# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:35:26 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{S})-2-azanyl-6-benzamido-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)c1ccccc1)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
 LBZ  LBZ  '(2~{S})-2-azanyl-6-benzamido-hexanoic acid'  L-peptide  35  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_LBZ
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
 LBZ  C4   C  CR16   0  -0.238  12.4500   0.7282  16.3038
 LBZ  C5   C  CR16   0  -0.252  13.3666   0.2080  15.4005
 LBZ  C6   C  CR16   0  -0.240  13.3237  -1.1420  15.0760
 LBZ  C11  C  CH2    0  -0.431   6.0233  -2.2262  16.0254
 LBZ  C8   C  CH2    0  -0.266   8.2197  -2.6276  18.1700
 LBZ  C9   C  CH2    0  -0.494   6.9705  -1.7877  18.3841
 LBZ  C10  C  CH2    0  -0.444   6.3505  -1.2079  17.1138
 LBZ  N1   N  NH1    0  -0.651   9.2744  -1.8497  17.5506
 LBZ  C3   C  CR16   0  -0.296  11.4868  -0.0937  16.8713
 LBZ  N    N  NH2    0  -0.793   4.9141  -4.2411  15.2674
 LBZ  CA   C  CH1    0  -0.195   5.0813  -3.3652  16.4267
 LBZ  C    C  C      0   0.390   3.7574  -2.7863  16.9794
 LBZ  O    O  O      0  -0.610   3.6177  -2.7543  18.2202
 LBZ  C1   C  CR16   0  -0.270  12.3682  -1.9654  15.6505
 LBZ  C2   C  CR6    0  -0.030  11.4323  -1.4476  16.5440
 LBZ  O1   O  O      0  -0.489  10.6637  -3.5889  17.2214
 LBZ  O2   O  OC    -1  -0.610   2.9412  -2.3720  16.1286
 LBZ  H1   H  HCR6   0   0.262  12.4861   1.7756  16.5731
 LBZ  H2   H  HCR6   0   0.261  14.1152   0.8506  14.9555
 LBZ  H3   H  HCR6   0   0.260  14.0376  -1.5548  14.3753
 LBZ  H4   H  HCH2   0   0.215   5.5750  -1.6918  15.1809
 LBZ  H5   H  HCH2   0   0.214   6.9479  -2.6677  15.6407
 LBZ  H6   H  HCH2   0   0.235   7.9880  -3.4942  17.5461
 LBZ  H7   H  HCH2   0   0.243   8.5625  -3.0183  19.1321
 LBZ  H8   H  HCH2   0   0.234   7.1993  -0.9721  19.0770
 LBZ  H9   H  HCH2   0   0.243   6.2331  -2.4138  18.8886
 LBZ  H10  H  HCH2   0   0.220   7.0143  -0.4518  16.6831
 LBZ  H11  H  HCH2   0   0.229   5.4476  -0.6621  17.3980
 LBZ  H12  H  HNH1   0   0.407   9.1078  -0.8680  17.4030
 LBZ  H13  H  HCR6   0   0.257  10.8000   0.3350  17.5907
 LBZ  H14  H  HNH2   0   0.332   4.3810  -5.0566  15.5471
 LBZ  H15  H  HNH2   0   0.321   4.3161  -3.7573  14.6058
 LBZ  H17  H  HCH1   0   0.201   5.5594  -3.9586  17.2129
 LBZ  H18  H  HCR6   0   0.257  12.3442  -3.0175  15.3991
 LBZ  C7   C  C      0   0.530  10.4295  -2.3896  17.1369

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
 LBZ  C11  C10  single    1.526  0.020  1.526
 LBZ  C11  CA   single    1.532  0.020  1.532
 LBZ  C6   C5   aromatic  1.389  0.020  1.389
 LBZ  C6   C1   aromatic  1.386  0.020  1.386
 LBZ  C5   C4   aromatic  1.388  0.020  1.388
 LBZ  C10  C9   single    1.528  0.020  1.528
 LBZ  C1   C2   aromatic  1.394  0.020  1.394
 LBZ  C4   C3   aromatic  1.388  0.020  1.388
 LBZ  N1   C8   single    1.450  0.020  1.450
 LBZ  N1   C7   single    1.340  0.020  1.340
 LBZ  C2   C3   aromatic  1.394  0.020  1.394
 LBZ  C2   C7   single    1.498  0.020  1.498
 LBZ  C8   C9   single    1.520  0.020  1.520
 LBZ  C    CA   single    1.525  0.021  1.525
 LBZ  C    O    deloc     1.231  0.020  1.231
 LBZ  C7   O1   double    1.225  0.020  1.225
 LBZ  CA   N    single    1.458  0.019  1.458
 LBZ  C    O2   deloc     1.250  0.020  1.250
 LBZ  C4   H1   single    0.930  0.020  1.080
 LBZ  C5   H2   single    0.930  0.020  1.080
 LBZ  C6   H3   single    0.930  0.020  1.080
 LBZ  C11  H4   single    0.970  0.020  1.090
 LBZ  C11  H5   single    0.970  0.020  1.090
 LBZ  C8   H6   single    0.970  0.020  1.090
 LBZ  C8   H7   single    0.970  0.020  1.090
 LBZ  C9   H8   single    0.970  0.020  1.090
 LBZ  C9   H9   single    0.970  0.020  1.090
 LBZ  C10  H10  single    0.970  0.020  1.090
 LBZ  C10  H11  single    0.970  0.020  1.090
 LBZ  N1   H12  single    0.860  0.020  1.020
 LBZ  C3   H13  single    0.930  0.020  1.080
 LBZ  N    H14  single    0.890  0.020  1.040
 LBZ  N    H15  single    0.890  0.020  1.040
 LBZ  CA   H17  single    0.970  0.020  1.090
 LBZ  C1   H18  single    0.930  0.020  1.080

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
 LBZ  H1   C4   C3   119.65  3.000
 LBZ  H1   C4   C5   120.18  3.000
 LBZ  C3   C4   C5   120.17  3.000
 LBZ  H2   C5   C6   120.15  3.000
 LBZ  H2   C5   C4   120.12  3.000
 LBZ  C6   C5   C4   119.72  3.000
 LBZ  H3   C6   C1   119.77  3.000
 LBZ  H3   C6   C5   120.11  3.000
 LBZ  C1   C6   C5   120.12  3.000
 LBZ  H5   C11  H4   105.76  3.000
 LBZ  H5   C11  CA   108.16  3.000
 LBZ  H4   C11  CA   108.25  3.000
 LBZ  H5   C11  C10  109.80  3.000
 LBZ  H4   C11  C10  108.18  3.000
 LBZ  CA   C11  C10  116.19  3.000
 LBZ  H7   C8   H6   106.58  3.000
 LBZ  H7   C8   N1   109.86  3.000
 LBZ  H6   C8   N1   109.63  3.000
 LBZ  H7   C8   C9   109.33  3.000
 LBZ  H6   C8   C9   110.14  3.000
 LBZ  N1   C8   C9   111.19  3.000
 LBZ  H9   C9   H8   106.03  3.000
 LBZ  H9   C9   C10  109.15  3.000
 LBZ  H8   C9   C10  109.18  3.000
 LBZ  H9   C9   C8   107.66  3.000
 LBZ  H8   C9   C8   109.21  3.000
 LBZ  C10  C9   C8   115.21  3.000
 LBZ  H11  C10  H10  104.98  3.000
 LBZ  H11  C10  C9   107.98  3.000
 LBZ  H10  C10  C9   110.07  3.000
 LBZ  H11  C10  C11  109.98  3.000
 LBZ  H10  C10  C11  108.08  3.000
 LBZ  C9   C10  C11  115.26  3.000
 LBZ  H12  N1   C8   117.75  3.000
 LBZ  H12  N1   C7   119.35  3.000
 LBZ  C8   N1   C7   122.86  3.000
 LBZ  H13  C3   C2   121.04  3.000
 LBZ  H13  C3   C4   118.51  3.000
 LBZ  C2   C3   C4   120.43  3.000
 LBZ  H15  N    H14  104.68  3.000
 LBZ  H15  N    CA   107.37  3.000
 LBZ  H14  N    CA   108.86  3.000
 LBZ  H17  CA   C    108.66  3.000
 LBZ  H17  CA   N    107.12  3.000
 LBZ  C    CA   N    111.00  2.800
 LBZ  H17  CA   C11  108.82  3.000
 LBZ  N    CA   C11  107.94  3.000
 LBZ  C    CA   C11  109.98  3.000
 LBZ  O2   C    O    126.50  3.000
 LBZ  O2   C    CA   116.09  3.000
 LBZ  O    C    CA   120.80  1.700
 LBZ  H18  C1   C2   119.70  3.000
 LBZ  H18  C1   C6   119.78  3.000
 LBZ  C2   C1   C6   120.52  3.000
 LBZ  C1   C2   C3   119.02  3.000
 LBZ  C3   C2   C7   122.95  3.000
 LBZ  C1   C2   C7   118.01  3.000
 LBZ  O1   C7   C2   120.99  3.000
 LBZ  O1   C7   N1   122.54  3.000
 LBZ  C2   C7   N1   116.46  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
 LBZ  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 LBZ  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 LBZ  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 LBZ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 LBZ  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 LBZ  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 LBZ  CONST_07  C7   C2   C3   C4    180.00   0.0  0
 LBZ  CONST_08  C7   C2   C1   C6    180.00   0.0  0
 LBZ  CONST_09  H3   C6   C5   C4    180.00   0.0  0
 LBZ  CONST_10  H18  C1   C6   C5    180.00   0.0  0
 LBZ  CONST_11  H13  C3   C4   C5    180.00   0.0  0
 LBZ  CONST_12  H1   C4   C5   C6    180.00   0.0  0
 LBZ  CONST_13  H2   C5   C4   C3    180.00   0.0  0
 LBZ  CONST_14  C2   C7   N1   C8    180.00   0.0  0
 LBZ  CONST_15  H12  N1   C7   C2      0.00   0.0  0
 LBZ  CONST_16  O1   C7   N1   C8      0.00   0.0  0
 LBZ  Var_01    C1   C2   C7   N1   -155.10  30.0  2
 LBZ  Var_02    C8   C9   C10  C11    54.54  30.0  3
 LBZ  Var_03    C9   C8   N1   C7   -173.28  30.0  3
 LBZ  Var_04    CA   C11  C10  C9     57.27  30.0  2
 LBZ  Var_05    N1   C8   C9   C10    60.32  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
 LBZ  chir_01  CA  C11  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
 LBZ  plan-1  C4   0.020
 LBZ  plan-1  C5   0.020
 LBZ  plan-1  C6   0.020
 LBZ  plan-1  C3   0.020
 LBZ  plan-1  C1   0.020
 LBZ  plan-1  C2   0.020
 LBZ  plan-1  H1   0.020
 LBZ  plan-1  H2   0.020
 LBZ  plan-1  H3   0.020
 LBZ  plan-1  H13  0.020
 LBZ  plan-1  H18  0.020
 LBZ  plan-1  C7   0.020
 LBZ  plan-2  C8   0.020
 LBZ  plan-2  N1   0.020
 LBZ  plan-2  C2   0.020
 LBZ  plan-2  O1   0.020
 LBZ  plan-2  H12  0.020
 LBZ  plan-2  C7   0.020
 LBZ  plan-3  CA   0.020
 LBZ  plan-3  C    0.020
 LBZ  plan-3  O    0.020
 LBZ  plan-3  O2   0.020

