# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:53:54 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(5-chloro-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(Cl)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
 CWD  CWD  "3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine"  L-peptide  22  15  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CWD
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
 CWD  N1    N   NR6    0  -0.525  -0.0332  -0.2350  -0.5564
 CWD  C2    C   CR6    0   0.717   0.3858  -1.5473  -0.5652
 CWD  O2    O   O      0  -0.469  -0.3391  -2.4819  -0.8300
 CWD  N3    N   NR16   0  -0.732   1.7123  -1.7239  -0.2508
 CWD  C4    C   CR6    0   0.605   2.6580  -0.7688   0.0655
 CWD  O4    O   O      0  -0.438   3.8042  -1.0670   0.3268
 CWD  C5    C   CR6    0  -0.299   2.1190   0.5746   0.0415
 CWD  CL5   CL  CL     0  -0.086   3.1827   1.8708   0.4002
 CWD  C6    C   CR16   0   0.147   0.8248   0.7776  -0.2587
 CWD  C7    C   CH2    0  -0.339  -1.4370   0.0921  -0.8158
 CWD  C8    C   CH1    0  -0.228  -2.2267   0.3633   0.4765
 CWD  N8    N   NH2    0  -0.781  -2.1706  -0.6905   1.4632
 CWD  C9    C   C      0   0.413  -3.6808   0.6857   0.0493
 CWD  O91   O   O      0  -0.592  -4.5691  -0.1136   0.3891
 CWD  O92   O   OC    -1  -0.615  -3.8168   1.7190  -0.6364
 CWD  HN3   H   HNR6   0   0.433   2.0290  -2.6864  -0.2493
 CWD  H6    H   HCR6   0   0.338   0.4022   1.7730  -0.2860
 CWD  H7    H   HCH2   0   0.272  -1.4586   0.9659  -1.4647
 CWD  H7A   H   HCH2   0   0.276  -1.8735  -0.7397  -1.3648
 CWD  H8    H   HCH1   0   0.232  -1.8094   1.2686   0.9342
 CWD  HN8   H   HNH2   0   0.334  -2.5719  -1.5420   1.0930
 CWD  HN8A  H   HNH2   0   0.337  -1.2153  -0.8954   1.7269

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
 CWD  N1  C2    single  1.378  0.020  1.378
 CWD  N1  C6    single  1.360  0.020  1.360
 CWD  N1  C7    single  1.465  0.020  1.465
 CWD  C2  O2    double  1.212  0.020  1.212
 CWD  C2  N3    single  1.375  0.020  1.375
 CWD  N3  C4    single  1.381  0.020  1.381
 CWD  N3  HN3   single  0.860  0.020  1.020
 CWD  C4  O4    double  1.213  0.020  1.213
 CWD  C4  C5    single  1.448  0.020  1.448
 CWD  C5  CL5   single  1.715  0.020  1.715
 CWD  C5  C6    double  1.344  0.020  1.344
 CWD  C6  H6    single  0.930  0.020  1.080
 CWD  C7  C8    single  1.539  0.020  1.539
 CWD  C7  H7    single  0.970  0.020  1.090
 CWD  C7  H7A   single  0.970  0.020  1.090
 CWD  C8  N8    single  1.445  0.020  1.445
 CWD  C8  C9    single  1.549  0.020  1.549
 CWD  C8  H8    single  0.970  0.020  1.090
 CWD  N8  HN8   single  0.890  0.020  1.040
 CWD  N8  HN8A  single  0.890  0.020  1.040
 CWD  C9  O91   deloc   1.242  0.020  1.242
 CWD  C9  O92   deloc   1.247  0.020  1.247

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
 CWD  C7    N1  C6   118.50  3.000
 CWD  C7    N1  C2   120.21  3.000
 CWD  C6    N1  C2   121.24  3.000
 CWD  N3    C2  O2   121.87  3.000
 CWD  N3    C2  N1   114.48  3.000
 CWD  O2    C2  N1   123.64  3.000
 CWD  HN3   N3  C4   116.27  3.000
 CWD  HN3   N3  C2   115.09  3.000
 CWD  C4    N3  C2   128.64  3.000
 CWD  C5    C4  O4   125.71  3.000
 CWD  C5    C4  N3   112.52  3.000
 CWD  O4    C4  N3   121.77  3.000
 CWD  C6    C5  CL5  122.00  3.000
 CWD  C6    C5  C4   120.16  3.000
 CWD  CL5   C5  C4   117.84  3.000
 CWD  H6    C6  C5   121.39  3.000
 CWD  H6    C6  N1   115.66  3.000
 CWD  C5    C6  N1   122.95  3.000
 CWD  H7A   C7  H7   107.76  3.000
 CWD  H7A   C7  C8   110.65  3.000
 CWD  H7    C7  C8   110.43  3.000
 CWD  H7A   C7  N1   107.65  3.000
 CWD  H7    C7  N1   107.69  3.000
 CWD  C8    C7  N1   112.49  3.000
 CWD  H8    C8  C9   107.48  3.000
 CWD  H8    C8  N8   107.59  3.000
 CWD  C9    C8  N8   112.12  3.000
 CWD  H8    C8  C7   107.50  3.000
 CWD  C9    C8  C7   106.67  3.000
 CWD  N8    C8  C7   115.16  3.000
 CWD  HN8A  N8  HN8  107.43  3.000
 CWD  HN8A  N8  C8   111.24  3.000
 CWD  HN8   N8  C8   110.40  3.000
 CWD  O92   C9  O91  127.25  3.000
 CWD  O92   C9  C8   115.22  3.000
 CWD  O91   C9  C8   117.50  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
 CWD  CONST_01  C4   N3  C2  N1      0.00   0.0  0
 CWD  CONST_02  C5   C4  N3  C2      0.00   0.0  0
 CWD  CONST_03  C6   N1  C2  N3      0.00   0.0  0
 CWD  CONST_04  O4   C4  N3  C2    180.00   0.0  0
 CWD  CONST_05  C6   N1  C2  O2    180.00   0.0  0
 CWD  CONST_06  C4   N3  C2  O2    180.00   0.0  0
 CWD  CONST_07  C7   N1  C2  N3    180.00   0.0  0
 CWD  CONST_08  HN3  N3  C2  N1    180.00   0.0  0
 CWD  CONST_09  HN3  N3  C4  C5    180.00   0.0  0
 CWD  CONST_10  C7   N1  C2  O2      0.00   0.0  0
 CWD  CONST_11  HN3  N3  C2  O2      0.00   0.0  0
 CWD  CONST_12  HN3  N3  C4  O4      0.00   0.0  0
 CWD  Var_01    CL5  C5  C6  N1    179.47  30.0  1
 CWD  Var_02    CL5  C5  C4  N3   -179.43  30.0  1
 CWD  Var_03    H6   C6  N1  C2    179.54  30.0  1
 CWD  Var_04    H6   C6  C5  C4   -179.77  30.0  1
 CWD  Var_05    C8   C7  N1  C2     99.87  30.0  3
 CWD  Var_06    CL5  C5  C4  O4      0.48  30.0  1
 CWD  Var_07    C8   C7  N1  C6    -77.64  30.0  3
 CWD  Var_08    H7   C7  N1  C2   -138.22  30.0  3
 CWD  Var_09    H7A  C7  N1  C2    -22.28  30.0  3
 CWD  Var_10    H6   C6  C5  CL5     0.02  30.0  1
 CWD  Var_11    H7   C7  N1  C6     44.27  30.0  3
 CWD  Var_12    H7A  C7  N1  C6    160.21  30.0  3
 CWD  Var_13    H6   C6  N1  C7     -2.98  30.0  1

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
 CWD  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
 CWD  plan-1  N1   0.020
 CWD  plan-1  C2   0.020
 CWD  plan-1  O2   0.020
 CWD  plan-1  N3   0.020
 CWD  plan-1  C4   0.020
 CWD  plan-1  O4   0.020
 CWD  plan-1  C5   0.020
 CWD  plan-1  C6   0.020
 CWD  plan-1  C7   0.020
 CWD  plan-1  HN3  0.020
 CWD  plan-2  C8   0.020
 CWD  plan-2  C9   0.020
 CWD  plan-2  O91  0.020
 CWD  plan-2  O92  0.020

