# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 09:08:12 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-methyl-1-(phenylmethyl)imidazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc(n1Cc2ccccc2)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
 HQ3  HQ3  "5-methyl-1-(phenylmethyl)imidazole-2-carboxylic acid"  ligand  27  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HQ3
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
 HQ3  O01  O  OC    -1  -0.576  28.5407  16.2419   -8.1687
 HQ3  C02  C  C      0   0.369  29.1386  17.1788   -8.7185
 HQ3  O03  O  O      0  -0.579  28.7319  18.3475   -8.8821
 HQ3  C04  C  CR5    0   0.246  30.5290  16.8479   -9.2298
 HQ3  N05  N  N      0  -0.447  31.1470  15.7173   -8.9702
 HQ3  C06  C  CR15   0  -0.271  32.3661  15.8001   -9.5624
 HQ3  C07  C  CR5    0   0.275  32.5081  16.9988  -10.2050
 HQ3  C08  C  CH3    0  -0.741  33.6373  17.5513  -10.9955
 HQ3  N09  N  NR5    0  -0.473  31.3283  17.6596   -9.9882
 HQ3  C10  C  CH2    0  -0.377  31.0594  18.9841  -10.5132
 HQ3  C11  C  CR6    0   0.100  31.7247  20.0762   -9.7145
 HQ3  C12  C  CR16   0  -0.283  31.6389  20.1027   -8.3241
 HQ3  C13  C  CR16   0  -0.239  32.2343  21.1261   -7.6017
 HQ3  C14  C  CR16   0  -0.267  32.9168  22.1439   -8.2577
 HQ3  C15  C  CR16   0  -0.241  33.0037  22.1268   -9.6424
 HQ3  C16  C  CR16   0  -0.308  32.4138  21.0956  -10.3632
 HQ3  H2   H  HCR5   0   0.237  33.0903  14.9998   -9.5072
 HQ3  H3   H  HCH3   0   0.249  34.0362  18.4703  -10.5617
 HQ3  H4   H  HCH3   0   0.259  34.4455  16.8229  -11.0325
 HQ3  H5   H  HCH3   0   0.247  33.3505  17.7769  -12.0249
 HQ3  H6   H  HCH2   0   0.267  31.4033  19.0225  -11.5481
 HQ3  H7   H  HCH2   0   0.293  29.9834  19.1290  -10.5186
 HQ3  H8   H  HCR6   0   0.250  31.1017  19.3212   -7.8021
 HQ3  H9   H  HCR6   0   0.252  32.1613  21.1321   -6.5216
 HQ3  H10  H  HCR6   0   0.252  33.3793  22.9423   -7.6917
 HQ3  H11  H  HCR6   0   0.252  33.5369  22.9111  -10.1643
 HQ3  H12  H  HCR6   0   0.250  32.4964  21.0815  -11.4440

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
 HQ3  C08  C07  single    1.485  0.020  1.485
 HQ3  C10  N09  single    1.450  0.020  1.450
 HQ3  C10  C11  single    1.508  0.020  1.508
 HQ3  C16  C11  aromatic  1.391  0.020  1.391
 HQ3  C16  C15  aromatic  1.390  0.020  1.390
 HQ3  C07  N09  aromatic  1.369  0.020  1.369
 HQ3  C07  C06  aromatic  1.367  0.020  1.367
 HQ3  N09  C04  aromatic  1.369  0.020  1.369
 HQ3  C11  C12  aromatic  1.393  0.020  1.393
 HQ3  O03  C02  deloc     1.248  0.020  1.248
 HQ3  C15  C14  aromatic  1.388  0.020  1.388
 HQ3  C06  N05  aromatic  1.358  0.020  1.358
 HQ3  C04  C02  single    1.518  0.020  1.518
 HQ3  C04  N05  aromatic  1.314  0.020  1.314
 HQ3  C02  O01  deloc     1.240  0.020  1.240
 HQ3  C12  C13  aromatic  1.387  0.020  1.387
 HQ3  C14  C13  aromatic  1.390  0.020  1.390
 HQ3  C06  H2   single    0.930  0.020  1.080
 HQ3  C08  H3   single    0.970  0.020  1.090
 HQ3  C08  H4   single    0.970  0.020  1.090
 HQ3  C08  H5   single    0.970  0.020  1.090
 HQ3  C10  H6   single    0.970  0.020  1.090
 HQ3  C10  H7   single    0.970  0.020  1.090
 HQ3  C12  H8   single    0.930  0.020  1.080
 HQ3  C13  H9   single    0.930  0.020  1.080
 HQ3  C14  H10  single    0.930  0.020  1.080
 HQ3  C15  H11  single    0.930  0.020  1.080
 HQ3  C16  H12  single    0.930  0.020  1.080

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
 HQ3  C04  C02  O03  117.28  3.000
 HQ3  C04  C02  O01  115.23  3.000
 HQ3  O03  C02  O01  127.48  3.000
 HQ3  N09  C04  N05  110.18  3.000
 HQ3  N05  C04  C02  123.48  3.000
 HQ3  N09  C04  C02  126.32  3.000
 HQ3  C06  N05  C04  106.47  3.000
 HQ3  H2   C06  C07  127.12  3.000
 HQ3  H2   C06  N05  122.29  3.000
 HQ3  C07  C06  N05  110.59  3.000
 HQ3  N09  C07  C08  124.04  3.000
 HQ3  N09  C07  C06  105.02  3.000
 HQ3  C08  C07  C06  130.94  3.000
 HQ3  H5   C08  H4   107.53  3.000
 HQ3  H5   C08  H3   107.26  3.000
 HQ3  H4   C08  H3   107.79  3.000
 HQ3  H5   C08  C07  112.26  3.000
 HQ3  H4   C08  C07  109.49  3.000
 HQ3  H3   C08  C07  112.30  3.000
 HQ3  C10  N09  C07  122.91  3.000
 HQ3  C07  N09  C04  107.74  3.000
 HQ3  C10  N09  C04  129.35  3.000
 HQ3  H7   C10  H6   107.64  3.000
 HQ3  H7   C10  C11  110.08  3.000
 HQ3  H6   C10  C11  109.75  3.000
 HQ3  H7   C10  N09  107.91  3.000
 HQ3  H6   C10  N09  108.49  3.000
 HQ3  C11  C10  N09  112.83  3.000
 HQ3  C16  C11  C12  118.82  3.000
 HQ3  C12  C11  C10  121.01  3.000
 HQ3  C16  C11  C10  120.16  3.000
 HQ3  H8   C12  C13  119.64  3.000
 HQ3  H8   C12  C11  119.87  3.000
 HQ3  C13  C12  C11  120.48  3.000
 HQ3  H9   C13  C14  120.00  3.000
 HQ3  H9   C13  C12  119.65  3.000
 HQ3  C14  C13  C12  120.36  3.000
 HQ3  H10  C14  C15  120.27  3.000
 HQ3  H10  C14  C13  120.21  3.000
 HQ3  C15  C14  C13  119.52  3.000
 HQ3  H11  C15  C16  119.78  3.000
 HQ3  H11  C15  C14  120.20  3.000
 HQ3  C16  C15  C14  120.01  3.000
 HQ3  H12  C16  C15  119.63  3.000
 HQ3  H12  C16  C11  119.55  3.000
 HQ3  C15  C16  C11  120.81  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
 HQ3  CONST_01  C06  C07  N09  C04     0.00   0.0  0
 HQ3  CONST_02  C07  C06  N05  C04     0.00   0.0  0
 HQ3  CONST_03  N09  C07  C06  N05     0.00   0.0  0
 HQ3  CONST_04  C07  N09  C04  N05     0.00   0.0  0
 HQ3  CONST_05  N09  C04  N05  C06     0.00   0.0  0
 HQ3  CONST_06  C14  C15  C16  C11     0.00   0.0  0
 HQ3  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 HQ3  CONST_08  C15  C16  C11  C12     0.00   0.0  0
 HQ3  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 HQ3  CONST_10  C16  C11  C12  C13     0.00   0.0  0
 HQ3  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 HQ3  CONST_12  C07  N09  C04  C02   180.00   0.0  0
 HQ3  CONST_13  C06  N05  C04  C02   180.00   0.0  0
 HQ3  CONST_14  C08  C07  N09  C04   180.00   0.0  0
 HQ3  CONST_15  C08  C07  C06  N05   180.00   0.0  0
 HQ3  CONST_16  C10  N09  C04  N05   180.00   0.0  0
 HQ3  CONST_17  C10  N09  C07  C06   180.00   0.0  0
 HQ3  CONST_18  C15  C16  C11  C10   180.00   0.0  0
 HQ3  CONST_19  C13  C12  C11  C10   180.00   0.0  0
 HQ3  CONST_20  H2   C06  N05  C04   180.00   0.0  0
 HQ3  CONST_21  H2   C06  C07  N09   180.00   0.0  0
 HQ3  CONST_22  H11  C15  C16  C11   180.00   0.0  0
 HQ3  CONST_23  H9   C13  C12  C11   180.00   0.0  0
 HQ3  CONST_24  H12  C16  C11  C12   180.00   0.0  0
 HQ3  CONST_25  H10  C14  C13  C12   180.00   0.0  0
 HQ3  CONST_26  H11  C15  C14  C13   180.00   0.0  0
 HQ3  CONST_27  H12  C16  C15  C14   180.00   0.0  0
 HQ3  CONST_28  H8   C12  C13  C14   180.00   0.0  0
 HQ3  CONST_29  H9   C13  C14  C15   180.00   0.0  0
 HQ3  CONST_30  H8   C12  C11  C16   180.00   0.0  0
 HQ3  CONST_31  H10  C14  C15  C16   180.00   0.0  0
 HQ3  Var_01    C11  C10  N09  C04   101.96  30.0  2
 HQ3  Var_02    C11  C10  N09  C07   -78.25  30.0  2
 HQ3  Var_03    C16  C11  C10  N09   133.79  30.0  2
 HQ3  Var_04    C12  C11  C10  N09   -47.62  30.0  2
 HQ3  Var_05    N09  C04  C02  O01   172.74  30.0  2
 HQ3  Var_06    N05  C04  C02  O01    -8.61  30.0  2
 HQ3  Var_07    N09  C04  C02  O03    -7.93  30.0  2
 HQ3  Var_08    N05  C04  C02  O03   170.73  30.0  2
 HQ3  Var_09    H6   C10  N09  C04  -136.22  30.0  2
 HQ3  Var_10    H7   C10  N09  C04   -19.87  30.0  2
 HQ3  Var_11    H3   C08  C07  C06  -119.15  30.0  2
 HQ3  Var_12    H4   C08  C07  C06     0.55  30.0  2
 HQ3  Var_13    H5   C08  C07  C06   119.90  30.0  2
 HQ3  Var_14    H6   C10  N09  C07    43.57  30.0  2
 HQ3  Var_15    H7   C10  N09  C07   159.91  30.0  2
 HQ3  Var_16    H3   C08  C07  N09    61.42  30.0  2
 HQ3  Var_17    H4   C08  C07  N09  -178.88  30.0  2
 HQ3  Var_18    H5   C08  C07  N09   -59.54  30.0  2
 HQ3  Var_19    H6   C10  C11  C12  -168.73  30.0  2
 HQ3  Var_20    H7   C10  C11  C12    72.98  30.0  2
 HQ3  Var_21    H6   C10  C11  C16    12.69  30.0  2
 HQ3  Var_22    H7   C10  C11  C16  -105.60  30.0  2

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
 HQ3  plan-1  C02  0.020
 HQ3  plan-1  C04  0.020
 HQ3  plan-1  N05  0.020
 HQ3  plan-1  C06  0.020
 HQ3  plan-1  C07  0.020
 HQ3  plan-1  C08  0.020
 HQ3  plan-1  N09  0.020
 HQ3  plan-1  C10  0.020
 HQ3  plan-1  H2   0.020
 HQ3  plan-2  C10  0.020
 HQ3  plan-2  C11  0.020
 HQ3  plan-2  C12  0.020
 HQ3  plan-2  C13  0.020
 HQ3  plan-2  C14  0.020
 HQ3  plan-2  C15  0.020
 HQ3  plan-2  C16  0.020
 HQ3  plan-2  H8   0.020
 HQ3  plan-2  H9   0.020
 HQ3  plan-2  H10  0.020
 HQ3  plan-2  H11  0.020
 HQ3  plan-2  H12  0.020
 HQ3  plan-3  O01  0.020
 HQ3  plan-3  C02  0.020
 HQ3  plan-3  O03  0.020
 HQ3  plan-3  C04  0.020

