# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:44:03 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (1S)-1-carboxy-2-(1H-imidazol-5-yl)-N,N,N-trimethylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)[C@@H](Cc1[nH]cnc1)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
 AVJ  AVJ  (1S)-1-carboxy-2-(1H-imidazol-5-yl)-N,N,N-trimethylethanaminium  ligand  30  14  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AVJ
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
 AVJ  CAA   C  CH3   0  -0.567   0.3207  -1.7468   1.0293
 AVJ  CAB   C  CH3   0  -0.561  -0.7731  -1.8226  -1.1398
 AVJ  CAC   C  CH3   0  -0.577  -2.0779  -1.7551   0.9125
 AVJ  CAM   C  CR15  0  -0.241   2.5711   0.1628  -1.1780
 AVJ  CAP   C  CH2   0  -0.581   0.1408   0.9578  -0.7064
 AVJ  NAR   N  NR15  0  -0.603   2.2151   1.1693   0.7075
 AVJ  NAT   N  N     0  -0.434   3.7655   0.2098  -0.5177
 AVJ  CAX   C  C     0   0.535  -2.2282   0.8361  -0.0908
 AVJ  CAY   C  CR5   0   0.278   1.5866   0.7526  -0.4333
 AVJ  CAZ   C  CR15  0   0.087   3.5141   0.8210   0.6107
 AVJ  CBC   C  CH1   0  -0.184  -0.8479   0.2767   0.2546
 AVJ  NBE   N  NT    1  -0.394  -0.8450  -1.2429   0.2350
 AVJ  HAA   H  HCH3  0   0.310   1.2506  -1.4034   0.5926
 AVJ  HAAA  H  HCH3  0   0.303   0.2299  -1.3952   2.0529
 AVJ  HAAB  H  HCH3  0   0.308   0.2944  -2.8321   1.0119
 AVJ  HAB   H  HCH3  0   0.306  -0.8685  -2.9010  -1.0517
 AVJ  HABA  H  HCH3  0   0.307  -1.5796  -1.4332  -1.7508
 AVJ  HABB  H  HCH3  0   0.293   0.1870  -1.5876  -1.5877
 AVJ  HAC   H  HCH3  0   0.308  -2.1953  -1.2562   1.8716
 AVJ  HACA  H  HCH3  0   0.306  -2.9489  -1.5890   0.2865
 AVJ  HACB  H  HCH3  0   0.312  -1.9606  -2.8228   1.0745
 AVJ  HAM   H  HCR5  0   0.264   2.4701  -0.2908  -2.1532
 AVJ  HAP   H  HCH2  0   0.323  -0.0833   2.0276  -0.6448
 AVJ  HAPA  H  HCH2  0   0.311  -0.0734   0.6725  -1.7359
 AVJ  HNAR  H  HNR5  0   0.422   1.7982   1.6640   1.4812
 AVJ  HAZ   H  HCR5  0   0.286   4.2279   1.0421   1.3889
 AVJ  HBC   H  HCH1  0   0.344  -0.6143   0.5423   1.2865
 AVJ  HOL   H  HOH1  0   0.500  -3.4922   2.0635   0.5960
 AVJ  OAH   O  O     0  -0.405  -2.8080   0.6029  -1.1180
 AVJ  OAL   O  OH1   0  -0.558  -2.6486   1.6546   0.8491

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
 AVJ  CAA  NBE   single    1.498  0.020  1.498
 AVJ  CAA  HAA   single    0.970  0.020  1.090
 AVJ  CAA  HAAA  single    0.970  0.020  1.090
 AVJ  CAA  HAAB  single    0.970  0.020  1.090
 AVJ  CAB  NBE   single    1.494  0.020  1.494
 AVJ  CAB  HAB   single    0.970  0.020  1.090
 AVJ  CAB  HABA  single    0.970  0.020  1.090
 AVJ  CAB  HABB  single    0.970  0.020  1.090
 AVJ  CAC  NBE   single    1.497  0.020  1.497
 AVJ  CAC  HAC   single    0.970  0.020  1.090
 AVJ  CAC  HACA  single    0.970  0.020  1.090
 AVJ  CAC  HACB  single    0.970  0.020  1.090
 AVJ  OAH  CAX   double    1.202  0.020  1.202
 AVJ  OAL  CAX   single    1.315  0.020  1.315
 AVJ  CAM  NAT   aromatic  1.366  0.020  1.366
 AVJ  CAM  CAY   aromatic  1.368  0.020  1.368
 AVJ  CAM  HAM   single    0.930  0.020  1.080
 AVJ  CAP  CAY   single    1.486  0.020  1.486
 AVJ  CAP  CBC   single    1.538  0.020  1.538
 AVJ  CAP  HAP   single    0.970  0.020  1.090
 AVJ  CAP  HAPA  single    0.970  0.020  1.090
 AVJ  NAR  CAY   aromatic  1.368  0.020  1.368
 AVJ  NAR  CAZ   aromatic  1.348  0.020  1.348
 AVJ  NAR  HNAR  single    0.860  0.020  1.020
 AVJ  NAT  CAZ   aromatic  1.308  0.020  1.308
 AVJ  CAX  CBC   single    1.529  0.020  1.529
 AVJ  CAZ  HAZ   single    0.930  0.020  1.080
 AVJ  CBC  NBE   single    1.520  0.020  1.520
 AVJ  CBC  HBC   single    0.970  0.020  1.090
 AVJ  OAL  HOL   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
 AVJ  HAAB  CAA  HAAA  109.67  3.000
 AVJ  HAAB  CAA  HAA   109.34  3.000
 AVJ  HAAA  CAA  HAA   110.43  3.000
 AVJ  HAAB  CAA  NBE   107.99  3.000
 AVJ  HAAA  CAA  NBE   109.01  3.000
 AVJ  HAA   CAA  NBE   110.34  3.000
 AVJ  HABB  CAB  HABA  110.35  3.000
 AVJ  HABB  CAB  HAB   109.04  3.000
 AVJ  HABA  CAB  HAB   109.69  3.000
 AVJ  HABB  CAB  NBE   109.78  3.000
 AVJ  HABA  CAB  NBE   110.09  3.000
 AVJ  HAB   CAB  NBE   107.85  3.000
 AVJ  HACB  CAC  HACA  108.84  3.000
 AVJ  HACB  CAC  HAC   109.33  3.000
 AVJ  HACA  CAC  HAC   110.60  3.000
 AVJ  HACB  CAC  NBE   108.35  3.000
 AVJ  HACA  CAC  NBE   110.33  3.000
 AVJ  HAC   CAC  NBE   109.34  3.000
 AVJ  HAM   CAM  CAY   127.24  3.000
 AVJ  HAM   CAM  NAT   122.19  3.000
 AVJ  CAY   CAM  NAT   110.57  3.000
 AVJ  HAPA  CAP  HAP   105.59  3.000
 AVJ  HAPA  CAP  CBC   110.37  3.000
 AVJ  HAP   CAP  CBC   105.43  3.000
 AVJ  HAPA  CAP  CAY   109.20  3.000
 AVJ  HAP   CAP  CAY   108.90  3.000
 AVJ  CBC   CAP  CAY   116.72  3.000
 AVJ  HNAR  NAR  CAZ   125.45  3.000
 AVJ  HNAR  NAR  CAY   126.83  3.000
 AVJ  CAZ   NAR  CAY   107.71  3.000
 AVJ  CAZ   NAT  CAM   105.38  3.000
 AVJ  CBC   CAX  OAL   110.78  3.000
 AVJ  CBC   CAX  OAH   123.88  3.000
 AVJ  OAL   CAX  OAH   125.24  3.000
 AVJ  NAR   CAY  CAP   123.96  3.000
 AVJ  NAR   CAY  CAM   104.76  3.000
 AVJ  CAP   CAY  CAM   131.29  3.000
 AVJ  HAZ   CAZ  NAT   126.23  3.000
 AVJ  HAZ   CAZ  NAR   122.19  3.000
 AVJ  NAT   CAZ  NAR   111.59  3.000
 AVJ  HBC   CBC  NBE   104.79  3.000
 AVJ  HBC   CBC  CAX   108.54  3.000
 AVJ  NBE   CBC  CAX   111.39  3.000
 AVJ  HBC   CBC  CAP   110.22  3.000
 AVJ  NBE   CBC  CAP   115.70  3.000
 AVJ  CAX   CBC  CAP   106.09  3.000
 AVJ  CBC   NBE  CAC   109.55  3.000
 AVJ  CBC   NBE  CAB   113.58  3.000
 AVJ  CAC   NBE  CAB   108.87  3.000
 AVJ  CBC   NBE  CAA   109.33  3.000
 AVJ  CAC   NBE  CAA   106.61  3.000
 AVJ  CAB   NBE  CAA   108.66  3.000
 AVJ  HOL   OAL  CAX   110.70  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
 AVJ  CONST_01  NAR   CAZ  NAT  CAM    0.00   0.0  0
 AVJ  CONST_02  CAZ   NAR  CAY  CAM    0.00   0.0  0
 AVJ  CONST_03  NAT   CAM  CAY  NAR    0.00   0.0  0
 AVJ  CONST_04  CAY   NAR  CAZ  NAT    0.00   0.0  0
 AVJ  CONST_05  CAZ   NAT  CAM  CAY    0.00   0.0  0
 AVJ  CONST_06  NAT   CAM  CAY  CAP  180.00   0.0  0
 AVJ  CONST_07  CAZ   NAR  CAY  CAP  180.00   0.0  0
 AVJ  CONST_08  HAZ   CAZ  NAT  CAM  180.00   0.0  0
 AVJ  CONST_09  HNAR  NAR  CAY  CAM  180.00   0.0  0
 AVJ  CONST_10  HAM   CAM  CAY  NAR  180.00   0.0  0
 AVJ  CONST_11  HOL   OAL  CAX  OAH    0.00   0.0  0
 AVJ  Var_01    CBC   CAP  CAY  CAM  118.01  30.0  2
 AVJ  Var_02    HAB   CAB  NBE  CAA   63.19  30.0  3
 AVJ  Var_03    HAC   CAC  NBE  CAA   69.00  30.0  3
 AVJ  Var_04    HAA   CAA  NBE  CAB   63.19  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
 AVJ  chir_01  CBC  CAP  CAX  NBE  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
 AVJ  plan-1  CAM   0.020
 AVJ  plan-1  CAP   0.020
 AVJ  plan-1  NAR   0.020
 AVJ  plan-1  NAT   0.020
 AVJ  plan-1  CAY   0.020
 AVJ  plan-1  CAZ   0.020
 AVJ  plan-1  HAM   0.020
 AVJ  plan-1  HNAR  0.020
 AVJ  plan-1  HAZ   0.020
 AVJ  plan-2  CAX   0.020
 AVJ  plan-2  CBC   0.020
 AVJ  plan-2  HOL   0.020
 AVJ  plan-2  OAH   0.020
 AVJ  plan-2  OAL   0.020

