# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 09:51:57 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5'-O-[(S)-hydroxy({[2-(trimethylammonio)ethoxy]phosphinato}oxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=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
 CDC  CDC  5'-O-[(S)-hydroxy({[2-(trimethylammonio)ethoxy]phosphinato}oxy)phosphoryl]cytidine  ligand  56  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CDC
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
 CDC  N1    N  NR6    0  -0.565   4.1780  -0.5326   0.5018
 CDC  C2    C  CR6    0   0.605   3.7318  -1.0068  -0.7489
 CDC  N3    N  N      0  -0.541   4.1339  -2.2325  -1.1437
 CDC  C4    C  CR6    0   0.514   4.9305  -2.9695  -0.3966
 CDC  C5    C  CR16   0  -0.476   5.4052  -2.5213   0.8740
 CDC  C6    C  CR16   0   0.096   4.9896  -1.3032   1.2691
 CDC  O2    O  O      0  -0.500   3.0079  -0.3055  -1.4387
 CDC  N4    N  NH2    0  -0.808   5.2921  -4.1681  -0.8513
 CDC  C1'   C  CR15   0   0.240   3.7804   0.7703   1.0070
 CDC  C2'   C  CR15   0  -0.060   4.1562   1.9697   0.1378
 CDC  O2'   O  OH1    0  -0.661   5.4834   2.3374   0.3983
 CDC  C3'   C  CR15   0  -0.037   3.1191   2.9992   0.6004
 CDC  C4'   C  CR15   0  -0.028   1.8977   2.1247   0.8664
 CDC  O4'   O  O      0  -0.489   2.3999   0.8293   1.2030
 CDC  O3'   O  OH1    0  -0.672   3.5135   3.6023   1.8075
 CDC  C5'   C  CH2    0  -0.132   0.9533   2.0610  -0.3155
 CDC  O5'   O  O2     0  -0.623  -0.1236   1.2152   0.0288
 CDC  PA    P  P      0   1.341  -1.4451   1.1632  -0.9458
 CDC  O1A   O  O      0  -0.795  -1.0592   1.5367  -2.3411
 CDC  O2A   O  OP    -1  -0.771  -2.5760   1.8513  -0.2488
 CDC  O3A   O  O2     0  -0.731  -1.6229  -0.4755  -0.8272
 CDC  PB    P  P      0   1.375  -2.9090  -1.3395  -1.3292
 CDC  O1B   O  O2     0  -0.614  -3.6429  -1.4644   0.1476
 CDC  O2B   O  OP    -1  -0.789  -3.7863  -0.5348  -2.2402
 CDC  O3B   O  O      0  -0.780  -2.4217  -2.6902  -1.7452
 CDC  C14   C  CH2    0  -0.189  -4.8357  -2.2073   0.2127
 CDC  C15   C  CH2    0  -0.339  -5.8771  -1.5343   1.0778
 CDC  N11   N  NT     1  -0.377  -6.4918  -0.2610   0.5561
 CDC  C16   C  CH3    0  -0.568  -6.9973  -0.4367  -0.8331
 CDC  C17   C  CH3    0  -0.557  -5.5227   0.8752   0.5865
 CDC  C18   C  CH3    0  -0.544  -7.6373   0.0700   1.4496
 CDC  H5    H  HCR6   0   0.289   6.0548  -3.1198   1.4941
 CDC  H6    H  HCR6   0   0.319   5.2885  -0.8861   2.2208
 CDC  H41   H  HNH2   0   0.414   5.9129  -4.7646  -0.3336
 CDC  H42   H  HNH2   0   0.403   4.9650  -4.4872  -1.7473
 CDC  H1'   H  HCR5   0   0.240   4.3044   0.8744   1.9657
 CDC  H2'   H  HCR5   0   0.268   3.9992   1.7502  -0.9194
 CDC  HO'2  H  HOH1   0   0.468   5.8410   2.7768  -0.3788
 CDC  H3'   H  HCR5   0   0.242   2.9225   3.7502  -0.1764
 CDC  H4'   H  HCR5   0   0.245   1.3466   2.5128   1.7299
 CDC  H3T   H  HOH1   0   0.447   4.4427   3.8469   1.7206
 CDC  H5'1  H  HCH2   0   0.224   1.4684   1.6963  -1.2058
 CDC  H5'2  H  HCH2   0   0.204   0.6151   3.0838  -0.5188
 CDC  H141  H  HCH2   0   0.258  -4.6512  -3.1759   0.6881
 CDC  H142  H  HCH2   0   0.233  -5.2538  -2.4310  -0.7738
 CDC  H151  H  HCH2   0   0.301  -5.4699  -1.3008   2.0615
 CDC  H152  H  HCH2   0   0.299  -6.6980  -2.2398   1.2110
 CDC  H161  H  HCH3   0   0.298  -6.1593  -0.5634  -1.5138
 CDC  H162  H  HCH3   0   0.289  -7.6525  -1.3036  -0.8700
 CDC  H163  H  HCH3   0   0.293  -7.5553   0.4531  -1.1134
 CDC  H171  H  HCH3   0   0.273  -6.0709   1.7905   0.3788
 CDC  H172  H  HCH3   0   0.275  -5.0802   0.9347   1.5768
 CDC  H173  H  HCH3   0   0.320  -4.7464   0.7357  -0.1536
 CDC  H181  H  HCH3   0   0.292  -8.3763  -0.7250   1.4015
 CDC  H182  H  HCH3   0   0.293  -7.2757   0.1761   2.4692
 CDC  H183  H  HCH3   0   0.291  -8.0835   1.0055   1.1234

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
 CDC  N1   C2    single  1.410  0.020  1.410
 CDC  N1   C6    single  1.357  0.020  1.357
 CDC  N1   C1'   single  1.453  0.020  1.453
 CDC  C2   N3    single  1.349  0.020  1.349
 CDC  C2   O2    double  1.221  0.020  1.221
 CDC  N3   C4    double  1.318  0.020  1.318
 CDC  C4   C5    single  1.429  0.020  1.429
 CDC  C4   N4    single  1.332  0.020  1.332
 CDC  C5   C6    double  1.346  0.020  1.346
 CDC  C5   H5    single  0.930  0.020  1.080
 CDC  C6   H6    single  0.930  0.020  1.080
 CDC  N4   H41   single  0.860  0.020  1.020
 CDC  N4   H42   single  0.860  0.020  1.020
 CDC  C1'  C2'   single  1.528  0.020  1.528
 CDC  C1'  O4'   single  1.396  0.020  1.396
 CDC  C1'  H1'   single  0.970  0.020  1.090
 CDC  C2'  O2'   single  1.402  0.020  1.402
 CDC  C2'  C3'   single  1.533  0.020  1.533
 CDC  C2'  H2'   single  0.970  0.020  1.090
 CDC  O2'  HO'2  single  0.850  0.020  0.980
 CDC  C3'  C4'   single  1.526  0.020  1.526
 CDC  C3'  O3'   single  1.406  0.020  1.406
 CDC  C3'  H3'   single  0.970  0.020  1.090
 CDC  C4'  O4'   single  1.430  0.020  1.430
 CDC  C4'  C5'   single  1.514  0.020  1.514
 CDC  C4'  H4'   single  0.970  0.020  1.090
 CDC  O3'  H3T   single  0.850  0.020  0.980
 CDC  C5'  O5'   single  1.412  0.020  1.412
 CDC  C5'  H5'1  single  0.970  0.020  1.090
 CDC  C5'  H5'2  single  0.970  0.020  1.090
 CDC  O5'  PA    single  1.643  0.020  1.643
 CDC  PA   O1A   deloc   1.495  0.020  1.495
 CDC  PA   O2A   deloc   1.496  0.020  1.496
 CDC  PA   O3A   single  1.653  0.020  1.653
 CDC  O3A  PB    single  1.629  0.020  1.629
 CDC  PB   O1B   single  1.654  0.020  1.654
 CDC  PB   O2B   deloc   1.499  0.020  1.499
 CDC  PB   O3B   deloc   1.495  0.020  1.495
 CDC  O1B  C14   single  1.407  0.020  1.407
 CDC  C14  C15   single  1.512  0.020  1.512
 CDC  C14  H141  single  0.970  0.020  1.090
 CDC  C14  H142  single  0.970  0.020  1.090
 CDC  C15  N11   single  1.507  0.020  1.507
 CDC  C15  H151  single  0.970  0.020  1.090
 CDC  C15  H152  single  0.970  0.020  1.090
 CDC  N11  C16   single  1.489  0.020  1.489
 CDC  N11  C17   single  1.494  0.020  1.494
 CDC  N11  C18   single  1.490  0.020  1.490
 CDC  C16  H161  single  0.970  0.020  1.090
 CDC  C16  H162  single  0.970  0.020  1.090
 CDC  C16  H163  single  0.970  0.020  1.090
 CDC  C17  H171  single  0.970  0.020  1.090
 CDC  C17  H172  single  0.970  0.020  1.090
 CDC  C17  H173  single  0.970  0.020  1.090
 CDC  C18  H181  single  0.970  0.020  1.090
 CDC  C18  H182  single  0.970  0.020  1.090
 CDC  C18  H183  single  0.970  0.020  1.090

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
 CDC  C1'   N1   C6    118.44  3.000
 CDC  C1'   N1   C2    121.56  3.000
 CDC  C6    N1   C2    119.99  3.000
 CDC  O2    C2   N3    122.21  3.000
 CDC  O2    C2   N1    119.70  3.000
 CDC  N3    C2   N1    118.09  3.000
 CDC  C4    N3   C2    121.50  3.000
 CDC  N4    C4   C5    119.72  3.000
 CDC  N4    C4   N3    118.30  3.000
 CDC  C5    C4   N3    121.99  3.000
 CDC  H5    C5   C6    121.27  3.000
 CDC  H5    C5   C4    122.48  3.000
 CDC  C6    C5   C4    116.25  3.000
 CDC  H6    C6   C5    121.46  3.000
 CDC  H6    C6   N1    116.36  3.000
 CDC  C5    C6   N1    122.17  3.000
 CDC  H42   N4   H41   118.14  3.000
 CDC  H42   N4   C4    120.08  3.000
 CDC  H41   N4   C4    121.75  3.000
 CDC  H1'   C1'  O4'   110.21  3.000
 CDC  H1'   C1'  C2'   107.76  3.000
 CDC  O4'   C1'  C2'   106.85  3.000
 CDC  H1'   C1'  N1    104.96  3.000
 CDC  O4'   C1'  N1    110.95  3.000
 CDC  C2'   C1'  N1    116.02  3.000
 CDC  H2'   C2'  C3'   109.28  3.000
 CDC  H2'   C2'  O2'   111.66  3.000
 CDC  C3'   C2'  O2'   114.11  3.000
 CDC  H2'   C2'  C1'   110.97  3.000
 CDC  C3'   C2'  C1'   100.90  3.000
 CDC  O2'   C2'  C1'   109.45  3.000
 CDC  HO'2  O2'  C2'   108.77  3.000
 CDC  H3'   C3'  O3'   111.36  3.000
 CDC  H3'   C3'  C4'   111.84  3.000
 CDC  O3'   C3'  C4'   108.72  3.000
 CDC  H3'   C3'  C2'   111.52  3.000
 CDC  O3'   C3'  C2'   110.95  3.000
 CDC  C4'   C3'  C2'   102.08  3.000
 CDC  H4'   C4'  C5'   108.44  3.000
 CDC  H4'   C4'  O4'   108.19  3.000
 CDC  C5'   C4'  O4'   111.39  3.000
 CDC  H4'   C4'  C3'   109.70  3.000
 CDC  C5'   C4'  C3'   112.79  3.000
 CDC  O4'   C4'  C3'   106.21  3.000
 CDC  C4'   O4'  C1'   110.66  3.000
 CDC  H3T   O3'  C3'   107.56  3.000
 CDC  H5'2  C5'  H5'1  107.83  3.000
 CDC  H5'2  C5'  O5'   111.65  3.000
 CDC  H5'1  C5'  O5'   111.02  3.000
 CDC  H5'2  C5'  C4'   107.33  3.000
 CDC  H5'1  C5'  C4'   110.88  3.000
 CDC  O5'   C5'  C4'   108.09  3.000
 CDC  PA    O5'  C5'   119.19  3.000
 CDC  O3A   PA   O2A   109.96  3.000
 CDC  O3A   PA   O1A   110.03  3.000
 CDC  O2A   PA   O1A   121.00  3.000
 CDC  O3A   PA   O5'    94.32  3.000
 CDC  O2A   PA   O5'   108.49  3.000
 CDC  O1A   PA   O5'   109.76  3.000
 CDC  PB    O3A  PA    126.08  3.000
 CDC  O3B   PB   O2B   120.44  3.000
 CDC  O3B   PB   O1B   108.96  3.000
 CDC  O2B   PB   O1B   108.87  3.000
 CDC  O3B   PB   O3A   107.92  3.000
 CDC  O2B   PB   O3A   111.39  3.000
 CDC  O1B   PB   O3A    96.62  3.000
 CDC  C14   O1B  PB    117.22  3.000
 CDC  H142  C14  H141  105.96  3.000
 CDC  H142  C14  C15   110.10  3.000
 CDC  H141  C14  C15   105.16  3.000
 CDC  H142  C14  O1B   112.96  3.000
 CDC  H141  C14  O1B   110.15  3.000
 CDC  C15   C14  O1B   112.05  3.000
 CDC  H152  C15  H151  108.03  3.000
 CDC  H152  C15  N11   106.37  3.000
 CDC  H151  C15  N11   106.49  3.000
 CDC  H152  C15  C14   107.47  3.000
 CDC  H151  C15  C14   110.76  3.000
 CDC  N11   C15  C14   117.32  3.000
 CDC  C18   N11  C17   108.52  3.000
 CDC  C18   N11  C16   108.96  3.000
 CDC  C17   N11  C16   109.21  3.000
 CDC  C18   N11  C15   107.08  3.000
 CDC  C17   N11  C15   111.77  3.000
 CDC  C16   N11  C15   111.22  3.000
 CDC  H163  C16  H162  109.55  3.000
 CDC  H163  C16  H161  109.25  3.000
 CDC  H162  C16  H161  110.51  3.000
 CDC  H163  C16  N11   108.56  3.000
 CDC  H162  C16  N11   109.29  3.000
 CDC  H161  C16  N11   109.65  3.000
 CDC  H173  C17  H172  109.79  3.000
 CDC  H173  C17  H171  109.87  3.000
 CDC  H172  C17  H171  109.48  3.000
 CDC  H173  C17  N11   110.71  3.000
 CDC  H172  C17  N11   108.94  3.000
 CDC  H171  C17  N11   108.02  3.000
 CDC  H183  C18  H182  109.53  3.000
 CDC  H183  C18  H181  109.72  3.000
 CDC  H182  C18  H181  109.83  3.000
 CDC  H183  C18  N11   109.08  3.000
 CDC  H182  C18  N11   109.17  3.000
 CDC  H181  C18  N11   109.49  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
 CDC  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CDC  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 CDC  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 CDC  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 CDC  CONST_05  N4    C4   N3   C2    180.00   0.0  0
 CDC  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 CDC  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 CDC  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 CDC  CONST_09  H41   N4   C4   N3    180.00   0.0  0
 CDC  CONST_10  H42   N4   C4   N3      0.00   0.0  0
 CDC  Var_01    O1A   PA   O5'  C5'    25.90  30.0  3
 CDC  Var_02    O1B   PB   O3A  PA    -98.51  30.0  3
 CDC  Var_03    C15   C14  O1B  PB   -137.88  30.0  3
 CDC  Var_04    N11   C15  C14  O1B    69.49  30.0  3
 CDC  Var_05    C16   N11  C15  C14    51.22  30.0  3
 CDC  Var_06    H5'1  C5'  O5'  PA    -69.17  30.0  2
 CDC  Var_07    H161  C16  N11  C15   -68.77  30.0  3
 CDC  Var_08    H171  C17  N11  C15  -169.59  30.0  3
 CDC  Var_09    H181  C18  N11  C15   -61.97  30.0  3

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
 CDC  chir_01  C1'  N1   C2'  O4'  negativ
 CDC  chir_02  C2'  O2'  C3'  C1'  positiv
 CDC  chir_03  C3'  O3'  C2'  C4'  negativ
 CDC  chir_04  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
 CDC  plan-1  N1   0.020
 CDC  plan-1  C2   0.020
 CDC  plan-1  N3   0.020
 CDC  plan-1  C4   0.020
 CDC  plan-1  C5   0.020
 CDC  plan-1  C6   0.020
 CDC  plan-1  O2   0.020
 CDC  plan-1  N4   0.020
 CDC  plan-1  C1'  0.020
 CDC  plan-1  H5   0.020
 CDC  plan-1  H6   0.020
 CDC  plan-1  H41  0.020
 CDC  plan-1  H42  0.020

