# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 07:01:45 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[C@@H](CCC(O)=O)C(O)=O)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
 SHR  SHR  'N-[(5S)-5-amino-5-carboxypentyl]-L-glutamic acid'  L-peptide  39  19  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SHR
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
 SHR  N1   N  NH2   0  -0.784   0.6092   1.7471   5.0088
 SHR  C10  C  CH1   0  -0.218  -0.0072   0.4404   4.9170
 SHR  C9   C  CH2   0  -0.435   0.2155  -0.3048   3.5861
 SHR  C8   C  CH2   0  -0.425  -0.3890   0.4202   2.3913
 SHR  C7   C  CH2   0  -0.446  -0.1314  -0.3164   1.0831
 SHR  C6   C  CH2   0  -0.258  -0.7249   0.4012  -0.1178
 SHR  N    N  NH1   0  -0.608  -0.4105  -0.3014  -1.3497
 SHR  C11  C  C     0   0.547   0.5010  -0.4258   6.0510
 SHR  O5   O  OH1   0  -0.595  -0.2840  -1.4765   6.2640
 SHR  O6   O  O     0  -0.441   1.5130  -0.2212   6.6724
 SHR  C4   C  CH1   0  -0.162  -0.8280   0.3975  -2.5411
 SHR  C3   C  CH2   0  -0.455  -0.1534  -0.1823  -3.7930
 SHR  C2   C  CH2   0  -0.594   1.3354   0.1295  -3.8383
 SHR  C1   C  C     0   0.558   2.0068  -0.3944  -5.0787
 SHR  O1   O  OH1   0  -0.595   3.3154  -0.1646  -5.0592
 SHR  O2   O  O     0  -0.441   1.4484  -0.9540  -5.9887
 SHR  C5   C  C     0   0.530  -2.3301   0.3094  -2.7496
 SHR  O3   O  OH1   0  -0.578  -2.8550  -0.8306  -2.3309
 SHR  O4   O  O     0  -0.446  -2.9711   1.1781  -3.2898
 SHR  H12  H  HNH2  0   0.344   1.5889   1.6868   4.7576
 SHR  H11  H  HNH2  0   0.357   0.1839   2.3673   4.3328
 SHR  H10  H  HCH1  0   0.268  -1.0858   0.5673   5.0576
 SHR  H92  H  HCH2  0   0.229   1.2929  -0.4351   3.4328
 SHR  H91  H  HCH2  0   0.235  -0.2153  -1.3073   3.6465
 SHR  H82  H  HCH2  0   0.223  -1.4676   0.5324   2.5448
 SHR  H81  H  HCH2  0   0.214   0.0200   1.4321   2.3150
 SHR  H72  H  HCH2  0   0.219   0.9499  -0.4229   0.9401
 SHR  H71  H  HCH2  0   0.224  -0.5385  -1.3301   1.1384
 SHR  H62  H  HCH2  0   0.221  -1.8126   0.4509  -0.0038
 SHR  H61  H  HCH2  0   0.196  -0.3699   1.4440  -0.1352
 SHR  H    H  HNH1  0   0.353   0.5892  -0.4527  -1.3842
 SHR  HO5  H  HOH1  0   0.481   0.0993  -2.0416   6.9512
 SHR  H4   H  HCH1  0   0.241  -0.6006   1.4754  -2.4997
 SHR  H32  H  HCH2  0   0.254  -0.3195  -1.2615  -3.8195
 SHR  H31  H  HCH2  0   0.261  -0.6306   0.2400  -4.6787
 SHR  H22  H  HCH2  0   0.290   1.4995   1.2110  -3.7949
 SHR  H21  H  HCH2  0   0.279   1.8704  -0.2830  -2.9785
 SHR  HO1  H  HOH1  0   0.481   3.7255  -0.5099  -5.8662
 SHR  HO3  H  HOH1  0   0.480  -3.8046  -0.8411  -2.5252

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
 SHR  N1   C10  single  1.448  0.020  1.448
 SHR  N1   H12  single  0.890  0.020  1.040
 SHR  N1   H11  single  0.890  0.020  1.040
 SHR  C10  C9   single  1.542  0.020  1.542
 SHR  C10  C11  single  1.515  0.020  1.515
 SHR  C10  H10  single  0.970  0.020  1.090
 SHR  C9   C8   single  1.523  0.020  1.523
 SHR  C9   H92  single  0.970  0.020  1.090
 SHR  C9   H91  single  0.970  0.020  1.090
 SHR  C8   C7   single  1.523  0.020  1.523
 SHR  C8   H82  single  0.970  0.020  1.090
 SHR  C8   H81  single  0.970  0.020  1.090
 SHR  C7   C6   single  1.520  0.020  1.520
 SHR  C7   H72  single  0.970  0.020  1.090
 SHR  C7   H71  single  0.970  0.020  1.090
 SHR  C6   N    single  1.453  0.020  1.453
 SHR  C6   H62  single  0.970  0.020  1.090
 SHR  C6   H61  single  0.970  0.020  1.090
 SHR  N    C4   single  1.443  0.020  1.443
 SHR  N    H    single  0.860  0.020  0.860
 SHR  C11  O5   single  1.329  0.020  1.329
 SHR  C11  O6   double  1.205  0.020  1.205
 SHR  O5   HO5  single  0.850  0.020  0.980
 SHR  C4   C3   single  1.536  0.020  1.536
 SHR  C4   C5   single  1.519  0.020  1.519
 SHR  C4   H4   single  0.970  0.020  1.090
 SHR  C3   C2   single  1.522  0.020  1.522
 SHR  C3   H32  single  0.970  0.020  1.090
 SHR  C3   H31  single  0.970  0.020  1.090
 SHR  C2   C1   single  1.505  0.020  1.505
 SHR  C2   H22  single  0.970  0.020  1.090
 SHR  C2   H21  single  0.970  0.020  1.090
 SHR  C1   O1   single  1.329  0.020  1.329
 SHR  C1   O2   double  1.205  0.020  1.205
 SHR  O1   HO1  single  0.850  0.020  0.980
 SHR  C5   O3   single  1.323  0.020  1.323
 SHR  C5   O4   double  1.207  0.020  1.207
 SHR  O3   HO3  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
 SHR  H11  N1   H12  106.11  3.000
 SHR  H11  N1   C10  109.40  3.000
 SHR  H12  N1   C10  110.02  3.000
 SHR  H10  C10  C11  107.50  3.000
 SHR  H10  C10  C9   108.01  3.000
 SHR  C11  C10  C9   108.75  3.000
 SHR  H10  C10  N1   107.85  3.000
 SHR  C11  C10  N1   109.01  3.000
 SHR  C9   C10  N1   115.44  3.000
 SHR  H91  C9   H92  106.63  3.000
 SHR  H91  C9   C8   108.89  3.000
 SHR  H92  C9   C8   109.71  3.000
 SHR  H91  C9   C10  109.80  3.000
 SHR  H92  C9   C10  108.68  3.000
 SHR  C8   C9   C10  112.95  3.000
 SHR  H81  C8   H82  106.45  3.000
 SHR  H81  C8   C7   108.91  3.000
 SHR  H82  C8   C7   109.66  3.000
 SHR  H81  C8   C9   110.28  3.000
 SHR  H82  C8   C9   109.26  3.000
 SHR  C7   C8   C9   112.11  3.000
 SHR  H71  C7   H72  106.49  3.000
 SHR  H71  C7   C6   109.40  3.000
 SHR  H72  C7   C6   109.15  3.000
 SHR  H71  C7   C8   109.98  3.000
 SHR  H72  C7   C8   109.02  3.000
 SHR  C6   C7   C8   112.60  3.000
 SHR  H61  C6   H62  106.19  3.000
 SHR  H61  C6   N    112.00  3.000
 SHR  H62  C6   N    108.99  3.000
 SHR  H61  C6   C7   109.49  3.000
 SHR  H62  C6   C7   109.10  3.000
 SHR  N    C6   C7   110.93  3.000
 SHR  H    N    C4   109.28  3.000
 SHR  H    N    C6   108.37  3.000
 SHR  C4   N    C6   113.79  3.000
 SHR  O6   C11  O5   123.21  3.000
 SHR  O6   C11  C10  124.80  3.000
 SHR  O5   C11  C10  111.96  3.000
 SHR  HO5  O5   C11  109.96  3.000
 SHR  H4   C4   C5   105.42  3.000
 SHR  H4   C4   C3   108.01  3.000
 SHR  C5   C4   C3   107.49  3.000
 SHR  H4   C4   N    112.51  3.000
 SHR  C5   C4   N    111.80  3.000
 SHR  C3   C4   N    111.29  3.000
 SHR  H31  C3   H32  107.23  3.000
 SHR  H31  C3   C2   108.93  3.000
 SHR  H32  C3   C2   110.52  3.000
 SHR  H31  C3   C4   108.88  3.000
 SHR  H32  C3   C4   109.03  3.000
 SHR  C2   C3   C4   112.13  3.000
 SHR  H21  C2   H22  105.56  3.000
 SHR  H21  C2   C1   107.37  3.000
 SHR  H22  C2   C1   108.05  3.000
 SHR  H21  C2   C3   112.20  3.000
 SHR  H22  C2   C3   110.36  3.000
 SHR  C1   C2   C3   112.94  3.000
 SHR  O2   C1   O1   123.20  3.000
 SHR  O2   C1   C2   125.26  3.000
 SHR  O1   C1   C2   111.54  3.000
 SHR  HO1  O1   C1   110.06  3.000
 SHR  O4   C5   O3   123.44  3.000
 SHR  O4   C5   C4   123.01  3.000
 SHR  O3   C5   C4   113.50  3.000
 SHR  HO3  O3   C5   109.54  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
 SHR  CONST_01  HO5  O5  C11  C10   180.00   0.0  0
 SHR  CONST_02  HO3  O3  C5   C4    180.00   0.0  0
 SHR  CONST_03  HO1  O1  C1   C2    180.00   0.0  0
 SHR  Var_01    C7   C8  C9   C10   178.74  30.0  3
 SHR  Var_02    C6   C7  C8   C9   -179.74  30.0  3
 SHR  Var_03    N    C6  C7   C8    177.60  30.0  3
 SHR  Var_04    C4   N   C6   C7   -174.06  30.0  3
 SHR  Var_05    C1   C2  C3   C4   -178.26  30.0  3
 SHR  Var_06    O1   C1  C2   C3   -176.94  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
 SHR  chir_01  C10  N1  C9  C11  negativ
 SHR  chir_02  C4   N   C3  C5   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
 SHR  plan-1  C10  0.020
 SHR  plan-1  C11  0.020
 SHR  plan-1  O5   0.020
 SHR  plan-1  O6   0.020
 SHR  plan-1  HO5  0.020
 SHR  plan-2  C2   0.020
 SHR  plan-2  C1   0.020
 SHR  plan-2  O1   0.020
 SHR  plan-2  O2   0.020
 SHR  plan-2  HO1  0.020
 SHR  plan-3  C4   0.020
 SHR  plan-3  C5   0.020
 SHR  plan-3  O3   0.020
 SHR  plan-3  O4   0.020
 SHR  plan-3  HO3  0.020

