# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:38:24 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-tert-butyl-3-(3-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Cc2nn(c3ncnc(N)c23)C(C)(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
 VGG  VGG  1-tert-butyl-3-(3-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  43  22  .  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_VGG
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
 VGG  C20   C  CH3   0  -0.648  -3.1414   2.9761  -0.8706
 VGG  C19   C  CT    0   0.063  -3.4016   1.6527  -0.1596
 VGG  C21   C  CH3   0  -0.648  -3.7232   1.9211   1.3110
 VGG  C22   C  CH3   0  -0.649  -4.5615   0.9291  -0.8435
 VGG  N7    N  NR5   0  -0.381  -2.1921   0.8098  -0.2403
 VGG  N8    N  N     0  -0.274  -1.0827   1.2389  -0.8675
 VGG  C3    C  CR56  0   0.592  -2.0016  -0.4248   0.2693
 VGG  N2    N  N     0  -0.464  -2.8800  -1.1819   0.9399
 VGG  C1    C  CR16  0   0.051  -2.3796  -2.3480   1.2873
 VGG  N6    N  N     0  -0.480  -1.1543  -2.8261   1.0723
 VGG  C5    C  CR6   0   0.426  -0.2773  -2.0647   0.4148
 VGG  N10   N  NH2   0  -0.822   0.9483  -2.5577   0.2055
 VGG  C4    C  CR56  0  -0.250  -0.6902  -0.7947  -0.0442
 VGG  C9    C  CR5   0   0.301  -0.1699   0.3060  -0.7735
 VGG  C11   C  CH2   0  -0.606   1.1759   0.4797  -1.3934
 VGG  C12   C  CR6   0   0.092   2.3059   0.4806  -0.3904
 VGG  C13   C  CR16  0  -0.374   3.4785  -0.2210  -0.6559
 VGG  C17   C  CR16  0  -0.295   2.2012   1.1882   0.8045
 VGG  C16   C  CR16  0  -0.225   3.2558   1.1884   1.7044
 VGG  C15   C  CR16  0  -0.312   4.4198   0.4833   1.4263
 VGG  C14   C  CR6   0   0.113   4.5480  -0.2312   0.2391
 VGG  C18   C  CH3   0  -0.723   5.8101  -0.9757  -0.0861
 VGG  H201  H  HCH3  0   0.238  -2.3276   3.5371  -0.4123
 VGG  H202  H  HCH3  0   0.238  -2.9108   2.8389  -1.9263
 VGG  H203  H  HCH3  0   0.237  -4.0464   3.5794  -0.7995
 VGG  H211  H  HCH3  0   0.234  -4.5835   2.5876   1.3819
 VGG  H212  H  HCH3  0   0.245  -3.9661   1.0028   1.8435
 VGG  H213  H  HCH3  0   0.235  -2.8823   2.4025   1.8121
 VGG  H221  H  HCH3  0   0.235  -4.3143   0.6894  -1.8786
 VGG  H222  H  HCH3  0   0.246  -4.8222   0.0078  -0.3257
 VGG  H223  H  HCH3  0   0.234  -5.4418   1.5731  -0.8491
 VGG  H1    H  HCR6  0   0.252  -3.0474  -3.0127   1.8257
 VGG  H101  H  HNH2  0   0.402   1.2008  -3.4204   0.6585
 VGG  H102  H  HNH2  0   0.415   1.7066  -1.9611  -0.0796
 VGG  H111  H  HCH2  0   0.269   1.3453  -0.3091  -2.1314
 VGG  H112  H  HCH2  0   0.284   1.1758   1.4213  -1.9488
 VGG  H13   H  HCR6  0   0.256   3.5590  -0.7783  -1.5844
 VGG  H17   H  HCR6  0   0.249   1.2948   1.7356   1.0352
 VGG  H16   H  HCR6  0   0.255   3.1700   1.7381   2.6334
 VGG  H15   H  HCR6  0   0.248   5.2332   0.4858   2.1421
 VGG  H181  H  HCH3  0   0.250   6.5131  -0.3339  -0.6212
 VGG  H182  H  HCH3  0   0.245   6.3135  -1.3266   0.8143
 VGG  H183  H  HCH3  0   0.244   5.6127  -1.8381  -0.7219

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
 VGG  C20  C19   single    1.525  0.020  1.525
 VGG  C19  C21   single    1.529  0.020  1.529
 VGG  C19  C22   single    1.529  0.020  1.529
 VGG  C19  N7    single    1.476  0.020  1.476
 VGG  N7   N8    aromatic  1.345  0.020  1.345
 VGG  N7   C3    aromatic  1.349  0.020  1.349
 VGG  N8   C9    aromatic  1.309  0.020  1.309
 VGG  C3   N2    aromatic  1.340  0.020  1.340
 VGG  C3   C4    aromatic  1.398  0.020  1.398
 VGG  N2   C1    aromatic  1.316  0.020  1.316
 VGG  C1   N6    aromatic  1.333  0.020  1.333
 VGG  N6   C5    aromatic  1.335  0.020  1.335
 VGG  C5   N10   single    1.338  0.020  1.338
 VGG  C5   C4    aromatic  1.412  0.020  1.412
 VGG  C4   C9    aromatic  1.419  0.020  1.419
 VGG  C9   C11   single    1.492  0.020  1.492
 VGG  C11  C12   single    1.511  0.020  1.511
 VGG  C12  C13   aromatic  1.392  0.020  1.392
 VGG  C12  C17   aromatic  1.393  0.020  1.393
 VGG  C13  C14   aromatic  1.395  0.020  1.395
 VGG  C17  C16   aromatic  1.386  0.020  1.386
 VGG  C16  C15   aromatic  1.389  0.020  1.389
 VGG  C15  C14   aromatic  1.392  0.020  1.392
 VGG  C14  C18   single    1.501  0.020  1.501
 VGG  C20  H201  single    0.970  0.020  1.090
 VGG  C20  H202  single    0.970  0.020  1.090
 VGG  C20  H203  single    0.970  0.020  1.090
 VGG  C21  H211  single    0.970  0.020  1.090
 VGG  C21  H212  single    0.970  0.020  1.090
 VGG  C21  H213  single    0.970  0.020  1.090
 VGG  C22  H221  single    0.970  0.020  1.090
 VGG  C22  H222  single    0.970  0.020  1.090
 VGG  C22  H223  single    0.970  0.020  1.090
 VGG  C1   H1    single    0.930  0.020  1.080
 VGG  N10  H101  single    0.890  0.020  1.040
 VGG  N10  H102  single    0.890  0.020  1.040
 VGG  C11  H111  single    0.970  0.020  1.090
 VGG  C11  H112  single    0.970  0.020  1.090
 VGG  C13  H13   single    0.930  0.020  1.080
 VGG  C17  H17   single    0.930  0.020  1.080
 VGG  C16  H16   single    0.930  0.020  1.080
 VGG  C15  H15   single    0.930  0.020  1.080
 VGG  C18  H181  single    0.970  0.020  1.090
 VGG  C18  H182  single    0.970  0.020  1.090
 VGG  C18  H183  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
 VGG  H203  C20  H202  107.98  3.000
 VGG  H203  C20  H201  107.92  3.000
 VGG  H202  C20  H201  108.33  3.000
 VGG  H203  C20  C19   107.96  3.000
 VGG  H202  C20  C19   112.26  3.000
 VGG  H201  C20  C19   112.23  3.000
 VGG  N7    C19  C22   109.08  3.000
 VGG  N7    C19  C21   108.97  3.000
 VGG  C22   C19  C21   110.72  3.000
 VGG  N7    C19  C20   109.28  3.000
 VGG  C22   C19  C20   109.37  3.000
 VGG  C21   C19  C20   109.39  3.000
 VGG  H213  C21  H212  108.63  3.000
 VGG  H213  C21  H211  107.97  3.000
 VGG  H212  C21  H211  107.92  3.000
 VGG  H213  C21  C19   110.92  3.000
 VGG  H212  C21  C19   111.67  3.000
 VGG  H211  C21  C19   109.61  3.000
 VGG  H223  C22  H222  107.99  3.000
 VGG  H223  C22  H221  107.93  3.000
 VGG  H222  C22  H221  108.64  3.000
 VGG  H223  C22  C19   109.59  3.000
 VGG  H222  C22  C19   111.68  3.000
 VGG  H221  C22  C19   110.89  3.000
 VGG  C3    N7   N8    110.59  3.000
 VGG  C3    N7   C19   128.13  3.000
 VGG  N8    N7   C19   121.28  3.000
 VGG  C9    N8   N7    108.33  3.000
 VGG  C4    C3   N2    125.29  3.000
 VGG  C4    C3   N7    106.85  3.000
 VGG  N2    C3   N7    127.86  3.000
 VGG  C1    N2   C3    112.56  3.000
 VGG  H1    C1   N6    115.22  3.000
 VGG  H1    C1   N2    116.09  3.000
 VGG  N6    C1   N2    128.69  3.000
 VGG  C5    N6   C1    118.62  3.000
 VGG  C4    C5   N10   123.27  3.000
 VGG  C4    C5   N6    118.75  3.000
 VGG  N10   C5   N6    117.97  3.000
 VGG  H102  N10  H101  116.53  3.000
 VGG  H102  N10  C5    121.09  3.000
 VGG  H101  N10  C5    118.38  3.000
 VGG  C9    C4   C5    139.23  3.000
 VGG  C9    C4   C3    104.71  3.000
 VGG  C5    C4   C3    116.06  3.000
 VGG  C11   C9   C4    129.39  3.000
 VGG  C11   C9   N8    121.09  3.000
 VGG  C4    C9   N8    109.52  3.000
 VGG  H112  C11  H111  106.17  3.000
 VGG  H112  C11  C12   109.68  3.000
 VGG  H111  C11  C12   109.43  3.000
 VGG  H112  C11  C9    108.15  3.000
 VGG  H111  C11  C9    109.64  3.000
 VGG  C12   C11  C9    113.51  3.000
 VGG  C17   C12  C13   118.89  3.000
 VGG  C17   C12  C11   120.91  3.000
 VGG  C13   C12  C11   120.20  3.000
 VGG  H13   C13  C14   119.22  3.000
 VGG  H13   C13  C12   118.96  3.000
 VGG  C14   C13  C12   121.82  3.000
 VGG  H17   C17  C16   119.86  3.000
 VGG  H17   C17  C12   120.14  3.000
 VGG  C16   C17  C12   119.99  3.000
 VGG  H16   C16  C15   119.73  3.000
 VGG  H16   C16  C17   119.78  3.000
 VGG  C15   C16  C17   120.49  3.000
 VGG  H15   C15  C14   119.71  3.000
 VGG  H15   C15  C16   119.71  3.000
 VGG  C14   C15  C16   120.57  3.000
 VGG  C18   C14  C15   121.13  3.000
 VGG  C18   C14  C13   120.62  3.000
 VGG  C15   C14  C13   118.24  3.000
 VGG  H183  C18  H182  108.12  3.000
 VGG  H183  C18  H181  107.21  3.000
 VGG  H182  C18  H181  107.26  3.000
 VGG  H183  C18  C14   111.52  3.000
 VGG  H182  C18  C14   111.67  3.000
 VGG  H181  C18  C14   110.85  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
 VGG  CONST_01  C4    C9   N8   N7     0.00   0.0  0
 VGG  CONST_02  C1    N2   C3   N7   180.00   0.0  0
 VGG  CONST_03  C5    C4   C3   N7   180.00   0.0  0
 VGG  CONST_04  C9    C4   C3   N7     0.00   0.0  0
 VGG  CONST_05  N2    C3   N7   N8   180.00   0.0  0
 VGG  CONST_06  C4    C3   N7   N8     0.00   0.0  0
 VGG  CONST_07  C3    C4   C9   N8     0.00   0.0  0
 VGG  CONST_08  C5    C4   C9   N8   180.00   0.0  0
 VGG  CONST_09  C9    N8   N7   C3     0.00   0.0  0
 VGG  CONST_10  N6    C1   N2   C3     0.00   0.0  0
 VGG  CONST_11  N6    C5   C4   C3     0.00   0.0  0
 VGG  CONST_12  C5    C4   C3   N2     0.00   0.0  0
 VGG  CONST_13  C9    C4   C3   N2   180.00   0.0  0
 VGG  CONST_14  C5    N6   C1   N2     0.00   0.0  0
 VGG  CONST_15  C4    C3   N2   C1     0.00   0.0  0
 VGG  CONST_16  C4    C5   N6   C1     0.00   0.0  0
 VGG  CONST_17  C9    C4   C5   N6   180.00   0.0  0
 VGG  CONST_18  C15   C14  C13  C12    0.00   0.0  0
 VGG  CONST_19  C15   C16  C17  C12    0.00   0.0  0
 VGG  CONST_20  C16   C17  C12  C13    0.00   0.0  0
 VGG  CONST_21  C16   C15  C14  C13    0.00   0.0  0
 VGG  CONST_22  C14   C13  C12  C17    0.00   0.0  0
 VGG  CONST_23  C14   C15  C16  C17    0.00   0.0  0
 VGG  CONST_24  C9    N8   N7   C19  180.00   0.0  0
 VGG  CONST_25  N2    C3   N7   C19    0.00   0.0  0
 VGG  CONST_26  C4    C3   N7   C19  180.00   0.0  0
 VGG  CONST_27  C11   C9   N8   N7   180.00   0.0  0
 VGG  CONST_28  N10   C5   C4   C3   180.00   0.0  0
 VGG  CONST_29  C11   C9   C4   C3   180.00   0.0  0
 VGG  CONST_30  N10   C5   N6   C1   180.00   0.0  0
 VGG  CONST_31  C11   C9   C4   C5     0.00   0.0  0
 VGG  CONST_32  C9    C4   C5   N10    0.00   0.0  0
 VGG  CONST_33  C14   C13  C12  C11  180.00   0.0  0
 VGG  CONST_34  C16   C17  C12  C11  180.00   0.0  0
 VGG  CONST_35  C18   C14  C13  C12  180.00   0.0  0
 VGG  CONST_36  C18   C14  C15  C16  180.00   0.0  0
 VGG  CONST_37  H1    C1   N2   C3   180.00   0.0  0
 VGG  CONST_38  H16   C16  C17  C12  180.00   0.0  0
 VGG  CONST_39  H17   C17  C12  C13  180.00   0.0  0
 VGG  CONST_40  H15   C15  C14  C13  180.00   0.0  0
 VGG  CONST_41  H13   C13  C12  C17  180.00   0.0  0
 VGG  CONST_42  H101  N10  C5   N6     0.00   0.0  0
 VGG  CONST_43  H102  N10  C5   N6   180.00   0.0  0
 VGG  Var_01    C12   C11  C9   N8   117.53  30.0  2
 VGG  Var_02    C13   C12  C11  C9   137.02  30.0  2
 VGG  Var_03    N8    N7   C19  C20    0.05  30.0  2
 VGG  Var_04    H181  C18  C14  C13   89.54  30.0  2
 VGG  Var_05    H201  C20  C19  N7   -61.28  30.0  3
 VGG  Var_06    H211  C21  C19  N7   176.95  30.0  3
 VGG  Var_07    H221  C22  C19  N7   -57.10  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
 VGG  plan-1  C11   0.020
 VGG  plan-1  C12   0.020
 VGG  plan-1  C13   0.020
 VGG  plan-1  C17   0.020
 VGG  plan-1  C16   0.020
 VGG  plan-1  C15   0.020
 VGG  plan-1  C14   0.020
 VGG  plan-1  C18   0.020
 VGG  plan-1  H13   0.020
 VGG  plan-1  H17   0.020
 VGG  plan-1  H16   0.020
 VGG  plan-1  H15   0.020
 VGG  plan-2  C19   0.020
 VGG  plan-2  N7    0.020
 VGG  plan-2  N8    0.020
 VGG  plan-2  C3    0.020
 VGG  plan-2  N2    0.020
 VGG  plan-2  C1    0.020
 VGG  plan-2  N6    0.020
 VGG  plan-2  C5    0.020
 VGG  plan-2  N10   0.020
 VGG  plan-2  C4    0.020
 VGG  plan-2  C9    0.020
 VGG  plan-2  C11   0.020
 VGG  plan-2  H1    0.020
 VGG  plan-3  C5    0.020
 VGG  plan-3  N10   0.020
 VGG  plan-3  H101  0.020
 VGG  plan-3  H102  0.020

