# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 10:43:37 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1[N+]([O-])=O)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[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
 N5C  N5C  '5-nitrocytidine 5'-(tetrahydrogen triphosphate)'  ligand  47  32  .  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
;

data_comp_N5C
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
 N5C  O4    O  O      0  -0.405  31.8417  -0.8702  -3.6014
 N5C  N5    N  N      1   0.373  31.0744  -1.6947  -3.1582
 N5C  O3    O  O     -1  -0.316  31.4019  -2.8421  -2.9198
 N5C  C5    C  CR6    0   0.014  29.7272  -1.3095  -2.9028
 N5C  C4    C  CR6    0   0.527  28.6812  -2.2026  -2.4675
 N5C  N4    N  NH2    0  -0.826  28.8769  -3.4862  -2.2182
 N5C  N3    N  N      0  -0.537  27.4557  -1.7376  -2.3118
 N5C  C2    C  CR6    0   0.602  27.1284  -0.4573  -2.5219
 N5C  O2    O  O      0  -0.478  26.0031  -0.0084  -2.4052
 N5C  C6    C  CR16   0   0.013  29.3964   0.0037  -3.1006
 N5C  N1    N  NR6    0  -0.402  28.1654   0.4410  -2.9017
 N5C  C1'   C  CR15   0   0.114  27.7810   1.8505  -3.1402
 N5C  O4'   O  O      0  -0.446  28.8288   2.5112  -3.7794
 N5C  C2'   C  CR15   0  -0.013  27.5113   2.5949  -1.8281
 N5C  O2'   O  OH1    0  -0.632  26.5365   3.5625  -2.1082
 N5C  C3'   C  CR15   0  -0.059  28.8750   3.2255  -1.5567
 N5C  O3'   O  OH1    0  -0.682  28.7731   4.3132  -0.6948
 N5C  C4'   C  CR15   0   0.056  29.3129   3.5878  -2.9778
 N5C  C5'   C  CH2    0  -0.259  30.7859   3.7945  -3.2006
 N5C  O5'   O  O2     0  -0.575  31.5098   2.6689  -2.6691
 N5C  PA    P  P      0   1.446  33.0721   2.6269  -2.4618
 N5C  O1A   O  OH1    0  -0.722  33.8187   3.0722  -3.7691
 N5C  O2A   O  O      0  -0.607  33.5236   1.3047  -1.9861
 N5C  O3A   O  O2     0  -0.651  33.3975   3.8375  -1.4321
 N5C  PB    P  P      0   1.436  32.8254   4.1672   0.0408
 N5C  O1B   O  O      0  -0.637  31.4148   4.5803   0.0834
 N5C  O2B   O  OH1    0  -0.683  33.9190   5.2008   0.4957
 N5C  O3B   O  O2     0  -0.604  33.0515   2.8197   0.8608
 N5C  PG    P  P      0   1.286  34.3636   1.9042   1.2670
 N5C  O1G   O  O      0  -0.719  34.4254   1.7016   2.7193
 N5C  O2G   O  OH1    0  -0.672  34.1573   0.6079   0.4146
 N5C  O3G   O  OH1    0  -0.667  35.5784   2.6524   0.5674
 N5C  HN4   H  HNH2   0   0.390  28.0887  -4.0453  -1.9350
 N5C  HN4A  H  HNH2   0   0.418  29.7802  -3.9165  -2.3077
 N5C  H6    H  HCR6   0   0.349  30.1325   0.7212  -3.4286
 N5C  H1'   H  HCR5   0   0.307  26.8967   1.8272  -3.7793
 N5C  H2'   H  HCR5   0   0.271  27.2034   1.9254  -1.0191
 N5C  HO2'  H  HOH1   0   0.462  26.4979   4.1774  -1.3673
 N5C  H3'   H  HCR5   0   0.226  29.5347   2.4467  -1.1506
 N5C  HO3'  H  HOH1   0   0.462  29.6537   4.4870  -0.3256
 N5C  H4'   H  HCR5   0   0.239  28.8252   4.5220  -3.2807
 N5C  H5'   H  HCH2   0   0.318  31.0038   3.8960  -4.2652
 N5C  H5'A  H  HCH2   0   0.269  31.0814   4.7184  -2.6998
 N5C  HO1A  H  HOH1   0   0.484  33.6718   3.9620  -4.1229
 N5C  HO2B  H  HOH1   0   0.538  33.6038   5.8923   1.0973
 N5C  HO2G  H  HOH1   0   0.494  33.9200   0.7583  -0.5454
 N5C  HO3G  H  HOH1   0   0.499  36.0440   3.2967   1.1198

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
 N5C  O4   N5    double  1.210  0.020  1.210
 N5C  N5   O3    single  1.217  0.020  1.217
 N5C  N5   C5    single  1.424  0.020  1.424
 N5C  C5   C4    single  1.443  0.020  1.443
 N5C  C5   C6    double  1.369  0.020  1.369
 N5C  C4   N4    single  1.322  0.020  1.322
 N5C  C4   N3    double  1.320  0.020  1.320
 N5C  N3   C2    single  1.338  0.020  1.338
 N5C  C2   O2    double  1.217  0.020  1.217
 N5C  C2   N1    single  1.424  0.020  1.424
 N5C  C6   N1    single  1.321  0.020  1.321
 N5C  N1   C1'   single  1.480  0.020  1.480
 N5C  C1'  O4'   single  1.394  0.020  1.394
 N5C  C1'  C2'   single  1.532  0.020  1.532
 N5C  O4'  C4'   single  1.427  0.020  1.427
 N5C  C2'  O2'   single  1.402  0.020  1.402
 N5C  C2'  C3'   single  1.527  0.020  1.527
 N5C  C3'  O3'   single  1.391  0.020  1.391
 N5C  C3'  C4'   single  1.531  0.020  1.531
 N5C  C4'  C5'   single  1.504  0.020  1.504
 N5C  C5'  O5'   single  1.440  0.020  1.440
 N5C  O5'  PA    single  1.577  0.020  1.577
 N5C  PA   O1A   single  1.570  0.020  1.570
 N5C  PA   O2A   double  1.476  0.020  1.476
 N5C  PA   O3A   single  1.622  0.020  1.622
 N5C  O3A  PB    single  1.614  0.020  1.614
 N5C  PB   O1B   double  1.471  0.020  1.471
 N5C  PB   O2B   single  1.572  0.020  1.572
 N5C  PB   O3B   single  1.594  0.020  1.594
 N5C  O3B  PG    single  1.651  0.020  1.651
 N5C  PG   O1G   double  1.468  0.020  1.468
 N5C  PG   O2G   single  1.565  0.020  1.565
 N5C  PG   O3G   single  1.589  0.020  1.589
 N5C  N4   HN4   single  0.860  0.020  1.020
 N5C  N4   HN4A  single  0.860  0.020  1.020
 N5C  C6   H6    single  0.930  0.020  1.080
 N5C  C1'  H1'   single  0.970  0.020  1.090
 N5C  C2'  H2'   single  0.970  0.020  1.090
 N5C  O2'  HO2'  single  0.850  0.020  0.980
 N5C  C3'  H3'   single  0.970  0.020  1.090
 N5C  O3'  HO3'  single  0.850  0.020  0.980
 N5C  C4'  H4'   single  0.970  0.020  1.090
 N5C  C5'  H5'   single  0.970  0.020  1.090
 N5C  C5'  H5'A  single  0.970  0.020  1.090
 N5C  O1A  HO1A  single  0.850  0.020  0.980
 N5C  O2B  HO2B  single  0.850  0.020  0.980
 N5C  O2G  HO2G  single  0.850  0.020  0.980
 N5C  O3G  HO3G  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
 N5C  C5    N5   O3   118.33  3.000
 N5C  C5    N5   O4   118.75  3.000
 N5C  O3    N5   O4   122.92  3.000
 N5C  C6    C5   C4   117.54  3.000
 N5C  C6    C5   N5   117.53  3.000
 N5C  C4    C5   N5   124.92  3.000
 N5C  N3    C4   N4   117.21  3.000
 N5C  N3    C4   C5   119.38  3.000
 N5C  N4    C4   C5   123.41  3.000
 N5C  HN4A  N4   HN4  119.41  3.000
 N5C  HN4A  N4   C4   122.16  3.000
 N5C  HN4   N4   C4   118.43  3.000
 N5C  C2    N3   C4   123.07  3.000
 N5C  N1    C2   O2   117.80  3.000
 N5C  N1    C2   N3   117.87  3.000
 N5C  O2    C2   N3   124.33  3.000
 N5C  H6    C6   N1   117.47  3.000
 N5C  H6    C6   C5   121.14  3.000
 N5C  N1    C6   C5   121.40  3.000
 N5C  C1'   N1   C6   122.19  3.000
 N5C  C1'   N1   C2   117.04  3.000
 N5C  C6    N1   C2   120.66  3.000
 N5C  H1'   C1'  C2'  111.66  3.000
 N5C  H1'   C1'  O4'  110.53  3.000
 N5C  C2'   C1'  O4'  107.14  3.000
 N5C  H1'   C1'  N1   106.53  3.000
 N5C  C2'   C1'  N1   111.73  3.000
 N5C  O4'   C1'  N1   109.27  3.000
 N5C  C4'   O4'  C1'  110.80  3.000
 N5C  H2'   C2'  C3'  111.87  3.000
 N5C  H2'   C2'  O2'  111.99  3.000
 N5C  C3'   C2'  O2'  111.81  3.000
 N5C  H2'   C2'  C1'  112.66  3.000
 N5C  C3'   C2'  C1'  101.28  3.000
 N5C  O2'   C2'  C1'  106.66  3.000
 N5C  HO2'  O2'  C2'  108.35  3.000
 N5C  H3'   C3'  C4'  109.83  3.000
 N5C  H3'   C3'  O3'  111.67  3.000
 N5C  C4'   C3'  O3'  114.27  3.000
 N5C  H3'   C3'  C2'  108.02  3.000
 N5C  C4'   C3'  C2'  100.85  3.000
 N5C  O3'   C3'  C2'  111.56  3.000
 N5C  HO3'  O3'  C3'  108.01  3.000
 N5C  H4'   C4'  C5'  106.11  3.000
 N5C  H4'   C4'  C3'  109.33  3.000
 N5C  C5'   C4'  C3'  116.76  3.000
 N5C  H4'   C4'  O4'  109.68  3.000
 N5C  C5'   C4'  O4'  110.65  3.000
 N5C  C3'   C4'  O4'  104.24  3.000
 N5C  H5'A  C5'  H5'  108.34  3.000
 N5C  H5'A  C5'  O5'  110.86  3.000
 N5C  H5'   C5'  O5'  109.41  3.000
 N5C  H5'A  C5'  C4'  108.27  3.000
 N5C  H5'   C5'  C4'  110.66  3.000
 N5C  O5'   C5'  C4'  109.28  3.000
 N5C  PA    O5'  C5'  124.58  3.000
 N5C  O3A   PA   O2A  113.75  3.000
 N5C  O3A   PA   O1A  102.80  3.000
 N5C  O2A   PA   O1A  112.15  3.000
 N5C  O3A   PA   O5'  105.21  3.000
 N5C  O2A   PA   O5'  111.68  3.000
 N5C  O1A   PA   O5'  110.74  3.000
 N5C  HO1A  O1A  PA   119.51  3.000
 N5C  PB    O3A  PA   131.34  3.000
 N5C  O3B   PB   O2B  107.96  3.000
 N5C  O3B   PB   O1B  111.02  3.000
 N5C  O2B   PB   O1B  118.31  3.000
 N5C  O3B   PB   O3A  104.28  3.000
 N5C  O2B   PB   O3A   98.73  3.000
 N5C  O1B   PB   O3A  115.08  3.000
 N5C  HO2B  O2B  PB   114.99  3.000
 N5C  PG    O3B  PB   135.10  3.000
 N5C  O3G   PG   O2G  104.54  3.000
 N5C  O3G   PG   O1G  117.93  3.000
 N5C  O2G   PG   O1G  115.48  3.000
 N5C  O3G   PG   O3B  103.78  3.000
 N5C  O2G   PG   O3B  102.75  3.000
 N5C  O1G   PG   O3B  110.70  3.000
 N5C  HO2G  O2G  PG   115.43  3.000
 N5C  HO3G  O3G  PG   115.46  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
 N5C  CONST_01  C2    N3   C4   C5     0.00   0.0  0
 N5C  CONST_02  N1    C2   N3   C4     0.00   0.0  0
 N5C  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 N5C  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 N5C  CONST_05  O2    C2   N3   C4   180.00   0.0  0
 N5C  CONST_06  C2    N3   C4   N4   180.00   0.0  0
 N5C  CONST_07  C6    N1   C2   O2   180.00   0.0  0
 N5C  CONST_08  C1'   N1   C2   O2     0.00   0.0  0
 N5C  CONST_09  HN4   N4   C4   C5   180.00   0.0  0
 N5C  CONST_10  HN4A  N4   C4   C5     0.00   0.0  0
 N5C  Var_01    C4    C5   N5   O4   175.35  30.0  2
 N5C  Var_02    O1A   PA   O5'  C5'  -50.38  30.0  3
 N5C  Var_03    O1B   PB   O3A  PA   -68.95  30.0  3
 N5C  Var_04    O1G   PG   O3B  PB   125.30  30.0  3
 N5C  Var_05    H5'   C5'  O5'  PA    70.77  30.0  1

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
 N5C  chir_01  C1'  N1   O4'  C2'  positiv
 N5C  chir_02  C2'  O2'  C1'  C3'  negativ
 N5C  chir_03  C3'  O3'  C4'  C2'  positiv
 N5C  chir_04  C4'  O4'  C3'  C5'  negativ
 N5C  chir_05  PA   O1A  O2A  O3A  both
 N5C  chir_06  PB   O2B  O1B  O3A  both

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
 N5C  plan-1  N5    0.020
 N5C  plan-1  C5    0.020
 N5C  plan-1  C4    0.020
 N5C  plan-1  N4    0.020
 N5C  plan-1  N3    0.020
 N5C  plan-1  C2    0.020
 N5C  plan-1  O2    0.020
 N5C  plan-1  C6    0.020
 N5C  plan-1  N1    0.020
 N5C  plan-1  C1'   0.020
 N5C  plan-1  HN4   0.020
 N5C  plan-1  HN4A  0.020
 N5C  plan-1  H6    0.020
 N5C  plan-2  O4    0.020
 N5C  plan-2  N5    0.020
 N5C  plan-2  O3    0.020
 N5C  plan-2  C5    0.020

