# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 15:28:23 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 3-(5-nitro-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(C(=O)NC1=O)[N+]([O-])=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
 NWD  NWD  3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine  L-peptide  25  17  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NWD
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
 NWD  N1    N  NR6    0  -0.518  -0.2189  -0.3201  -0.5421
 NWD  O1    O  O      0  -0.400   2.4465   2.5293   0.2489
 NWD  C2    C  CR6    0   0.743   0.1063  -1.6775  -0.5650
 NWD  N2    N  N      1   0.348   2.9067   1.4069   0.2273
 NWD  O2    O  O      0  -0.439  -0.7032  -2.5364  -0.8116
 NWD  N3    N  NR16   0  -0.736   1.4168  -1.9425  -0.2888
 NWD  O3    O  O     -1  -0.371   4.0743   1.1574   0.4019
 NWD  C4    C  CR6    0   0.568   2.4550  -1.0669  -0.0022
 NWD  O4    O  O      0  -0.412   3.5607  -1.4935   0.2269
 NWD  C5    C  CR6    0   0.011   2.0087   0.3189  -0.0220
 NWD  C6    C  CR16   0   0.101   0.7079   0.6093  -0.2830
 NWD  C7    C  CH2    0  -0.355  -1.5986   0.0950  -0.7925
 NWD  C8    C  CH1    0  -0.229  -2.3411   0.3753   0.5334
 NWD  N8    N  NH2    0  -0.778  -2.3410  -0.6912   1.4941
 NWD  C9    C  C      0   0.557  -3.7715   0.7701   0.2008
 NWD  O91   O  O      0  -0.422  -4.7455   0.1556   0.5434
 NWD  O92   O  OH1    0  -0.592  -3.8100   1.8742  -0.5328
 NWD  HN3   H  HNR6   0   0.443   1.6664  -2.9254  -0.2945
 NWD  H6    H  HCR6   0   0.361   0.3621   1.6339  -0.3009
 NWD  H7    H  HCH2   0   0.305  -1.5653   0.9793  -1.4259
 NWD  H7A   H  HCH2   0   0.307  -2.0908  -0.6960  -1.3534
 NWD  H8    H  HCH1   0   0.299  -1.8722   1.2482   1.0021
 NWD  HN8   H  HNH2   0   0.356  -2.6427  -1.5682   1.0912
 NWD  HN8A  H  HNH2   0   0.364  -1.4231  -0.8262   1.8934
 NWD  H81   H  HOH1   0   0.487  -4.7262   2.1011  -0.7546

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
 NWD  N1   C2    single  1.396  0.020  1.396
 NWD  N1   C6    single  1.338  0.020  1.338
 NWD  N1   C7    single  1.462  0.020  1.462
 NWD  O1   N2    double  1.213  0.020  1.213
 NWD  C2   O2    double  1.206  0.020  1.206
 NWD  C2   N3    single  1.365  0.020  1.365
 NWD  N2   O3    single  1.207  0.020  1.207
 NWD  N2   C5    single  1.433  0.020  1.433
 NWD  N3   C4    single  1.388  0.020  1.388
 NWD  N3   HN3   single  0.860  0.020  1.020
 NWD  C4   O4    double  1.207  0.020  1.207
 NWD  C4   C5    single  1.456  0.020  1.456
 NWD  C5   C6    double  1.358  0.020  1.358
 NWD  C6   H6    single  0.930  0.020  1.080
 NWD  C7   C8    single  1.545  0.020  1.545
 NWD  C7   H7    single  0.970  0.020  1.090
 NWD  C7   H7A   single  0.970  0.020  1.090
 NWD  C8   N8    single  1.435  0.020  1.435
 NWD  C8   C9    single  1.521  0.020  1.521
 NWD  C8   H8    single  0.970  0.020  1.090
 NWD  N8   HN8   single  0.890  0.020  1.040
 NWD  N8   HN8A  single  0.890  0.020  1.040
 NWD  C9   O91   double  1.201  0.020  1.201
 NWD  C9   O92   single  1.326  0.020  1.326
 NWD  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
 NWD  C7    N1   C6   119.31  3.000
 NWD  C7    N1   C2   119.54  3.000
 NWD  C6    N1   C2   121.15  3.000
 NWD  N3    C2   O2   123.20  3.000
 NWD  N3    C2   N1   114.15  3.000
 NWD  O2    C2   N1   122.65  3.000
 NWD  C5    N2   O3   118.33  3.000
 NWD  C5    N2   O1   117.90  3.000
 NWD  O3    N2   O1   123.76  3.000
 NWD  HN3   N3   C4   115.37  3.000
 NWD  HN3   N3   C2   115.04  3.000
 NWD  C4    N3   C2   129.59  3.000
 NWD  C5    C4   O4   128.30  3.000
 NWD  C5    C4   N3   111.62  3.000
 NWD  O4    C4   N3   120.09  3.000
 NWD  C6    C5   C4   119.98  3.000
 NWD  C6    C5   N2   118.13  3.000
 NWD  C4    C5   N2   121.90  3.000
 NWD  H6    C6   C5   120.79  3.000
 NWD  H6    C6   N1   115.68  3.000
 NWD  C5    C6   N1   123.52  3.000
 NWD  H7A   C7   H7   107.74  3.000
 NWD  H7A   C7   C8   110.92  3.000
 NWD  H7    C7   C8   111.52  3.000
 NWD  H7A   C7   N1   107.99  3.000
 NWD  H7    C7   N1   107.55  3.000
 NWD  C8    C7   N1   110.97  3.000
 NWD  H8    C8   C9   106.81  3.000
 NWD  H8    C8   N8   107.79  3.000
 NWD  C9    C8   N8   109.84  3.000
 NWD  H8    C8   C7   107.81  3.000
 NWD  C9    C8   C7   108.14  3.000
 NWD  N8    C8   C7   116.07  3.000
 NWD  HN8A  N8   HN8  108.23  3.000
 NWD  HN8A  N8   C8   111.34  3.000
 NWD  HN8   N8   C8   112.19  3.000
 NWD  O92   C9   O91  124.06  3.000
 NWD  O92   C9   C8   111.37  3.000
 NWD  O91   C9   C8   124.56  3.000
 NWD  H81   O92  C9   110.41  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
 NWD  CONST_01  C4   N3   C2  N1     0.00   0.0  0
 NWD  CONST_02  C5   C4   N3  C2     0.00   0.0  0
 NWD  CONST_03  C6   N1   C2  N3     0.00   0.0  0
 NWD  CONST_04  O4   C4   N3  C2   180.00   0.0  0
 NWD  CONST_05  C6   N1   C2  O2   180.00   0.0  0
 NWD  CONST_06  C4   N3   C2  O2   180.00   0.0  0
 NWD  CONST_07  C7   N1   C2  N3   180.00   0.0  0
 NWD  CONST_08  HN3  N3   C2  N1   180.00   0.0  0
 NWD  CONST_09  C7   N1   C2  O2     0.00   0.0  0
 NWD  CONST_10  H81  O92  C9  C8   180.00   0.0  0
 NWD  Var_01    C4   C5   N2  O1  -176.94  30.0  2
 NWD  Var_02    C8   C7   N1  C2    98.92  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
 NWD  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
 NWD  plan-1  N1   0.020
 NWD  plan-1  C2   0.020
 NWD  plan-1  N2   0.020
 NWD  plan-1  O2   0.020
 NWD  plan-1  N3   0.020
 NWD  plan-1  C4   0.020
 NWD  plan-1  O4   0.020
 NWD  plan-1  C5   0.020
 NWD  plan-1  C6   0.020
 NWD  plan-1  C7   0.020
 NWD  plan-1  HN3  0.020
 NWD  plan-1  H6   0.020
 NWD  plan-2  C8   0.020
 NWD  plan-2  C9   0.020
 NWD  plan-2  O91  0.020
 NWD  plan-2  O92  0.020
 NWD  plan-2  H81  0.020
 NWD  plan-3  O1   0.020
 NWD  plan-3  N2   0.020
 NWD  plan-3  O3   0.020
 NWD  plan-3  C5   0.020

