# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 06:38:50 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: {[(1R)-2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1-(hydroxymethyl)ethoxy]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C[C@H](CO)OC[P](O)(O)=O)C=C1
#
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
 CFV  CFV  '{[(1R)-2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1-(hydroxymethyl)ethoxy]methyl}phosphonic acid'  ligand  30  18  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CFV
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
 CFV  OAN   O  OP    -1  -0.914  -0.8625   3.5687   0.0924
 CFV  PAM   P  P      0   1.173  -0.3914   2.1094   0.2269
 CFV  OAO   O  O      0  -0.874   0.8457   1.7806  -0.6102
 CFV  OAP   O  OP    -1  -0.882  -0.3323   1.6358   1.6892
 CFV  CAL   C  CH2    0  -0.467  -1.8125   1.1858  -0.5653
 CFV  OAK   O  O2     0  -0.502  -1.6565  -0.2243  -0.6890
 CFV  CAJ   C  CH1    0   0.013  -1.7672  -0.9270   0.5205
 CFV  CAQ   C  CH2    0  -0.165  -3.1667  -1.4773   0.7320
 CFV  OAR   O  OH1    0  -0.674  -3.4810  -2.4189  -0.2694
 CFV  CAA   C  CH2    0  -0.331  -0.7205  -2.0340   0.5288
 CFV  NAB   N  NT     0  -0.499   0.6235  -1.5043   0.3597
 CFV  CAC   C  C1     0   0.149   1.2301  -0.9067   1.4054
 CFV  CAD   C  C1     0  -0.465   2.4675  -0.3814   1.3029
 CFV  CAE   C  C      0   0.516   3.0549  -0.4207   0.0123
 CFV  NAF   N  NH2    0  -0.825   4.2724   0.1136  -0.1810
 CFV  NAG   N  N      0  -0.553   2.4762  -1.0121  -1.0111
 CFV  CAH   C  C      0   0.587   1.2450  -1.5493  -0.8915
 CFV  OAI   O  O      0  -0.545   0.6855  -2.1063  -1.8319
 CFV  HAL   H  HCH2   0   0.159  -2.7544   1.4218  -0.0422
 CFV  HALA  H  HCH2   0   0.184  -1.9468   1.5510  -1.5898
 CFV  HAJ   H  HCH1   0   0.234  -1.5616  -0.2586   1.3639
 CFV  HAQ   H  HCH2   0   0.189  -3.2131  -1.9210   1.7364
 CFV  HAQA  H  HCH2   0   0.202  -3.8741  -0.6365   0.7290
 CFV  HOAR  H  HOH1   0   0.454  -4.3696  -2.7444  -0.1031
 CFV  HAA   H  HCH2   0   0.247  -0.7644  -2.5705   1.4793
 CFV  HAAA  H  HCH2   0   0.259  -0.9003  -2.7553  -0.2628
 CFV  HAC   H  H      0   0.282   0.6826  -0.9021   2.3356
 CFV  HAD   H  H      0   0.260   2.9476   0.0944   2.1443
 CFV  HNAF  H  HNH2   0   0.399   4.6815   0.7101   0.5159
 CFV  HNAA  H  HNH2   0   0.388   4.6208   0.2035  -1.1200

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
 CFV  OAN  PAM   deloc   1.539  0.020  1.539
 CFV  PAM  OAO   deloc   1.529  0.020  1.529
 CFV  PAM  OAP   deloc   1.538  0.020  1.538
 CFV  PAM  CAL   single  1.871  0.020  1.871
 CFV  CAL  OAK   single  1.424  0.020  1.424
 CFV  OAK  CAJ   single  1.403  0.020  1.403
 CFV  CAJ  CAQ   single  1.519  0.020  1.519
 CFV  CAJ  CAA   single  1.524  0.020  1.524
 CFV  CAQ  OAR   single  1.410  0.020  1.410
 CFV  CAA  NAB   single  1.454  0.020  1.454
 CFV  NAB  CAC   single  1.349  0.020  1.349
 CFV  NAB  CAH   single  1.398  0.020  1.398
 CFV  CAC  CAD   double  1.348  0.020  1.348
 CFV  CAD  CAE   single  1.419  0.020  1.419
 CFV  CAE  NAF   single  1.344  0.020  1.344
 CFV  CAE  NAG   double  1.316  0.020  1.316
 CFV  NAG  CAH   single  1.349  0.020  1.349
 CFV  CAH  OAI   double  1.228  0.020  1.228
 CFV  CAL  HAL   single  0.970  0.020  1.090
 CFV  CAL  HALA  single  0.970  0.020  1.090
 CFV  CAJ  HAJ   single  0.970  0.020  1.090
 CFV  CAQ  HAQ   single  0.970  0.020  1.090
 CFV  CAQ  HAQA  single  0.970  0.020  1.090
 CFV  OAR  HOAR  single  0.850  0.020  0.980
 CFV  CAA  HAA   single  0.970  0.020  1.090
 CFV  CAA  HAAA  single  0.970  0.020  1.090
 CFV  CAC  HAC   single  0.930  0.020  1.080
 CFV  CAD  HAD   single  0.930  0.020  1.080
 CFV  NAF  HNAF  single  0.890  0.020  1.040
 CFV  NAF  HNAA  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
 CFV  CAL   PAM  OAP   106.24  3.000
 CFV  CAL   PAM  OAO   106.06  3.000
 CFV  OAP   PAM  OAO   115.02  3.000
 CFV  CAL   PAM  OAN   101.46  3.000
 CFV  OAP   PAM  OAN   112.75  3.000
 CFV  OAO   PAM  OAN   113.80  3.000
 CFV  HALA  CAL  HAL   105.51  3.000
 CFV  HALA  CAL  OAK   105.20  3.000
 CFV  HAL   CAL  OAK   110.28  3.000
 CFV  HALA  CAL  PAM   108.93  3.000
 CFV  HAL   CAL  PAM   110.01  3.000
 CFV  OAK   CAL  PAM   116.26  3.000
 CFV  CAJ   OAK  CAL   114.35  3.000
 CFV  HAJ   CAJ  CAA   108.06  3.000
 CFV  HAJ   CAJ  CAQ   106.67  3.000
 CFV  CAA   CAJ  CAQ   111.66  3.000
 CFV  HAJ   CAJ  OAK   110.08  3.000
 CFV  CAA   CAJ  OAK   108.33  3.000
 CFV  CAQ   CAJ  OAK   111.98  3.000
 CFV  HAQA  CAQ  HAQ   106.52  3.000
 CFV  HAQA  CAQ  OAR   111.44  3.000
 CFV  HAQ   CAQ  OAR   111.72  3.000
 CFV  HAQA  CAQ  CAJ   108.40  3.000
 CFV  HAQ   CAQ  CAJ   108.21  3.000
 CFV  OAR   CAQ  CAJ   110.39  3.000
 CFV  HOAR  OAR  CAQ   108.03  3.000
 CFV  HAAA  CAA  HAA   107.54  3.000
 CFV  HAAA  CAA  NAB   108.07  3.000
 CFV  HAA   CAA  NAB   108.49  3.000
 CFV  HAAA  CAA  CAJ   111.40  3.000
 CFV  HAA   CAA  CAJ   109.52  3.000
 CFV  NAB   CAA  CAJ   111.69  3.000
 CFV  CAH   NAB  CAC   120.56  3.000
 CFV  CAH   NAB  CAA   120.21  3.000
 CFV  CAC   NAB  CAA   119.13  3.000
 CFV  HAC   CAC  CAD   121.97  3.000
 CFV  HAC   CAC  NAB   116.23  3.000
 CFV  CAD   CAC  NAB   121.78  3.000
 CFV  HAD   CAD  CAE   122.51  3.000
 CFV  HAD   CAD  CAC   121.38  3.000
 CFV  CAE   CAD  CAC   116.00  3.000
 CFV  NAG   CAE  NAF   117.73  3.000
 CFV  NAG   CAE  CAD   122.54  3.000
 CFV  NAF   CAE  CAD   119.68  3.000
 CFV  HNAA  NAF  HNAF  116.98  3.000
 CFV  HNAA  NAF  CAE   118.95  3.000
 CFV  HNAF  NAF  CAE   120.36  3.000
 CFV  CAH   NAG  CAE   120.76  3.000
 CFV  OAI   CAH  NAG   121.93  3.000
 CFV  OAI   CAH  NAB   119.84  3.000
 CFV  NAG   CAH  NAB   118.19  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
 CFV  CONST_01  CAE   NAG  CAH  NAB    0.00   0.0  0
 CFV  CONST_02  NAG   CAH  NAB  CAC    0.00   0.0  0
 CFV  CONST_03  CAH   NAG  CAE  CAD    0.00   0.0  0
 CFV  CONST_04  NAG   CAH  NAB  CAA  180.00   0.0  0
 CFV  CONST_05  OAI   CAH  NAB  CAC  180.00   0.0  0
 CFV  CONST_06  OAI   CAH  NAG  CAE  180.00   0.0  0
 CFV  CONST_07  CAH   NAG  CAE  NAF  180.00   0.0  0
 CFV  CONST_08  OAI   CAH  NAB  CAA    0.00   0.0  0
 CFV  CONST_09  HNAF  NAF  CAE  CAD    0.00   0.0  0
 CFV  CONST_10  HNAA  NAF  CAE  CAD  180.00   0.0  0
 CFV  Var_01    CAC   NAB  CAA  CAJ   76.56  30.0  3
 CFV  Var_02    OAK   CAL  PAM  OAN  175.97  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
 CFV  chir_01  CAJ  OAK  CAQ  CAA  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
 CFV  plan-1  CAA   0.020
 CFV  plan-1  NAB   0.020
 CFV  plan-1  CAC   0.020
 CFV  plan-1  CAD   0.020
 CFV  plan-1  CAE   0.020
 CFV  plan-1  NAF   0.020
 CFV  plan-1  NAG   0.020
 CFV  plan-1  CAH   0.020
 CFV  plan-1  OAI   0.020
 CFV  plan-1  HAC   0.020
 CFV  plan-1  HAD   0.020
 CFV  plan-1  HNAF  0.020
 CFV  plan-1  HNAA  0.020

