# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 22:14:54 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: tert-butyl {4-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-2-methoxyphenyl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1NC(=O)OC(C)(C)C)c2nn(C(C)C)c3ncnc(N)c23
#
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
 VSH  VSH  'tert-butyl {4-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-2-methoxyphenyl}carbamate'  ligand  55  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VSH
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
 VSH  O27  O  O     0  -0.492  -4.0031  -1.6339   1.0205
 VSH  C12  C  C     0   0.761  -4.1923  -0.6631   0.3231
 VSH  O29  O  O2    0  -0.502  -5.3739  -0.1712  -0.0300
 VSH  C20  C  CT    0   0.187  -6.6352  -0.7259   0.4398
 VSH  C17  C  CH3   0  -0.672  -6.7469  -0.6051   1.9543
 VSH  C16  C  CH3   0  -0.660  -7.6689   0.1680  -0.2335
 VSH  C15  C  CH3   0  -0.671  -6.8124  -2.1638  -0.0310
 VSH  N26  N  NH1   0  -0.760  -3.2167   0.1081  -0.2349
 VSH  C7   C  CR6   0   0.279  -1.8370  -0.0453  -0.1313
 VSH  C2   C  CR16  0  -0.305  -1.1896  -1.1376   0.4328
 VSH  C8   C  CR6   0   0.359  -1.0504   0.9973  -0.6670
 VSH  O28  O  O2    0  -0.483  -1.7396   2.0181  -1.2109
 VSH  C18  C  CH3   0  -0.436  -1.0295   3.1223  -1.7378
 VSH  C3   C  CR16  0  -0.485   0.3308   0.9257  -0.6247
 VSH  C6   C  CR6   0   0.056   0.9712  -0.1676  -0.0342
 VSH  C1   C  CR16  0  -0.309   0.1973  -1.1948   0.4827
 VSH  C9   C  CR5   0   0.264   2.4342  -0.2366   0.0024
 VSH  N23  N  N     0  -0.273   3.0558  -1.3604  -0.2715
 VSH  N24  N  NR5   0  -0.362   4.3717  -1.1380  -0.1632
 VSH  C19  C  CH1   0  -0.119   5.3287  -2.1996  -0.4412
 VSH  C14  C  CH3   0  -0.650   5.0828  -3.3914   0.4722
 VSH  C13  C  CH3   0  -0.648   5.2922  -2.5783  -1.9148
 VSH  C10  C  CR56  0   0.579   4.6261   0.1390   0.1722
 VSH  N21  N  N     0  -0.465   5.8258   0.6999   0.3547
 VSH  C5   C  CR56  0  -0.268   3.3880   0.7749   0.3074
 VSH  C11  C  CR6   0   0.429   3.4416   2.1159   0.7553
 VSH  N25  N  NH2   0  -0.817   2.3569   2.8511   1.0178
 VSH  N22  N  N     0  -0.477   4.6360   2.6877   0.9237
 VSH  C4   C  CR16  0   0.054   5.7341   1.9643   0.7080
 VSH  H1   H  HCH3  0   0.237  -6.5584   0.4188   2.2812
 VSH  H2   H  HCH3  0   0.237  -7.7612  -0.8659   2.2588
 VSH  H3   H  HCH3  0   0.247  -6.0632  -1.2706   2.4770
 VSH  H4   H  HCH3  0   0.239  -7.5413   1.2125   0.0542
 VSH  H5   H  HCH3  0   0.239  -7.6044   0.0985  -1.3204
 VSH  H6   H  HCH3  0   0.233  -8.6710  -0.1399   0.0628
 VSH  H7   H  HCH3  0   0.236  -7.8357  -2.4809   0.1747
 VSH  H8   H  HCH3  0   0.237  -6.6533  -2.2468  -1.1074
 VSH  H9   H  HCH3  0   0.248  -6.1439  -2.8562   0.4751
 VSH  H10  H  HNH1  0   0.415  -3.5296   0.9148  -0.7542
 VSH  H11  H  HCR6  0   0.283  -1.7590  -1.9525   0.8479
 VSH  H12  H  HCH3  0   0.268  -1.7768   3.8336  -2.0790
 VSH  H13  H  HCH3  0   0.229  -0.4054   3.6003  -0.9780
 VSH  H14  H  HCH3  0   0.235  -0.4020   2.8345  -2.5848
 VSH  H15  H  HCR6  0   0.294   0.9264   1.7053  -1.0817
 VSH  H16  H  HCR6  0   0.253   0.6717  -2.0512   0.9423
 VSH  H17  H  HCH1  0   0.263   6.3036  -1.7696  -0.2074
 VSH  H18  H  HCH3  0   0.233   4.1151  -3.8503   0.2711
 VSH  H19  H  HCH3  0   0.238   5.8546  -4.1423   0.3072
 VSH  H20  H  HCH3  0   0.240   5.1156  -3.0976   1.5213
 VSH  H21  H  HCH3  0   0.239   5.5049  -1.7177  -2.5492
 VSH  H22  H  HCH3  0   0.237   6.0430  -3.3413  -2.1199
 VSH  H23  H  HCH3  0   0.233   4.3173  -2.9802  -2.1917
 VSH  H24  H  HNH2  0   0.414   1.4483   2.4271   1.0910
 VSH  H25  H  HNH2  0   0.405   2.4770   3.7531   1.4484
 VSH  H26  H  HCR6  0   0.254   6.6714   2.4904   0.8572

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
 VSH  C15  C20  single    1.523  0.020  1.523
 VSH  C16  C20  single    1.523  0.020  1.523
 VSH  C20  C17  single    1.523  0.020  1.523
 VSH  C20  O29  single    1.456  0.020  1.456
 VSH  O27  C12  double    1.210  0.020  1.210
 VSH  O29  C12  single    1.328  0.020  1.328
 VSH  C12  N26  single    1.363  0.020  1.363
 VSH  C2   C1   aromatic  1.389  0.020  1.389
 VSH  C2   C7   aromatic  1.389  0.020  1.389
 VSH  C1   C6   aromatic  1.386  0.020  1.386
 VSH  N26  C7   single    1.392  0.020  1.392
 VSH  C7   C8   aromatic  1.412  0.020  1.412
 VSH  C14  C19  single    1.522  0.020  1.522
 VSH  C6   C9   single    1.465  0.020  1.465
 VSH  C6   C3   aromatic  1.398  0.020  1.398
 VSH  C8   C3   aromatic  1.384  0.020  1.384
 VSH  C8   O28  single    1.346  0.020  1.346
 VSH  C9   N23  aromatic  1.313  0.020  1.313
 VSH  C9   C5   aromatic  1.423  0.020  1.423
 VSH  N23  N24  aromatic  1.339  0.020  1.339
 VSH  N25  C11  single    1.336  0.020  1.336
 VSH  C5   C11  aromatic  1.415  0.020  1.415
 VSH  C5   C10  aromatic  1.398  0.020  1.398
 VSH  C11  N22  aromatic  1.335  0.020  1.335
 VSH  N24  C10  aromatic  1.345  0.020  1.345
 VSH  N24  C19  single    1.456  0.020  1.456
 VSH  O28  C18  single    1.415  0.020  1.415
 VSH  C10  N21  aromatic  1.337  0.020  1.337
 VSH  C19  C13  single    1.522  0.020  1.522
 VSH  N22  C4   aromatic  1.332  0.020  1.332
 VSH  N21  C4   aromatic  1.316  0.020  1.316
 VSH  C17  H1   single    0.970  0.020  1.090
 VSH  C17  H2   single    0.970  0.020  1.090
 VSH  C17  H3   single    0.970  0.020  1.090
 VSH  C16  H4   single    0.970  0.020  1.090
 VSH  C16  H5   single    0.970  0.020  1.090
 VSH  C16  H6   single    0.970  0.020  1.090
 VSH  C15  H7   single    0.970  0.020  1.090
 VSH  C15  H8   single    0.970  0.020  1.090
 VSH  C15  H9   single    0.970  0.020  1.090
 VSH  N26  H10  single    0.860  0.020  1.020
 VSH  C2   H11  single    0.930  0.020  1.080
 VSH  C18  H12  single    0.970  0.020  1.090
 VSH  C18  H13  single    0.970  0.020  1.090
 VSH  C18  H14  single    0.970  0.020  1.090
 VSH  C3   H15  single    0.930  0.020  1.080
 VSH  C1   H16  single    0.930  0.020  1.080
 VSH  C19  H17  single    0.970  0.020  1.090
 VSH  C14  H18  single    0.970  0.020  1.090
 VSH  C14  H19  single    0.970  0.020  1.090
 VSH  C14  H20  single    0.970  0.020  1.090
 VSH  C13  H21  single    0.970  0.020  1.090
 VSH  C13  H22  single    0.970  0.020  1.090
 VSH  C13  H23  single    0.970  0.020  1.090
 VSH  N25  H24  single    0.890  0.020  1.040
 VSH  N25  H25  single    0.890  0.020  1.040
 VSH  C4   H26  single    0.930  0.020  1.080

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
 VSH  N26  C12  O29  108.57  3.000
 VSH  N26  C12  O27  125.30  3.000
 VSH  O29  C12  O27  126.12  3.000
 VSH  C20  O29  C12  122.97  3.000
 VSH  C15  C20  C16  109.77  3.000
 VSH  C16  C20  C17  110.07  3.000
 VSH  C15  C20  C17  111.93  3.000
 VSH  C17  C20  O29  110.74  3.000
 VSH  C16  C20  O29  102.81  3.000
 VSH  C15  C20  O29  111.15  3.000
 VSH  H3   C17  H2   107.70  3.000
 VSH  H3   C17  H1   108.75  3.000
 VSH  H2   C17  H1   107.54  3.000
 VSH  H3   C17  C20  112.53  3.000
 VSH  H2   C17  C20  109.08  3.000
 VSH  H1   C17  C20  111.07  3.000
 VSH  H6   C16  H5   107.90  3.000
 VSH  H6   C16  H4   107.84  3.000
 VSH  H5   C16  H4   108.47  3.000
 VSH  H6   C16  C20  109.76  3.000
 VSH  H5   C16  C20  111.27  3.000
 VSH  H4   C16  C20  111.46  3.000
 VSH  H9   C15  H8   108.73  3.000
 VSH  H9   C15  H7   107.69  3.000
 VSH  H8   C15  H7   107.50  3.000
 VSH  H9   C15  C20  112.68  3.000
 VSH  H8   C15  C20  111.08  3.000
 VSH  H7   C15  C20  108.98  3.000
 VSH  H10  N26  C7   115.70  3.000
 VSH  H10  N26  C12  116.17  3.000
 VSH  C7   N26  C12  128.07  3.000
 VSH  C8   C7   C2   118.36  3.000
 VSH  C8   C7   N26  116.27  3.000
 VSH  C2   C7   N26  125.35  3.000
 VSH  H11  C2   C1   118.86  3.000
 VSH  H11  C2   C7   120.33  3.000
 VSH  C1   C2   C7   120.81  3.000
 VSH  C3   C8   O28  124.23  3.000
 VSH  O28  C8   C7   115.34  3.000
 VSH  C3   C8   C7   120.42  3.000
 VSH  C18  O28  C8   119.03  3.000
 VSH  H14  C18  H13  109.03  3.000
 VSH  H14  C18  H12  108.90  3.000
 VSH  H13  C18  H12  108.94  3.000
 VSH  H14  C18  O28  111.80  3.000
 VSH  H13  C18  O28  111.65  3.000
 VSH  H12  C18  O28  106.42  3.000
 VSH  H15  C3   C6   119.31  3.000
 VSH  H15  C3   C8   119.94  3.000
 VSH  C6   C3   C8   120.71  3.000
 VSH  C9   C6   C1   120.89  3.000
 VSH  C9   C6   C3   120.32  3.000
 VSH  C1   C6   C3   118.77  3.000
 VSH  H16  C1   C6   120.03  3.000
 VSH  H16  C1   C2   119.07  3.000
 VSH  C6   C1   C2   120.90  3.000
 VSH  C5   C9   N23  109.61  3.000
 VSH  C5   C9   C6   129.87  3.000
 VSH  N23  C9   C6   120.52  3.000
 VSH  N24  N23  C9   107.83  3.000
 VSH  C10  N24  C19  128.00  3.000
 VSH  C19  N24  N23  120.62  3.000
 VSH  C10  N24  N23  111.34  3.000
 VSH  H17  C19  C13  109.09  3.000
 VSH  H17  C19  C14  108.94  3.000
 VSH  C13  C19  C14  112.48  3.000
 VSH  H17  C19  N24  105.02  3.000
 VSH  C13  C19  N24  110.52  3.000
 VSH  C14  C19  N24  110.50  3.000
 VSH  H20  C14  H19  108.07  3.000
 VSH  H20  C14  H18  108.53  3.000
 VSH  H19  C14  H18  108.12  3.000
 VSH  H20  C14  C19  111.21  3.000
 VSH  H19  C14  C19  109.55  3.000
 VSH  H18  C14  C19  111.26  3.000
 VSH  H23  C13  H22  108.07  3.000
 VSH  H23  C13  H21  108.52  3.000
 VSH  H22  C13  H21  107.98  3.000
 VSH  H23  C13  C19  111.05  3.000
 VSH  H22  C13  C19  109.87  3.000
 VSH  H21  C13  C19  111.24  3.000
 VSH  C5   C10  N21  126.19  3.000
 VSH  N21  C10  N24  127.04  3.000
 VSH  C5   C10  N24  106.77  3.000
 VSH  C4   N21  C10  112.16  3.000
 VSH  C11  C5   C10  115.35  3.000
 VSH  C10  C5   C9   104.44  3.000
 VSH  C11  C5   C9   140.07  3.000
 VSH  N22  C11  N25  117.76  3.000
 VSH  N22  C11  C5   118.67  3.000
 VSH  N25  C11  C5   123.56  3.000
 VSH  H25  N25  H24  117.04  3.000
 VSH  H25  N25  C11  118.69  3.000
 VSH  H24  N25  C11  121.05  3.000
 VSH  C4   N22  C11  118.97  3.000
 VSH  H26  C4   N22  115.24  3.000
 VSH  H26  C4   N21  116.26  3.000
 VSH  N22  C4   N21  128.50  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
 VSH  CONST_01  C6   C1   C2   C7      0.00   0.0  0
 VSH  CONST_02  C6   C3   C8   C7      0.00   0.0  0
 VSH  CONST_03  C9   C6   C1   C2    180.00   0.0  0
 VSH  CONST_04  C3   C6   C1   C2      0.00   0.0  0
 VSH  CONST_05  C3   C8   C7   C2      0.00   0.0  0
 VSH  CONST_06  C1   C2   C7   C8      0.00   0.0  0
 VSH  CONST_07  C1   C6   C3   C8      0.00   0.0  0
 VSH  CONST_08  C9   C6   C3   C8    180.00   0.0  0
 VSH  CONST_11  N24  N23  C9   C6    180.00   0.0  0
 VSH  CONST_12  C11  C5   C9   C6      0.00   0.0  0
 VSH  CONST_13  C10  C5   C9   C6    180.00   0.0  0
 VSH  CONST_16  C10  N24  N23  C9      0.00   0.0  0
 VSH  CONST_17  N22  C11  C5   C9    180.00   0.0  0
 VSH  CONST_18  N24  C10  C5   C9      0.00   0.0  0
 VSH  CONST_19  N21  C10  C5   C9    180.00   0.0  0
 VSH  CONST_20  C11  C5   C9   N23   180.00   0.0  0
 VSH  CONST_21  C10  C5   C9   N23     0.00   0.0  0
 VSH  CONST_22  C5   C10  N24  N23     0.00   0.0  0
 VSH  CONST_23  N21  C10  N24  N23   180.00   0.0  0
 VSH  CONST_24  C5   C9   N23  N24     0.00   0.0  0
 VSH  CONST_25  C11  C5   C10  N24   180.00   0.0  0
 VSH  CONST_26  C4   N21  C10  N24   180.00   0.0  0
 VSH  CONST_27  N22  C11  C5   C10     0.00   0.0  0
 VSH  CONST_28  N22  C4   N21  C10     0.00   0.0  0
 VSH  CONST_29  C11  C5   C10  N21     0.00   0.0  0
 VSH  CONST_30  C11  N22  C4   N21     0.00   0.0  0
 VSH  CONST_31  C4   N22  C11  C5      0.00   0.0  0
 VSH  CONST_32  C4   N21  C10  C5      0.00   0.0  0
 VSH  CONST_33  C1   C2   C7   N26   180.00   0.0  0
 VSH  CONST_34  C3   C8   C7   N26   180.00   0.0  0
 VSH  CONST_35  O28  C8   C7   C2    180.00   0.0  0
 VSH  CONST_36  C6   C3   C8   O28   180.00   0.0  0
 VSH  CONST_37  C19  N24  N23  C9    180.00   0.0  0
 VSH  CONST_38  N25  C11  C5   C9      0.00   0.0  0
 VSH  CONST_39  C5   C10  N24  C19   180.00   0.0  0
 VSH  CONST_40  N21  C10  N24  C19     0.00   0.0  0
 VSH  CONST_41  N25  C11  C5   C10   180.00   0.0  0
 VSH  CONST_42  C4   N22  C11  N25   180.00   0.0  0
 VSH  CONST_43  H16  C1   C2   C7    180.00   0.0  0
 VSH  CONST_44  H15  C3   C8   C7    180.00   0.0  0
 VSH  CONST_45  H11  C2   C7   C8    180.00   0.0  0
 VSH  CONST_46  H26  C4   N21  C10   180.00   0.0  0
 VSH  CONST_47  C2   C7   N26  C12     0.00   0.0  0
 VSH  CONST_48  C8   C7   N26  C12   180.00   0.0  0
 VSH  CONST_49  H10  N26  C7   C2    180.00   0.0  0
 VSH  CONST_50  H24  N25  C11  C5      0.00   0.0  0
 VSH  CONST_51  H25  N25  C11  C5    180.00   0.0  0
 VSH  CONST_52  C7   N26  C12  O27     0.00   0.0  0
 VSH  CONST_53  C7   N26  C12  O29   180.00   0.0  0
 VSH  Var_01    C3   C8   O28  C18    -2.33  30.0  2
 VSH  Var_02    C14  C19  N24  N23   -58.70  30.0  2
 VSH  Var_03    H12  C18  O28  C8   -177.59  30.0  3
 VSH  Var_04    H18  C14  C19  N24    65.04  30.0  3
 VSH  Var_05    H21  C13  C19  N24    57.95  30.0  3
 VSH  Var_06    C15  C20  O29  C12   -62.59  30.0  3
 VSH  Var_07    N26  C12  O29  C20  -177.43  30.0  3
 VSH  Var_08    H7   C15  C20  O29  -169.44  30.0  3
 VSH  Var_09    H4   C16  C20  O29   -59.38  30.0  3
 VSH  Var_10    H1   C17  C20  O29    51.95  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
 VSH  plan-1  N26  0.020
 VSH  plan-1  C7   0.020
 VSH  plan-1  C2   0.020
 VSH  plan-1  C8   0.020
 VSH  plan-1  O28  0.020
 VSH  plan-1  C3   0.020
 VSH  plan-1  C6   0.020
 VSH  plan-1  C1   0.020
 VSH  plan-1  C9   0.020
 VSH  plan-1  H11  0.020
 VSH  plan-1  H15  0.020
 VSH  plan-1  H16  0.020
 VSH  plan-2  C6   0.020
 VSH  plan-2  C9   0.020
 VSH  plan-2  N23  0.020
 VSH  plan-2  N24  0.020
 VSH  plan-2  C19  0.020
 VSH  plan-2  C10  0.020
 VSH  plan-2  N21  0.020
 VSH  plan-2  C5   0.020
 VSH  plan-2  C11  0.020
 VSH  plan-2  N25  0.020
 VSH  plan-2  N22  0.020
 VSH  plan-2  C4   0.020
 VSH  plan-2  H26  0.020
 VSH  plan-3  C12  0.020
 VSH  plan-3  N26  0.020
 VSH  plan-3  C7   0.020
 VSH  plan-3  H10  0.020
 VSH  plan-4  C11  0.020
 VSH  plan-4  N25  0.020
 VSH  plan-4  H24  0.020
 VSH  plan-4  H25  0.020
 VSH  plan-5  O27  0.020
 VSH  plan-5  C12  0.020
 VSH  plan-5  O29  0.020
 VSH  plan-5  N26  0.020

