# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:20:00 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](N)CN1C=C(F)C(=O)NC1=O
#
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
 4WR  4WR  1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione  ligand  25  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4WR
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
 4WR  C2   C  CR6   0   0.723  -0.5317   1.2866  -0.5377
 4WR  C4   C  CR6   0   0.470  -2.6773   0.2651   0.1935
 4WR  C5   C  CR6   0   0.284  -2.0103  -1.0093   0.0542
 4WR  F5   F  F     0  -0.294  -2.7284  -2.1051   0.3122
 4WR  C6   C  CR16  0  -0.076  -0.7295  -1.0850  -0.3211
 4WR  O2   O  O     0  -0.474   0.0760   2.3010  -0.8078
 4WR  N3   N  NR16  0  -0.734  -1.8416   1.3188  -0.1136
 4WR  O4   O  O     0  -0.449  -3.8302   0.4264   0.5352
 4WR  N1   N  NR6   0  -0.520   0.0098   0.0263  -0.6172
 4WR  CAB  C  CH2   0  -0.330   1.4113  -0.1440  -0.9936
 4WR  CAM  C  CH1   0  -0.117   2.3248  -0.3610   0.2237
 4WR  NAA  N  NH2   0  -0.776   2.2281   0.6535   1.2499
 4WR  CAL  C  CH2   0  -0.264   3.7562  -0.4912  -0.2909
 4WR  NAJ  N  NH2   0  -0.792   4.6776  -0.9082   0.7501
 4WR  H1   H  HCR6  0   0.339  -0.2253  -2.0364  -0.4238
 4WR  H2   H  HNR6  0   0.434  -2.2444   2.2454  -0.0393
 4WR  H3   H  HCH2  0   0.272   1.4628  -1.0019  -1.6657
 4WR  H4   H  HCH2  0   0.277   1.7177   0.7301  -1.5649
 4WR  H5   H  HCH1  0   0.237   2.0458  -1.3191   0.6799
 4WR  H6   H  HNH2  0   0.339   2.4127   1.5702   0.8604
 4WR  H7   H  HNH2  0   0.347   1.2980   0.6847   1.6463
 4WR  H9   H  HCH2  0   0.201   3.7440  -1.1672  -1.1586
 4WR  H10  H  HCH2  0   0.219   4.0793   0.4839  -0.6700
 4WR  H11  H  HNH2  0   0.336   4.4356  -1.8429   1.0560
 4WR  H12  H  HNH2  0   0.347   5.6057  -0.9857   0.3541

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
 4WR  F5   C5   single  1.335  0.020  1.335
 4WR  O4   C4   double  1.213  0.020  1.213
 4WR  C4   C5   single  1.445  0.020  1.445
 4WR  C4   N3   single  1.379  0.020  1.379
 4WR  C5   C6   double  1.337  0.020  1.337
 4WR  N3   C2   single  1.377  0.020  1.377
 4WR  C6   N1   single  1.367  0.020  1.367
 4WR  C2   N1   single  1.374  0.020  1.374
 4WR  C2   O2   double  1.213  0.020  1.213
 4WR  N1   CAB  single  1.461  0.020  1.461
 4WR  CAL  NAJ  single  1.451  0.020  1.451
 4WR  CAL  CAM  single  1.527  0.020  1.527
 4WR  CAB  CAM  single  1.537  0.020  1.537
 4WR  CAM  NAA  single  1.446  0.020  1.446
 4WR  C6   H1   single  0.930  0.020  1.080
 4WR  N3   H2   single  0.860  0.020  1.020
 4WR  CAB  H3   single  0.970  0.020  1.090
 4WR  CAB  H4   single  0.970  0.020  1.090
 4WR  CAM  H5   single  0.970  0.020  1.090
 4WR  NAA  H6   single  0.890  0.020  1.040
 4WR  NAA  H7   single  0.890  0.020  1.040
 4WR  CAL  H9   single  0.970  0.020  1.090
 4WR  CAL  H10  single  0.970  0.020  1.090
 4WR  NAJ  H11  single  0.890  0.020  1.040
 4WR  NAJ  H12  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
 4WR  N1   C2   N3   114.46  3.000
 4WR  N1   C2   O2   123.83  3.000
 4WR  N3   C2   O2   121.70  3.000
 4WR  O4   C4   N3   122.47  3.000
 4WR  N3   C4   C5   111.88  3.000
 4WR  O4   C4   C5   125.66  3.000
 4WR  C6   C5   F5   121.54  3.000
 4WR  C6   C5   C4   121.28  3.000
 4WR  F5   C5   C4   117.19  3.000
 4WR  H1   C6   N1   116.25  3.000
 4WR  H1   C6   C5   121.54  3.000
 4WR  N1   C6   C5   122.20  3.000
 4WR  H2   N3   C4   116.19  3.000
 4WR  H2   N3   C2   114.97  3.000
 4WR  C4   N3   C2   128.82  3.000
 4WR  CAB  N1   C6   118.67  3.000
 4WR  CAB  N1   C2   119.99  3.000
 4WR  C6   N1   C2   121.33  3.000
 4WR  H4   CAB  H3   107.15  3.000
 4WR  H4   CAB  CAM  111.21  3.000
 4WR  H3   CAB  CAM  110.41  3.000
 4WR  H4   CAB  N1   108.16  3.000
 4WR  H3   CAB  N1   107.20  3.000
 4WR  CAM  CAB  N1   112.48  3.000
 4WR  H5   CAM  CAL  107.70  3.000
 4WR  H5   CAM  NAA  107.49  3.000
 4WR  CAL  CAM  NAA  111.20  3.000
 4WR  H5   CAM  CAB  107.54  3.000
 4WR  NAA  CAM  CAB  115.03  3.000
 4WR  CAL  CAM  CAB  107.60  3.000
 4WR  H7   NAA  H6   106.88  3.000
 4WR  H7   NAA  CAM  111.17  3.000
 4WR  H6   NAA  CAM  110.47  3.000
 4WR  H10  CAL  H9   106.11  3.000
 4WR  H10  CAL  NAJ  108.47  3.000
 4WR  H9   CAL  NAJ  113.35  3.000
 4WR  H10  CAL  CAM  108.50  3.000
 4WR  H9   CAL  CAM  107.93  3.000
 4WR  NAJ  CAL  CAM  112.21  3.000
 4WR  H12  NAJ  H11  105.46  3.000
 4WR  H12  NAJ  CAL  108.88  3.000
 4WR  H11  NAJ  CAL  109.28  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
 4WR  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 4WR  CONST_02  N3   C2   N1   C6     0.00   0.0  0
 4WR  CONST_03  O2   C2   N3   C4   180.00   0.0  0
 4WR  CONST_04  O2   C2   N1   C6   180.00   0.0  0
 4WR  CONST_05  CAB  N1   C2   N3   180.00   0.0  0
 4WR  CONST_06  H2   N3   C2   N1   180.00   0.0  0
 4WR  CONST_07  CAB  N1   C2   O2     0.00   0.0  0
 4WR  Var_01    CAM  CAB  N1   C2    99.11  30.0  3
 4WR  Var_02    H11  NAJ  CAL  CAM   64.82  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
 4WR  chir_01  CAM  CAL  CAB  NAA  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
 4WR  plan-1  C2   0.020
 4WR  plan-1  C4   0.020
 4WR  plan-1  C5   0.020
 4WR  plan-1  F5   0.020
 4WR  plan-1  C6   0.020
 4WR  plan-1  O2   0.020
 4WR  plan-1  N3   0.020
 4WR  plan-1  O4   0.020
 4WR  plan-1  N1   0.020
 4WR  plan-1  CAB  0.020
 4WR  plan-1  H1   0.020
 4WR  plan-1  H2   0.020

