H  HCH1   0   0.265  -4.3315   0.7199   1.0066
 610  H3    H  HCH1   0   0.295  -3.8052   0.8855  -1.6707
 610  H5    H  HCH1   0   0.268  -2.9025   4.0464  -0.3604
 610  H6    H  H      0   0.272  -0.8358   4.1547   1.1901
 610  HO8   H  HOH1   0   0.471  -3.7737   3.0590   2.8037
 610  HO9   H  HOH1   0   0.454  -5.3468   2.9553   0.5813
 610  H10   H  H      0   0.267   0.0882   2.7796  -1.3888
 610  H11   H  HCR5   0   0.280  -0.4037   0.7477  -0.2430
 610  H13   H  HCH2   0   0.275   2.1324   4.1438  -0.7593
 610  H13A  H  HCH2   0   0.278   1.5555   4.2535   0.8988
 610  HN14  H  HNH1   0   0.421   1.9385   1.9442   1.1965
 610  H19   H  HCR6   0   0.314   3.7901  -3.5655   0.2698
 610  H21   H  HCR6   0   0.277   1.7090   0.0170   1.3116
 610  HO23  H  HOH1   0   0.486   4.4408   1.0407  -2.1173
 610  HO24  H  HOH1   0   0.484   5.3906  -3.3287  -1.3881
 610  H30   H  HCR6   0   0.279  -1.2177  -4.1700   0.3306
 610  H32   H  HCR6   0   0.264  -5.1870  -3.4789  -0.5526

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
 610  C1   C2    single    1.532  0.020  1.532
 610  C1   C5    single    1.534  0.020  1.534
 610  C1   O8    single    1.397  0.020  1.397
 610  C2   C3    single    1.526  0.020  1.526
 610  C2   O9    single    1.399  0.020  1.399
 610  C3   O4    single    1.394  0.020  1.394
 610  C3   N7    single    1.464  0.020  1.464
 610  O4   C5    single    1.424  0.020  1.424
 610  C5   C6    single    1.492  0.020  1.492
 610  C6   C10   double    1.327  0.020  1.327
 610  N7   C11   aromatic  1.369  0.020  1.369
 610  N7   C28   aromatic  1.362  0.020  1.362
 610  C10  C13   single    1.499  0.020  1.499
 610  C11  N12   aromatic  1.300  0.020  1.300
 610  N12  C29   aromatic  1.370  0.020  1.370
 610  C13  N14   single    1.455  0.020  1.455
 610  N14  C15   single    1.335  0.020  1.335
 610  C15  C16   single    1.487  0.020  1.487
 610  C15  O25   double    1.238  0.020  1.238
 610  C16  C17   aromatic  1.404  0.020  1.404
 610  C16  C21   aromatic  1.393  0.020  1.393
 610  C17  C18   aromatic  1.413  0.020  1.413
 610  C17  O23   single    1.320  0.020  1.320
 610  C18  C19   aromatic  1.375  0.020  1.375
 610  C18  O24   single    1.341  0.020  1.341
 610  C19  C20   aromatic  1.395  0.020  1.395
 610  C20  C21   aromatic  1.375  0.020  1.375
 610  C20  N22   single    1.443  0.020  1.443
 610  N22  O26   double    1.211  0.020  1.211
 610  N22  O27   single    1.209  0.020  1.209
 610  C28  C29   aromatic  1.401  0.020  1.401
 610  C28  N33   aromatic  1.319  0.020  1.319
 610  C29  C30   aromatic  1.384  0.020  1.384
 610  C30  N31   aromatic  1.327  0.020  1.327
 610  N31  C32   aromatic  1.334  0.020  1.334
 610  C32  N33   aromatic  1.325  0.020  1.325
 610  C1   H1    single    0.970  0.020  1.090
 610  C2   H2    single    0.970  0.020  1.090
 610  C3   H3    single    0.970  0.020  1.090
 610  C5   H5    single    0.970  0.020  1.090
 610  C6   H6    single    0.930  0.020  1.080
 610  O8   HO8   single    0.850  0.020  0.980
 610  O9   HO9   single    0.850  0.020  0.980
 610  C10  H10   single    0.930  0.020  1.080
 610  C11  H11   single    0.930  0.020  1.080
 610  C13  H13   single    0.970  0.020  1.090
 610  C13  H13A  single    0.970  0.020  1.090
 610  N14  HN14  single    0.860  0.020  1.020
 610  C19  H19   single    0.930  0.020  1.080
 610  C21  H21   single    0.930  0.020  1.080
 610  O23  HO23  single    0.850  0.020  0.980
 610  O24  HO24  single    0.850  0.020  0.980
 610  C30  H30   single    0.930  0.020  1.080
 610  C32  H32   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
 610  H1    C1   O8   111.55  3.000
 610  H1    C1   C5   109.93  3.000
 610  O8    C1   C5   109.80  3.000
 610  H1    C1   C2   109.22  3.000
 610  O8    C1   C2   114.29  3.000
 610  C5    C1   C2   101.59  3.000
 610  H2    C2   O9   111.99  3.000
 610  H2    C2   C3   112.15  3.000
 610  O9    C2   C3   107.55  3.000
 610  H2    C2   C1   112.72  3.000
 610  O9    C2   C1   111.21  3.000
 610  C3    C2   C1   100.57  3.000
 610  H3    C3   N7   107.11  3.000
 610  H3    C3   O4   110.26  3.000
 610  N7    C3   O4   109.65  3.000
 610  H3    C3   C2   112.12  3.000
 610  N7    C3   C2   111.05  3.000
 610  O4    C3   C2   106.66  3.000
 610  C5    O4   C3   111.26  3.000
 610  H5    C5   C6   109.32  3.000
 610  H5    C5   O4   109.10  3.000
 610  C6    C5   O4   111.96  3.000
 610  H5    C5   C1   108.61  3.000
 610  C6    C5   C1   112.57  3.000
 610  O4    C5   C1   105.13  3.000
 610  H6    C6   C10  119.90  3.000
 610  H6    C6   C5   114.20  3.000
 610  C10   C6   C5   125.89  3.000
 610  C28   N7   C11  105.68  3.000
 610  C28   N7   C3   125.23  3.000
 610  C11   N7   C3   129.09  3.000
 610  HO8   O8   C1   109.02  3.000
 610  HO9   O9   C2   107.79  3.000
 610  H10   C10  C13  115.41  3.000
 610  H10   C10  C6   120.72  3.000
 610  C13   C10  C6   123.67  3.000
 610  H11   C11  N12  124.40  3.000
 610  H11   C11  N7   121.45  3.000
 610  N12   C11  N7   114.15  3.000
 610  C29   N12  C11  104.37  3.000
 610  H13A  C13  H13  107.76  3.000
 610  H13A  C13  N14  108.40  3.000
 610  H13   C13  N14  108.96  3.000
 610  H13A  C13  C10  111.46  3.000
 610  H13   C13  C10  111.92  3.000
 610  N14   C13  C10  108.27  3.000
 610  HN14  N14  C15  119.31  3.000
 610  HN14  N14  C13  115.54  3.000
 610  C15   N14  C13  123.83  3.000
 610  O25   C15  C16  119.79  3.000
 610  O25   C15  N14  122.11  3.000
 610  C16   C15  N14  118.08  3.000
 610  C21   C16  C17  119.70  3.000
 610  C21   C16  C15  122.15  3.000
 610  C17   C16  C15  117.92  3.000
 610  O23   C17  C18  117.04  3.000
 610  O23   C17  C16  123.41  3.000
 610  C18   C17  C16  119.55  3.000
 610  O24   C18  C19  124.11  3.000
 610  O24   C18  C17  115.81  3.000
 610  C19   C18  C17  120.06  3.000
 610  H19   C19  C20  120.87  3.000
 610  H19   C19  C18  119.82  3.000
 610  C20   C19  C18  119.31  3.000
 610  N22   C20  C21  118.99  3.000
 610  N22   C20  C19  119.23  3.000
 610  C21   C20  C19  121.75  3.000
 610  H21   C21  C20  118.84  3.000
 610  H21   C21  C16  121.55  3.000
 610  C20   C21  C16  119.54  3.000
 610  O27   N22  O26  123.72  3.000
 610  O27   N22  C20  118.38  3.000
 610  O26   N22  C20  117.90  3.000
 610  HO23  O23  C17  106.56  3.000
 610  HO24  O24  C18  110.63  3.000
 610  N33   C28  C29  125.72  3.000
 610  N33   C28  N7   128.69  3.000
 610  C29   C28  N7   105.59  3.000
 610  C30   C29  C28  115.73  3.000
 610  C30   C29  N12  134.06  3.000
 610  C28   C29  N12  110.21  3.000
 610  H30   C30  N31  118.07  3.000
 610  H30   C30  C29  122.31  3.000
 610  N31   C30  C29  119.62  3.000
 610  C32   N31  C30  118.74  3.000
 610  H32   C32  N33  116.36  3.000
 610  H32   C32  N31  116.30  3.000
 610  N33   C32  N31  127.35  3.000
 610  C32   N33  C28  112.84  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
 610  CONST_01  C29   N12  C11  N7      0.00   0.0  0
 610  CONST_02  N12   C29  C28  N7      0.00   0.0  0
 610  CONST_03  C30   C29  C28  N7    180.00   0.0  0
 610  CONST_04  C32   N33  C28  N7    180.00   0.0  0
 610  CONST_05  C29   C28  N7   C11     0.00   0.0  0
 610  CONST_06  N33   C28  N7   C11   180.00   0.0  0
 610  CONST_07  C28   C29  N12  C11     0.00   0.0  0
 610  CONST_08  C30   C29  N12  C11   180.00   0.0  0
 610  CONST_09  C28   N7   C11  N12     0.00   0.0  0
 610  CONST_10  N33   C28  C29  N12   180.00   0.0  0
 610  CONST_11  N31   C30  C29  N12   180.00   0.0  0
 610  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 610  CONST_13  C19   C20  C21  C16     0.00   0.0  0
 610  CONST_14  C20   C21  C16  C17     0.00   0.0  0
 610  CONST_15  C20   C19  C18  C17     0.00   0.0  0
 610  CONST_16  C21   C16  C17  C18     0.00   0.0  0
 610  CONST_17  C21   C20  C19  C18     0.00   0.0  0
 610  CONST_18  N31   C30  C29  C28     0.00   0.0  0
 610  CONST_19  N31   C32  N33  C28     0.00   0.0  0
 610  CONST_20  C32   N33  C28  C29     0.00   0.0  0
 610  CONST_21  C32   N31  C30  C29     0.00   0.0  0
 610  CONST_22  N33   C28  C29  C30     0.00   0.0  0
 610  CONST_23  N33   C32  N31  C30     0.00   0.0  0
 610  CONST_24  N12   C11  N7   C3    180.00   0.0  0
 610  CONST_25  C29   C28  N7   C3    180.00   0.0  0
 610  CONST_26  N33   C28  N7   C3      0.00   0.0  0
 610  CONST_27  C18   C17  C16  C15   180.00   0.0  0
 610  CONST_28  C20   C21  C16  C15   180.00   0.0  0
 610  CONST_29  O24   C18  C17  C16   180.00   0.0  0
 610  CONST_30  N22   C20  C21  C16   180.00   0.0  0
 610  CONST_31  N22   C20  C19  C18   180.00   0.0  0
 610  CONST_32  O23   C17  C18  C19   180.00   0.0  0
 610  CONST_33  O24   C18  C19  C20   180.00   0.0  0
 610  CONST_34  O23   C17  C16  C21   180.00   0.0  0
 610  CONST_35  H11   C11  N7   C3      0.00   0.0  0
 610  CONST_36  H30   C30  C29  N12     0.00   0.0  0
 610  CONST_37  H21   C21  C16  C17   180.00   0.0  0
 610  CONST_38  H19   C19  C18  C17   180.00   0.0  0
 610  CONST_39  H32   C32  N33  C28   180.00   0.0  0
 610  CONST_40  O26   N22  C20  C19     0.00   0.0  0
 610  CONST_41  O27   N22  C20  C19   180.00   0.0  0
 610  CONST_42  O26   N22  C20  C21   180.00   0.0  0
 610  CONST_43  O27   N22  C20  C21     0.00   0.0  0
 610  CONST_45  HN14  N14  C15  C16     0.00   0.0  0
 610  Var_01    C17   C16  C15  N14  -169.67  30.0  2
 610  Var_02    C13   C10  C6   C5   -172.31   0.0  2
 610  Var_03    N14   C13  C10  C6    108.63  30.0  3
 610  Var_04    C15   N14  C13  C10    91.29  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
 610  chir_01  C1  C2  C5  O8  negativ
 610  chir_02  C2  O9  C3  C1  negativ
 610  chir_03  C3  O4  N7  C2  negativ
 610  chir_04  C5  O4  C6  C1  positiv

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
 610  plan-1  C15   0.020
 610  plan-1  C16   0.020
 610  plan-1  C17   0.020
 610  plan-1  C18   0.020
 610  plan-1  C19   0.020
 610  plan-1  C20   0.020
 610  plan-1  C21   0.020
 610  plan-1  N22   0.020
 610  plan-1  O23   0.020
 610  plan-1  O24   0.020
 610  plan-1  H19   0.020
 610  plan-1  H21   0.020
 610  plan-2  C3    0.020
 610  plan-2  N7    0.020
 610  plan-2  C11   0.020
 610  plan-2  N12   0.020
 610  plan-2  C28   0.020
 610  plan-2  C29   0.020
 610  plan-2  C30   0.020
 610  plan-2  N31   0.020
 610  plan-2  C32   0.020
 610  plan-2  N33   0.020
 610  plan-2  H11   0.020
 610  plan-2  H30   0.020
 610  plan-2  H32   0.020
 610  plan-3  C20   0.020
 610  plan-3  N22   0.020
 610  plan-3  O26   0.020
 610  plan-3  O27   0.020
 610  plan-4  C13   0.020
 610  plan-4  N14   0.020
 610  plan-4  C15   0.020
 610  plan-4  C16   0.020
 610  plan-4  O25   0.020
 610  plan-4  HN14  0.020
 610  plan-5  C5    0.020
 610  plan-5  C6    0.020
 610  plan-5  C10   0.020
 610  plan-5  C13   0.020
 610  plan-5  H6    0.020
 610  plan-5  H10   0.020

