# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:37:38 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(5-fluoro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C=C(F)C(=O)NC1=O)C(O)=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
 FWD  FWD  3-(5-fluoro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine  ligand  22  15  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FWD
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
 FWD  N1   N  NR6    0  -0.500   0.2337  -0.0107  -0.6088
 FWD  C2   C  CR6    0   0.735   0.7791  -1.2697  -0.6053
 FWD  O2   O  O      0  -0.481   0.1818  -2.2694  -0.9440
 FWD  N3   N  NR16   0  -0.736   2.0978  -1.3205  -0.2063
 FWD  C4   C  CR6    0   0.466   2.9172  -0.2869   0.1960
 FWD  O4   O  O      0  -0.456   4.0722  -0.4633   0.5287
 FWD  C5   C  CR6    0   0.277   2.2363   0.9849   0.1640
 FWD  F5   F  F      0  -0.297   2.9393   2.0638   0.5233
 FWD  C6   C  CR16   0  -0.073   0.9575   1.0770  -0.2177
 FWD  C7   C  CH2    0  -0.330  -1.1941   0.1626  -0.8576
 FWD  C8   C  CH1    0  -0.225  -1.9902   0.2660   0.4455
 FWD  N8   N  NH2    0  -0.779  -1.6685  -0.8494   1.3109
 FWD  C9   C  C      0   0.394  -3.4865   0.4592   0.0805
 FWD  O91  O  O      0  -0.595  -4.2930  -0.3957   0.4870
 FWD  O92  O  OC    -1  -0.617  -3.7415   1.4689  -0.6077
 FWD  H3   H  HNR6   0   0.430   2.5103  -2.2455  -0.2083
 FWD  H6   H  HCR6   0   0.333   0.4437   2.0289  -0.2450
 FWD  H71  H  HCH2   0   0.274  -1.3239   1.0626  -1.4554
 FWD  H72  H  HCH2   0   0.272  -1.5338  -0.6797  -1.4567
 FWD  H8   H  HCH1   0   0.233  -1.6639   1.1807   0.9554
 FWD  H81  H  HNH2   0   0.344  -2.0805  -0.6827   2.2203
 FWD  H82  H  HNH2   0   0.330  -2.1348  -1.6790   0.9626

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
 FWD  N1  C2   single  1.372  0.020  1.372
 FWD  N1  C6   single  1.364  0.020  1.364
 FWD  N1  C7   single  1.460  0.020  1.460
 FWD  C2  O2   double  1.213  0.020  1.213
 FWD  C2  N3   single  1.379  0.020  1.379
 FWD  N3  C4   single  1.379  0.020  1.379
 FWD  N3  H3   single  0.860  0.020  1.020
 FWD  C4  O4   double  1.215  0.020  1.215
 FWD  C4  C5   single  1.443  0.020  1.443
 FWD  C5  F5   single  1.337  0.020  1.337
 FWD  C5  C6   double  1.338  0.020  1.338
 FWD  C6  H6   single  0.930  0.020  1.080
 FWD  C7  C8   single  1.531  0.020  1.531
 FWD  C7  H71  single  0.970  0.020  1.090
 FWD  C7  H72  single  0.970  0.020  1.090
 FWD  C8  N8   single  1.448  0.020  1.448
 FWD  C8  C9   single  1.552  0.020  1.552
 FWD  C8  H8   single  0.970  0.020  1.090
 FWD  N8  H81  single  0.890  0.020  1.040
 FWD  N8  H82  single  0.890  0.020  1.040
 FWD  C9  O91  deloc   1.244  0.020  1.244
 FWD  C9  O92  deloc   1.248  0.020  1.248

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
 FWD  C7   N1  C6   118.25  3.000
 FWD  C7   N1  C2   119.88  3.000
 FWD  C6   N1  C2   121.34  3.000
 FWD  N3   C2  O2   121.44  3.000
 FWD  N3   C2  N1   114.50  3.000
 FWD  O2   C2  N1   124.05  3.000
 FWD  H3   N3  C4   116.30  3.000
 FWD  H3   N3  C2   115.00  3.000
 FWD  C4   N3  C2   128.70  3.000
 FWD  C5   C4  O4   125.64  3.000
 FWD  C5   C4  N3   111.95  3.000
 FWD  O4   C4  N3   122.42  3.000
 FWD  C6   C5  F5   121.59  3.000
 FWD  C6   C5  C4   121.20  3.000
 FWD  F5   C5  C4   117.21  3.000
 FWD  H6   C6  C5   121.44  3.000
 FWD  H6   C6  N1   116.26  3.000
 FWD  C5   C6  N1   122.29  3.000
 FWD  H72  C7  H71  107.50  3.000
 FWD  H72  C7  C8   111.02  3.000
 FWD  H71  C7  C8   110.48  3.000
 FWD  H72  C7  N1   107.89  3.000
 FWD  H71  C7  N1   107.97  3.000
 FWD  C8   C7  N1   111.82  3.000
 FWD  H8   C8  C9   106.99  3.000
 FWD  H8   C8  N8   107.36  3.000
 FWD  C9   C8  N8   116.78  3.000
 FWD  H8   C8  C7   107.30  3.000
 FWD  C9   C8  C7   108.03  3.000
 FWD  N8   C8  C7   109.96  3.000
 FWD  H82  N8  H81  104.85  3.000
 FWD  H82  N8  C8   108.84  3.000
 FWD  H81  N8  C8   108.65  3.000
 FWD  O92  C9  O91  127.14  3.000
 FWD  O92  C9  C8   115.29  3.000
 FWD  O91  C9  C8   117.56  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
 FWD  CONST_01  C4  N3  C2  N1    0.00   0.0  0
 FWD  CONST_02  C5  C4  N3  C2    0.00   0.0  0
 FWD  CONST_03  C6  N1  C2  N3    0.00   0.0  0
 FWD  CONST_04  O4  C4  N3  C2  180.00   0.0  0
 FWD  CONST_05  C6  N1  C2  O2  180.00   0.0  0
 FWD  CONST_06  C4  N3  C2  O2  180.00   0.0  0
 FWD  CONST_07  C7  N1  C2  N3  180.00   0.0  0
 FWD  CONST_08  H3  N3  C2  N1  180.00   0.0  0
 FWD  CONST_09  C7  N1  C2  O2    0.00   0.0  0
 FWD  Var_01    C8  C7  N1  C2   95.80  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
 FWD  chir_01  C8  C7  N8  C9  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
 FWD  plan-1  N1   0.020
 FWD  plan-1  C2   0.020
 FWD  plan-1  O2   0.020
 FWD  plan-1  N3   0.020
 FWD  plan-1  C4   0.020
 FWD  plan-1  O4   0.020
 FWD  plan-1  C5   0.020
 FWD  plan-1  F5   0.020
 FWD  plan-1  C6   0.020
 FWD  plan-1  C7   0.020
 FWD  plan-1  H3   0.020
 FWD  plan-1  H6   0.020
 FWD  plan-2  C8   0.020
 FWD  plan-2  C9   0.020
 FWD  plan-2  O91  0.020
 FWD  plan-2  O92  0.020

