# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 13:00:14 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)N[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
 8CP  8CP  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine  ligand  45  28  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8CP
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
 8CP  N1   N  NR6   0  -0.549   6.8515  7.7952  10.4911
 8CP  C2   C  CR6   0   0.594   7.7525  7.9702   9.4304
 8CP  N3   N  N     0  -0.539   9.0721  7.9355   9.6962
 8CP  C4   C  CR6   0   0.515   9.5108  7.7014  10.9189
 8CP  C5   C  CR16  0  -0.477   8.6215  7.4870  12.0132
 8CP  C6   C  CR16  0   0.080   7.3009  7.5515  11.7405
 8CP  O2   O  O     0  -0.528   7.3048  8.1440   8.3020
 8CP  N4   N  NH2   0  -0.811  10.8283  7.6712  11.1199
 8CP  C1'  C  CH1   0   0.202   5.4163  7.8312  10.1583
 8CP  C2'  C  CH2   0  -0.533   4.9153  6.5058   9.5915
 8CP  C3'  C  CH1   0  -0.000   4.2972  5.8203  10.8034
 8CP  C4'  C  CH1   0   0.016   3.7363  7.0352  11.5506
 8CP  O4'  O  O2    0  -0.500   4.6736  8.0783  11.3223
 8CP  O3'  O  OH1   0  -0.695   3.3099  4.8980  10.4505
 8CP  C5'  C  CH2   0  -0.229   3.4803  6.8795  13.0281
 8CP  O5'  O  O2    0  -0.578   4.7095  6.6028  13.7121
 8CP  PA   P  P     0   1.501   4.9661  5.5097  14.8208
 8CP  O1A  O  O     0  -0.655   6.3326  5.5543  15.3491
 8CP  O2A  O  OH1   0  -0.732   3.7494  5.7111  15.8120
 8CP  O3A  O  O2    0  -0.707   4.7100  4.0889  14.0764
 8CP  PB   P  P     0   1.491   3.6054  3.0143  13.6465
 8CP  O1B  O  OH1   0  -0.727   2.2994  3.6665  14.2675
 8CP  O2B  O  O     0  -0.673   3.5843  2.7518  12.1903
 8CP  PG   P  P     0   1.458   4.5113  1.5720  16.1169
 8CP  O1G  O  O     0  -0.679   4.2730  0.2481  16.7177
 8CP  O2G  O  OH1   0  -0.725   6.0113  2.0863  16.0246
 8CP  O3G  O  OH1   0  -0.761   3.7934  2.8226  16.8215
 8CP  N3B  N  NH1   0  -0.945   4.0086  1.6603  14.5168
 8CP  H1   H  HCR6  0   0.283   8.9747  7.2938  13.0147
 8CP  H2   H  HCR6  0   0.321   6.5602  7.4223  12.5126
 8CP  H3   H  HNH2  0   0.401  11.4602  7.8263  10.3533
 8CP  H4   H  HNH2  0   0.413  11.2196  7.4830  12.0257
 8CP  H5   H  HCH1  0   0.270   5.2841  8.6542   9.4568
 8CP  H6   H  HCH2  0   0.262   4.1347  6.6970   8.8512
 8CP  H7   H  HCH2  0   0.278   5.6985  5.9235   9.1100
 8CP  H8   H  HCH1  0   0.227   5.0874  5.3478  11.4015
 8CP  H9   H  HCH1  0   0.250   2.7670  7.2930  11.1006
 8CP  H10  H  HOH1  0   0.461   3.3723  4.1214  11.0313
 8CP  H11  H  HCH2  0   0.284   3.0664  7.7962  13.4493
 8CP  H12  H  HCH2  0   0.252   2.7377  6.0914  13.1704
 8CP  H13  H  HOH1  0   0.502   3.6756  5.0550  16.5221
 8CP  H14  H  HOH1  0   0.513   1.4847  3.1682  14.1046
 8CP  H15  H  HOH1  0   0.504   6.4829  2.1206  16.8690
 8CP  H16  H  HOH1  0   0.508   2.9098  2.6278  17.1657
 8CP  H17  H  HNH1  0   0.456   4.0114  0.7898  13.9964

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
 8CP  O2   C2   double  1.226  0.020  1.226
 8CP  C2   N3   single  1.347  0.020  1.347
 8CP  C2   N1   single  1.403  0.020  1.403
 8CP  N3   C4   double  1.320  0.020  1.320
 8CP  C2'  C1'  single  1.526  0.020  1.526
 8CP  C2'  C3'  single  1.523  0.020  1.523
 8CP  C1'  N1   single  1.474  0.020  1.474
 8CP  C1'  O4'  single  1.403  0.020  1.403
 8CP  N1   C6   single  1.350  0.020  1.350
 8CP  O3'  C3'  single  1.396  0.020  1.396
 8CP  C4   N4   single  1.333  0.020  1.333
 8CP  C4   C5   single  1.426  0.020  1.426
 8CP  C3'  C4'  single  1.533  0.020  1.533
 8CP  O4'  C4'  single  1.421  0.020  1.421
 8CP  C6   C5   double  1.350  0.020  1.350
 8CP  C4'  C5'  single  1.508  0.020  1.508
 8CP  O2B  PB   double  1.480  0.020  1.480
 8CP  C5'  O5'  single  1.434  0.020  1.434
 8CP  O5'  PA   single  1.578  0.020  1.578
 8CP  PB   O3A  single  1.600  0.020  1.600
 8CP  PB   O1B  single  1.586  0.020  1.586
 8CP  PB   N3B  single  1.659  0.020  1.659
 8CP  O3A  PA   single  1.624  0.020  1.624
 8CP  N3B  PG   single  1.679  0.020  1.679
 8CP  PA   O1A  double  1.466  0.020  1.466
 8CP  PA   O2A  single  1.582  0.020  1.582
 8CP  PG   O1G  double  1.473  0.020  1.473
 8CP  PG   O3G  single  1.605  0.020  1.605
 8CP  PG   O2G  single  1.588  0.020  1.588
 8CP  C5   H1   single  0.930  0.020  1.080
 8CP  C6   H2   single  0.930  0.020  1.080
 8CP  N4   H3   single  0.860  0.020  1.020
 8CP  N4   H4   single  0.860  0.020  1.020
 8CP  C1'  H5   single  0.970  0.020  1.090
 8CP  C2'  H6   single  0.970  0.020  1.090
 8CP  C2'  H7   single  0.970  0.020  1.090
 8CP  C3'  H8   single  0.970  0.020  1.090
 8CP  C4'  H9   single  0.970  0.020  1.090
 8CP  O3'  H10  single  0.850  0.020  0.980
 8CP  C5'  H11  single  0.970  0.020  1.090
 8CP  C5'  H12  single  0.970  0.020  1.090
 8CP  O2A  H13  single  0.850  0.020  0.980
 8CP  O1B  H14  single  0.850  0.020  0.980
 8CP  O2G  H15  single  0.850  0.020  0.980
 8CP  O3G  H16  single  0.850  0.020  0.980
 8CP  N3B  H17  single  0.860  0.020  1.020

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
 8CP  C1'  N1   C6   122.52  3.000
 8CP  C6   N1   C2   120.57  3.000
 8CP  C1'  N1   C2   116.85  3.000
 8CP  O2   C2   N3   122.89  3.000
 8CP  N3   C2   N1   118.49  3.000
 8CP  O2   C2   N1   118.62  3.000
 8CP  C4   N3   C2   120.87  3.000
 8CP  N4   C4   C5   119.81  3.000
 8CP  C5   C4   N3   122.02  3.000
 8CP  N4   C4   N3   118.17  3.000
 8CP  H1   C5   C6   121.06  3.000
 8CP  H1   C5   C4   122.33  3.000
 8CP  C6   C5   C4   116.60  3.000
 8CP  H2   C6   C5   121.46  3.000
 8CP  H2   C6   N1   117.12  3.000
 8CP  C5   C6   N1   121.41  3.000
 8CP  H4   N4   H3   118.14  3.000
 8CP  H4   N4   C4   121.68  3.000
 8CP  H3   N4   C4   120.18  3.000
 8CP  H5   C1'  O4'  109.70  3.000
 8CP  H5   C1'  C2'  112.15  3.000
 8CP  O4'  C1'  C2'  106.70  3.000
 8CP  H5   C1'  N1   106.38  3.000
 8CP  O4'  C1'  N1   109.42  3.000
 8CP  C2'  C1'  N1   112.48  3.000
 8CP  H7   C2'  H6   107.94  3.000
 8CP  H7   C2'  C3'  113.78  3.000
 8CP  H6   C2'  C3'  109.14  3.000
 8CP  H7   C2'  C1'  113.13  3.000
 8CP  H6   C2'  C1'  109.52  3.000
 8CP  C3'  C2'  C1'  103.21  3.000
 8CP  H8   C3'  O3'  111.25  3.000
 8CP  H8   C3'  C4'  109.81  3.000
 8CP  O3'  C3'  C4'  112.83  3.000
 8CP  H8   C3'  C2'  109.58  3.000
 8CP  C4'  C3'  C2'  100.35  3.000
 8CP  O3'  C3'  C2'  112.52  3.000
 8CP  H9   C4'  C5'  106.00  3.000
 8CP  H9   C4'  O4'  110.10  3.000
 8CP  C5'  C4'  O4'  110.20  3.000
 8CP  H9   C4'  C3'  108.00  3.000
 8CP  C5'  C4'  C3'  117.27  3.000
 8CP  O4'  C4'  C3'  105.21  3.000
 8CP  C4'  O4'  C1'  110.69  3.000
 8CP  H10  O3'  C3'  109.35  3.000
 8CP  H12  C5'  H11  107.35  3.000
 8CP  H12  C5'  O5'  112.43  3.000
 8CP  H11  C5'  O5'  107.66  3.000
 8CP  H12  C5'  C4'  108.52  3.000
 8CP  H11  C5'  C4'  110.87  3.000
 8CP  O5'  C5'  C4'  109.99  3.000
 8CP  PA   O5'  C5'  127.47  3.000
 8CP  O3A  PA   O2A  106.09  3.000
 8CP  O2A  PA   O1A  119.16  3.000
 8CP  O3A  PA   O1A  109.80  3.000
 8CP  O2A  PA   O5'  103.12  3.000
 8CP  O1A  PA   O5'  112.57  3.000
 8CP  O3A  PA   O5'  104.97  3.000
 8CP  H13  O2A  PA   115.54  3.000
 8CP  PB   O3A  PA   145.04  3.000
 8CP  N3B  PB   O2B  112.02  3.000
 8CP  N3B  PB   O1B  109.29  3.000
 8CP  O2B  PB   O1B  116.51  3.000
 8CP  N3B  PB   O3A  103.85  3.000
 8CP  O1B  PB   O3A  100.78  3.000
 8CP  O2B  PB   O3A  113.16  3.000
 8CP  H14  O1B  PB   114.52  3.000
 8CP  N3B  PG   O3G  104.09  3.000
 8CP  O3G  PG   O2G  101.28  3.000
 8CP  N3B  PG   O2G  102.14  3.000
 8CP  O2G  PG   O1G  117.86  3.000
 8CP  O3G  PG   O1G  116.67  3.000
 8CP  N3B  PG   O1G  112.79  3.000
 8CP  H15  O2G  PG   114.90  3.000
 8CP  H16  O3G  PG   114.05  3.000
 8CP  H17  N3B  PG   116.29  3.000
 8CP  H17  N3B  PB   115.59  3.000
 8CP  PG   N3B  PB   127.98  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
 8CP  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 8CP  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 8CP  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 8CP  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 8CP  CONST_05  N4   C4   N3   C2   180.00   0.0  0
 8CP  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 8CP  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 8CP  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 8CP  CONST_09  H3   N4   C4   N3     0.00   0.0  0
 8CP  CONST_10  H4   N4   C4   N3   180.00   0.0  0
 8CP  Var_01    O3A  PA   O5'  C5'   63.49  30.0  3
 8CP  Var_02    O2B  PB   O3A  PA   122.87  30.0  1
 8CP  Var_03    PG   N3B  PB   O3A   41.35  30.0  3
 8CP  Var_04    O1G  PG   N3B  PB   157.11  30.0  3
 8CP  Var_05    H11  C5'  O5'  PA   104.41  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
 8CP  chir_01  C1'  C2'  N1   O4'  positiv
 8CP  chir_02  C3'  O3'  C4'  C2'  positiv
 8CP  chir_03  C4'  O4'  C3'  C5'  negativ
 8CP  chir_04  PA   O3A  O1A  O2A  both
 8CP  chir_05  PB   O3A  O2B  N3B  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
 8CP  plan-1  N1   0.020
 8CP  plan-1  C2   0.020
 8CP  plan-1  N3   0.020
 8CP  plan-1  C4   0.020
 8CP  plan-1  C5   0.020
 8CP  plan-1  C6   0.020
 8CP  plan-1  O2   0.020
 8CP  plan-1  N4   0.020
 8CP  plan-1  C1'  0.020
 8CP  plan-1  H1   0.020
 8CP  plan-1  H2   0.020
 8CP  plan-1  H3   0.020
 8CP  plan-1  H4   0.020

