# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:43:17 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(SCc4ccc(cc4)[N+]([O-])=O)ncnc23
#
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
 NBM  NBM  6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine  ligand  46  29  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NBM
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
 NBM  C01   C  CR16   0  -0.274  -4.8691  -0.4391  -1.0745
 NBM  C02   C  CR16   0  -0.251  -6.1009   0.1579  -1.2739
 NBM  C03   C  CR6    0   0.242  -6.7938   0.6405  -0.1730
 NBM  C04   C  CR16   0  -0.250  -6.2822   0.5382   1.1122
 NBM  C05   C  CR16   0  -0.276  -5.0497  -0.0644   1.2913
 NBM  C06   C  CR6    0   0.109  -4.3357  -0.5635   0.2057
 NBM  C07   C  CH2    0  -0.625  -2.9983  -1.2072   0.4087
 NBM  C09   C  CR6    0   0.046  -0.2685  -0.7871   0.4655
 NBM  C11   C  CR16   0   0.047   0.8698  -2.7290   0.8908
 NBM  C13   C  CR56   0   0.502   2.0871  -0.9297   0.5447
 NBM  C14   C  CR56   0   0.114   0.9568  -0.1315   0.3637
 NBM  C16   C  CR15   0   0.119   2.6157   1.1493   0.1422
 NBM  C18   C  CH1    0   0.213   4.5508  -0.4475   0.4397
 NBM  C19   C  CH1    0  -0.013   5.1372  -0.7574  -0.9415
 NBM  C20   C  CH1    0  -0.033   6.5898  -0.3101  -0.7608
 NBM  C21   C  CH1    0  -0.056   6.3889   0.9357   0.1003
 NBM  C23   C  CH2    0  -0.167   6.1321   2.1767  -0.7354
 NBM  N10   N  N      0  -0.435  -0.2883  -2.0841   0.7281
 NBM  N12   N  N      0  -0.421   2.0881  -2.2268   0.8117
 NBM  N15   N  N      0  -0.447   1.3138   1.1639   0.1163
 NBM  N17   N  NR5    0  -0.538   3.1452  -0.0856   0.3951
 NBM  N27   N  N      1   0.331  -8.0911   1.2688  -0.3711
 NBM  O22   O  O2     0  -0.490   5.2729   0.6302   0.9444
 NBM  O24   O  OH1    0  -0.666   5.7400   3.2203   0.1201
 NBM  O25   O  OH1    0  -0.666   7.2720  -1.3304  -0.0841
 NBM  O26   O  OH1    0  -0.650   4.9279  -2.0959  -1.2525
 NBM  O28   O  O      0  -0.378  -8.5403   1.3034  -1.4924
 NBM  O29   O  O     -1  -0.377  -8.6543   1.7259   0.5953
 NBM  S08   S  S2     0   0.098  -1.7479   0.1081   0.2425
 NBM  H011  H  HCR6   0   0.279  -4.3213  -0.8189  -1.9273
 NBM  H021  H  HCR6   0   0.300  -6.5029   0.2422  -2.2727
 NBM  H041  H  HCR6   0   0.300  -6.8272   0.9133   1.9658
 NBM  H051  H  HCR6   0   0.279  -4.6456  -0.1545   2.2912
 NBM  H071  H  HCH2   0   0.310  -2.9175  -1.6564   1.3971
 NBM  H072  H  HCH2   0   0.310  -2.8087  -1.9728  -0.3416
 NBM  H111  H  HCR6   0   0.266   0.7926  -3.7871   1.1110
 NBM  H161  H  HCR5   0   0.304   3.2431   2.0182   0.0086
 NBM  H181  H  HCH1   0   0.268   4.6231  -1.3244   1.0919
 NBM  H191  H  HCH1   0   0.245   4.6674  -0.0953  -1.6814
 NBM  H201  H  HCH1   0   0.255   7.0657  -0.0640  -1.7189
 NBM  H211  H  HCH1   0   0.265   7.2483   1.1182   0.7528
 NBM  H231  H  HCH2   0   0.228   7.0602   2.4099  -1.2734
 NBM  H232  H  HCH2   0   0.200   5.3682   1.9760  -1.4992
 NBM  H241  H  HOH1   0   0.461   5.5972   4.0063  -0.4147
 NBM  H251  H  HOH1   0   0.458   8.1784  -1.0438   0.0664
 NBM  H261  H  HOH1   0   0.464   5.1479  -2.2354  -2.1790

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
 NBM  C23  O24   single    1.405  0.020  1.405
 NBM  C23  C21   single    1.518  0.020  1.518
 NBM  C16  N15   aromatic  1.302  0.020  1.302
 NBM  C16  N17   aromatic  1.367  0.020  1.367
 NBM  N15  C14   aromatic  1.366  0.020  1.366
 NBM  O22  C21   single    1.432  0.020  1.432
 NBM  O22  C18   single    1.392  0.020  1.392
 NBM  C20  C21   single    1.528  0.020  1.528
 NBM  C20  C19   single    1.531  0.020  1.531
 NBM  C20  O25   single    1.402  0.020  1.402
 NBM  N17  C18   single    1.452  0.020  1.452
 NBM  N17  C13   aromatic  1.362  0.020  1.362
 NBM  S08  C09   single    1.744  0.020  1.744
 NBM  S08  C07   single    1.822  0.020  1.822
 NBM  C19  C18   single    1.532  0.020  1.532
 NBM  C19  O26   single    1.390  0.020  1.390
 NBM  C14  C13   aromatic  1.396  0.020  1.396
 NBM  C14  C09   aromatic  1.393  0.020  1.393
 NBM  C01  C02   aromatic  1.383  0.020  1.383
 NBM  C01  C06   aromatic  1.392  0.020  1.392
 NBM  C02  C03   aromatic  1.387  0.020  1.387
 NBM  O29  N27   single    1.208  0.020  1.208
 NBM  C13  N12   aromatic  1.324  0.020  1.324
 NBM  C09  N10   aromatic  1.323  0.020  1.323
 NBM  C07  C06   single    1.498  0.020  1.498
 NBM  C06  C05   aromatic  1.392  0.020  1.392
 NBM  C03  N27   single    1.455  0.020  1.455
 NBM  C03  C04   aromatic  1.387  0.020  1.387
 NBM  N27  O28   double    1.208  0.020  1.208
 NBM  N10  C11   aromatic  1.335  0.020  1.335
 NBM  N12  C11   aromatic  1.320  0.020  1.320
 NBM  C05  C04   aromatic  1.384  0.020  1.384
 NBM  C01  H011  single    0.930  0.020  1.080
 NBM  C02  H021  single    0.930  0.020  1.080
 NBM  C04  H041  single    0.930  0.020  1.080
 NBM  C05  H051  single    0.930  0.020  1.080
 NBM  C07  H071  single    0.970  0.020  1.090
 NBM  C07  H072  single    0.970  0.020  1.090
 NBM  C11  H111  single    0.930  0.020  1.080
 NBM  C16  H161  single    0.930  0.020  1.080
 NBM  C18  H181  single    0.970  0.020  1.090
 NBM  C19  H191  single    0.970  0.020  1.090
 NBM  C20  H201  single    0.970  0.020  1.090
 NBM  C21  H211  single    0.970  0.020  1.090
 NBM  C23  H231  single    0.970  0.020  1.090
 NBM  C23  H232  single    0.970  0.020  1.090
 NBM  O24  H241  single    0.850  0.020  0.980
 NBM  O25  H251  single    0.850  0.020  0.980
 NBM  O26  H261  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
 NBM  H011  C01  C06   119.95  3.000
 NBM  H011  C01  C02   119.24  3.000
 NBM  C06   C01  C02   120.81  3.000
 NBM  H021  C02  C03   121.38  3.000
 NBM  H021  C02  C01   119.89  3.000
 NBM  C03   C02  C01   118.72  3.000
 NBM  N27   C03  C04   119.13  3.000
 NBM  C04   C03  C02   121.69  3.000
 NBM  N27   C03  C02   119.18  3.000
 NBM  H041  C04  C05   119.90  3.000
 NBM  H041  C04  C03   121.37  3.000
 NBM  C05   C04  C03   118.73  3.000
 NBM  H051  C05  C06   119.95  3.000
 NBM  H051  C05  C04   119.25  3.000
 NBM  C06   C05  C04   120.81  3.000
 NBM  C07   C06  C05   120.42  3.000
 NBM  C05   C06  C01   119.25  3.000
 NBM  C07   C06  C01   120.33  3.000
 NBM  H072  C07  H071  108.82  3.000
 NBM  H072  C07  S08   108.99  3.000
 NBM  H071  C07  S08   109.25  3.000
 NBM  H072  C07  C06   111.36  3.000
 NBM  H071  C07  C06   111.50  3.000
 NBM  S08   C07  C06   106.86  3.000
 NBM  S08   C09  N10   121.06  3.000
 NBM  N10   C09  C14   119.26  3.000
 NBM  S08   C09  C14   119.68  3.000
 NBM  H111  C11  N12   116.70  3.000
 NBM  H111  C11  N10   115.76  3.000
 NBM  N12   C11  N10   127.54  3.000
 NBM  N17   C13  N12   128.95  3.000
 NBM  N12   C13  C14   125.94  3.000
 NBM  N17   C13  C14   105.10  3.000
 NBM  N15   C14  C13   110.74  3.000
 NBM  C13   C14  C09   115.70  3.000
 NBM  N15   C14  C09   133.56  3.000
 NBM  H161  C16  N17   121.63  3.000
 NBM  H161  C16  N15   124.70  3.000
 NBM  N17   C16  N15   113.64  3.000
 NBM  H181  C18  O22   111.70  3.000
 NBM  H181  C18  N17   106.37  3.000
 NBM  O22   C18  N17   108.69  3.000
 NBM  H181  C18  C19   110.46  3.000
 NBM  N17   C18  C19   113.15  3.000
 NBM  O22   C18  C19   106.55  3.000
 NBM  H191  C19  O26   111.43  3.000
 NBM  H191  C19  C20   108.02  3.000
 NBM  O26   C19  C20   116.79  3.000
 NBM  H191  C19  C18   108.76  3.000
 NBM  O26   C19  C18   109.80  3.000
 NBM  C20   C19  C18   101.40  3.000
 NBM  H201  C20  O25   111.94  3.000
 NBM  H201  C20  C21   111.48  3.000
 NBM  O25   C20  C21   112.67  3.000
 NBM  H201  C20  C19   111.95  3.000
 NBM  O25   C20  C19   107.83  3.000
 NBM  C21   C20  C19   100.37  3.000
 NBM  H211  C21  O22   107.22  3.000
 NBM  H211  C21  C23   108.95  3.000
 NBM  O22   C21  C23   111.53  3.000
 NBM  H211  C21  C20   111.64  3.000
 NBM  O22   C21  C20   105.11  3.000
 NBM  C23   C21  C20   112.25  3.000
 NBM  H232  C23  H231  106.61  3.000
 NBM  H232  C23  O24   111.40  3.000
 NBM  H231  C23  O24   112.12  3.000
 NBM  H232  C23  C21   110.55  3.000
 NBM  H231  C23  C21   107.48  3.000
 NBM  O24   C23  C21   108.61  3.000
 NBM  C11   N10  C09   118.97  3.000
 NBM  C13   N12  C11   112.58  3.000
 NBM  C16   N15  C14   104.30  3.000
 NBM  C18   N17  C16   127.28  3.000
 NBM  C18   N17  C13   126.46  3.000
 NBM  C16   N17  C13   106.21  3.000
 NBM  O29   N27  O28   123.92  3.000
 NBM  O28   N27  C03   118.05  3.000
 NBM  O29   N27  C03   118.04  3.000
 NBM  C21   O22  C18   110.84  3.000
 NBM  H241  O24  C23   108.06  3.000
 NBM  H251  O25  C20   108.49  3.000
 NBM  H261  O26  C19   108.69  3.000
 NBM  C09   S08  C07   101.53  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
 NBM  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 NBM  CONST_02  C04   C05  C06  C01    0.00   0.0  0
 NBM  CONST_03  C05   C06  C01  C02    0.00   0.0  0
 NBM  CONST_04  C05   C04  C03  C02    0.00   0.0  0
 NBM  CONST_05  C06   C01  C02  C03    0.00   0.0  0
 NBM  CONST_06  C06   C05  C04  C03    0.00   0.0  0
 NBM  CONST_07  C16   N15  C14  C09  180.00   0.0  0
 NBM  CONST_08  N17   C13  C14  C09  180.00   0.0  0
 NBM  CONST_09  N12   C13  C14  C09    0.00   0.0  0
 NBM  CONST_10  N12   C11  N10  C09    0.00   0.0  0
 NBM  CONST_11  C14   C09  N10  C11    0.00   0.0  0
 NBM  CONST_12  N17   C13  N12  C11  180.00   0.0  0
 NBM  CONST_13  C14   C13  N12  C11    0.00   0.0  0
 NBM  CONST_14  N15   C16  N17  C13    0.00   0.0  0
 NBM  CONST_15  C16   N15  C14  C13    0.00   0.0  0
 NBM  CONST_16  N10   C09  C14  C13    0.00   0.0  0
 NBM  CONST_17  N10   C11  N12  C13    0.00   0.0  0
 NBM  CONST_18  N17   C16  N15  C14    0.00   0.0  0
 NBM  CONST_19  C16   N17  C13  C14    0.00   0.0  0
 NBM  CONST_20  N12   C13  N17  C16  180.00   0.0  0
 NBM  CONST_21  N15   C14  C09  N10  180.00   0.0  0
 NBM  CONST_22  N15   C14  C13  N12  180.00   0.0  0
 NBM  CONST_23  N17   C13  C14  N15    0.00   0.0  0
 NBM  CONST_24  C18   N17  C13  C14  180.00   0.0  0
 NBM  CONST_25  N15   C16  N17  C18  180.00   0.0  0
 NBM  CONST_26  N12   C13  N17  C18    0.00   0.0  0
 NBM  CONST_27  N27   C03  C02  C01  180.00   0.0  0
 NBM  CONST_28  C07   C06  C01  C02  180.00   0.0  0
 NBM  CONST_29  C07   C06  C05  C04  180.00   0.0  0
 NBM  CONST_30  N27   C03  C04  C05  180.00   0.0  0
 NBM  CONST_31  S08   C09  N10  C11  180.00   0.0  0
 NBM  CONST_32  S08   C09  C14  C13  180.00   0.0  0
 NBM  CONST_33  S08   C09  C14  N15    0.00   0.0  0
 NBM  CONST_34  H051  C05  C06  C01  180.00   0.0  0
 NBM  CONST_35  H041  C04  C03  C02  180.00   0.0  0
 NBM  CONST_36  H011  C01  C02  C03  180.00   0.0  0
 NBM  CONST_37  H021  C02  C03  C04  180.00   0.0  0
 NBM  CONST_38  H111  C11  N10  C09  180.00   0.0  0
 NBM  CONST_39  H161  C16  N17  C13  180.00   0.0  0
 NBM  CONST_40  O29   N27  C03  C02  180.00   0.0  0
 NBM  CONST_41  O28   N27  C03  C02    0.00   0.0  0
 NBM  CONST_42  O29   N27  C03  C04    0.00   0.0  0
 NBM  CONST_43  O28   N27  C03  C04  180.00   0.0  0
 NBM  Var_01    S08   C07  C06  C01   87.78  30.0  2
 NBM  Var_02    C14   C09  S08  C07  177.79  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
 NBM  chir_01  C18  O22  N17  C19  negativ
 NBM  chir_02  C19  O26  C18  C20  negativ
 NBM  chir_03  C20  O25  C21  C19  positiv
 NBM  chir_04  C21  O22  C20  C23  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
 NBM  plan-1  C01   0.020
 NBM  plan-1  C02   0.020
 NBM  plan-1  C03   0.020
 NBM  plan-1  C04   0.020
 NBM  plan-1  C05   0.020
 NBM  plan-1  C06   0.020
 NBM  plan-1  C07   0.020
 NBM  plan-1  N27   0.020
 NBM  plan-1  H011  0.020
 NBM  plan-1  H021  0.020
 NBM  plan-1  H041  0.020
 NBM  plan-1  H051  0.020
 NBM  plan-2  C09   0.020
 NBM  plan-2  C11   0.020
 NBM  plan-2  C13   0.020
 NBM  plan-2  C14   0.020
 NBM  plan-2  C16   0.020
 NBM  plan-2  C18   0.020
 NBM  plan-2  N10   0.020
 NBM  plan-2  N12   0.020
 NBM  plan-2  N15   0.020
 NBM  plan-2  N17   0.020
 NBM  plan-2  S08   0.020
 NBM  plan-2  H111  0.020
 NBM  plan-2  H161  0.020
 NBM  plan-3  C03   0.020
 NBM  plan-3  N27   0.020
 NBM  plan-3  O28   0.020
 NBM  plan-3  O29   0.020

