# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 08:57:55 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (5S)-5-[(2S)-2-amino-2-carboxyethyl]-4,5-dihydroisoxazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@H]1CC(=NO1)C(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
 DA3  DA3  '(5S)-5-[(2S)-2-amino-2-carboxyethyl]-4,5-dihydroisoxazole-3-carboxylic acid'  ligand  22  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DA3
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
 DA3  N1    N  NH2    0  -0.798   0.0175   1.6556   2.8627
 DA3  C2    C  CH1    0  -0.208  -0.3254   0.3589   2.3033
 DA3  C1    C  C      0   0.404  -0.1505  -0.7567   3.3575
 DA3  O1    O  O      0  -0.606   0.6126  -0.5270   4.3156
 DA3  O2    O  OC    -1  -0.622  -0.7662  -1.8193   3.1349
 DA3  O3    O  O      0  -0.416  -1.0296   0.9777  -0.5486
 DA3  O4    O  O      0  -0.587   1.2109  -1.0061  -3.8793
 DA3  N2    N  N      0  -0.108  -1.2005   0.2371  -1.6898
 DA3  C3    C  CH2    0  -0.448   0.4801  -0.0422   1.0553
 DA3  C4    C  CR15   0   0.006   0.3542   0.9051  -0.1259
 DA3  C5    C  CH2    0  -0.552   1.0825   0.4069  -1.3699
 DA3  C6    C  CR5    0   0.045  -0.0742  -0.1060  -2.1670
 DA3  C7    C  C      0   0.384   0.0465  -0.8985  -3.4542
 DA3  O5    O  OC    -1  -0.591  -1.0000  -1.3470  -3.9476
 DA3  HN11  H  HNH2   0   0.334   0.0067   2.3729   2.1487
 DA3  HN12  H  HNH2   0   0.327   0.9603   1.6188   3.2289
 DA3  H2    H  HCH1   0   0.211  -1.3839   0.3830   2.0248
 DA3  H31   H  HCH2   0   0.224   1.5425  -0.1037   1.3185
 DA3  H32   H  HCH2   0   0.227   0.1795  -1.0451   0.7350
 DA3  H4    H  HCR5   0   0.238   0.6574   1.9183   0.1479
 DA3  H51   H  HCH2   0   0.270   1.6014   1.1999  -1.9149
 DA3  H52   H  HCH2   0   0.265   1.8189  -0.3679  -1.1526

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
 DA3  N1  C2    single  1.453  0.020  1.453
 DA3  N1  HN11  single  0.890  0.020  1.040
 DA3  N1  HN12  single  0.890  0.020  1.040
 DA3  C2  C1    single  1.545  0.020  1.545
 DA3  C2  C3    single  1.539  0.020  1.539
 DA3  C2  H2    single  0.970  0.020  1.090
 DA3  C1  O1    deloc   1.246  0.020  1.246
 DA3  C1  O2    deloc   1.248  0.020  1.248
 DA3  O3  N2    single  1.371  0.020  1.371
 DA3  O3  C4    single  1.449  0.020  1.449
 DA3  O4  C7    deloc   1.244  0.020  1.244
 DA3  N2  C6    double  1.270  0.020  1.270
 DA3  C3  C4    single  1.519  0.020  1.519
 DA3  C3  H31   single  0.970  0.020  1.090
 DA3  C3  H32   single  0.970  0.020  1.090
 DA3  C4  C5    single  1.525  0.020  1.525
 DA3  C4  H4    single  0.970  0.020  1.090
 DA3  C5  C6    single  1.495  0.020  1.495
 DA3  C5  H51   single  0.970  0.020  1.090
 DA3  C5  H52   single  0.970  0.020  1.090
 DA3  C6  C7    single  1.516  0.020  1.516
 DA3  C7  O5    deloc   1.241  0.020  1.241

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
 DA3  HN12  N1  HN11  106.91  3.000
 DA3  HN12  N1  C2    109.06  3.000
 DA3  HN11  N1  C2    111.00  3.000
 DA3  H2    C2  C3    107.79  3.000
 DA3  H2    C2  C1    107.40  3.000
 DA3  C3    C2  C1    107.82  3.000
 DA3  H2    C2  N1    107.84  3.000
 DA3  C3    C2  N1    114.92  3.000
 DA3  C1    C2  N1    110.79  3.000
 DA3  O2    C1  O1    126.59  3.000
 DA3  O2    C1  C2    115.93  3.000
 DA3  O1    C1  C2    117.44  3.000
 DA3  C4    O3  N2    109.57  3.000
 DA3  C6    N2  O3    110.36  3.000
 DA3  H32   C3  H31   106.55  3.000
 DA3  H32   C3  C4    108.72  3.000
 DA3  H31   C3  C4    107.58  3.000
 DA3  H32   C3  C2    109.41  3.000
 DA3  H31   C3  C2    109.10  3.000
 DA3  C4    C3  C2    115.13  3.000
 DA3  H4    C4  C5    112.01  3.000
 DA3  H4    C4  C3    111.13  3.000
 DA3  C5    C4  C3    113.01  3.000
 DA3  H4    C4  O3    106.97  3.000
 DA3  C5    C4  O3    103.56  3.000
 DA3  C3    C4  O3    109.71  3.000
 DA3  H52   C5  H51   107.10  3.000
 DA3  H52   C5  C6    112.63  3.000
 DA3  H51   C5  C6    110.50  3.000
 DA3  H52   C5  C4    113.08  3.000
 DA3  H51   C5  C4    113.34  3.000
 DA3  C6    C5  C4    100.22  3.000
 DA3  C7    C6  C5    124.76  3.000
 DA3  C7    C6  N2    122.04  3.000
 DA3  C5    C6  N2    113.14  3.000
 DA3  O5    C7  C6    117.34  3.000
 DA3  O5    C7  O4    128.47  3.000
 DA3  C6    C7  O4    114.19  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
 DA3  Var_01  C5  C6  N2  O3   -0.86  30.0  1
 DA3  Var_02  C4  C5  C6  N2   11.23  30.0  1
 DA3  Var_03  N2  C6  C7  O4  171.13  30.0  2

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
 DA3  chir_01  C2  N1  C1  C3  positiv
 DA3  chir_02  C4  O3  C3  C5  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
 DA3  plan-1  C2  0.020
 DA3  plan-1  C1  0.020
 DA3  plan-1  O1  0.020
 DA3  plan-1  O2  0.020
 DA3  plan-2  O4  0.020
 DA3  plan-2  C6  0.020
 DA3  plan-2  C7  0.020
 DA3  plan-2  O5  0.020

