# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 03:48:08 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N)NC(=O)[N+](=C1)[C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2
#
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
 523  523  '2'-deoxy-5-methylcytidine 5'-(tetrahydrogen triphosphate)'  ligand  48  29  .  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_523
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
 523  N1    N  NR6   1  -0.582  59.0252  127.1946  57.6388
 523  C2    C  CR6   0   0.752  57.9913  126.3754  57.4710
 523  N3    N  NR16  0  -0.621  58.3287  125.0748  57.1667
 523  C4    C  CR6   0   0.505  59.5736  124.5864  57.0285
 523  C5    C  CR6   0  -0.103  60.6479  125.4945  57.2018
 523  C5A   C  CH3   0  -0.778  62.0655  125.0435  57.0473
 523  C6    C  CR16  0   0.164  60.3049  126.7666  57.5068
 523  O2    O  OC    0  -0.398  56.8468  126.7227  57.5860
 523  N4    N  NH2   0  -0.775  59.7514  123.3235  56.7401
 523  C1'   C  CH1   0   0.278  58.6820  128.6010  57.9845
 523  C2'   C  CH2   0  -0.627  58.2718  128.7473  59.4425
 523  C3'   C  CH1   0   0.038  59.5809  129.1537  60.1082
 523  C4'   C  CH1   0   0.054  60.2179  130.0018  59.0168
 523  O4'   O  O2    0  -0.527  59.8068  129.3991  57.7939
 523  O3'   O  OH1   0  -0.691  59.4496  129.9083  61.2771
 523  C5'   C  CH2   0  -0.249  61.7209  130.0586  59.0891
 523  O5'   O  O2    0  -0.564  62.2107  130.9350  58.0660
 523  PA    P  P     0   1.484  63.1708  130.4950  56.8909
 523  O1A   O  OH1   0  -0.642  62.6731  129.0904  56.3403
 523  O2A   O  O     0  -0.713  63.4067  131.5794  55.9190
 523  O3A   O  O2    0  -0.672  64.4851  130.0049  57.7146
 523  PB    P  P     0   1.426  65.9629  129.8139  57.0937
 523  O1B   O  OH1   0  -0.637  66.6964  128.9753  58.2104
 523  O2B   O  O     0  -0.736  65.9846  129.3378  55.7065
 523  O3B   O  O2    0  -0.604  66.5497  131.2894  57.3644
 523  PG    P  P     0   1.380  68.0196  131.9032  57.0304
 523  O1G   O  O     0  -0.741  67.9230  133.1967  56.3251
 523  O2G   O  OH1   0  -0.679  68.6239  131.8669  58.4895
 523  O3G   O  OH1   0  -0.679  68.7797  130.7173  56.2938
 523  HN3   H  HNR6  0   0.460  57.5447  124.4584  57.0464
 523  H5A1  H  HCH3  0   0.280  62.2631  124.6351  56.0548
 523  H5A2  H  HCH3  0   0.262  62.7362  125.8900  57.1782
 523  H5A3  H  HCH3  0   0.267  62.2762  124.2695  57.7870
 523  H6    H  HCR6  0   0.369  61.0710  127.5192  57.6316
 523  HN41  H  HNH2  0   0.417  60.6773  122.9450  56.6207
 523  HN42  H  HNH2  0   0.424  58.9813  122.6877  56.6051
 523  H1'   H  HCH1  0   0.322  57.9002  128.8951  57.2847
 523  H2'1  H  HCH2  0   0.298  57.5526  129.5626  59.5334
 523  H2'2  H  HCH2  0   0.327  57.8140  127.8480  59.8523
 523  H3'   H  HCH1  0   0.220  60.2025  128.2603  60.2756
 523  H4'   H  HCH1  0   0.192  59.8135  131.0204  59.0721
 523  HO3'  H  HOH1  0   0.457  59.2564  129.2983  61.9951
 523  H5'1  H  HCH2  0   0.284  62.1520  129.0577  59.0099
 523  H5'2  H  HCH2  0   0.237  62.0211  130.4713  60.0527
 523  HO1A  H  HOH1  0   0.538  62.0572  129.1536  55.5960
 523  HO1B  H  HOH1  0   0.532  66.6932  128.0169  58.0698
 523  HO2G  H  HOH1  0   0.539  69.3930  132.4381  58.6123
 523  HO3G  H  HOH1  0   0.512  68.7348  130.7766  55.3296

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
 523  N1   C6    aromatic  1.356  0.020  1.356
 523  N1   C1'   single    1.488  0.020  1.488
 523  N1   C2    aromatic  1.330  0.020  1.330
 523  C2   N3    aromatic  1.378  0.020  1.378
 523  C2   O2    double    1.202  0.020  1.202
 523  N3   C4    aromatic  1.344  0.020  1.344
 523  N3   HN3   single    0.860  0.020  1.020
 523  C4   C5    aromatic  1.417  0.020  1.417
 523  C4   N4    single    1.308  0.020  1.308
 523  C5   C5A   single    1.496  0.020  1.496
 523  C5   C6    aromatic  1.352  0.020  1.352
 523  C5A  H5A1  single    0.970  0.020  1.090
 523  C5A  H5A2  single    0.970  0.020  1.090
 523  C5A  H5A3  single    0.970  0.020  1.090
 523  C6   H6    single    0.930  0.020  1.080
 523  N4   HN41  single    0.860  0.020  1.020
 523  N4   HN42  single    0.860  0.020  1.020
 523  C1'  O4'   single    1.392  0.020  1.392
 523  C1'  C2'   single    1.522  0.020  1.522
 523  C1'  H1'   single    0.970  0.020  1.090
 523  C2'  C3'   single    1.524  0.020  1.524
 523  C2'  H2'1  single    0.970  0.020  1.090
 523  C2'  H2'2  single    0.970  0.020  1.090
 523  C3'  C4'   single    1.522  0.020  1.522
 523  C3'  O3'   single    1.398  0.020  1.398
 523  C3'  H3'   single    0.970  0.020  1.090
 523  C4'  O4'   single    1.424  0.020  1.424
 523  C4'  C5'   single    1.506  0.020  1.506
 523  C4'  H4'   single    0.970  0.020  1.090
 523  O3'  HO3'  single    0.850  0.020  0.980
 523  C5'  O5'   single    1.433  0.020  1.433
 523  C5'  H5'1  single    0.970  0.020  1.090
 523  C5'  H5'2  single    0.970  0.020  1.090
 523  O5'  PA    single    1.580  0.020  1.580
 523  PA   O2A   double    1.475  0.020  1.475
 523  PA   O1A   single    1.589  0.020  1.589
 523  PA   O3A   single    1.627  0.020  1.627
 523  O1A  HO1A  single    0.850  0.020  0.980
 523  O3A  PB    single    1.614  0.020  1.614
 523  PB   O2B   double    1.467  0.020  1.467
 523  PB   O3B   single    1.611  0.020  1.611
 523  PB   O1B   single    1.577  0.020  1.577
 523  O1B  HO1B  single    0.850  0.020  0.980
 523  O3B  PG    single    1.628  0.020  1.628
 523  PG   O1G   double    1.477  0.020  1.477
 523  PG   O3G   single    1.589  0.020  1.589
 523  PG   O2G   single    1.580  0.020  1.580
 523  O2G  HO2G  single    0.850  0.020  0.980
 523  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
 523  C1'   N1   C6    122.59  3.000
 523  C1'   N1   C2    115.61  3.000
 523  C6    N1   C2    121.81  3.000
 523  O2    C2   N3    121.82  3.000
 523  O2    C2   N1    123.40  3.000
 523  N3    C2   N1    114.78  3.000
 523  HN3   N3   C4    119.17  3.000
 523  HN3   N3   C2    114.49  3.000
 523  C4    N3   C2    126.33  3.000
 523  N4    C4   C5    122.87  3.000
 523  N4    C4   N3    119.97  3.000
 523  C5    C4   N3    117.16  3.000
 523  C6    C5   C5A   123.19  3.000
 523  C6    C5   C4    115.98  3.000
 523  C5A   C5   C4    120.84  3.000
 523  H5A3  C5A  H5A2  110.57  3.000
 523  H5A3  C5A  H5A1  108.43  3.000
 523  H5A2  C5A  H5A1  106.80  3.000
 523  H5A3  C5A  C5    109.07  3.000
 523  H5A2  C5A  C5    109.71  3.000
 523  H5A1  C5A  C5    112.24  3.000
 523  H6    C6   C5    120.08  3.000
 523  H6    C6   N1    115.96  3.000
 523  C5    C6   N1    123.94  3.000
 523  HN42  N4   HN41  116.71  3.000
 523  HN42  N4   C4    122.34  3.000
 523  HN41  N4   C4    120.93  3.000
 523  H1'   C1'  O4'   109.69  3.000
 523  H1'   C1'  C2'   113.33  3.000
 523  O4'   C1'  C2'   107.09  3.000
 523  H1'   C1'  N1    105.74  3.000
 523  C2'   C1'  N1    112.06  3.000
 523  O4'   C1'  N1    108.88  3.000
 523  H2'2  C2'  H2'1  107.97  3.000
 523  H2'2  C2'  C3'   114.65  3.000
 523  H2'1  C2'  C3'   109.31  3.000
 523  H2'2  C2'  C1'   113.23  3.000
 523  H2'1  C2'  C1'   109.23  3.000
 523  C3'   C2'  C1'   102.28  3.000
 523  H3'   C3'  O3'   111.34  3.000
 523  H3'   C3'  C4'   108.96  3.000
 523  O3'   C3'  C4'   109.77  3.000
 523  H3'   C3'  C2'   109.57  3.000
 523  O3'   C3'  C2'   115.38  3.000
 523  C4'   C3'  C2'   101.24  3.000
 523  H4'   C4'  C5'   109.29  3.000
 523  H4'   C4'  O4'   109.25  3.000
 523  C5'   C4'  O4'   110.20  3.000
 523  H4'   C4'  C3'   109.08  3.000
 523  C5'   C4'  C3'   113.85  3.000
 523  O4'   C4'  C3'   105.02  3.000
 523  C4'   O4'  C1'   110.99  3.000
 523  HO3'  O3'  C3'   107.51  3.000
 523  H5'2  C5'  H5'1  107.58  3.000
 523  H5'2  C5'  O5'   107.78  3.000
 523  H5'1  C5'  O5'   111.94  3.000
 523  H5'2  C5'  C4'   109.36  3.000
 523  H5'1  C5'  C4'   110.84  3.000
 523  O5'   C5'  C4'   109.26  3.000
 523  PA    O5'  C5'   124.62  3.000
 523  O3A   PA   O2A   115.21  3.000
 523  O3A   PA   O1A    99.34  3.000
 523  O2A   PA   O1A   118.15  3.000
 523  O3A   PA   O5'   101.44  3.000
 523  O1A   PA   O5'   108.28  3.000
 523  O2A   PA   O5'   112.48  3.000
 523  HO1A  O1A  PA    114.08  3.000
 523  PB    O3A  PA    125.49  3.000
 523  O3B   PB   O2B   116.80  3.000
 523  O3B   PB   O1B   101.46  3.000
 523  O2B   PB   O1B   119.35  3.000
 523  O1B   PB   O3A   102.49  3.000
 523  O3B   PB   O3A    99.23  3.000
 523  O2B   PB   O3A   114.56  3.000
 523  HO1B  O1B  PB    114.94  3.000
 523  PG    O3B  PB    129.79  3.000
 523  O3G   PG   O2G   103.18  3.000
 523  O2G   PG   O1G   119.10  3.000
 523  O3G   PG   O1G   117.61  3.000
 523  O2G   PG   O3B    98.47  3.000
 523  O3G   PG   O3B   104.22  3.000
 523  O1G   PG   O3B   111.67  3.000
 523  HO2G  O2G  PG    114.11  3.000
 523  HO3G  O3G  PG    113.21  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
 523  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 523  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 523  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 523  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 523  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 523  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 523  CONST_07  C1'   N1   C2   N3   180.00   0.0  0
 523  CONST_08  C1'   N1   C6   C5   180.00   0.0  0
 523  CONST_09  C5A   C5   C6   N1   180.00   0.0  0
 523  CONST_10  N4    C4   N3   C2   180.00   0.0  0
 523  CONST_11  C5A   C5   C4   N3   180.00   0.0  0
 523  CONST_12  O2    C2   N3   C4   180.00   0.0  0
 523  CONST_13  O2    C2   N1   C6   180.00   0.0  0
 523  CONST_14  N4    C4   C5   C6   180.00   0.0  0
 523  CONST_15  C1'   N1   C2   O2     0.00   0.0  0
 523  CONST_16  HN3   N3   C2   N1   180.00   0.0  0
 523  CONST_17  H6    C6   N1   C2   180.00   0.0  0
 523  CONST_18  HN41  N4   C4   N3   180.00   0.0  0
 523  CONST_19  HN42  N4   C4   N3     0.00   0.0  0
 523  Var_01    H5A1  C5A  C5   C4    59.13  30.0  2
 523  Var_02    O2A   PA   O5'  C5'  174.65  30.0  3
 523  Var_03    O2B   PB   O3A  PA   -34.47  30.0  3
 523  Var_04    O1G   PG   O3B  PB   130.32  30.0  3
 523  Var_05    H5'1  C5'  O5'  PA     4.47  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
 523  chir_01  C1'  N1   O4'  C2'  positiv
 523  chir_02  C3'  O3'  C4'  C2'  positiv
 523  chir_03  C4'  O4'  C3'  C5'  negativ
 523  chir_04  PA   O2A  O1A  O3A  both
 523  chir_05  PB   O2B  O3B  O1B  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
 523  plan-1  N1    0.020
 523  plan-1  C2    0.020
 523  plan-1  N3    0.020
 523  plan-1  C4    0.020
 523  plan-1  C5    0.020
 523  plan-1  C5A   0.020
 523  plan-1  C6    0.020
 523  plan-1  O2    0.020
 523  plan-1  N4    0.020
 523  plan-1  C1'   0.020
 523  plan-1  HN3   0.020
 523  plan-1  H6    0.020
 523  plan-2  C4    0.020
 523  plan-2  N4    0.020
 523  plan-2  HN41  0.020
 523  plan-2  HN42  0.020

