# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:28:14 2021
#   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  36  18  .  2022-09-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (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  -0.241  11.5477   0.4882  15.1035
 LBZ  C5   C  CR16  0  -0.253  12.9283   0.3991  15.2163
 LBZ  C6   C  CR16  0  -0.242  13.4948  -0.6107  15.9846
 LBZ  C11  C  CH2   0  -0.451   5.9225  -1.6122  16.8183
 LBZ  C8   C  CH2   0  -0.310   8.3019  -3.6116  17.3463
 LBZ  C9   C  CH2   0  -0.429   7.5070  -2.9064  18.4395
 LBZ  C10  C  CH2   0  -0.446   6.8786  -1.5847  18.0105
 LBZ  N1   N  NH1   0  -0.640   9.2862  -2.7617  16.7057
 LBZ  C3   C  CR16  0  -0.292  10.7357  -0.4357  15.7464
 LBZ  N    N  NH2   0  -0.774   4.8744  -3.8419  16.9055
 LBZ  CA   C  CH1   0  -0.189   4.6353  -2.4218  17.0434
 LBZ  C    C  C     0   0.517   3.5577  -1.8510  16.1305
 LBZ  O    O  O     0  -0.451   2.7872  -0.9800  16.4555
 LBZ  C1   C  CR16  0  -0.270  12.6840  -1.5244  16.6396
 LBZ  C2   C  CR6   0  -0.026  11.2982  -1.4530  16.5151
 LBZ  O1   O  O     0  -0.492  10.8562  -2.9298  18.3173
 LBZ  O2   O  OH1   0  -0.591   3.5770  -2.3856  14.9158
 LBZ  H1   H  HCR6  0   0.264  11.0990   1.2826  14.5219
 LBZ  H2   H  HCR6  0   0.264  13.5610   1.1182  14.7126
 LBZ  H3   H  HCR6  0   0.262  14.5705  -0.6831  16.0780
 LBZ  H4   H  HCH2  0   0.251   5.6574  -0.5738  16.6019
 LBZ  H5   H  HCH2  0   0.231   6.4210  -1.9808  15.9154
 LBZ  H6   H  HCH2  0   0.247   7.6323  -3.9665  16.5648
 LBZ  H7   H  HCH2  0   0.250   8.7969  -4.4922  17.7591
 LBZ  H8   H  HCH2  0   0.227   8.1631  -2.7143  19.2920
 LBZ  H9   H  HCH2  0   0.235   6.7379  -3.5970  18.7883
 LBZ  H10  H  HCH2  0   0.228   7.6753  -0.8714  17.7804
 LBZ  H11  H  HCH2  0   0.233   6.3466  -1.1592  18.8661
 LBZ  H12  H  HNH1  0   0.405   9.0661  -2.3974  15.7943
 LBZ  H13  H  HCR6  0   0.255   9.6605  -0.3324  15.6632
 LBZ  H14  H  HNH2  0   0.356   4.0293  -4.3675  17.0895
 LBZ  H15  H  HNH2  0   0.348   5.1606  -4.0687  15.9620
 LBZ  H17  H  HCH1  0   0.263   4.2877  -2.2320  18.0629
 LBZ  H18  H  HCR6  0   0.259  13.1303  -2.3032  17.2440
 LBZ  H19  H  HOH1  0   0.481   2.8999  -1.9720  14.3596
 LBZ  C7   C  C     0   0.521  10.4637  -2.4441  17.2636

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    1.528  0.020  1.528
 LBZ  C11  CA   single    1.537  0.020  1.537
 LBZ  C6   C5   aromatic  1.390  0.020  1.390
 LBZ  C6   C1   aromatic  1.386  0.020  1.386
 LBZ  C5   C4   aromatic  1.388  0.020  1.388
 LBZ  C10  C9   single    1.525  0.020  1.525
 LBZ  C1   C2   aromatic  1.393  0.020  1.393
 LBZ  C4   C3   aromatic  1.388  0.020  1.388
 LBZ  N1   C8   single    1.450  0.020  1.450
 LBZ  N1   C7   single    1.341  0.020  1.341
 LBZ  C2   C3   aromatic  1.394  0.020  1.394
 LBZ  C2   C7   single    1.496  0.020  1.496
 LBZ  C8   C9   single    1.525  0.020  1.525
 LBZ  C    CA   single    1.525  0.021  1.525
 LBZ  C    O    double    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   single    1.327  0.020  1.327
 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
 LBZ  O2   H19  single    0.850  0.020  0.980

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   119.68  3.000
 LBZ  H1   C4   C5   120.22  3.000
 LBZ  C3   C4   C5   120.10  3.000
 LBZ  H2   C5   C6   120.12  3.000
 LBZ  H2   C5   C4   120.07  3.000
 LBZ  C6   C5   C4   119.81  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   105.48  3.000
 LBZ  H5   C11  CA   108.93  3.000
 LBZ  H4   C11  CA   109.03  3.000
 LBZ  H5   C11  C10  111.37  3.000
 LBZ  H4   C11  C10  106.80  3.000
 LBZ  CA   C11  C10  114.77  3.000
 LBZ  H7   C8   H6   106.71  3.000
 LBZ  H7   C8   N1   109.40  3.000
 LBZ  H6   C8   N1   106.95  3.000
 LBZ  H7   C8   C9   109.79  3.000
 LBZ  H6   C8   C9   110.18  3.000
 LBZ  N1   C8   C9   113.56  3.000
 LBZ  H9   C9   H8   106.57  3.000
 LBZ  H9   C9   C10  110.37  3.000
 LBZ  H8   C9   C10  108.33  3.000
 LBZ  H9   C9   C8   107.69  3.000
 LBZ  H8   C9   C8   109.12  3.000
 LBZ  C10  C9   C8   114.46  3.000
 LBZ  H11  C10  H10  105.37  3.000
 LBZ  H11  C10  C9   108.52  3.000
 LBZ  H10  C10  C9   108.92  3.000
 LBZ  H11  C10  C11  108.24  3.000
 LBZ  H10  C10  C11  107.65  3.000
 LBZ  C9   C10  C11  117.49  3.000
 LBZ  H12  N1   C8   117.66  3.000
 LBZ  H12  N1   C7   118.90  3.000
 LBZ  C8   N1   C7   123.44  3.000
 LBZ  H13  C3   C2   120.84  3.000
 LBZ  H13  C3   C4   118.79  3.000
 LBZ  C2   C3   C4   120.35  3.000
 LBZ  H15  N    H14  106.81  3.000
 LBZ  H15  N    CA   110.84  3.000
 LBZ  H14  N    CA   110.76  3.000
 LBZ  H17  CA   C    105.59  3.000
 LBZ  H17  CA   N    108.16  3.000
 LBZ  C    CA   N    111.00  2.800
 LBZ  H17  CA   C11  108.13  3.000
 LBZ  N    CA   C11  111.39  3.000
 LBZ  C    CA   C11  107.89  3.000
 LBZ  O2   C    O    123.10  3.000
 LBZ  O2   C    CA   112.78  3.000
 LBZ  O    C    CA   120.80  1.700
 LBZ  H18  C1   C2   119.80  3.000
 LBZ  H18  C1   C6   119.81  3.000
 LBZ  C2   C1   C6   120.38  3.000
 LBZ  C1   C2   C3   119.23  3.000
 LBZ  C3   C2   C7   122.30  3.000
 LBZ  C1   C2   C7   118.43  3.000
 LBZ  H19  O2   C    110.08  3.000
 LBZ  O1   C7   C2   120.95  3.000
 LBZ  O1   C7   N1   123.05  3.000
 LBZ  C2   C7   N1   116.00  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  CONST_17  H19  O2   C    CA    180.00   0.0  0
 LBZ  Var_01    C1   C2   C7   N1   -150.75  30.0  2
 LBZ  Var_02    C8   C9   C10  C11    57.61  30.0  3
 LBZ  Var_03    C9   C8   N1   C7     77.13  30.0  3
 LBZ  Var_04    CA   C11  C10  C9     64.56  30.0  2
 LBZ  Var_05    N1   C8   C9   C10    51.62  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
 LBZ  plan-3  H19  0.020

