# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:14:27 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 3,5-dimethyl-1H-pyrazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc(C)c1C(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
 KYD  KYD  '3,5-dimethyl-1H-pyrazole-4-carboxylic acid'  ligand  17  10  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KYD
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
 KYD  C1    C  CH3    0  -0.714   0.3931   2.5596   0.1517
 KYD  C2    C  CR5    0   0.257   0.7291   1.1078   0.1160
 KYD  N3    N  N      0  -0.307   1.9859   0.7260   0.2374
 KYD  N4    N  NR15   0  -0.483   1.9533  -0.6066   0.1628
 KYD  C6    C  CR5    0   0.406   0.7188  -1.1072  -0.0047
 KYD  C7    C  CH3    0  -0.746   0.4916  -2.5738  -0.1130
 KYD  C8    C  CR5    0  -0.409  -0.1321  -0.0109  -0.0409
 KYD  C9    C  C      0   0.342  -1.6218   0.0057  -0.2012
 KYD  O10   O  OC    -1  -0.595  -2.1713   1.1267  -0.1810
 KYD  O11   O  O      0  -0.601  -2.2042  -1.0914  -0.3462
 KYD  H11C  H  HCH3   0   0.232  -0.0729   2.8851  -0.7777
 KYD  H12C  H  HCH3   0   0.233  -0.3114   2.7884   0.9499
 KYD  H13C  H  HCH3   0   0.221   1.2967   3.1485   0.3073
 KYD  H4    H  HNR5   0   0.406   2.8127  -1.1284   0.2291
 KYD  H71C  H  HCH3   0   0.246   0.8194  -3.0941   0.7889
 KYD  H72C  H  HCH3   0   0.266  -0.5641  -2.7698  -0.2631
 KYD  H73C  H  HCH3   0   0.246   1.0472  -2.9972  -0.9517

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
 KYD  C1  C2    single    1.491  0.020  1.491
 KYD  C2  N3    aromatic  1.319  0.020  1.319
 KYD  C2  C8    aromatic  1.420  0.020  1.420
 KYD  N3  N4    aromatic  1.335  0.020  1.335
 KYD  N4  C6    aromatic  1.343  0.020  1.343
 KYD  C6  C7    single    1.488  0.020  1.488
 KYD  C6  C8    aromatic  1.388  0.020  1.388
 KYD  C8  C9    single    1.498  0.020  1.498
 KYD  C9  O10   deloc     1.249  0.020  1.249
 KYD  C9  O11   deloc     1.250  0.020  1.250
 KYD  C1  H11C  single    0.970  0.020  1.090
 KYD  C1  H12C  single    0.970  0.020  1.090
 KYD  C1  H13C  single    0.970  0.020  1.090
 KYD  N4  H4    single    0.860  0.020  1.020
 KYD  C7  H71C  single    0.970  0.020  1.090
 KYD  C7  H72C  single    0.970  0.020  1.090
 KYD  C7  H73C  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
 KYD  H13C  C1  H12C  108.56  3.000
 KYD  H13C  C1  H11C  108.36  3.000
 KYD  H12C  C1  H11C  106.61  3.000
 KYD  H13C  C1  C2    110.05  3.000
 KYD  H12C  C1  C2    111.59  3.000
 KYD  H11C  C1  C2    111.53  3.000
 KYD  C8    C2  N3    111.09  3.000
 KYD  C8    C2  C1    129.28  3.000
 KYD  N3    C2  C1    119.63  3.000
 KYD  N4    N3  C2    105.10  3.000
 KYD  H4    N4  C6    126.83  3.000
 KYD  H4    N4  N3    119.50  3.000
 KYD  C6    N4  N3    113.68  3.000
 KYD  C8    C6  C7    133.06  3.000
 KYD  C8    C6  N4    105.81  3.000
 KYD  C7    C6  N4    121.13  3.000
 KYD  H73C  C7  H72C  108.61  3.000
 KYD  H73C  C7  H71C  107.29  3.000
 KYD  H72C  C7  H71C  108.70  3.000
 KYD  H73C  C7  C6    111.13  3.000
 KYD  H72C  C7  C6    109.69  3.000
 KYD  H71C  C7  C6    111.33  3.000
 KYD  C9    C8  C6    128.39  3.000
 KYD  C9    C8  C2    127.29  3.000
 KYD  C6    C8  C2    104.33  3.000
 KYD  O11   C9  O10   125.78  3.000
 KYD  O11   C9  C8    117.75  3.000
 KYD  O10   C9  C8    116.47  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
 KYD  CONST_01  C6    N4  N3  C2    0.00   0.0  0
 KYD  CONST_02  N4    C6  C8  C2    0.00   0.0  0
 KYD  CONST_03  C6    C8  C2  N3    0.00   0.0  0
 KYD  CONST_04  C8    C6  N4  N3    0.00   0.0  0
 KYD  CONST_05  C8    C2  N3  N4    0.00   0.0  0
 KYD  CONST_06  N4    N3  C2  C1  180.00   0.0  0
 KYD  CONST_07  C6    C8  C2  C1  180.00   0.0  0
 KYD  CONST_08  C7    C6  C8  C2  180.00   0.0  0
 KYD  CONST_09  C9    C8  C2  N3  180.00   0.0  0
 KYD  CONST_10  C7    C6  N4  N3  180.00   0.0  0
 KYD  CONST_11  C9    C8  C6  N4  180.00   0.0  0
 KYD  CONST_12  H4    N4  N3  C2  180.00   0.0  0
 KYD  Var_01    O10   C9  C8  C2   -0.81  30.0  2
 KYD  Var_02    H11C  C1  C2  N3  118.92  30.0  2
 KYD  Var_03    H71C  C7  C6  N4   60.75  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
 KYD  plan-1  C1   0.020
 KYD  plan-1  C2   0.020
 KYD  plan-1  N3   0.020
 KYD  plan-1  N4   0.020
 KYD  plan-1  C6   0.020
 KYD  plan-1  C7   0.020
 KYD  plan-1  C8   0.020
 KYD  plan-1  C9   0.020
 KYD  plan-1  H4   0.020
 KYD  plan-2  C8   0.020
 KYD  plan-2  C9   0.020
 KYD  plan-2  O10  0.020
 KYD  plan-2  O11  0.020

