# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 03:07:45 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-amino-2'-deoxycytidine 5'-(tetrahydrogen triphosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N
#
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
 CSG  CSG  '2'-amino-2'-deoxycytidine 5'-(tetrahydrogen triphosphate)'  ligand  46  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_CSG
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
 CSG  C5    C  CR16  0  -0.474  29.4713  -1.3112  -3.0850
 CSG  C4    C  CR6   0   0.514  28.3104  -2.0586  -2.7272
 CSG  N4    N  NH2   0  -0.811  28.3934  -3.3809  -2.5804
 CSG  N3    N  N     0  -0.538  27.1400  -1.4812  -2.5309
 CSG  C2    C  CR6   0   0.594  26.9974  -0.1483  -2.6566
 CSG  O2    O  O     0  -0.523  25.9304   0.4279  -2.4782
 CSG  C6    C  CR16  0   0.085  29.3165   0.0233  -3.2152
 CSG  N1    N  NR6   0  -0.554  28.1210   0.6165  -3.0057
 CSG  C1'   C  CH1   0   0.219  27.9159   2.0684  -3.1469
 CSG  O4'   O  O2    0  -0.501  29.0115   2.6285  -3.8182
 CSG  C2'   C  CH1   0  -0.198  27.8048   2.7836  -1.7915
 CSG  N2'   N  NH2   0  -0.788  26.8411   3.8606  -1.8666
 CSG  C3'   C  CH1   0   0.009  29.2633   3.2076  -1.5730
 CSG  O3'   O  OH1   0  -0.679  29.3875   4.2397  -0.6459
 CSG  C4'   C  CH1   0  -0.014  29.6653   3.5906  -2.9978
 CSG  C5'   C  CH2   0  -0.202  31.1362   3.6574  -3.3084
 CSG  O5'   O  O2    0  -0.600  31.7658   2.4245  -2.9228
 CSG  PA    P  P     0   1.495  33.3461   2.2737  -2.8365
 CSG  O1A   O  O     0  -0.666  34.1262   3.3795  -3.4061
 CSG  O2A   O  OH1   0  -0.704  33.6380   0.7953  -3.3139
 CSG  O3A   O  O2    0  -0.677  33.6175   2.0033  -1.2537
 CSG  PB    P  P     0   1.520  32.8863   2.6173   0.0291
 CSG  O1B   O  OH1   0  -0.698  32.0606   1.3631   0.5057
 CSG  O2B   O  O     0  -0.686  32.1759   3.8921  -0.1831
 CSG  O3B   O  O2    0  -0.674  34.0902   2.6972   1.0830
 CSG  PG    P  P     0   1.478  35.1527   3.9436   1.2115
 CSG  O1G   O  OH1   0  -0.719  34.5012   4.9328   2.2531
 CSG  O2G   O  OH1   0  -0.716  36.3243   3.2633   2.0267
 CSG  O3G   O  O     0  -0.678  35.4383   4.5698  -0.0848
 CSG  H5    H  HCR6  0   0.283  30.4289  -1.7795  -3.2555
 CSG  HN4   H  HNH2  0   0.413  29.2493  -3.8768  -2.7556
 CSG  HN4A  H  HNH2  0   0.402  27.5733  -3.9172  -2.3535
 CSG  H6    H  HCR6  0   0.315  30.1410   0.6593  -3.4947
 CSG  H1'   H  HCH1  0   0.271  27.0069   2.2053  -3.7355
 CSG  H2'   H  HCH1  0   0.278  27.4759   2.0964  -1.0120
 CSG  HN2'  H  HNH2  0   0.358  26.7984   4.3365  -0.9746
 CSG  HN2A  H  HNH2  0   0.350  27.1149   4.5652  -2.5416
 CSG  H3'   H  HCH1  0   0.216  29.8306   2.3198  -1.2594
 CSG  HO3'  H  HOH1  0   0.462  30.3181   4.2776  -0.3781
 CSG  H4'   H  HCH1  0   0.247  29.2797   4.5958  -3.2199
 CSG  H5'   H  HCH2  0   0.276  31.2950   3.8287  -4.3743
 CSG  H5'A  H  HCH2  0   0.258  31.5614   4.5004  -2.7621
 CSG  HO2A  H  HOH1  0   0.514  33.7412   0.6967  -4.2716
 CSG  HO1B  H  HOH1  0   0.519  31.4703   1.5089   1.2597
 CSG  HO1G  H  HOH1  0   0.510  34.2597   4.5814   3.1217
 CSG  HO2G  H  HOH1  0   0.514  36.9086   2.6869   1.5133

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
 CSG  C6   C5    double  1.350  0.020  1.350
 CSG  C5   C4    single  1.426  0.020  1.426
 CSG  C5   H5    single  0.930  0.020  1.080
 CSG  C4   N3    double  1.320  0.020  1.320
 CSG  C4   N4    single  1.333  0.020  1.333
 CSG  N4   HN4   single  0.860  0.020  1.020
 CSG  N4   HN4A  single  0.860  0.020  1.020
 CSG  C2   N3    single  1.346  0.020  1.346
 CSG  N1   C2    single  1.403  0.020  1.403
 CSG  O2   C2    double  1.226  0.020  1.226
 CSG  C6   N1    single  1.351  0.020  1.351
 CSG  C6   H6    single  0.930  0.020  1.080
 CSG  C1'  N1    single  1.473  0.020  1.473
 CSG  O4'  C1'   single  1.402  0.020  1.402
 CSG  C1'  C2'   single  1.537  0.020  1.537
 CSG  C1'  H1'   single  0.970  0.020  1.090
 CSG  O4'  C4'   single  1.423  0.020  1.423
 CSG  N2'  C2'   single  1.447  0.020  1.447
 CSG  C2'  C3'   single  1.534  0.020  1.534
 CSG  C2'  H2'   single  0.970  0.020  1.090
 CSG  N2'  HN2'  single  0.890  0.020  1.040
 CSG  N2'  HN2A  single  0.890  0.020  1.040
 CSG  C4'  C3'   single  1.529  0.020  1.529
 CSG  C3'  O3'   single  1.393  0.020  1.393
 CSG  C3'  H3'   single  0.970  0.020  1.090
 CSG  O3'  HO3'  single  0.850  0.020  0.980
 CSG  C5'  C4'   single  1.505  0.020  1.505
 CSG  C4'  H4'   single  0.970  0.020  1.090
 CSG  C5'  O5'   single  1.437  0.020  1.437
 CSG  C5'  H5'   single  0.970  0.020  1.090
 CSG  C5'  H5'A  single  0.970  0.020  1.090
 CSG  O5'  PA    single  1.590  0.020  1.590
 CSG  O1A  PA    double  1.468  0.020  1.468
 CSG  O2A  PA    single  1.581  0.020  1.581
 CSG  PA   O3A   single  1.628  0.020  1.628
 CSG  O2A  HO2A  single  0.850  0.020  0.980
 CSG  O3A  PB    single  1.599  0.020  1.599
 CSG  O2B  PB    double  1.475  0.020  1.475
 CSG  PB   O1B   single  1.575  0.020  1.575
 CSG  PB   O3B   single  1.602  0.020  1.602
 CSG  O1B  HO1B  single  0.850  0.020  0.980
 CSG  PG   O3B   single  1.643  0.020  1.643
 CSG  O3G  PG    double  1.468  0.020  1.468
 CSG  PG   O2G   single  1.581  0.020  1.581
 CSG  PG   O1G   single  1.577  0.020  1.577
 CSG  O1G  HO1G  single  0.850  0.020  0.980
 CSG  O2G  HO2G  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
 CSG  H5    C5   C6    121.03  3.000
 CSG  H5    C5   C4    122.30  3.000
 CSG  C6    C5   C4    116.67  3.000
 CSG  N3    C4   N4    118.22  3.000
 CSG  N4    C4   C5    119.78  3.000
 CSG  N3    C4   C5    122.00  3.000
 CSG  HN4A  N4   HN4   118.09  3.000
 CSG  HN4A  N4   C4    120.20  3.000
 CSG  HN4   N4   C4    121.57  3.000
 CSG  C2    N3   C4    120.87  3.000
 CSG  N1    C2   O2    118.49  3.000
 CSG  O2    C2   N3    122.95  3.000
 CSG  N1    C2   N3    118.55  3.000
 CSG  H6    C6   N1    117.26  3.000
 CSG  H6    C6   C5    121.37  3.000
 CSG  N1    C6   C5    121.37  3.000
 CSG  C1'   N1   C6    122.76  3.000
 CSG  C1'   N1   C2    116.71  3.000
 CSG  C6    N1   C2    120.52  3.000
 CSG  H1'   C1'  C2'   110.92  3.000
 CSG  H1'   C1'  O4'   110.03  3.000
 CSG  C2'   C1'  O4'   107.04  3.000
 CSG  H1'   C1'  N1    106.93  3.000
 CSG  C2'   C1'  N1    112.60  3.000
 CSG  O4'   C1'  N1    109.32  3.000
 CSG  C4'   O4'  C1'   110.67  3.000
 CSG  H2'   C2'  C3'   111.05  3.000
 CSG  H2'   C2'  N2'   107.78  3.000
 CSG  C3'   C2'  N2'   115.76  3.000
 CSG  H2'   C2'  C1'   111.05  3.000
 CSG  C3'   C2'  C1'   100.69  3.000
 CSG  N2'   C2'  C1'   110.41  3.000
 CSG  HN2A  N2'  HN2'  105.76  3.000
 CSG  HN2A  N2'  C2'   111.85  3.000
 CSG  HN2'  N2'  C2'   109.41  3.000
 CSG  H3'   C3'  C4'   109.42  3.000
 CSG  H3'   C3'  O3'   111.25  3.000
 CSG  C4'   C3'  O3'   114.28  3.000
 CSG  H3'   C3'  C2'   107.93  3.000
 CSG  O3'   C3'  C2'   112.60  3.000
 CSG  C4'   C3'  C2'   100.75  3.000
 CSG  HO3'  O3'  C3'   107.37  3.000
 CSG  H4'   C4'  C5'   105.11  3.000
 CSG  H4'   C4'  C3'   108.97  3.000
 CSG  C5'   C4'  C3'   117.41  3.000
 CSG  H4'   C4'  O4'   109.91  3.000
 CSG  C5'   C4'  O4'   111.10  3.000
 CSG  C3'   C4'  O4'   104.30  3.000
 CSG  H5'A  C5'  H5'   108.13  3.000
 CSG  H5'A  C5'  O5'   110.97  3.000
 CSG  H5'   C5'  O5'   109.45  3.000
 CSG  H5'A  C5'  C4'   108.17  3.000
 CSG  H5'   C5'  C4'   110.54  3.000
 CSG  O5'   C5'  C4'   109.56  3.000
 CSG  PA    O5'  C5'   122.11  3.000
 CSG  O3A   PA   O2A    96.17  3.000
 CSG  O3A   PA   O1A   114.43  3.000
 CSG  O2A   PA   O1A   119.28  3.000
 CSG  O3A   PA   O5'   103.55  3.000
 CSG  O2A   PA   O5'   104.82  3.000
 CSG  O1A   PA   O5'   115.82  3.000
 CSG  HO2A  O2A  PA    114.43  3.000
 CSG  PB    O3A  PA    129.77  3.000
 CSG  O3B   PB   O2B   114.43  3.000
 CSG  O3B   PB   O1B   103.56  3.000
 CSG  O2B   PB   O1B   118.64  3.000
 CSG  O3B   PB   O3A   101.73  3.000
 CSG  O1B   PB   O3A   100.18  3.000
 CSG  O2B   PB   O3A   115.89  3.000
 CSG  HO1B  O1B  PB    115.79  3.000
 CSG  PG    O3B  PB    125.12  3.000
 CSG  O3G   PG   O2G   119.66  3.000
 CSG  O2G   PG   O1G   103.62  3.000
 CSG  O3G   PG   O1G   113.33  3.000
 CSG  O1G   PG   O3B   105.09  3.000
 CSG  O2G   PG   O3B   101.14  3.000
 CSG  O3G   PG   O3B   112.36  3.000
 CSG  HO1G  O1G  PG    117.91  3.000
 CSG  HO2G  O2G  PG    115.47  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
 CSG  CONST_01  C2    N3   C4   C5     0.00   0.0  0
 CSG  CONST_02  N1    C2   N3   C4     0.00   0.0  0
 CSG  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 CSG  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 CSG  CONST_05  O2    C2   N3   C4   180.00   0.0  0
 CSG  CONST_06  C2    N3   C4   N4   180.00   0.0  0
 CSG  CONST_07  C6    N1   C2   O2   180.00   0.0  0
 CSG  CONST_08  C1'   N1   C2   O2     0.00   0.0  0
 CSG  CONST_09  HN4   N4   C4   C5     0.00   0.0  0
 CSG  CONST_10  HN4A  N4   C4   C5   180.00   0.0  0
 CSG  Var_01    O1A   PA   O5'  C5'  -10.81  30.0  3
 CSG  Var_02    O2B   PB   O3A  PA   -21.57  30.0  3
 CSG  Var_03    O3G   PG   O3B  PB   -33.27  30.0  2
 CSG  Var_04    H5'   C5'  O5'  PA    71.48  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
 CSG  chir_01  C1'  N1   O4'  C2'  positiv
 CSG  chir_02  C2'  N2'  C3'  C1'  positiv
 CSG  chir_03  C3'  O3'  C4'  C2'  positiv
 CSG  chir_04  C4'  O4'  C3'  C5'  negativ
 CSG  chir_05  PA   O1A  O2A  O3A  both
 CSG  chir_06  PB   O1B  O2B  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
 CSG  plan-1  C5    0.020
 CSG  plan-1  C4    0.020
 CSG  plan-1  N4    0.020
 CSG  plan-1  N3    0.020
 CSG  plan-1  C2    0.020
 CSG  plan-1  O2    0.020
 CSG  plan-1  C6    0.020
 CSG  plan-1  N1    0.020
 CSG  plan-1  C1'   0.020
 CSG  plan-1  H5    0.020
 CSG  plan-1  HN4   0.020
 CSG  plan-1  HN4A  0.020
 CSG  plan-1  H6    0.020

