# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:20:31 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (2S)-2-amino-4-[5-(5-aminopentyl)-1,3,4-oxadiazol-2-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCc1oc(CC[C@H](N)C(O)=O)nn1
#
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
 5A6  5A6  '(2S)-2-amino-4-[5-(5-aminopentyl)-1,3,4-oxadiazol-2-yl]butanoic acid'  peptide  37  18  .  2016-04-22  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_5A6
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
 5A6  O    O  O      0  -0.597  -4.7722  2.9753   7.8826
 5A6  C    C  C      0   0.414  -4.1136  3.9409   7.4470
 5A6  N18  N  NH2    0  -0.797  -0.8474  4.1679   0.4181
 5A6  C19  C  CH2    0  -0.274  -0.2367  4.4353   1.7136
 5A6  C20  C  CH2    0  -0.433   0.6134  3.2553   2.1640
 5A6  C21  C  CH2    0  -0.435   1.2381  3.4436   3.5440
 5A6  C22  C  CH2    0  -0.441   2.3571  4.4788   3.5713
 5A6  C23  C  CH2    0  -0.544   3.0451  4.6318   4.9349
 5A6  CA   C  CH1    0  -0.225  -2.8946  4.3995   8.2954
 5A6  C29  C  CH2    0  -0.406  -1.6935  4.7142   7.4059
 5A6  C30  C  CH2    0  -0.547  -0.4949  5.2085   8.2205
 5A6  C31  C  CR5    0   0.464   0.6576  5.5787   7.3713
 5A6  N32  N  N      0  -0.319   1.2258  6.7214   7.2225
 5A6  N33  N  N      0  -0.316   2.2305  6.5505   6.3003
 5A6  C34  C  CR5    0   0.454   2.2049  5.3163   5.9445
 5A6  O35  O  O      0  -0.407   1.2350  4.6448   6.5922
 5A6  N    N  NH2    0  -0.821  -2.5406  3.4024   9.2953
 5A6  H2   H  HNH2   0   0.343  -1.4255  4.9543   0.1503
 5A6  H3   H  HNH2   0   0.335  -0.1203  4.1170  -0.2854
 5A6  H5   H  HCH2   0   0.192   0.3665  5.3538   1.7240
 5A6  H6   H  HCH2   0   0.210  -1.0360  4.5883   2.4444
 5A6  H7   H  HCH2   0   0.224  -0.0171  2.3622   2.1725
 5A6  H8   H  HCH2   0   0.211   1.4020  3.0688   1.4260
 5A6  H9   H  HCH2   0   0.221   0.4477  3.7100   4.2519
 5A6  H10  H  HCH2   0   0.226   1.6428  2.4870   3.8870
 5A6  H11  H  HCH2   0   0.239   3.1247  4.1853   2.8504
 5A6  H12  H  HCH2   0   0.236   1.9930  5.4571   3.2493
 5A6  H13  H  HCH2   0   0.267   3.3510  3.6531   5.3128
 5A6  H14  H  HCH2   0   0.279   3.9501  5.2282   4.8173
 5A6  H15  H  HCH1   0   0.204  -3.2040  5.3482   8.7659
 5A6  H16  H  HCH2   0   0.218  -1.4115  3.8138   6.8519
 5A6  H17  H  HCH2   0   0.227  -1.9691  5.4727   6.6729
 5A6  H18  H  HCH2   0   0.266  -0.1877  4.4397   8.9342
 5A6  H19  H  HCH2   0   0.262  -0.7689  6.0937   8.7979
 5A6  H20  H  HNH2   0   0.333  -2.2843  3.8472  10.1658
 5A6  H21  H  HNH2   0   0.337  -3.3693  2.8500   9.4776
 5A6  OXT  O  OC    -1  -0.602  -4.3467  4.5992   6.4156

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
 5A6  N18  C19  single    1.457  0.020  1.457
 5A6  C20  C19  single    1.523  0.020  1.523
 5A6  C20  C21  single    1.526  0.020  1.526
 5A6  C21  C22  single    1.525  0.020  1.525
 5A6  C22  C23  single    1.535  0.020  1.535
 5A6  C23  C34  single    1.481  0.020  1.481
 5A6  C34  N33  aromatic  1.285  0.020  1.285
 5A6  C34  O35  aromatic  1.346  0.020  1.346
 5A6  N33  N32  aromatic  1.374  0.020  1.374
 5A6  O    C    deloc     1.231  0.020  1.231
 5A6  O35  C31  aromatic  1.346  0.020  1.346
 5A6  N32  C31  aromatic  1.285  0.020  1.285
 5A6  C    CA   single    1.525  0.021  1.525
 5A6  C31  C30  single    1.479  0.020  1.479
 5A6  C29  CA   single    1.527  0.020  1.527
 5A6  C29  C30  single    1.531  0.020  1.531
 5A6  CA   N    single    1.458  0.019  1.458
 5A6  N18  H2   single    0.890  0.020  1.040
 5A6  N18  H3   single    0.890  0.020  1.040
 5A6  C19  H5   single    0.970  0.020  1.090
 5A6  C19  H6   single    0.970  0.020  1.090
 5A6  C20  H7   single    0.970  0.020  1.090
 5A6  C20  H8   single    0.970  0.020  1.090
 5A6  C21  H9   single    0.970  0.020  1.090
 5A6  C21  H10  single    0.970  0.020  1.090
 5A6  C22  H11  single    0.970  0.020  1.090
 5A6  C22  H12  single    0.970  0.020  1.090
 5A6  C23  H13  single    0.970  0.020  1.090
 5A6  C23  H14  single    0.970  0.020  1.090
 5A6  CA   H15  single    0.970  0.020  1.090
 5A6  C29  H16  single    0.970  0.020  1.090
 5A6  C29  H17  single    0.970  0.020  1.090
 5A6  C30  H18  single    0.970  0.020  1.090
 5A6  C30  H19  single    0.970  0.020  1.090
 5A6  N    H20  single    0.890  0.020  1.040
 5A6  N    H21  single    0.890  0.020  1.040
 5A6  C    OXT  deloc     1.246  0.020  1.246

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
 5A6  OXT  C    CA   120.80  1.700
 5A6  OXT  C    O    126.83  3.000
 5A6  CA   C    O    120.80  1.700
 5A6  H3   N18  H2   105.38  3.000
 5A6  H3   N18  C19  109.02  3.000
 5A6  H2   N18  C19  109.39  3.000
 5A6  H6   C19  H5   106.13  3.000
 5A6  H6   C19  C20  108.59  3.000
 5A6  H5   C19  C20  109.79  3.000
 5A6  H6   C19  N18  108.27  3.000
 5A6  H5   C19  N18  113.07  3.000
 5A6  C20  C19  N18  110.78  3.000
 5A6  H8   C20  H7   106.33  3.000
 5A6  H8   C20  C21  109.59  3.000
 5A6  H7   C20  C21  109.26  3.000
 5A6  H8   C20  C19  109.54  3.000
 5A6  H7   C20  C19  108.26  3.000
 5A6  C21  C20  C19  113.60  3.000
 5A6  H10  C21  H9   106.11  3.000
 5A6  H10  C21  C22  108.46  3.000
 5A6  H9   C21  C22  110.69  3.000
 5A6  H10  C21  C20  109.09  3.000
 5A6  H9   C21  C20  108.62  3.000
 5A6  C22  C21  C20  113.59  3.000
 5A6  H12  C22  H11  106.27  3.000
 5A6  H12  C22  C23  108.79  3.000
 5A6  H11  C22  C23  107.33  3.000
 5A6  H12  C22  C21  110.99  3.000
 5A6  H11  C22  C21  108.73  3.000
 5A6  C23  C22  C21  114.36  3.000
 5A6  H14  C23  H13  107.15  3.000
 5A6  H14  C23  C34  106.95  3.000
 5A6  H13  C23  C34  109.70  3.000
 5A6  H14  C23  C22  109.31  3.000
 5A6  H13  C23  C22  110.09  3.000
 5A6  C34  C23  C22  113.41  3.000
 5A6  H15  CA   N    111.36  3.000
 5A6  H15  CA   C29  106.96  3.000
 5A6  N    CA   C29  110.48  3.000
 5A6  H15  CA   C    105.46  3.000
 5A6  N    CA   C    111.00  2.800
 5A6  C29  CA   C    111.08  3.000
 5A6  H17  C29  H16  107.29  3.000
 5A6  H17  C29  C30  109.33  3.000
 5A6  H16  C29  C30  109.47  3.000
 5A6  H17  C29  CA   109.64  3.000
 5A6  H16  C29  CA   109.15  3.000
 5A6  C30  C29  CA   111.86  3.000
 5A6  H19  C30  H18  107.19  3.000
 5A6  H19  C30  C31  107.24  3.000
 5A6  H18  C30  C31  109.39  3.000
 5A6  H19  C30  C29  110.28  3.000
 5A6  H18  C30  C29  109.89  3.000
 5A6  C31  C30  C29  112.67  3.000
 5A6  O35  C31  N32  111.11  3.000
 5A6  N32  C31  C30  129.34  3.000
 5A6  O35  C31  C30  119.54  3.000
 5A6  N33  N32  C31  106.88  3.000
 5A6  C34  N33  N32  106.90  3.000
 5A6  O35  C34  N33  111.13  3.000
 5A6  O35  C34  C23  120.41  3.000
 5A6  N33  C34  C23  128.43  3.000
 5A6  C34  O35  C31  103.97  3.000
 5A6  H21  N    H20  107.01  3.000
 5A6  H21  N    CA   107.35  3.000
 5A6  H20  N    CA   110.60  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
 5A6  CONST_01  N33  C34  O35  C31     0.00   0.0  0
 5A6  CONST_02  C34  N33  N32  C31     0.00   0.0  0
 5A6  CONST_03  O35  C34  N33  N32     0.00   0.0  0
 5A6  CONST_04  C34  O35  C31  N32     0.00   0.0  0
 5A6  CONST_05  O35  C31  N32  N33     0.00   0.0  0
 5A6  CONST_06  N32  N33  C34  C23   180.00   0.0  0
 5A6  CONST_07  C31  O35  C34  C23   180.00   0.0  0
 5A6  CONST_08  C34  O35  C31  C30   180.00   0.0  0
 5A6  CONST_09  N33  N32  C31  C30   180.00   0.0  0
 5A6  Var_01    N33  C34  C23  C22   -98.30  30.0  2
 5A6  Var_02    O35  C31  C30  C29   -61.26  30.0  1
 5A6  Var_03    C34  C23  C22  C21   -72.30  30.0  3
 5A6  Var_04    C31  C30  C29  CA   -177.32  30.0  3
 5A6  Var_05    C21  C20  C19  N18  -177.58  30.0  2
 5A6  Var_06    C22  C21  C20  C19   -71.14  30.0  3
 5A6  Var_07    C23  C22  C21  C20  -177.09  30.0  3
 5A6  Var_08    H2   N18  C19  C20   178.56  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
 5A6  chir_01  CA  C  C29  N  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
 5A6  plan-1  C23  0.020
 5A6  plan-1  C30  0.020
 5A6  plan-1  C31  0.020
 5A6  plan-1  N32  0.020
 5A6  plan-1  N33  0.020
 5A6  plan-1  C34  0.020
 5A6  plan-1  O35  0.020
 5A6  plan-2  O    0.020
 5A6  plan-2  C    0.020
 5A6  plan-2  CA   0.020
 5A6  plan-2  OXT  0.020

