# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 06:25:50 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine
#   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)[C@H](Cl)[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
 FF7  FF7  5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine  ligand  42  29  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FF7
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
 FF7  C4   C   CR6    0   0.513  -5.8626  -2.8735   0.1091
 FF7  N4   N   NH2    0  -0.809  -6.3028  -4.0247   0.6157
 FF7  C5   C   CR16   0  -0.478  -5.8090  -2.7020  -1.3079
 FF7  C6   C   CR16   0   0.099  -5.3507  -1.5134  -1.7460
 FF7  N3   N   N      0  -0.542  -5.4873  -1.9249   0.9439
 FF7  C2   C   CR6    0   0.601  -5.0345  -0.7357   0.4944
 FF7  O2   O   O      0  -0.505  -4.6825   0.1585   1.2500
 FF7  N1   N   NR6    0  -0.554  -4.9756  -0.5292  -0.8940
 FF7  C1'  C   CR15   0   0.223  -4.4609   0.7203  -1.4432
 FF7  C2'  C   CH2    0  -0.555  -5.1654   2.0008  -0.9841
 FF7  C3'  C   CR15   0   0.024  -4.1092   2.7664  -0.1877
 FF7  O3'  O   OH1    0  -0.671  -4.0842   4.1539  -0.4190
 FF7  O4'  O   O      0  -0.491  -3.1046   0.8440  -1.1207
 FF7  C4'  C   CR15   0   0.018  -2.7991   2.1588  -0.6926
 FF7  C5'  C   CH2    0  -0.152  -1.7256   2.1232   0.3677
 FF7  O5'  O   O2     0  -0.628  -0.5434   1.5776  -0.1695
 FF7  PA   P   P      0   1.335   0.8749   1.9309   0.6138
 FF7  O1A  O   OP    -1  -0.808   0.6777   1.6872   2.0789
 FF7  O2A  O   O      0  -0.813   1.3602   3.2692   0.1425
 FF7  O3A  O   O2     0  -0.751   1.6914   0.7243  -0.1045
 FF7  PB   P   P      0   1.308   3.3635   0.6028  -0.1552
 FF7  O1B  O   O      0  -0.805   3.9198   1.3275   1.0340
 FF7  O2B  O   OP    -1  -0.800   3.7815   0.9922  -1.5450
 FF7  C3B  C   CH1    0  -0.765   3.4930  -1.2139   0.0057
 FF7  PG   P   P      0   1.185   5.2069  -1.9553  -0.2835
 FF7  O2G  O   OP    -1  -0.901   5.0821  -3.3959   0.2153
 FF7  O1G  O   OP    -1  -0.894   5.3742  -1.8423  -1.7985
 FF7  O3G  O   O      0  -0.893   6.1668  -1.0902   0.5296
 FF7  CL   CL  CL     0  -0.243   2.8730  -1.6726   1.6528
 FF7  H1   H   HNH2   0   0.413  -6.5891  -4.7841   0.0239
 FF7  H2   H   HNH2   0   0.402  -6.3242  -4.1652   1.6112
 FF7  H3   H   HCR6   0   0.287  -6.1079  -3.4771  -1.9971
 FF7  H4   H   HCR6   0   0.317  -5.2654  -1.2928  -2.8012
 FF7  H5   H   HCR5   0   0.243  -4.5765   0.6088  -2.5251
 FF7  H6   H   HCH2   0   0.259  -5.4417   2.5822  -1.8660
 FF7  H7   H   HCH2   0   0.270  -6.0771   1.8066  -0.4223
 FF7  H8   H   HCR5   0   0.230  -4.2278   2.5551   0.8785
 FF7  H9   H   HOH1   0   0.455  -4.8097   4.5532   0.0694
 FF7  H10  H   HCR5   0   0.219  -2.4473   2.7548  -1.5485
 FF7  H11  H   HCH2   0   0.201  -1.5833   3.1536   0.7182
 FF7  H12  H   HCH2   0   0.207  -2.0801   1.5342   1.2214
 FF7  H15  H   HCH1   0   0.250   2.7927  -1.6775  -0.6937

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
 FF7  O2   C2   double  1.222  0.020  1.222
 FF7  C2   N3   single  1.350  0.020  1.350
 FF7  C2   N1   single  1.405  0.020  1.405
 FF7  C2'  C1'  single  1.532  0.020  1.532
 FF7  C2'  C3'  single  1.528  0.020  1.528
 FF7  N3   C4   double  1.318  0.020  1.318
 FF7  C1'  N1   single  1.459  0.020  1.459
 FF7  C1'  O4'  single  1.400  0.020  1.400
 FF7  N1   C6   single  1.355  0.020  1.355
 FF7  O3'  C3'  single  1.407  0.020  1.407
 FF7  C4   N4   single  1.333  0.020  1.333
 FF7  C4   C5   single  1.428  0.020  1.428
 FF7  C3'  C4'  single  1.530  0.020  1.530
 FF7  O4'  C4'  single  1.416  0.020  1.416
 FF7  C4'  C5'  single  1.509  0.020  1.509
 FF7  C6   C5   double  1.347  0.020  1.347
 FF7  O1B  PB   deloc   1.500  0.020  1.500
 FF7  C5'  O5'  single  1.409  0.020  1.409
 FF7  O5'  PA   single  1.658  0.020  1.658
 FF7  O3A  PB   single  1.677  0.020  1.677
 FF7  O3A  PA   single  1.624  0.020  1.624
 FF7  PB   O2B  deloc   1.503  0.020  1.503
 FF7  PB   C3B  single  1.828  0.020  1.828
 FF7  CL   C3B  single  1.819  0.020  1.819
 FF7  PA   O2A  deloc   1.500  0.020  1.500
 FF7  PA   O1A  deloc   1.498  0.020  1.498
 FF7  C3B  PG   single  1.890  0.020  1.890
 FF7  O3G  PG   deloc   1.527  0.020  1.527
 FF7  PG   O2G  deloc   1.530  0.020  1.530
 FF7  PG   O1G  deloc   1.528  0.020  1.528
 FF7  N4   H1   single  0.860  0.020  1.020
 FF7  N4   H2   single  0.860  0.020  1.020
 FF7  C5   H3   single  0.930  0.020  1.080
 FF7  C6   H4   single  0.930  0.020  1.080
 FF7  C1'  H5   single  0.970  0.020  1.090
 FF7  C2'  H6   single  0.970  0.020  1.090
 FF7  C2'  H7   single  0.970  0.020  1.090
 FF7  C3'  H8   single  0.970  0.020  1.090
 FF7  O3'  H9   single  0.850  0.020  0.980
 FF7  C4'  H10  single  0.970  0.020  1.090
 FF7  C5'  H11  single  0.970  0.020  1.090
 FF7  C5'  H12  single  0.970  0.020  1.090
 FF7  C3B  H15  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
 FF7  N3   C4   C5   122.09  3.000
 FF7  C5   C4   N4   119.56  3.000
 FF7  N3   C4   N4   118.36  3.000
 FF7  H2   N4   H1   118.13  3.000
 FF7  H2   N4   C4   120.27  3.000
 FF7  H1   N4   C4   121.56  3.000
 FF7  H3   C5   C6   121.34  3.000
 FF7  H3   C5   C4   122.47  3.000
 FF7  C6   C5   C4   116.19  3.000
 FF7  H4   C6   N1   116.33  3.000
 FF7  H4   C6   C5   121.61  3.000
 FF7  N1   C6   C5   122.05  3.000
 FF7  C2   N3   C4   121.25  3.000
 FF7  N1   C2   O2   119.42  3.000
 FF7  N1   C2   N3   118.21  3.000
 FF7  O2   C2   N3   122.37  3.000
 FF7  C1'  N1   C2   120.85  3.000
 FF7  C1'  N1   C6   118.90  3.000
 FF7  C2   N1   C6   120.20  3.000
 FF7  H5   C1'  O4'  109.84  3.000
 FF7  H5   C1'  C2'  109.45  3.000
 FF7  O4'  C1'  C2'  107.62  3.000
 FF7  H5   C1'  N1   104.35  3.000
 FF7  O4'  C1'  N1   109.33  3.000
 FF7  C2'  C1'  N1   116.16  3.000
 FF7  H7   C2'  H6   107.45  3.000
 FF7  H7   C2'  C3'  113.54  3.000
 FF7  H6   C2'  C3'  109.22  3.000
 FF7  H7   C2'  C1'  113.00  3.000
 FF7  H6   C2'  C1'  108.63  3.000
 FF7  C3'  C2'  C1'  104.89  3.000
 FF7  H8   C3'  C4'  109.76  3.000
 FF7  H8   C3'  O3'  110.66  3.000
 FF7  C4'  C3'  O3'  108.80  3.000
 FF7  H8   C3'  C2'  109.66  3.000
 FF7  C4'  C3'  C2'  102.76  3.000
 FF7  O3'  C3'  C2'  114.87  3.000
 FF7  H9   O3'  C3'  108.22  3.000
 FF7  C4'  O4'  C1'  111.15  3.000
 FF7  H10  C4'  C5'  109.38  3.000
 FF7  H10  C4'  O4'  109.67  3.000
 FF7  C5'  C4'  O4'  110.12  3.000
 FF7  H10  C4'  C3'  108.38  3.000
 FF7  C5'  C4'  C3'  112.74  3.000
 FF7  O4'  C4'  C3'  106.49  3.000
 FF7  H12  C5'  H11  107.32  3.000
 FF7  H12  C5'  O5'  111.12  3.000
 FF7  H11  C5'  O5'  112.12  3.000
 FF7  H12  C5'  C4'  109.26  3.000
 FF7  H11  C5'  C4'  107.12  3.000
 FF7  O5'  C5'  C4'  109.76  3.000
 FF7  PA   O5'  C5'  117.08  3.000
 FF7  O3A  PA   O2A  111.18  3.000
 FF7  O2A  PA   O1A  119.67  3.000
 FF7  O3A  PA   O1A  112.19  3.000
 FF7  O1A  PA   O5'  108.34  3.000
 FF7  O2A  PA   O5'  108.57  3.000
 FF7  O3A  PA   O5'   93.60  3.000
 FF7  PB   O3A  PA   124.63  3.000
 FF7  C3B  PB   O2B  108.61  3.000
 FF7  C3B  PB   O1B  112.59  3.000
 FF7  O2B  PB   O1B  120.34  3.000
 FF7  C3B  PB   O3A   98.04  3.000
 FF7  O2B  PB   O3A  106.65  3.000
 FF7  O1B  PB   O3A  108.11  3.000
 FF7  H15  C3B  CL   104.72  3.000
 FF7  H15  C3B  PG   108.47  3.000
 FF7  CL   C3B  PG   110.41  3.000
 FF7  H15  C3B  PB   108.66  3.000
 FF7  PG   C3B  PB   116.14  3.000
 FF7  CL   C3B  PB   107.83  3.000
 FF7  O3G  PG   O1G  114.66  3.000
 FF7  O1G  PG   O2G  113.69  3.000
 FF7  O3G  PG   O2G  114.28  3.000
 FF7  O1G  PG   C3B  102.83  3.000
 FF7  O2G  PG   C3B  104.22  3.000
 FF7  O3G  PG   C3B  105.45  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
 FF7  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 FF7  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 FF7  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 FF7  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 FF7  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 FF7  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 FF7  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 FF7  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 FF7  CONST_09  H1   N4   C4   C5     0.00   0.0  0
 FF7  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 FF7  Var_01    O3A  PA   O5'  C5'  162.98  30.0  3
 FF7  Var_02    O1B  PB   O3A  PA    26.52  30.0  3
 FF7  Var_03    H11  C5'  O5'  PA    39.87  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
 FF7  chir_01  C1'  C2'  N1   O4'  positiv
 FF7  chir_02  C3'  O3'  C4'  C2'  positiv
 FF7  chir_03  C4'  O4'  C3'  C5'  negativ
 FF7  chir_06  C3B  PB   CL   PG   positiv

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
 FF7  plan-1  C4   0.020
 FF7  plan-1  N4   0.020
 FF7  plan-1  C5   0.020
 FF7  plan-1  C6   0.020
 FF7  plan-1  N3   0.020
 FF7  plan-1  C2   0.020
 FF7  plan-1  O2   0.020
 FF7  plan-1  N1   0.020
 FF7  plan-1  C1'  0.020
 FF7  plan-1  H1   0.020
 FF7  plan-1  H2   0.020
 FF7  plan-1  H3   0.020
 FF7  plan-1  H4   0.020

