# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:12:35 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: (2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(Nc2nc(N[C@@H](CO)c3ccccc3)nc4[nH]ncc24)cc1C(C)(C)C
#
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
 UYD  UYD  (2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethan-1-ol  ligand  56  30  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UYD
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
 UYD  C10  C  CH1   0  -0.163  -39.5132  23.4088  -67.1930
 UYD  C11  C  CH2   0  -0.160  -41.0201  23.6157  -67.2936
 UYD  C13  C  CR6   0   0.144  -38.8954  23.1762  -68.5613
 UYD  C14  C  CR16  0  -0.300  -39.1952  22.0030  -69.2505
 UYD  C15  C  CR16  0  -0.242  -38.6657  21.7562  -70.5082
 UYD  C16  C  CR16  0  -0.273  -37.8211  22.6862  -71.1017
 UYD  C17  C  CR16  0  -0.240  -37.5167  23.8577  -70.4238
 UYD  C18  C  CR16  0  -0.316  -38.0510  24.1007  -69.1637
 UYD  C20  C  CR56  0   0.553  -36.1827  25.6290  -64.7520
 UYD  C23  C  CR15  0  -0.129  -34.2935  24.9065  -63.8159
 UYD  C01  C  CH3   0  -0.535  -34.8761  17.4852  -65.1340
 UYD  C04  C  CR5   0   0.472  -35.7236  20.8426  -65.3041
 UYD  C06  C  CR6   0   0.541  -35.9905  23.2860  -65.0660
 UYD  C08  C  CR6   0   0.609  -37.7605  24.5257  -65.8432
 UYD  C24  C  CR56  0  -0.268  -35.4309  24.4715  -64.5380
 UYD  C25  C  CR15  0  -0.580  -36.7675  20.3966  -66.1286
 UYD  C26  C  CR5   0   0.522  -36.6207  19.0201  -66.1629
 UYD  C27  C  CT    0  -0.195  -37.4745  18.0077  -66.8910
 UYD  C28  C  CH3   0  -0.644  -36.6307  17.1347  -67.8299
 UYD  C29  C  CH3   0  -0.638  -38.2469  17.1346  -65.8916
 UYD  C30  C  CH3   0  -0.658  -38.4951  18.7591  -67.7490
 UYD  N02  N  NR5   0  -0.338  -35.5507  18.7382  -65.3861
 UYD  N03  N  N     0  -0.338  -34.9931  19.8377  -64.8666
 UYD  N07  N  N     0  -0.529  -37.1412  23.3362  -65.7131
 UYD  N09  N  NH1   0  -0.669  -38.9474  24.5266  -66.4857
 UYD  N19  N  N     0  -0.523  -37.3441  25.7081  -65.3944
 UYD  N21  N  NR15  0  -0.531  -35.4892  26.6272  -64.1779
 UYD  N22  N  N     0  -0.248  -34.3449  26.1972  -63.6097
 UYD  O12  O  OH1   0  -0.668  -41.2612  24.7890  -68.0323
 UYD  H1   H  HCH1  0   0.271  -39.3659  22.5101  -66.5886
 UYD  H2   H  HCH2  0   0.214  -41.4663  22.7332  -67.7667
 UYD  H3   H  HCH2  0   0.224  -41.4280  23.6818  -66.2783
 UYD  H4   H  HCR6  0   0.249  -39.8530  21.2680  -68.8009
 UYD  H5   H  HCR6  0   0.254  -38.9115  20.8361  -71.0233
 UYD  H6   H  HCR6  0   0.253  -37.4034  22.4966  -72.0819
 UYD  H7   H  HCR6  0   0.253  -36.8599  24.5898  -70.8762
 UYD  H8   H  HCR6  0   0.244  -37.7955  25.0209  -68.6538
 UYD  H9   H  HCR5  0   0.267  -33.4574  24.3303  -63.4483
 UYD  H10  H  HCH3  0   0.273  -34.3827  17.5538  -64.1685
 UYD  H11  H  HCH3  0   0.254  -35.5798  16.6611  -65.0972
 UYD  H12  H  HCH3  0   0.256  -34.1272  17.2772  -65.8981
 UYD  H13  H  HCR5  0   0.283  -37.5088  20.9947  -66.6235
 UYD  H14  H  HCH3  0   0.237  -35.9540  16.4629  -67.3037
 UYD  H15  H  HCH3  0   0.238  -37.2906  16.5121  -68.4361
 UYD  H16  H  HCH3  0   0.235  -36.0363  17.7492  -68.5077
 UYD  H17  H  HCH3  0   0.236  -38.8710  17.7482  -65.2403
 UYD  H18  H  HCH3  0   0.236  -38.8998  16.4441  -66.4294
 UYD  H19  H  HCH3  0   0.233  -37.5942  16.5348  -65.2581
 UYD  H20  H  HCH3  0   0.230  -39.1576  19.3783  -67.1430
 UYD  H21  H  HCH3  0   0.238  -38.0072  19.3996  -68.4844
 UYD  H22  H  HCH3  0   0.241  -39.1158  18.0440  -68.2900
 UYD  H23  H  HNH1  0   0.413  -34.4878  22.1417  -64.3708
 UYD  H24  H  HNH1  0   0.388  -39.3545  25.4341  -66.6503
 UYD  H25  H  HNR5  0   0.413  -35.7373  27.6025  -64.1369
 UYD  H26  H  HOH1  0   0.462  -42.1902  25.0195  -67.9427
 UYD  N05  N  NH1   0  -0.750  -35.3453  22.1154  -64.9023

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
 UYD  C16  C15  aromatic  1.389  0.020  1.389
 UYD  C16  C17  aromatic  1.387  0.020  1.387
 UYD  C15  C14  aromatic  1.387  0.020  1.387
 UYD  C17  C18  aromatic  1.390  0.020  1.390
 UYD  C14  C13  aromatic  1.393  0.020  1.393
 UYD  C18  C13  aromatic  1.389  0.020  1.389
 UYD  C13  C10  single    1.519  0.020  1.519
 UYD  C28  C27  single    1.535  0.020  1.535
 UYD  C11  C10  single    1.524  0.020  1.524
 UYD  C11  O12  single    1.407  0.020  1.407
 UYD  C10  N09  single    1.439  0.020  1.439
 UYD  C30  C27  single    1.530  0.020  1.530
 UYD  N09  C08  single    1.350  0.020  1.350
 UYD  C27  C26  single    1.511  0.020  1.511
 UYD  C27  C29  single    1.536  0.020  1.536
 UYD  C26  C25  aromatic  1.385  0.020  1.385
 UYD  C26  N02  aromatic  1.352  0.020  1.352
 UYD  C08  N07  aromatic  1.347  0.020  1.347
 UYD  C08  N19  aromatic  1.331  0.020  1.331
 UYD  C25  C04  aromatic  1.403  0.020  1.403
 UYD  N07  C06  aromatic  1.321  0.020  1.321
 UYD  N19  C20  aromatic  1.330  0.020  1.330
 UYD  N02  C01  single    1.445  0.020  1.445
 UYD  N02  N03  aromatic  1.338  0.020  1.338
 UYD  C04  N03  aromatic  1.317  0.020  1.317
 UYD  C04  N05  single    1.387  0.020  1.387
 UYD  C06  N05  single    1.347  0.020  1.347
 UYD  C06  C24  aromatic  1.413  0.020  1.413
 UYD  C20  C24  aromatic  1.397  0.020  1.397
 UYD  C20  N21  aromatic  1.344  0.020  1.344
 UYD  C24  C23  aromatic  1.416  0.020  1.416
 UYD  N21  N22  aromatic  1.348  0.020  1.348
 UYD  C23  N22  aromatic  1.308  0.020  1.308
 UYD  C10  H1   single    0.970  0.020  1.090
 UYD  C11  H2   single    0.970  0.020  1.090
 UYD  C11  H3   single    0.970  0.020  1.090
 UYD  C14  H4   single    0.930  0.020  1.080
 UYD  C15  H5   single    0.930  0.020  1.080
 UYD  C16  H6   single    0.930  0.020  1.080
 UYD  C17  H7   single    0.930  0.020  1.080
 UYD  C18  H8   single    0.930  0.020  1.080
 UYD  C23  H9   single    0.930  0.020  1.080
 UYD  C01  H10  single    0.970  0.020  1.090
 UYD  C01  H11  single    0.970  0.020  1.090
 UYD  C01  H12  single    0.970  0.020  1.090
 UYD  C25  H13  single    0.930  0.020  1.080
 UYD  C28  H14  single    0.970  0.020  1.090
 UYD  C28  H15  single    0.970  0.020  1.090
 UYD  C28  H16  single    0.970  0.020  1.090
 UYD  C29  H17  single    0.970  0.020  1.090
 UYD  C29  H18  single    0.970  0.020  1.090
 UYD  C29  H19  single    0.970  0.020  1.090
 UYD  C30  H20  single    0.970  0.020  1.090
 UYD  C30  H21  single    0.970  0.020  1.090
 UYD  C30  H22  single    0.970  0.020  1.090
 UYD  N05  H23  single    0.860  0.020  1.020
 UYD  N09  H24  single    0.860  0.020  1.020
 UYD  N21  H25  single    0.860  0.020  1.020
 UYD  O12  H26  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
 UYD  H1   C10  N09  108.30  3.000
 UYD  H1   C10  C13  108.50  3.000
 UYD  N09  C10  C13  113.69  3.000
 UYD  H1   C10  C11  106.34  3.000
 UYD  N09  C10  C11  108.41  3.000
 UYD  C13  C10  C11  111.31  3.000
 UYD  H3   C11  H2   107.26  3.000
 UYD  H3   C11  O12  111.85  3.000
 UYD  H2   C11  O12  112.02  3.000
 UYD  H3   C11  C10  108.36  3.000
 UYD  H2   C11  C10  108.76  3.000
 UYD  O12  C11  C10  108.50  3.000
 UYD  C18  C13  C14  118.46  3.000
 UYD  C18  C13  C10  122.40  3.000
 UYD  C14  C13  C10  119.14  3.000
 UYD  H4   C14  C15  119.16  3.000
 UYD  H4   C14  C13  119.75  3.000
 UYD  C15  C14  C13  121.09  3.000
 UYD  H5   C15  C16  120.24  3.000
 UYD  H5   C15  C14  119.74  3.000
 UYD  C16  C15  C14  120.02  3.000
 UYD  H6   C16  C17  120.39  3.000
 UYD  H6   C16  C15  120.28  3.000
 UYD  C17  C16  C15  119.34  3.000
 UYD  H7   C17  C18  119.59  3.000
 UYD  H7   C17  C16  120.00  3.000
 UYD  C18  C17  C16  120.41  3.000
 UYD  H8   C18  C17  119.00  3.000
 UYD  H8   C18  C13  120.31  3.000
 UYD  C17  C18  C13  120.69  3.000
 UYD  N21  C20  N19  127.80  3.000
 UYD  N21  C20  C24  105.80  3.000
 UYD  N19  C20  C24  126.40  3.000
 UYD  H9   C23  N22  120.22  3.000
 UYD  H9   C23  C24  129.18  3.000
 UYD  N22  C23  C24  110.61  3.000
 UYD  H12  C01  H11  108.95  3.000
 UYD  H12  C01  H10  108.85  3.000
 UYD  H11  C01  H10  108.22  3.000
 UYD  H12  C01  N02  111.34  3.000
 UYD  H11  C01  N02  111.22  3.000
 UYD  H10  C01  N02  108.19  3.000
 UYD  N05  C04  N03  116.91  3.000
 UYD  N05  C04  C25  131.66  3.000
 UYD  N03  C04  C25  111.43  3.000
 UYD  N07  C06  N05  120.66  3.000
 UYD  N05  C06  C24  119.61  3.000
 UYD  N07  C06  C24  119.73  3.000
 UYD  N19  C08  N09  115.77  3.000
 UYD  N19  C08  N07  127.43  3.000
 UYD  N09  C08  N07  116.79  3.000
 UYD  C06  C24  C23  140.03  3.000
 UYD  C23  C24  C20  104.83  3.000
 UYD  C06  C24  C20  115.14  3.000
 UYD  H13  C25  C26  128.00  3.000
 UYD  H13  C25  C04  127.43  3.000
 UYD  C26  C25  C04  104.57  3.000
 UYD  N02  C26  C27  125.75  3.000
 UYD  N02  C26  C25  106.08  3.000
 UYD  C27  C26  C25  128.16  3.000
 UYD  C30  C27  C29  107.98  3.000
 UYD  C29  C27  C28  110.56  3.000
 UYD  C30  C27  C28  107.63  3.000
 UYD  C29  C27  C26  110.58  3.000
 UYD  C30  C27  C26  108.54  3.000
 UYD  C28  C27  C26  111.42  3.000
 UYD  H16  C28  H15  107.80  3.000
 UYD  H16  C28  H14  108.01  3.000
 UYD  H15  C28  H14  106.99  3.000
 UYD  H16  C28  C27  111.05  3.000
 UYD  H15  C28  C27  109.38  3.000
 UYD  H14  C28  C27  113.39  3.000
 UYD  H19  C29  H18  107.25  3.000
 UYD  H19  C29  H17  107.77  3.000
 UYD  H18  C29  H17  107.92  3.000
 UYD  H19  C29  C27  112.96  3.000
 UYD  H18  C29  C27  109.87  3.000
 UYD  H17  C29  C27  110.89  3.000
 UYD  H22  C30  H21  107.77  3.000
 UYD  H22  C30  H20  107.59  3.000
 UYD  H21  C30  H20  108.25  3.000
 UYD  H22  C30  C27  109.62  3.000
 UYD  H21  C30  C27  111.60  3.000
 UYD  H20  C30  C27  111.86  3.000
 UYD  N03  N02  C26  112.43  3.000
 UYD  N03  N02  C01  116.76  3.000
 UYD  C26  N02  C01  130.57  3.000
 UYD  N02  N03  C04  105.48  3.000
 UYD  C08  N07  C06  118.76  3.000
 UYD  H24  N09  C08  115.69  3.000
 UYD  H24  N09  C10  117.40  3.000
 UYD  C08  N09  C10  125.41  3.000
 UYD  C08  N19  C20  112.53  3.000
 UYD  H25  N21  N22  120.05  3.000
 UYD  H25  N21  C20  127.54  3.000
 UYD  N22  N21  C20  112.41  3.000
 UYD  N21  N22  C23  106.36  3.000
 UYD  H26  O12  C11  108.46  3.000
 UYD  H23  N05  C06  116.65  3.000
 UYD  H23  N05  C04  114.09  3.000
 UYD  C06  N05  C04  129.17  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
 UYD  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 UYD  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 UYD  CONST_03  C17  C16  C15  C14     0.00   0.0  0
 UYD  CONST_04  C17  C18  C13  C14     0.00   0.0  0
 UYD  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 UYD  CONST_06  C18  C13  C14  C15     0.00   0.0  0
 UYD  CONST_07  N07  C08  N19  C20     0.00   0.0  0
 UYD  CONST_08  N07  C06  C24  C20     0.00   0.0  0
 UYD  CONST_09  N22  C23  C24  C20     0.00   0.0  0
 UYD  CONST_10  C23  N22  N21  C20     0.00   0.0  0
 UYD  CONST_11  N07  C06  C24  C23   180.00   0.0  0
 UYD  CONST_12  N19  C20  C24  C23   180.00   0.0  0
 UYD  CONST_13  N21  C20  C24  C23     0.00   0.0  0
 UYD  CONST_14  N02  C26  C25  C04     0.00   0.0  0
 UYD  CONST_15  C26  N02  N03  C04     0.00   0.0  0
 UYD  CONST_16  N19  C08  N07  C06     0.00   0.0  0
 UYD  CONST_17  N19  C20  C24  C06     0.00   0.0  0
 UYD  CONST_18  N21  C20  C24  C06   180.00   0.0  0
 UYD  CONST_19  N22  C23  C24  C06   180.00   0.0  0
 UYD  CONST_20  C24  C06  N07  C08     0.00   0.0  0
 UYD  CONST_21  C24  C20  N19  C08     0.00   0.0  0
 UYD  CONST_22  N21  C20  N19  C08   180.00   0.0  0
 UYD  CONST_23  N22  N21  C20  C24     0.00   0.0  0
 UYD  CONST_24  N21  N22  C23  C24     0.00   0.0  0
 UYD  CONST_25  N03  N02  C26  C25     0.00   0.0  0
 UYD  CONST_26  N02  N03  C04  C25     0.00   0.0  0
 UYD  CONST_27  N03  C04  C25  C26     0.00   0.0  0
 UYD  CONST_28  N22  N21  C20  N19   180.00   0.0  0
 UYD  CONST_29  C15  C14  C13  C10   180.00   0.0  0
 UYD  CONST_30  C17  C18  C13  C10   180.00   0.0  0
 UYD  CONST_31  N09  C08  N19  C20   180.00   0.0  0
 UYD  CONST_32  N05  C06  C24  C20   180.00   0.0  0
 UYD  CONST_33  N05  C06  C24  C23     0.00   0.0  0
 UYD  CONST_34  C25  C26  N02  C01   180.00   0.0  0
 UYD  CONST_35  C04  N03  N02  C01   180.00   0.0  0
 UYD  CONST_36  C27  C26  C25  C04   180.00   0.0  0
 UYD  CONST_37  N09  C08  N07  C06   180.00   0.0  0
 UYD  CONST_38  N05  C06  N07  C08   180.00   0.0  0
 UYD  CONST_39  N05  C04  C25  C26   180.00   0.0  0
 UYD  CONST_40  N03  N02  C26  C27   180.00   0.0  0
 UYD  CONST_41  N05  C04  N03  N02   180.00   0.0  0
 UYD  CONST_42  H5   C15  C14  C13   180.00   0.0  0
 UYD  CONST_43  H7   C17  C18  C13   180.00   0.0  0
 UYD  CONST_44  H6   C16  C15  C14   180.00   0.0  0
 UYD  CONST_45  H8   C18  C13  C14   180.00   0.0  0
 UYD  CONST_46  H4   C14  C15  C16   180.00   0.0  0
 UYD  CONST_47  H9   C23  C24  C20   180.00   0.0  0
 UYD  CONST_48  H25  N21  N22  C23   180.00   0.0  0
 UYD  CONST_49  H13  C25  C26  N02   180.00   0.0  0
 UYD  CONST_50  N07  C08  N09  C10     0.00   0.0  0
 UYD  CONST_51  N19  C08  N09  C10   180.00   0.0  0
 UYD  CONST_52  H24  N09  C08  N07   180.00   0.0  0
 UYD  Var_01    N07  C06  N05  C04    -1.63  30.0  2
 UYD  Var_02    C25  C04  N05  C06     9.31  30.0  1
 UYD  Var_03    C28  C27  C26  C25   124.37  30.0  3
 UYD  Var_04    H10  C01  N02  C26  -154.96  30.0  2
 UYD  Var_05    H14  C28  C27  C26    68.33  30.0  3
 UYD  Var_06    H20  C30  C27  C26   -61.25  30.0  3
 UYD  Var_07    H17  C29  C27  C26    57.77  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 UYD  chir_01  C10  C13  C11  N09  positiv

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
 UYD  plan-1  C01  0.020
 UYD  plan-1  C04  0.020
 UYD  plan-1  C25  0.020
 UYD  plan-1  C26  0.020
 UYD  plan-1  C27  0.020
 UYD  plan-1  N02  0.020
 UYD  plan-1  N03  0.020
 UYD  plan-1  H13  0.020
 UYD  plan-1  N05  0.020
 UYD  plan-2  C10  0.020
 UYD  plan-2  C13  0.020
 UYD  plan-2  C14  0.020
 UYD  plan-2  C15  0.020
 UYD  plan-2  C16  0.020
 UYD  plan-2  C17  0.020
 UYD  plan-2  C18  0.020
 UYD  plan-2  H4   0.020
 UYD  plan-2  H5   0.020
 UYD  plan-2  H6   0.020
 UYD  plan-2  H7   0.020
 UYD  plan-2  H8   0.020
 UYD  plan-3  C20  0.020
 UYD  plan-3  C23  0.020
 UYD  plan-3  C06  0.020
 UYD  plan-3  C08  0.020
 UYD  plan-3  C24  0.020
 UYD  plan-3  N07  0.020
 UYD  plan-3  N09  0.020
 UYD  plan-3  N19  0.020
 UYD  plan-3  N21  0.020
 UYD  plan-3  N22  0.020
 UYD  plan-3  H9   0.020
 UYD  plan-3  H25  0.020
 UYD  plan-3  N05  0.020
 UYD  plan-4  C10  0.020
 UYD  plan-4  C08  0.020
 UYD  plan-4  N09  0.020
 UYD  plan-4  H24  0.020

