# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 10:51:17 2020
#   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  41  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.554   4.7032  -0.4826   0.8551
 8CP  C2   C  CR6    0   0.601   4.8159  -0.6373  -0.5367
 8CP  N3   N  N      0  -0.541   5.3256  -1.7929  -1.0109
 8CP  C4   C  CR6    0   0.513   5.7088  -2.7565  -0.1971
 8CP  C5   C  CR16   0  -0.478   5.6044  -2.6368   1.2224
 8CP  C6   C  CR16   0   0.098   5.0873  -1.4820   1.6851
 8CP  O2   O  O      0  -0.505   4.4576   0.2707  -1.2726
 8CP  N4   N  NH2    0  -0.809   6.2057  -3.8730  -0.7283
 8CP  C1'  C  CH1    0   0.223   4.1205   0.7248   1.4302
 8CP  C2'  C  CH2    0  -0.555   4.7834   2.0497   1.0415
 8CP  C3'  C  CH1    0   0.023   3.7244   2.7986   0.2329
 8CP  C4'  C  CH1    0   0.018   2.4242   2.1183   0.6652
 8CP  O4'  O  O2     0  -0.492   2.7705   0.8060   1.0702
 8CP  O3'  O  OH1    0  -0.671   3.6316   4.1745   0.5135
 8CP  C5'  C  CH2    0  -0.151   1.3985   2.0643  -0.4404
 8CP  O5'  O  O2     0  -0.628   0.2105   1.4816   0.0420
 8CP  PA   P  P      0   1.337  -1.1308   1.5928  -0.9293
 8CP  O1A  O  O      0  -0.815  -1.7414   2.9502  -0.7450
 8CP  O2A  O  OP    -1  -0.816  -0.7508   1.1313  -2.3051
 8CP  O3A  O  O2     0  -0.755  -1.9459   0.4516  -0.1155
 8CP  PB   P  P      0   1.294  -3.6143   0.2247  -0.2203
 8CP  O1B  O  OP    -1  -0.823  -4.2266   0.8919   0.9770
 8CP  O2B  O  O      0  -0.831  -4.0097   0.6702  -1.6047
 8CP  PG   P  P      0   1.191  -5.0393  -2.3016   0.6430
 8CP  O1G  O  O      0  -0.910  -4.9119  -2.1876   2.1593
 8CP  O2G  O  OP    -1  -0.918  -4.8081  -3.7156   0.1019
 8CP  O3G  O  OP    -1  -0.913  -6.2810  -1.6155   0.0708
 8CP  N3B  N  NH1    0  -0.972  -3.6314  -1.4383  -0.0190
 8CP  H1   H  HCR6   0   0.287   5.9097  -3.4246   1.8943
 8CP  H2   H  HCR6   0   0.318   4.9589  -1.3023   2.7439
 8CP  H3   H  HNH2   0   0.402   6.2582  -3.9791  -1.7269
 8CP  H4   H  HNH2   0   0.413   6.4968  -4.6442  -0.1543
 8CP  H5   H  HCH1   0   0.243   4.2078   0.5787   2.5107
 8CP  H6   H  HCH2   0   0.259   5.0002   2.6102   1.9530
 8CP  H7   H  HCH2   0   0.270   5.7235   1.9168   0.5090
 8CP  H8   H  HCH1   0   0.230   3.8909   2.6344  -0.8351
 8CP  H9   H  HCH1   0   0.219   2.0121   2.6730   1.5218
 8CP  H10  H  HOH1   0   0.455   4.3577   4.6207   0.0685
 8CP  H11  H  HCH2   0   0.200   1.2354   3.0933  -0.7877
 8CP  H12  H  HCH2   0   0.207   1.8082   1.4946  -1.2819
 8CP  H17  H  HNH1   0   0.339  -3.2609  -1.9287  -0.8238

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  1.222  0.020  1.222
 8CP  C2   N3   single  1.349  0.020  1.349
 8CP  C2   N1   single  1.405  0.020  1.405
 8CP  N3   C4   double  1.318  0.020  1.318
 8CP  C2'  C1'  single  1.532  0.020  1.532
 8CP  C2'  C3'  single  1.528  0.020  1.528
 8CP  C1'  N1   single  1.459  0.020  1.459
 8CP  C1'  O4'  single  1.400  0.020  1.400
 8CP  N1   C6   single  1.355  0.020  1.355
 8CP  O3'  C3'  single  1.407  0.020  1.407
 8CP  C4   N4   single  1.333  0.020  1.333
 8CP  C4   C5   single  1.428  0.020  1.428
 8CP  C3'  C4'  single  1.530  0.020  1.530
 8CP  O4'  C4'  single  1.416  0.020  1.416
 8CP  C6   C5   double  1.347  0.020  1.347
 8CP  C4'  C5'  single  1.509  0.020  1.509
 8CP  O2B  PB   deloc   1.507  0.020  1.507
 8CP  C5'  O5'  single  1.408  0.020  1.408
 8CP  O5'  PA   single  1.660  0.020  1.660
 8CP  PB   O3A  single  1.687  0.020  1.687
 8CP  PB   O1B  deloc   1.501  0.020  1.501
 8CP  PB   N3B  single  1.675  0.020  1.675
 8CP  O3A  PA   single  1.621  0.020  1.621
 8CP  N3B  PG   single  1.779  0.020  1.779
 8CP  PA   O1A  deloc   1.500  0.020  1.500
 8CP  PA   O2A  deloc   1.500  0.020  1.500
 8CP  PG   O1G  deloc   1.526  0.020  1.526
 8CP  PG   O3G  deloc   1.530  0.020  1.530
 8CP  PG   O2G  deloc   1.532  0.020  1.532
 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  N3B  H17  single  0.890  0.020  1.040

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   118.84  3.000
 8CP  C6   N1   C2   120.20  3.000
 8CP  C1'  N1   C2   120.91  3.000
 8CP  O2   C2   N3   122.37  3.000
 8CP  N3   C2   N1   118.22  3.000
 8CP  O2   C2   N1   119.41  3.000
 8CP  C4   N3   C2   121.26  3.000
 8CP  N4   C4   C5   119.58  3.000
 8CP  C5   C4   N3   122.07  3.000
 8CP  N4   C4   N3   118.35  3.000
 8CP  H1   C5   C6   121.36  3.000
 8CP  H1   C5   C4   122.46  3.000
 8CP  C6   C5   C4   116.18  3.000
 8CP  H2   C6   C5   121.61  3.000
 8CP  H2   C6   N1   116.33  3.000
 8CP  C5   C6   N1   122.06  3.000
 8CP  H4   N4   H3   118.13  3.000
 8CP  H4   N4   C4   121.57  3.000
 8CP  H3   N4   C4   120.24  3.000
 8CP  H5   C1'  O4'  109.80  3.000
 8CP  H5   C1'  C2'  109.37  3.000
 8CP  O4'  C1'  C2'  107.58  3.000
 8CP  H5   C1'  N1   104.30  3.000
 8CP  O4'  C1'  N1   109.38  3.000
 8CP  C2'  C1'  N1   116.30  3.000
 8CP  H7   C2'  H6   107.43  3.000
 8CP  H7   C2'  C3'  113.54  3.000
 8CP  H6   C2'  C3'  109.13  3.000
 8CP  H7   C2'  C1'  113.10  3.000
 8CP  H6   C2'  C1'  108.55  3.000
 8CP  C3'  C2'  C1'  104.96  3.000
 8CP  H8   C3'  O3'  110.59  3.000
 8CP  H8   C3'  C4'  109.79  3.000
 8CP  O3'  C3'  C4'  108.81  3.000
 8CP  H8   C3'  C2'  109.73  3.000
 8CP  C4'  C3'  C2'  102.80  3.000
 8CP  O3'  C3'  C2'  114.79  3.000
 8CP  H9   C4'  C5'  109.50  3.000
 8CP  H9   C4'  O4'  109.63  3.000
 8CP  C5'  C4'  O4'  110.03  3.000
 8CP  H9   C4'  C3'  108.30  3.000
 8CP  C5'  C4'  C3'  112.74  3.000
 8CP  O4'  C4'  C3'  106.56  3.000
 8CP  C4'  O4'  C1'  111.29  3.000
 8CP  H10  O3'  C3'  108.17  3.000
 8CP  H12  C5'  H11  107.45  3.000
 8CP  H12  C5'  O5'  111.30  3.000
 8CP  H11  C5'  O5'  111.76  3.000
 8CP  H12  C5'  C4'  109.10  3.000
 8CP  H11  C5'  C4'  107.41  3.000
 8CP  O5'  C5'  C4'  109.70  3.000
 8CP  PA   O5'  C5'  116.97  3.000
 8CP  O3A  PA   O2A  111.78  3.000
 8CP  O2A  PA   O1A  119.63  3.000
 8CP  O3A  PA   O1A  111.76  3.000
 8CP  O2A  PA   O5'  108.14  3.000
 8CP  O1A  PA   O5'  108.53  3.000
 8CP  O3A  PA   O5'   93.74  3.000
 8CP  PB   O3A  PA   124.09  3.000
 8CP  N3B  PB   O2B  113.65  3.000
 8CP  N3B  PB   O1B  109.95  3.000
 8CP  O2B  PB   O1B  119.62  3.000
 8CP  N3B  PB   O3A   97.82  3.000
 8CP  O1B  PB   O3A  107.10  3.000
 8CP  O2B  PB   O3A  106.07  3.000
 8CP  N3B  PG   O3G  106.59  3.000
 8CP  O3G  PG   O2G  113.86  3.000
 8CP  N3B  PG   O2G  101.36  3.000
 8CP  O2G  PG   O1G  114.05  3.000
 8CP  O3G  PG   O1G  113.95  3.000
 8CP  N3B  PG   O1G  105.51  3.000
 8CP  H17  N3B  PG   110.50  3.000
 8CP  H17  N3B  PB   112.42  3.000
 8CP  PG   N3B  PB   122.31  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'  164.62  30.0  3
 8CP  Var_02    O2B  PB   O3A  PA    29.53  30.0  1
 8CP  Var_03    PG   N3B  PB   O3A  153.90  30.0  3
 8CP  Var_04    O1G  PG   N3B  PB   -83.05  30.0  3
 8CP  Var_05    H11  C5'  O5'  PA    49.64  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
 8CP  chir_01  C1'  C2'  N1   O4'  positiv
 8CP  chir_02  C3'  O3'  C4'  C2'  positiv
 8CP  chir_03  C4'  O4'  C3'  C5'  negativ

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

