# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 18:50:40 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(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)O[P](O)(=O)C(F)(F)[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
 FFJ  FFJ  2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(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_FFJ
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
 FFJ  C4   C  CR6   0   0.515   9.4816   7.6460  11.0545
 FFJ  N4   N  NH2   0  -0.811  10.7912   7.7423  11.2837
 FFJ  C5   C  CR16  0  -0.476   8.5990   7.3048  12.1217
 FFJ  C6   C  CR16  0   0.084   7.2837   7.2447  11.8238
 FFJ  N3   N  N     0  -0.539   9.0441   7.8762   9.8307
 FFJ  C2   C  CR6   0   0.595   7.7324   7.7897   9.5388
 FFJ  O2   O  O     0  -0.528   7.2883   7.9623   8.4088
 FFJ  N1   N  NR6   0  -0.549   6.8350   7.4862  10.5732
 FFJ  C1'  C  CH1   0   0.202   5.4073   7.4135  10.2160
 FFJ  C2'  C  CH2   0  -0.534   5.0258   6.0764   9.5826
 FFJ  C3'  C  CH1   0   0.009   4.4774   5.2907  10.7632
 FFJ  O3'  O  OH1   0  -0.685   3.6124   4.2688  10.3703
 FFJ  O4'  O  O2    0  -0.500   4.6343   7.5442  11.3793
 FFJ  C4'  C  CH1   0   0.002   3.7860   6.4158  11.5398
 FFJ  C5'  C  CH2   0  -0.226   3.5006   6.1710  12.9977
 FFJ  O5'  O  O2    0  -0.588   4.7184   5.8094  13.6651
 FFJ  PA   P  P     0   1.521   4.8366   5.2236  15.1317
 FFJ  O1A  O  OH1   0  -0.727   3.5073   5.5943  15.9086
 FFJ  O2A  O  O     0  -0.651   6.1350   5.4979  15.7531
 FFJ  O3A  O  O2    0  -0.691   4.6118   3.6200  14.9653
 FFJ  PB   P  P     0   1.361   3.6531   2.6523  14.1349
 FFJ  O1B  O  OH1   0  -0.713   2.2329   2.9768  14.7511
 FFJ  O2B  O  O     0  -0.659   3.7915   2.6804  12.6656
 FFJ  C3B  C  CT    0   0.280   4.1708   1.0183  14.8446
 FFJ  F3B  F  F     0  -0.322   5.5168   0.9305  14.7232
 FFJ  F4B  F  F     0  -0.332   3.6205   0.0686  14.0424
 FFJ  PG   P  P     0   1.331   3.6530   0.5973  16.5811
 FFJ  O2G  O  OH1   0  -0.728   4.3667   1.7958  17.3328
 FFJ  O1G  O  OH1   0  -0.726   4.5610  -0.6661  16.9229
 FFJ  O3G  O  O     0  -0.670   2.1947   0.4248  16.7089
 FFJ  H1   H  HNH2  0   0.402  11.4196   7.9796  10.5352
 FFJ  H2   H  HNH2  0   0.413  11.1819   7.5667  12.1924
 FFJ  H3   H  HCR6  0   0.283   8.9529   7.1137  13.1234
 FFJ  H4   H  HCR6  0   0.316   6.5474   7.0118  12.5764
 FFJ  H5   H  HCH1  0   0.271   5.2144   8.2527   9.5483
 FFJ  H6   H  HCH2  0   0.262   4.2337   6.2343   8.8466
 FFJ  H7   H  HCH2  0   0.279   5.8603   5.5897   9.0817
 FFJ  H8   H  HCH1  0   0.227   5.3137   4.8956  11.3543
 FFJ  H9   H  HOH1  0   0.460   3.5478   3.6428  11.1077
 FFJ  H10  H  HCH1  0   0.253   2.8104   6.6103  11.0719
 FFJ  H11  H  HCH2  0   0.285   3.0825   7.0647  13.4635
 FFJ  H12  H  HCH2  0   0.247   2.7527   5.3780  13.0681
 FFJ  H13  H  HOH1  0   0.515   3.5139   6.4568  16.3492
 FFJ  H14  H  HOH1  0   0.520   1.4675   2.7228  14.2137
 FFJ  H15  H  HOH1  0   0.513   4.1436   1.9007  18.2698
 FFJ  H16  H  HOH1  0   0.509   4.1025  -1.5171  16.8818

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
 FFJ  O2   C2   double  1.226  0.020  1.226
 FFJ  C2   N3   single  1.347  0.020  1.347
 FFJ  C2   N1   single  1.403  0.020  1.403
 FFJ  N3   C4   double  1.320  0.020  1.320
 FFJ  C2'  C1'  single  1.528  0.020  1.528
 FFJ  C2'  C3'  single  1.521  0.020  1.521
 FFJ  C1'  N1   single  1.474  0.020  1.474
 FFJ  C1'  O4'  single  1.403  0.020  1.403
 FFJ  N1   C6   single  1.350  0.020  1.350
 FFJ  O3'  C3'  single  1.395  0.020  1.395
 FFJ  C3'  C4'  single  1.532  0.020  1.532
 FFJ  C4   N4   single  1.333  0.020  1.333
 FFJ  C4   C5   single  1.426  0.020  1.426
 FFJ  O4'  C4'  single  1.421  0.020  1.421
 FFJ  C4'  C5'  single  1.506  0.020  1.506
 FFJ  C6   C5   double  1.350  0.020  1.350
 FFJ  O2B  PB   double  1.476  0.020  1.476
 FFJ  C5'  O5'  single  1.435  0.020  1.435
 FFJ  O5'  PA   single  1.584  0.020  1.584
 FFJ  PB   O3A  single  1.595  0.020  1.595
 FFJ  PB   O1B  single  1.582  0.020  1.582
 FFJ  PB   C3B  single  1.855  0.020  1.855
 FFJ  O3A  PA   single  1.628  0.020  1.628
 FFJ  F4B  C3B  single  1.360  0.020  1.360
 FFJ  C3B  F3B  single  1.354  0.020  1.354
 FFJ  C3B  PG   single  1.860  0.020  1.860
 FFJ  PA   O2A  double  1.465  0.020  1.465
 FFJ  PA   O1A  single  1.584  0.020  1.584
 FFJ  PG   O3G  double  1.474  0.020  1.474
 FFJ  PG   O2G  single  1.585  0.020  1.585
 FFJ  PG   O1G  single  1.593  0.020  1.593
 FFJ  N4   H1   single  0.860  0.020  1.020
 FFJ  N4   H2   single  0.860  0.020  1.020
 FFJ  C5   H3   single  0.930  0.020  1.080
 FFJ  C6   H4   single  0.930  0.020  1.080
 FFJ  C1'  H5   single  0.970  0.020  1.090
 FFJ  C2'  H6   single  0.970  0.020  1.090
 FFJ  C2'  H7   single  0.970  0.020  1.090
 FFJ  C3'  H8   single  0.970  0.020  1.090
 FFJ  O3'  H9   single  0.850  0.020  0.980
 FFJ  C4'  H10  single  0.970  0.020  1.090
 FFJ  C5'  H11  single  0.970  0.020  1.090
 FFJ  C5'  H12  single  0.970  0.020  1.090
 FFJ  O1A  H13  single  0.850  0.020  0.980
 FFJ  O1B  H14  single  0.850  0.020  0.980
 FFJ  O2G  H15  single  0.850  0.020  0.980
 FFJ  O1G  H16  single  0.850  0.020  0.980

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
 FFJ  N3   C4   C5   122.03  3.000
 FFJ  C5   C4   N4   119.77  3.000
 FFJ  N3   C4   N4   118.20  3.000
 FFJ  H2   N4   H1   118.13  3.000
 FFJ  H2   N4   C4   121.66  3.000
 FFJ  H1   N4   C4   120.20  3.000
 FFJ  H3   C5   C6   121.09  3.000
 FFJ  H3   C5   C4   122.26  3.000
 FFJ  C6   C5   C4   116.64  3.000
 FFJ  H4   C6   N1   117.27  3.000
 FFJ  H4   C6   C5   121.39  3.000
 FFJ  N1   C6   C5   121.34  3.000
 FFJ  C2   N3   C4   120.84  3.000
 FFJ  N1   C2   O2   118.58  3.000
 FFJ  N1   C2   N3   118.51  3.000
 FFJ  O2   C2   N3   122.92  3.000
 FFJ  C1'  N1   C2   116.86  3.000
 FFJ  C1'  N1   C6   122.52  3.000
 FFJ  C2   N1   C6   120.60  3.000
 FFJ  H5   C1'  O4'  109.81  3.000
 FFJ  H5   C1'  C2'  112.07  3.000
 FFJ  O4'  C1'  C2'  106.72  3.000
 FFJ  H5   C1'  N1   106.38  3.000
 FFJ  O4'  C1'  N1   109.17  3.000
 FFJ  C2'  C1'  N1   112.68  3.000
 FFJ  H7   C2'  H6   108.09  3.000
 FFJ  H7   C2'  C3'  113.76  3.000
 FFJ  H6   C2'  C3'  109.64  3.000
 FFJ  H7   C2'  C1'  113.00  3.000
 FFJ  H6   C2'  C1'  109.50  3.000
 FFJ  C3'  C2'  C1'  102.73  3.000
 FFJ  H8   C3'  C4'  109.59  3.000
 FFJ  H8   C3'  O3'  111.12  3.000
 FFJ  C4'  C3'  O3'  113.64  3.000
 FFJ  H8   C3'  C2'  109.23  3.000
 FFJ  C4'  C3'  C2'  100.18  3.000
 FFJ  O3'  C3'  C2'  112.54  3.000
 FFJ  H9   O3'  C3'  107.46  3.000
 FFJ  C4'  O4'  C1'  110.40  3.000
 FFJ  H10  C4'  C5'  105.82  3.000
 FFJ  H10  C4'  O4'  109.95  3.000
 FFJ  C5'  C4'  O4'  110.59  3.000
 FFJ  H10  C4'  C3'  108.34  3.000
 FFJ  C5'  C4'  C3'  117.19  3.000
 FFJ  O4'  C4'  C3'  104.87  3.000
 FFJ  H12  C5'  H11  107.74  3.000
 FFJ  H12  C5'  O5'  111.60  3.000
 FFJ  H11  C5'  O5'  109.45  3.000
 FFJ  H12  C5'  C4'  108.08  3.000
 FFJ  H11  C5'  C4'  110.66  3.000
 FFJ  O5'  C5'  C4'  109.30  3.000
 FFJ  PA   O5'  C5'  125.96  3.000
 FFJ  O3A  PA   O2A  110.50  3.000
 FFJ  O2A  PA   O1A  119.47  3.000
 FFJ  O3A  PA   O1A   99.48  3.000
 FFJ  O1A  PA   O5'  107.76  3.000
 FFJ  O2A  PA   O5'  112.93  3.000
 FFJ  O3A  PA   O5'  105.03  3.000
 FFJ  H13  O1A  PA   115.21  3.000
 FFJ  PB   O3A  PA   137.20  3.000
 FFJ  C3B  PB   O2B  111.80  3.000
 FFJ  C3B  PB   O1B  106.39  3.000
 FFJ  O2B  PB   O1B  117.91  3.000
 FFJ  C3B  PB   O3A   99.64  3.000
 FFJ  O1B  PB   O3A  102.25  3.000
 FFJ  O2B  PB   O3A  116.76  3.000
 FFJ  H14  O1B  PB   116.06  3.000
 FFJ  PG   C3B  F4B  106.26  3.000
 FFJ  PG   C3B  F3B  110.22  3.000
 FFJ  F4B  C3B  F3B  107.71  3.000
 FFJ  PG   C3B  PB   118.61  3.000
 FFJ  F3B  C3B  PB   107.46  3.000
 FFJ  F4B  C3B  PB   106.06  3.000
 FFJ  O3G  PG   O1G  116.91  3.000
 FFJ  O1G  PG   O2G  103.97  3.000
 FFJ  O3G  PG   O2G  119.54  3.000
 FFJ  O1G  PG   C3B  102.77  3.000
 FFJ  O2G  PG   C3B   98.41  3.000
 FFJ  O3G  PG   C3B  112.50  3.000
 FFJ  H15  O2G  PG   115.91  3.000
 FFJ  H16  O1G  PG   114.73  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
 FFJ  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 FFJ  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 FFJ  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 FFJ  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 FFJ  CONST_05  O2   C2   N3   C4    180.00   0.0  0
 FFJ  CONST_06  C2   N3   C4   N4    180.00   0.0  0
 FFJ  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 FFJ  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 FFJ  CONST_09  H1   N4   C4   C5    180.00   0.0  0
 FFJ  CONST_10  H2   N4   C4   C5      0.00   0.0  0
 FFJ  Var_01    O3A  PA   O5'  C5'    84.95  30.0  3
 FFJ  Var_02    O2B  PB   O3A  PA     64.58  30.0  1
 FFJ  Var_03    F4B  C3B  PB   O3A  -168.32  30.0  3
 FFJ  Var_04    O3G  PG   C3B  PB     66.53  30.0  3
 FFJ  Var_05    H11  C5'  O5'  PA     70.13  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
 FFJ  chir_01  C1'  C2'  N1   O4'  positiv
 FFJ  chir_02  C3'  O3'  C4'  C2'  positiv
 FFJ  chir_03  C4'  O4'  C3'  C5'  negativ
 FFJ  chir_04  PA   O3A  O2A  O1A  both
 FFJ  chir_05  PB   O3A  O1B  C3B  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
 FFJ  plan-1  C4   0.020
 FFJ  plan-1  N4   0.020
 FFJ  plan-1  C5   0.020
 FFJ  plan-1  C6   0.020
 FFJ  plan-1  N3   0.020
 FFJ  plan-1  C2   0.020
 FFJ  plan-1  O2   0.020
 FFJ  plan-1  N1   0.020
 FFJ  plan-1  C1'  0.020
 FFJ  plan-1  H1   0.020
 FFJ  plan-1  H2   0.020
 FFJ  plan-1  H3   0.020
 FFJ  plan-1  H4   0.020

