# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar  4 20:36:45 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S)-2-ammonio-4-[(2,4-dinitrophenyl)amino]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H](CCNc1ccc(cc1[N+]([O-])=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
 01W  01W  (2S)-2-ammonio-4-[(2,4-dinitrophenyl)amino]butanoate  L-peptide  32  20  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_01W
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
 01W  O52   O  O     -1  -0.387  -13.9087  38.8704  -21.2752
 01W  N5    N  N      1   0.320  -13.5582  38.9413  -20.1180
 01W  O5    O  O      0  -0.384  -13.9641  39.7780  -19.3418
 01W  C5    C  CR6    0   0.243  -12.6074  37.9788  -19.6293
 01W  C6    C  CR16   0  -0.246  -12.1797  38.0269  -18.2967
 01W  C7    C  CR16   0  -0.356  -11.2891  37.1047  -17.8342
 01W  C4    C  CR16   0  -0.342  -12.1239  37.0105  -20.4753
 01W  C3    C  CR6    0   0.208  -11.2119  36.0724  -20.0136
 01W  N3    N  N      1   0.348  -10.7606  35.1008  -20.9746
 01W  O32   O  O     -1  -0.410   -9.9391  34.2727  -20.6256
 01W  O3    O  O      0  -0.376  -11.2090  35.1382  -22.0965
 01W  C2    C  CR6    0   0.432  -10.7559  36.0747  -18.6583
 01W  N13   N  NH1    0  -0.658   -9.8885  35.1995  -18.1551
 01W  C1    C  CH2    0  -0.325   -9.4693  35.1359  -16.7712
 01W  CB    C  CH2    0  -0.466  -10.5069  34.4330  -15.8965
 01W  CA    C  CH1    0  -0.228  -10.0428  34.2662  -14.4516
 01W  N     N  NT3    1  -0.790  -11.0306  33.4248  -13.7175
 01W  C     C  C      0   0.453   -9.9654  35.6304  -13.7108
 01W  O     O  O      0  -0.580  -10.9605  35.9098  -13.0157
 01W  OXT   O  OC    -1  -0.564   -8.9480  36.2995  -13.9254
 01W  H6    H  HCR6   0   0.307  -12.5465  38.7870  -17.6221
 01W  H7    H  HCR6   0   0.302  -10.9821  37.1722  -16.8013
 01W  H4    H  HCR6   0   0.328  -12.4474  36.9737  -21.5047
 01W  HN13  H  HNH1   0   0.422   -9.5540  34.4766  -18.7714
 01W  H11   H  HCH2   0   0.283   -8.5357  34.5747  -16.7558
 01W  H21   H  HCH2   0   0.269   -9.2370  36.1311  -16.3986
 01W  H1B   H  HCH2   0   0.260  -11.4543  34.9795  -15.9134
 01W  H2B   H  HCH2   0   0.268  -10.7001  33.4477  -16.3305
 01W  HA    H  HCH1   0   0.294   -9.0846  33.7474  -14.4219
 01W  H1N   H  HNT3   0   0.466  -10.6007  32.9349  -12.9334
 01W  H2N   H  HNT3   0   0.447  -11.7269  34.0709  -13.3202
 01W  H3N   H  HNT3   0   0.461  -11.4947  32.7226  -14.2933

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
 01W  O3   N3    double    1.209  0.020  1.209
 01W  N3   O32   single    1.218  0.020  1.218
 01W  N3   C3    single    1.439  0.020  1.439
 01W  O52  N5    single    1.211  0.020  1.211
 01W  C4   C3    aromatic  1.387  0.020  1.387
 01W  C4   C5    aromatic  1.374  0.020  1.374
 01W  C3   C2    aromatic  1.430  0.020  1.430
 01W  N5   C5    single    1.439  0.020  1.439
 01W  N5   O5    double    1.211  0.020  1.211
 01W  C5   C6    aromatic  1.400  0.020  1.400
 01W  C2   N13   single    1.331  0.020  1.331
 01W  C2   C7    aromatic  1.423  0.020  1.423
 01W  N13  C1    single    1.447  0.020  1.447
 01W  C6   C7    aromatic  1.363  0.020  1.363
 01W  C1   CB    single    1.528  0.020  1.528
 01W  CB   CA    single    1.521  0.033  1.521
 01W  CA   C     single    1.525  0.021  1.525
 01W  CA   N     single    1.458  0.019  1.458
 01W  C    O     deloc     1.231  0.020  1.231
 01W  C    OXT   deloc     1.237  0.020  1.237
 01W  C6   H6    single    0.930  0.020  1.080
 01W  C7   H7    single    0.930  0.020  1.080
 01W  C4   H4    single    0.930  0.020  1.080
 01W  N13  HN13  single    0.860  0.020  1.020
 01W  C1   H11   single    0.970  0.020  1.090
 01W  C1   H21   single    0.970  0.020  1.090
 01W  CB   H1B   single    0.970  0.020  1.090
 01W  CB   H2B   single    0.970  0.020  1.090
 01W  CA   HA    single    0.970  0.020  0.970
 01W  N    H1N   single    0.890  0.020  1.040
 01W  N    H2N   single    0.890  0.020  1.040
 01W  N    H3N   single    0.890  0.020  1.040

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
 01W  C5    N5   O5   117.77  3.000
 01W  O5    N5   O52  123.76  3.000
 01W  C5    N5   O52  118.46  3.000
 01W  C4    C5   C6   120.18  3.000
 01W  C6    C5   N5   120.14  3.000
 01W  C4    C5   N5   119.67  3.000
 01W  H6    C6   C7   119.07  3.000
 01W  H6    C6   C5   120.98  3.000
 01W  C7    C6   C5   119.95  3.000
 01W  H7    C7   C2   119.52  3.000
 01W  H7    C7   C6   117.91  3.000
 01W  C2    C7   C6   122.56  3.000
 01W  H4    C4   C3   119.42  3.000
 01W  H4    C4   C5   120.38  3.000
 01W  C3    C4   C5   120.20  3.000
 01W  C2    C3   N3   122.27  3.000
 01W  C2    C3   C4   121.60  3.000
 01W  N3    C3   C4   116.13  3.000
 01W  O3    N3   O32  122.50  3.000
 01W  O32   N3   C3   118.65  3.000
 01W  O3    N3   C3   118.85  3.000
 01W  N13   C2   C3   124.41  3.000
 01W  N13   C2   C7   120.09  3.000
 01W  C3    C2   C7   115.50  3.000
 01W  HN13  N13  C1   117.22  3.000
 01W  HN13  N13  C2   117.20  3.000
 01W  C1    N13  C2   125.39  3.000
 01W  H21   C1   H11  106.47  3.000
 01W  H21   C1   CB   111.70  3.000
 01W  H11   C1   CB   109.69  3.000
 01W  H21   C1   N13  110.43  3.000
 01W  H11   C1   N13  106.52  3.000
 01W  CB    C1   N13  111.77  3.000
 01W  H2B   CB   H1B  106.91  3.000
 01W  H2B   CB   CA   109.31  3.000
 01W  H1B   CB   CA   109.42  3.000
 01W  H2B   CB   C1   107.88  3.000
 01W  H1B   CB   C1   110.45  3.000
 01W  CA    CB   C1   112.68  3.000
 01W  HA    CA   C    110.00  3.000
 01W  HA    CA   N    110.00  3.000
 01W  C     CA   N    111.00  2.800
 01W  HA    CA   CB   109.00  3.000
 01W  N     CA   CB   110.40  1.500
 01W  C     CA   CB   110.50  1.500
 01W  H3N   N    H2N  110.01  3.000
 01W  H3N   N    H1N  107.18  3.000
 01W  H2N   N    H1N  106.85  3.000
 01W  H3N   N    CA   114.33  3.000
 01W  H2N   N    CA   106.50  3.000
 01W  H1N   N    CA   111.74  3.000
 01W  OXT   C    O    129.26  3.000
 01W  OXT   C    CA   120.80  1.700
 01W  O     C    CA   120.80  1.700

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
 01W  CONST_01  C2    C3   C4   C5     0.00   0.0  0
 01W  CONST_02  C2    C7   C6   C5     0.00   0.0  0
 01W  CONST_03  C3    C4   C5   C6     0.00   0.0  0
 01W  CONST_04  C3    C2   C7   C6     0.00   0.0  0
 01W  CONST_05  C4    C3   C2   C7     0.00   0.0  0
 01W  CONST_06  C4    C5   C6   C7     0.00   0.0  0
 01W  CONST_07  C3    C4   C5   N5   180.00   0.0  0
 01W  CONST_08  C7    C6   C5   N5   180.00   0.0  0
 01W  CONST_09  N3    C3   C4   C5   180.00   0.0  0
 01W  CONST_10  N13   C2   C7   C6   180.00   0.0  0
 01W  CONST_11  N3    C3   C2   C7   180.00   0.0  0
 01W  CONST_12  N13   C2   C3   C4   180.00   0.0  0
 01W  CONST_13  H7    C7   C6   C5   180.00   0.0  0
 01W  CONST_14  H4    C4   C5   C6   180.00   0.0  0
 01W  CONST_15  H6    C6   C5   C4   180.00   0.0  0
 01W  CONST_16  C4    C5   N5   O52    0.00   0.0  0
 01W  CONST_17  C6    C5   N5   O52  180.00   0.0  0
 01W  CONST_18  C4    C5   N5   O5   180.00   0.0  0
 01W  CONST_19  C6    C5   N5   O5     0.00   0.0  0
 01W  CONST_20  C1    N13  C2   C7     0.00   0.0  0
 01W  CONST_21  O3    N3   C3   C4     0.00   0.0  0
 01W  CONST_22  O32   N3   C3   C4   180.00   0.0  0
 01W  CONST_23  C1    N13  C2   C3   180.00   0.0  0
 01W  CONST_24  C2    C3   N3   O32    0.00   0.0  0
 01W  CONST_25  C2    C3   N3   O3   180.00   0.0  0
 01W  CONST_26  HN13  N13  C2   C7   180.00   0.0  0
 01W  Var_01    CB    C1   N13  C2    79.46  30.0  3
 01W  Var_02    CA    CB   C1   N13  175.93  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
 01W  chir_01  CA  CB  C  N  negativ

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
 01W  plan-1  N5    0.020
 01W  plan-1  C5    0.020
 01W  plan-1  C6    0.020
 01W  plan-1  C7    0.020
 01W  plan-1  C4    0.020
 01W  plan-1  C3    0.020
 01W  plan-1  N3    0.020
 01W  plan-1  C2    0.020
 01W  plan-1  N13   0.020
 01W  plan-1  H6    0.020
 01W  plan-1  H7    0.020
 01W  plan-1  H4    0.020
 01W  plan-2  O52   0.020
 01W  plan-2  N5    0.020
 01W  plan-2  O5    0.020
 01W  plan-2  C5    0.020
 01W  plan-3  C3    0.020
 01W  plan-3  N3    0.020
 01W  plan-3  O32   0.020
 01W  plan-3  O3    0.020
 01W  plan-4  C2    0.020
 01W  plan-4  N13   0.020
 01W  plan-4  C1    0.020
 01W  plan-4  HN13  0.020
 01W  plan-5  CA    0.020
 01W  plan-5  C     0.020
 01W  plan-5  O     0.020
 01W  plan-5  OXT   0.020

