# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:49:24 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  24  17  .  2022-07-22  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_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  -0.514  -0.1986  -0.3237  -0.5690
 NWD  O1    O  O      0  -0.404   2.4742   2.5407   0.1327
 NWD  C2    C  CR6    0   0.733   0.1280  -1.6792  -0.5673
 NWD  N2    N  N      1   0.347   2.9187   1.4135   0.2055
 NWD  O2    O  O      0  -0.440  -0.6772  -2.5461  -0.8021
 NWD  N3    N  NR16   0  -0.735   1.4388  -1.9403  -0.2816
 NWD  O3    O  O     -1  -0.376   4.0693   1.1648   0.4747
 NWD  C4    C  CR6    0   0.565   2.4752  -1.0610  -0.0031
 NWD  O4    O  O      0  -0.417   3.5825  -1.4851   0.2284
 NWD  C5    C  CR6    0   0.006   2.0268   0.3226  -0.0409
 NWD  C6    C  CR16   0   0.100   0.7247   0.6063  -0.3155
 NWD  C7    C  CH2    0  -0.345  -1.5876   0.0911  -0.8089
 NWD  C8    C  CH1    0  -0.230  -2.3315   0.4162   0.4986
 NWD  N8    N  NH2    0  -0.780  -2.2960  -0.6168   1.5055
 NWD  C9    C  C      0   0.415  -3.7817   0.7917   0.0960
 NWD  O91   O  O      0  -0.589  -4.6968   0.0553   0.4985
 NWD  O92   O  OC    -1  -0.614  -3.8841   1.7971  -0.6347
 NWD  HN3   H  HNR6   0   0.440   1.6884  -2.9230  -0.2741
 NWD  H6    H  HCR6   0   0.357   0.3764   1.6298  -0.3453
 NWD  H7    H  HCH2   0   0.283  -1.5598   0.9611  -1.4614
 NWD  H7A   H  HCH2   0   0.284  -2.0791  -0.7153  -1.3485
 NWD  H8    H  HCH1   0   0.238  -1.8646   1.3120   0.9262
 NWD  HN8   H  HNH2   0   0.337  -2.7266  -1.4663   1.1656
 NWD  HN8A  H  HNH2   0   0.338  -1.3483  -0.8399   1.7804

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  1.394  0.020  1.394
 NWD  N1  C6    single  1.335  0.020  1.335
 NWD  N1  C7    single  1.469  0.020  1.469
 NWD  O1  N2    double  1.214  0.020  1.214
 NWD  C2  O2    double  1.206  0.020  1.206
 NWD  C2  N3    single  1.367  0.020  1.367
 NWD  N2  O3    single  1.208  0.020  1.208
 NWD  N2  C5    single  1.430  0.020  1.430
 NWD  N3  C4    single  1.387  0.020  1.387
 NWD  N3  HN3   single  0.860  0.020  1.020
 NWD  C4  O4    double  1.208  0.020  1.208
 NWD  C4  C5    single  1.455  0.020  1.455
 NWD  C5  C6    double  1.361  0.020  1.361
 NWD  C6  H6    single  0.930  0.020  1.080
 NWD  C7  C8    single  1.539  0.020  1.539
 NWD  C7  H7    single  0.970  0.020  1.090
 NWD  C7  H7A   single  0.970  0.020  1.090
 NWD  C8  N8    single  1.443  0.020  1.443
 NWD  C8  C9    single  1.551  0.020  1.551
 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   deloc   1.242  0.020  1.242
 NWD  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
 NWD  C7    N1  C6   119.23  3.000
 NWD  C7    N1  C2   119.74  3.000
 NWD  C6    N1  C2   121.00  3.000
 NWD  N3    C2  O2   122.93  3.000
 NWD  N3    C2  N1   114.25  3.000
 NWD  O2    C2  N1   122.82  3.000
 NWD  C5    N2  O3   118.39  3.000
 NWD  C5    N2  O1   118.01  3.000
 NWD  O3    N2  O1   123.61  3.000
 NWD  HN3   N3  C4   115.39  3.000
 NWD  HN3   N3  C2   115.02  3.000
 NWD  C4    N3  C2   129.59  3.000
 NWD  C5    C4  O4   128.41  3.000
 NWD  C5    C4  N3   111.55  3.000
 NWD  O4    C4  N3   120.04  3.000
 NWD  C6    C5  C4   119.90  3.000
 NWD  C6    C5  N2   118.19  3.000
 NWD  C4    C5  N2   121.91  3.000
 NWD  H6    C6  C5   120.73  3.000
 NWD  H6    C6  N1   115.56  3.000
 NWD  C5    C6  N1   123.71  3.000
 NWD  H7A   C7  H7   107.88  3.000
 NWD  H7A   C7  C8   111.08  3.000
 NWD  H7    C7  C8   110.67  3.000
 NWD  H7A   C7  N1   107.39  3.000
 NWD  H7    C7  N1   107.43  3.000
 NWD  C8    C7  N1   112.20  3.000
 NWD  H8    C8  C9   107.55  3.000
 NWD  H8    C8  N8   107.59  3.000
 NWD  C9    C8  N8   112.17  3.000
 NWD  H8    C8  C7   107.33  3.000
 NWD  C9    C8  C7   106.41  3.000
 NWD  N8    C8  C7   115.45  3.000
 NWD  HN8A  N8  HN8  107.76  3.000
 NWD  HN8A  N8  C8   111.75  3.000
 NWD  HN8   N8  C8   110.88  3.000
 NWD  O92   C9  O91  127.41  3.000
 NWD  O92   C9  C8   115.08  3.000
 NWD  O91   C9  C8   117.47  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  Var_01    C4   C5  N2  O1  178.73  30.0  2
 NWD  Var_02    C8   C7  N1  C2   99.32  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-3  O1   0.020
 NWD  plan-3  N2   0.020
 NWD  plan-3  O3   0.020
 NWD  plan-3  C5   0.020

