# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:15:58 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[3-cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)COc1ccc(cc1C#N)n2cc(cn2)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
 YSH  YSH  '1-[3-cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid'  ligand  38  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YSH
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
 YSH  C1    C  CR15   0   0.041   0.6175  -0.1686  -3.3920
 YSH  N2    N  NR5    0  -0.406  -0.2908   0.2118  -2.4664
 YSH  N3    N  N      0  -0.286  -1.4171   0.6722  -3.0243
 YSH  C4    C  CR15   0  -0.050  -1.2173   0.5845  -4.3217
 YSH  C5    C  CR5    0  -0.345   0.0559   0.0595  -4.6249
 YSH  C6    C  CR6    0   0.375  -0.1684   0.1485  -1.0677
 YSH  C7    C  CR16   0  -0.288  -1.2981   0.0066  -0.2794
 YSH  C8    C  CR6    0  -0.100  -1.1649  -0.0565   1.1033
 YSH  C9    C  CR6    0   0.430   0.0948   0.0061   1.7200
 YSH  C10   C  CR16   0  -0.374   1.2190   0.1494   0.9118
 YSH  C11   C  CR16   0  -0.281   1.0816   0.2290  -0.4635
 YSH  C12   C  CSP    0   0.072  -2.3228  -0.1890   1.9212
 YSH  N13   N  NS     0  -0.251  -3.2684  -0.2883   2.5722
 YSH  O14   O  O2     0  -0.454   0.1040  -0.0757   3.0467
 YSH  C15   C  CH2    0  -0.153   1.3234   0.1139   3.7549
 YSH  C16   C  CT     0  -0.146   1.0465   0.0413   5.2518
 YSH  C17   C  CH3    0  -0.644   2.3767   0.3102   5.9585
 YSH  C18   C  CH3    0  -0.639   0.5410  -1.3507   5.6331
 YSH  C19   C  CH3    0  -0.640   0.0265   1.1044   5.6615
 YSH  C20   C  C      0   0.351   0.6634  -0.2104  -5.9685
 YSH  O21   O  OC    -1  -0.600  -0.0445   0.0626  -6.9573
 YSH  O22   O  O      0  -0.601   1.8167  -0.6843  -5.9712
 YSH  H1    H  HCR5   0   0.295   1.5710  -0.5896  -3.1194
 YSH  H4    H  HCR5   0   0.261  -1.9857   0.9022  -5.0103
 YSH  H7    H  HCR6   0   0.297  -2.2800  -0.0544  -0.7271
 YSH  H10   H  HCR6   0   0.302   2.2099   0.2145   1.3387
 YSH  H11   H  HCR6   0   0.297   1.9714   0.3672  -1.0637
 YSH  H151  H  HCH2   0   0.239   1.7497   1.0899   3.4945
 YSH  H152  H  HCH2   0   0.238   2.0461  -0.6600   3.4706
 YSH  H171  H  HCH3   0   0.235   2.2483   0.2548   7.0405
 YSH  H172  H  HCH3   0   0.229   3.1365  -0.4230   5.6788
 YSH  H173  H  HCH3   0   0.229   2.7658   1.3029   5.7210
 YSH  H181  H  HCH3   0   0.223   1.2696  -2.1202   5.3681
 YSH  H182  H  HCH3   0   0.228   0.3734  -1.4134   6.7100
 YSH  H183  H  HCH3   0   0.233  -0.4004  -1.5946   5.1396
 YSH  H191  H  HCH3   0   0.223   0.3507   2.1032   5.3606
 YSH  H192  H  HCH3   0   0.234  -0.9538   0.9215   5.2201
 YSH  H193  H  HCH3   0   0.227  -0.0971   1.1095   6.7460

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
 YSH  C1   N2    aromatic  1.351  0.020  1.351
 YSH  C1   C5    aromatic  1.374  0.020  1.374
 YSH  C1   H1    single    0.930  0.020  1.080
 YSH  N2   N3    aromatic  1.339  0.020  1.339
 YSH  N2   C6    single    1.406  0.020  1.406
 YSH  N3   C4    aromatic  1.316  0.020  1.316
 YSH  C4   C5    aromatic  1.410  0.020  1.410
 YSH  C4   H4    single    0.930  0.020  1.080
 YSH  C5   C20   single    1.499  0.020  1.499
 YSH  C6   C7    aromatic  1.385  0.020  1.385
 YSH  C6   C11   aromatic  1.391  0.020  1.391
 YSH  C7   C8    aromatic  1.390  0.020  1.390
 YSH  C7   H7    single    0.930  0.020  1.080
 YSH  C8   C9    aromatic  1.404  0.020  1.404
 YSH  C8   C12   single    1.424  0.020  1.424
 YSH  C9   C10   aromatic  1.392  0.020  1.392
 YSH  C9   O14   single    1.329  0.020  1.329
 YSH  C10  C11   aromatic  1.384  0.020  1.384
 YSH  C10  H10   single    0.930  0.020  1.080
 YSH  C11  H11   single    0.930  0.020  1.080
 YSH  C12  N13   triple    1.152  0.020  1.152
 YSH  O14  C15   single    1.423  0.020  1.423
 YSH  C15  C16   single    1.524  0.020  1.524
 YSH  C15  H151  single    0.970  0.020  1.090
 YSH  C15  H152  single    0.970  0.020  1.090
 YSH  C16  C17   single    1.530  0.020  1.530
 YSH  C16  C18   single    1.529  0.020  1.529
 YSH  C16  C19   single    1.529  0.020  1.529
 YSH  C17  H171  single    0.970  0.020  1.090
 YSH  C17  H172  single    0.970  0.020  1.090
 YSH  C17  H173  single    0.970  0.020  1.090
 YSH  C18  H181  single    0.970  0.020  1.090
 YSH  C18  H182  single    0.970  0.020  1.090
 YSH  C18  H183  single    0.970  0.020  1.090
 YSH  C19  H191  single    0.970  0.020  1.090
 YSH  C19  H192  single    0.970  0.020  1.090
 YSH  C19  H193  single    0.970  0.020  1.090
 YSH  C20  O21   deloc     1.246  0.020  1.246
 YSH  C20  O22   deloc     1.247  0.020  1.247

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
 YSH  H1    C1   C5    130.82  3.000
 YSH  H1    C1   N2    122.11  3.000
 YSH  C5    C1   N2    107.05  3.000
 YSH  C6    N2   N3    120.23  3.000
 YSH  C6    N2   C1    127.62  3.000
 YSH  N3    N2   C1    112.14  3.000
 YSH  C4    N3   N2    105.09  3.000
 YSH  H4    C4   C5    127.95  3.000
 YSH  H4    C4   N3    120.08  3.000
 YSH  C5    C4   N3    111.96  3.000
 YSH  C20   C5   C4    128.73  3.000
 YSH  C20   C5   C1    127.50  3.000
 YSH  C4    C5   C1    103.76  3.000
 YSH  C11   C6   C7    119.47  3.000
 YSH  C11   C6   N2    120.53  3.000
 YSH  C7    C6   N2    120.00  3.000
 YSH  H7    C7   C8    119.76  3.000
 YSH  H7    C7   C6    120.74  3.000
 YSH  C8    C7   C6    119.51  3.000
 YSH  C12   C8   C9    118.78  3.000
 YSH  C12   C8   C7    119.84  3.000
 YSH  C9    C8   C7    121.38  3.000
 YSH  O14   C9   C10   125.46  3.000
 YSH  O14   C9   C8    116.23  3.000
 YSH  C10   C9   C8    118.31  3.000
 YSH  H10   C10  C11   118.68  3.000
 YSH  H10   C10  C9    121.15  3.000
 YSH  C11   C10  C9    120.17  3.000
 YSH  H11   C11  C10   118.47  3.000
 YSH  H11   C11  C6    120.37  3.000
 YSH  C10   C11  C6    121.16  3.000
 YSH  N13   C12  C8    180.00  3.000
 YSH  C15   O14  C9    119.64  3.000
 YSH  H152  C15  H151  108.09  3.000
 YSH  H152  C15  C16   109.93  3.000
 YSH  H151  C15  C16   110.26  3.000
 YSH  H152  C15  O14   109.98  3.000
 YSH  H151  C15  O14   109.49  3.000
 YSH  C16   C15  O14   109.07  3.000
 YSH  C19   C16  C18   110.21  3.000
 YSH  C19   C16  C17   109.51  3.000
 YSH  C18   C16  C17   109.40  3.000
 YSH  C19   C16  C15   110.56  3.000
 YSH  C18   C16  C15   110.39  3.000
 YSH  C17   C16  C15   106.69  3.000
 YSH  H173  C17  H172  107.85  3.000
 YSH  H173  C17  H171  107.68  3.000
 YSH  H172  C17  H171  107.56  3.000
 YSH  H173  C17  C16   111.65  3.000
 YSH  H172  C17  C16   111.63  3.000
 YSH  H171  C17  C16   110.29  3.000
 YSH  H183  C18  H182  107.52  3.000
 YSH  H183  C18  H181  107.96  3.000
 YSH  H182  C18  H181  107.53  3.000
 YSH  H183  C18  C16   112.10  3.000
 YSH  H182  C18  C16   110.43  3.000
 YSH  H181  C18  C16   111.12  3.000
 YSH  H193  C19  H192  107.53  3.000
 YSH  H193  C19  H191  107.64  3.000
 YSH  H192  C19  H191  107.98  3.000
 YSH  H193  C19  C16   110.18  3.000
 YSH  H192  C19  C16   112.00  3.000
 YSH  H191  C19  C16   111.34  3.000
 YSH  O22   C20  O21   127.37  3.000
 YSH  O22   C20  C5    116.44  3.000
 YSH  O21   C20  C5    116.20  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
 YSH  CONST_01  C4    N3   N2   C1      0.00   0.0  0
 YSH  CONST_04  N3    C4   C5   C1      0.00   0.0  0
 YSH  CONST_05  C4    C5   C1   N2      0.00   0.0  0
 YSH  CONST_06  C5    C4   N3   N2      0.00   0.0  0
 YSH  CONST_07  C8    C7   C6   N2    180.00   0.0  0
 YSH  CONST_08  C10   C11  C6   N2    180.00   0.0  0
 YSH  CONST_09  C5    C1   N2   N3      0.00   0.0  0
 YSH  CONST_12  C6    N2   N3   C4    180.00   0.0  0
 YSH  CONST_13  C6    N2   C1   C5    180.00   0.0  0
 YSH  CONST_14  C9    C8   C7   C6      0.00   0.0  0
 YSH  CONST_15  C9    C10  C11  C6      0.00   0.0  0
 YSH  CONST_16  C10   C11  C6   C7      0.00   0.0  0
 YSH  CONST_17  C10   C9   C8   C7      0.00   0.0  0
 YSH  CONST_18  C11   C6   C7   C8      0.00   0.0  0
 YSH  CONST_19  C11   C10  C9   C8      0.00   0.0  0
 YSH  CONST_20  C20   C5   C1   N2    180.00   0.0  0
 YSH  CONST_21  C20   C5   C4   N3    180.00   0.0  0
 YSH  CONST_22  C12   C8   C7   C6    180.00   0.0  0
 YSH  CONST_23  O14   C9   C8   C7    180.00   0.0  0
 YSH  CONST_24  C12   C8   C9   C10   180.00   0.0  0
 YSH  CONST_25  O14   C9   C10  C11   180.00   0.0  0
 YSH  CONST_26  H4    C4   C5   C1    180.00   0.0  0
 YSH  CONST_27  H7    C7   C6   N2      0.00   0.0  0
 YSH  CONST_28  H11   C11  C6   N2      0.00   0.0  0
 YSH  CONST_29  H1    C1   N2   N3    180.00   0.0  0
 YSH  CONST_30  H10   C10  C11  C6    180.00   0.0  0
 YSH  Var_01    O21   C20  C5   C1    179.08  30.0  2
 YSH  Var_02    C16   C15  O14  C9    177.08  30.0  3
 YSH  Var_03    C17   C16  C15  O14  -177.66  30.0  3
 YSH  Var_04    H171  C17  C16  C15  -179.02  30.0  3
 YSH  Var_05    H181  C18  C16  C15    58.92  30.0  3
 YSH  Var_06    H191  C19  C16  C15   -55.35  30.0  3

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
 YSH  plan-1  C1   0.020
 YSH  plan-1  N2   0.020
 YSH  plan-1  N3   0.020
 YSH  plan-1  C4   0.020
 YSH  plan-1  C5   0.020
 YSH  plan-1  C6   0.020
 YSH  plan-1  C20  0.020
 YSH  plan-1  H1   0.020
 YSH  plan-1  H4   0.020
 YSH  plan-2  N2   0.020
 YSH  plan-2  C6   0.020
 YSH  plan-2  C7   0.020
 YSH  plan-2  C8   0.020
 YSH  plan-2  C9   0.020
 YSH  plan-2  C10  0.020
 YSH  plan-2  C11  0.020
 YSH  plan-2  C12  0.020
 YSH  plan-2  N13  0.020
 YSH  plan-2  O14  0.020
 YSH  plan-2  H7   0.020
 YSH  plan-2  H10  0.020
 YSH  plan-2  H11  0.020
 YSH  plan-3  C5   0.020
 YSH  plan-3  C20  0.020
 YSH  plan-3  O21  0.020
 YSH  plan-3  O22  0.020

