# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 07:47:21 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (1S,9S)-9-amino-6,10-dioxooctahydro-6H-pyridazino[1,2-a][1,2]diazepine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCC(=O)N2CCC[C@H](N2C1=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
 ODA  ODA  '(1S,9S)-9-amino-6,10-dioxooctahydro-6H-pyridazino[1,2-a][1,2]diazepine-1-carboxylic acid'  peptide  31  17  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ODA
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
 ODA  N     N  NH2    0  -0.774  19.8593  33.3594  27.9767
 ODA  CA    C  CH1    0  -0.227  19.2203  32.0665  27.9240
 ODA  CB    C  CH2    0  -0.416  17.8066  32.2168  27.3391
 ODA  CG    C  CH2    0  -0.606  17.1458  30.8928  26.9344
 ODA  CD    C  C      0   0.534  17.3301  29.8310  27.9892
 ODA  OE1   O  O      0  -0.474  16.4270  29.4383  28.7085
 ODA  NE2   N  NT     0  -0.325  18.6144  29.4160  28.1759
 ODA  C     C  C      0   0.512  19.9996  31.0254  27.1165
 ODA  O     O  O      0  -0.473  20.8814  31.3421  26.3348
 ODA  N2    N  NT     0  -0.308  19.6033  29.7382  27.2716
 ODA  CA2   C  CH1    0  -0.237  20.2488  28.6048  26.6200
 ODA  CB2   C  CH2    0  -0.436  20.7893  27.6683  27.7020
 ODA  CG2   C  CH2    0  -0.457  19.6890  27.2811  28.6817
 ODA  CD2   C  CH2    0  -0.284  19.0352  28.5317  29.2496
 ODA  C2    C  C      0   0.428  19.3362  27.8675  25.6019
 ODA  O2    O  O      0  -0.575  18.2066  28.3341  25.3755
 ODA  OXT   O  OC    -1  -0.596  19.8599  26.8647  25.0834
 ODA  H     H  HNH2   0   0.349  20.7441  33.2911  28.4636
 ODA  H2    H  HNH2   0   0.340  20.0821  33.6696  27.0382
 ODA  HA1   H  HCH1   0   0.268  19.1328  31.7035  28.9522
 ODA  HB2   H  HCH2   0   0.250  17.1925  32.7409  28.0728
 ODA  HB3   H  HCH2   0   0.245  17.8554  32.8568  26.4542
 ODA  HG2   H  HCH2   0   0.265  16.0769  31.0458  26.7924
 ODA  HG3   H  HCH2   0   0.283  17.5528  30.5331  25.9911
 ODA  HA2   H  HCH1   0   0.268  21.0912  29.0126  26.0604
 ODA  HB23  H  HCH2   0   0.243  21.2242  26.7880  27.2319
 ODA  HB22  H  HCH2   0   0.225  21.5935  28.1730  28.2466
 ODA  HG23  H  HCH2   0   0.232  18.9347  26.6627  28.1871
 ODA  HG22  H  HCH2   0   0.244  20.0954  26.6882  29.5033
 ODA  HD22  H  HCH2   0   0.240  19.7462  29.0711  29.8839
 ODA  HD23  H  HCH2   0   0.264  18.1651  28.2904  29.8537

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
 ODA  N    CA    single  1.458  0.019  1.458
 ODA  N    H     single  0.860  0.020  0.860
 ODA  N    H2    single  0.890  0.020  1.040
 ODA  CA   CB    single  1.521  0.033  1.521
 ODA  CA   C     single  1.525  0.021  1.525
 ODA  CA   HA1   single  0.970  0.020  1.090
 ODA  CB   CG    single  1.534  0.020  1.534
 ODA  CB   HB2   single  0.970  0.020  1.090
 ODA  CB   HB3   single  0.970  0.020  1.090
 ODA  CG   CD    single  1.508  0.020  1.508
 ODA  CG   HG2   single  0.970  0.020  1.090
 ODA  CG   HG3   single  0.970  0.020  1.090
 ODA  CD   OE1   double  1.220  0.020  1.220
 ODA  CD   NE2   single  1.363  0.020  1.363
 ODA  NE2  N2    single  1.378  0.020  1.378
 ODA  NE2  CD2   single  1.453  0.020  1.453
 ODA  C    O     double  1.231  0.020  1.231
 ODA  C    N2    single  1.356  0.020  1.356
 ODA  N2   CA2   single  1.458  0.020  1.458
 ODA  CA2  CB2   single  1.530  0.020  1.530
 ODA  CA2  C2    single  1.553  0.020  1.553
 ODA  CA2  HA2   single  0.970  0.020  1.090
 ODA  CB2  CG2   single  1.523  0.020  1.523
 ODA  CB2  HB23  single  0.970  0.020  1.090
 ODA  CB2  HB22  single  0.970  0.020  1.090
 ODA  CG2  CD2   single  1.521  0.020  1.521
 ODA  CG2  HG23  single  0.970  0.020  1.090
 ODA  CG2  HG22  single  0.970  0.020  1.090
 ODA  CD2  HD22  single  0.970  0.020  1.090
 ODA  CD2  HD23  single  0.970  0.020  1.090
 ODA  C2   O2    deloc   1.243  0.020  1.243
 ODA  C2   OXT   deloc   1.244  0.020  1.244

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
 ODA  H2    N    H     105.90  3.000
 ODA  H2    N    CA    109.74  3.000
 ODA  H     N    CA    114.00  3.000
 ODA  HA1   CA   C     108.11  3.000
 ODA  HA1   CA   CB    108.45  3.000
 ODA  C     CA   CB    110.50  1.500
 ODA  HA1   CA   N     107.36  3.000
 ODA  C     CA   N     111.00  2.800
 ODA  CB    CA   N     110.40  1.500
 ODA  HB3   CB   HB2   106.75  3.000
 ODA  HB3   CB   CG    108.12  3.000
 ODA  HB2   CB   CG    110.46  3.000
 ODA  HB3   CB   CA    108.91  3.000
 ODA  HB2   CB   CA    107.98  3.000
 ODA  CG    CB   CA    114.34  3.000
 ODA  HG3   CG   HG2   107.47  3.000
 ODA  HG3   CG   CD    109.14  3.000
 ODA  HG2   CG   CD    108.06  3.000
 ODA  HG3   CG   CB    110.66  3.000
 ODA  HG2   CG   CB    109.63  3.000
 ODA  CD    CG   CB    111.75  3.000
 ODA  NE2   CD   OE1   121.27  3.000
 ODA  NE2   CD   CG    115.18  3.000
 ODA  OE1   CD   CG    123.29  3.000
 ODA  CD2   NE2  N2    114.79  3.000
 ODA  CD2   NE2  CD    124.02  3.000
 ODA  N2    NE2  CD    121.01  3.000
 ODA  N2    C    O     122.06  3.000
 ODA  N2    C    CA    115.89  3.000
 ODA  O     C    CA    120.80  1.700
 ODA  CA2   N2   C     123.89  3.000
 ODA  CA2   N2   NE2   115.42  3.000
 ODA  C     N2   NE2   120.44  3.000
 ODA  HA2   CA2  C2    107.16  3.000
 ODA  HA2   CA2  CB2   108.61  3.000
 ODA  C2    CA2  CB2   112.37  3.000
 ODA  HA2   CA2  N2    106.30  3.000
 ODA  C2    CA2  N2    113.69  3.000
 ODA  CB2   CA2  N2    108.44  3.000
 ODA  HB22  CB2  HB23  107.11  3.000
 ODA  HB22  CB2  CG2   109.14  3.000
 ODA  HB23  CB2  CG2   111.15  3.000
 ODA  HB22  CB2  CA2   109.22  3.000
 ODA  HB23  CB2  CA2   109.31  3.000
 ODA  CG2   CB2  CA2   110.82  3.000
 ODA  HG22  CG2  HG23  106.86  3.000
 ODA  HG22  CG2  CD2   108.99  3.000
 ODA  HG23  CG2  CD2   109.71  3.000
 ODA  HG22  CG2  CB2   110.69  3.000
 ODA  HG23  CG2  CB2   110.55  3.000
 ODA  CD2   CG2  CB2   109.97  3.000
 ODA  HD23  CD2  HD22  107.91  3.000
 ODA  HD23  CD2  CG2   111.67  3.000
 ODA  HD22  CD2  CG2   110.01  3.000
 ODA  HD23  CD2  NE2   108.31  3.000
 ODA  HD22  CD2  NE2   108.44  3.000
 ODA  CG2   CD2  NE2   110.41  3.000
 ODA  OXT   C2   O2    127.52  3.000
 ODA  OXT   C2   CA2   114.10  3.000
 ODA  O2    C2   CA2   118.37  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
 ODA  Var_01  CB2  CG2  CD2  NE2   52.20  30.0  1
 ODA  Var_02  CD2  CG2  CB2  CA2  -54.31  30.0  1

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
 ODA  chir_01  CA   N   CB   C   negativ
 ODA  chir_02  CA2  N2  CB2  C2  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
 ODA  plan-1  CG   0.020
 ODA  plan-1  CD   0.020
 ODA  plan-1  OE1  0.020
 ODA  plan-1  NE2  0.020
 ODA  plan-1  N2   0.020
 ODA  plan-1  CD2  0.020
 ODA  plan-2  CA   0.020
 ODA  plan-2  NE2  0.020
 ODA  plan-2  C    0.020
 ODA  plan-2  O    0.020
 ODA  plan-2  N2   0.020
 ODA  plan-2  CA2  0.020
 ODA  plan-3  CA2  0.020
 ODA  plan-3  C2   0.020
 ODA  plan-3  O2   0.020
 ODA  plan-3  OXT  0.020

