# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:27:50 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-methyl-N-(3-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc2c(Nc3cccc(C)c3)ncnc12
#
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
 JJM  JJM  1-methyl-N-(3-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  31  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JJM
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
 JJM  C10   C  CR56  0  -0.249   1.7313   0.4385  -0.0914
 JJM  N12   N  N     0  -0.247   3.5083   1.7855  -0.2416
 JJM  C02   C  CR6   0   0.113  -4.3146   0.6395  -0.1211
 JJM  C03   C  CR16  0  -0.316  -4.6967  -0.6898   0.0573
 JJM  C04   C  CR16  0  -0.231  -3.7311  -1.6736   0.1902
 JJM  C05   C  CR16  0  -0.330  -2.3755  -1.3738   0.1499
 JJM  C06   C  CR6   0   0.391  -1.9819  -0.0480  -0.0294
 JJM  C07   C  CR16  0  -0.422  -2.9614   0.9417  -0.1648
 JJM  N08   N  NH1   0  -0.769  -0.6574   0.3941  -0.0873
 JJM  C09   C  CR6   0   0.546   0.5129  -0.2727  -0.0121
 JJM  C11   C  CR15  0  -0.112   2.1987   1.7643  -0.2396
 JJM  N13   N  NR5   0  -0.359   3.9287   0.5193  -0.0994
 JJM  C14   C  CR56  0   0.578   2.8922  -0.3321  -0.0049
 JJM  N15   N  N     0  -0.454   2.9397  -1.6607   0.1431
 JJM  C16   C  CR16  0   0.073   1.7426  -2.1980   0.2026
 JJM  N17   N  N     0  -0.497   0.5527  -1.5904   0.1351
 JJM  C18   C  CH3   0  -0.521   5.3357   0.2091  -0.0666
 JJM  H011  H  HCH3  0   0.250  -5.6741   2.0545   0.7508
 JJM  H012  H  HCH3  0   0.244  -4.9520   2.6001  -0.7560
 JJM  H013  H  HCH3  0   0.245  -6.2269   1.3821  -0.7740
 JJM  H031  H  HCR6  0   0.246  -5.7477  -0.9502   0.0912
 JJM  H041  H  HCR6  0   0.254  -4.0311  -2.7048   0.3275
 JJM  H051  H  HCR6  0   0.286  -1.6427  -2.1561   0.2514
 JJM  H071  H  HCR6  0   0.261  -2.6555   1.9729  -0.3113
 JJM  H081  H  HNH1  0   0.422  -0.5656   1.3922  -0.2015
 JJM  H111  H  HCR5  0   0.273   1.6391   2.6818  -0.3440
 JJM  H161  H  HCR6  0   0.258   1.7030  -3.2751   0.3218
 JJM  H181  H  HCH3  0   0.262   5.8190   0.7330   0.7556
 JJM  H182  H  HCH3  0   0.263   5.4499  -0.8609   0.0797
 JJM  H183  H  HCH3  0   0.262   5.8105   0.4922  -1.0042
 JJM  C01   C  CH3   0  -0.723  -5.3435   1.7262  -0.2366

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
 JJM  C18  N13   single    1.441  0.020  1.441
 JJM  N12  N13   aromatic  1.342  0.020  1.342
 JJM  N12  C11   aromatic  1.310  0.020  1.310
 JJM  N13  C14   aromatic  1.345  0.020  1.345
 JJM  C11  C10   aromatic  1.414  0.020  1.414
 JJM  C14  N15   aromatic  1.338  0.020  1.338
 JJM  C14  C10   aromatic  1.396  0.020  1.396
 JJM  N15  C16   aromatic  1.314  0.020  1.314
 JJM  C10  C09   aromatic  1.413  0.020  1.413
 JJM  C16  N17   aromatic  1.338  0.020  1.338
 JJM  C09  N17   aromatic  1.327  0.020  1.327
 JJM  C09  N08   single    1.349  0.020  1.349
 JJM  N08  C06   single    1.397  0.020  1.397
 JJM  C06  C05   aromatic  1.395  0.020  1.395
 JJM  C06  C07   aromatic  1.399  0.020  1.399
 JJM  C05  C04   aromatic  1.389  0.020  1.389
 JJM  C07  C02   aromatic  1.387  0.020  1.387
 JJM  C04  C03   aromatic  1.385  0.020  1.385
 JJM  C02  C03   aromatic  1.395  0.020  1.395
 JJM  C02  C01   single    1.501  0.020  1.501
 JJM  C01  H011  single    0.970  0.020  1.090
 JJM  C01  H012  single    0.970  0.020  1.090
 JJM  C01  H013  single    0.970  0.020  1.090
 JJM  C03  H031  single    0.930  0.020  1.080
 JJM  C04  H041  single    0.930  0.020  1.080
 JJM  C05  H051  single    0.930  0.020  1.080
 JJM  C07  H071  single    0.930  0.020  1.080
 JJM  N08  H081  single    0.860  0.020  1.020
 JJM  C11  H111  single    0.930  0.020  1.080
 JJM  C16  H161  single    0.930  0.020  1.080
 JJM  C18  H181  single    0.970  0.020  1.090
 JJM  C18  H182  single    0.970  0.020  1.090
 JJM  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
 JJM  C14   C10  C11   104.43  3.000
 JJM  C14   C10  C09   115.83  3.000
 JJM  C11   C10  C09   139.74  3.000
 JJM  N13   N12  C11   107.33  3.000
 JJM  C07   C02  C03   118.61  3.000
 JJM  C03   C02  C01   120.81  3.000
 JJM  C07   C02  C01   120.57  3.000
 JJM  H031  C03  C04   120.18  3.000
 JJM  H031  C03  C02   119.93  3.000
 JJM  C04   C03  C02   119.89  3.000
 JJM  H041  C04  C05   118.66  3.000
 JJM  H041  C04  C03   119.71  3.000
 JJM  C05   C04  C03   121.63  3.000
 JJM  H051  C05  C06   120.71  3.000
 JJM  H051  C05  C04   120.31  3.000
 JJM  C06   C05  C04   118.97  3.000
 JJM  N08   C06  C07   115.83  3.000
 JJM  C07   C06  C05   119.17  3.000
 JJM  N08   C06  C05   125.00  3.000
 JJM  H071  C07  C06   119.19  3.000
 JJM  H071  C07  C02   119.08  3.000
 JJM  C06   C07  C02   121.73  3.000
 JJM  H081  N08  C09   114.61  3.000
 JJM  H081  N08  C06   113.82  3.000
 JJM  C09   N08  C06   131.57  3.000
 JJM  N17   C09  N08   121.54  3.000
 JJM  N08   C09  C10   119.74  3.000
 JJM  N17   C09  C10   118.71  3.000
 JJM  H111  C11  N12   120.28  3.000
 JJM  H111  C11  C10   129.48  3.000
 JJM  N12   C11  C10   110.24  3.000
 JJM  C18   N13  C14   127.93  3.000
 JJM  C14   N13  N12   111.32  3.000
 JJM  C18   N13  N12   120.76  3.000
 JJM  N15   C14  N13   127.54  3.000
 JJM  N15   C14  C10   125.78  3.000
 JJM  N13   C14  C10   106.69  3.000
 JJM  C16   N15  C14   112.26  3.000
 JJM  H161  C16  N17   115.10  3.000
 JJM  H161  C16  N15   116.39  3.000
 JJM  N17   C16  N15   128.51  3.000
 JJM  C16   N17  C09   118.91  3.000
 JJM  H183  C18  H182  109.06  3.000
 JJM  H183  C18  H181  109.39  3.000
 JJM  H182  C18  H181  109.02  3.000
 JJM  H183  C18  N13   110.50  3.000
 JJM  H182  C18  N13   108.53  3.000
 JJM  H181  C18  N13   110.31  3.000
 JJM  H013  C01  H012  108.03  3.000
 JJM  H013  C01  H011  107.18  3.000
 JJM  H012  C01  H011  107.39  3.000
 JJM  H013  C01  C02   111.41  3.000
 JJM  H012  C01  C02   111.78  3.000
 JJM  H011  C01  C02   110.83  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
 JJM  CONST_01  N13   N12  C11  C10     0.00   0.0  0
 JJM  CONST_02  N12   N13  C14  C10     0.00   0.0  0
 JJM  CONST_03  C16   N15  C14  C10     0.00   0.0  0
 JJM  CONST_04  C16   N17  C09  C10     0.00   0.0  0
 JJM  CONST_05  N15   C14  N13  N12   180.00   0.0  0
 JJM  CONST_06  C14   C10  C11  N12     0.00   0.0  0
 JJM  CONST_07  C09   C10  C11  N12   180.00   0.0  0
 JJM  CONST_08  C05   C06  C07  C02     0.00   0.0  0
 JJM  CONST_09  C05   C04  C03  C02     0.00   0.0  0
 JJM  CONST_10  C06   C05  C04  C03     0.00   0.0  0
 JJM  CONST_11  C06   C07  C02  C03     0.00   0.0  0
 JJM  CONST_12  C07   C06  C05  C04     0.00   0.0  0
 JJM  CONST_13  C07   C02  C03  C04     0.00   0.0  0
 JJM  CONST_14  N13   C14  C10  C09   180.00   0.0  0
 JJM  CONST_15  N15   C14  C10  C09     0.00   0.0  0
 JJM  CONST_16  N15   C16  N17  C09     0.00   0.0  0
 JJM  CONST_17  C14   N13  N12  C11     0.00   0.0  0
 JJM  CONST_18  N13   C14  C10  C11     0.00   0.0  0
 JJM  CONST_19  N15   C14  C10  C11   180.00   0.0  0
 JJM  CONST_20  N17   C09  C10  C11   180.00   0.0  0
 JJM  CONST_21  C16   N15  C14  N13   180.00   0.0  0
 JJM  CONST_22  N17   C16  N15  C14     0.00   0.0  0
 JJM  CONST_23  N17   C09  C10  C14     0.00   0.0  0
 JJM  CONST_24  C18   N13  C14  C10   180.00   0.0  0
 JJM  CONST_25  C06   C07  C02  C01   180.00   0.0  0
 JJM  CONST_26  C04   C03  C02  C01   180.00   0.0  0
 JJM  CONST_27  N08   C06  C07  C02   180.00   0.0  0
 JJM  CONST_28  N08   C06  C05  C04   180.00   0.0  0
 JJM  CONST_29  C11   C10  C09  N08     0.00   0.0  0
 JJM  CONST_30  C14   C10  C09  N08   180.00   0.0  0
 JJM  CONST_31  C16   N17  C09  N08   180.00   0.0  0
 JJM  CONST_32  C18   N13  N12  C11   180.00   0.0  0
 JJM  CONST_33  C18   N13  C14  N15     0.00   0.0  0
 JJM  CONST_34  H041  C04  C03  C02   180.00   0.0  0
 JJM  CONST_35  H051  C05  C04  C03   180.00   0.0  0
 JJM  CONST_36  H071  C07  C02  C03   180.00   0.0  0
 JJM  CONST_37  H031  C03  C04  C05   180.00   0.0  0
 JJM  CONST_38  H111  C11  C10  C09     0.00   0.0  0
 JJM  CONST_39  H161  C16  N17  C09   180.00   0.0  0
 JJM  Var_01    C06   N08  C09  C10  -179.52  30.0  2
 JJM  Var_02    C09   N08  C06  C05     0.97  30.0  2
 JJM  Var_03    H181  C18  N13  N12    59.20  30.0  2
 JJM  Var_04    H011  C01  C02  C03    83.26  30.0  2

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
 JJM  plan-1  C02   0.020
 JJM  plan-1  C03   0.020
 JJM  plan-1  C04   0.020
 JJM  plan-1  C05   0.020
 JJM  plan-1  C06   0.020
 JJM  plan-1  C07   0.020
 JJM  plan-1  N08   0.020
 JJM  plan-1  H031  0.020
 JJM  plan-1  H041  0.020
 JJM  plan-1  H051  0.020
 JJM  plan-1  H071  0.020
 JJM  plan-1  C01   0.020
 JJM  plan-2  C10   0.020
 JJM  plan-2  N12   0.020
 JJM  plan-2  N08   0.020
 JJM  plan-2  C09   0.020
 JJM  plan-2  C11   0.020
 JJM  plan-2  N13   0.020
 JJM  plan-2  C14   0.020
 JJM  plan-2  N15   0.020
 JJM  plan-2  C16   0.020
 JJM  plan-2  N17   0.020
 JJM  plan-2  C18   0.020
 JJM  plan-2  H111  0.020
 JJM  plan-2  H161  0.020

