# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Nov 14 07:49:16 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (3S)-3-amino-N-cyclopropyl-2-oxohexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](N)C(=O)C(=O)NC1CC1
#
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
 03A  03A  "(3S)-3-amino-N-cyclopropyl-2-oxohexanamide"  ligand  29  13  .  2022-11-14  2022-11-14
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_03A
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
 03A  NAA   N  NH1   0  -0.631   1.9667  -0.0100  -0.6152
 03A  NAE   N  NH2   0  -0.775  -2.4331   1.9549   0.2188
 03A  CAH   C  CH1   0  -0.193  -1.5994   0.7809   0.3248
 03A  CAI   C  C     0   0.271  -0.2359   0.9327  -0.3210
 03A  CAJ   C  CH2   0  -0.425  -2.2879  -0.4335  -0.3198
 03A  CAK   C  CH2   0  -0.416  -3.5896  -0.8179   0.3726
 03A  CAL   C  CH3   0  -0.665  -4.2684  -2.0018  -0.3018
 03A  CAM   C  C     0   0.476   0.8592  -0.0516   0.1274
 03A  CAN   C  CH1   0  -0.084   3.0908  -0.8492  -0.3572
 03A  CAO   C  CH2   0  -0.512   4.4505  -0.2771  -0.5832
 03A  CAP   C  CH2   0  -0.483   3.9732  -0.5450   0.8116
 03A  OBS   O  O     0  -0.461   0.6879  -0.7817   1.0891
 03A  HNAA  H  HNH1  0   0.409   1.9934   0.6141  -1.4073
 03A  H2    H  HNH2  0   0.343  -2.5370   2.2254  -0.7519
 03A  HAH   H  HCH1  0   0.262  -1.4459   0.5568   1.3843
 03A  OBR   O  O     0  -0.358   0.0111   1.7639  -1.1598
 03A  HAJ   H  HCH2  0   0.227  -2.4806  -0.2087  -1.3749
 03A  HAJA  H  HCH2  0   0.239  -1.6118  -1.2922  -0.3069
 03A  HAK   H  HCH2  0   0.215  -3.3803  -1.0598   1.4189
 03A  HAKA  H  HCH2  0   0.225  -4.2639   0.0397   0.3825
 03A  HAL   H  HCH3  0   0.218  -4.5368  -1.7682  -1.3337
 03A  HALA  H  HCH3  0   0.217  -3.6177  -2.8781  -0.3211
 03A  HALB  H  HCH3  0   0.229  -5.1840  -2.2826   0.2197
 03A  HAN   H  HCH1  0   0.276   2.9408  -1.8946  -0.6068
 03A  HAO   H  HCH2  0   0.263   5.2020  -0.9260  -1.0123
 03A  HAOA  H  HCH2  0   0.262   4.5142   0.7553  -0.9044
 03A  HAP   H  HCH2  0   0.259   3.7128   0.3068   1.4261
 03A  HAPA  H  HCH2  0   0.258   4.3931  -1.3824   1.3529
 03A  HNAE  H  HNH2  0   0.354  -2.0016   2.7401   0.6898

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
 03A  NAA  CAM   single  1.334  0.020  1.465
 03A  CAH  NAE   single  1.444  0.020  1.451
 03A  CAH  CAI   single  1.516  0.020  1.531
 03A  CAH  CAJ   single  1.538  0.020  1.534
 03A  CAK  CAJ   single  1.524  0.020  1.547
 03A  CAK  CAL   single  1.522  0.020  1.544
 03A  CAM  CAI   single  1.539  0.020  1.540
 03A  CAM  OBS   double  1.220  0.020  1.188
 03A  CAN  NAA   single  1.426  0.020  1.467
 03A  CAO  CAN   single  1.492  0.020  1.532
 03A  CAP  CAN   single  1.496  0.020  1.532
 03A  CAP  CAO   single  1.498  0.020  1.532
 03A  NAA  HNAA  single  0.860  0.020  1.020
 03A  NAE  HNAE  single  0.890  0.020  1.040
 03A  NAE  H2    single  0.890  0.020  1.040
 03A  CAH  HAH   single  0.970  0.020  1.090
 03A  CAI  OBR   double  1.206  0.020  1.189
 03A  CAJ  HAJ   single  0.970  0.020  1.090
 03A  CAJ  HAJA  single  0.970  0.020  1.090
 03A  CAK  HAK   single  0.970  0.020  1.090
 03A  CAK  HAKA  single  0.970  0.020  1.090
 03A  CAL  HAL   single  0.970  0.020  1.090
 03A  CAL  HALA  single  0.970  0.020  1.090
 03A  CAL  HALB  single  0.970  0.020  1.090
 03A  CAN  HAN   single  0.970  0.020  1.090
 03A  CAO  HAO   single  0.970  0.020  1.090
 03A  CAO  HAOA  single  0.970  0.020  1.090
 03A  CAP  HAP   single  0.970  0.020  1.090
 03A  CAP  HAPA  single  0.970  0.020  1.090

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
 03A  HNAA  NAA  CAN   119.02  3.000
 03A  HNAA  NAA  CAM   118.58  3.000
 03A  CAN   NAA  CAM   122.36  3.000
 03A  H2    NAE  HNAE  106.40  3.000
 03A  H2    NAE  CAH   110.28  3.000
 03A  HNAE  NAE  CAH   110.51  3.000
 03A  HAH   CAH  CAJ   107.88  3.000
 03A  HAH   CAH  CAI   107.87  3.000
 03A  CAJ   CAH  CAI   107.65  3.000
 03A  HAH   CAH  NAE   108.59  3.000
 03A  CAJ   CAH  NAE   110.66  3.000
 03A  CAI   CAH  NAE   113.99  3.000
 03A  OBR   CAI  CAM   119.83  3.000
 03A  OBR   CAI  CAH   123.31  3.000
 03A  CAM   CAI  CAH   116.85  3.000
 03A  HAJA  CAJ  HAJ   106.33  3.000
 03A  HAJA  CAJ  CAK   108.96  3.000
 03A  HAJ   CAJ  CAK   109.82  3.000
 03A  HAJA  CAJ  CAH   109.79  3.000
 03A  HAJ   CAJ  CAH   108.68  3.000
 03A  CAK   CAJ  CAH   113.03  3.000
 03A  HAKA  CAK  HAK   106.46  3.000
 03A  HAKA  CAK  CAL   109.86  3.000
 03A  HAK   CAK  CAL   109.70  3.000
 03A  HAKA  CAK  CAJ   109.50  3.000
 03A  HAK   CAK  CAJ   109.08  3.000
 03A  CAL   CAK  CAJ   112.07  3.000
 03A  HALB  CAL  HALA  107.59  3.000
 03A  HALB  CAL  HAL   107.50  3.000
 03A  HALA  CAL  HAL   107.56  3.000
 03A  HALB  CAL  CAK   111.27  3.000
 03A  HALA  CAL  CAK   111.49  3.000
 03A  HAL   CAL  CAK   111.23  3.000
 03A  OBS   CAM  CAI   120.84  3.000
 03A  OBS   CAM  NAA   125.04  3.000
 03A  CAI   CAM  NAA   114.12  3.000
 03A  HAN   CAN  CAP   117.21  3.000
 03A  HAN   CAN  CAO   117.41  3.000
 03A  CAP   CAN  CAO    60.19  3.000
 03A  HAN   CAN  NAA   114.60  3.000
 03A  CAP   CAN  NAA   119.12  3.000
 03A  CAO   CAN  NAA   117.72  3.000
 03A  HAOA  CAO  HAO   114.42  3.000
 03A  HAOA  CAO  CAP   117.73  3.000
 03A  HAO   CAO  CAP   118.90  3.000
 03A  HAOA  CAO  CAN   117.64  3.000
 03A  HAO   CAO  CAN   117.59  3.000
 03A  CAP   CAO  CAN    60.02  3.000
 03A  HAPA  CAP  HAP   114.74  3.000
 03A  HAPA  CAP  CAO   118.72  3.000
 03A  HAP   CAP  CAO   117.68  3.000
 03A  HAPA  CAP  CAN   117.55  3.000
 03A  HAP   CAP  CAN   117.51  3.000
 03A  CAO   CAP  CAN    59.79  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
 03A  CONST_01  CAN   NAA  CAM  CAI   180.00   0.0  0
 03A  CONST_02  OBS   CAM  NAA  CAN     0.00   0.0  0
 03A  CONST_03  HNAA  NAA  CAM  CAI     0.00   0.0  0
 03A  CONST_04  HNAA  NAA  CAM  OBS   180.00   0.0  0
 03A  Var_01    CAP   CAO  CAN  NAA   109.42  30.0  1
 03A  Var_02    HAP   CAP  CAO  CAN  -107.34  30.0  1
 03A  Var_03    HAPA  CAP  CAO  CAN   106.93  30.0  1
 03A  Var_04    HAO   CAO  CAP  CAN  -106.99  30.0  1
 03A  Var_05    HAOA  CAO  CAP  CAN   107.57  30.0  1
 03A  Var_06    HAN   CAN  CAP  CAO   107.58  30.0  1
 03A  Var_07    CAO   CAN  NAA  CAM  -143.83  30.0  1
 03A  Var_08    CAP   CAN  NAA  CAM   -74.33  30.0  1
 03A  Var_09    HAO   CAO  CAN  NAA  -141.42  30.0  1
 03A  Var_10    HAOA  CAO  CAN  NAA     1.71  30.0  1
 03A  Var_11    HAP   CAP  CAN  NAA     0.51  30.0  1
 03A  Var_12    HAPA  CAP  CAN  NAA   144.01  30.0  1
 03A  Var_13    HNAA  NAA  CAN  CAO    38.49  30.0  3
 03A  Var_14    HNAA  NAA  CAN  CAP   108.00  30.0  3
 03A  Var_15    HAN   CAN  NAA  CAM    71.83  30.0  1
 03A  Var_16    CAH   CAI  CAM  NAA   170.08  30.0  2
 03A  Var_17    OBR   CAI  CAM  NAA    -9.15  30.0  2
 03A  Var_18    OBS   CAM  CAI  CAH   -10.32  30.0  1
 03A  Var_19    CAL   CAK  CAJ  CAH   178.70  30.0  1
 03A  Var_20    OBR   CAI  CAM  OBS   170.44  30.0  2
 03A  Var_21    HAK   CAK  CAJ  CAH   -59.62  30.0  1
 03A  Var_22    HAKA  CAK  CAJ  CAH    56.52  30.0  1
 03A  Var_23    HAL   CAL  CAK  CAJ   -61.70  30.0  3
 03A  Var_24    HALA  CAL  CAK  CAJ    58.36  30.0  3
 03A  Var_25    HALB  CAL  CAK  CAJ   178.47  30.0  3
 03A  Var_26    HAJ   CAJ  CAK  CAL    57.15  30.0  3
 03A  Var_27    HAJA  CAJ  CAK  CAL   -58.95  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
 03A  chir_01  CAH  NAE  CAI  CAJ  positiv
 03A  chir_02  CAN  NAA  CAO  CAP  both

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
 03A  plan-1  NAA   0.020
 03A  plan-1  CAI   0.020
 03A  plan-1  CAM   0.020
 03A  plan-1  CAN   0.020
 03A  plan-1  OBS   0.020
 03A  plan-1  HNAA  0.020
 03A  plan-2  CAH   0.020
 03A  plan-2  CAI   0.020
 03A  plan-2  CAM   0.020
 03A  plan-2  OBR   0.020

