# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 17:43:25 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CC#C)c2nc(Nc3ccc4C(=O)NNc4c3)ncc2N(CC#C)C1=O
#
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
 KWJ  KWJ  (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one  ligand  46  29  .  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_KWJ
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
 KWJ  C4   C  C     0   0.589  -4.6740  -0.7481   0.1256
 KWJ  C14  C  CR16  0  -0.289   4.3282  -1.3688   0.0329
 KWJ  C5   C  CH1   0  -0.221  -4.4222   0.7229  -0.1959
 KWJ  C6   C  CH3   0  -0.697  -5.6527   1.5501   0.1302
 KWJ  C11  C  CR6   0   0.604   0.1361   0.1506   0.2855
 KWJ  C8   C  CSP   0   0.257  -2.8180   3.2972  -0.6609
 KWJ  C9   C  CSP1  0  -0.513  -2.6732   3.8322  -1.7273
 KWJ  C10  C  CR6   0   0.548  -2.1150   0.4252   0.3800
 KWJ  C12  C  CR6   0   0.386   2.6423   0.3597   0.2370
 KWJ  C13  C  CR16  0  -0.330   3.0011  -1.0025   0.1115
 KWJ  N1   N  NT    0  -0.576  -3.5700  -1.5096   0.3477
 KWJ  N2   N  NT    0  -0.499  -3.2251   1.2016   0.5020
 KWJ  C3   C  CH2   0  -0.488  -3.7315  -2.9307   0.6041
 KWJ  N3   N  N     0  -0.509  -0.9160   0.9650   0.4094
 KWJ  C1   C  CSP1  0  -0.498  -3.5949  -4.3772  -1.6257
 KWJ  C2   C  CSP   0   0.261  -3.6620  -3.7281  -0.6174
 KWJ  O1   O  O     0  -0.453  -5.7934  -1.2170   0.1424
 KWJ  N4   N  NH1   0  -0.778   1.3373   0.8053   0.3370
 KWJ  C15  C  CR56  0  -0.206   5.3104  -0.3878   0.0724
 KWJ  C16  C  CR5   0   0.526   6.7641  -0.4472   0.0369
 KWJ  O2   O  O     0  -0.488   7.5149  -1.4018  -0.1068
 KWJ  N5   N  NR15  0  -0.513   7.1589   0.8554   0.1977
 KWJ  N6   N  NR15  0  -0.537   6.0841   1.7401   0.1236
 KWJ  C17  C  CR56  0   0.417   4.9512   0.9529   0.1684
 KWJ  C18  C  CR16  0  -0.427   3.6284   1.3498   0.2670
 KWJ  N7   N  N     0  -0.478   0.0825  -1.1548   0.1113
 KWJ  C19  C  CR16  0  -0.051  -1.1352  -1.7030   0.0978
 KWJ  C20  C  CR6   0   0.193  -2.2851  -0.9686   0.2471
 KWJ  H1   H  HCR6  0   0.264   4.5933  -2.4150  -0.0519
 KWJ  H2   H  HCH1  0   0.291  -4.2559   0.7737  -1.2837
 KWJ  H3   H  HCH3  0   0.248  -5.8416   1.5842   1.2031
 KWJ  H4   H  HCH3  0   0.254  -5.5516   2.5671  -0.2433
 KWJ  H5   H  HCH3  0   0.268  -6.5210   1.1183  -0.3596
 KWJ  H6   H  HCH2  0   0.311  -2.1792   2.8124   1.2792
 KWJ  H7   H  HCH2  0   0.311  -3.8968   3.0706   1.1250
 KWJ  H8   H  H     0   0.284  -2.5338   4.3067  -2.6716
 KWJ  H9   H  HCR6  0   0.292   2.2325  -1.7551   0.0827
 KWJ  H10  H  HCH2  0   0.310  -2.9621  -3.2505   1.3092
 KWJ  H11  H  HCH2  0   0.320  -4.6898  -3.0903   1.0962
 KWJ  H12  H  H     0   0.285  -3.5385  -4.9514  -2.5221
 KWJ  H13  H  HNH1  0   0.413   1.2298   1.8032   0.4419
 KWJ  H14  H  HCR6  0   0.281   3.3620   2.3960   0.3574
 KWJ  H15  H  HCR6  0   0.282  -1.1654  -2.7786  -0.0314
 KWJ  H16  H  HNR5  0   0.418   8.0397   1.1939  -0.1617
 KWJ  H17  H  HNR5  0   0.410   6.1503   2.4884   0.8027
 KWJ  C7   C  CH2   0  -0.471  -3.0320   2.6347   0.6261

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
 KWJ  C1   C2   triple    1.201  0.020  1.201
 KWJ  C2   C3   single    1.460  0.020  1.460
 KWJ  N7   C19  aromatic  1.335  0.020  1.335
 KWJ  N7   C11  aromatic  1.318  0.020  1.318
 KWJ  C19  C20  aromatic  1.373  0.020  1.373
 KWJ  N4   C11  single    1.369  0.020  1.369
 KWJ  N4   C12  single    1.383  0.020  1.383
 KWJ  C3   N1   single    1.453  0.020  1.453
 KWJ  C11  N3   aromatic  1.336  0.020  1.336
 KWJ  C13  C12  aromatic  1.414  0.020  1.414
 KWJ  C13  C14  aromatic  1.379  0.020  1.379
 KWJ  C12  C18  aromatic  1.398  0.020  1.398
 KWJ  C20  N1   single    1.398  0.020  1.398
 KWJ  C20  C10  aromatic  1.410  0.020  1.410
 KWJ  N1   C4   single    1.359  0.020  1.359
 KWJ  C14  C15  aromatic  1.389  0.020  1.389
 KWJ  N3   C10  aromatic  1.315  0.020  1.315
 KWJ  C10  N2   single    1.360  0.020  1.360
 KWJ  C18  C17  aromatic  1.385  0.020  1.385
 KWJ  C4   O1   double    1.214  0.020  1.214
 KWJ  C4   C5   single    1.527  0.020  1.527
 KWJ  C15  C17  aromatic  1.391  0.020  1.391
 KWJ  C15  C16  single    1.455  0.020  1.455
 KWJ  C17  N6   single    1.380  0.020  1.380
 KWJ  N2   C5   single    1.466  0.020  1.466
 KWJ  N2   C7   single    1.451  0.020  1.451
 KWJ  C16  O2   double    1.223  0.020  1.223
 KWJ  C16  N5   single    1.371  0.020  1.371
 KWJ  C5   C6   single    1.518  0.020  1.518
 KWJ  C7   C8   single    1.463  0.020  1.463
 KWJ  N6   N5   single    1.394  0.020  1.394
 KWJ  C8   C9   triple    1.202  0.020  1.202
 KWJ  C14  H1   single    0.929  0.020  1.085
 KWJ  C5   H2   single    0.939  0.020  1.096
 KWJ  C6   H3   single    0.939  0.020  1.096
 KWJ  C6   H4   single    0.939  0.020  1.096
 KWJ  C6   H5   single    0.939  0.020  1.096
 KWJ  C7   H6   single    0.939  0.020  1.096
 KWJ  C7   H7   single    0.939  0.020  1.096
 KWJ  C9   H8   single    0.913  0.020  1.066
 KWJ  C13  H9   single    0.929  0.020  1.085
 KWJ  C3   H10  single    0.939  0.020  1.096
 KWJ  C3   H11  single    0.939  0.020  1.096
 KWJ  C1   H12  single    0.913  0.020  1.066
 KWJ  N4   H13  single    0.868  0.020  1.013
 KWJ  C18  H14  single    0.929  0.020  1.085
 KWJ  C19  H15  single    0.929  0.020  1.085
 KWJ  N5   H16  single    0.868  0.020  1.013
 KWJ  N6   H17  single    0.868  0.020  1.013

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
 KWJ  O1   C4   N1   122.03  3.000
 KWJ  O1   C4   C5   121.82  3.000
 KWJ  N1   C4   C5   116.11  3.000
 KWJ  H1   C14  C15  120.77  3.000
 KWJ  H1   C14  C13  119.79  3.000
 KWJ  C15  C14  C13  119.43  3.000
 KWJ  H2   C5   N2   109.38  3.000
 KWJ  H2   C5   C6   108.01  3.000
 KWJ  N2   C5   C6   112.44  3.000
 KWJ  H2   C5   C4   106.10  3.000
 KWJ  C6   C5   C4   110.25  3.000
 KWJ  N2   C5   C4   110.43  3.000
 KWJ  H5   C6   H4   106.92  3.000
 KWJ  H5   C6   H3   108.52  3.000
 KWJ  H4   C6   H3   108.95  3.000
 KWJ  H5   C6   C5   109.54  3.000
 KWJ  H4   C6   C5   111.11  3.000
 KWJ  H3   C6   C5   111.65  3.000
 KWJ  N7   C11  N4   120.95  3.000
 KWJ  N4   C11  N3   113.32  3.000
 KWJ  N7   C11  N3   125.72  3.000
 KWJ  C9   C8   C7   180.00  3.000
 KWJ  H8   C9   C8   180.00  3.000
 KWJ  C20  C10  N3   121.18  3.000
 KWJ  N3   C10  N2   120.52  3.000
 KWJ  C20  C10  N2   118.30  3.000
 KWJ  C18  C12  N4   115.85  3.000
 KWJ  C18  C12  C13  120.34  3.000
 KWJ  N4   C12  C13  123.81  3.000
 KWJ  H9   C13  C12  119.66  3.000
 KWJ  H9   C13  C14  120.00  3.000
 KWJ  C12  C13  C14  120.34  3.000
 KWJ  C20  N1   C3   119.56  3.000
 KWJ  C20  N1   C4   121.20  3.000
 KWJ  C3   N1   C4   119.10  3.000
 KWJ  C10  N2   C7   117.56  3.000
 KWJ  C7   N2   C5   118.15  3.000
 KWJ  C10  N2   C5   115.94  3.000
 KWJ  H11  C3   H10  106.58  3.000
 KWJ  H11  C3   C2   109.87  3.000
 KWJ  H10  C3   C2   110.29  3.000
 KWJ  H11  C3   N1   108.72  3.000
 KWJ  H10  C3   N1   108.80  3.000
 KWJ  C2   C3   N1   112.41  3.000
 KWJ  C10  N3   C11  117.74  3.000
 KWJ  H12  C1   C2   180.00  3.000
 KWJ  C1   C2   C3   180.00  3.000
 KWJ  H13  N4   C12  115.27  3.000
 KWJ  H13  N4   C11  112.54  3.000
 KWJ  C12  N4   C11  132.17  3.000
 KWJ  C17  C15  C16  107.39  3.000
 KWJ  C16  C15  C14  132.60  3.000
 KWJ  C17  C15  C14  120.00  3.000
 KWJ  N5   C16  O2   125.37  3.000
 KWJ  N5   C16  C15  104.24  3.000
 KWJ  O2   C16  C15  130.39  3.000
 KWJ  H16  N5   N6   116.16  3.000
 KWJ  H16  N5   C16  121.87  3.000
 KWJ  N6   N5   C16  112.01  3.000
 KWJ  H17  N6   C17  116.96  3.000
 KWJ  H17  N6   N5   112.51  3.000
 KWJ  C17  N6   N5   105.62  3.000
 KWJ  C18  C17  N6   128.54  3.000
 KWJ  N6   C17  C15  109.60  3.000
 KWJ  C18  C17  C15  121.86  3.000
 KWJ  H14  C18  C17  121.17  3.000
 KWJ  H14  C18  C12  120.82  3.000
 KWJ  C17  C18  C12  118.00  3.000
 KWJ  C19  N7   C11  116.42  3.000
 KWJ  H15  C19  C20  121.38  3.000
 KWJ  H15  C19  N7   115.72  3.000
 KWJ  C20  C19  N7   122.90  3.000
 KWJ  C19  C20  N1   124.81  3.000
 KWJ  N1   C20  C10  119.12  3.000
 KWJ  C19  C20  C10  115.97  3.000
 KWJ  H7   C7   H6   106.36  3.000
 KWJ  H7   C7   N2   109.18  3.000
 KWJ  H6   C7   N2   108.46  3.000
 KWJ  H7   C7   C8   109.74  3.000
 KWJ  H6   C7   C8   109.83  3.000
 KWJ  N2   C7   C8   113.04  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
 KWJ  CONST_01  C18  C12  C13  C14     0.00   0.0  0
 KWJ  CONST_02  C18  C17  C15  C14     0.00   0.0  0
 KWJ  CONST_03  C20  C19  N7   C11     0.00   0.0  0
 KWJ  CONST_04  C20  C10  N3   C11     0.00   0.0  0
 KWJ  CONST_05  N7   C19  C20  C10     0.00   0.0  0
 KWJ  CONST_06  N7   C11  N3   C10     0.00   0.0  0
 KWJ  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 KWJ  CONST_08  C15  C17  C18  C12     0.00   0.0  0
 KWJ  CONST_09  C17  C18  C12  C13     0.00   0.0  0
 KWJ  CONST_10  C17  C15  C14  C13     0.00   0.0  0
 KWJ  CONST_11  C19  N7   C11  N3      0.00   0.0  0
 KWJ  CONST_12  C19  C20  C10  N3      0.00   0.0  0
 KWJ  CONST_13  C20  N1   C4   C5      0.00   0.0  0
 KWJ  CONST_14  N6   N5   C16  C15     0.00   0.0  0
 KWJ  CONST_15  N4   C12  C13  C14   180.00   0.0  0
 KWJ  CONST_16  N4   C11  N3   C10   180.00   0.0  0
 KWJ  CONST_17  C19  N7   C11  N4    180.00   0.0  0
 KWJ  CONST_18  C17  C18  C12  N4    180.00   0.0  0
 KWJ  CONST_19  C3   N1   C4   C5    180.00   0.0  0
 KWJ  CONST_20  C20  N1   C4   O1    180.00   0.0  0
 KWJ  CONST_21  N6   N5   C16  O2    180.00   0.0  0
 KWJ  CONST_22  H15  C19  N7   C11   180.00   0.0  0
 KWJ  CONST_23  H1   C14  C13  C12   180.00   0.0  0
 KWJ  CONST_24  H14  C18  C12  C13   180.00   0.0  0
 KWJ  CONST_25  H9   C13  C14  C15   180.00   0.0  0
 KWJ  CONST_27  O1   C4   N1   C3      0.00   0.0  0
 KWJ  Var_01    C19  C20  N1   C4   -161.65  30.0  1
 KWJ  Var_02    C20  C10  N2   C5    -31.74  30.0  1
 KWJ  Var_03    C13  C12  N4   C11    -3.34  30.0  2
 KWJ  Var_04    N7   C11  N4   C12     0.00  30.0  2
 KWJ  Var_05    C2   C3   N1   C4     91.59  30.0  2
 KWJ  Var_06    C8   C7   N2   C5    -65.53  30.0  3
 KWJ  Var_07    N2   C7   C8   C9     63.38  30.0  1

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
 KWJ  chir_01  C5  C4  N2  C6  positiv

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
 KWJ  plan-1  C14  0.020
 KWJ  plan-1  C12  0.020
 KWJ  plan-1  C13  0.020
 KWJ  plan-1  N4   0.020
 KWJ  plan-1  C15  0.020
 KWJ  plan-1  C16  0.020
 KWJ  plan-1  O2   0.020
 KWJ  plan-1  N5   0.020
 KWJ  plan-1  N6   0.020
 KWJ  plan-1  C17  0.020
 KWJ  plan-1  C18  0.020
 KWJ  plan-1  H1   0.020
 KWJ  plan-1  H9   0.020
 KWJ  plan-1  H14  0.020
 KWJ  plan-1  H16  0.020
 KWJ  plan-1  H17  0.020
 KWJ  plan-2  C11  0.020
 KWJ  plan-2  C10  0.020
 KWJ  plan-2  N1   0.020
 KWJ  plan-2  N2   0.020
 KWJ  plan-2  N3   0.020
 KWJ  plan-2  N4   0.020
 KWJ  plan-2  N7   0.020
 KWJ  plan-2  C19  0.020
 KWJ  plan-2  C20  0.020
 KWJ  plan-2  H15  0.020
 KWJ  plan-3  C4   0.020
 KWJ  plan-3  C5   0.020
 KWJ  plan-3  N1   0.020
 KWJ  plan-3  C3   0.020
 KWJ  plan-3  O1   0.020
 KWJ  plan-3  C20  0.020

