# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 00:09:31 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N~2~-(tert-butoxycarbonyl)-N-[(1S)-1-(formylamino)ethyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC=O)NC(=O)[C@H](C)NC(=O)OC(C)(C)C
#
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
 BAF  BAF  N~2~-(tert-butoxycarbonyl)-N-[(1S)-1-(formylamino)ethyl]-L-alaninamide  ligand  39  18  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BAF
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
 BAF  N3    N  NH1   0  -0.599   0.3532  -0.3518  -4.8451
 BAF  C1    C  C1    0   0.261  -0.3901  -1.4686  -4.8491
 BAF  O1    O  O     0  -0.477  -1.2958  -1.7085  -4.0729
 BAF  CA1   C  CH1   0   0.073   0.2049   0.6950  -3.8579
 BAF  CB1   C  CH3   0  -0.681   0.9898   1.9201  -4.2919
 BAF  N1    N  NH1   0  -0.630   0.6315   0.2309  -2.5549
 BAF  C2    C  C     0   0.570  -0.1833   0.0840  -1.4982
 BAF  O2    O  O     0  -0.485  -1.3396   0.4723  -1.4607
 BAF  CA2   C  CH1   0  -0.209   0.4448  -0.6605  -0.3249
 BAF  CB2   C  CH3   0  -0.644   0.2983  -2.1679  -0.5478
 BAF  N2    N  NH1   0  -0.659  -0.1941  -0.2174   0.8870
 BAF  C3    C  C     0   0.765   0.4261  -0.2506   2.0832
 BAF  O3    O  O     0  -0.522   1.5818  -0.5928   2.2414
 BAF  O4    O  O2    0  -0.504  -0.4073   0.1517   3.0423
 BAF  C4    C  CT    0   0.189  -0.0028   0.2887   4.4311
 BAF  C41   C  CH3   0  -0.658  -1.2715   0.7983   5.1052
 BAF  C42   C  CH3   0  -0.671   0.3945  -1.0592   5.0200
 BAF  C43   C  CH3   0  -0.673   1.1063   1.3243   4.5740
 BAF  HN3   H  HNH1  0   0.411   1.1128  -0.2888  -5.5048
 BAF  H1    H  H     0   0.209  -0.0924  -2.1613  -5.6508
 BAF  HA1   H  HCH1  0   0.268  -0.8498   0.9511  -3.7690
 BAF  HB11  H  HCH3  0   0.239   2.0557   1.6995  -4.3742
 BAF  HB12  H  HCH3  0   0.250   0.6376   2.2795  -5.2584
 BAF  HB13  H  HCH3  0   0.255   0.8631   2.7181  -3.5629
 BAF  HN1   H  HNH1  0   0.402   1.5864  -0.0854  -2.4745
 BAF  HA2   H  HCH1  0   0.275   1.5068  -0.4130  -0.2649
 BAF  HB21  H  HCH3  0   0.235  -0.7533  -2.4504  -0.6024
 BAF  HB22  H  HCH3  0   0.236   0.7844  -2.4806  -1.4717
 BAF  HB23  H  HCH3  0   0.247   0.7585  -2.7112   0.2767
 BAF  HN2   H  HNH1  0   0.395  -1.1717   0.0259   0.8373
 BAF  H411  H  HCH3  0   0.230  -1.0901   0.9592   6.1675
 BAF  H412  H  HCH3  0   0.237  -1.5923   1.7473   4.6731
 BAF  H413  H  HCH3  0   0.237  -2.0880   0.0806   5.0108
 BAF  H421  H  HCH3  0   0.234  -0.3990  -1.7950   4.8801
 BAF  H422  H  HCH3  0   0.246   1.3118  -1.4465   4.5833
 BAF  H423  H  HCH3  0   0.233   0.5558  -0.9494   6.0930
 BAF  H431  H  HCH3  0   0.235   0.8190   2.2671   4.1054
 BAF  H432  H  HCH3  0   0.234   1.2787   1.5222   5.6323
 BAF  H433  H  HCH3  0   0.246   2.0468   0.9906   4.1421

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
 BAF  N3   C1    single  1.342  0.020  1.342
 BAF  N3   CA1   single  1.446  0.020  1.446
 BAF  N3   HN3   single  0.860  0.020  1.020
 BAF  C1   O1    double  1.217  0.020  1.217
 BAF  C1   H1    single  0.930  0.020  1.080
 BAF  CA1  CB1   single  1.518  0.020  1.518
 BAF  CA1  N1    single  1.448  0.020  1.448
 BAF  CA1  HA1   single  0.970  0.020  1.090
 BAF  CB1  HB11  single  0.970  0.020  1.090
 BAF  CB1  HB12  single  0.970  0.020  1.090
 BAF  CB1  HB13  single  0.970  0.020  1.090
 BAF  N1   C2    single  1.342  0.020  1.342
 BAF  N1   HN1   single  0.860  0.020  1.020
 BAF  C2   O2    double  1.220  0.020  1.220
 BAF  C2   CA2   single  1.525  0.020  1.525
 BAF  CA2  CB2   single  1.531  0.020  1.531
 BAF  CA2  N2    single  1.440  0.020  1.440
 BAF  CA2  HA2   single  0.970  0.020  1.090
 BAF  CB2  HB21  single  0.970  0.020  1.090
 BAF  CB2  HB22  single  0.970  0.020  1.090
 BAF  CB2  HB23  single  0.970  0.020  1.090
 BAF  N2   C3    single  1.348  0.020  1.348
 BAF  N2   HN2   single  0.860  0.020  1.020
 BAF  C3   O3    double  1.216  0.020  1.216
 BAF  C3   O4    single  1.333  0.020  1.333
 BAF  O4   C4    single  1.453  0.020  1.453
 BAF  C4   C41   single  1.524  0.020  1.524
 BAF  C4   C42   single  1.524  0.020  1.524
 BAF  C4   C43   single  1.524  0.020  1.524
 BAF  C41  H411  single  0.970  0.020  1.090
 BAF  C41  H412  single  0.970  0.020  1.090
 BAF  C41  H413  single  0.970  0.020  1.090
 BAF  C42  H421  single  0.970  0.020  1.090
 BAF  C42  H422  single  0.970  0.020  1.090
 BAF  C42  H423  single  0.970  0.020  1.090
 BAF  C43  H431  single  0.970  0.020  1.090
 BAF  C43  H432  single  0.970  0.020  1.090
 BAF  C43  H433  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
 BAF  HN3   N3   CA1   118.60  3.000
 BAF  HN3   N3   C1    117.88  3.000
 BAF  CA1   N3   C1    123.21  3.000
 BAF  H1    C1   O1    122.81  3.000
 BAF  H1    C1   N3    112.11  3.000
 BAF  O1    C1   N3    125.08  3.000
 BAF  HA1   CA1  N1    106.70  3.000
 BAF  HA1   CA1  CB1   109.53  3.000
 BAF  N1    CA1  CB1   111.32  3.000
 BAF  HA1   CA1  N3    108.98  3.000
 BAF  N1    CA1  N3    110.62  3.000
 BAF  CB1   CA1  N3    109.63  3.000
 BAF  HB13  CB1  HB12  108.34  3.000
 BAF  HB13  CB1  HB11  108.20  3.000
 BAF  HB12  CB1  HB11  108.39  3.000
 BAF  HB13  CB1  CA1   109.88  3.000
 BAF  HB12  CB1  CA1   110.64  3.000
 BAF  HB11  CB1  CA1   111.30  3.000
 BAF  HN1   N1   C2    118.51  3.000
 BAF  HN1   N1   CA1   116.81  3.000
 BAF  C2    N1   CA1   124.39  3.000
 BAF  CA2   C2   O2    121.46  3.000
 BAF  CA2   C2   N1    114.15  3.000
 BAF  O2    C2   N1    124.36  3.000
 BAF  HA2   CA2  N2    108.39  3.000
 BAF  HA2   CA2  CB2   108.92  3.000
 BAF  N2    CA2  CB2   112.52  3.000
 BAF  HA2   CA2  C2    109.40  3.000
 BAF  N2    CA2  C2    108.34  3.000
 BAF  CB2   CA2  C2    109.23  3.000
 BAF  HB23  CB2  HB22  108.06  3.000
 BAF  HB23  CB2  HB21  108.43  3.000
 BAF  HB22  CB2  HB21  108.26  3.000
 BAF  HB23  CB2  CA2   109.91  3.000
 BAF  HB22  CB2  CA2   111.30  3.000
 BAF  HB21  CB2  CA2   110.78  3.000
 BAF  HN2   N2   C3    119.72  3.000
 BAF  HN2   N2   CA2   117.57  3.000
 BAF  C3    N2   CA2   122.36  3.000
 BAF  O4    C3   O3    125.86  3.000
 BAF  O4    C3   N2    110.09  3.000
 BAF  O3    C3   N2    124.05  3.000
 BAF  C4    O4   C3    122.83  3.000
 BAF  C43   C4   C42   112.03  3.000
 BAF  C43   C4   C41   109.70  3.000
 BAF  C42   C4   C41   109.99  3.000
 BAF  C43   C4   O4    110.87  3.000
 BAF  C42   C4   O4    111.02  3.000
 BAF  C41   C4   O4    102.85  3.000
 BAF  H413  C41  H412  108.53  3.000
 BAF  H413  C41  H411  107.82  3.000
 BAF  H412  C41  H411  107.85  3.000
 BAF  H413  C41  C4    111.39  3.000
 BAF  H412  C41  C4    111.13  3.000
 BAF  H411  C41  C4    109.99  3.000
 BAF  H423  C42  H422  107.84  3.000
 BAF  H423  C42  H421  107.55  3.000
 BAF  H422  C42  H421  108.77  3.000
 BAF  H423  C42  C4    109.25  3.000
 BAF  H422  C42  C4    112.33  3.000
 BAF  H421  C42  C4    110.94  3.000
 BAF  H433  C43  H432  107.72  3.000
 BAF  H433  C43  H431  108.80  3.000
 BAF  H432  C43  H431  107.55  3.000
 BAF  H433  C43  C4    112.56  3.000
 BAF  H432  C43  C4    109.23  3.000
 BAF  H431  C43  C4    110.80  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
 BAF  CONST_01  CA1   N3   C1  O1      0.00   0.0  0
 BAF  CONST_02  O2    C2   N1  CA1     0.00   0.0  0
 BAF  CONST_03  CA2   C2   N1  CA1   180.00   0.0  0
 BAF  CONST_04  HN3   N3   C1  O1    180.00   0.0  0
 BAF  CONST_05  HN1   N1   C2  O2    180.00   0.0  0
 BAF  Var_01    O3    C3   N2  CA2     3.48  30.0  2
 BAF  Var_02    C41   C4   O4  C3    178.61  30.0  3
 BAF  Var_03    H411  C41  C4  O4   -179.08  30.0  3
 BAF  Var_04    H421  C42  C4  O4    -53.65  30.0  3
 BAF  Var_05    H431  C43  C4  O4     52.75  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
 BAF  chir_01  CA1  N3  CB1  N1   positiv
 BAF  chir_02  CA2  N2  C2   CB2  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
 BAF  plan-1  N3   0.020
 BAF  plan-1  C1   0.020
 BAF  plan-1  O1   0.020
 BAF  plan-1  CA1  0.020
 BAF  plan-1  HN3  0.020
 BAF  plan-1  H1   0.020
 BAF  plan-2  CA1  0.020
 BAF  plan-2  N1   0.020
 BAF  plan-2  C2   0.020
 BAF  plan-2  O2   0.020
 BAF  plan-2  CA2  0.020
 BAF  plan-2  HN1  0.020
 BAF  plan-3  N2   0.020
 BAF  plan-3  C3   0.020
 BAF  plan-3  O3   0.020
 BAF  plan-3  O4   0.020

