# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:22:35 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N~8~-(cyclopropylmethyl)-N~4~-(2-methylphenyl)-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1Nc2nc(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
 XNA  XNA  N~8~-(cyclopropylmethyl)-N~4~-(2-methylphenyl)-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine  ligand  55  29  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XNA
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
 XNA  C01   C  CH3   0  -0.769  -3.8700   3.6674   0.9935
 XNA  C02   C  CR6   0   0.045  -4.4181   2.3925   0.4202
 XNA  C03   C  CR16  0  -0.301  -5.7845   2.1423   0.4390
 XNA  C04   C  CR16  0  -0.258  -6.3187   0.9691  -0.0767
 XNA  C05   C  CR16  0  -0.270  -5.4685   0.0275  -0.6341
 XNA  C06   C  CR16  0  -0.295  -4.0998   0.2515  -0.6753
 XNA  C07   C  CR6   0   0.309  -3.5673   1.4265  -0.1461
 XNA  N08   N  NH1   0  -0.770  -2.2020   1.7218  -0.1766
 XNA  C09   C  CR6   0   0.531  -1.1296   0.9090  -0.2344
 XNA  N10   N  N     0  -0.524  -1.2288  -0.3926  -0.3106
 XNA  C11   C  CR6   0   0.648  -0.0938  -1.1309  -0.3485
 XNA  N12   N  N     0  -0.552   1.1376  -0.6421  -0.3211
 XNA  C13   C  CR66  0   0.160   1.2345   0.6928  -0.2400
 XNA  C14   C  CR6   0   0.506   2.5262   1.3336  -0.1858
 XNA  N15   N  N     0  -0.479   2.6174   2.6489  -0.0904
 XNA  C16   C  CR16  0   0.033   1.4801   3.3585  -0.0583
 XNA  N17   N  N     0  -0.474   0.2600   2.8988  -0.1020
 XNA  C18   C  CR66  0   0.069   0.1560   1.5522  -0.1919
 XNA  N19   N  NH1   0  -0.648   3.6190   0.5766  -0.2354
 XNA  C20   C  CH2   0  -0.258   4.9692   1.0885  -0.1410
 XNA  C21   C  CH1   0  -0.292   5.9527   0.0158  -0.5120
 XNA  C22   C  CH2   0  -0.485   6.2753  -1.0629   0.4800
 XNA  C23   C  CH2   0  -0.491   7.2905  -0.0096   0.1566
 XNA  N24   N  NT    0  -0.501  -0.2518  -2.4697  -0.4255
 XNA  C25   C  CH2   0  -0.319   0.8721  -3.3843  -0.4983
 XNA  C26   C  CH2   0  -0.314   0.7837  -4.4118   0.6256
 XNA  N27   N  NH1   0  -0.580  -0.4908  -5.1082   0.6748
 XNA  C28   C  CH2   0  -0.315  -1.5980  -4.1678   0.6898
 XNA  C29   C  CH2   0  -0.318  -1.5424  -3.1319  -0.4301
 XNA  H01   H  HCH3  0   0.251  -3.4146   4.3010   0.2276
 XNA  H01A  H  HCH3  0   0.267  -4.6609   4.2514   1.4596
 XNA  H01B  H  HCH3  0   0.252  -3.1084   3.4790   1.7531
 XNA  H03   H  HCR6  0   0.250  -6.4422   2.8841   0.8764
 XNA  H04   H  HCR6  0   0.253  -7.3863   0.7965  -0.0435
 XNA  H05   H  HCR6  0   0.256  -5.8652  -0.8899  -1.0491
 XNA  H06   H  HCR6  0   0.277  -3.4511  -0.4840  -1.1238
 XNA  HN08  H  HNH1  0   0.422  -1.9448   2.6966  -0.0883
 XNA  H16   H  HCR6  0   0.249   1.6007   4.4341   0.0155
 XNA  HN19  H  HNH1  0   0.403   3.4802  -0.4230  -0.2412
 XNA  H20   H  HCH2  0   0.250   5.0746   1.9474  -0.8068
 XNA  H20A  H  HCH2  0   0.233   5.1719   1.4488   0.8740
 XNA  H21   H  HCH1  0   0.268   5.9288  -0.2801  -1.5557
 XNA  H22   H  HCH2  0   0.249   5.7939  -1.0226   1.4501
 XNA  H22A  H  HCH2  0   0.254   6.4404  -2.0659   0.1088
 XNA  H23   H  HCH2  0   0.256   8.1511  -0.2894  -0.4368
 XNA  H23A  H  HCH2  0   0.249   7.4944   0.7443   0.9075
 XNA  H25   H  HCH2  0   0.231   0.8478  -3.8993  -1.4670
 XNA  H25A  H  HCH2  0   0.270   1.8032  -2.8274  -0.4434
 XNA  H26   H  HCH2  0   0.242   1.5877  -5.1413   0.5132
 XNA  H26A  H  HCH2  0   0.224   0.9386  -3.9058   1.5840
 XNA  HN27  H  HNH1  0   0.343  -0.5721  -5.7061  -0.1402
 XNA  H28   H  HCH2  0   0.242  -2.5385  -4.7185   0.6277
 XNA  H28A  H  HCH2  0   0.224  -1.5928  -3.6453   1.6519
 XNA  H29   H  HCH2  0   0.272  -2.3361  -2.4005  -0.3118
 XNA  H29A  H  HCH2  0   0.229  -1.6870  -3.6261  -1.3989

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
 XNA  C01  C02   single    1.502  0.020  1.502
 XNA  C01  H01   single    0.970  0.020  1.090
 XNA  C01  H01A  single    0.970  0.020  1.090
 XNA  C01  H01B  single    0.970  0.020  1.090
 XNA  C03  C02   aromatic  1.389  0.020  1.389
 XNA  C02  C07   aromatic  1.406  0.020  1.406
 XNA  C03  C04   aromatic  1.388  0.020  1.388
 XNA  C03  H03   single    0.930  0.020  1.080
 XNA  C04  C05   aromatic  1.386  0.020  1.386
 XNA  C04  H04   single    0.930  0.020  1.080
 XNA  C05  C06   aromatic  1.388  0.020  1.388
 XNA  C05  H05   single    0.930  0.020  1.080
 XNA  C07  C06   aromatic  1.394  0.020  1.394
 XNA  C06  H06   single    0.930  0.020  1.080
 XNA  C07  N08   single    1.397  0.020  1.397
 XNA  N08  C09   single    1.347  0.020  1.347
 XNA  N08  HN08  single    0.860  0.020  1.020
 XNA  C09  N10   aromatic  1.308  0.020  1.308
 XNA  C09  C18   aromatic  1.438  0.020  1.438
 XNA  N10  C11   aromatic  1.354  0.020  1.354
 XNA  C11  N12   aromatic  1.325  0.020  1.325
 XNA  C11  N24   single    1.350  0.020  1.350
 XNA  C13  N12   aromatic  1.341  0.020  1.341
 XNA  C18  C13   aromatic  1.380  0.020  1.380
 XNA  C13  C14   aromatic  1.443  0.020  1.443
 XNA  N15  C14   aromatic  1.322  0.020  1.322
 XNA  C14  N19   single    1.330  0.020  1.330
 XNA  C16  N15   aromatic  1.341  0.020  1.341
 XNA  N17  C16   aromatic  1.305  0.020  1.305
 XNA  C16  H16   single    0.930  0.020  1.080
 XNA  N17  C18   aromatic  1.354  0.020  1.354
 XNA  N19  C20   single    1.447  0.020  1.447
 XNA  N19  HN19  single    0.860  0.020  1.020
 XNA  C21  C20   single    1.502  0.020  1.502
 XNA  C20  H20   single    0.970  0.020  1.090
 XNA  C20  H20A  single    0.970  0.020  1.090
 XNA  C21  C23   single    1.496  0.020  1.496
 XNA  C21  C22   single    1.501  0.020  1.501
 XNA  C21  H21   single    0.970  0.020  1.090
 XNA  C23  C22   single    1.498  0.020  1.498
 XNA  C22  H22   single    0.970  0.020  1.090
 XNA  C22  H22A  single    0.970  0.020  1.090
 XNA  C23  H23   single    0.970  0.020  1.090
 XNA  C23  H23A  single    0.970  0.020  1.090
 XNA  C25  N24   single    1.451  0.020  1.451
 XNA  N24  C29   single    1.451  0.020  1.451
 XNA  C26  C25   single    1.525  0.020  1.525
 XNA  C25  H25   single    0.970  0.020  1.090
 XNA  C25  H25A  single    0.970  0.020  1.090
 XNA  C26  N27   single    1.453  0.020  1.453
 XNA  C26  H26   single    0.970  0.020  1.090
 XNA  C26  H26A  single    0.970  0.020  1.090
 XNA  N27  C28   single    1.453  0.020  1.453
 XNA  N27  HN27  single    0.890  0.020  1.040
 XNA  C28  C29   single    1.527  0.020  1.527
 XNA  C28  H28   single    0.970  0.020  1.090
 XNA  C28  H28A  single    0.970  0.020  1.090
 XNA  C29  H29   single    0.970  0.020  1.090
 XNA  C29  H29A  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
 XNA  H01B  C01  H01A  107.55  3.000
 XNA  H01B  C01  H01   107.27  3.000
 XNA  H01A  C01  H01   106.96  3.000
 XNA  H01B  C01  C02   111.95  3.000
 XNA  H01A  C01  C02   110.73  3.000
 XNA  H01   C01  C02   112.12  3.000
 XNA  C07   C02  C03   118.48  3.000
 XNA  C07   C02  C01   121.07  3.000
 XNA  C03   C02  C01   120.45  3.000
 XNA  H03   C03  C04   119.66  3.000
 XNA  H03   C03  C02   118.63  3.000
 XNA  C04   C03  C02   121.71  3.000
 XNA  H04   C04  C05   120.61  3.000
 XNA  H04   C04  C03   120.20  3.000
 XNA  C05   C04  C03   119.18  3.000
 XNA  H05   C05  C06   119.15  3.000
 XNA  H05   C05  C04   120.36  3.000
 XNA  C06   C05  C04   120.49  3.000
 XNA  H06   C06  C07   120.19  3.000
 XNA  H06   C06  C05   119.71  3.000
 XNA  C07   C06  C05   120.10  3.000
 XNA  N08   C07  C06   122.89  3.000
 XNA  N08   C07  C02   117.05  3.000
 XNA  C06   C07  C02   120.04  3.000
 XNA  HN08  N08  C09   112.50  3.000
 XNA  HN08  N08  C07   116.74  3.000
 XNA  C09   N08  C07   130.65  3.000
 XNA  C18   C09  N10   120.98  3.000
 XNA  C18   C09  N08   116.14  3.000
 XNA  N10   C09  N08   122.88  3.000
 XNA  C11   N10  C09   118.73  3.000
 XNA  N24   C11  N12   118.40  3.000
 XNA  N24   C11  N10   116.36  3.000
 XNA  N12   C11  N10   125.24  3.000
 XNA  C13   N12  C11   115.82  3.000
 XNA  C18   C13  C14   114.95  3.000
 XNA  C14   C13  N12   120.60  3.000
 XNA  C18   C13  N12   124.45  3.000
 XNA  N19   C14  N15   120.80  3.000
 XNA  N19   C14  C13   118.77  3.000
 XNA  N15   C14  C13   120.42  3.000
 XNA  C16   N15  C14   118.02  3.000
 XNA  H16   C16  N17   117.10  3.000
 XNA  H16   C16  N15   115.60  3.000
 XNA  N17   C16  N15   127.30  3.000
 XNA  C18   N17  C16   115.12  3.000
 XNA  N17   C18  C13   124.18  3.000
 XNA  N17   C18  C09   121.04  3.000
 XNA  C13   C18  C09   114.78  3.000
 XNA  HN19  N19  C20   118.62  3.000
 XNA  HN19  N19  C14   116.79  3.000
 XNA  C20   N19  C14   124.25  3.000
 XNA  H20A  C20  H20   106.75  3.000
 XNA  H20A  C20  C21   110.03  3.000
 XNA  H20   C20  C21   110.37  3.000
 XNA  H20A  C20  N19   110.44  3.000
 XNA  H20   C20  N19   109.18  3.000
 XNA  C21   C20  N19   110.02  3.000
 XNA  H21   C21  C23   116.42  3.000
 XNA  H21   C21  C22   116.39  3.000
 XNA  C23   C21  C22    60.00  3.000
 XNA  H21   C21  C20   114.71  3.000
 XNA  C22   C21  C20   119.40  3.000
 XNA  C23   C21  C20   119.17  3.000
 XNA  H22A  C22  H22   114.16  3.000
 XNA  H22A  C22  C23   118.31  3.000
 XNA  H22   C22  C23   117.91  3.000
 XNA  H22A  C22  C21   118.18  3.000
 XNA  H22   C22  C21   118.00  3.000
 XNA  C23   C22  C21    59.84  3.000
 XNA  H23A  C23  H23   114.23  3.000
 XNA  H23A  C23  C22   117.84  3.000
 XNA  H23   C23  C22   118.38  3.000
 XNA  H23A  C23  C21   117.79  3.000
 XNA  H23   C23  C21   118.07  3.000
 XNA  C22   C23  C21    60.16  3.000
 XNA  C29   N24  C25   113.66  3.000
 XNA  C29   N24  C11   123.84  3.000
 XNA  C25   N24  C11   122.50  3.000
 XNA  H25A  C25  H25   107.71  3.000
 XNA  H25A  C25  C26   110.96  3.000
 XNA  H25   C25  C26   109.45  3.000
 XNA  H25A  C25  N24   109.77  3.000
 XNA  H25   C25  N24   108.84  3.000
 XNA  C26   C25  N24   110.05  3.000
 XNA  H26A  C26  H26   107.16  3.000
 XNA  H26A  C26  N27   108.42  3.000
 XNA  H26   C26  N27   109.22  3.000
 XNA  H26A  C26  C25   108.99  3.000
 XNA  H26   C26  C25   109.37  3.000
 XNA  N27   C26  C25   113.48  3.000
 XNA  HN27  N27  C28   109.20  3.000
 XNA  HN27  N27  C26   109.01  3.000
 XNA  C28   N27  C26   111.01  3.000
 XNA  H28A  C28  H28   107.15  3.000
 XNA  H28A  C28  C29   108.70  3.000
 XNA  H28   C28  C29   109.39  3.000
 XNA  H28A  C28  N27   108.33  3.000
 XNA  H28   C28  N27   109.24  3.000
 XNA  C29   C28  N27   113.82  3.000
 XNA  H29A  C29  H29   107.66  3.000
 XNA  H29A  C29  C28   109.72  3.000
 XNA  H29   C29  C28   110.52  3.000
 XNA  H29A  C29  N24   109.01  3.000
 XNA  H29   C29  N24   110.03  3.000
 XNA  C28   C29  N24   109.87  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
 XNA  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 XNA  CONST_02  C05   C06  C07  C02     0.00   0.0  0
 XNA  CONST_03  C06   C07  C02  C03     0.00   0.0  0
 XNA  CONST_04  C06   C05  C04  C03     0.00   0.0  0
 XNA  CONST_05  C07   C02  C03  C04     0.00   0.0  0
 XNA  CONST_06  C07   C06  C05  C04     0.00   0.0  0
 XNA  CONST_07  N12   C11  N10  C09     0.00   0.0  0
 XNA  CONST_08  N12   C13  C18  C09     0.00   0.0  0
 XNA  CONST_09  C14   C13  C18  C09   180.00   0.0  0
 XNA  CONST_10  C16   N17  C18  C09   180.00   0.0  0
 XNA  CONST_11  C13   C18  C09  N10     0.00   0.0  0
 XNA  CONST_12  N17   C18  C09  N10   180.00   0.0  0
 XNA  CONST_13  C13   N12  C11  N10     0.00   0.0  0
 XNA  CONST_14  C18   C09  N10  C11     0.00   0.0  0
 XNA  CONST_15  C18   C13  N12  C11     0.00   0.0  0
 XNA  CONST_16  C14   C13  N12  C11   180.00   0.0  0
 XNA  CONST_17  N17   C18  C13  N12   180.00   0.0  0
 XNA  CONST_18  N15   C14  C13  N12   180.00   0.0  0
 XNA  CONST_19  C16   N17  C18  C13     0.00   0.0  0
 XNA  CONST_20  C16   N15  C14  C13     0.00   0.0  0
 XNA  CONST_21  N17   C18  C13  C14     0.00   0.0  0
 XNA  CONST_22  N17   C16  N15  C14     0.00   0.0  0
 XNA  CONST_23  C18   C13  C14  N15     0.00   0.0  0
 XNA  CONST_24  C18   N17  C16  N15     0.00   0.0  0
 XNA  CONST_25  N24   C11  N10  C09   180.00   0.0  0
 XNA  CONST_26  N24   C11  N12  C13   180.00   0.0  0
 XNA  CONST_27  C04   C03  C02  C01   180.00   0.0  0
 XNA  CONST_28  C06   C07  C02  C01   180.00   0.0  0
 XNA  CONST_29  N08   C07  C02  C03   180.00   0.0  0
 XNA  CONST_30  N08   C07  C06  C05   180.00   0.0  0
 XNA  CONST_31  C11   N10  C09  N08   180.00   0.0  0
 XNA  CONST_32  C13   C18  C09  N08   180.00   0.0  0
 XNA  CONST_33  N17   C18  C09  N08     0.00   0.0  0
 XNA  CONST_34  N19   C14  C13  N12     0.00   0.0  0
 XNA  CONST_35  N19   C14  N15  C16   180.00   0.0  0
 XNA  CONST_36  N19   C14  C13  C18   180.00   0.0  0
 XNA  CONST_37  H04   C04  C03  C02   180.00   0.0  0
 XNA  CONST_38  H06   C06  C07  C02   180.00   0.0  0
 XNA  CONST_39  H05   C05  C04  C03   180.00   0.0  0
 XNA  CONST_40  H03   C03  C04  C05   180.00   0.0  0
 XNA  CONST_41  H16   C16  N15  C14   180.00   0.0  0
 XNA  CONST_42  C20   N19  C14  C13   180.00   0.0  0
 XNA  CONST_43  C20   N19  C14  N15     0.00   0.0  0
 XNA  CONST_44  HN19  N19  C14  C13     0.00   0.0  0
 XNA  Var_01    C25   N24  C11  N10   178.84  30.0  2
 XNA  Var_02    C26   C25  N24  C11   124.47  30.0  1
 XNA  Var_03    C28   C29  N24  C11  -124.81  30.0  1
 XNA  Var_04    N27   C26  C25  N24    53.24  30.0  1
 XNA  Var_05    N27   C28  C29  N24   -52.83  30.0  1
 XNA  Var_06    C28   N27  C26  C25   -51.99  30.0  1
 XNA  Var_07    C29   C28  N27  C26    51.92  30.0  1
 XNA  Var_08    C09   N08  C07  C02   156.00  30.0  2
 XNA  Var_09    N10   C09  N08  C07     1.92  30.0  2
 XNA  Var_10    C22   C23  C21  C20   109.08  30.0  1
 XNA  Var_11    H22   C22  C23  C21  -107.86  30.0  1
 XNA  Var_12    C21   C20  N19  C14  -168.45  30.0  3
 XNA  Var_13    C23   C21  C20  N19  -147.36  30.0  1
 XNA  Var_14    H01   C01  C02  C03  -114.62  30.0  2

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
 XNA  chir_01  C21  C20  C23  C22  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
 XNA  plan-1  C01   0.020
 XNA  plan-1  C02   0.020
 XNA  plan-1  C03   0.020
 XNA  plan-1  C04   0.020
 XNA  plan-1  C05   0.020
 XNA  plan-1  C06   0.020
 XNA  plan-1  C07   0.020
 XNA  plan-1  N08   0.020
 XNA  plan-1  H03   0.020
 XNA  plan-1  H04   0.020
 XNA  plan-1  H05   0.020
 XNA  plan-1  H06   0.020
 XNA  plan-2  C14   0.020
 XNA  plan-2  N19   0.020
 XNA  plan-2  C20   0.020
 XNA  plan-2  HN19  0.020
 XNA  plan-3  N08   0.020
 XNA  plan-3  C09   0.020
 XNA  plan-3  N10   0.020
 XNA  plan-3  C11   0.020
 XNA  plan-3  N12   0.020
 XNA  plan-3  C13   0.020
 XNA  plan-3  C14   0.020
 XNA  plan-3  N15   0.020
 XNA  plan-3  C16   0.020
 XNA  plan-3  N17   0.020
 XNA  plan-3  C18   0.020
 XNA  plan-3  N19   0.020
 XNA  plan-3  N24   0.020
 XNA  plan-3  H16   0.020

