# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:30:21 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2S)-5-amino-2-[(1-propyl-1H-imidazol-4-yl)methyl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1cnc(C[C@H](CCCN)C(O)=O)c1
#
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
 720  720  '(2S)-5-amino-2-[(1-propyl-1H-imidazol-4-yl)methyl]pentanoic acid'  ligand  37  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_720
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
 720  N     N  NH2    0  -0.792   1.7028  -5.9573  -1.8985
 720  CA    C  CH2    0  -0.282   1.4124  -4.5311  -1.8609
 720  CG    C  CR15   0   0.076  -3.5606   0.7018   2.2297
 720  CE1   C  CH3    0  -0.669  -2.4180   1.3049   6.7794
 720  CE2   C  CH2    0  -0.291  -2.4996   1.6383   4.2902
 720  CZ    C  CH2    0  -0.431  -2.4180   0.6207   5.4200
 720  CH    C  CH2    0  -0.443   0.3193  -4.0996  -0.8869
 720  CM    C  CH2    0  -0.410   0.0660  -2.5979  -0.9245
 720  CA2   C  CH1    0  -0.318  -0.9287  -2.0985   0.1231
 720  CB2   C  CH2    0  -0.502  -1.0558  -0.5719   0.0275
 720  CG2   C  CR5    0   0.138  -1.8540   0.0464   1.1249
 720  CD3   C  CR15   0  -0.145  -1.3860   0.6077   2.2827
 720  N2    N  N      0  -0.462  -3.2206   0.1159   1.1087
 720  C     C  C      0   0.424  -2.2986  -2.7805  -0.0474
 720  N1    N  NR5    0  -0.397  -2.4874   1.0273   2.9770
 720  O     O  O      0  -0.625  -2.8654  -2.6112  -1.1485
 720  OXT   O  OC    -1  -0.622  -2.7314  -3.4598   0.9039
 720  HN1   H  HNH2   0   0.336   0.8532  -6.4632  -2.1197
 720  HN2   H  HNH2   0   0.336   1.9639  -6.2685  -0.9704
 720  HAC1  H  HCH2   0   0.209   1.1396  -4.2118  -2.8716
 720  HAC2  H  HCH2   0   0.209   2.3392  -4.0015  -1.6185
 720  HHC1  H  HCH2   0   0.204   0.6020  -4.4025   0.1278
 720  HHC2  H  HCH2   0   0.211  -0.6023  -4.6403  -1.1276
 720  HE21  H  HCH2   0   0.256  -1.6641   2.3374   4.3491
 720  HE22  H  HCH2   0   0.258  -3.4139   2.2274   4.3765
 720  HZC1  H  HCH2   0   0.232  -1.5116   0.0208   5.3038
 720  HZC2  H  HCH2   0   0.231  -3.2636  -0.0674   5.3442
 720  HE11  H  HCH3   0   0.224  -1.5671   1.9809   6.8825
 720  HE12  H  HCH3   0   0.237  -2.3602   0.5755   7.5866
 720  HE13  H  HCH3   0   0.224  -3.3261   1.8922   6.9271
 720  HG    H  HCR5   0   0.270  -4.5683   0.9267   2.5483
 720  HMC1  H  HCH2   0   0.203  -0.2878  -2.3133  -1.9206
 720  HMC2  H  HCH2   0   0.203   1.0185  -2.0739  -0.7803
 720  HA2   H  HCH1   0   0.191  -0.5344  -2.3436   1.1161
 720  HB21  H  HCH2   0   0.220  -1.4980  -0.3156  -0.9387
 720  HB22  H  HCH2   0   0.222  -0.0520  -0.1379   0.0369
 720  HD3   H  HCR5   0   0.277  -0.3846   0.7516   2.6554

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
 720  N    CA    single    1.456  0.020  1.456
 720  N    HN1   single    0.890  0.020  1.040
 720  N    HN2   single    0.890  0.020  1.040
 720  CA   CH    single    1.526  0.020  1.526
 720  CA   HAC1  single    0.970  0.020  1.090
 720  CA   HAC2  single    0.970  0.020  1.090
 720  CG   N2    aromatic  1.310  0.020  1.310
 720  CG   N1    aromatic  1.348  0.020  1.348
 720  CG   HG    single    0.930  0.020  1.080
 720  CE1  CZ    single    1.522  0.020  1.522
 720  CE1  HE11  single    0.970  0.020  1.090
 720  CE1  HE12  single    0.970  0.020  1.090
 720  CE1  HE13  single    0.970  0.020  1.090
 720  CE2  CZ    single    1.523  0.020  1.523
 720  CE2  N1    single    1.448  0.020  1.448
 720  CE2  HE21  single    0.970  0.020  1.090
 720  CE2  HE22  single    0.970  0.020  1.090
 720  CZ   HZC1  single    0.970  0.020  1.090
 720  CZ   HZC2  single    0.970  0.020  1.090
 720  CH   CM    single    1.523  0.020  1.523
 720  CH   HHC1  single    0.970  0.020  1.090
 720  CH   HHC2  single    0.970  0.020  1.090
 720  CM   CA2   single    1.529  0.020  1.529
 720  CM   HMC1  single    0.970  0.020  1.090
 720  CM   HMC2  single    0.970  0.020  1.090
 720  CA2  CB2   single    1.535  0.020  1.535
 720  CA2  C     single    1.540  0.020  1.540
 720  CA2  HA2   single    0.970  0.020  1.090
 720  CB2  CG2   single    1.491  0.020  1.491
 720  CB2  HB21  single    0.970  0.020  1.090
 720  CB2  HB22  single    0.970  0.020  1.090
 720  CG2  CD3   aromatic  1.369  0.020  1.369
 720  CG2  N2    aromatic  1.368  0.020  1.368
 720  CD3  N1    aromatic  1.368  0.020  1.368
 720  CD3  HD3   single    0.930  0.020  1.080
 720  C    O     deloc     1.250  0.020  1.250
 720  C    OXT   deloc     1.247  0.020  1.247

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
 720  HN2   N    HN1   105.24  3.000
 720  HN2   N    CA    109.18  3.000
 720  HN1   N    CA    109.12  3.000
 720  HAC2  CA   HAC1  105.92  3.000
 720  HAC2  CA   CH    109.16  3.000
 720  HAC1  CA   CH    109.16  3.000
 720  HAC2  CA   N     108.11  3.000
 720  HAC1  CA   N     108.16  3.000
 720  CH    CA   N     115.87  3.000
 720  HG    CG   N1    121.93  3.000
 720  HG    CG   N2    125.98  3.000
 720  N1    CG   N2    112.08  3.000
 720  HE13  CE1  HE12  107.71  3.000
 720  HE13  CE1  HE11  107.61  3.000
 720  HE12  CE1  HE11  107.65  3.000
 720  HE13  CE1  CZ    111.28  3.000
 720  HE12  CE1  CZ    111.15  3.000
 720  HE11  CE1  CZ    111.27  3.000
 720  HE22  CE2  HE21  106.94  3.000
 720  HE22  CE2  N1    107.85  3.000
 720  HE21  CE2  N1    108.23  3.000
 720  HE22  CE2  CZ    110.31  3.000
 720  HE21  CE2  CZ    110.32  3.000
 720  N1    CE2  CZ    112.97  3.000
 720  HZC2  CZ   HZC1  106.78  3.000
 720  HZC2  CZ   CE2   109.14  3.000
 720  HZC1  CZ   CE2   109.41  3.000
 720  HZC2  CZ   CE1   110.19  3.000
 720  HZC1  CZ   CE1   109.98  3.000
 720  CE2   CZ   CE1   111.24  3.000
 720  HHC2  CH   HHC1  106.50  3.000
 720  HHC2  CH   CM    109.96  3.000
 720  HHC1  CH   CM    109.77  3.000
 720  HHC2  CH   CA    108.83  3.000
 720  HHC1  CH   CA    109.14  3.000
 720  CM    CH   CA    112.46  3.000
 720  HMC2  CM   HMC1  106.03  3.000
 720  HMC2  CM   CA2   108.60  3.000
 720  HMC1  CM   CA2   109.17  3.000
 720  HMC2  CM   CH    108.87  3.000
 720  HMC1  CM   CH    109.42  3.000
 720  CA2   CM   CH    114.42  3.000
 720  HA2   CA2  C     108.74  3.000
 720  HA2   CA2  CB2   107.98  3.000
 720  C     CA2  CB2   111.10  3.000
 720  HA2   CA2  CM    108.28  3.000
 720  C     CA2  CM    111.00  3.000
 720  CB2   CA2  CM    109.64  3.000
 720  HB22  CB2  HB21  106.61  3.000
 720  HB22  CB2  CG2   108.69  3.000
 720  HB21  CB2  CG2   109.68  3.000
 720  HB22  CB2  CA2   108.55  3.000
 720  HB21  CB2  CA2   108.77  3.000
 720  CG2   CB2  CA2   114.26  3.000
 720  N2    CG2  CD3   109.30  3.000
 720  N2    CG2  CB2   123.15  3.000
 720  CD3   CG2  CB2   127.54  3.000
 720  HD3   CD3  N1    122.11  3.000
 720  HD3   CD3  CG2   131.64  3.000
 720  N1    CD3  CG2   106.24  3.000
 720  CG2   N2   CG    105.77  3.000
 720  OXT   C    O     126.06  3.000
 720  OXT   C    CA2   117.76  3.000
 720  O     C    CA2   116.17  3.000
 720  CD3   N1   CE2   126.60  3.000
 720  CD3   N1   CG    106.60  3.000
 720  CE2   N1   CG    126.72  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
 720  CONST_01  CD3   CG2  N2   CG      0.00   0.0  0
 720  CONST_02  CG2   CD3  N1   CG      0.00   0.0  0
 720  CONST_03  N1    CG   N2   CG2     0.00   0.0  0
 720  CONST_04  N2    CG   N1   CD3     0.00   0.0  0
 720  CONST_05  N1    CD3  CG2  N2      0.00   0.0  0
 720  CONST_06  CB2   CG2  N2   CG    180.00   0.0  0
 720  CONST_07  N2    CG   N1   CE2   180.00   0.0  0
 720  CONST_08  CG2   CD3  N1   CE2   180.00   0.0  0
 720  CONST_09  N1    CD3  CG2  CB2   180.00   0.0  0
 720  CONST_10  HD3   CD3  N1   CG    180.00   0.0  0
 720  CONST_11  HG    CG   N2   CG2   180.00   0.0  0
 720  Var_01    CZ    CE2  N1   CG     94.61  30.0  2
 720  Var_02    CD3   CG2  CB2  CA2    96.07  30.0  2
 720  Var_03    N1    CE2  CZ   CE1   179.37  30.0  2
 720  Var_04    CM    CH   CA   N    -179.21  30.0  3
 720  Var_05    CA2   CM   CH   CA   -174.67  30.0  3
 720  Var_06    HE11  CE1  CZ   CE2   -60.07  30.0  3
 720  Var_07    HN1   N    CA   CH     57.01  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
 720  chir_01  CA2  CM  CB2  C  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
 720  plan-1  CG   0.020
 720  plan-1  CE2  0.020
 720  plan-1  CB2  0.020
 720  plan-1  CG2  0.020
 720  plan-1  CD3  0.020
 720  plan-1  N2   0.020
 720  plan-1  N1   0.020
 720  plan-1  HG   0.020
 720  plan-1  HD3  0.020
 720  plan-2  CA2  0.020
 720  plan-2  C    0.020
 720  plan-2  O    0.020
 720  plan-2  OXT  0.020

