# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 22:33:24 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-2-{[7-(benzylamino)-3-(propan-2-yl)-1H-pyrazolo[4,3-d]pyrimidin-5-yl]amino}butan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](CO)Nc1nc(NCc2ccccc2)c3[nH]nc(C(C)C)c3n1
#
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
 404  404  (2R)-2-{[7-(benzylamino)-3-(propan-2-yl)-1H-pyrazolo[4,3-d]pyrimidin-5-yl]amino}butan-1-ol  ligand  52  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_404
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
 404  C1    C  CR6   0   0.562  -0.2773  -0.5208   0.5345
 404  C2    C  CR56  0   0.218   0.7202  -1.5275   0.5111
 404  C3    C  CR56  0   0.080   2.0353  -1.1237   0.3290
 404  N4    N  N     0  -0.526   2.4172   0.1578   0.1674
 404  C5    C  CR6   0   0.560   1.4138   1.0198   0.2071
 404  N6    N  N     0  -0.527   0.1070   0.7304   0.3921
 404  N7    N  NR15  0  -0.540   0.7402  -2.8793   0.6320
 404  N8    N  N     0  -0.247   1.9769  -3.3533   0.5438
 404  C9    C  CR5   0   0.180   2.7886  -2.3322   0.3574
 404  C10   C  CH1   0  -0.314   4.2679  -2.4790   0.1840
 404  C11   C  CH3   0  -0.652   4.7648  -3.8705   0.5562
 404  C12   C  CH3   0  -0.653   4.6705  -2.1093  -1.2463
 404  N13   N  NH1   0  -0.661  -1.5817  -0.8009   0.6784
 404  C14   C  CH2   0  -0.327  -2.6035   0.2232   0.7630
 404  C15   C  CR6   0   0.069  -3.9547  -0.3722   0.4774
 404  C16   C  CR16  0  -0.300  -4.8850  -0.5458   1.4956
 404  C17   C  CR16  0  -0.241  -6.1280  -1.1092   1.2308
 404  C18   C  CR16  0  -0.264  -6.4488  -1.5070  -0.0589
 404  C19   C  CR16  0  -0.242  -5.5231  -1.3390  -1.0830
 404  C20   C  CR16  0  -0.284  -4.2842  -0.7769  -0.8150
 404  N21   N  NH1   0  -0.668   1.7282   2.3320   0.0739
 404  C22   C  CH1   0  -0.118   0.7909   3.4216  -0.0848
 404  C23   C  CH2   0  -0.411   0.7097   3.9042  -1.5362
 404  C24   C  CH3   0  -0.668   0.2297   2.8295  -2.5003
 404  C25   C  CH2   0  -0.148   1.1253   4.5461   0.8823
 404  O26   O  OH1   0  -0.675   2.4069   5.0533   0.5810
 404  H10   H  HCH1  0   0.236   4.7439  -1.7542   0.8541
 404  H11   H  HCH3  0   0.218   4.3256  -4.6346  -0.0865
 404  H11A  H  HCH3  0   0.228   5.8484  -3.9247   0.4456
 404  H11B  H  HCH3  0   0.228   4.5216  -4.1240   1.5883
 404  H12   H  HCH3  0   0.227   5.7542  -2.1539  -1.3661
 404  H12A  H  HCH3  0   0.218   4.2235  -2.7983  -1.9655
 404  H12B  H  HCH3  0   0.235   4.3471  -1.0995  -1.4982
 404  HN13  H  HNH1  0   0.401  -1.8487  -1.7386   0.9280
 404  H14   H  HCH2  0   0.251  -2.6010   0.7001   1.7485
 404  H14A  H  HCH2  0   0.265  -2.3682   1.0018   0.0363
 404  H16   H  HCR6  0   0.254  -4.6359  -0.2401   2.5049
 404  H17   H  HCR6  0   0.257  -6.8424  -1.2378   2.0335
 404  H18   H  HCR6  0   0.257  -7.4155  -1.9463  -0.2690
 404  H19   H  HCR6  0   0.258  -5.7703  -1.6435  -2.0917
 404  H20   H  HCR6  0   0.254  -3.5673  -0.6469  -1.6175
 404  HN21  H  HNH1  0   0.373   2.6966   2.5220  -0.1287
 404  H22   H  HCH1  0   0.259  -0.1905   3.0440   0.2049
 404  H23   H  HCH2  0   0.216   0.0249   4.7567  -1.5723
 404  H23A  H  HCH2  0   0.219   1.6846   4.2805  -1.8576
 404  H24   H  HCH3  0   0.229   0.1270   3.2311  -3.5090
 404  H24A  H  HCH3  0   0.221   0.9271   1.9930  -2.5525
 404  H24B  H  HCH3  0   0.218  -0.7406   2.4300  -2.2003
 404  H25   H  HCH2  0   0.196   0.3526   5.3213   0.7973
 404  H25A  H  HCH2  0   0.205   1.0794   4.1531   1.9056
 404  HO26  H  HOH1  0   0.457   2.6354   5.7106   1.2436
 404  HN7   H  HNR5  0   0.415  -0.0220  -3.5154   0.7937

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
 404  C2   C1    aromatic  1.417  0.020  1.417
 404  C1   N13   single    1.342  0.020  1.342
 404  C1   N6    aromatic  1.317  0.020  1.317
 404  N7   C2    aromatic  1.357  0.020  1.357
 404  C2   C3    aromatic  1.388  0.020  1.388
 404  C9   C3    aromatic  1.424  0.020  1.424
 404  C3   N4    aromatic  1.347  0.020  1.347
 404  N4   C5    aromatic  1.323  0.020  1.323
 404  C5   N6    aromatic  1.351  0.020  1.351
 404  C5   N21   single    1.356  0.020  1.356
 404  N8   N7    aromatic  1.327  0.020  1.327
 404  N8   C9    aromatic  1.318  0.020  1.318
 404  C10  C9    single    1.497  0.020  1.497
 404  C11  C10   single    1.524  0.020  1.524
 404  C10  C12   single    1.531  0.020  1.531
 404  C10  H10   single    0.970  0.020  1.090
 404  C11  H11   single    0.970  0.020  1.090
 404  C11  H11A  single    0.970  0.020  1.090
 404  C11  H11B  single    0.970  0.020  1.090
 404  C12  H12   single    0.970  0.020  1.090
 404  C12  H12A  single    0.970  0.020  1.090
 404  C12  H12B  single    0.970  0.020  1.090
 404  N13  C14   single    1.449  0.020  1.449
 404  N13  HN13  single    0.860  0.020  1.020
 404  C14  C15   single    1.504  0.020  1.504
 404  C14  H14   single    0.970  0.020  1.090
 404  C14  H14A  single    0.970  0.020  1.090
 404  C20  C15   aromatic  1.394  0.020  1.394
 404  C15  C16   aromatic  1.390  0.020  1.390
 404  C16  C17   aromatic  1.390  0.020  1.390
 404  C16  H16   single    0.930  0.020  1.080
 404  C18  C17   aromatic  1.387  0.020  1.387
 404  C17  H17   single    0.930  0.020  1.080
 404  C19  C18   aromatic  1.391  0.020  1.391
 404  C18  H18   single    0.930  0.020  1.080
 404  C20  C19   aromatic  1.387  0.020  1.387
 404  C19  H19   single    0.930  0.020  1.080
 404  C20  H20   single    0.930  0.020  1.080
 404  N21  C22   single    1.446  0.020  1.446
 404  N21  HN21  single    0.860  0.020  1.020
 404  C25  C22   single    1.520  0.020  1.520
 404  C22  C23   single    1.532  0.020  1.532
 404  C22  H22   single    0.970  0.020  1.090
 404  C23  C24   single    1.522  0.020  1.522
 404  C23  H23   single    0.970  0.020  1.090
 404  C23  H23A  single    0.970  0.020  1.090
 404  C24  H24   single    0.970  0.020  1.090
 404  C24  H24A  single    0.970  0.020  1.090
 404  C24  H24B  single    0.970  0.020  1.090
 404  O26  C25   single    1.411  0.020  1.411
 404  C25  H25   single    0.970  0.020  1.090
 404  C25  H25A  single    0.970  0.020  1.090
 404  O26  HO26  single    0.850  0.020  0.980
 404  N7   HN7   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
 404  N13   C1   N6    119.59  3.000
 404  N6    C1   C2    117.89  3.000
 404  N13   C1   C2    122.52  3.000
 404  N7    C2   C3    106.70  3.000
 404  C3    C2   C1    117.55  3.000
 404  N7    C2   C1    135.75  3.000
 404  C9    C3   N4    131.28  3.000
 404  N4    C3   C2    124.14  3.000
 404  C9    C3   C2    104.58  3.000
 404  C5    N4   C3    113.65  3.000
 404  N21   C5   N6    116.42  3.000
 404  N21   C5   N4    116.85  3.000
 404  N6    C5   N4    126.72  3.000
 404  C5    N6   C1    120.05  3.000
 404  HN7   N7   N8    119.40  3.000
 404  HN7   N7   C2    129.27  3.000
 404  N8    N7   C2    111.32  3.000
 404  C9    N8   N7    107.85  3.000
 404  C10   C9   N8    123.31  3.000
 404  C10   C9   C3    127.13  3.000
 404  N8    C9   C3    109.55  3.000
 404  H10   C10  C12   107.30  3.000
 404  H10   C10  C11   108.24  3.000
 404  C12   C10  C11   111.28  3.000
 404  H10   C10  C9    107.07  3.000
 404  C12   C10  C9    110.15  3.000
 404  C11   C10  C9    112.56  3.000
 404  H11B  C11  H11A  107.82  3.000
 404  H11B  C11  H11   107.76  3.000
 404  H11A  C11  H11   107.79  3.000
 404  H11B  C11  C10   111.77  3.000
 404  H11A  C11  C10   110.16  3.000
 404  H11   C11  C10   111.38  3.000
 404  H12B  C12  H12A  108.12  3.000
 404  H12B  C12  H12   107.89  3.000
 404  H12A  C12  H12   107.97  3.000
 404  H12B  C12  C10   111.20  3.000
 404  H12A  C12  C10   110.81  3.000
 404  H12   C12  C10   110.72  3.000
 404  HN13  N13  C14   117.19  3.000
 404  HN13  N13  C1    118.62  3.000
 404  C14   N13  C1    122.96  3.000
 404  H14A  C14  H14   106.76  3.000
 404  H14A  C14  C15   110.48  3.000
 404  H14   C14  C15   110.21  3.000
 404  H14A  C14  N13   108.27  3.000
 404  H14   C14  N13   111.02  3.000
 404  C15   C14  N13   110.04  3.000
 404  C20   C15  C16   119.00  3.000
 404  C16   C15  C14   120.77  3.000
 404  C20   C15  C14   120.23  3.000
 404  H16   C16  C17   119.82  3.000
 404  H16   C16  C15   119.55  3.000
 404  C17   C16  C15   120.62  3.000
 404  H17   C17  C18   120.19  3.000
 404  H17   C17  C16   119.80  3.000
 404  C18   C17  C16   120.01  3.000
 404  H18   C18  C19   120.04  3.000
 404  H18   C18  C17   120.22  3.000
 404  C19   C18  C17   119.74  3.000
 404  H19   C19  C20   119.88  3.000
 404  H19   C19  C18   120.02  3.000
 404  C20   C19  C18   120.10  3.000
 404  H20   C20  C19   119.77  3.000
 404  H20   C20  C15   119.69  3.000
 404  C19   C20  C15   120.54  3.000
 404  HN21  N21  C22   117.32  3.000
 404  HN21  N21  C5    115.16  3.000
 404  C22   N21  C5    126.14  3.000
 404  H22   C22  C25   106.56  3.000
 404  H22   C22  C23   108.25  3.000
 404  C25   C22  C23   112.42  3.000
 404  H22   C22  N21   107.05  3.000
 404  C23   C22  N21   112.07  3.000
 404  C25   C22  N21   110.18  3.000
 404  H23A  C23  H23   106.28  3.000
 404  H23A  C23  C24   109.76  3.000
 404  H23   C23  C24   109.39  3.000
 404  H23A  C23  C22   109.86  3.000
 404  H23   C23  C22   108.06  3.000
 404  C24   C23  C22   113.24  3.000
 404  H24B  C24  H24A  107.52  3.000
 404  H24B  C24  H24   107.78  3.000
 404  H24A  C24  H24   107.37  3.000
 404  H24B  C24  C23   111.40  3.000
 404  H24A  C24  C23   111.74  3.000
 404  H24   C24  C23   110.84  3.000
 404  H25A  C25  H25   107.20  3.000
 404  H25A  C25  O26   111.46  3.000
 404  H25   C25  O26   111.66  3.000
 404  H25A  C25  C22   108.61  3.000
 404  H25   C25  C22   108.56  3.000
 404  O26   C25  C22   109.26  3.000
 404  HO26  O26  C25   108.34  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
 404  CONST_01  N8    N7   C2   C1   180.00   0.0  0
 404  CONST_02  C9    C3   C2   C1   180.00   0.0  0
 404  CONST_03  N4    C3   C2   C1     0.00   0.0  0
 404  CONST_04  N4    C5   N6   C1     0.00   0.0  0
 404  CONST_05  C5    N6   C1   C2     0.00   0.0  0
 404  CONST_06  C9    N8   N7   C2     0.00   0.0  0
 404  CONST_07  N8    C9   C3   C2     0.00   0.0  0
 404  CONST_08  C5    N4   C3   C2     0.00   0.0  0
 404  CONST_09  N6    C1   C2   C3     0.00   0.0  0
 404  CONST_10  N8    N7   C2   C3     0.00   0.0  0
 404  CONST_11  N7    N8   C9   C3     0.00   0.0  0
 404  CONST_12  N6    C5   N4   C3     0.00   0.0  0
 404  CONST_13  N7    C2   C3   N4   180.00   0.0  0
 404  CONST_14  N8    C9   C3   N4   180.00   0.0  0
 404  CONST_15  C9    C3   N4   C5   180.00   0.0  0
 404  CONST_16  N7    C2   C1   N6   180.00   0.0  0
 404  CONST_17  C9    C3   C2   N7     0.00   0.0  0
 404  CONST_18  C18   C19  C20  C15    0.00   0.0  0
 404  CONST_19  C18   C17  C16  C15    0.00   0.0  0
 404  CONST_20  C19   C20  C15  C16    0.00   0.0  0
 404  CONST_21  C19   C18  C17  C16    0.00   0.0  0
 404  CONST_22  C20   C15  C16  C17    0.00   0.0  0
 404  CONST_23  C20   C19  C18  C17    0.00   0.0  0
 404  CONST_24  N21   C5   N6   C1   180.00   0.0  0
 404  CONST_25  C10   C9   C3   C2   180.00   0.0  0
 404  CONST_26  N13   C1   C2   C3   180.00   0.0  0
 404  CONST_27  N21   C5   N4   C3   180.00   0.0  0
 404  CONST_28  C10   C9   C3   N4     0.00   0.0  0
 404  CONST_29  N13   C1   N6   C5   180.00   0.0  0
 404  CONST_30  N13   C1   C2   N7     0.00   0.0  0
 404  CONST_31  C10   C9   N8   N7   180.00   0.0  0
 404  CONST_32  C19   C20  C15  C14  180.00   0.0  0
 404  CONST_33  C17   C16  C15  C14  180.00   0.0  0
 404  CONST_34  HN7   N7   C2   C1     0.00   0.0  0
 404  CONST_35  H19   C19  C20  C15  180.00   0.0  0
 404  CONST_36  H17   C17  C16  C15  180.00   0.0  0
 404  CONST_37  H20   C20  C15  C16  180.00   0.0  0
 404  CONST_38  H18   C18  C17  C16  180.00   0.0  0
 404  CONST_39  H16   C16  C17  C18  180.00   0.0  0
 404  CONST_40  C14   N13  C1   C2   180.00   0.0  0
 404  CONST_41  C22   N21  C5   N4   180.00   0.0  0
 404  CONST_42  C14   N13  C1   N6     0.00   0.0  0
 404  CONST_43  C22   N21  C5   N6     0.00   0.0  0
 404  CONST_44  HN13  N13  C1   C2     0.00   0.0  0
 404  CONST_45  HN21  N21  C5   N4     0.00   0.0  0
 404  Var_01    C15   C14  N13  C1   161.90  30.0  3
 404  Var_02    C11   C10  C9   C3   168.17  30.0  2
 404  Var_03    C20   C15  C14  N13  -70.93  30.0  2
 404  Var_04    H11   C11  C10  C9    62.22  30.0  3
 404  Var_05    H12   C12  C10  C9   176.52  30.0  3
 404  Var_06    H24   C24  C23  C22  176.46  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
 404  chir_01  C22  N21  C25  C23  negativ

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
 404  plan-1  C14   0.020
 404  plan-1  C15   0.020
 404  plan-1  C16   0.020
 404  plan-1  C17   0.020
 404  plan-1  C18   0.020
 404  plan-1  C19   0.020
 404  plan-1  C20   0.020
 404  plan-1  H16   0.020
 404  plan-1  H17   0.020
 404  plan-1  H18   0.020
 404  plan-1  H19   0.020
 404  plan-1  H20   0.020
 404  plan-2  C1    0.020
 404  plan-2  C2    0.020
 404  plan-2  C3    0.020
 404  plan-2  N4    0.020
 404  plan-2  C5    0.020
 404  plan-2  N6    0.020
 404  plan-2  N7    0.020
 404  plan-2  N8    0.020
 404  plan-2  C9    0.020
 404  plan-2  C10   0.020
 404  plan-2  N13   0.020
 404  plan-2  N21   0.020
 404  plan-2  HN7   0.020
 404  plan-3  C1    0.020
 404  plan-3  N13   0.020
 404  plan-3  C14   0.020
 404  plan-3  HN13  0.020
 404  plan-4  C5    0.020
 404  plan-4  N21   0.020
 404  plan-4  C22   0.020
 404  plan-4  HN21  0.020

