# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:28:32 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CCN(C)C)C(=O)c1cnn(c2cc(ccn2)C(O)=O)c1c3ccc(OC)cc3
#
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
 H5Y  H5Y  '2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid'  ligand  58  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5Y
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
 H5Y  C10  C  CR6    0   0.379   0.3675  -3.9370  -0.2376
 H5Y  C20  C  CR6    0   0.006   5.0135   1.0599  -0.2295
 H5Y  C21  C  C      0   0.413   6.1486   1.7377  -0.9988
 H5Y  C24  C  CR16   0  -0.378   3.6925   1.4265  -0.4459
 H5Y  C26  C  CR15   0  -0.046  -0.2875   2.4584  -0.0241
 H5Y  C28  C  CH2    0  -0.330  -4.5390   0.6127   0.3498
 H5Y  C01  C  CH3    0  -0.659  -2.6229   0.8002   2.9818
 H5Y  C02  C  CH2    0  -0.326  -2.9234   1.7519   1.8361
 H5Y  C05  C  CR5    0  -0.389  -0.8275   1.1579  -0.0464
 H5Y  C06  C  CR5    0   0.483   0.2691   0.3210   0.0157
 H5Y  C07  C  CR6    0   0.052   0.3306  -1.1387  -0.0586
 H5Y  C08  C  CR16   0  -0.263   1.1835  -1.7863  -0.9554
 H5Y  C09  C  CR16   0  -0.333   1.2057  -3.1624  -1.0456
 H5Y  C11  C  CR16   0  -0.373  -0.4934  -3.3028   0.6542
 H5Y  C12  C  CR16   0  -0.283  -0.5030  -1.9171   0.7329
 H5Y  C16  C  CR6    0   0.472   2.7065   0.7774   0.2810
 H5Y  C18  C  CR16   0  -0.059   4.1971  -0.5314   1.3588
 H5Y  C19  C  CR16   0  -0.364   5.2637   0.0512   0.6948
 H5Y  C29  C  CH2    0  -0.260  -5.3308   1.6087  -0.4925
 H5Y  C31  C  CH3    0  -0.527  -7.5380   1.1787   0.3781
 H5Y  C32  C  CH3    0  -0.517  -7.2621   1.8576  -1.8859
 H5Y  N03  N  NT     0  -0.440  -3.1756   1.0644   0.5755
 H5Y  N15  N  NR5    0  -0.452   1.3506   1.1375   0.0918
 H5Y  N17  N  N      0  -0.402   2.9337  -0.1693   1.1687
 H5Y  N25  N  N      0  -0.268   1.0227   2.4324   0.0535
 H5Y  N30  N  NT     0  -0.410  -6.6702   1.1356  -0.7799
 H5Y  O13  O  O2     0  -0.467   0.4573  -5.2690  -0.3912
 H5Y  O22  O  OC    -1  -0.581   7.2991   1.3630  -0.7164
 H5Y  O23  O  O      0  -0.579   5.8071   2.5962  -1.8303
 H5Y  O27  O  O      0  -0.484  -2.4604   0.0498  -1.3103
 H5Y  H1   H  HCR6   0   0.271   3.4423   2.1918  -1.1670
 H5Y  H2   H  HCR5   0   0.278  -0.8114   3.4009  -0.0832
 H5Y  H3   H  HCH2   0   0.252  -5.0012   0.4691   1.3276
 H5Y  H4   H  HCH2   0   0.253  -4.5340  -0.3574  -0.1449
 H5Y  H5   H  HCH3   0   0.242  -2.5361   1.3531   3.9171
 H5Y  H6   H  HCH3   0   0.232  -3.4106   0.0551   3.1045
 H5Y  H7   H  HCH3   0   0.229  -1.6816   0.2755   2.8165
 H5Y  H8   H  HCH2   0   0.257  -3.8101   2.3451   2.0635
 H5Y  H9   H  HCH2   0   0.262  -2.1098   2.4631   1.7225
 H5Y  H10  H  HCR6   0   0.257   1.8299  -1.2101  -1.6055
 H5Y  H11  H  HCR6   0   0.266   1.8678  -3.6515  -1.7493
 H5Y  H12  H  HCR6   0   0.281  -1.1593  -3.8634   1.2955
 H5Y  H13  H  HCR6   0   0.254  -1.1740  -1.4452   1.4398
 H5Y  H14  H  HCH3   0   0.230  -0.1749  -5.9744   1.4676
 H5Y  H15  H  HCH3   0   0.231  -1.4311  -5.9196   0.2110
 H5Y  H16  H  HCH3   0   0.261  -0.1351  -7.1243   0.1206
 H5Y  H17  H  HCR6   0   0.265   4.3646  -1.3184   2.0850
 H5Y  H18  H  HCR6   0   0.263   6.2734  -0.2774   0.8949
 H5Y  H19  H  HCH2   0   0.195  -5.3362   2.5949   0.0034
 H5Y  H20  H  HCH2   0   0.238  -4.8060   1.7401  -1.4411
 H5Y  H21  H  HCH3   0   0.235  -8.5140   0.7629   0.1235
 H5Y  H22  H  HCH3   0   0.236  -7.1366   0.5797   1.1956
 H5Y  H23  H  HCH3   0   0.192  -7.6977   2.2005   0.7579
 H5Y  H24  H  HCH3   0   0.191  -7.4138   2.9285  -1.6784
 H5Y  H25  H  HCH3   0   0.233  -6.6295   1.7763  -2.7710
 H5Y  H26  H  HCH3   0   0.232  -8.2348   1.4282  -2.1303
 H5Y  C14  C  CH3    0  -0.439  -0.3699  -6.1004   0.3997
 H5Y  C04  C  C      0   0.487  -2.2215   0.7158  -0.3106

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
 H5Y  C31  N30  single    1.448  0.020  1.448
 H5Y  N30  C32  single    1.447  0.020  1.447
 H5Y  N30  C29  single    1.449  0.020  1.449
 H5Y  C29  C28  single    1.526  0.020  1.526
 H5Y  C28  N03  single    1.454  0.020  1.454
 H5Y  C02  N03  single    1.458  0.020  1.458
 H5Y  C02  C01  single    1.519  0.020  1.519
 H5Y  N03  C04  single    1.348  0.020  1.348
 H5Y  C04  O27  double    1.225  0.020  1.225
 H5Y  C04  C05  single    1.486  0.020  1.486
 H5Y  C26  C05  aromatic  1.408  0.020  1.408
 H5Y  C26  N25  aromatic  1.313  0.020  1.313
 H5Y  C05  C06  aromatic  1.381  0.020  1.381
 H5Y  N25  N15  aromatic  1.336  0.020  1.336
 H5Y  C06  N15  aromatic  1.357  0.020  1.357
 H5Y  C06  C07  single    1.463  0.020  1.463
 H5Y  N15  C16  single    1.416  0.020  1.416
 H5Y  C07  C08  aromatic  1.397  0.020  1.397
 H5Y  C07  C12  aromatic  1.388  0.020  1.388
 H5Y  N17  C16  aromatic  1.318  0.020  1.318
 H5Y  N17  C18  aromatic  1.328  0.020  1.328
 H5Y  C08  C09  aromatic  1.379  0.020  1.379
 H5Y  C16  C24  aromatic  1.386  0.020  1.386
 H5Y  C12  C11  aromatic  1.388  0.020  1.388
 H5Y  C18  C19  aromatic  1.385  0.020  1.385
 H5Y  C09  C10  aromatic  1.398  0.020  1.398
 H5Y  C11  C10  aromatic  1.392  0.020  1.392
 H5Y  C24  C20  aromatic  1.388  0.020  1.388
 H5Y  C10  O13  single    1.344  0.020  1.344
 H5Y  C19  C20  aromatic  1.391  0.020  1.391
 H5Y  C20  C21  single    1.530  0.020  1.530
 H5Y  O13  C14  single    1.415  0.020  1.415
 H5Y  C21  O23  deloc     1.243  0.020  1.243
 H5Y  C21  O22  deloc     1.243  0.020  1.243
 H5Y  C24  H1   single    0.930  0.020  1.080
 H5Y  C26  H2   single    0.930  0.020  1.080
 H5Y  C28  H3   single    0.970  0.020  1.090
 H5Y  C28  H4   single    0.970  0.020  1.090
 H5Y  C01  H5   single    0.970  0.020  1.090
 H5Y  C01  H6   single    0.970  0.020  1.090
 H5Y  C01  H7   single    0.970  0.020  1.090
 H5Y  C02  H8   single    0.970  0.020  1.090
 H5Y  C02  H9   single    0.970  0.020  1.090
 H5Y  C08  H10  single    0.930  0.020  1.080
 H5Y  C09  H11  single    0.930  0.020  1.080
 H5Y  C11  H12  single    0.930  0.020  1.080
 H5Y  C12  H13  single    0.930  0.020  1.080
 H5Y  C14  H14  single    0.970  0.020  1.090
 H5Y  C14  H15  single    0.970  0.020  1.090
 H5Y  C14  H16  single    0.970  0.020  1.090
 H5Y  C18  H17  single    0.930  0.020  1.080
 H5Y  C19  H18  single    0.930  0.020  1.080
 H5Y  C29  H19  single    0.970  0.020  1.090
 H5Y  C29  H20  single    0.970  0.020  1.090
 H5Y  C31  H21  single    0.970  0.020  1.090
 H5Y  C31  H22  single    0.970  0.020  1.090
 H5Y  C31  H23  single    0.970  0.020  1.090
 H5Y  C32  H24  single    0.970  0.020  1.090
 H5Y  C32  H25  single    0.970  0.020  1.090
 H5Y  C32  H26  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
 H5Y  O13  C10  C11  124.47  3.000
 H5Y  O13  C10  C09  116.29  3.000
 H5Y  C11  C10  C09  119.23  3.000
 H5Y  C19  C20  C24  117.80  3.000
 H5Y  C19  C20  C21  121.48  3.000
 H5Y  C24  C20  C21  120.72  3.000
 H5Y  O23  C21  O22  127.93  3.000
 H5Y  O22  C21  C20  116.05  3.000
 H5Y  O23  C21  C20  116.02  3.000
 H5Y  H1   C24  C16  121.11  3.000
 H5Y  H1   C24  C20  120.76  3.000
 H5Y  C16  C24  C20  118.13  3.000
 H5Y  H2   C26  N25  120.31  3.000
 H5Y  H2   C26  C05  128.25  3.000
 H5Y  N25  C26  C05  111.43  3.000
 H5Y  H4   C28  H3   106.97  3.000
 H5Y  H4   C28  N03  110.06  3.000
 H5Y  H3   C28  N03  107.40  3.000
 H5Y  H4   C28  C29  109.45  3.000
 H5Y  H3   C28  C29  111.15  3.000
 H5Y  N03  C28  C29  111.68  3.000
 H5Y  H7   C01  H6   108.16  3.000
 H5Y  H7   C01  H5   107.78  3.000
 H5Y  H6   C01  H5   107.90  3.000
 H5Y  H7   C01  C02  110.97  3.000
 H5Y  H6   C01  C02  111.70  3.000
 H5Y  H5   C01  C02  110.18  3.000
 H5Y  H9   C02  H8   105.94  3.000
 H5Y  H9   C02  N03  110.35  3.000
 H5Y  H8   C02  N03  107.22  3.000
 H5Y  H9   C02  C01  109.92  3.000
 H5Y  H8   C02  C01  110.13  3.000
 H5Y  N03  C02  C01  113.00  3.000
 H5Y  C06  C05  C04  124.93  3.000
 H5Y  C06  C05  C26  104.74  3.000
 H5Y  C04  C05  C26  129.58  3.000
 H5Y  N15  C06  C07  124.73  3.000
 H5Y  C07  C06  C05  129.48  3.000
 H5Y  N15  C06  C05  105.70  3.000
 H5Y  C12  C07  C08  118.21  3.000
 H5Y  C12  C07  C06  120.35  3.000
 H5Y  C08  C07  C06  121.39  3.000
 H5Y  H10  C08  C09  118.82  3.000
 H5Y  H10  C08  C07  120.21  3.000
 H5Y  C09  C08  C07  120.96  3.000
 H5Y  H11  C09  C08  120.19  3.000
 H5Y  H11  C09  C10  119.46  3.000
 H5Y  C08  C09  C10  120.35  3.000
 H5Y  H12  C11  C12  118.67  3.000
 H5Y  H12  C11  C10  121.64  3.000
 H5Y  C12  C11  C10  119.69  3.000
 H5Y  H13  C12  C11  118.45  3.000
 H5Y  H13  C12  C07  120.00  3.000
 H5Y  C11  C12  C07  121.55  3.000
 H5Y  N17  C16  N15  115.98  3.000
 H5Y  N17  C16  C24  124.54  3.000
 H5Y  N15  C16  C24  119.48  3.000
 H5Y  H17  C18  N17  116.16  3.000
 H5Y  H17  C18  C19  120.51  3.000
 H5Y  N17  C18  C19  123.32  3.000
 H5Y  H18  C19  C18  120.19  3.000
 H5Y  H18  C19  C20  120.78  3.000
 H5Y  C18  C19  C20  119.03  3.000
 H5Y  H20  C29  H19  106.57  3.000
 H5Y  H20  C29  N30  108.13  3.000
 H5Y  H19  C29  N30  112.10  3.000
 H5Y  H20  C29  C28  107.98  3.000
 H5Y  H19  C29  C28  109.74  3.000
 H5Y  N30  C29  C28  112.08  3.000
 H5Y  H23  C31  H22  107.73  3.000
 H5Y  H23  C31  H21  107.72  3.000
 H5Y  H22  C31  H21  107.16  3.000
 H5Y  H23  C31  N30  112.97  3.000
 H5Y  H22  C31  N30  111.27  3.000
 H5Y  H21  C31  N30  109.77  3.000
 H5Y  H26  C32  H25  107.81  3.000
 H5Y  H26  C32  H24  107.58  3.000
 H5Y  H25  C32  H24  107.77  3.000
 H5Y  H26  C32  N30  109.84  3.000
 H5Y  H25  C32  N30  110.22  3.000
 H5Y  H24  C32  N30  113.42  3.000
 H5Y  C04  N03  C02  124.60  3.000
 H5Y  C04  N03  C28  118.77  3.000
 H5Y  C02  N03  C28  116.30  3.000
 H5Y  N25  N15  C16  119.04  3.000
 H5Y  C16  N15  C06  128.15  3.000
 H5Y  N25  N15  C06  112.70  3.000
 H5Y  C18  N17  C16  117.16  3.000
 H5Y  N15  N25  C26  105.41  3.000
 H5Y  C32  N30  C31  110.56  3.000
 H5Y  C32  N30  C29  111.51  3.000
 H5Y  C31  N30  C29  112.68  3.000
 H5Y  C14  O13  C10  118.66  3.000
 H5Y  H16  C14  H15  108.75  3.000
 H5Y  H16  C14  H14  108.72  3.000
 H5Y  H15  C14  H14  108.84  3.000
 H5Y  H16  C14  O13  106.48  3.000
 H5Y  H15  C14  O13  111.96  3.000
 H5Y  H14  C14  O13  111.97  3.000
 H5Y  O27  C04  N03  122.63  3.000
 H5Y  O27  C04  C05  119.33  3.000
 H5Y  N03  C04  C05  118.04  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
 H5Y  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 H5Y  CONST_02  C07  C12  C11  C10     0.00   0.0  0
 H5Y  CONST_03  N15  C16  C24  C20   180.00   0.0  0
 H5Y  CONST_04  N17  C16  C24  C20     0.00   0.0  0
 H5Y  CONST_05  N17  C18  C19  C20     0.00   0.0  0
 H5Y  CONST_08  C18  N17  C16  C24     0.00   0.0  0
 H5Y  CONST_09  C18  C19  C20  C24     0.00   0.0  0
 H5Y  CONST_10  N15  C06  C05  C26     0.00   0.0  0
 H5Y  CONST_11  C07  C06  C05  C26   180.00   0.0  0
 H5Y  CONST_12  C06  N15  N25  C26     0.00   0.0  0
 H5Y  CONST_13  C16  N15  N25  C26   180.00   0.0  0
 H5Y  CONST_14  N15  N25  C26  C05     0.00   0.0  0
 H5Y  CONST_15  N25  N15  C06  C05     0.00   0.0  0
 H5Y  CONST_16  C16  N15  C06  C05   180.00   0.0  0
 H5Y  CONST_19  N25  C26  C05  C06     0.00   0.0  0
 H5Y  CONST_21  C09  C08  C07  C06   180.00   0.0  0
 H5Y  CONST_22  C11  C12  C07  C06   180.00   0.0  0
 H5Y  CONST_23  N25  N15  C06  C07   180.00   0.0  0
 H5Y  CONST_24  C16  N15  C06  C07     0.00   0.0  0
 H5Y  CONST_26  C11  C12  C07  C08     0.00   0.0  0
 H5Y  CONST_27  C11  C10  C09  C08     0.00   0.0  0
 H5Y  CONST_28  C12  C07  C08  C09     0.00   0.0  0
 H5Y  CONST_29  C12  C11  C10  C09     0.00   0.0  0
 H5Y  CONST_31  C19  C18  N17  C16     0.00   0.0  0
 H5Y  CONST_32  C19  C20  C24  C16     0.00   0.0  0
 H5Y  CONST_33  N15  C16  N17  C18   180.00   0.0  0
 H5Y  CONST_35  C16  C24  C20  C21   180.00   0.0  0
 H5Y  CONST_36  C18  C19  C20  C21   180.00   0.0  0
 H5Y  CONST_37  N25  C26  C05  C04   180.00   0.0  0
 H5Y  CONST_38  N15  C06  C05  C04   180.00   0.0  0
 H5Y  CONST_39  C07  C06  C05  C04     0.00   0.0  0
 H5Y  CONST_40  O13  C10  C09  C08   180.00   0.0  0
 H5Y  CONST_41  O13  C10  C11  C12   180.00   0.0  0
 H5Y  CONST_42  H10  C08  C09  C10   180.00   0.0  0
 H5Y  CONST_43  H13  C12  C11  C10   180.00   0.0  0
 H5Y  CONST_44  H17  C18  C19  C20   180.00   0.0  0
 H5Y  CONST_45  H18  C19  C20  C24   180.00   0.0  0
 H5Y  CONST_46  H2   C26  C05  C06   180.00   0.0  0
 H5Y  CONST_47  H11  C09  C08  C07   180.00   0.0  0
 H5Y  CONST_48  H12  C11  C12  C07   180.00   0.0  0
 H5Y  CONST_49  H1   C24  C20  C19   180.00   0.0  0
 H5Y  CONST_50  C05  C04  N03  C28   180.00   0.0  0
 H5Y  CONST_51  C05  C04  N03  C02     0.00   0.0  0
 H5Y  CONST_52  O27  C04  N03  C28     0.00   0.0  0
 H5Y  CONST_53  O27  C04  N03  C02   180.00   0.0  0
 H5Y  Var_01    O23  C21  C20  C24    -1.50  30.0  2
 H5Y  Var_02    N03  C04  C05  C26   -65.94  30.0  2
 H5Y  Var_03    H14  C14  O13  C10   -61.08  30.0  3
 H5Y  Var_04    C31  N30  C29  C28    72.58  30.0  1
 H5Y  Var_05    C01  C02  N03  C28    85.46  30.0  1
 H5Y  Var_06    C29  C28  N03  C02    96.59  30.0  1
 H5Y  Var_07    N30  C29  C28  N03   177.08  30.0  1
 H5Y  Var_08    H21  C31  N30  C29  -176.92  30.0  3
 H5Y  Var_09    H24  C32  N30  C29   -64.08  30.0  3
 H5Y  Var_10    H5   C01  C02  N03  -174.62  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
 H5Y  plan-1  C26  0.020
 H5Y  plan-1  C05  0.020
 H5Y  plan-1  C06  0.020
 H5Y  plan-1  C07  0.020
 H5Y  plan-1  C16  0.020
 H5Y  plan-1  N15  0.020
 H5Y  plan-1  N25  0.020
 H5Y  plan-1  H2   0.020
 H5Y  plan-1  C04  0.020
 H5Y  plan-2  C10  0.020
 H5Y  plan-2  C06  0.020
 H5Y  plan-2  C07  0.020
 H5Y  plan-2  C08  0.020
 H5Y  plan-2  C09  0.020
 H5Y  plan-2  C11  0.020
 H5Y  plan-2  C12  0.020
 H5Y  plan-2  O13  0.020
 H5Y  plan-2  H10  0.020
 H5Y  plan-2  H11  0.020
 H5Y  plan-2  H12  0.020
 H5Y  plan-2  H13  0.020
 H5Y  plan-3  C20  0.020
 H5Y  plan-3  C21  0.020
 H5Y  plan-3  C24  0.020
 H5Y  plan-3  C16  0.020
 H5Y  plan-3  C18  0.020
 H5Y  plan-3  C19  0.020
 H5Y  plan-3  N15  0.020
 H5Y  plan-3  N17  0.020
 H5Y  plan-3  H1   0.020
 H5Y  plan-3  H17  0.020
 H5Y  plan-3  H18  0.020
 H5Y  plan-4  C28  0.020
 H5Y  plan-4  C02  0.020
 H5Y  plan-4  C05  0.020
 H5Y  plan-4  N03  0.020
 H5Y  plan-4  O27  0.020
 H5Y  plan-4  C04  0.020
 H5Y  plan-5  C20  0.020
 H5Y  plan-5  C21  0.020
 H5Y  plan-5  O22  0.020
 H5Y  plan-5  O23  0.020

