# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 05:13:12 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 1-[(2~{R})-butan-2-yl]imidazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)n1ccnc1C(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
 HL3  HL3  "1-[(2~{R})-butan-2-yl]imidazole-2-carboxylic acid"  ligand  23  12  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HL3
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
 HL3  C01  C  CR15   0  -0.225  32.4221  16.3913   -8.9924
 HL3  C02  C  CR15   0  -0.119  32.7050  17.5444   -9.6669
 HL3  N03  N  NR5    0  -0.426  31.5004  18.1210   -9.9435
 HL3  C04  C  CR5    0   0.265  30.5347  17.3092   -9.4245
 HL3  N05  N  N      0  -0.456  31.0797  16.2571   -8.8458
 HL3  C06  C  C      0   0.367  29.0312  17.5195   -9.5102
 HL3  O07  O  OC    -1  -0.577  28.3544  16.8051   -8.7558
 HL3  O08  O  O      0  -0.580  28.6156  18.3618  -10.3307
 HL3  C09  C  CH1    0  -0.134  31.3705  19.4310  -10.5833
 HL3  C10  C  CH2    0  -0.413  32.0025  20.5178   -9.7154
 HL3  C11  C  CH3    0  -0.665  31.4134  20.5961   -8.3147
 HL3  C12  C  CH3    0  -0.652  31.9607  19.3990  -11.9859
 HL3  H1   H  HCR5   0   0.236  33.1195  15.6590   -8.6133
 HL3  H2   H  HCR5   0   0.282  33.6415  17.9926   -9.9567
 HL3  H4   H  HCH1   0   0.276  30.3032  19.6163  -10.6584
 HL3  H5   H  HCH2   0   0.218  33.0857  20.3712   -9.6612
 HL3  H6   H  HCH2   0   0.232  31.8521  21.4706  -10.2295
 HL3  H7   H  HCH3   0   0.232  31.8449  21.4278   -7.7572
 HL3  H8   H  HCH3   0   0.220  30.3328  20.7459   -8.3485
 HL3  H9   H  HCH3   0   0.224  31.6046  19.6866   -7.7439
 HL3  H10  H  HCH3   0   0.235  31.7899  20.3562  -12.4791
 HL3  H11  H  HCH3   0   0.224  33.0371  19.2205  -11.9729
 HL3  H12  H  HCH3   0   0.237  31.4923  18.6224  -12.5908

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
 HL3  C12  C09  single    1.522  0.020  1.522
 HL3  C09  N03  single    1.464  0.020  1.464
 HL3  C09  C10  single    1.528  0.020  1.528
 HL3  O08  C06  deloc     1.247  0.020  1.247
 HL3  N03  C02  aromatic  1.364  0.020  1.364
 HL3  N03  C04  aromatic  1.364  0.020  1.364
 HL3  C02  C01  aromatic  1.366  0.020  1.366
 HL3  C10  C11  single    1.522  0.020  1.522
 HL3  C04  C06  single    1.521  0.020  1.521
 HL3  C04  N05  aromatic  1.319  0.020  1.319
 HL3  C06  O07  deloc     1.240  0.020  1.240
 HL3  C01  N05  aromatic  1.357  0.020  1.357
 HL3  C01  H1   single    0.930  0.020  1.080
 HL3  C02  H2   single    0.930  0.020  1.080
 HL3  C09  H4   single    0.970  0.020  1.090
 HL3  C10  H5   single    0.970  0.020  1.090
 HL3  C10  H6   single    0.970  0.020  1.090
 HL3  C11  H7   single    0.970  0.020  1.090
 HL3  C11  H8   single    0.970  0.020  1.090
 HL3  C11  H9   single    0.970  0.020  1.090
 HL3  C12  H10  single    0.970  0.020  1.090
 HL3  C12  H11  single    0.970  0.020  1.090
 HL3  C12  H12  single    0.970  0.020  1.090

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
 HL3  H1   C01  N05  122.26  3.000
 HL3  H1   C01  C02  127.75  3.000
 HL3  N05  C01  C02  109.99  3.000
 HL3  H2   C02  N03  122.49  3.000
 HL3  H2   C02  C01  131.60  3.000
 HL3  N03  C02  C01  105.91  3.000
 HL3  C09  N03  C04  129.50  3.000
 HL3  C04  N03  C02  107.25  3.000
 HL3  C09  N03  C02  123.05  3.000
 HL3  C06  C04  N05  122.94  3.000
 HL3  N05  C04  N03  110.44  3.000
 HL3  C06  C04  N03  126.60  3.000
 HL3  C04  N05  C01  106.41  3.000
 HL3  O08  C06  O07  127.41  3.000
 HL3  O07  C06  C04  115.19  3.000
 HL3  O08  C06  C04  117.39  3.000
 HL3  H4   C09  C12  108.72  3.000
 HL3  H4   C09  C10  108.94  3.000
 HL3  C12  C09  C10  112.22  3.000
 HL3  H4   C09  N03  105.68  3.000
 HL3  C10  C09  N03  110.59  3.000
 HL3  C12  C09  N03  110.46  3.000
 HL3  H6   C10  H5   106.04  3.000
 HL3  H6   C10  C11  109.57  3.000
 HL3  H5   C10  C11  110.15  3.000
 HL3  H6   C10  C09  107.22  3.000
 HL3  H5   C10  C09  110.01  3.000
 HL3  C11  C10  C09  113.54  3.000
 HL3  H9   C11  H8   107.71  3.000
 HL3  H9   C11  H7   107.41  3.000
 HL3  H8   C11  H7   107.63  3.000
 HL3  H9   C11  C10  111.78  3.000
 HL3  H8   C11  C10  111.21  3.000
 HL3  H7   C11  C10  110.90  3.000
 HL3  H12  C12  H11  108.29  3.000
 HL3  H12  C12  H10  107.89  3.000
 HL3  H11  C12  H10  107.67  3.000
 HL3  H12  C12  C09  111.08  3.000
 HL3  H11  C12  C09  112.02  3.000
 HL3  H10  C12  C09  109.74  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
 HL3  CONST_01  C04  N03  C02  C01     0.00   0.0  0
 HL3  CONST_02  N03  C04  N05  C01     0.00   0.0  0
 HL3  CONST_03  N05  C04  N03  C02     0.00   0.0  0
 HL3  CONST_04  C04  N05  C01  C02     0.00   0.0  0
 HL3  CONST_05  N05  C01  C02  N03     0.00   0.0  0
 HL3  CONST_06  C09  N03  C02  C01   180.00   0.0  0
 HL3  CONST_07  C06  C04  N05  C01   180.00   0.0  0
 HL3  CONST_08  C06  C04  N03  C02   180.00   0.0  0
 HL3  CONST_09  C09  N03  C04  N05   180.00   0.0  0
 HL3  CONST_10  H1   C01  C02  N03   180.00   0.0  0
 HL3  CONST_11  H2   C02  N03  C04   180.00   0.0  0
 HL3  CONST_12  H1   C01  N05  C04   180.00   0.0  0
 HL3  CONST_13  H2   C02  C01  N05   180.00   0.0  0
 HL3  Var_01    O08  C06  C04  N03    14.36  30.0  2
 HL3  Var_02    O07  C06  C04  N03  -166.67  30.0  2
 HL3  Var_03    O08  C06  C04  N05  -163.69  30.0  2
 HL3  Var_04    O07  C06  C04  N05    15.28  30.0  2
 HL3  Var_05    H7   C11  C10  C09  -176.05  30.0  3
 HL3  Var_06    H8   C11  C10  C09   -56.31  30.0  3
 HL3  Var_07    H9   C11  C10  C09    64.12  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
 HL3  chir_01  C09  C12  N03  C10  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
 HL3  plan-1  C01  0.020
 HL3  plan-1  C02  0.020
 HL3  plan-1  N03  0.020
 HL3  plan-1  C04  0.020
 HL3  plan-1  N05  0.020
 HL3  plan-1  C06  0.020
 HL3  plan-1  C09  0.020
 HL3  plan-1  H1   0.020
 HL3  plan-1  H2   0.020
 HL3  plan-2  C04  0.020
 HL3  plan-2  C06  0.020
 HL3  plan-2  O07  0.020
 HL3  plan-2  O08  0.020

