# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:23:31 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  59  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   0.3586  -4.0012  -0.2418
 H5Y  C20  C  CR6   0   0.031   4.9970   1.1749  -0.1557
 H5Y  C21  C  C     0   0.551   6.0610   1.9978  -0.8027
 H5Y  C24  C  CR16  0  -0.356   3.6743   1.5257  -0.3760
 H5Y  C26  C  CR15  0  -0.035  -0.3125   2.3906  -0.0648
 H5Y  C28  C  CH2   0  -0.329  -4.5552   0.5740   0.3388
 H5Y  C01  C  CH3   0  -0.659  -2.6740   0.7653   2.9774
 H5Y  C02  C  CH2   0  -0.326  -2.9265   1.7066   1.8119
 H5Y  C05  C  CR5   0  -0.395  -0.8398   1.0833  -0.0717
 H5Y  C06  C  CR5   0   0.487   0.2624   0.2568  -0.0097
 H5Y  C07  C  CR6   0   0.054   0.3264  -1.2034  -0.0771
 H5Y  C08  C  CR16  0  -0.263   1.1468  -1.8545  -1.0008
 H5Y  C09  C  CR16  0  -0.332   1.1667  -3.2307  -1.0841
 H5Y  C11  C  CR16  0  -0.373  -0.4712  -3.3629   0.6761
 H5Y  C12  C  CR16  0  -0.283  -0.4788  -1.9766   0.7475
 H5Y  C16  C  CR6   0   0.501   2.6964   0.7554   0.2379
 H5Y  C18  C  CR16  0  -0.045   4.2168  -0.6185   1.1998
 H5Y  C19  C  CR16  0  -0.343   5.2808   0.0734   0.6443
 H5Y  C29  C  CH2   0  -0.260  -5.3168   1.5607  -0.5415
 H5Y  C31  C  CH3   0  -0.526  -7.5000   1.4337   0.4670
 H5Y  C32  C  CH3   0  -0.518  -7.2871   1.8306  -1.8711
 H5Y  N03  N  NT    0  -0.440  -3.1839   1.0043   0.5605
 H5Y  N15  N  NR5   0  -0.461   1.3387   1.0866   0.0534
 H5Y  N17  N  N     0  -0.392   2.9494  -0.2778   1.0136
 H5Y  N25  N  N     0  -0.266   0.9962   2.3794   0.0043
 H5Y  N30  N  NT    0  -0.411  -6.7042   1.1804  -0.7163
 H5Y  O13  O  O2    0  -0.467   0.4453  -5.3337  -0.3905
 H5Y  O22  O  OH1   0  -0.584   7.2767   1.5770  -0.5078
 H5Y  O23  O  O     0  -0.420   5.8225   2.9424  -1.5113
 H5Y  O27  O  O     0  -0.483  -2.4778  -0.0512  -1.3065
 H5Y  H1   H  HCR6  0   0.295   3.4102   2.3650  -1.0027
 H5Y  H2   H  HCR5  0   0.283  -0.8471   3.3268  -0.1279
 H5Y  H3   H  HCH2  0   0.250  -5.0272   0.4762   1.3171
 H5Y  H4   H  HCH2  0   0.255  -4.5700  -0.4138  -0.1194
 H5Y  H5   H  HCH3  0   0.241  -2.5808   1.3313   3.9042
 H5Y  H6   H  HCH3  0   0.233  -3.4880   0.0498   3.1028
 H5Y  H7   H  HCH3  0   0.231  -1.7496   0.2050   2.8345
 H5Y  H8   H  HCH2  0   0.256  -3.7959   2.3336   2.0159
 H5Y  H9   H  HCH2  0   0.263  -2.0881   2.3883   1.6993
 H5Y  H10  H  HCR6  0   0.258   1.7682  -1.2812  -1.6776
 H5Y  H11  H  HCR6  0   0.266   1.8027  -3.7235  -1.8088
 H5Y  H12  H  HCR6  0   0.282  -1.1128  -3.9203   1.3445
 H5Y  H13  H  HCR6  0   0.259  -1.1242  -1.5004   1.4753
 H5Y  H14  H  HCH3  0   0.231  -0.1383  -6.0352   1.4857
 H5Y  H15  H  HCH3  0   0.231  -1.4280  -5.9761   0.2636
 H5Y  H16  H  HCH3  0   0.262  -0.1396  -7.1864   0.1394
 H5Y  H17  H  HCR6  0   0.282   4.3964  -1.4789   1.8324
 H5Y  H18  H  HCR6  0   0.288   6.2913  -0.2514   0.8428
 H5Y  H19  H  HCH2  0   0.195  -5.2166   2.5808  -0.1310
 H5Y  H20  H  HCH2  0   0.239  -4.8382   1.5740  -1.5229
 H5Y  H21  H  HCH3  0   0.236  -8.5253   1.1004   0.3017
 H5Y  H22  H  HCH3  0   0.234  -7.1188   0.8826   1.3271
 H5Y  H23  H  HCH3  0   0.193  -7.5337   2.5001   0.7414
 H5Y  H24  H  HCH3  0   0.192  -7.3109   2.9285  -1.7889
 H5Y  H25  H  HCH3  0   0.233  -6.7244   1.5758  -2.7702
 H5Y  H26  H  HCH3  0   0.232  -8.3135   1.4887  -2.0115
 H5Y  H28  H  HOH1  0   0.495   7.9410   2.1355  -0.9395
 H5Y  C04  C  C     0   0.490  -2.2345   0.6332  -0.3207
 H5Y  C14  C  CH3   0  -0.439  -0.3630  -6.1614   0.4237

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    1.448  0.020  1.448
 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    1.347  0.020  1.347
 H5Y  C04  O27  double    1.225  0.020  1.225
 H5Y  C04  C05  single    1.487  0.020  1.487
 H5Y  C26  C05  aromatic  1.410  0.020  1.410
 H5Y  C26  N25  aromatic  1.311  0.020  1.311
 H5Y  C05  C06  aromatic  1.379  0.020  1.379
 H5Y  N25  N15  aromatic  1.338  0.020  1.338
 H5Y  C06  N15  aromatic  1.361  0.020  1.361
 H5Y  C06  C07  single    1.463  0.020  1.463
 H5Y  N15  C16  single    1.410  0.020  1.410
 H5Y  C07  C08  aromatic  1.396  0.020  1.396
 H5Y  C07  C12  aromatic  1.388  0.020  1.388
 H5Y  N17  C16  aromatic  1.317  0.020  1.317
 H5Y  N17  C18  aromatic  1.326  0.020  1.326
 H5Y  C08  C09  aromatic  1.379  0.020  1.379
 H5Y  C16  C24  aromatic  1.388  0.020  1.388
 H5Y  C12  C11  aromatic  1.388  0.020  1.388
 H5Y  C18  C19  aromatic  1.385  0.020  1.385
 H5Y  C09  C10  aromatic  1.399  0.020  1.399
 H5Y  C11  C10  aromatic  1.392  0.020  1.392
 H5Y  C24  C20  aromatic  1.386  0.020  1.386
 H5Y  C10  O13  single    1.344  0.020  1.344
 H5Y  C19  C20  aromatic  1.391  0.020  1.391
 H5Y  C20  C21  single    1.493  0.020  1.493
 H5Y  O13  C14  single    1.415  0.020  1.415
 H5Y  C21  O23  double    1.205  0.020  1.205
 H5Y  C21  O22  single    1.320  0.020  1.320
 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
 H5Y  O22  H28  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
 H5Y  O13  C10  C11  124.48  3.000
 H5Y  O13  C10  C09  116.26  3.000
 H5Y  C11  C10  C09  119.26  3.000
 H5Y  C19  C20  C24  119.12  3.000
 H5Y  C19  C20  C21  122.73  3.000
 H5Y  C24  C20  C21  118.15  3.000
 H5Y  O23  C21  O22  124.32  3.000
 H5Y  O22  C21  C20  112.58  3.000
 H5Y  O23  C21  C20  123.11  3.000
 H5Y  H1   C24  C16  121.04  3.000
 H5Y  H1   C24  C20  121.47  3.000
 H5Y  C16  C24  C20  117.49  3.000
 H5Y  H2   C26  N25  120.32  3.000
 H5Y  H2   C26  C05  128.21  3.000
 H5Y  N25  C26  C05  111.46  3.000
 H5Y  H4   C28  H3   106.87  3.000
 H5Y  H4   C28  N03  110.21  3.000
 H5Y  H3   C28  N03  107.33  3.000
 H5Y  H4   C28  C29  109.69  3.000
 H5Y  H3   C28  C29  111.07  3.000
 H5Y  N03  C28  C29  111.55  3.000
 H5Y  H7   C01  H6   108.10  3.000
 H5Y  H7   C01  H5   107.80  3.000
 H5Y  H6   C01  H5   107.85  3.000
 H5Y  H7   C01  C02  111.02  3.000
 H5Y  H6   C01  C02  111.75  3.000
 H5Y  H5   C01  C02  110.17  3.000
 H5Y  H9   C02  H8   105.89  3.000
 H5Y  H9   C02  N03  110.46  3.000
 H5Y  H8   C02  N03  107.25  3.000
 H5Y  H9   C02  C01  109.88  3.000
 H5Y  H8   C02  C01  110.19  3.000
 H5Y  N03  C02  C01  112.91  3.000
 H5Y  C06  C05  C04  125.16  3.000
 H5Y  C06  C05  C26  104.88  3.000
 H5Y  C04  C05  C26  129.24  3.000
 H5Y  N15  C06  C07  125.18  3.000
 H5Y  C07  C06  C05  129.13  3.000
 H5Y  N15  C06  C05  105.59  3.000
 H5Y  C12  C07  C08  118.30  3.000
 H5Y  C12  C07  C06  120.21  3.000
 H5Y  C08  C07  C06  121.43  3.000
 H5Y  H10  C08  C09  118.84  3.000
 H5Y  H10  C08  C07  120.24  3.000
 H5Y  C09  C08  C07  120.91  3.000
 H5Y  H11  C09  C08  120.21  3.000
 H5Y  H11  C09  C10  119.45  3.000
 H5Y  C08  C09  C10  120.34  3.000
 H5Y  H12  C11  C12  118.67  3.000
 H5Y  H12  C11  C10  121.66  3.000
 H5Y  C12  C11  C10  119.67  3.000
 H5Y  H13  C12  C11  118.48  3.000
 H5Y  H13  C12  C07  120.01  3.000
 H5Y  C11  C12  C07  121.51  3.000
 H5Y  N17  C16  N15  116.53  3.000
 H5Y  N17  C16  C24  124.11  3.000
 H5Y  N15  C16  C24  119.36  3.000
 H5Y  H17  C18  N17  116.41  3.000
 H5Y  H17  C18  C19  120.24  3.000
 H5Y  N17  C18  C19  123.34  3.000
 H5Y  H18  C19  C18  119.65  3.000
 H5Y  H18  C19  C20  122.35  3.000
 H5Y  C18  C19  C20  118.00  3.000
 H5Y  H20  C29  H19  106.44  3.000
 H5Y  H20  C29  N30  108.33  3.000
 H5Y  H19  C29  N30  111.98  3.000
 H5Y  H20  C29  C28  107.91  3.000
 H5Y  H19  C29  C28  109.73  3.000
 H5Y  N30  C29  C28  112.19  3.000
 H5Y  H23  C31  H22  107.67  3.000
 H5Y  H23  C31  H21  107.74  3.000
 H5Y  H22  C31  H21  107.08  3.000
 H5Y  H23  C31  N30  112.93  3.000
 H5Y  H22  C31  N30  111.34  3.000
 H5Y  H21  C31  N30  109.83  3.000
 H5Y  H26  C32  H25  107.82  3.000
 H5Y  H26  C32  H24  107.56  3.000
 H5Y  H25  C32  H24  107.79  3.000
 H5Y  H26  C32  N30  109.92  3.000
 H5Y  H25  C32  N30  110.17  3.000
 H5Y  H24  C32  N30  113.38  3.000
 H5Y  C04  N03  C02  124.73  3.000
 H5Y  C04  N03  C28  118.89  3.000
 H5Y  C02  N03  C28  116.10  3.000
 H5Y  N25  N15  C16  118.57  3.000
 H5Y  C16  N15  C06  128.66  3.000
 H5Y  N25  N15  C06  112.64  3.000
 H5Y  C18  N17  C16  117.92  3.000
 H5Y  N15  N25  C26  105.41  3.000
 H5Y  C32  N30  C31  110.61  3.000
 H5Y  C32  N30  C29  111.33  3.000
 H5Y  C31  N30  C29  112.43  3.000
 H5Y  C14  O13  C10  118.66  3.000
 H5Y  H28  O22  C21  110.37  3.000
 H5Y  O27  C04  N03  122.71  3.000
 H5Y  O27  C04  C05  119.37  3.000
 H5Y  N03  C04  C05  117.91  3.000
 H5Y  H16  C14  H15  108.77  3.000
 H5Y  H16  C14  H14  108.72  3.000
 H5Y  H15  C14  H14  108.85  3.000
 H5Y  H16  C14  O13  106.49  3.000
 H5Y  H15  C14  O13  111.92  3.000
 H5Y  H14  C14  O13  111.98  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  H28  O22  C21  C20   180.00   0.0  0
 H5Y  CONST_53  O27  C04  N03  C28     0.00   0.0  0
 H5Y  CONST_54  O27  C04  N03  C02   180.00   0.0  0
 H5Y  Var_01    O23  C21  C20  C24    -0.53  30.0  2
 H5Y  Var_02    N03  C04  C05  C26   -64.81  30.0  2
 H5Y  Var_03    H14  C14  O13  C10   -61.49  30.0  3
 H5Y  Var_04    C31  N30  C29  C28    74.54  30.0  2
 H5Y  Var_05    C01  C02  N03  C28    84.39  30.0  1
 H5Y  Var_06    C29  C28  N03  C02    97.58  30.0  1
 H5Y  Var_07    N30  C29  C28  N03  -177.09  30.0  2
 H5Y  Var_08    H21  C31  N30  C29  -178.00  30.0  3
 H5Y  Var_09    H24  C32  N30  C29   -62.54  30.0  3
 H5Y  Var_10    H5   C01  C02  N03  -174.67  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
 H5Y  plan-5  H28  0.020

