# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:38:59 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-[(2S)-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
 M5F  M5F  1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione  ligand  25  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M5F
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
 M5F  F5   F  F     0  -0.294  -2.7119  -2.0915  -0.4103
 M5F  C5   C  CR6   0   0.285  -2.0100  -0.9976  -0.1045
 M5F  C6   C  CR16  0  -0.076  -0.7354  -1.0712   0.2911
 M5F  N1   N  NR6   0  -0.519  -0.0095   0.0407   0.6196
 M5F  CAB  C  CH2   0  -0.332   1.3918  -0.1296   0.9933
 M5F  CAM  C  CH1   0  -0.119   2.3042  -0.3435  -0.2250
 M5F  CAL  C  CH2   0  -0.262   3.7325  -0.5112   0.2876
 M5F  NAJ  N  NH2   0  -0.792   4.6424  -0.9421  -0.7576
 M5F  NAA  N  NH2   0  -0.776   2.2236   0.6939  -1.2303
 M5F  C2   C  CR6   0   0.724  -0.5603   1.2982   0.5553
 M5F  O2   O  O     0  -0.475   0.0415   2.3131   0.8367
 M5F  N3   N  NR16  0  -0.734  -1.8739   1.3270   0.1437
 M5F  C4   C  CR6   0   0.471  -2.6905   0.2724  -0.2097
 M5F  O4   O  O     0  -0.449  -3.8412   0.4296  -0.5609
 M5F  H1   H  HCR6  0   0.338  -0.2244  -2.0206   0.3789
 M5F  H2   H  HCH2  0   0.277   1.7021   0.7526   1.5499
 M5F  H3   H  HCH2  0   0.273   1.4514  -0.9808   1.6728
 M5F  H4   H  HCH1  0   0.236   2.0072  -1.2855  -0.7027
 M5F  H5   H  HCH2  0   0.218   4.0785   0.4533   0.6734
 M5F  H6   H  HCH2  0   0.201   3.7052  -1.1919   1.1513
 M5F  H7   H  HNH2  0   0.347   5.5710  -1.0341  -0.3658
 M5F  H8   H  HNH2  0   0.337   4.3844  -1.8734  -1.0612
 M5F  H10  H  HNH2  0   0.347   1.3061   0.7163  -1.6558
 M5F  H11  H  HNH2  0   0.339   2.3746   1.6047  -0.8132
 M5F  H13  H  HNR6  0   0.434  -2.2849   2.2513   0.0869

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
 M5F  F5   C5   single  1.335  0.020  1.335
 M5F  O4   C4   double  1.213  0.020  1.213
 M5F  C4   C5   single  1.445  0.020  1.445
 M5F  C4   N3   single  1.380  0.020  1.380
 M5F  C5   C6   double  1.337  0.020  1.337
 M5F  N3   C2   single  1.377  0.020  1.377
 M5F  C6   N1   single  1.368  0.020  1.368
 M5F  C2   N1   single  1.374  0.020  1.374
 M5F  C2   O2   double  1.213  0.020  1.213
 M5F  N1   CAB  single  1.460  0.020  1.460
 M5F  NAA  CAM  single  1.447  0.020  1.447
 M5F  CAB  CAM  single  1.537  0.020  1.537
 M5F  CAM  CAL  single  1.527  0.020  1.527
 M5F  CAL  NAJ  single  1.451  0.020  1.451
 M5F  C6   H1   single  0.930  0.020  1.080
 M5F  CAB  H2   single  0.970  0.020  1.090
 M5F  CAB  H3   single  0.970  0.020  1.090
 M5F  CAM  H4   single  0.970  0.020  1.090
 M5F  CAL  H5   single  0.970  0.020  1.090
 M5F  CAL  H6   single  0.970  0.020  1.090
 M5F  NAJ  H7   single  0.890  0.020  1.040
 M5F  NAJ  H8   single  0.890  0.020  1.040
 M5F  NAA  H10  single  0.890  0.020  1.040
 M5F  NAA  H11  single  0.890  0.020  1.040
 M5F  N3   H13  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
 M5F  C4   C5   C6   121.28  3.000
 M5F  C6   C5   F5   121.60  3.000
 M5F  C4   C5   F5   117.12  3.000
 M5F  H1   C6   N1   116.31  3.000
 M5F  H1   C6   C5   121.52  3.000
 M5F  N1   C6   C5   122.16  3.000
 M5F  C2   N1   CAB  120.22  3.000
 M5F  CAB  N1   C6   118.42  3.000
 M5F  C2   N1   C6   121.32  3.000
 M5F  H3   CAB  H2   107.37  3.000
 M5F  H3   CAB  CAM  110.66  3.000
 M5F  H2   CAB  CAM  110.42  3.000
 M5F  H3   CAB  N1   107.63  3.000
 M5F  H2   CAB  N1   108.05  3.000
 M5F  CAM  CAB  N1   112.52  3.000
 M5F  H4   CAM  NAA  107.34  3.000
 M5F  H4   CAM  CAL  107.76  3.000
 M5F  NAA  CAM  CAL  111.36  3.000
 M5F  H4   CAM  CAB  107.69  3.000
 M5F  CAL  CAM  CAB  107.72  3.000
 M5F  NAA  CAM  CAB  114.70  3.000
 M5F  H6   CAL  H5   106.04  3.000
 M5F  H6   CAL  NAJ  113.41  3.000
 M5F  H5   CAL  NAJ  108.49  3.000
 M5F  H6   CAL  CAM  107.97  3.000
 M5F  H5   CAL  CAM  108.49  3.000
 M5F  NAJ  CAL  CAM  112.17  3.000
 M5F  H8   NAJ  H7   105.44  3.000
 M5F  H8   NAJ  CAL  109.21  3.000
 M5F  H7   NAJ  CAL  108.87  3.000
 M5F  H11  NAA  H10  106.77  3.000
 M5F  H11  NAA  CAM  110.50  3.000
 M5F  H10  NAA  CAM  111.02  3.000
 M5F  N3   C2   O2   121.68  3.000
 M5F  O2   C2   N1   123.77  3.000
 M5F  N3   C2   N1   114.55  3.000
 M5F  H13  N3   C4   116.28  3.000
 M5F  H13  N3   C2   115.02  3.000
 M5F  C4   N3   C2   128.70  3.000
 M5F  O4   C4   N3   122.44  3.000
 M5F  N3   C4   C5   111.99  3.000
 M5F  O4   C4   C5   125.57  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
 M5F  CONST_01  C2   N3   C4   C5     0.00   0.0  0
 M5F  CONST_02  N3   C2   N1   C6     0.00   0.0  0
 M5F  CONST_03  C4   N3   C2   N1     0.00   0.0  0
 M5F  CONST_04  O2   C2   N1   C6   180.00   0.0  0
 M5F  CONST_05  N3   C2   N1   CAB  180.00   0.0  0
 M5F  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 M5F  CONST_07  C4   N3   C2   O2   180.00   0.0  0
 M5F  CONST_08  H13  N3   C4   C5   180.00   0.0  0
 M5F  CONST_09  O2   C2   N1   CAB    0.00   0.0  0
 M5F  Var_01    CAM  CAB  N1   C6    77.87  30.0  3
 M5F  Var_02    H7   NAJ  CAL  CAM  179.81  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
 M5F  chir_01  CAM  NAA  CAB  CAL  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
 M5F  plan-1  F5   0.020
 M5F  plan-1  C5   0.020
 M5F  plan-1  C6   0.020
 M5F  plan-1  N1   0.020
 M5F  plan-1  CAB  0.020
 M5F  plan-1  C2   0.020
 M5F  plan-1  O2   0.020
 M5F  plan-1  N3   0.020
 M5F  plan-1  C4   0.020
 M5F  plan-1  O4   0.020
 M5F  plan-1  H1   0.020
 M5F  plan-1  H13  0.020

