# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:14:42 2021
#   Inital geometry file: a 115 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)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C[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
 CH1  CH1  '3'-deoxycytidine 5'-(tetrahydrogen triphosphate)'  ligand  44  28  .  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_CH1
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
 CH1  N1    N  NR6   0  -0.559   -7.2620  89.8291  18.7821
 CH1  C2    C  CR6   0   0.598   -7.2265  88.5112  19.2780
 CH1  N3    N  N     0  -0.542   -7.9258  88.2389  20.3981
 CH1  C4    C  CR6   0   0.518   -8.6150  89.1741  21.0204
 CH1  C5    C  CR16  0  -0.476   -8.6554  90.5260  20.5554
 CH1  C6    C  CR16  0   0.106   -7.9594  90.7925  19.4358
 CH1  O2    O  O     0  -0.516   -6.5763  87.6596  18.6879
 CH1  N4    N  NH2   0  -0.806   -9.2864  88.8393  22.1197
 CH1  C1'   C  CR15  0   0.189   -6.5352  90.1719  17.5788
 CH1  C2'   C  CR15  0   0.015   -7.4056  90.6626  16.4236
 CH1  O2'   O  OH1   0  -0.656   -7.9550  89.5576  15.7659
 CH1  C3'   C  CH2   0  -0.557   -6.3917  91.4760  15.6289
 CH1  C4'   C  CR15  0   0.020   -5.4614  92.0414  16.7081
 CH1  O4'   O  O     0  -0.496   -5.6480  91.2239  17.8622
 CH1  C5'   C  CH2   0  -0.210   -5.6978  93.4872  17.0739
 CH1  O5'   O  O2    0  -0.572   -7.0534  93.6466  17.5393
 CH1  PA    P  P     0   1.539   -7.9995  94.8352  17.1262
 CH1  O1A   O  O     0  -0.709   -7.3025  96.1127  16.8378
 CH1  O2A   O  OH1   0  -0.693   -9.1465  94.8141  18.2009
 CH1  O3A   O  O2    0  -0.680   -8.8373  94.2592  15.8701
 CH1  PB    P  P     0   1.512   -8.9964  94.8294  14.3687
 CH1  O1B   O  O     0  -0.635   -9.9247  94.0240  13.5744
 CH1  O2B   O  OH1   0  -0.733   -7.4754  94.9071  13.9395
 CH1  O3B   O  O2    0  -0.704   -9.4935  96.3313  14.6280
 CH1  PG    P  P     0   1.458   -8.8153  97.7759  14.2204
 CH1  O1G   O  O     0  -0.689   -8.0860  97.7000  12.9453
 CH1  O2G   O  OH1   0  -0.713  -10.0674  98.7363  14.1365
 CH1  O3G   O  OH1   0  -0.765   -8.0375  98.1950  15.5195
 CH1  H5    H  HCR6  0   0.290   -9.2099  91.2967  21.0689
 CH1  H6    H  HCR6  0   0.307   -7.9236  91.7888  19.0204
 CH1  HN41  H  HNH2  0   0.415   -9.8491  89.5069  22.6167
 CH1  HN42  H  HNH2  0   0.404   -9.2821  87.8879  22.4459
 CH1  H1'   H  HCR5  0   0.269   -6.0015  89.2708  17.2694
 CH1  H2'   H  HCR5  0   0.226   -8.1966  91.3193  16.8074
 CH1  HO2'  H  HOH1  0   0.462   -8.6013  89.8736  15.1276
 CH1  H3'2  H  HCH2  0   0.260   -6.8414  92.2462  15.0024
 CH1  H3'   H  HCH2  0   0.273   -5.8333  90.8070  14.9713
 CH1  H4'   H  HCR5  0   0.266   -4.4171  91.9799  16.3847
 CH1  H5'1  H  HCH2  0   0.259   -5.4939  94.1173  16.2063
 CH1  H5'2  H  HCH2  0   0.280   -5.0362  93.7985  17.8824
 CH1  HOA2  H  HOH1  0   0.522   -8.9118  95.1757  19.0688
 CH1  HOB2  H  HOH1  0   0.514   -7.3041  95.1129  13.0080
 CH1  HOG2  H  HOH1  0   0.507  -10.5249  98.9229  14.9682
 CH1  HOG3  H  HOH1  0   0.504   -7.6999  97.4425  16.0874

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
 CH1  N1   C2    single  1.409  0.020  1.409
 CH1  N1   C6    single  1.357  0.020  1.357
 CH1  N1   C1'   single  1.447  0.020  1.447
 CH1  C2   N3    single  1.348  0.020  1.348
 CH1  C2   O2    double  1.223  0.020  1.223
 CH1  N3   C4    double  1.318  0.020  1.318
 CH1  C4   C5    single  1.430  0.020  1.430
 CH1  C4   N4    single  1.331  0.020  1.331
 CH1  C5   C6    double  1.345  0.020  1.345
 CH1  C5   H5    single  0.930  0.020  1.080
 CH1  C6   H6    single  0.930  0.020  1.080
 CH1  N4   HN41  single  0.860  0.020  1.020
 CH1  N4   HN42  single  0.860  0.020  1.020
 CH1  C1'  C2'   single  1.527  0.020  1.527
 CH1  C1'  O4'   single  1.405  0.020  1.405
 CH1  C1'  H1'   single  0.970  0.020  1.090
 CH1  C2'  O2'   single  1.398  0.020  1.398
 CH1  C2'  C3'   single  1.524  0.020  1.524
 CH1  C2'  H2'   single  0.970  0.020  1.090
 CH1  O2'  HO2'  single  0.850  0.020  0.980
 CH1  C3'  C4'   single  1.533  0.020  1.533
 CH1  C3'  H3'2  single  0.970  0.020  1.090
 CH1  C3'  H3'   single  0.970  0.020  1.090
 CH1  C4'  O4'   single  1.427  0.020  1.427
 CH1  C4'  C5'   single  1.510  0.020  1.510
 CH1  C4'  H4'   single  0.970  0.020  1.090
 CH1  C5'  O5'   single  1.442  0.020  1.442
 CH1  C5'  H5'1  single  0.970  0.020  1.090
 CH1  C5'  H5'2  single  0.970  0.020  1.090
 CH1  O5'  PA    single  1.574  0.020  1.574
 CH1  PA   O1A   double  1.483  0.020  1.483
 CH1  PA   O2A   single  1.572  0.020  1.572
 CH1  PA   O3A   single  1.616  0.020  1.616
 CH1  O2A  HOA2  single  0.850  0.020  0.980
 CH1  O3A  PB    single  1.614  0.020  1.614
 CH1  PB   O1B   double  1.463  0.020  1.463
 CH1  PB   O2B   single  1.582  0.020  1.582
 CH1  PB   O3B   single  1.603  0.020  1.603
 CH1  O2B  HOB2  single  0.850  0.020  0.980
 CH1  O3B  PG    single  1.647  0.020  1.647
 CH1  PG   O1G   double  1.471  0.020  1.471
 CH1  PG   O2G   single  1.580  0.020  1.580
 CH1  PG   O3G   single  1.571  0.020  1.571
 CH1  O2G  HOG2  single  0.850  0.020  0.980
 CH1  O3G  HOG3  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
 CH1  C1'   N1   C6    119.37  3.000
 CH1  C1'   N1   C2    120.12  3.000
 CH1  C6    N1   C2    120.51  3.000
 CH1  O2    C2   N3    122.40  3.000
 CH1  O2    C2   N1    119.67  3.000
 CH1  N3    C2   N1    117.93  3.000
 CH1  C4    N3   C2    121.35  3.000
 CH1  N4    C4   C5    119.47  3.000
 CH1  N4    C4   N3    118.38  3.000
 CH1  C5    C4   N3    122.14  3.000
 CH1  H5    C5   C6    121.36  3.000
 CH1  H5    C5   C4    122.33  3.000
 CH1  C6    C5   C4    116.31  3.000
 CH1  H6    C6   C5    121.34  3.000
 CH1  H6    C6   N1    116.91  3.000
 CH1  C5    C6   N1    121.75  3.000
 CH1  HN42  N4   HN41  118.07  3.000
 CH1  HN42  N4   C4    120.24  3.000
 CH1  HN41  N4   C4    121.61  3.000
 CH1  H1'   C1'  O4'   111.49  3.000
 CH1  H1'   C1'  C2'   109.23  3.000
 CH1  O4'   C1'  C2'   105.77  3.000
 CH1  H1'   C1'  N1    106.59  3.000
 CH1  O4'   C1'  N1    109.08  3.000
 CH1  C2'   C1'  N1    114.76  3.000
 CH1  H2'   C2'  C3'   110.04  3.000
 CH1  H2'   C2'  O2'   110.75  3.000
 CH1  C3'   C2'  O2'   115.97  3.000
 CH1  H2'   C2'  C1'   109.78  3.000
 CH1  C3'   C2'  C1'   100.76  3.000
 CH1  O2'   C2'  C1'   109.01  3.000
 CH1  HO2'  O2'  C2'   108.46  3.000
 CH1  H3'   C3'  H3'2  107.34  3.000
 CH1  H3'   C3'  C4'   109.85  3.000
 CH1  H3'2  C3'  C4'   113.23  3.000
 CH1  H3'   C3'  C2'   109.12  3.000
 CH1  H3'2  C3'  C2'   113.73  3.000
 CH1  C4'   C3'  C2'   103.51  3.000
 CH1  H4'   C4'  C5'   105.94  3.000
 CH1  H4'   C4'  O4'   109.36  3.000
 CH1  C5'   C4'  O4'   109.40  3.000
 CH1  H4'   C4'  C3'   110.50  3.000
 CH1  C5'   C4'  C3'   115.38  3.000
 CH1  O4'   C4'  C3'   106.19  3.000
 CH1  C4'   O4'  C1'   110.40  3.000
 CH1  H5'2  C5'  H5'1  108.14  3.000
 CH1  H5'2  C5'  O5'   107.44  3.000
 CH1  H5'1  C5'  O5'   111.61  3.000
 CH1  H5'2  C5'  C4'   110.98  3.000
 CH1  H5'1  C5'  C4'   109.32  3.000
 CH1  O5'   C5'  C4'   109.34  3.000
 CH1  PA    O5'  C5'   124.31  3.000
 CH1  O3A   PA   O2A    98.53  3.000
 CH1  O3A   PA   O1A   113.54  3.000
 CH1  O2A   PA   O1A   119.16  3.000
 CH1  O3A   PA   O5'   104.26  3.000
 CH1  O2A   PA   O5'   104.42  3.000
 CH1  O1A   PA   O5'   114.76  3.000
 CH1  HOA2  O2A  PA    115.50  3.000
 CH1  PB    O3A  PA    130.41  3.000
 CH1  O3B   PB   O2B   107.21  3.000
 CH1  O3B   PB   O1B   114.00  3.000
 CH1  O2B   PB   O1B   119.31  3.000
 CH1  O3B   PB   O3A   102.19  3.000
 CH1  O2B   PB   O3A   100.07  3.000
 CH1  O1B   PB   O3A   111.91  3.000
 CH1  HOB2  O2B  PB    116.17  3.000
 CH1  PG    O3B  PB    130.84  3.000
 CH1  O3G   PG   O2G   105.90  3.000
 CH1  O3G   PG   O1G   119.02  3.000
 CH1  O2G   PG   O1G   112.22  3.000
 CH1  O3G   PG   O3B   103.48  3.000
 CH1  O2G   PG   O3B   102.70  3.000
 CH1  O1G   PG   O3B   111.93  3.000
 CH1  HOG2  O2G  PG    116.50  3.000
 CH1  HOG3  O3G  PG    115.81  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
 CH1  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CH1  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 CH1  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 CH1  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 CH1  CONST_05  N4    C4   N3   C2    180.00   0.0  0
 CH1  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 CH1  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 CH1  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 CH1  CONST_09  HN41  N4   C4   N3    180.00   0.0  0
 CH1  CONST_10  HN42  N4   C4   N3      0.00   0.0  0
 CH1  Var_01    O1A   PA   O5'  C5'   -30.65  30.0  3
 CH1  Var_02    O1B   PB   O3A  PA   -176.53  30.0  3
 CH1  Var_03    O1G   PG   O3B  PB     33.31  30.0  3
 CH1  Var_04    H5'1  C5'  O5'  PA    -15.57  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
 CH1  chir_01  C1'  N1   C2'  O4'  negativ
 CH1  chir_02  C2'  O2'  C1'  C3'  negativ
 CH1  chir_03  C4'  O4'  C5'  C3'  positiv
 CH1  chir_04  PA   O1A  O2A  O3A  both
 CH1  chir_05  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
 CH1  plan-1  N1    0.020
 CH1  plan-1  C2    0.020
 CH1  plan-1  N3    0.020
 CH1  plan-1  C4    0.020
 CH1  plan-1  C5    0.020
 CH1  plan-1  C6    0.020
 CH1  plan-1  O2    0.020
 CH1  plan-1  N4    0.020
 CH1  plan-1  C1'   0.020
 CH1  plan-1  H5    0.020
 CH1  plan-1  H6    0.020
 CH1  plan-1  HN41  0.020
 CH1  plan-1  HN42  0.020

