# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 22:00:07 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  32  18  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OH1   0  -0.747  -1.0717   3.6220  -0.0494
 CFV  PAM   P  P     0   1.351  -0.4522   2.1404   0.0393
 CFV  OAO   O  O     0  -0.691   0.7828   1.8823  -0.7329
 CFV  OAP   O  OH1   0  -0.743  -0.1840   1.8524   1.6012
 CFV  CAL   C  CH2   0  -0.461  -1.9210   1.1776  -0.4668
 CFV  OAK   O  O2    0  -0.475  -1.5943  -0.1771  -0.6077
 CFV  CAJ   C  CH1   0  -0.001  -1.7381  -0.9700   0.5532
 CFV  CAQ   C  CH2   0  -0.160  -3.1425  -1.5300   0.6870
 CFV  OAR   O  OH1   0  -0.668  -3.4257  -2.3606  -0.4108
 CFV  CAA   C  CH2   0  -0.333  -0.6889  -2.0721   0.4896
 CFV  NAB   N  NR6   0  -0.511   0.6554  -1.5361   0.3524
 CFV  CAC   C  CR16  0   0.106   1.2872  -1.0474   1.4423
 CFV  CAD   C  CR16  0  -0.466   2.5191  -0.5065   1.3705
 CFV  CAE   C  CR6   0   0.522   3.1073  -0.4597   0.0722
 CFV  NAF   N  NH2   0  -0.817   4.3131   0.0922  -0.0848
 CFV  NAG   N  N     0  -0.545   2.5079  -0.9565  -0.9894
 CFV  CAH   C  CR6   0   0.595   1.2753  -1.4985  -0.9062
 CFV  OAI   O  O     0  -0.527   0.7044  -1.9789  -1.8770
 CFV  HOAN  H  HOH1  0   0.496  -0.4327   4.3366   0.0799
 CFV  HOAP  H  HOH1  0   0.488  -0.9108   2.0839   2.1943
 CFV  HAL   H  HCH2  0   0.257  -2.7524   1.3542   0.2271
 CFV  HALA  H  HCH2  0   0.287  -2.2404   1.5525  -1.4426
 CFV  HAJ   H  HCH1  0   0.231  -1.5593  -0.3749   1.4582
 CFV  HAQ   H  HCH2  0   0.208  -3.1980  -2.0688   1.6423
 CFV  HAQA  H  HCH2  0   0.213  -3.8519  -0.6943   0.7593
 CFV  HOAR  H  HOH1  0   0.460  -4.3077  -2.7236  -0.2923
 CFV  HAA   H  HCH2  0   0.269  -0.7396  -2.6625   1.4060
 CFV  HAAA  H  HCH2  0   0.278  -0.8751  -2.7433  -0.3434
 CFV  HAC   H  HCR6  0   0.303   0.7549  -1.1260   2.3804
 CFV  HAD   H  HCR6  0   0.277   3.0147  -0.1209   2.2482
 CFV  HNAF  H  HNH2  0   0.409   4.8363   0.4476   0.6954
 CFV  HNAA  H  HNH2  0   0.397   4.7432   0.1150  -0.9932

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   single  1.608  0.020  1.608
 CFV  PAM  OAO   double  1.479  0.020  1.479
 CFV  PAM  OAP   single  1.611  0.020  1.611
 CFV  PAM  CAL   single  1.828  0.020  1.828
 CFV  CAL  OAK   single  1.401  0.020  1.401
 CFV  OAK  CAJ   single  1.413  0.020  1.413
 CFV  CAJ  CAQ   single  1.518  0.020  1.518
 CFV  CAJ  CAA   single  1.523  0.020  1.523
 CFV  CAQ  OAR   single  1.406  0.020  1.406
 CFV  CAA  NAB   single  1.454  0.020  1.454
 CFV  NAB  CAC   single  1.351  0.020  1.351
 CFV  NAB  CAH   single  1.403  0.020  1.403
 CFV  CAC  CAD   double  1.347  0.020  1.347
 CFV  CAD  CAE   single  1.426  0.020  1.426
 CFV  CAE  NAF   single  1.335  0.020  1.335
 CFV  CAE  NAG   double  1.316  0.020  1.316
 CFV  NAG  CAH   single  1.349  0.020  1.349
 CFV  CAH  OAI   double  1.224  0.020  1.224
 CFV  OAN  HOAN  single  0.850  0.020  0.980
 CFV  OAP  HOAP  single  0.850  0.020  0.980
 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  0.860  0.020  1.020
 CFV  NAF  HNAA  single  0.860  0.020  1.020

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  HOAN  OAN  PAM   114.75  3.000
 CFV  CAL   PAM  OAP   107.95  3.000
 CFV  CAL   PAM  OAO   115.75  3.000
 CFV  OAP   PAM  OAO   109.63  3.000
 CFV  CAL   PAM  OAN    99.23  3.000
 CFV  OAP   PAM  OAN   106.40  3.000
 CFV  OAO   PAM  OAN   116.97  3.000
 CFV  HOAP  OAP  PAM   115.29  3.000
 CFV  HALA  CAL  HAL   106.74  3.000
 CFV  HALA  CAL  OAK   108.07  3.000
 CFV  HAL   CAL  OAK   113.33  3.000
 CFV  HALA  CAL  PAM   107.54  3.000
 CFV  HAL   CAL  PAM   110.43  3.000
 CFV  OAK   CAL  PAM   110.48  3.000
 CFV  CAJ   OAK  CAL   115.87  3.000
 CFV  HAJ   CAJ  CAA   108.33  3.000
 CFV  HAJ   CAJ  CAQ   106.14  3.000
 CFV  CAA   CAJ  CAQ   111.97  3.000
 CFV  HAJ   CAJ  OAK   110.88  3.000
 CFV  CAA   CAJ  OAK   107.55  3.000
 CFV  CAQ   CAJ  OAK   111.93  3.000
 CFV  HAQA  CAQ  HAQ   106.46  3.000
 CFV  HAQA  CAQ  OAR   111.77  3.000
 CFV  HAQ   CAQ  OAR   112.29  3.000
 CFV  HAQA  CAQ  CAJ   108.83  3.000
 CFV  HAQ   CAQ  CAJ   107.73  3.000
 CFV  OAR   CAQ  CAJ   109.61  3.000
 CFV  HOAR  OAR  CAQ   108.17  3.000
 CFV  HAAA  CAA  HAA   107.57  3.000
 CFV  HAAA  CAA  NAB   108.30  3.000
 CFV  HAA   CAA  NAB   108.77  3.000
 CFV  HAAA  CAA  CAJ   111.17  3.000
 CFV  HAA   CAA  CAJ   108.93  3.000
 CFV  NAB   CAA  CAJ   111.98  3.000
 CFV  CAH   NAB  CAC   120.47  3.000
 CFV  CAH   NAB  CAA   120.20  3.000
 CFV  CAC   NAB  CAA   119.31  3.000
 CFV  HAC   CAC  CAD   121.70  3.000
 CFV  HAC   CAC  NAB   116.31  3.000
 CFV  CAD   CAC  NAB   121.98  3.000
 CFV  HAD   CAD  CAE   122.64  3.000
 CFV  HAD   CAD  CAC   121.33  3.000
 CFV  CAE   CAD  CAC   116.03  3.000
 CFV  NAG   CAE  NAF   118.18  3.000
 CFV  NAG   CAE  CAD   122.27  3.000
 CFV  NAF   CAE  CAD   119.54  3.000
 CFV  HNAA  NAF  HNAF  118.10  3.000
 CFV  HNAA  NAF  CAE   120.13  3.000
 CFV  HNAF  NAF  CAE   121.68  3.000
 CFV  CAH   NAG  CAE   121.19  3.000
 CFV  OAI   CAH  NAG   122.33  3.000
 CFV  OAI   CAH  NAB   119.64  3.000
 CFV  NAG   CAH  NAB   118.01  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   78.84  30.0  3
 CFV  Var_02    OAK   CAL  PAM  OAN  173.74  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

