# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 07:16:16 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2S)-2-amino-2-methyldec-8-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CCCCCC[C@](C)(N)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
 ZS8  ZS8  '(2S)-2-amino-2-methyldec-8-ynoic acid'  ligand  32  14  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZS8
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
 ZS8  N    N  NH2    0  -0.804  -2.7661   1.5421   0.8132
 ZS8  CA   C  CT     0  -0.033  -2.7116   0.4307  -0.1324
 ZS8  C    C  C      0   0.424  -3.9315  -0.4980   0.1125
 ZS8  O    O  O      0  -0.612  -4.2783  -1.2298  -0.8360
 ZS8  CB2  C  CH3    0  -0.646  -2.7548   1.0126  -1.5437
 ZS8  CB1  C  CH2    0  -0.410  -1.4620  -0.4632   0.0472
 ZS8  CG1  C  CH2    0  -0.430  -0.1144   0.2352  -0.0993
 ZS8  CD1  C  CH2    0  -0.413   1.0534  -0.7337   0.0477
 ZS8  CZ1  C  CH2    0  -0.419   2.4122  -0.0496  -0.0228
 ZS8  CE1  C  CH2    0  -0.601   3.5623  -1.0563   0.0715
 ZS8  CT1  C  CSP    0   0.150   4.8806  -0.4309   0.0431
 ZS8  CI1  C  CSP    0  -0.074   5.9621   0.0989   0.0231
 ZS8  CK1  C  CH3    0  -0.817   7.2733   0.7322  -0.0026
 ZS8  H1   H  HNH2   0   0.327  -2.8554   1.1704   1.7500
 ZS8  H2   H  HNH2   0   0.327  -1.8952   2.0592   0.7887
 ZS8  H7   H  HCH3   0   0.217  -3.7071   1.5116  -1.7306
 ZS8  H8   H  HCH3   0   0.207  -1.9685   1.7569  -1.6902
 ZS8  H9   H  HCH3   0   0.214  -2.6248   0.2401  -2.3002
 ZS8  H10  H  HCH2   0   0.209  -1.5061  -0.9251   1.0414
 ZS8  H11  H  HCH2   0   0.205  -1.5136  -1.2865  -0.6732
 ZS8  H12  H  HCH2   0   0.217  -0.0455   0.7284  -1.0738
 ZS8  H13  H  HCH2   0   0.202  -0.0149   1.0241   0.6533
 ZS8  H14  H  HCH2   0   0.212   0.9682  -1.2680   1.0006
 ZS8  H15  H  HCH2   0   0.213   0.9885  -1.4982  -0.7344
 ZS8  H16  H  HCH2   0   0.224   2.4987   0.5119  -0.9574
 ZS8  H17  H  HCH2   0   0.224   2.5020   0.6793   0.7874
 ZS8  H18  H  HCH2   0   0.255   3.4611  -1.6396   0.9918
 ZS8  H19  H  HCH2   0   0.256   3.4842  -1.7741  -0.7502
 ZS8  H20  H  HCH3   0   0.262   8.0640   0.0065   0.1907
 ZS8  H21  H  HCH3   0   0.262   7.4720   1.1883  -0.9728
 ZS8  H22  H  HCH3   0   0.262   7.3501   1.5142   0.7532
 ZS8  OXT  O  OC    -1  -0.611  -4.4405  -0.4810   1.2520

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
 ZS8  CK1  CI1  single  1.456  0.020  1.456
 ZS8  CI1  CT1  triple  1.204  0.020  1.204
 ZS8  CT1  CE1  single  1.459  0.020  1.459
 ZS8  CE1  CZ1  single  1.531  0.020  1.531
 ZS8  CZ1  CD1  single  1.523  0.020  1.523
 ZS8  CD1  CG1  single  1.524  0.020  1.524
 ZS8  CG1  CB1  single  1.525  0.020  1.525
 ZS8  CB1  CA   single  1.547  0.020  1.547
 ZS8  CA   C    single  1.553  0.020  1.553
 ZS8  CA   N    single  1.460  0.020  1.460
 ZS8  CA   CB2  single  1.527  0.020  1.527
 ZS8  C    O    deloc   1.247  0.020  1.247
 ZS8  N    H1   single  0.890  0.020  1.040
 ZS8  N    H2   single  0.890  0.020  1.040
 ZS8  CB2  H7   single  0.970  0.020  1.090
 ZS8  CB2  H8   single  0.970  0.020  1.090
 ZS8  CB2  H9   single  0.970  0.020  1.090
 ZS8  CB1  H10  single  0.970  0.020  1.090
 ZS8  CB1  H11  single  0.970  0.020  1.090
 ZS8  CG1  H12  single  0.970  0.020  1.090
 ZS8  CG1  H13  single  0.970  0.020  1.090
 ZS8  CD1  H14  single  0.970  0.020  1.090
 ZS8  CD1  H15  single  0.970  0.020  1.090
 ZS8  CZ1  H16  single  0.970  0.020  1.090
 ZS8  CZ1  H17  single  0.970  0.020  1.090
 ZS8  CE1  H18  single  0.970  0.020  1.090
 ZS8  CE1  H19  single  0.970  0.020  1.090
 ZS8  CK1  H20  single  0.970  0.020  1.090
 ZS8  CK1  H21  single  0.970  0.020  1.090
 ZS8  CK1  H22  single  0.970  0.020  1.090
 ZS8  C    OXT  deloc   1.248  0.020  1.248

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
 ZS8  H2   N    H1   106.61  3.000
 ZS8  H2   N    CA   109.92  3.000
 ZS8  H1   N    CA   108.86  3.000
 ZS8  CB1  CA   CB2  110.51  3.000
 ZS8  CB2  CA   C    110.57  3.000
 ZS8  CB1  CA   C    105.71  3.000
 ZS8  CB2  CA   N    107.90  3.000
 ZS8  C    CA   N    108.89  3.000
 ZS8  CB1  CA   N    113.25  3.000
 ZS8  OXT  C    O    126.08  3.000
 ZS8  OXT  C    CA   117.14  3.000
 ZS8  O    C    CA   116.71  3.000
 ZS8  H9   CB2  H8   107.71  3.000
 ZS8  H9   CB2  H7   108.03  3.000
 ZS8  H8   CB2  H7   107.07  3.000
 ZS8  H9   CB2  CA   111.61  3.000
 ZS8  H8   CB2  CA   111.29  3.000
 ZS8  H7   CB2  CA   110.93  3.000
 ZS8  H11  CB1  H10  106.13  3.000
 ZS8  H11  CB1  CG1  108.83  3.000
 ZS8  H10  CB1  CG1  108.38  3.000
 ZS8  H11  CB1  CA   108.66  3.000
 ZS8  H10  CB1  CA   108.42  3.000
 ZS8  CG1  CB1  CA   115.98  3.000
 ZS8  H13  CG1  H12  106.36  3.000
 ZS8  H13  CG1  CD1  108.79  3.000
 ZS8  H12  CG1  CD1  108.91  3.000
 ZS8  H13  CG1  CB1  110.14  3.000
 ZS8  H12  CG1  CB1  110.34  3.000
 ZS8  CD1  CG1  CB1  112.12  3.000
 ZS8  H15  CD1  H14  106.02  3.000
 ZS8  H15  CD1  CZ1  109.46  3.000
 ZS8  H14  CD1  CZ1  109.19  3.000
 ZS8  H15  CD1  CG1  109.22  3.000
 ZS8  H14  CD1  CG1  109.52  3.000
 ZS8  CZ1  CD1  CG1  113.17  3.000
 ZS8  H17  CZ1  H16  106.52  3.000
 ZS8  H17  CZ1  CE1  109.32  3.000
 ZS8  H16  CZ1  CE1  109.31  3.000
 ZS8  H17  CZ1  CD1  109.78  3.000
 ZS8  H16  CZ1  CD1  109.92  3.000
 ZS8  CE1  CZ1  CD1  111.83  3.000
 ZS8  H19  CE1  H18  105.98  3.000
 ZS8  H19  CE1  CT1  109.33  3.000
 ZS8  H18  CE1  CT1  109.17  3.000
 ZS8  H19  CE1  CZ1  109.37  3.000
 ZS8  H18  CE1  CZ1  109.43  3.000
 ZS8  CT1  CE1  CZ1  113.30  3.000
 ZS8  CI1  CT1  CE1  180.00  3.000
 ZS8  CK1  CI1  CT1  180.00  3.000
 ZS8  H22  CK1  H21  107.69  3.000
 ZS8  H22  CK1  H20  107.66  3.000
 ZS8  H21  CK1  H20  107.69  3.000
 ZS8  H22  CK1  CI1  111.29  3.000
 ZS8  H21  CK1  CI1  111.21  3.000
 ZS8  H20  CK1  CI1  111.12  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
 ZS8  Var_01  CD1  CG1  CB1  CA   -178.09  30.0  1
 ZS8  Var_02  CZ1  CD1  CG1  CB1  -177.03  30.0  1
 ZS8  Var_03  CE1  CZ1  CD1  CG1  -177.70  30.0  1
 ZS8  Var_04  CT1  CE1  CZ1  CD1  -178.45  30.0  1
 ZS8  Var_05  H20  CK1  CI1  CT1   -22.71  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
 ZS8  chir_01  CA  C  N  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
 ZS8  plan-1  CA   0.020
 ZS8  plan-1  C    0.020
 ZS8  plan-1  O    0.020
 ZS8  plan-1  OXT  0.020

