# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:49:02 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  18  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.731   0.3281   2.5284   0.1793
 KYD  C2    C  CR5   0   0.301   0.6973   1.0886   0.0857
 KYD  N3    N  N     0  -0.288   1.9613   0.7358   0.0075
 KYD  N4    N  NR15  0  -0.481   1.9572  -0.6000  -0.0625
 KYD  C6    C  CR5   0   0.468   0.7412  -1.1424  -0.0331
 KYD  C7    C  CH3   0  -0.728   0.5204  -2.6084  -0.0968
 KYD  C8    C  CR5   0  -0.359  -0.1337  -0.0647   0.0650
 KYD  C9    C  C     0   0.450  -1.5788  -0.1852   0.1206
 KYD  O10   O  OH1   0  -0.601  -2.1967   0.9915   0.1942
 KYD  O11   O  O     0  -0.458  -2.1803  -1.2378   0.1011
 KYD  H11C  H  HCH3  0   0.248  -0.3065   2.8355  -0.6515
 KYD  H12C  H  HCH3  0   0.247  -0.2158   2.7442   1.0986
 KYD  H13C  H  HCH3  0   0.245   1.2277   3.1412   0.1652
 KYD  H4    H  HNR5  0   0.421   2.8331  -1.0956  -0.1323
 KYD  H71C  H  HCH3  0   0.264   0.0495  -2.9704   0.8162
 KYD  H72C  H  HCH3  0   0.264  -0.1358  -2.8684  -0.9255
 KYD  H73C  H  HCH3  0   0.255   1.4630  -3.1374  -0.2273
 KYD  H10   H  HOH1  0   0.482  -3.1545   0.8519   0.2228

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    1.489  0.020  1.489
 KYD  C2   N3    aromatic  1.315  0.020  1.315
 KYD  C2   C8    aromatic  1.422  0.020  1.422
 KYD  N3   N4    aromatic  1.338  0.020  1.338
 KYD  N4   C6    aromatic  1.332  0.020  1.332
 KYD  C6   C7    single    1.484  0.020  1.484
 KYD  C6   C8    aromatic  1.392  0.020  1.392
 KYD  C8   C9    single    1.451  0.020  1.451
 KYD  C9   O10   single    1.331  0.020  1.331
 KYD  C9   O11   double    1.213  0.020  1.213
 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
 KYD  O10  H10   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
 KYD  H13C  C1   H12C  108.17  3.000
 KYD  H13C  C1   H11C  108.22  3.000
 KYD  H12C  C1   H11C  107.26  3.000
 KYD  H13C  C1   C2    109.79  3.000
 KYD  H12C  C1   C2    111.61  3.000
 KYD  H11C  C1   C2    111.65  3.000
 KYD  C8    C2   N3    110.08  3.000
 KYD  C8    C2   C1    129.82  3.000
 KYD  N3    C2   C1    120.10  3.000
 KYD  N4    N3   C2    105.56  3.000
 KYD  H4    N4   C6    126.46  3.000
 KYD  H4    N4   N3    119.44  3.000
 KYD  C6    N4   N3    114.10  3.000
 KYD  C8    C6   C7    132.42  3.000
 KYD  C8    C6   N4    105.09  3.000
 KYD  C7    C6   N4    122.49  3.000
 KYD  H73C  C7   H72C  108.34  3.000
 KYD  H73C  C7   H71C  108.26  3.000
 KYD  H72C  C7   H71C  107.35  3.000
 KYD  H73C  C7   C6    110.87  3.000
 KYD  H72C  C7   C6    111.00  3.000
 KYD  H71C  C7   C6    110.89  3.000
 KYD  C9    C8   C6    124.37  3.000
 KYD  C9    C8   C2    130.45  3.000
 KYD  C6    C8   C2    105.17  3.000
 KYD  O11   C9   O10   122.55  3.000
 KYD  O11   C9   C8    124.43  3.000
 KYD  O10   C9   C8    113.02  3.000
 KYD  H10   O10  C9    109.47  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  CONST_13  H10   O10  C9  C8  180.00   0.0  0
 KYD  Var_01    O10   C9   C8  C2    0.45  30.0  2
 KYD  Var_02    H11C  C1   C2  N3  120.26  30.0  2
 KYD  Var_03    H71C  C7   C6  N4  116.94  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
 KYD  plan-2  H10  0.020

