# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:55:43 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (3~{S})-4-(6-azanyl-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl)-~{N}-(4-methoxy-2-methyl-phenyl)-3-methyl-piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)N2CCN([C@@H](C)C2)c3nc(N)nc4n(C)ncc34)c(C)c1
#
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
 EMW  EMW  (3~{S})-4-(6-azanyl-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl)-~{N}-(4-methoxy-2-methyl-phenyl)-3-methyl-piperazine-1-carboxamide  ligand  56  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EMW
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
 EMW  C1   C  CH3   0  -0.436   8.3902  -0.5059   1.7288
 EMW  C3   C  CR6   0   0.395   6.2438  -0.7241   0.7452
 EMW  C4   C  CR16  0  -0.407   6.0596   0.6535   0.6790
 EMW  C5   C  CR16  0  -0.255   4.8872   1.1573   0.1314
 EMW  C6   C  CR6   0   0.258   3.8895   0.3148  -0.3317
 EMW  C8   C  C     0   0.711   1.8367   1.6172  -0.1956
 EMW  O9   O  O     0  -0.523   2.0886   1.9889   0.9425
 EMW  N10  N  NT    0  -0.488   0.6944   2.0019  -0.8491
 EMW  C11  C  CH2   0  -0.353   0.1309   1.3307  -1.9983
 EMW  C12  C  CH1   0  -0.067  -0.8450   0.2068  -1.6332
 EMW  C16  C  CH2   0  -0.310  -1.3291   1.5473   0.4039
 EMW  C17  C  CH2   0  -0.337  -0.3692   2.6128  -0.0788
 EMW  C18  C  CR6   0   0.512  -2.8941  -0.0950  -0.3393
 EMW  N22  N  N     0  -0.509  -4.9680  -1.8565   0.3474
 EMW  C23  C  CR56  0   0.588  -5.0226  -0.5551   0.6187
 EMW  C24  C  CR56  0  -0.231  -4.0455   0.4029   0.3185
 EMW  C31  C  CR16  0  -0.408   5.2448  -1.5725   0.2665
 EMW  O2   O  O2    0  -0.474   7.3419  -1.3222   1.2481
 EMW  N7   N  NH1   0  -0.781   2.7064   0.8345  -0.8994
 EMW  C14  C  CH3   0  -0.687  -1.4514  -0.2730  -2.9470
 EMW  N15  N  NT    0  -0.509  -1.8517   0.7270  -0.6982
 EMW  N19  N  N     0  -0.520  -2.8294  -1.3806  -0.6175
 EMW  C20  C  CR6   0   0.548  -3.8534  -2.1965  -0.2849
 EMW  N21  N  NH2   0  -0.823  -3.7105  -3.4834  -0.6600
 EMW  C25  C  CR15  0  -0.114  -4.6159   1.6241   0.7555
 EMW  N26  N  N     0  -0.263  -5.7979   1.4247   1.2773
 EMW  N27  N  NR5   0  -0.371  -6.0437   0.1018   1.1977
 EMW  C28  C  CH3   0  -0.522  -7.2807  -0.4446   1.6902
 EMW  C29  C  CR6   0   0.100   4.0643  -1.0735  -0.2627
 EMW  H1   H  HCH3  0   0.228   8.8062   0.1308   0.9432
 EMW  H2   H  HCH3  0   0.227   8.0689   0.1273   2.5602
 EMW  H3   H  HCH3  0   0.259   9.1685  -1.1779   2.0824
 EMW  H4   H  HCR6  0   0.278   6.8109   1.3455   1.0342
 EMW  H5   H  HCR6  0   0.261   4.7597   2.2291   0.0598
 EMW  H6   H  HCH2  0   0.266  -0.3990   2.0815  -2.5915
 EMW  H7   H  HCH2  0   0.266   0.8946   0.9275  -2.6608
 EMW  H8   H  HCH1  0   0.230  -0.2774  -0.6114  -1.1667
 EMW  H9   H  HCH2  0   0.239  -0.8141   0.9091   1.1339
 EMW  H10  H  HCH2  0   0.268  -2.1497   2.0278   0.9283
 EMW  H11  H  HCH2  0   0.276   0.0311   3.1540   0.7736
 EMW  H12  H  HCH2  0   0.257  -0.8864   3.3316  -0.7187
 EMW  H13  H  HCH3  0   0.249   2.0232  -1.7616  -0.3399
 EMW  H14  H  HCH3  0   0.250   2.8995  -1.9559  -1.8486
 EMW  H15  H  HCH3  0   0.256   3.2289  -3.0374  -0.5036
 EMW  H16  H  HCR6  0   0.256   5.3960  -2.6443   0.3227
 EMW  H17  H  HNH1  0   0.402   2.4582   0.4873  -1.8096
 EMW  H18  H  HCH3  0   0.229  -2.0667   0.5118  -3.3906
 EMW  H19  H  HCH3  0   0.236  -0.6477  -0.4994  -3.6498
 EMW  H20  H  HCH3  0   0.264  -2.0526  -1.1679  -2.8326
 EMW  H21  H  HNH2  0   0.394  -4.3381  -4.1724  -0.2835
 EMW  H22  H  HNH2  0   0.395  -2.8052  -3.8014  -0.9578
 EMW  H23  H  HCR5  0   0.264  -4.2167   2.6254   0.6985
 EMW  H24  H  HCH3  0   0.257  -8.1288   0.0139   1.1850
 EMW  H25  H  HCH3  0   0.260  -7.2901  -1.5129   1.4946
 EMW  H26  H  HCH3  0   0.256  -7.3720  -0.2824   2.7631
 EMW  C30  C  CH3   0  -0.745   2.9998  -2.0052  -0.7620

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
 EMW  N26  N27  aromatic  1.348  0.020  1.348
 EMW  N26  C25  aromatic  1.307  0.020  1.307
 EMW  C28  N27  single    1.439  0.020  1.439
 EMW  N27  C23  aromatic  1.345  0.020  1.345
 EMW  C25  C24  aromatic  1.417  0.020  1.417
 EMW  C23  C24  aromatic  1.401  0.020  1.401
 EMW  C23  N22  aromatic  1.330  0.020  1.330
 EMW  C24  C18  aromatic  1.416  0.020  1.416
 EMW  C14  C12  single    1.524  0.020  1.524
 EMW  N22  C20  aromatic  1.326  0.020  1.326
 EMW  C18  N15  single    1.375  0.020  1.375
 EMW  C18  N19  aromatic  1.317  0.020  1.317
 EMW  C12  N15  single    1.469  0.020  1.469
 EMW  C12  C11  single    1.533  0.020  1.533
 EMW  N15  C16  single    1.470  0.020  1.470
 EMW  C20  N19  aromatic  1.351  0.020  1.351
 EMW  C20  N21  single    1.348  0.020  1.348
 EMW  C16  C17  single    1.513  0.020  1.513
 EMW  C30  C29  single    1.500  0.020  1.500
 EMW  C11  N10  single    1.445  0.020  1.445
 EMW  N10  C17  single    1.448  0.020  1.448
 EMW  N10  C8   single    1.371  0.020  1.371
 EMW  C29  C31  aromatic  1.387  0.020  1.387
 EMW  C29  C6   aromatic  1.401  0.020  1.401
 EMW  N7   C8   single    1.365  0.020  1.365
 EMW  N7   C6   single    1.411  0.020  1.411
 EMW  C8   O9   double    1.223  0.020  1.223
 EMW  C31  C3   aromatic  1.395  0.020  1.395
 EMW  C6   C5   aromatic  1.386  0.020  1.386
 EMW  C3   O2   single    1.348  0.020  1.348
 EMW  C3   C4   aromatic  1.391  0.020  1.391
 EMW  C5   C4   aromatic  1.389  0.020  1.389
 EMW  O2   C1   single    1.413  0.020  1.413
 EMW  C1   H1   single    0.970  0.020  1.090
 EMW  C1   H2   single    0.970  0.020  1.090
 EMW  C1   H3   single    0.970  0.020  1.090
 EMW  C4   H4   single    0.930  0.020  1.080
 EMW  C5   H5   single    0.930  0.020  1.080
 EMW  C11  H6   single    0.970  0.020  1.090
 EMW  C11  H7   single    0.970  0.020  1.090
 EMW  C12  H8   single    0.970  0.020  1.090
 EMW  C16  H9   single    0.970  0.020  1.090
 EMW  C16  H10  single    0.970  0.020  1.090
 EMW  C17  H11  single    0.970  0.020  1.090
 EMW  C17  H12  single    0.970  0.020  1.090
 EMW  C30  H13  single    0.970  0.020  1.090
 EMW  C30  H14  single    0.970  0.020  1.090
 EMW  C30  H15  single    0.970  0.020  1.090
 EMW  C31  H16  single    0.930  0.020  1.080
 EMW  N7   H17  single    0.860  0.020  1.020
 EMW  C14  H18  single    0.970  0.020  1.090
 EMW  C14  H19  single    0.970  0.020  1.090
 EMW  C14  H20  single    0.970  0.020  1.090
 EMW  N21  H21  single    0.890  0.020  1.040
 EMW  N21  H22  single    0.890  0.020  1.040
 EMW  C25  H23  single    0.930  0.020  1.080
 EMW  C28  H24  single    0.970  0.020  1.090
 EMW  C28  H25  single    0.970  0.020  1.090
 EMW  C28  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
 EMW  H3   C1   H2   108.73  3.000
 EMW  H3   C1   H1   108.74  3.000
 EMW  H2   C1   H1   108.71  3.000
 EMW  H3   C1   O2   106.54  3.000
 EMW  H2   C1   O2   112.04  3.000
 EMW  H1   C1   O2   111.98  3.000
 EMW  O2   C3   C31  116.20  3.000
 EMW  O2   C3   C4   124.40  3.000
 EMW  C31  C3   C4   119.39  3.000
 EMW  H4   C4   C5   118.94  3.000
 EMW  H4   C4   C3   121.73  3.000
 EMW  C5   C4   C3   119.32  3.000
 EMW  H5   C5   C6   119.70  3.000
 EMW  H5   C5   C4   119.02  3.000
 EMW  C6   C5   C4   121.28  3.000
 EMW  C29  C6   N7   119.30  3.000
 EMW  N7   C6   C5   120.94  3.000
 EMW  C29  C6   C5   119.75  3.000
 EMW  N7   C8   N10  116.48  3.000
 EMW  N7   C8   O9   121.50  3.000
 EMW  N10  C8   O9   121.98  3.000
 EMW  C17  N10  C11  109.42  3.000
 EMW  C17  N10  C8   118.47  3.000
 EMW  C11  N10  C8   125.00  3.000
 EMW  H7   C11  H6   105.31  3.000
 EMW  H7   C11  C12  108.67  3.000
 EMW  H6   C11  C12  108.91  3.000
 EMW  H7   C11  N10  112.49  3.000
 EMW  H6   C11  N10  107.54  3.000
 EMW  C12  C11  N10  113.55  3.000
 EMW  H8   C12  N15  110.31  3.000
 EMW  H8   C12  C14  109.68  3.000
 EMW  N15  C12  C14  112.79  3.000
 EMW  H8   C12  C11  108.54  3.000
 EMW  N15  C12  C11  109.16  3.000
 EMW  C14  C12  C11  106.19  3.000
 EMW  H10  C16  H9   106.89  3.000
 EMW  H10  C16  N15  109.90  3.000
 EMW  H9   C16  N15  109.94  3.000
 EMW  H10  C16  C17  108.77  3.000
 EMW  H9   C16  C17  108.90  3.000
 EMW  N15  C16  C17  112.29  3.000
 EMW  H12  C17  H11  107.84  3.000
 EMW  H12  C17  C16  110.48  3.000
 EMW  H11  C17  C16  109.53  3.000
 EMW  H12  C17  N10  108.27  3.000
 EMW  H11  C17  N10  110.91  3.000
 EMW  C16  C17  N10  109.79  3.000
 EMW  N19  C18  N15  119.42  3.000
 EMW  N19  C18  C24  118.77  3.000
 EMW  N15  C18  C24  121.81  3.000
 EMW  C20  N22  C23  112.49  3.000
 EMW  N27  C23  C24  106.72  3.000
 EMW  C24  C23  N22  126.63  3.000
 EMW  N27  C23  N22  126.63  3.000
 EMW  C25  C24  C23  104.04  3.000
 EMW  C23  C24  C18  115.21  3.000
 EMW  C25  C24  C18  140.67  3.000
 EMW  H16  C31  C29  119.64  3.000
 EMW  H16  C31  C3   118.92  3.000
 EMW  C29  C31  C3   121.45  3.000
 EMW  C3   O2   C1   118.37  3.000
 EMW  H17  N7   C8   120.49  3.000
 EMW  H17  N7   C6   116.36  3.000
 EMW  C8   N7   C6   122.52  3.000
 EMW  H20  C14  H19  107.77  3.000
 EMW  H20  C14  H18  108.89  3.000
 EMW  H19  C14  H18  107.62  3.000
 EMW  H20  C14  C12  112.92  3.000
 EMW  H19  C14  C12  109.10  3.000
 EMW  H18  C14  C12  110.38  3.000
 EMW  C18  N15  C16  114.04  3.000
 EMW  C16  N15  C12  115.54  3.000
 EMW  C18  N15  C12  118.28  3.000
 EMW  C20  N19  C18  120.02  3.000
 EMW  N21  C20  N19  115.32  3.000
 EMW  N21  C20  N22  117.82  3.000
 EMW  N19  C20  N22  126.86  3.000
 EMW  H22  N21  H21  117.17  3.000
 EMW  H22  N21  C20  118.70  3.000
 EMW  H21  N21  C20  118.94  3.000
 EMW  H23  C25  N26  119.80  3.000
 EMW  H23  C25  C24  129.36  3.000
 EMW  N26  C25  C24  110.83  3.000
 EMW  N27  N26  C25  106.92  3.000
 EMW  C28  N27  N26  120.60  3.000
 EMW  C28  N27  C23  127.90  3.000
 EMW  N26  N27  C23  111.49  3.000
 EMW  H26  C28  H25  108.86  3.000
 EMW  H26  C28  H24  109.22  3.000
 EMW  H25  C28  H24  108.90  3.000
 EMW  H26  C28  N27  110.66  3.000
 EMW  H25  C28  N27  108.61  3.000
 EMW  H24  C28  N27  110.54  3.000
 EMW  C31  C29  C30  120.50  3.000
 EMW  C31  C29  C6   118.80  3.000
 EMW  C30  C29  C6   120.70  3.000
 EMW  H15  C30  H14  107.36  3.000
 EMW  H15  C30  H13  107.95  3.000
 EMW  H14  C30  H13  107.01  3.000
 EMW  H15  C30  C29  111.14  3.000
 EMW  H14  C30  C29  111.60  3.000
 EMW  H13  C30  C29  111.56  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
 EMW  CONST_01  C6   C29  C31  C3      0.00   0.0  0
 EMW  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 EMW  CONST_03  C29  C31  C3   C4      0.00   0.0  0
 EMW  CONST_04  C29  C6   C5   C4      0.00   0.0  0
 EMW  CONST_05  C31  C29  C6   C5      0.00   0.0  0
 EMW  CONST_06  C31  C3   C4   C5      0.00   0.0  0
 EMW  CONST_07  N26  C25  C24  C18   180.00   0.0  0
 EMW  CONST_08  N27  C23  C24  C18   180.00   0.0  0
 EMW  CONST_09  N22  C23  C24  C18     0.00   0.0  0
 EMW  CONST_10  N22  C20  N19  C18     0.00   0.0  0
 EMW  CONST_11  N26  N27  C23  N22   180.00   0.0  0
 EMW  CONST_12  C25  C24  C23  N22   180.00   0.0  0
 EMW  CONST_13  C25  N26  N27  C23     0.00   0.0  0
 EMW  CONST_14  N26  C25  C24  C23     0.00   0.0  0
 EMW  CONST_15  N19  C18  C24  C23     0.00   0.0  0
 EMW  CONST_16  N19  C20  N22  C23     0.00   0.0  0
 EMW  CONST_17  N27  N26  C25  C24     0.00   0.0  0
 EMW  CONST_18  N26  N27  C23  C24     0.00   0.0  0
 EMW  CONST_19  C20  N22  C23  C24     0.00   0.0  0
 EMW  CONST_20  C20  N19  C18  C24     0.00   0.0  0
 EMW  CONST_21  C25  C24  C18  N19   180.00   0.0  0
 EMW  CONST_22  N27  C23  N22  C20   180.00   0.0  0
 EMW  CONST_23  N27  C23  C24  C25     0.00   0.0  0
 EMW  CONST_24  N15  C18  C24  C23   180.00   0.0  0
 EMW  CONST_25  C25  C24  C18  N15     0.00   0.0  0
 EMW  CONST_26  C20  N19  C18  N15   180.00   0.0  0
 EMW  CONST_27  C30  C29  C31  C3    180.00   0.0  0
 EMW  CONST_28  N7   C6   C5   C4    180.00   0.0  0
 EMW  CONST_29  C30  C29  C6   C5    180.00   0.0  0
 EMW  CONST_30  O2   C3   C4   C5    180.00   0.0  0
 EMW  CONST_31  N21  C20  N19  C18   180.00   0.0  0
 EMW  CONST_32  C28  N27  C23  N22     0.00   0.0  0
 EMW  CONST_33  N21  C20  N22  C23   180.00   0.0  0
 EMW  CONST_34  C28  N27  C23  C24   180.00   0.0  0
 EMW  CONST_35  N7   C6   C29  C31   180.00   0.0  0
 EMW  CONST_36  C29  C31  C3   O2    180.00   0.0  0
 EMW  CONST_37  C28  N27  N26  C25   180.00   0.0  0
 EMW  CONST_38  H5   C5   C4   C3    180.00   0.0  0
 EMW  CONST_39  H16  C31  C3   C4    180.00   0.0  0
 EMW  CONST_40  H4   C4   C5   C6    180.00   0.0  0
 EMW  CONST_41  H23  C25  C24  C18     0.00   0.0  0
 EMW  CONST_43  C17  N10  C8   O9      0.00   0.0  0
 EMW  CONST_45  N10  C8   N7   C6    180.00   0.0  0
 EMW  CONST_48  N7   C8   N10  C17   180.00   0.0  0
 EMW  CONST_50  H21  N21  C20  N22     0.00   0.0  0
 EMW  CONST_51  H22  N21  C20  N22   180.00   0.0  0
 EMW  CONST_52  O9   C8   N7   C6      0.00   0.0  0
 EMW  Var_01    N15  C16  C17  N10   -54.83  30.0  1
 EMW  Var_02    C16  C17  N10  C11    60.77  30.0  1
 EMW  Var_03    C24  C18  N15  C12  -166.38  30.0  2
 EMW  Var_04    C17  C16  N15  C12    48.62  30.0  1
 EMW  Var_05    C17  N10  C11  C12   -61.10  30.0  1
 EMW  Var_06    C31  C3   O2   C1    179.14  30.0  2
 EMW  Var_07    H13  C30  C29  C6    -51.17  30.0  2
 EMW  Var_08    H24  C28  N27  C23  -121.12  30.0  2
 EMW  Var_09    H1   C1   O2   C3    -61.10  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
 EMW  chir_01  C12  C14  N15  C11  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
 EMW  plan-1  C3   0.020
 EMW  plan-1  C4   0.020
 EMW  plan-1  C5   0.020
 EMW  plan-1  C6   0.020
 EMW  plan-1  C31  0.020
 EMW  plan-1  O2   0.020
 EMW  plan-1  N7   0.020
 EMW  plan-1  C29  0.020
 EMW  plan-1  H4   0.020
 EMW  plan-1  H5   0.020
 EMW  plan-1  H16  0.020
 EMW  plan-1  C30  0.020
 EMW  plan-2  C18  0.020
 EMW  plan-2  N22  0.020
 EMW  plan-2  C23  0.020
 EMW  plan-2  C24  0.020
 EMW  plan-2  N15  0.020
 EMW  plan-2  N19  0.020
 EMW  plan-2  C20  0.020
 EMW  plan-2  N21  0.020
 EMW  plan-2  C25  0.020
 EMW  plan-2  N26  0.020
 EMW  plan-2  N27  0.020
 EMW  plan-2  C28  0.020
 EMW  plan-2  H23  0.020
 EMW  plan-3  C6   0.020
 EMW  plan-3  C8   0.020
 EMW  plan-3  O9   0.020
 EMW  plan-3  N10  0.020
 EMW  plan-3  C11  0.020
 EMW  plan-3  C17  0.020
 EMW  plan-3  N7   0.020
 EMW  plan-3  H17  0.020
 EMW  plan-4  C20  0.020
 EMW  plan-4  N21  0.020
 EMW  plan-4  H21  0.020
 EMW  plan-4  H22  0.020

