# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:34:44 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 8-[(3R)-3-aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CCn1c(nc2N(C)C(=O)N(Cc3nc(C)c4ccccc4n3)C(=O)c12)N5CCC[C@@H](N)C5
#
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
 356  356  8-[(3R)-3-aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-dione  ligand  63  35  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_356
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
 356  C1    C  CR56  0   0.122  -0.9808   0.4078  -0.6092
 356  N2    N  NR5   0  -0.536  -2.1805   0.5195   0.0721
 356  C3    C  CR56  0   0.456  -1.0290  -0.8241  -1.2033
 356  C4    C  CR6   0   0.562   0.1362   1.2709  -0.7137
 356  C5    C  CR5   0   0.719  -2.8668  -0.6179  -0.1832
 356  C6    C  CH2   0  -0.497  -2.5421   1.5635   1.0108
 356  N7    N  N     0  -0.506  -2.1847  -1.4574  -0.9526
 356  N8    N  NR6   0  -0.599   0.0032  -1.3000  -1.9571
 356  N9    N  NR6   0  -0.603   1.1296   0.7301  -1.5447
 356  O10   O  O     0  -0.470   0.2745   2.3583  -0.1780
 356  N11   N  NT    0  -0.529  -4.0977  -0.8622   0.3499
 356  C12   C  CSP   0   0.106  -3.0336   2.7715   0.3570
 356  C13   C  CR6   0   0.756   1.1313  -0.5378  -2.1136
 356  C14   C  CH3   0  -0.533  -0.0410  -2.6210  -2.5623
 356  C15   C  CH2   0  -0.401   2.3654   1.4712  -1.6660
 356  C16   C  CH2   0  -0.283  -4.4882  -2.2603   0.4617
 356  C17   C  CH2   0  -0.329  -5.2048   0.0178  -0.0354
 356  C18   C  CSP   0   0.016  -3.4493   3.7662  -0.1758
 356  O19   O  O     0  -0.492   2.0893  -0.9504  -2.7389
 356  C20   C  CR6   0   0.350   3.3915   1.0442  -0.6509
 356  C21   C  CH1   0  -0.100  -5.5805  -2.4136   1.5162
 356  C22   C  CH2   0  -0.441  -6.3061  -0.0545   1.0050
 356  C23   C  CH3   0  -0.818  -3.9471   4.9678  -0.8250
 356  N24   N  N     0  -0.429   3.0651   0.1649   0.2443
 356  N25   N  N     0  -0.444   4.5906   1.6554  -0.7833
 356  C26   C  CH2   0  -0.450  -6.7608  -1.4960   1.1999
 356  N27   N  NH2   0  -0.792  -5.9184  -3.8241   1.6245
 356  C28   C  CR66  0   0.265   4.0222  -0.1849   1.1395
 356  C29   C  CR6   0   0.279   5.5383   1.3467   0.0627
 356  C30   C  CR66  0   0.003   5.3100   0.3895   1.0938
 356  C31   C  CR16  0  -0.306   3.7237  -1.1404   2.1317
 356  C32   C  CH3   0  -0.756   6.8621   2.0215  -0.0852
 356  C33   C  CR16  0  -0.312   6.2805   0.0010   2.0397
 356  C34   C  CR16  0  -0.244   4.6836  -1.5019   3.0402
 356  C35   C  CR16  0  -0.251   5.9703  -0.9300   2.9959
 356  H61   H  HCH2  0   0.302  -3.2988   1.1514   1.6808
 356  H62   H  HCH2  0   0.311  -1.6705   1.7935   1.6234
 356  H141  H  HCH3  0   0.258   0.6962  -3.2813  -2.1091
 356  H142  H  HCH3  0   0.268  -1.0303  -3.0356  -2.4020
 356  H143  H  HCH3  0   0.259   0.1462  -2.5574  -3.6315
 356  H151  H  HCH2  0   0.296   2.7725   1.3545  -2.6689
 356  H152  H  HCH2  0   0.300   2.1539   2.5314  -1.5354
 356  H161  H  HCH2  0   0.214  -4.8484  -2.6480  -0.5030
 356  H162  H  HCH2  0   0.258  -3.6218  -2.8536   0.7513
 356  H171  H  HCH2  0   0.266  -4.8474   1.0407  -0.1455
 356  H172  H  HCH2  0   0.238  -5.5952  -0.2904  -1.0156
 356  H21   H  HCH1  0   0.227  -5.1516  -2.1046   2.4759
 356  H221  H  HCH2  0   0.227  -5.9389   0.3565   1.9501
 356  H222  H  HCH2  0   0.243  -7.1407   0.5725   0.6854
 356  H231  H  HCH3  0   0.270  -4.4686   5.6063  -0.1121
 356  H232  H  HCH3  0   0.269  -3.1325   5.5464  -1.2603
 356  H233  H  HCH3  0   0.270  -4.6464   4.7185  -1.6231
 356  H261  H  HCH2  0   0.213  -7.2457  -1.8502   0.2822
 356  H262  H  HCH2  0   0.238  -7.5049  -1.5612   1.9975
 356  H271  H  HNH2  0   0.349  -6.5730  -3.9536   2.3865
 356  H272  H  HNH2  0   0.337  -6.4148  -4.1165   0.7900
 356  H31   H  HCR6  0   0.265   2.7322  -1.5736   2.1556
 356  H321  H  HCH3  0   0.264   7.6564   1.2915  -0.2482
 356  H322  H  HCH3  0   0.268   6.8438   2.7098  -0.9260
 356  H323  H  HCH3  0   0.264   7.1206   2.5781   0.8170
 356  H33   H  HCR6  0   0.270   7.2708   0.4358   2.0128
 356  H34   H  HCR6  0   0.271   4.4556  -2.2346   3.8034
 356  H35   H  HCR6  0   0.269   6.7138  -1.2299   3.7220

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
 356  C14  N8    single    1.454  0.020  1.454
 356  C22  C17   single    1.517  0.020  1.517
 356  C22  C26   single    1.524  0.020  1.524
 356  O19  C13   double    1.216  0.020  1.216
 356  N8   C13   single    1.370  0.020  1.370
 356  N8   C3    single    1.364  0.020  1.364
 356  C17  N11   single    1.466  0.020  1.466
 356  C26  C21   single    1.528  0.020  1.528
 356  N7   C3    aromatic  1.341  0.020  1.341
 356  N7   C5    aromatic  1.327  0.020  1.327
 356  C13  N9    single    1.390  0.020  1.390
 356  C3   C1    aromatic  1.369  0.020  1.369
 356  N11  C5    single    1.363  0.020  1.363
 356  N11  C16   single    1.456  0.020  1.456
 356  C5   N2    aromatic  1.353  0.020  1.353
 356  C21  C16   single    1.526  0.020  1.526
 356  C21  N27   single    1.454  0.020  1.454
 356  C32  C29   single    1.493  0.020  1.493
 356  N9   C15   single    1.446  0.020  1.446
 356  N9   C4    single    1.404  0.020  1.404
 356  C33  C35   aromatic  1.370  0.020  1.370
 356  C33  C30   aromatic  1.410  0.020  1.410
 356  C1   N2    aromatic  1.384  0.020  1.384
 356  C1   C4    single    1.415  0.020  1.415
 356  C29  C30   aromatic  1.425  0.020  1.425
 356  C29  N25   aromatic  1.307  0.020  1.307
 356  C35  C34   aromatic  1.409  0.020  1.409
 356  C30  C28   aromatic  1.411  0.020  1.411
 356  N25  C20   aromatic  1.352  0.020  1.352
 356  C34  C31   aromatic  1.370  0.020  1.370
 356  C28  C31   aromatic  1.410  0.020  1.410
 356  C28  N24   aromatic  1.356  0.020  1.356
 356  C20  N24   aromatic  1.297  0.020  1.297
 356  C20  C15   single    1.505  0.020  1.505
 356  N2   C6    single    1.450  0.020  1.450
 356  C4   O10   double    1.220  0.020  1.220
 356  C6   C12   single    1.459  0.020  1.459
 356  C12  C18   triple    1.203  0.020  1.203
 356  C18  C23   single    1.454  0.020  1.454
 356  C6   H61   single    0.970  0.020  1.090
 356  C6   H62   single    0.970  0.020  1.090
 356  C14  H141  single    0.970  0.020  1.090
 356  C14  H142  single    0.970  0.020  1.090
 356  C14  H143  single    0.970  0.020  1.090
 356  C15  H151  single    0.970  0.020  1.090
 356  C15  H152  single    0.970  0.020  1.090
 356  C16  H161  single    0.970  0.020  1.090
 356  C16  H162  single    0.970  0.020  1.090
 356  C17  H171  single    0.970  0.020  1.090
 356  C17  H172  single    0.970  0.020  1.090
 356  C21  H21   single    0.970  0.020  1.090
 356  C22  H221  single    0.970  0.020  1.090
 356  C22  H222  single    0.970  0.020  1.090
 356  C23  H231  single    0.970  0.020  1.090
 356  C23  H232  single    0.970  0.020  1.090
 356  C23  H233  single    0.970  0.020  1.090
 356  C26  H261  single    0.970  0.020  1.090
 356  C26  H262  single    0.970  0.020  1.090
 356  N27  H271  single    0.890  0.020  1.040
 356  N27  H272  single    0.890  0.020  1.040
 356  C31  H31   single    0.930  0.020  1.080
 356  C32  H321  single    0.970  0.020  1.090
 356  C32  H322  single    0.970  0.020  1.090
 356  C32  H323  single    0.970  0.020  1.090
 356  C33  H33   single    0.930  0.020  1.080
 356  C34  H34   single    0.930  0.020  1.080
 356  C35  H35   single    0.930  0.020  1.080

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
 356  C4    C1   C3    123.00  3.000
 356  C4    C1   N2    132.15  3.000
 356  C3    C1   N2    104.82  3.000
 356  C6    N2   C5    126.95  3.000
 356  C6    N2   C1    126.37  3.000
 356  C5    N2   C1    106.20  3.000
 356  N8    C3   N7    126.20  3.000
 356  N7    C3   C1    111.98  3.000
 356  N8    C3   C1    121.83  3.000
 356  O10   C4   N9    121.54  3.000
 356  O10   C4   C1    126.91  3.000
 356  N9    C4   C1    111.55  3.000
 356  N11   C5   N7    125.25  3.000
 356  N11   C5   N2    122.34  3.000
 356  N7    C5   N2    112.36  3.000
 356  H62   C6   H61   106.80  3.000
 356  H62   C6   C12   110.28  3.000
 356  H61   C6   C12   110.75  3.000
 356  H62   C6   N2    108.45  3.000
 356  H61   C6   N2    107.37  3.000
 356  C12   C6   N2    112.96  3.000
 356  C5    N7   C3    104.62  3.000
 356  C14   N8   C13   118.87  3.000
 356  C13   N8   C3    119.47  3.000
 356  C14   N8   C3    121.61  3.000
 356  C15   N9   C13   115.61  3.000
 356  C15   N9   C4    117.20  3.000
 356  C13   N9   C4    126.50  3.000
 356  C17   N11  C16   113.21  3.000
 356  C16   N11  C5    116.38  3.000
 356  C17   N11  C5    118.13  3.000
 356  C18   C12  C6    180.00  3.000
 356  O19   C13  N9    121.40  3.000
 356  N9    C13  N8    117.37  3.000
 356  O19   C13  N8    121.23  3.000
 356  H143  C14  H142  108.95  3.000
 356  H143  C14  H141  109.17  3.000
 356  H142  C14  H141  108.92  3.000
 356  H143  C14  N8    110.55  3.000
 356  H142  C14  N8    108.27  3.000
 356  H141  C14  N8    110.94  3.000
 356  H152  C15  H151  106.71  3.000
 356  H152  C15  C20   109.13  3.000
 356  H151  C15  C20   109.63  3.000
 356  H152  C15  N9    108.84  3.000
 356  H151  C15  N9    109.99  3.000
 356  C20   C15  N9    112.37  3.000
 356  H162  C16  H161  107.55  3.000
 356  H162  C16  C21   109.33  3.000
 356  H161  C16  C21   109.65  3.000
 356  H162  C16  N11   109.27  3.000
 356  H161  C16  N11   111.03  3.000
 356  C21   C16  N11   109.97  3.000
 356  H172  C17  H171  106.84  3.000
 356  H172  C17  C22   109.90  3.000
 356  H171  C17  C22   110.63  3.000
 356  H172  C17  N11   109.53  3.000
 356  H171  C17  N11   110.04  3.000
 356  C22   C17  N11   109.84  3.000
 356  C23   C18  C12   180.00  3.000
 356  N25   C20  N24   126.68  3.000
 356  N24   C20  C15   119.11  3.000
 356  N25   C20  C15   114.22  3.000
 356  H21   C21  N27   107.41  3.000
 356  H21   C21  C26   108.32  3.000
 356  N27   C21  C26   114.73  3.000
 356  H21   C21  C16   107.26  3.000
 356  N27   C21  C16   108.37  3.000
 356  C26   C21  C16   110.46  3.000
 356  H222  C22  H221  107.08  3.000
 356  H222  C22  C26   110.65  3.000
 356  H221  C22  C26   110.18  3.000
 356  H222  C22  C17   109.09  3.000
 356  H221  C22  C17   109.32  3.000
 356  C26   C22  C17   110.45  3.000
 356  H233  C23  H232  107.97  3.000
 356  H233  C23  H231  107.81  3.000
 356  H232  C23  H231  107.93  3.000
 356  H233  C23  C18   110.96  3.000
 356  H232  C23  C18   111.18  3.000
 356  H231  C23  C18   110.85  3.000
 356  C28   N24  C20   116.93  3.000
 356  C29   N25  C20   118.21  3.000
 356  H262  C26  H261  106.89  3.000
 356  H262  C26  C22   110.67  3.000
 356  H261  C26  C22   109.29  3.000
 356  H262  C26  C21   109.82  3.000
 356  H261  C26  C21   108.71  3.000
 356  C22   C26  C21   111.35  3.000
 356  H272  N27  H271  105.42  3.000
 356  H272  N27  C21   109.40  3.000
 356  H271  N27  C21   109.28  3.000
 356  C31   C28  C30   119.48  3.000
 356  C31   C28  N24   119.33  3.000
 356  C30   C28  N24   121.18  3.000
 356  C32   C29  C30   121.14  3.000
 356  C30   C29  N25   120.70  3.000
 356  C32   C29  N25   118.16  3.000
 356  C33   C30  C29   124.07  3.000
 356  C29   C30  C28   116.30  3.000
 356  C33   C30  C28   119.63  3.000
 356  H31   C31  C34   121.44  3.000
 356  H31   C31  C28   118.75  3.000
 356  C34   C31  C28   119.82  3.000
 356  H323  C32  H322  108.70  3.000
 356  H323  C32  H321  107.00  3.000
 356  H322  C32  H321  108.69  3.000
 356  H323  C32  C29   111.02  3.000
 356  H322  C32  C29   110.36  3.000
 356  H321  C32  C29   110.97  3.000
 356  H33   C33  C35   119.85  3.000
 356  H33   C33  C30   120.17  3.000
 356  C35   C33  C30   119.98  3.000
 356  H34   C34  C35   119.30  3.000
 356  H34   C34  C31   119.91  3.000
 356  C35   C34  C31   120.79  3.000
 356  H35   C35  C34   119.61  3.000
 356  H35   C35  C33   120.09  3.000
 356  C34   C35  C33   120.30  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
 356  CONST_01  C5    N7   C3   C1      0.00   0.0  0
 356  CONST_02  N7    C5   N2   C1      0.00   0.0  0
 356  CONST_03  C3    N7   C5   N2      0.00   0.0  0
 356  CONST_04  N7    C3   C1   N2      0.00   0.0  0
 356  CONST_05  C5    N2   C1   C3      0.00   0.0  0
 356  CONST_06  C30   C29  N25  C20     0.00   0.0  0
 356  CONST_07  C30   C28  N24  C20     0.00   0.0  0
 356  CONST_08  C31   C28  N24  C20   180.00   0.0  0
 356  CONST_09  C33   C30  C28  N24   180.00   0.0  0
 356  CONST_10  C29   C30  C28  N24     0.00   0.0  0
 356  CONST_11  C34   C31  C28  N24   180.00   0.0  0
 356  CONST_12  C29   N25  C20  N24     0.00   0.0  0
 356  CONST_13  C33   C30  C29  N25   180.00   0.0  0
 356  CONST_14  C28   C30  C29  N25     0.00   0.0  0
 356  CONST_15  C28   N24  C20  N25     0.00   0.0  0
 356  CONST_16  C35   C33  C30  C28     0.00   0.0  0
 356  CONST_17  C35   C34  C31  C28     0.00   0.0  0
 356  CONST_18  C35   C33  C30  C29   180.00   0.0  0
 356  CONST_19  C31   C28  C30  C29   180.00   0.0  0
 356  CONST_20  C34   C35  C33  C30     0.00   0.0  0
 356  CONST_21  C34   C31  C28  C30     0.00   0.0  0
 356  CONST_22  C33   C35  C34  C31     0.00   0.0  0
 356  CONST_23  C33   C30  C28  C31     0.00   0.0  0
 356  CONST_24  N11   C5   N2   C1    180.00   0.0  0
 356  CONST_25  N11   C5   N7   C3    180.00   0.0  0
 356  CONST_26  C13   N9   C4   C1      0.00   0.0  0
 356  CONST_27  N9    C13  N8   C3      0.00   0.0  0
 356  CONST_28  N8    C13  N9   C4      0.00   0.0  0
 356  CONST_29  C6    N2   C1   C3    180.00   0.0  0
 356  CONST_30  C6    N2   C1   C4      0.00   0.0  0
 356  CONST_31  N7    C5   N2   C6    180.00   0.0  0
 356  CONST_32  N11   C5   N2   C6      0.00   0.0  0
 356  CONST_33  C29   N25  C20  C15   180.00   0.0  0
 356  CONST_34  C28   N24  C20  C15   180.00   0.0  0
 356  CONST_35  C32   C29  N25  C20   180.00   0.0  0
 356  CONST_36  C32   C29  C30  C28   180.00   0.0  0
 356  CONST_37  C33   C30  C29  C32     0.00   0.0  0
 356  CONST_38  C15   N9   C4   C1    180.00   0.0  0
 356  CONST_39  O19   C13  N8   C3    180.00   0.0  0
 356  CONST_40  O19   C13  N9   C4    180.00   0.0  0
 356  CONST_41  C15   N9   C13  N8    180.00   0.0  0
 356  CONST_42  C14   N8   C13  N9    180.00   0.0  0
 356  CONST_43  C13   N9   C4   O10   180.00   0.0  0
 356  CONST_44  H31   C31  C28  N24     0.00   0.0  0
 356  CONST_45  H33   C33  C30  C28   180.00   0.0  0
 356  CONST_46  H34   C34  C31  C28   180.00   0.0  0
 356  CONST_47  H35   C35  C33  C30   180.00   0.0  0
 356  CONST_48  C15   N9   C4   O10     0.00   0.0  0
 356  CONST_49  O19   C13  N8   C14     0.00   0.0  0
 356  CONST_50  O19   C13  N9   C15     0.00   0.0  0
 356  Var_01    C17   N11  C5   N2     64.20  30.0  1
 356  Var_02    C22   C17  N11  C5   -158.58  30.0  1
 356  Var_03    C21   C16  N11  C5    158.36  30.0  1
 356  Var_04    C26   C22  C17  N11   -55.84  30.0  1
 356  Var_05    C21   C26  C22  C17    53.63  30.0  1
 356  Var_06    C20   C15  N9   C4     91.29  30.0  3
 356  Var_07    N25   C20  C15  N9    176.13  30.0  1
 356  Var_08    C12   C6   N2   C1     82.78  30.0  2
 356  Var_09    H141  C14  N8   C3   -112.69  30.0  3
 356  Var_10    H321  C32  C29  N25  -120.69  30.0  2
 356  Var_11    H231  C23  C18  C12  -158.81  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
 356  chir_01  C21  C26  C16  N27  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
 356  plan-1  C1   0.020
 356  plan-1  N2   0.020
 356  plan-1  C3   0.020
 356  plan-1  C4   0.020
 356  plan-1  C5   0.020
 356  plan-1  C6   0.020
 356  plan-1  N7   0.020
 356  plan-1  N8   0.020
 356  plan-1  N9   0.020
 356  plan-1  O10  0.020
 356  plan-1  N11  0.020
 356  plan-1  C13  0.020
 356  plan-1  C14  0.020
 356  plan-1  C15  0.020
 356  plan-1  O19  0.020
 356  plan-2  C15  0.020
 356  plan-2  C20  0.020
 356  plan-2  N24  0.020
 356  plan-2  N25  0.020
 356  plan-2  C28  0.020
 356  plan-2  C29  0.020
 356  plan-2  C30  0.020
 356  plan-2  C31  0.020
 356  plan-2  C32  0.020
 356  plan-2  C33  0.020
 356  plan-2  C34  0.020
 356  plan-2  C35  0.020
 356  plan-2  H31  0.020
 356  plan-2  H33  0.020
 356  plan-2  H34  0.020
 356  plan-2  H35  0.020

