# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:36:46 2020
#   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  23  15  .  2022-09-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.528  -0.0684  -0.2214  -0.5571
 CWD  C2    C   CR6   0   0.728   0.3483  -1.5366  -0.5792
 CWD  O2    O   O     0  -0.466  -0.3832  -2.4644  -0.8467
 CWD  N3    N   NR16  0  -0.733   1.6747  -1.7166  -0.2752
 CWD  C4    C   CR6   0   0.608   2.6238  -0.7643   0.0428
 CWD  O4    O   O     0  -0.431   3.7702  -1.0648   0.2947
 CWD  C5    C   CR6   0  -0.296   2.0871   0.5822   0.0332
 CWD  CL5   CL  CL    0  -0.080   3.1555   1.8708   0.3985
 CWD  C6    C   CR16  0   0.146   0.7932   0.7913  -0.2580
 CWD  C7    C   CH2   0  -0.349  -1.4654   0.1022  -0.8176
 CWD  C8    C   CH1   0  -0.229  -2.2381   0.3361   0.5006
 CWD  N8    N   NH2   0  -0.778  -2.1660  -0.7271   1.4647
 CWD  C9    C   C     0   0.556  -3.6909   0.6224   0.1594
 CWD  O91   O   O     0  -0.425  -4.6192  -0.0650   0.4919
 CWD  O92   O   OH1   0  -0.593  -3.8098   1.7226  -0.5725
 CWD  HN3   H   HNR6  0   0.436   1.9908  -2.6795  -0.2844
 CWD  H6    H   HCR6  0   0.342   0.3731   1.7879  -0.2767
 CWD  H7    H   HCH2  0   0.295  -1.4897   0.9861  -1.4532
 CWD  H7A   H   HCH2  0   0.299  -1.9051  -0.7195  -1.3785
 CWD  H8    H   HCH1  0   0.295  -1.8384   1.2417   0.9707
 CWD  HN8   H   HNH2  0   0.354  -2.3887  -1.6237   1.0531
 CWD  HN8A  H   HNH2  0   0.363  -1.2399  -0.7913   1.8632
 CWD  H81   H   HOH1  0   0.486  -4.7390   1.8735  -0.8042

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  1.380  0.020  1.380
 CWD  N1   C6    single  1.363  0.020  1.363
 CWD  N1   C7    single  1.457  0.020  1.457
 CWD  C2   O2    double  1.211  0.020  1.211
 CWD  C2   N3    single  1.373  0.020  1.373
 CWD  N3   C4    single  1.382  0.020  1.382
 CWD  N3   HN3   single  0.860  0.020  1.020
 CWD  C4   O4    double  1.212  0.020  1.212
 CWD  C4   C5    single  1.450  0.020  1.450
 CWD  C5   CL5   single  1.713  0.020  1.713
 CWD  C5   C6    double  1.343  0.020  1.343
 CWD  C6   H6    single  0.930  0.020  1.080
 CWD  C7   C8    single  1.546  0.020  1.546
 CWD  C7   H7    single  0.970  0.020  1.090
 CWD  C7   H7A   single  0.970  0.020  1.090
 CWD  C8   N8    single  1.437  0.020  1.437
 CWD  C8   C9    single  1.520  0.020  1.520
 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   double  1.202  0.020  1.202
 CWD  C9   O92   single  1.327  0.020  1.327
 CWD  O92  H81   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
 CWD  C7    N1   C6   118.69  3.000
 CWD  C7    N1   C2   119.89  3.000
 CWD  C6    N1   C2   121.39  3.000
 CWD  N3    C2   O2   122.13  3.000
 CWD  N3    C2   N1   114.41  3.000
 CWD  O2    C2   N1   123.45  3.000
 CWD  HN3   N3   C4   116.28  3.000
 CWD  HN3   N3   C2   115.08  3.000
 CWD  C4    N3   C2   128.64  3.000
 CWD  C5    C4   O4   125.59  3.000
 CWD  C5    C4   N3   112.61  3.000
 CWD  O4    C4   N3   121.80  3.000
 CWD  C6    C5   CL5  122.01  3.000
 CWD  C6    C5   C4   120.19  3.000
 CWD  CL5   C5   C4   117.80  3.000
 CWD  H6    C6   C5   121.44  3.000
 CWD  H6    C6   N1   115.80  3.000
 CWD  C5    C6   N1   122.76  3.000
 CWD  H7A   C7   H7   107.65  3.000
 CWD  H7A   C7   C8   110.61  3.000
 CWD  H7    C7   C8   111.33  3.000
 CWD  H7A   C7   N1   108.17  3.000
 CWD  H7    C7   N1   107.82  3.000
 CWD  C8    C7   N1   111.12  3.000
 CWD  H8    C8   C9   106.82  3.000
 CWD  H8    C8   N8   107.78  3.000
 CWD  C9    C8   N8   109.76  3.000
 CWD  H8    C8   C7   107.97  3.000
 CWD  C9    C8   C7   108.35  3.000
 CWD  N8    C8   C7   115.79  3.000
 CWD  HN8A  N8   HN8  107.82  3.000
 CWD  HN8A  N8   C8   110.96  3.000
 CWD  HN8   N8   C8   111.83  3.000
 CWD  O92   C9   O91  123.89  3.000
 CWD  O92   C9   C8   111.46  3.000
 CWD  O91   C9   C8   124.65  3.000
 CWD  H81   O92  C9   110.29  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  C7   N1   C2  O2    0.00   0.0  0
 CWD  CONST_10  H81  O92  C9  C8  180.00   0.0  0
 CWD  Var_01    C8   C7   N1  C2   99.20  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
 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  CL5  0.020
 CWD  plan-1  C6   0.020
 CWD  plan-1  C7   0.020
 CWD  plan-1  HN3  0.020
 CWD  plan-1  H6   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
 CWD  plan-2  H81  0.020

