# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:52:16 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  23  15  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.504   0.2241   0.0111  -0.5829
 FWD  C2    C  CR6   0   0.744   0.7705  -1.2504  -0.5798
 FWD  O2    O  O     0  -0.476   0.1639  -2.2481  -0.9041
 FWD  N3    N  NR16  0  -0.736   2.0919  -1.2979  -0.1970
 FWD  C4    C  CR6   0   0.469   2.9132  -0.2613   0.1956
 FWD  O4    O  O     0  -0.449   4.0707  -0.4339   0.5162
 FWD  C5    C  CR6   0   0.283   2.2307   1.0117   0.1696
 FWD  F5    F  F     0  -0.294   2.9373   2.0886   0.5214
 FWD  C6    C  CR16  0  -0.075   0.9500   1.1045  -0.2011
 FWD  C7    C  CH2   0  -0.341  -1.1965   0.1773  -0.8358
 FWD  C8    C  CH1   0  -0.220  -1.9810   0.2696   0.4850
 FWD  N8    N  NH2   0  -0.770  -1.6591  -0.8368   1.3415
 FWD  C9    C  C     0   0.532  -3.4663   0.4165   0.1716
 FWD  O91   O  O     0  -0.428  -4.3124  -0.3699   0.5098
 FWD  O92   O  OH1   0  -0.591  -3.7173   1.5197  -0.5205
 FWD  H3    H  HNR6  0   0.433   2.5065  -2.2222  -0.2026
 FWD  H6    H  HCR6  0   0.338   0.4369   2.0567  -0.2294
 FWD  H71   H  HCH2  0   0.297  -1.3306   1.0755  -1.4362
 FWD  H72   H  HCH2  0   0.296  -1.5405  -0.6660  -1.4305
 FWD  H8    H  HCH1  0   0.291  -1.6758   1.1918   0.9924
 FWD  H81   H  HNH2  0   0.364  -2.0506  -0.6950   2.2627
 FWD  H82   H  HNH2  0   0.351  -2.0512  -1.6988   0.9846
 FWD  H92O  H  HOH1  0   0.486  -4.6639   1.5852  -0.7197

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  1.375  0.020  1.375
 FWD  N1   C6    single  1.367  0.020  1.367
 FWD  N1   C7    single  1.453  0.020  1.453
 FWD  C2   O2    double  1.212  0.020  1.212
 FWD  C2   N3    single  1.377  0.020  1.377
 FWD  N3   C4    single  1.380  0.020  1.380
 FWD  N3   H3    single  0.860  0.020  1.020
 FWD  C4   O4    double  1.213  0.020  1.213
 FWD  C4   C5    single  1.445  0.020  1.445
 FWD  C5   F5    single  1.335  0.020  1.335
 FWD  C5   C6    double  1.336  0.020  1.336
 FWD  C6   H6    single  0.930  0.020  1.080
 FWD  C7   C8    single  1.539  0.020  1.539
 FWD  C7   H71   single  0.970  0.020  1.090
 FWD  C7   H72   single  0.970  0.020  1.090
 FWD  C8   N8    single  1.436  0.020  1.436
 FWD  C8   C9    single  1.525  0.020  1.525
 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   double  1.204  0.020  1.204
 FWD  C9   O92   single  1.326  0.020  1.326
 FWD  O92  H92O  single  0.850  0.020  0.980

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   118.46  3.000
 FWD  C7    N1   C2   119.61  3.000
 FWD  C6    N1   C2   121.49  3.000
 FWD  N3    C2   O2   121.77  3.000
 FWD  N3    C2   N1   114.45  3.000
 FWD  O2    C2   N1   123.78  3.000
 FWD  H3    N3   C4   116.33  3.000
 FWD  H3    N3   C2   115.01  3.000
 FWD  C4    N3   C2   128.66  3.000
 FWD  C5    C4   O4   125.50  3.000
 FWD  C5    C4   N3   112.07  3.000
 FWD  O4    C4   N3   122.43  3.000
 FWD  C6    C5   F5   121.62  3.000
 FWD  C6    C5   C4   121.26  3.000
 FWD  F5    C5   C4   117.12  3.000
 FWD  H6    C6   C5   121.52  3.000
 FWD  H6    C6   N1   116.41  3.000
 FWD  C5    C6   N1   122.06  3.000
 FWD  H72   C7   H71  107.41  3.000
 FWD  H72   C7   C8   110.77  3.000
 FWD  H71   C7   C8   111.16  3.000
 FWD  H72   C7   N1   108.41  3.000
 FWD  H71   C7   N1   108.11  3.000
 FWD  C8    C7   N1   110.86  3.000
 FWD  H8    C8   C9   106.58  3.000
 FWD  H8    C8   N8   108.05  3.000
 FWD  C9    C8   N8   114.53  3.000
 FWD  H8    C8   C7   107.81  3.000
 FWD  C9    C8   C7   109.01  3.000
 FWD  N8    C8   C7   110.57  3.000
 FWD  H82   N8   H81  106.90  3.000
 FWD  H82   N8   C8   111.05  3.000
 FWD  H81   N8   C8   110.41  3.000
 FWD  O92   C9   O91  123.86  3.000
 FWD  O92   C9   C8   111.81  3.000
 FWD  O91   C9   C8   124.33  3.000
 FWD  H92O  O92  C9   110.37  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  CONST_10  H92O  O92  C9  C8  180.00   0.0  0
 FWD  Var_01    C8    C7   N1  C2   95.63  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
 FWD  plan-2  H92O  0.020

