# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 04:24:04 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)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)C(F)(F)[P](O)(=O)O[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
 6CF  6CF  2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine  ligand  46  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6CF
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
 6CF  N1    N  NR6   0  -0.549   6.9336   6.9263  10.5216
 6CF  P1    P  P     0   1.368   4.4277   6.5135  15.2937
 6CF  C2    C  CR6   0   0.595   7.9431   6.7055   9.5736
 6CF  O2    O  O     0  -0.528   7.6183   6.4760   8.4135
 6CF  P2    P  P     0   1.380   3.8431   3.4302  15.0927
 6CF  N3    N  N     0  -0.539   9.2267   6.7521   9.9776
 6CF  P3    P  P     0   1.469   4.3895   0.5865  15.1885
 6CF  C4    C  CR6   0   0.514   9.5306   6.9789  11.2420
 6CF  N4    N  NH2   0  -0.811  10.8185   7.0072  11.5848
 6CF  C5    C  CR16  0  -0.475   8.5282   7.1917  12.2338
 6CF  C6    C  CR16  0   0.084   7.2453   7.1583  11.8146
 6CF  C1'   C  CH1   0   0.203   5.5418   6.8674  10.0352
 6CF  F1A   F  F     0  -0.325   6.1284   4.6174  14.6373
 6CF  O1A   O  OH1   0  -0.740   2.8931   6.3668  15.6918
 6CF  O1B   O  O     0  -0.661   3.1237   3.6586  13.8236
 6CF  O1G   O  OH1   0  -0.712   4.7916   0.1165  16.6417
 6CF  C2'   C  CH2   0  -0.532   5.0487   5.4325   9.8625
 6CF  F2A   F  F     0  -0.322   5.5135   4.6091  16.7389
 6CF  O2A   O  O     0  -0.651   5.2644   7.4682  16.0388
 6CF  O2B   O  OH1   0  -0.722   2.9765   3.2785  16.4083
 6CF  O2G   O  OH1   0  -0.707   5.5661  -0.0823  14.3775
 6CF  C3'   C  CH1   0   0.010   4.3397   5.1675  11.1810
 6CF  O3'   O  OH1   0  -0.685   3.4092   4.1326  11.0845
 6CF  C3A   C  CT    0   0.258   5.0674   4.7727  15.4705
 6CF  O3B   O  O2    0  -0.697   4.8318   2.1721  15.1698
 6CF  O3G   O  O     0  -0.678   2.9960   0.4194  14.7507
 6CF  C4'   C  CH1   0   0.003   3.7158   6.5440  11.4320
 6CF  O4'   O  O2    0  -0.502   4.6945   7.4710  10.9759
 6CF  C5'   C  CH2   0  -0.202   3.2956   6.8671  12.8416
 6CF  O5'   O  O2    0  -0.599   4.4132   6.6718  13.7215
 6CF  HN4   H  HNH2  0   0.402  11.5301   6.8550  10.8908
 6CF  HN4A  H  HNH2  0   0.413  11.1093   7.1884  12.5291
 6CF  H5    H  HCR6  0   0.284   8.7716   7.3814  13.2681
 6CF  H6    H  HCR6  0   0.314   6.4266   7.3237  12.4961
 6CF  H1'   H  HCH1  0   0.271   5.5171   7.4315   9.1030
 6CF  HO1A  H  HOH1  0   0.518   2.6517   6.7069  16.5660
 6CF  HO1G  H  HOH1  0   0.515   4.0488   0.0079  17.2519
 6CF  H2'   H  HCH2  0   0.262   4.3264   5.3895   9.0433
 6CF  H2'A  H  HCH2  0   0.279   5.8502   4.7293   9.6455
 6CF  HO2B  H  HOH1  0   0.516   2.0525   3.5599  16.3388
 6CF  HO2G  H  HOH1  0   0.515   5.5410   0.0603  13.4206
 6CF  H3'   H  HCH1  0   0.217   5.0878   4.9580  11.9574
 6CF  HO3'  H  HOH1  0   0.460   3.2201   3.8275  11.9845
 6CF  H4'   H  HCH1  0   0.252   2.8079   6.6280  10.8182
 6CF  H5'   H  HCH2  0   0.275   2.9567   7.9012  12.9182
 6CF  H5'A  H  HCH2  0   0.260   2.4669   6.2143  13.1168

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
 6CF  C2   N1    single  1.402  0.020  1.402
 6CF  C1'  N1    single  1.476  0.020  1.476
 6CF  N1   C6    single  1.350  0.020  1.350
 6CF  O5'  P1    single  1.580  0.020  1.580
 6CF  C3A  P1    single  1.863  0.020  1.863
 6CF  P1   O2A   double  1.472  0.020  1.472
 6CF  P1   O1A   single  1.592  0.020  1.592
 6CF  O2   C2    double  1.226  0.020  1.226
 6CF  C2   N3    single  1.346  0.020  1.346
 6CF  O1B  P2    double  1.476  0.020  1.476
 6CF  P2   O2B   single  1.583  0.020  1.583
 6CF  P2   C3A   single  1.856  0.020  1.856
 6CF  P2   O3B   single  1.602  0.020  1.602
 6CF  N3   C4    double  1.320  0.020  1.320
 6CF  O3B  P3    single  1.646  0.020  1.646
 6CF  P3   O3G   double  1.470  0.020  1.470
 6CF  P3   O1G   single  1.579  0.020  1.579
 6CF  P3   O2G   single  1.578  0.020  1.578
 6CF  C4   N4    single  1.333  0.020  1.333
 6CF  C4   C5    single  1.426  0.020  1.426
 6CF  N4   HN4   single  0.860  0.020  1.020
 6CF  N4   HN4A  single  0.860  0.020  1.020
 6CF  C6   C5    double  1.350  0.020  1.350
 6CF  C5   H5    single  0.930  0.020  1.080
 6CF  C6   H6    single  0.930  0.020  1.080
 6CF  C2'  C1'   single  1.527  0.020  1.527
 6CF  C1'  O4'   single  1.402  0.020  1.402
 6CF  C1'  H1'   single  0.970  0.020  1.090
 6CF  F1A  C3A   single  1.358  0.020  1.358
 6CF  O1A  HO1A  single  0.850  0.020  0.980
 6CF  O1G  HO1G  single  0.850  0.020  0.980
 6CF  C2'  C3'   single  1.520  0.020  1.520
 6CF  C2'  H2'   single  0.970  0.020  1.090
 6CF  C2'  H2'A  single  0.970  0.020  1.090
 6CF  C3A  F2A   single  1.354  0.020  1.354
 6CF  O2B  HO2B  single  0.850  0.020  0.980
 6CF  O2G  HO2G  single  0.850  0.020  0.980
 6CF  O3'  C3'   single  1.395  0.020  1.395
 6CF  C3'  C4'   single  1.532  0.020  1.532
 6CF  C3'  H3'   single  0.970  0.020  1.090
 6CF  O3'  HO3'  single  0.850  0.020  0.980
 6CF  O4'  C4'   single  1.423  0.020  1.423
 6CF  C4'  C5'   single  1.506  0.020  1.506
 6CF  C4'  H4'   single  0.970  0.020  1.090
 6CF  C5'  O5'   single  1.436  0.020  1.436
 6CF  C5'  H5'   single  0.970  0.020  1.090
 6CF  C5'  H5'A  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
 6CF  C1'   N1   C6   122.71  3.000
 6CF  C6    N1   C2   120.55  3.000
 6CF  C1'   N1   C2   116.74  3.000
 6CF  O5'   P1   C3A  101.02  3.000
 6CF  C3A   P1   O2A  111.27  3.000
 6CF  O5'   P1   O2A  116.35  3.000
 6CF  O2A   P1   O1A  118.76  3.000
 6CF  C3A   P1   O1A  102.77  3.000
 6CF  O5'   P1   O1A  104.43  3.000
 6CF  N3    C2   O2   122.87  3.000
 6CF  N3    C2   N1   118.55  3.000
 6CF  O2    C2   N1   118.57  3.000
 6CF  O3B   P2   C3A   98.69  3.000
 6CF  O3B   P2   O2B  102.86  3.000
 6CF  C3A   P2   O2B  105.15  3.000
 6CF  O3B   P2   O1B  117.62  3.000
 6CF  C3A   P2   O1B  112.61  3.000
 6CF  O2B   P2   O1B  117.55  3.000
 6CF  C4    N3   C2   120.85  3.000
 6CF  O3G   P3   O3B  111.15  3.000
 6CF  O3G   P3   O2G  120.37  3.000
 6CF  O3B   P3   O2G  101.65  3.000
 6CF  O2G   P3   O1G   99.03  3.000
 6CF  O3G   P3   O1G  118.79  3.000
 6CF  O3B   P3   O1G  103.22  3.000
 6CF  C5    C4   N4   119.81  3.000
 6CF  C5    C4   N3   122.00  3.000
 6CF  N4    C4   N3   118.19  3.000
 6CF  HN4A  N4   HN4  118.12  3.000
 6CF  HN4A  N4   C4   121.68  3.000
 6CF  HN4   N4   C4   120.20  3.000
 6CF  H5    C5   C6   121.08  3.000
 6CF  H5    C5   C4   122.28  3.000
 6CF  C6    C5   C4   116.64  3.000
 6CF  H6    C6   C5   121.44  3.000
 6CF  H6    C6   N1   117.16  3.000
 6CF  C5    C6   N1   121.40  3.000
 6CF  H1'   C1'  O4'  109.71  3.000
 6CF  H1'   C1'  C2'  112.48  3.000
 6CF  O4'   C1'  C2'  106.57  3.000
 6CF  H1'   C1'  N1   106.42  3.000
 6CF  O4'   C1'  N1   109.36  3.000
 6CF  C2'   C1'  N1   112.30  3.000
 6CF  HO1A  O1A  P1   115.69  3.000
 6CF  HO1G  O1G  P3   114.72  3.000
 6CF  H2'A  C2'  H2'  108.17  3.000
 6CF  H2'A  C2'  C3'  113.82  3.000
 6CF  H2'   C2'  C3'  109.57  3.000
 6CF  H2'A  C2'  C1'  113.07  3.000
 6CF  H2'   C2'  C1'  109.58  3.000
 6CF  C3'   C2'  C1'  102.49  3.000
 6CF  HO2B  O2B  P2   115.78  3.000
 6CF  HO2G  O2G  P3   115.24  3.000
 6CF  H3'   C3'  C4'  109.45  3.000
 6CF  H3'   C3'  O3'  111.21  3.000
 6CF  C4'   C3'  O3'  113.97  3.000
 6CF  H3'   C3'  C2'  109.18  3.000
 6CF  C4'   C3'  C2'  100.10  3.000
 6CF  O3'   C3'  C2'  112.35  3.000
 6CF  HO3'  O3'  C3'  107.43  3.000
 6CF  F2A   C3A  F1A  107.67  3.000
 6CF  F2A   C3A  P2   108.70  3.000
 6CF  F1A   C3A  P2   107.93  3.000
 6CF  F2A   C3A  P1   108.35  3.000
 6CF  F1A   C3A  P1   108.48  3.000
 6CF  P2    C3A  P1   115.47  3.000
 6CF  P3    O3B  P2   126.24  3.000
 6CF  H4'   C4'  C5'  106.01  3.000
 6CF  H4'   C4'  O4'  109.83  3.000
 6CF  C5'   C4'  O4'  110.62  3.000
 6CF  H4'   C4'  C3'  108.27  3.000
 6CF  C5'   C4'  C3'  117.37  3.000
 6CF  O4'   C4'  C3'  104.64  3.000
 6CF  C4'   O4'  C1'  110.49  3.000
 6CF  H5'A  C5'  H5'  108.28  3.000
 6CF  H5'A  C5'  O5'  110.82  3.000
 6CF  H5'   C5'  O5'  109.13  3.000
 6CF  H5'A  C5'  C4'  108.66  3.000
 6CF  H5'   C5'  C4'  110.84  3.000
 6CF  O5'   C5'  C4'  109.10  3.000
 6CF  C5'   O5'  P1   129.09  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
 6CF  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 6CF  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 6CF  CONST_03  C1'   N1   C2   N3   180.00   0.0  0
 6CF  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 6CF  CONST_05  N4    C4   N3   C2   180.00   0.0  0
 6CF  CONST_06  C1'   N1   C2   O2     0.00   0.0  0
 6CF  CONST_07  C6    N1   C2   O2   180.00   0.0  0
 6CF  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 6CF  CONST_09  HN4   N4   C4   N3     0.00   0.0  0
 6CF  CONST_10  HN4A  N4   C4   N3   180.00   0.0  0
 6CF  Var_01    C4'   C5'  O5'  P1  -162.86  30.0  1
 6CF  Var_02    O1B   P2   C3A  P1    47.90  30.0  2
 6CF  Var_03    O5'   P1   C3A  P2   -75.74  30.0  3
 6CF  Var_04    O3G   P3   O3B  P2    15.94  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
 6CF  chir_03  C1'  N1   C2'  O4'  negativ
 6CF  chir_04  C3'  O3'  C4'  C2'  positiv
 6CF  chir_05  C4'  O4'  C3'  C5'  negativ
 6CF  chir_06  P1   C3A  O2A  O1A  both
 6CF  chir_07  P2   O2B  O1B  C3A  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
 6CF  plan-1  N1    0.020
 6CF  plan-1  C2    0.020
 6CF  plan-1  O2    0.020
 6CF  plan-1  N3    0.020
 6CF  plan-1  C4    0.020
 6CF  plan-1  N4    0.020
 6CF  plan-1  C5    0.020
 6CF  plan-1  C6    0.020
 6CF  plan-1  C1'   0.020
 6CF  plan-1  HN4   0.020
 6CF  plan-1  HN4A  0.020
 6CF  plan-1  H5    0.020
 6CF  plan-1  H6    0.020

