# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Sep 25 19:44:41 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: cytidine 5'-(tetrahydrogen triphosphate)
#   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@@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
 CTP  CTP  "CYTIDINE-5'-TRIPHOSPHATE"  ligand  45  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_CTP
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
 CTP  N1    N  NT    0  -0.559  20.4188  27.5724  -15.7223
 CTP  C2    C  C     0   0.594  20.9283  28.8849  -15.6500
 CTP  N3    N  N     0  -0.540  20.6788  29.7164  -16.6831
 CTP  C4    C  C     0   0.515  19.9799  29.3202  -17.7276
 CTP  C5    C  C1    0  -0.475  19.4489  27.9959  -17.8310
 CTP  C6    C  C1    0   0.102  19.7058  27.1668  -16.8030
 CTP  O2    O  O     0  -0.507  21.5714  29.2280  -14.6687
 CTP  N4    N  NH2   0  -0.807  19.7709  30.1897  -18.7148
 CTP  C1'   C  CR15  0   0.187  20.6955  26.6315  -14.6577
 CTP  C2'   C  CR15  0  -0.001  19.4609  26.1294  -13.9125
 CTP  O2'   O  OH1   0  -0.652  19.0418  27.0935  -12.9997
 CTP  C3'   C  CR15  0  -0.056  19.9838  24.8137  -13.3295
 CTP  C4'   C  CR15  0  -0.003  20.9341  24.3329  -14.4444
 CTP  O4'   O  O     0  -0.494  21.2840  25.4825  -15.2093
 CTP  O3'   O  OH1   0  -0.661  20.6735  25.1117  -12.1444
 CTP  C5'   C  CH2   0  -0.209  20.3728  23.2597  -15.3467
 CTP  O5'   O  O2    0  -0.580  19.1278  23.6999  -15.9124
 CTP  PA    P  P     0   1.478  17.8266  22.7969  -15.8933
 CTP  O1A   O  O     0  -0.675  17.5444  22.0097  -14.6842
 CTP  O2A   O  OH1   0  -0.708  17.9426  22.0139  -17.2664
 CTP  O3A   O  O2    0  -0.674  16.7356  23.9551  -16.2247
 CTP  PB    P  P     0   1.510  15.4343  24.4206  -15.3994
 CTP  O1B   O  O     0  -0.647  14.7429  25.5239  -16.0711
 CTP  O2B   O  OH1   0  -0.725  15.8978  24.6230  -13.8990
 CTP  O3B   O  O2    0  -0.693  14.6601  23.0174  -15.3045
 CTP  PG    P  P     0   1.459  13.1640  22.7334  -14.7236
 CTP  O1G   O  O     0  -0.677  12.6955  23.7365  -13.7570
 CTP  O2G   O  OH1   0  -0.712  13.2936  21.2333  -14.2282
 CTP  O3G   O  OH1   0  -0.717  12.3965  22.5845  -16.0996
 CTP  H5    H  H     0   0.286  18.8822  27.6677  -18.6892
 CTP  H6    H  H     0   0.314  19.3577  26.1436  -16.8078
 CTP  HN41  H  HNH2  0   0.414  19.2486  29.9402  -19.5368
 CTP  HN42  H  HNH2  0   0.402  20.1454  31.1215  -18.6549
 CTP  H1'   H  HCR5  0   0.270  21.3704  27.1370  -13.9643
 CTP  H2'   H  HCR5  0   0.241  18.6697  25.8929  -14.6352
 CTP  HO2'  H  HOH1  0   0.461  18.1806  26.8422  -12.6520
 CTP  H3'   H  HCR5  0   0.247  19.1785  24.0895  -13.1514
 CTP  H4'   H  HCR5  0   0.264  21.8397  23.9059  -13.9959
 CTP  HO3'  H  HOH1  0   0.455  21.0219  24.2919  -11.7793
 CTP  H5'1  H  HCH2  0   0.275  21.0597  23.0459  -16.1664
 CTP  H5'2  H  HCH2  0   0.257  20.2440  22.3450  -14.7639
 CTP  HOA2  H  HOH1  0   0.508  17.3540  21.2500  -17.3522
 CTP  HOB2  H  HOH1  0   0.515  16.1331  25.5329  -13.6639
 CTP  HOG2  H  HOH1  0   0.508  13.5808  21.1320  -13.3090
 CTP  HOG3  H  HOH1  0   0.510  11.4310  22.5851  -16.0299

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
 CTP  N1   C2    single  1.410  0.020  1.410
 CTP  N1   C6    single  1.357  0.020  1.357
 CTP  N1   C1'   single  1.448  0.020  1.448
 CTP  C2   N3    single  1.349  0.020  1.349
 CTP  C2   O2    double  1.222  0.020  1.222
 CTP  N3   C4    double  1.318  0.020  1.318
 CTP  C4   C5    single  1.430  0.020  1.430
 CTP  C4   N4    single  1.332  0.020  1.332
 CTP  C5   C6    double  1.345  0.020  1.345
 CTP  C5   H5    single  0.930  0.020  1.080
 CTP  C6   H6    single  0.930  0.020  1.080
 CTP  N4   HN41  single  0.860  0.020  1.020
 CTP  N4   HN42  single  0.860  0.020  1.020
 CTP  C1'  C2'   single  1.527  0.020  1.527
 CTP  C1'  O4'   single  1.404  0.020  1.404
 CTP  C1'  H1'   single  0.970  0.020  1.090
 CTP  C2'  O2'   single  1.392  0.020  1.392
 CTP  C2'  C3'   single  1.531  0.020  1.531
 CTP  C2'  H2'   single  0.970  0.020  1.090
 CTP  O2'  HO2'  single  0.850  0.020  0.980
 CTP  C3'  C4'   single  1.542  0.020  1.542
 CTP  C3'  O3'   single  1.403  0.020  1.403
 CTP  C3'  H3'   single  0.970  0.020  1.090
 CTP  C4'  O4'   single  1.424  0.020  1.424
 CTP  C4'  C5'   single  1.510  0.020  1.510
 CTP  C4'  H4'   single  0.970  0.020  1.090
 CTP  O3'  HO3'  single  0.850  0.020  0.980
 CTP  C5'  O5'   single  1.437  0.020  1.437
 CTP  C5'  H5'1  single  0.970  0.020  1.090
 CTP  C5'  H5'2  single  0.970  0.020  1.090
 CTP  O5'  PA    single  1.584  0.020  1.584
 CTP  PA   O1A   double  1.470  0.020  1.470
 CTP  PA   O2A   single  1.585  0.020  1.585
 CTP  PA   O3A   single  1.625  0.020  1.625
 CTP  O2A  HOA2  single  0.850  0.020  0.980
 CTP  O3A  PB    single  1.610  0.020  1.610
 CTP  PB   O1B   double  1.465  0.020  1.465
 CTP  PB   O2B   single  1.583  0.020  1.583
 CTP  PB   O3B   single  1.605  0.020  1.605
 CTP  O2B  HOB2  single  0.850  0.020  0.980
 CTP  O3B  PG    single  1.630  0.020  1.630
 CTP  PG   O1G   double  1.470  0.020  1.470
 CTP  PG   O2G   single  1.585  0.020  1.585
 CTP  PG   O3G   single  1.583  0.020  1.583
 CTP  O2G  HOG2  single  0.850  0.020  0.980
 CTP  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
 CTP  C1'   N1   C6    119.47  3.000
 CTP  C1'   N1   C2    119.89  3.000
 CTP  C6    N1   C2    120.60  3.000
 CTP  O2    C2   N3    122.61  3.000
 CTP  O2    C2   N1    119.51  3.000
 CTP  N3    C2   N1    117.88  3.000
 CTP  C4    N3   C2    121.31  3.000
 CTP  N4    C4   C5    119.50  3.000
 CTP  N4    C4   N3    118.32  3.000
 CTP  C5    C4   N3    122.18  3.000
 CTP  H5    C5   C6    121.35  3.000
 CTP  H5    C5   C4    122.26  3.000
 CTP  C6    C5   C4    116.39  3.000
 CTP  H6    C6   C5    121.23  3.000
 CTP  H6    C6   N1    117.11  3.000
 CTP  C5    C6   N1    121.65  3.000
 CTP  HN42  N4   HN41  118.16  3.000
 CTP  HN42  N4   C4    120.14  3.000
 CTP  HN41  N4   C4    121.70  3.000
 CTP  H1'   C1'  O4'   111.68  3.000
 CTP  H1'   C1'  C2'   110.01  3.000
 CTP  O4'   C1'  C2'   105.16  3.000
 CTP  H1'   C1'  N1    106.52  3.000
 CTP  O4'   C1'  N1    108.85  3.000
 CTP  C2'   C1'  N1    114.72  3.000
 CTP  H2'   C2'  C3'   108.17  3.000
 CTP  H2'   C2'  O2'   111.35  3.000
 CTP  C3'   C2'  O2'   116.63  3.000
 CTP  H2'   C2'  C1'   109.41  3.000
 CTP  C3'   C2'  C1'   101.08  3.000
 CTP  O2'   C2'  C1'   109.61  3.000
 CTP  HO2'  O2'  C2'   109.00  3.000
 CTP  H3'   C3'  O3'   111.33  3.000
 CTP  H3'   C3'  C4'   111.34  3.000
 CTP  O3'   C3'  C4'   111.96  3.000
 CTP  H3'   C3'  C2'   112.22  3.000
 CTP  O3'   C3'  C2'   107.88  3.000
 CTP  C4'   C3'  C2'   101.72  3.000
 CTP  H4'   C4'  C5'   105.93  3.000
 CTP  H4'   C4'  O4'   109.32  3.000
 CTP  C5'   C4'  O4'   110.12  3.000
 CTP  H4'   C4'  C3'   109.55  3.000
 CTP  C5'   C4'  C3'   115.12  3.000
 CTP  O4'   C4'  C3'   106.74  3.000
 CTP  C4'   O4'  C1'   110.28  3.000
 CTP  HO3'  O3'  C3'   108.50  3.000
 CTP  H5'2  C5'  H5'1  108.13  3.000
 CTP  H5'2  C5'  O5'   111.38  3.000
 CTP  H5'1  C5'  O5'   108.06  3.000
 CTP  H5'2  C5'  C4'   108.67  3.000
 CTP  H5'1  C5'  C4'   110.75  3.000
 CTP  O5'   C5'  C4'   109.86  3.000
 CTP  PA    O5'  C5'   122.18  3.000
 CTP  O3A   PA   O2A   102.98  3.000
 CTP  O3A   PA   O1A   114.86  3.000
 CTP  O2A   PA   O1A   117.52  3.000
 CTP  O3A   PA   O5'    98.20  3.000
 CTP  O2A   PA   O5'   102.18  3.000
 CTP  O1A   PA   O5'   118.22  3.000
 CTP  HOA2  O2A  PA    114.96  3.000
 CTP  PB    O3A  PA    130.11  3.000
 CTP  O3B   PB   O2B   101.35  3.000
 CTP  O3B   PB   O1B   117.25  3.000
 CTP  O2B   PB   O1B   118.45  3.000
 CTP  O3B   PB   O3A    99.64  3.000
 CTP  O2B   PB   O3A   106.62  3.000
 CTP  O1B   PB   O3A   111.36  3.000
 CTP  HOB2  O2B  PB    114.90  3.000
 CTP  PG    O3B  PB    128.03  3.000
 CTP  O3G   PG   O2G   102.85  3.000
 CTP  O3G   PG   O1G   118.78  3.000
 CTP  O2G   PG   O1G   117.81  3.000
 CTP  O3G   PG   O3B    98.73  3.000
 CTP  O2G   PG   O3B   101.61  3.000
 CTP  O1G   PG   O3B   114.08  3.000
 CTP  HOG2  O2G  PG    114.83  3.000
 CTP  HOG3  O3G  PG    114.90  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
 CTP  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CTP  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 CTP  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 CTP  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 CTP  CONST_05  N4    C4   N3   C2    180.00   0.0  0
 CTP  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 CTP  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 CTP  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 CTP  CONST_09  HN41  N4   C4   N3    180.00   0.0  0
 CTP  CONST_10  HN42  N4   C4   N3      0.00   0.0  0
 CTP  CONST_11  HN41  N4   C4   C5      0.00   0.0  0
 CTP  CONST_12  HN42  N4   C4   C5    180.00   0.0  0
 CTP  Var_01    H5    C5   C6   N1    179.91  30.0  1
 CTP  Var_02    H6    C6   N1   C2    178.89  30.0  1
 CTP  Var_03    H5    C5   C4   N3   -179.55  30.0  1
 CTP  Var_04    H6    C6   C5   C4   -178.87  30.0  1
 CTP  Var_05    H6    C6   N1   C1'     1.03  30.0  1
 CTP  Var_06    H5    C5   C4   N4      0.26  30.0  1
 CTP  Var_07    PA    O5'  C5'  C4'  -131.01  30.0  3
 CTP  Var_08    O1A   PA   O5'  C5'    39.76  30.0  3
 CTP  Var_09    O2A   PA   O5'  C5'   -90.96  30.0  3
 CTP  Var_10    O3A   PA   O5'  C5'   163.77  30.0  3
 CTP  Var_11    PB    O3A  PA   O5'  -123.11  30.0  3
 CTP  Var_12    O1B   PB   O3A  PA    179.36  30.0  3
 CTP  Var_13    O2B   PB   O3A  PA     48.78  30.0  3
 CTP  Var_14    O3B   PB   O3A  PA    -56.23  30.0  3
 CTP  Var_15    PB    O3A  PA   O1A     3.28  30.0  3
 CTP  Var_16    PB    O3A  PA   O2A   132.29  30.0  3
 CTP  Var_17    PG    O3B  PB   O3A  -173.29  30.0  3
 CTP  Var_18    O1G   PG   O3B  PB    -24.32  30.0  3
 CTP  Var_19    O2G   PG   O3B  PB   -152.16  30.0  3
 CTP  Var_20    O3G   PG   O3B  PB    102.70  30.0  3
 CTP  Var_21    PG    O3B  PB   O1B   -53.09  30.0  3
 CTP  Var_22    PG    O3B  PB   O2B    77.44  30.0  3
 CTP  Var_23    H5'1  C5'  O5'  PA    108.07  30.0  1
 CTP  Var_24    H5'2  C5'  O5'  PA    -10.55  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
 CTP  chir_01  C1'  N1   C2'  O4'  negativ
 CTP  chir_02  C2'  O2'  C3'  C1'  positiv
 CTP  chir_03  C3'  O3'  C2'  C4'  negativ
 CTP  chir_04  C4'  O4'  C3'  C5'  negativ
 CTP  chir_05  PA   O1A  O2A  O3A  both
 CTP  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
 CTP  plan-1  N1    0.020
 CTP  plan-1  C2    0.020
 CTP  plan-1  N3    0.020
 CTP  plan-1  C4    0.020
 CTP  plan-1  C5    0.020
 CTP  plan-1  C6    0.020
 CTP  plan-1  O2    0.020
 CTP  plan-1  N4    0.020
 CTP  plan-1  C1'   0.020
 CTP  plan-1  HN41  0.020
 CTP  plan-1  HN42  0.020

