# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:08:07 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N~8~-(cyclopropylmethyl)-N~4~-[2-(methylsulfanyl)phenyl]-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccccc1Nc2nc(nc3c(NCC4CC4)ncnc23)N5CCNCC5
#
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
 XNB  XNB  N~8~-(cyclopropylmethyl)-N~4~-[2-(methylsulfanyl)phenyl]-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine  ligand  56  30  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XNB
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
 XNB  C01   C  CH3   0  -0.794   5.5258  -2.9104  -1.7225
 XNB  S02   S  S2    0   0.043   3.9168  -2.3320  -1.1560
 XNB  C03   C  CR6   0  -0.167   4.3192  -0.9390  -0.1525
 XNB  C04   C  CR16  0  -0.269   5.5748  -0.3382  -0.1323
 XNB  C05   C  CR16  0  -0.247   5.8030   0.7872   0.6457
 XNB  C06   C  CR16  0  -0.275   4.7804   1.3216   1.4157
 XNB  C07   C  CR16  0  -0.262   3.5323   0.7188   1.4205
 XNB  C08   C  CR6   0   0.346   3.2918  -0.4072   0.6413
 XNB  N09   N  NH1   0  -0.771   2.0499  -1.0591   0.6501
 XNB  C10   C  CR6   0   0.515   0.8350  -0.4860   0.5591
 XNB  N11   N  N     0  -0.510   0.7005   0.8091   0.4448
 XNB  C12   C  CR6   0   0.641  -0.5435   1.3290   0.3482
 XNB  N13   N  N     0  -0.551  -1.6681   0.6278   0.3601
 XNB  C14   C  CR66  0   0.158  -1.5234  -0.7016   0.4654
 XNB  C15   C  CR6   0   0.505  -2.6786  -1.5660   0.4606
 XNB  N16   N  N     0  -0.478  -2.5344  -2.8768   0.5458
 XNB  C17   C  CR16  0   0.029  -1.2907  -3.3679   0.6536
 XNB  N18   N  N     0  -0.467  -0.1730  -2.6956   0.6741
 XNB  C19   C  CR66  0   0.079  -0.3099  -1.3524   0.5735
 XNB  N20   N  NH1   0  -0.648  -3.8869  -1.0165   0.3689
 XNB  C21   C  CH2   0  -0.260  -5.1191  -1.7687   0.2693
 XNB  C22   C  CH1   0  -0.291  -6.2946  -0.8515   0.4468
 XNB  C23   C  CH2   0  -0.491  -7.5671  -1.1363  -0.2855
 XNB  C24   C  CH2   0  -0.486  -6.7194   0.0314  -0.6897
 XNB  N25   N  NT    0  -0.510  -0.6204   2.6724   0.2263
 XNB  C26   C  CH2   0  -0.300  -1.8851   3.3794   0.1705
 XNB  C27   C  CH2   0  -0.296  -1.8846   4.3578  -0.9919
 XNB  N28   N  NH1   0  -0.602  -0.7514   5.2568  -0.8745
 XNB  C29   C  CH2   0  -0.294   0.4956   4.5149  -0.9050
 XNB  C30   C  CH2   0  -0.302   0.5397   3.5431   0.2622
 XNB  H01   H  HCH3  0   0.297   5.3315  -3.8230  -2.2824
 XNB  H01A  H  HCH3  0   0.276   6.0049  -2.1934  -2.3858
 XNB  H01B  H  HCH3  0   0.279   6.1819  -3.1456  -0.8865
 XNB  H04   H  HCR6  0   0.269   6.3811  -0.7326  -0.7348
 XNB  H05   H  HCR6  0   0.261   6.7832   1.2454   0.6435
 XNB  H06   H  HCR6  0   0.260   4.9524   2.1996   2.0236
 XNB  H07   H  HCR6  0   0.269   2.7400   1.1211   2.0351
 XNB  HN09  H  HNH1  0   0.409   2.0427  -2.0712   0.6935
 XNB  H17   H  HCR6  0   0.248  -1.2187  -4.4480   0.7277
 XNB  HN20  H  HNH1  0   0.403  -3.9199  -0.0156   0.2442
 XNB  H21   H  HCH2  0   0.234  -5.1769  -2.2766  -0.7003
 XNB  H21A  H  HCH2  0   0.250  -5.1271  -2.5496   1.0322
 XNB  H22   H  HCH1  0   0.267  -6.3953  -0.4332   1.4433
 XNB  H23   H  HCH2  0   0.249  -7.5926  -1.9965  -0.9435
 XNB  H23A  H  HCH2  0   0.256  -8.5011  -0.9402   0.2244
 XNB  H24   H  HCH2  0   0.254  -7.0725   1.0273  -0.4558
 XNB  H24A  H  HCH2  0   0.249  -6.1698  -0.0381  -1.6211
 XNB  H26   H  HCH2  0   0.269  -2.6984   2.6682   0.0646
 XNB  H26A  H  HCH2  0   0.228  -2.0341   3.9271   1.1086
 XNB  H27   H  HCH2  0   0.197  -1.8773   3.7839  -1.9323
 XNB  H27A  H  HCH2  0   0.239  -2.8104   4.9357  -0.9693
 XNB  HN28  H  HNH1  0   0.357  -0.7684   5.9268  -1.6317
 XNB  H29   H  HCH2  0   0.197   0.6292   3.9468  -1.8394
 XNB  H29A  H  HCH2  0   0.239   1.3338   5.2088  -0.8199
 XNB  H30   H  HCH2  0   0.226   0.5407   4.1058   1.2034
 XNB  H30A  H  HCH2  0   0.274   1.4467   2.9473   0.2266

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
 XNB  S02  C01   single    1.801  0.020  1.801
 XNB  C01  H01   single    0.970  0.020  1.090
 XNB  C01  H01A  single    0.970  0.020  1.090
 XNB  C01  H01B  single    0.970  0.020  1.090
 XNB  C03  S02   single    1.763  0.020  1.763
 XNB  C08  C03   aromatic  1.403  0.020  1.403
 XNB  C03  C04   aromatic  1.392  0.020  1.392
 XNB  C05  C04   aromatic  1.387  0.020  1.387
 XNB  C04  H04   single    0.930  0.020  1.080
 XNB  C06  C05   aromatic  1.387  0.020  1.387
 XNB  C05  H05   single    0.930  0.020  1.080
 XNB  C07  C06   aromatic  1.386  0.020  1.386
 XNB  C06  H06   single    0.930  0.020  1.080
 XNB  C07  C08   aromatic  1.390  0.020  1.390
 XNB  C07  H07   single    0.930  0.020  1.080
 XNB  N09  C08   single    1.403  0.020  1.403
 XNB  C10  N09   single    1.346  0.020  1.346
 XNB  N09  HN09  single    0.860  0.020  1.020
 XNB  N11  C10   aromatic  1.307  0.020  1.307
 XNB  C19  C10   aromatic  1.436  0.020  1.436
 XNB  C12  N11   aromatic  1.352  0.020  1.352
 XNB  N25  C12   single    1.351  0.020  1.351
 XNB  N13  C12   aromatic  1.325  0.020  1.325
 XNB  N13  C14   aromatic  1.341  0.020  1.341
 XNB  C15  C14   aromatic  1.443  0.020  1.443
 XNB  C14  C19   aromatic  1.381  0.020  1.381
 XNB  N20  C15   single    1.331  0.020  1.331
 XNB  C15  N16   aromatic  1.321  0.020  1.321
 XNB  N16  C17   aromatic  1.342  0.020  1.342
 XNB  C17  N18   aromatic  1.304  0.020  1.304
 XNB  C17  H17   single    0.930  0.020  1.080
 XNB  C19  N18   aromatic  1.354  0.020  1.354
 XNB  C21  N20   single    1.447  0.020  1.447
 XNB  N20  HN20  single    0.860  0.020  1.020
 XNB  C22  C21   single    1.502  0.020  1.502
 XNB  C21  H21   single    0.970  0.020  1.090
 XNB  C21  H21A  single    0.970  0.020  1.090
 XNB  C24  C22   single    1.501  0.020  1.501
 XNB  C23  C22   single    1.496  0.020  1.496
 XNB  C22  H22   single    0.970  0.020  1.090
 XNB  C24  C23   single    1.498  0.020  1.498
 XNB  C23  H23   single    0.970  0.020  1.090
 XNB  C23  H23A  single    0.970  0.020  1.090
 XNB  C24  H24   single    0.970  0.020  1.090
 XNB  C24  H24A  single    0.970  0.020  1.090
 XNB  C26  N25   single    1.450  0.020  1.450
 XNB  N25  C30   single    1.451  0.020  1.451
 XNB  C27  C26   single    1.519  0.020  1.519
 XNB  C26  H26   single    0.970  0.020  1.090
 XNB  C26  H26A  single    0.970  0.020  1.090
 XNB  C27  N28   single    1.451  0.020  1.451
 XNB  C27  H27   single    0.970  0.020  1.090
 XNB  C27  H27A  single    0.970  0.020  1.090
 XNB  N28  C29   single    1.451  0.020  1.451
 XNB  N28  HN28  single    0.890  0.020  1.040
 XNB  C29  C30   single    1.519  0.020  1.519
 XNB  C29  H29   single    0.970  0.020  1.090
 XNB  C29  H29A  single    0.970  0.020  1.090
 XNB  C30  H30   single    0.970  0.020  1.090
 XNB  C30  H30A  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
 XNB  H01B  C01  H01A  110.20  3.000
 XNB  H01B  C01  H01   108.76  3.000
 XNB  H01A  C01  H01   108.52  3.000
 XNB  H01B  C01  S02   111.48  3.000
 XNB  H01A  C01  S02   111.93  3.000
 XNB  H01   C01  S02   105.76  3.000
 XNB  C03   S02  C01   103.23  3.000
 XNB  C08   C03  C04   119.25  3.000
 XNB  C04   C03  S02   123.72  3.000
 XNB  C08   C03  S02   117.02  3.000
 XNB  H04   C04  C05   119.07  3.000
 XNB  H04   C04  C03   120.47  3.000
 XNB  C05   C04  C03   120.45  3.000
 XNB  H05   C05  C06   120.38  3.000
 XNB  H05   C05  C04   119.45  3.000
 XNB  C06   C05  C04   120.17  3.000
 XNB  H06   C06  C07   119.62  3.000
 XNB  H06   C06  C05   120.50  3.000
 XNB  C07   C06  C05   119.88  3.000
 XNB  H07   C07  C08   119.57  3.000
 XNB  H07   C07  C06   120.02  3.000
 XNB  C08   C07  C06   120.40  3.000
 XNB  N09   C08  C07   121.74  3.000
 XNB  N09   C08  C03   118.41  3.000
 XNB  C07   C08  C03   119.83  3.000
 XNB  HN09  N09  C10   114.95  3.000
 XNB  HN09  N09  C08   118.09  3.000
 XNB  C10   N09  C08   126.92  3.000
 XNB  C19   C10  N11   121.11  3.000
 XNB  C19   C10  N09   117.51  3.000
 XNB  N11   C10  N09   121.37  3.000
 XNB  C12   N11  C10   118.82  3.000
 XNB  N25   C12  N13   118.59  3.000
 XNB  N13   C12  N11   125.22  3.000
 XNB  N25   C12  N11   116.18  3.000
 XNB  C14   N13  C12   115.69  3.000
 XNB  C19   C14  C15   114.92  3.000
 XNB  C19   C14  N13   124.60  3.000
 XNB  C15   C14  N13   120.47  3.000
 XNB  N20   C15  N16   120.88  3.000
 XNB  N16   C15  C14   120.45  3.000
 XNB  N20   C15  C14   118.68  3.000
 XNB  C17   N16  C15   118.00  3.000
 XNB  H17   C17  N18   117.07  3.000
 XNB  H17   C17  N16   115.56  3.000
 XNB  N18   C17  N16   127.37  3.000
 XNB  C19   N18  C17   115.06  3.000
 XNB  N18   C19  C14   124.20  3.000
 XNB  N18   C19  C10   121.25  3.000
 XNB  C14   C19  C10   114.55  3.000
 XNB  HN20  N20  C21   118.63  3.000
 XNB  HN20  N20  C15   116.60  3.000
 XNB  C21   N20  C15   124.29  3.000
 XNB  H21A  C21  H21   106.63  3.000
 XNB  H21A  C21  C22   110.40  3.000
 XNB  H21   C21  C22   110.26  3.000
 XNB  H21A  C21  N20   109.26  3.000
 XNB  H21   C21  N20   110.28  3.000
 XNB  C22   C21  N20   109.94  3.000
 XNB  H22   C22  C24   116.25  3.000
 XNB  H22   C22  C23   116.36  3.000
 XNB  C24   C22  C23    60.02  3.000
 XNB  H22   C22  C21   114.62  3.000
 XNB  C23   C22  C21   119.47  3.000
 XNB  C24   C22  C21   119.44  3.000
 XNB  H23A  C23  H23   114.19  3.000
 XNB  H23A  C23  C24   118.31  3.000
 XNB  H23   C23  C24   117.92  3.000
 XNB  H23A  C23  C22   117.98  3.000
 XNB  H23   C23  C22   117.95  3.000
 XNB  C24   C23  C22    60.16  3.000
 XNB  H24A  C24  H24   114.22  3.000
 XNB  H24A  C24  C23   117.95  3.000
 XNB  H24   C24  C23   118.31  3.000
 XNB  H24A  C24  C22   118.01  3.000
 XNB  H24   C24  C22   118.04  3.000
 XNB  C23   C24  C22    59.83  3.000
 XNB  C30   N25  C26   113.94  3.000
 XNB  C30   N25  C12   123.29  3.000
 XNB  C26   N25  C12   122.54  3.000
 XNB  H26A  C26  H26   107.99  3.000
 XNB  H26A  C26  C27   109.44  3.000
 XNB  H26   C26  C27   110.34  3.000
 XNB  H26A  C26  N25   109.22  3.000
 XNB  H26   C26  N25   109.74  3.000
 XNB  C27   C26  N25   110.07  3.000
 XNB  H27A  C27  H27   107.40  3.000
 XNB  H27A  C27  N28   109.43  3.000
 XNB  H27   C27  N28   112.75  3.000
 XNB  H27A  C27  C26   108.95  3.000
 XNB  H27   C27  C26   108.51  3.000
 XNB  N28   C27  C26   109.71  3.000
 XNB  HN28  N28  C29   109.72  3.000
 XNB  HN28  N28  C27   109.68  3.000
 XNB  C29   N28  C27   110.64  3.000
 XNB  H29A  C29  H29   107.51  3.000
 XNB  H29A  C29  C30   108.93  3.000
 XNB  H29   C29  C30   108.55  3.000
 XNB  H29A  C29  N28   109.46  3.000
 XNB  H29   C29  N28   112.68  3.000
 XNB  C30   C29  N28   109.62  3.000
 XNB  H30A  C30  H30   108.00  3.000
 XNB  H30A  C30  C29   110.49  3.000
 XNB  H30   C30  C29   109.34  3.000
 XNB  H30A  C30  N25   109.74  3.000
 XNB  H30   C30  N25   109.26  3.000
 XNB  C29   C30  N25   109.97  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
 XNB  CONST_01  C06   C07  C08  C03     0.00   0.0  0
 XNB  CONST_02  C06   C05  C04  C03     0.00   0.0  0
 XNB  CONST_03  C07   C08  C03  C04     0.00   0.0  0
 XNB  CONST_04  C07   C06  C05  C04     0.00   0.0  0
 XNB  CONST_05  C08   C03  C04  C05     0.00   0.0  0
 XNB  CONST_06  C08   C07  C06  C05     0.00   0.0  0
 XNB  CONST_07  N13   C12  N11  C10     0.00   0.0  0
 XNB  CONST_08  N13   C14  C19  C10     0.00   0.0  0
 XNB  CONST_09  C15   C14  C19  C10   180.00   0.0  0
 XNB  CONST_10  C17   N18  C19  C10   180.00   0.0  0
 XNB  CONST_11  C14   C19  C10  N11     0.00   0.0  0
 XNB  CONST_12  N18   C19  C10  N11   180.00   0.0  0
 XNB  CONST_13  C14   N13  C12  N11     0.00   0.0  0
 XNB  CONST_14  C19   C10  N11  C12     0.00   0.0  0
 XNB  CONST_15  C15   C14  N13  C12   180.00   0.0  0
 XNB  CONST_16  C19   C14  N13  C12     0.00   0.0  0
 XNB  CONST_17  N16   C15  C14  N13   180.00   0.0  0
 XNB  CONST_18  N18   C19  C14  N13   180.00   0.0  0
 XNB  CONST_19  C17   N16  C15  C14     0.00   0.0  0
 XNB  CONST_20  C17   N18  C19  C14     0.00   0.0  0
 XNB  CONST_21  N18   C19  C14  C15     0.00   0.0  0
 XNB  CONST_22  N18   C17  N16  C15     0.00   0.0  0
 XNB  CONST_23  C19   C14  C15  N16     0.00   0.0  0
 XNB  CONST_24  C19   N18  C17  N16     0.00   0.0  0
 XNB  CONST_25  N25   C12  N11  C10   180.00   0.0  0
 XNB  CONST_26  N25   C12  N13  C14   180.00   0.0  0
 XNB  CONST_27  C07   C08  C03  S02   180.00   0.0  0
 XNB  CONST_28  C05   C04  C03  S02   180.00   0.0  0
 XNB  CONST_29  N09   C08  C03  C04   180.00   0.0  0
 XNB  CONST_30  N09   C08  C07  C06   180.00   0.0  0
 XNB  CONST_31  C12   N11  C10  N09   180.00   0.0  0
 XNB  CONST_32  C14   C19  C10  N09   180.00   0.0  0
 XNB  CONST_33  N18   C19  C10  N09     0.00   0.0  0
 XNB  CONST_34  N20   C15  C14  N13     0.00   0.0  0
 XNB  CONST_35  N20   C15  N16  C17   180.00   0.0  0
 XNB  CONST_36  N20   C15  C14  C19   180.00   0.0  0
 XNB  CONST_37  H07   C07  C08  C03   180.00   0.0  0
 XNB  CONST_38  H05   C05  C04  C03   180.00   0.0  0
 XNB  CONST_39  H06   C06  C05  C04   180.00   0.0  0
 XNB  CONST_40  H04   C04  C05  C06   180.00   0.0  0
 XNB  CONST_41  H17   C17  N16  C15   180.00   0.0  0
 XNB  CONST_42  C21   N20  C15  C14   180.00   0.0  0
 XNB  CONST_43  C21   N20  C15  N16     0.00   0.0  0
 XNB  CONST_44  HN20  N20  C15  C14     0.00   0.0  0
 XNB  Var_01    C26   N25  C12  N11  -177.29  30.0  3
 XNB  Var_02    C27   C26  N25  C12  -131.51  30.0  1
 XNB  Var_03    C29   C30  N25  C12   131.39  30.0  1
 XNB  Var_04    N28   C27  C26  N25   -55.73  30.0  1
 XNB  Var_05    N28   C29  C30  N25    56.05  30.0  1
 XNB  Var_06    C29   N28  C27  C26    60.66  30.0  1
 XNB  Var_07    C30   C29  N28  C27   -60.82  30.0  1
 XNB  Var_08    C10   N09  C08  C03  -135.09  30.0  2
 XNB  Var_09    N11   C10  N09  C08     0.14  30.0  2
 XNB  Var_10    C23   C24  C22  C21   109.06  30.0  1
 XNB  Var_11    H23   C23  C24  C22  -107.91  30.0  1
 XNB  Var_12    C08   C03  S02  C01  -168.51  30.0  1
 XNB  Var_13    C22   C21  N20  C15   169.21  30.0  1
 XNB  Var_14    C24   C22  C21  N20    77.28  30.0  2
 XNB  Var_15    H01   C01  S02  C03   175.47  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
 XNB  chir_01  C22  C21  C24  C23  both

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
 XNB  plan-1  S02   0.020
 XNB  plan-1  C03   0.020
 XNB  plan-1  C04   0.020
 XNB  plan-1  C05   0.020
 XNB  plan-1  C06   0.020
 XNB  plan-1  C07   0.020
 XNB  plan-1  C08   0.020
 XNB  plan-1  N09   0.020
 XNB  plan-1  H04   0.020
 XNB  plan-1  H05   0.020
 XNB  plan-1  H06   0.020
 XNB  plan-1  H07   0.020
 XNB  plan-2  C15   0.020
 XNB  plan-2  N20   0.020
 XNB  plan-2  C21   0.020
 XNB  plan-2  HN20  0.020
 XNB  plan-3  N09   0.020
 XNB  plan-3  C10   0.020
 XNB  plan-3  N11   0.020
 XNB  plan-3  C12   0.020
 XNB  plan-3  N13   0.020
 XNB  plan-3  C14   0.020
 XNB  plan-3  C15   0.020
 XNB  plan-3  N16   0.020
 XNB  plan-3  C17   0.020
 XNB  plan-3  N18   0.020
 XNB  plan-3  C19   0.020
 XNB  plan-3  N20   0.020
 XNB  plan-3  N25   0.020
 XNB  plan-3  H17   0.020

