# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 08:40:02 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-nitro-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n(cnc1[N+]([O-])=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
#
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
 NIA  NIA  4-nitro-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazol-5-amine  ligand  35  22  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NIA
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
 NIA  O8    O  OH1    0  -0.738   2.4725  -2.6379   0.7708
 NIA  P     P  P      0   1.458   3.6457  -1.5877   0.4838
 NIA  O6    O  O      0  -0.705   4.3552  -1.2759   1.7375
 NIA  O7    O  OH1    0  -0.728   4.4803  -2.1394  -0.7544
 NIA  O5'   O  O2     0  -0.590   2.9845  -0.3424  -0.2683
 NIA  C5'   C  CH2    0  -0.172   2.4458   0.7421   0.4884
 NIA  C4'   C  CH1    0  -0.052   1.6587   1.6109  -0.4679
 NIA  C3'   C  CH1    0  -0.031   0.9804   2.7831   0.2303
 NIA  O3'   O  OH1    0  -0.663   0.8225   3.8168  -0.7029
 NIA  C2'   C  CH1    0  -0.039  -0.3708   2.1640   0.6007
 NIA  O2'   O  OH1    0  -0.655  -1.4193   3.0769   0.7439
 NIA  O4'   O  O2     0  -0.489   0.6062   0.8587  -1.0819
 NIA  C1'   C  CH1    0   0.215  -0.6363   1.2698  -0.6116
 NIA  N1    N  NR5    0  -0.521  -1.4279   0.0929  -0.2939
 NIA  C5    C  CR5    0   0.518  -2.7852   0.0374  -0.2752
 NIA  N6    N  NH2    0  -0.837  -3.5741   1.0849  -0.5560
 NIA  C4    C  CR5    0   0.218  -3.0559  -1.2969   0.0344
 NIA  N7    N  N      1   0.343  -4.3146  -1.8674   0.1768
 NIA  O72   O  O      0  -0.454  -5.2907  -1.1507  -0.0186
 NIA  O71   O  O     -1  -0.428  -4.4033  -3.0395   0.4860
 NIA  N3    N  N      0  -0.420  -1.9051  -2.0091   0.2081
 NIA  C2    C  CR15   0   0.140  -0.9535  -1.1629   0.0127
 NIA  HO8   H  HOH1   0   0.498   2.0855  -3.0587  -0.0086
 NIA  HO7   H  HOH1   0   0.506   4.9730  -2.9519  -0.5756
 NIA  H5'1  H  HCH2   0   0.268   3.2527   1.3320   0.9283
 NIA  H5'2  H  HCH2   0   0.240   1.8147   0.3754   1.3038
 NIA  H4'   H  HCH1   0   0.283   2.3258   1.9650  -1.2584
 NIA  H3'   H  HCH1   0   0.263   1.5362   3.1107   1.1183
 NIA  H1    H  HOH1   0   0.454   0.1585   4.4284  -0.3641
 NIA  H2'   H  HCH1   0   0.264  -0.2537   1.5408   1.4954
 NIA  H2    H  HOH1   0   0.477  -1.4749   3.3602   1.6623
 NIA  H1'   H  HCH1   0   0.272  -1.1838   1.8245  -1.3842
 NIA  HN61  H  HNH2   0   0.411  -3.2394   2.0133  -0.3463
 NIA  HN62  H  HNH2   0   0.416  -4.5614   0.9504  -0.4143
 NIA  H3    H  HCR5   0   0.276   0.1004  -1.3772   0.0681

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
 NIA  O8   P     single    1.600  0.020  1.600
 NIA  O8   HO8   single    0.850  0.020  0.980
 NIA  P    O6    double    1.474  0.020  1.474
 NIA  P    O7    single    1.592  0.020  1.592
 NIA  P    O5'   single    1.598  0.020  1.598
 NIA  O7   HO7   single    0.850  0.020  0.980
 NIA  O5'  C5'   single    1.428  0.020  1.428
 NIA  C5'  C4'   single    1.513  0.020  1.513
 NIA  C5'  H5'1  single    0.970  0.020  1.090
 NIA  C5'  H5'2  single    0.970  0.020  1.090
 NIA  C4'  C3'   single    1.524  0.020  1.524
 NIA  C4'  O4'   single    1.432  0.020  1.432
 NIA  C4'  H4'   single    0.970  0.020  1.090
 NIA  C3'  O3'   single    1.402  0.020  1.402
 NIA  C3'  C2'   single    1.532  0.020  1.532
 NIA  C3'  H3'   single    0.970  0.020  1.090
 NIA  O3'  H1    single    0.850  0.020  0.980
 NIA  C2'  O2'   single    1.398  0.020  1.398
 NIA  C2'  C1'   single    1.530  0.020  1.530
 NIA  C2'  H2'   single    0.970  0.020  1.090
 NIA  O2'  H2    single    0.850  0.020  0.980
 NIA  O4'  C1'   single    1.391  0.020  1.391
 NIA  C1'  N1    single    1.453  0.020  1.453
 NIA  C1'  H1'   single    0.970  0.020  1.090
 NIA  N1   C5    aromatic  1.359  0.020  1.359
 NIA  N1   C2    aromatic  1.377  0.020  1.377
 NIA  C5   N6    single    1.341  0.020  1.341
 NIA  C5   C4    aromatic  1.396  0.020  1.396
 NIA  N6   HN61  single    0.890  0.020  1.040
 NIA  N6   HN62  single    0.890  0.020  1.040
 NIA  C4   N7    single    1.389  0.020  1.389
 NIA  C4   N3    aromatic  1.364  0.020  1.364
 NIA  N7   O72   double    1.227  0.020  1.227
 NIA  N7   O71   single    1.215  0.020  1.215
 NIA  N3   C2    aromatic  1.288  0.020  1.288
 NIA  C2   H3    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
 NIA  HO8   O8   P     115.75  3.000
 NIA  O5'   P    O7     96.94  3.000
 NIA  O5'   P    O6    115.77  3.000
 NIA  O7    P    O6    118.85  3.000
 NIA  O5'   P    O8    107.00  3.000
 NIA  O7    P    O8    107.24  3.000
 NIA  O6    P    O8    109.82  3.000
 NIA  HO7   O7   P     114.49  3.000
 NIA  C5'   O5'  P     119.90  3.000
 NIA  H5'2  C5'  H5'1  107.88  3.000
 NIA  H5'2  C5'  C4'   111.31  3.000
 NIA  H5'1  C5'  C4'   109.20  3.000
 NIA  H5'2  C5'  O5'   110.97  3.000
 NIA  H5'1  C5'  O5'   110.18  3.000
 NIA  C4'   C5'  O5'   107.30  3.000
 NIA  H4'   C4'  O4'   107.98  3.000
 NIA  H4'   C4'  C3'   110.72  3.000
 NIA  O4'   C4'  C3'   105.87  3.000
 NIA  H4'   C4'  C5'   109.00  3.000
 NIA  O4'   C4'  C5'   110.59  3.000
 NIA  C3'   C4'  C5'   112.56  3.000
 NIA  H3'   C3'  C2'   111.82  3.000
 NIA  H3'   C3'  O3'   112.06  3.000
 NIA  C2'   C3'  O3'   111.08  3.000
 NIA  H3'   C3'  C4'   112.02  3.000
 NIA  C2'   C3'  C4'   101.10  3.000
 NIA  O3'   C3'  C4'   108.21  3.000
 NIA  H1    O3'  C3'   108.15  3.000
 NIA  H2'   C2'  C1'   109.44  3.000
 NIA  H2'   C2'  O2'   111.58  3.000
 NIA  C1'   C2'  O2'   109.44  3.000
 NIA  H2'   C2'  C3'   109.44  3.000
 NIA  C1'   C2'  C3'   101.40  3.000
 NIA  O2'   C2'  C3'   115.00  3.000
 NIA  H2    O2'  C2'   109.47  3.000
 NIA  C1'   O4'  C4'   110.88  3.000
 NIA  H1'   C1'  N1    106.94  3.000
 NIA  H1'   C1'  O4'   110.92  3.000
 NIA  N1    C1'  O4'   108.74  3.000
 NIA  H1'   C1'  C2'   110.43  3.000
 NIA  N1    C1'  C2'   113.25  3.000
 NIA  O4'   C1'  C2'   106.61  3.000
 NIA  C2    N1   C5    107.69  3.000
 NIA  C2    N1   C1'   126.83  3.000
 NIA  C5    N1   C1'   125.47  3.000
 NIA  C4    C5   N6    132.75  3.000
 NIA  C4    C5   N1    103.64  3.000
 NIA  N6    C5   N1    123.57  3.000
 NIA  HN62  N6   HN61  114.78  3.000
 NIA  HN62  N6   C5    116.31  3.000
 NIA  HN61  N6   C5    118.69  3.000
 NIA  N3    C4   N7    122.47  3.000
 NIA  N3    C4   C5    111.32  3.000
 NIA  N7    C4   C5    126.21  3.000
 NIA  O71   N7   O72   123.08  3.000
 NIA  O71   N7   C4    119.22  3.000
 NIA  O72   N7   C4    117.70  3.000
 NIA  C2    N3   C4    105.12  3.000
 NIA  H3    C2   N3    125.76  3.000
 NIA  H3    C2   N1    122.02  3.000
 NIA  N3    C2   N1    112.23  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
 NIA  CONST_01  N3    C4   C5   N1      0.00   0.0  0
 NIA  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 NIA  CONST_03  N3    C2   N1   C5      0.00   0.0  0
 NIA  CONST_04  C2    N3   C4   C5      0.00   0.0  0
 NIA  CONST_05  C2    N1   C5   C4      0.00   0.0  0
 NIA  CONST_06  C4    C5   N1   C1'   180.00   0.0  0
 NIA  CONST_07  N3    C2   N1   C1'   180.00   0.0  0
 NIA  CONST_08  N6    C5   N1   C1'     0.00   0.0  0
 NIA  CONST_09  N7    C4   C5   N1    180.00   0.0  0
 NIA  CONST_10  C2    N1   C5   N6    180.00   0.0  0
 NIA  CONST_11  N3    C4   C5   N6    180.00   0.0  0
 NIA  CONST_12  C2    N3   C4   N7    180.00   0.0  0
 NIA  CONST_13  H3    C2   N1   C1'     0.00   0.0  0
 NIA  CONST_14  O72   N7   C4   C5      0.00   0.0  0
 NIA  CONST_15  O71   N7   C4   C5    180.00   0.0  0
 NIA  CONST_16  N3    C4   N7   O72   180.00   0.0  0
 NIA  CONST_17  N3    C4   N7   O71     0.00   0.0  0
 NIA  CONST_19  HN62  N6   C5   N1    180.00   0.0  0
 NIA  Var_01    C4'   C5'  O5'  P    -168.84  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
 NIA  chir_01  C4'  C5'  C3'  O4'  positiv
 NIA  chir_02  C3'  O3'  C2'  C4'  negativ
 NIA  chir_03  C2'  O2'  C1'  C3'  negativ
 NIA  chir_04  C1'  O4'  N1   C2'  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
 NIA  plan-1  C1'   0.020
 NIA  plan-1  N1    0.020
 NIA  plan-1  C5    0.020
 NIA  plan-1  N6    0.020
 NIA  plan-1  C4    0.020
 NIA  plan-1  N7    0.020
 NIA  plan-1  N3    0.020
 NIA  plan-1  C2    0.020
 NIA  plan-1  H3    0.020
 NIA  plan-2  C5    0.020
 NIA  plan-2  N6    0.020
 NIA  plan-2  HN61  0.020
 NIA  plan-2  HN62  0.020
 NIA  plan-3  C4    0.020
 NIA  plan-3  N7    0.020
 NIA  plan-3  O72   0.020
 NIA  plan-3  O71   0.020

