# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:22:47 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-chloranyl-1-[(4-methoxy-3,5-dimethyl-pyridin-2-yl)methyl]pyrazolo[3,4-d]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(C)cnc(Cn2ncc3c(Cl)nc(N)nc23)c1C
#
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
 8M9  8M9  4-chloranyl-1-[(4-methoxy-3,5-dimethyl-pyridin-2-yl)methyl]pyrazolo[3,4-d]pyrimidin-6-amine  ligand  37  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8M9
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
 8M9  C10  C   CH2   0  -0.374   0.5897  -0.7573   1.8715
 8M9  C13  C   CR6   0   0.389   3.3413   0.6438  -0.3255
 8M9  C15  C   CR16  0  -0.133   2.7722  -1.5765  -0.9044
 8M9  N01  N   N     0  -0.487  -1.3756   1.0613   0.4902
 8M9  C02  C   CR6   0   0.576  -2.3745   1.6243  -0.1797
 8M9  N03  N   N     0  -0.455  -3.4686   0.9819  -0.6752
 8M9  C04  C   CR6   0   0.122  -3.5592  -0.2981  -0.4888
 8M9  C05  C   CR56  0  -0.105  -2.5902  -1.0263   0.1897
 8M9  C06  C   CR56  0   0.638  -1.5200  -0.2457   0.6529
 8M9  C07  C   CR15  0  -0.107  -2.2815  -2.3439   0.6091
 8M9  N08  N   N     0  -0.237  -1.1481  -2.3568   1.2550
 8M9  N09  N   NR5   0  -0.371  -0.6906  -1.0861   1.2922
 8M9  C11  C   CR6   0   0.173   1.6512  -0.5781   0.8115
 8M9  C12  C   CR6   0  -0.028   2.3560   0.6194   0.6657
 8M9  C14  C   CR6   0  -0.065   3.5660  -0.4627  -1.1419
 8M9  N16  N   N     0  -0.405   1.8556  -1.6426   0.0472
 8M9  C19  C   CH3   0  -0.415   5.2035   1.8988   0.3232
 8M9  CL1  CL  CL    0  -0.080  -4.9468  -1.1048  -1.1183
 8M9  N22  N   NH2   0  -0.818  -2.3206   2.9391  -0.4188
 8M9  H1   H   HCH2  0   0.284   0.4744   0.1277   2.4935
 8M9  H2   H   HCH2  0   0.297   0.8598  -1.5813   2.5307
 8M9  H3   H   HCR6  0   0.255   2.9002  -2.4643  -1.5164
 8M9  H4   H   HCH3  0   0.263   0.9862   2.0360   1.5071
 8M9  H5   H   HCH3  0   0.255   2.3760   1.7011   2.5359
 8M9  H6   H   HCH3  0   0.263   2.5541   2.7169   1.1128
 8M9  H7   H   HCH3  0   0.251   4.4491   0.3822  -2.9145
 8M9  H8   H   HCH3  0   0.248   5.6085  -0.3573  -1.8240
 8M9  H9   H   HCH3  0   0.248   4.5601  -1.3725  -2.8036
 8M9  H10  H   HCR5  0   0.278  -2.8457  -3.2514   0.4602
 8M9  H11  H   HCH3  0   0.230   4.9054   1.9564   1.3729
 8M9  H12  H   HCH3  0   0.230   5.8997   1.0652   0.2036
 8M9  H13  H   HCH3  0   0.246   5.7079   2.8227   0.0495
 8M9  H14  H   HNH2  0   0.405  -1.5901   3.4946  -0.0094
 8M9  H15  H   HNH2  0   0.407  -3.1094   3.4111  -0.8237
 8M9  O18  O   O2    0  -0.483   4.0775   1.7653  -0.5372
 8M9  C17  C   CH3   0  -0.774   2.0569   1.8312   1.5006
 8M9  C20  C   CH3   0  -0.719   4.5984  -0.4498  -2.2264

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
 8M9  C20  C14  single    1.497  0.020  1.497
 8M9  C19  O18  single    1.423  0.020  1.423
 8M9  C15  C14  aromatic  1.388  0.020  1.388
 8M9  C15  N16  aromatic  1.323  0.020  1.323
 8M9  C14  C13  aromatic  1.393  0.020  1.393
 8M9  N16  C11  aromatic  1.326  0.020  1.326
 8M9  C13  O18  single    1.358  0.020  1.358
 8M9  C13  C12  aromatic  1.398  0.020  1.398
 8M9  C11  C12  aromatic  1.397  0.020  1.397
 8M9  C11  C10  single    1.511  0.020  1.511
 8M9  C12  C17  single    1.502  0.020  1.502
 8M9  C10  N09  single    1.443  0.020  1.443
 8M9  N09  N08  aromatic  1.351  0.020  1.351
 8M9  N09  C06  aromatic  1.343  0.020  1.343
 8M9  N01  C06  aromatic  1.325  0.020  1.325
 8M9  N01  C02  aromatic  1.328  0.020  1.328
 8M9  N08  C07  aromatic  1.305  0.020  1.305
 8M9  C06  C05  aromatic  1.403  0.020  1.403
 8M9  N22  C02  single    1.337  0.020  1.337
 8M9  C02  N03  aromatic  1.362  0.020  1.362
 8M9  C07  C05  aromatic  1.417  0.020  1.417
 8M9  C05  C04  aromatic  1.389  0.020  1.389
 8M9  N03  C04  aromatic  1.297  0.020  1.297
 8M9  C04  CL1  single    1.724  0.020  1.724
 8M9  C10  H1   single    0.970  0.020  1.090
 8M9  C10  H2   single    0.970  0.020  1.090
 8M9  C15  H3   single    0.930  0.020  1.080
 8M9  C17  H4   single    0.970  0.020  1.090
 8M9  C17  H5   single    0.970  0.020  1.090
 8M9  C17  H6   single    0.970  0.020  1.090
 8M9  C20  H7   single    0.970  0.020  1.090
 8M9  C20  H8   single    0.970  0.020  1.090
 8M9  C20  H9   single    0.970  0.020  1.090
 8M9  C07  H10  single    0.930  0.020  1.080
 8M9  C19  H11  single    0.970  0.020  1.090
 8M9  C19  H12  single    0.970  0.020  1.090
 8M9  C19  H13  single    0.970  0.020  1.090
 8M9  N22  H14  single    0.860  0.020  1.020
 8M9  N22  H15  single    0.860  0.020  1.020

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
 8M9  H2   C10  H1   107.19  3.000
 8M9  H2   C10  C11  109.88  3.000
 8M9  H1   C10  C11  112.28  3.000
 8M9  H2   C10  N09  106.89  3.000
 8M9  H1   C10  N09  108.71  3.000
 8M9  C11  C10  N09  111.64  3.000
 8M9  O18  C13  C14  118.49  3.000
 8M9  O18  C13  C12  120.47  3.000
 8M9  C14  C13  C12  121.02  3.000
 8M9  H3   C15  N16  116.50  3.000
 8M9  H3   C15  C14  119.48  3.000
 8M9  N16  C15  C14  124.01  3.000
 8M9  C06  N01  C02  113.47  3.000
 8M9  N22  C02  N03  115.53  3.000
 8M9  N03  C02  N01  126.00  3.000
 8M9  N22  C02  N01  118.47  3.000
 8M9  C04  N03  C02  118.00  3.000
 8M9  CL1  C04  C05  119.64  3.000
 8M9  CL1  C04  N03  117.75  3.000
 8M9  C05  C04  N03  122.61  3.000
 8M9  C07  C05  C06  104.68  3.000
 8M9  C07  C05  C04  141.64  3.000
 8M9  C06  C05  C04  113.68  3.000
 8M9  N09  C06  C05  106.26  3.000
 8M9  C05  C06  N01  126.25  3.000
 8M9  N09  C06  N01  127.49  3.000
 8M9  H10  C07  N08  120.96  3.000
 8M9  H10  C07  C05  128.86  3.000
 8M9  N08  C07  C05  110.19  3.000
 8M9  N09  N08  C07  107.37  3.000
 8M9  N08  N09  C06  111.49  3.000
 8M9  C06  N09  C10  126.62  3.000
 8M9  N08  N09  C10  121.72  3.000
 8M9  N16  C11  C12  123.37  3.000
 8M9  C12  C11  C10  121.96  3.000
 8M9  N16  C11  C10  114.67  3.000
 8M9  C11  C12  C17  122.22  3.000
 8M9  C17  C12  C13  121.37  3.000
 8M9  C11  C12  C13  116.40  3.000
 8M9  C20  C14  C15  121.67  3.000
 8M9  C15  C14  C13  116.40  3.000
 8M9  C20  C14  C13  121.92  3.000
 8M9  C11  N16  C15  118.76  3.000
 8M9  H13  C19  H12  108.97  3.000
 8M9  H13  C19  H11  108.88  3.000
 8M9  H12  C19  H11  108.62  3.000
 8M9  H13  C19  O18  107.12  3.000
 8M9  H12  C19  O18  111.48  3.000
 8M9  H11  C19  O18  111.70  3.000
 8M9  H15  N22  H14  118.37  3.000
 8M9  H15  N22  C02  120.16  3.000
 8M9  H14  N22  C02  120.00  3.000
 8M9  C19  O18  C13  114.34  3.000
 8M9  H6   C17  H5   107.56  3.000
 8M9  H6   C17  H4   107.35  3.000
 8M9  H5   C17  H4   107.69  3.000
 8M9  H6   C17  C12  111.60  3.000
 8M9  H5   C17  C12  111.90  3.000
 8M9  H4   C17  C12  110.52  3.000
 8M9  H9   C20  H8   107.44  3.000
 8M9  H9   C20  H7   107.90  3.000
 8M9  H8   C20  H7   107.15  3.000
 8M9  H9   C20  C14  110.63  3.000
 8M9  H8   C20  C14  111.83  3.000
 8M9  H7   C20  C14  111.68  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
 8M9  CONST_01  N16  C15  C14  C13    0.00   0.0  0
 8M9  CONST_02  N16  C11  C12  C13    0.00   0.0  0
 8M9  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 8M9  CONST_04  C12  C11  N16  C15    0.00   0.0  0
 8M9  CONST_05  N08  N09  C06  N01  180.00   0.0  0
 8M9  CONST_06  C07  C05  C06  N01  180.00   0.0  0
 8M9  CONST_07  C04  C05  C06  N01    0.00   0.0  0
 8M9  CONST_08  C04  N03  C02  N01    0.00   0.0  0
 8M9  CONST_09  N09  C06  N01  C02  180.00   0.0  0
 8M9  CONST_10  C05  C06  N01  C02    0.00   0.0  0
 8M9  CONST_11  C05  C04  N03  C02    0.00   0.0  0
 8M9  CONST_12  C06  N01  C02  N03    0.00   0.0  0
 8M9  CONST_13  C06  C05  C04  N03    0.00   0.0  0
 8M9  CONST_14  C07  C05  C04  N03  180.00   0.0  0
 8M9  CONST_15  N09  C06  C05  C04  180.00   0.0  0
 8M9  CONST_16  N08  C07  C05  C04  180.00   0.0  0
 8M9  CONST_17  N08  N09  C06  C05    0.00   0.0  0
 8M9  CONST_18  N09  N08  C07  C05    0.00   0.0  0
 8M9  CONST_19  C07  N08  N09  C06    0.00   0.0  0
 8M9  CONST_20  N08  C07  C05  C06    0.00   0.0  0
 8M9  CONST_21  N09  C06  C05  C07    0.00   0.0  0
 8M9  CONST_22  C14  C15  N16  C11    0.00   0.0  0
 8M9  CONST_23  C14  C13  C12  C11    0.00   0.0  0
 8M9  CONST_24  C15  N16  C11  C10  180.00   0.0  0
 8M9  CONST_25  C13  C12  C11  C10  180.00   0.0  0
 8M9  CONST_26  C07  N08  N09  C10  180.00   0.0  0
 8M9  CONST_27  N01  C06  N09  C10    0.00   0.0  0
 8M9  CONST_28  C05  C06  N09  C10  180.00   0.0  0
 8M9  CONST_29  O18  C13  C14  C15  180.00   0.0  0
 8M9  CONST_30  C14  C13  C12  C17  180.00   0.0  0
 8M9  CONST_31  N16  C11  C12  C17  180.00   0.0  0
 8M9  CONST_32  N16  C15  C14  C20  180.00   0.0  0
 8M9  CONST_33  C12  C13  C14  C20  180.00   0.0  0
 8M9  CONST_34  CL1  C04  N03  C02  180.00   0.0  0
 8M9  CONST_35  N22  C02  N03  C04  180.00   0.0  0
 8M9  CONST_36  N22  C02  N01  C06  180.00   0.0  0
 8M9  CONST_37  CL1  C04  C05  C06  180.00   0.0  0
 8M9  CONST_38  CL1  C04  C05  C07    0.00   0.0  0
 8M9  CONST_39  O18  C13  C12  C11  180.00   0.0  0
 8M9  CONST_40  H3   C15  C14  C13  180.00   0.0  0
 8M9  CONST_41  H10  C07  C05  C04    0.00   0.0  0
 8M9  CONST_42  H14  N22  C02  N01    0.00   0.0  0
 8M9  CONST_43  H15  N22  C02  N01  180.00   0.0  0
 8M9  Var_01    C11  C10  N09  C06  -74.91  30.0  2
 8M9  Var_02    N16  C11  C10  N09  -59.29  30.0  1
 8M9  Var_03    H7   C20  C14  C13  -54.89  30.0  2
 8M9  Var_04    H4   C17  C12  C13  129.70  30.0  2
 8M9  Var_05    H11  C19  O18  C13  -61.30  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
 8M9  plan-1  C10  0.020
 8M9  plan-1  C13  0.020
 8M9  plan-1  C15  0.020
 8M9  plan-1  C11  0.020
 8M9  plan-1  C12  0.020
 8M9  plan-1  C14  0.020
 8M9  plan-1  N16  0.020
 8M9  plan-1  H3   0.020
 8M9  plan-1  O18  0.020
 8M9  plan-1  C17  0.020
 8M9  plan-1  C20  0.020
 8M9  plan-2  C10  0.020
 8M9  plan-2  N01  0.020
 8M9  plan-2  C02  0.020
 8M9  plan-2  N03  0.020
 8M9  plan-2  C04  0.020
 8M9  plan-2  C05  0.020
 8M9  plan-2  C06  0.020
 8M9  plan-2  C07  0.020
 8M9  plan-2  N08  0.020
 8M9  plan-2  N09  0.020
 8M9  plan-2  CL1  0.020
 8M9  plan-2  N22  0.020
 8M9  plan-2  H10  0.020
 8M9  plan-3  C02  0.020
 8M9  plan-3  N22  0.020
 8M9  plan-3  H14  0.020
 8M9  plan-3  H15  0.020

