# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:52:54 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(c3ccc(NC(=O)c4ccccc4)cc3)c12)C5CCCC5
#
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
 VS0  VS0  N-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]benzamide  ligand  53  30  .  2021-08-24  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_VS0
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
 VS0  O30  O  O     0  -0.460  -4.3183  -1.7853  -0.7400
 VS0  C19  C  C     0   0.525  -4.6434  -0.7034  -0.2832
 VS0  C15  C  CR6   0  -0.045  -6.0800  -0.3384  -0.0986
 VS0  C6   C  CR16  0  -0.294  -6.5345   0.9782  -0.1548
 VS0  C2   C  CR16  0  -0.240  -7.8852   1.2586  -0.0050
 VS0  C1   C  CR16  0  -0.249  -8.7910   0.2287   0.2073
 VS0  C3   C  CR16  0  -0.242  -8.3442  -1.0861   0.2573
 VS0  C7   C  CR16  0  -0.264  -6.9977  -1.3699   0.0940
 VS0  N29  N  NH1   0  -0.757  -3.7559   0.2472   0.1076
 VS0  C16  C  CR6   0   0.365  -2.3591   0.1976   0.0494
 VS0  C8   C  CR16  0  -0.287  -1.6433  -0.6128  -0.8321
 VS0  C4   C  CR16  0  -0.309  -0.2583  -0.5641  -0.8426
 VS0  C13  C  CR6   0   0.012   0.4596   0.2716   0.0128
 VS0  C5   C  CR16  0  -0.336  -0.2704   1.0755   0.8908
 VS0  C9   C  CR16  0  -0.327  -1.6528   1.0424   0.9069
 VS0  C14  C  CR5   0  -0.011   1.9248   0.2651   0.0091
 VS0  C12  C  CR56  0  -0.117   2.8488   1.3621   0.0254
 VS0  C18  C  CR6   0   0.392   2.8040   2.7704  -0.0467
 VS0  N28  N  NH2   0  -0.825   1.6588   3.4684  -0.1341
 VS0  N26  N  N     0  -0.475   3.9445   3.4646  -0.0112
 VS0  C11  C  CR16  0   0.040   5.0967   2.8017   0.0541
 VS0  N25  N  N     0  -0.463   5.2824   1.4988   0.0718
 VS0  C17  C  CR56  0   0.509   4.1383   0.8113   0.0490
 VS0  N27  N  NR5   0  -0.518   4.0296  -0.5405   0.0326
 VS0  C10  C  CR15  0  -0.052   2.6979  -0.8641   0.0103
 VS0  C24  C  CH1   0  -0.101   5.1319  -1.4861   0.0902
 VS0  C23  C  CH2   0  -0.463   5.1014  -2.3796   1.3546
 VS0  C21  C  CH2   0  -0.448   4.8179  -3.7947   0.8503
 VS0  C20  C  CH2   0  -0.447   5.5047  -3.8176  -0.5125
 VS0  C22  C  CH2   0  -0.461   5.1374  -2.4596  -1.1077
 VS0  H1   H  HCR6  0   0.266  -5.8518   1.7975  -0.3436
 VS0  H2   H  HCR6  0   0.266  -8.2285   2.2831  -0.0609
 VS0  H3   H  HCR6  0   0.266  -9.8438   0.4480   0.3279
 VS0  H4   H  HCR6  0   0.265  -9.0471  -1.8923   0.4200
 VS0  H5   H  HCR6  0   0.262  -6.6560  -2.3960   0.1255
 VS0  H6   H  HNH1  0   0.421  -4.1280   1.0295   0.6237
 VS0  H7   H  HCR6  0   0.275  -2.1482  -1.2667  -1.5248
 VS0  H8   H  HCR6  0   0.252   0.2764  -1.1846  -1.5512
 VS0  H9   H  HCR6  0   0.266   0.2439   1.7174   1.5955
 VS0  H10  H  HCR6  0   0.272  -2.1902   1.6715   1.6071
 VS0  H11  H  HNH2  0   0.408   0.7995   3.0136  -0.3878
 VS0  H12  H  HNH2  0   0.396   1.7191   4.4544  -0.3253
 VS0  H13  H  HCR6  0   0.245   5.9898   3.4179   0.0863
 VS0  H14  H  HCR5  0   0.297   2.3760  -1.8941   0.0240
 VS0  H15  H  HCH1  0   0.276   6.0330  -0.8755   0.0872
 VS0  H16  H  HCH2  0   0.247   6.0842  -2.3517   1.8291
 VS0  H17  H  HCH2  0   0.250   4.3818  -2.0254   2.0937
 VS0  H18  H  HCH2  0   0.239   5.1830  -4.5637   1.5318
 VS0  H19  H  HCH2  0   0.223   3.7425  -3.9543   0.7277
 VS0  H20  H  HCH2  0   0.225   6.5872  -3.9001  -0.3822
 VS0  H21  H  HCH2  0   0.238   5.1878  -4.6485  -1.1438
 VS0  H22  H  HCH2  0   0.242   4.1381  -2.5149  -1.5478
 VS0  H23  H  HCH2  0   0.252   5.8141  -2.1309  -1.8967

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
 VS0  C2   C6   aromatic  1.388  0.020  1.388
 VS0  C2   C1   aromatic  1.388  0.020  1.388
 VS0  C6   C15  aromatic  1.394  0.020  1.394
 VS0  O30  C19  double    1.219  0.020  1.219
 VS0  C1   C3   aromatic  1.389  0.020  1.389
 VS0  C15  C19  single    1.494  0.020  1.494
 VS0  C15  C7   aromatic  1.394  0.020  1.394
 VS0  C19  N29  single    1.358  0.020  1.358
 VS0  C3   C7   aromatic  1.386  0.020  1.386
 VS0  C8   C4   aromatic  1.386  0.020  1.386
 VS0  C8   C16  aromatic  1.395  0.020  1.395
 VS0  C4   C13  aromatic  1.395  0.020  1.395
 VS0  N29  C16  single    1.399  0.020  1.399
 VS0  C16  C9   aromatic  1.396  0.020  1.396
 VS0  C23  C21  single    1.529  0.020  1.529
 VS0  C23  C24  single    1.549  0.020  1.549
 VS0  C13  C14  single    1.465  0.020  1.465
 VS0  C13  C5   aromatic  1.396  0.020  1.396
 VS0  C21  C20  single    1.526  0.020  1.526
 VS0  C9   C5   aromatic  1.383  0.020  1.383
 VS0  C14  C10  aromatic  1.369  0.020  1.369
 VS0  C14  C12  aromatic  1.434  0.020  1.434
 VS0  C10  N27  aromatic  1.371  0.020  1.371
 VS0  N28  C18  single    1.344  0.020  1.344
 VS0  C12  C18  aromatic  1.411  0.020  1.411
 VS0  C12  C17  aromatic  1.402  0.020  1.402
 VS0  N27  C24  single    1.453  0.020  1.453
 VS0  N27  C17  aromatic  1.356  0.020  1.356
 VS0  C24  C22  single    1.544  0.020  1.544
 VS0  C18  N26  aromatic  1.336  0.020  1.336
 VS0  C17  N25  aromatic  1.335  0.020  1.335
 VS0  N26  C11  aromatic  1.331  0.020  1.331
 VS0  N25  C11  aromatic  1.316  0.020  1.316
 VS0  C20  C22  single    1.528  0.020  1.528
 VS0  C6   H1   single    0.930  0.020  1.080
 VS0  C2   H2   single    0.930  0.020  1.080
 VS0  C1   H3   single    0.930  0.020  1.080
 VS0  C3   H4   single    0.930  0.020  1.080
 VS0  C7   H5   single    0.930  0.020  1.080
 VS0  N29  H6   single    0.860  0.020  1.020
 VS0  C8   H7   single    0.930  0.020  1.080
 VS0  C4   H8   single    0.930  0.020  1.080
 VS0  C5   H9   single    0.930  0.020  1.080
 VS0  C9   H10  single    0.930  0.020  1.080
 VS0  N28  H11  single    0.890  0.020  1.040
 VS0  N28  H12  single    0.890  0.020  1.040
 VS0  C11  H13  single    0.930  0.020  1.080
 VS0  C10  H14  single    0.930  0.020  1.080
 VS0  C24  H15  single    0.970  0.020  1.090
 VS0  C23  H16  single    0.970  0.020  1.090
 VS0  C23  H17  single    0.970  0.020  1.090
 VS0  C21  H18  single    0.970  0.020  1.090
 VS0  C21  H19  single    0.970  0.020  1.090
 VS0  C20  H20  single    0.970  0.020  1.090
 VS0  C20  H21  single    0.970  0.020  1.090
 VS0  C22  H22  single    0.970  0.020  1.090
 VS0  C22  H23  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
 VS0  N29  C19  C15  114.96  3.000
 VS0  N29  C19  O30  123.71  3.000
 VS0  C15  C19  O30  121.33  3.000
 VS0  C7   C15  C6   119.33  3.000
 VS0  C7   C15  C19  118.00  3.000
 VS0  C6   C15  C19  122.64  3.000
 VS0  H1   C6   C2   118.66  3.000
 VS0  H1   C6   C15  121.06  3.000
 VS0  C2   C6   C15  120.26  3.000
 VS0  H2   C2   C1   120.23  3.000
 VS0  H2   C2   C6   119.65  3.000
 VS0  C1   C2   C6   120.12  3.000
 VS0  H3   C1   C3   120.04  3.000
 VS0  H3   C1   C2   120.10  3.000
 VS0  C3   C1   C2   119.85  3.000
 VS0  H4   C3   C7   119.76  3.000
 VS0  H4   C3   C1   120.11  3.000
 VS0  C7   C3   C1   120.13  3.000
 VS0  H5   C7   C3   119.84  3.000
 VS0  H5   C7   C15  119.86  3.000
 VS0  C3   C7   C15  120.29  3.000
 VS0  H6   N29  C16  114.67  3.000
 VS0  H6   N29  C19  116.69  3.000
 VS0  C16  N29  C19  128.01  3.000
 VS0  C9   C16  C8   118.70  3.000
 VS0  C9   C16  N29  117.27  3.000
 VS0  C8   C16  N29  124.00  3.000
 VS0  H7   C8   C4   118.97  3.000
 VS0  H7   C8   C16  121.21  3.000
 VS0  C4   C8   C16  119.81  3.000
 VS0  H8   C4   C13  119.37  3.000
 VS0  H8   C4   C8   118.57  3.000
 VS0  C13  C4   C8   122.06  3.000
 VS0  C14  C13  C5   121.80  3.000
 VS0  C5   C13  C4   117.48  3.000
 VS0  C14  C13  C4   120.70  3.000
 VS0  H9   C5   C9   118.77  3.000
 VS0  H9   C5   C13  120.13  3.000
 VS0  C9   C5   C13  121.08  3.000
 VS0  H10  C9   C5   119.29  3.000
 VS0  H10  C9   C16  119.83  3.000
 VS0  C5   C9   C16  120.88  3.000
 VS0  C10  C14  C12  105.49  3.000
 VS0  C12  C14  C13  129.85  3.000
 VS0  C10  C14  C13  124.65  3.000
 VS0  C17  C12  C18  114.97  3.000
 VS0  C17  C12  C14  106.99  3.000
 VS0  C18  C12  C14  137.93  3.000
 VS0  N26  C18  N28  117.35  3.000
 VS0  N26  C18  C12  119.36  3.000
 VS0  N28  C18  C12  123.28  3.000
 VS0  H12  N28  H11  116.54  3.000
 VS0  H12  N28  C18  118.05  3.000
 VS0  H11  N28  C18  120.67  3.000
 VS0  C11  N26  C18  118.80  3.000
 VS0  H13  C11  N25  116.45  3.000
 VS0  H13  C11  N26  115.53  3.000
 VS0  N25  C11  N26  128.01  3.000
 VS0  C17  N25  C11  112.87  3.000
 VS0  N27  C17  N25  125.60  3.000
 VS0  N25  C17  C12  125.88  3.000
 VS0  N27  C17  C12  108.52  3.000
 VS0  C24  N27  C10  125.73  3.000
 VS0  C24  N27  C17  125.96  3.000
 VS0  C10  N27  C17  108.26  3.000
 VS0  H14  C10  N27  120.99  3.000
 VS0  H14  C10  C14  128.24  3.000
 VS0  N27  C10  C14  110.74  3.000
 VS0  H15  C24  C22  110.41  3.000
 VS0  H15  C24  C23  110.01  3.000
 VS0  C22  C24  C23  105.65  3.000
 VS0  H15  C24  N27  105.24  3.000
 VS0  C22  C24  N27  112.47  3.000
 VS0  C23  C24  N27  113.13  3.000
 VS0  H17  C23  H16  106.92  3.000
 VS0  H17  C23  C21  113.69  3.000
 VS0  H16  C23  C21  109.51  3.000
 VS0  H17  C23  C24  112.27  3.000
 VS0  H16  C23  C24  108.81  3.000
 VS0  C21  C23  C24  105.57  3.000
 VS0  H19  C21  H18  107.23  3.000
 VS0  H19  C21  C20  109.88  3.000
 VS0  H18  C21  C20  113.38  3.000
 VS0  H19  C21  C23  110.75  3.000
 VS0  H18  C21  C23  112.61  3.000
 VS0  C20  C21  C23  103.00  3.000
 VS0  H21  C20  H20  107.41  3.000
 VS0  H21  C20  C22  112.45  3.000
 VS0  H20  C20  C22  110.58  3.000
 VS0  H21  C20  C21  113.42  3.000
 VS0  H20  C20  C21  109.89  3.000
 VS0  C22  C20  C21  103.09  3.000
 VS0  H23  C22  H22  106.93  3.000
 VS0  H23  C22  C20  113.63  3.000
 VS0  H22  C22  C20  109.37  3.000
 VS0  H23  C22  C24  111.94  3.000
 VS0  H22  C22  C24  109.94  3.000
 VS0  C20  C22  C24  105.02  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
 VS0  CONST_01  C1   C2   C6   C15     0.00   0.0  0
 VS0  CONST_02  C1   C3   C7   C15     0.00   0.0  0
 VS0  CONST_03  C3   C1   C2   C6      0.00   0.0  0
 VS0  CONST_04  C3   C7   C15  C6      0.00   0.0  0
 VS0  CONST_05  C7   C15  C6   C2      0.00   0.0  0
 VS0  CONST_06  C7   C3   C1   C2      0.00   0.0  0
 VS0  CONST_07  C13  C4   C8   C16     0.00   0.0  0
 VS0  CONST_08  C13  C5   C9   C16     0.00   0.0  0
 VS0  CONST_09  C14  C13  C4   C8    180.00   0.0  0
 VS0  CONST_10  C5   C13  C4   C8      0.00   0.0  0
 VS0  CONST_11  C5   C9   C16  C8      0.00   0.0  0
 VS0  CONST_12  C9   C16  C8   C4      0.00   0.0  0
 VS0  CONST_15  C9   C5   C13  C4      0.00   0.0  0
 VS0  CONST_16  N27  C10  C14  C13   180.00   0.0  0
 VS0  CONST_17  C18  C12  C14  C13     0.00   0.0  0
 VS0  CONST_18  C17  C12  C14  C13   180.00   0.0  0
 VS0  CONST_21  C14  C13  C5   C9    180.00   0.0  0
 VS0  CONST_22  C17  N27  C10  C14     0.00   0.0  0
 VS0  CONST_23  N26  C18  C12  C14   180.00   0.0  0
 VS0  CONST_24  N27  C17  C12  C14     0.00   0.0  0
 VS0  CONST_25  N25  C17  C12  C14   180.00   0.0  0
 VS0  CONST_26  N27  C10  C14  C12     0.00   0.0  0
 VS0  CONST_27  C11  N26  C18  C12     0.00   0.0  0
 VS0  CONST_28  C10  N27  C17  C12     0.00   0.0  0
 VS0  CONST_29  C11  N25  C17  C12     0.00   0.0  0
 VS0  CONST_30  C10  C14  C12  C18   180.00   0.0  0
 VS0  CONST_31  N27  C17  C12  C18   180.00   0.0  0
 VS0  CONST_32  N25  C17  C12  C18     0.00   0.0  0
 VS0  CONST_33  N25  C11  N26  C18     0.00   0.0  0
 VS0  CONST_34  C17  C12  C18  N26     0.00   0.0  0
 VS0  CONST_35  C17  N25  C11  N26     0.00   0.0  0
 VS0  CONST_36  N27  C17  N25  C11   180.00   0.0  0
 VS0  CONST_37  C10  N27  C17  N25   180.00   0.0  0
 VS0  CONST_38  C10  C14  C12  C17     0.00   0.0  0
 VS0  CONST_39  C24  N27  C10  C14   180.00   0.0  0
 VS0  CONST_40  C24  N27  C17  C12   180.00   0.0  0
 VS0  CONST_41  C24  N27  C17  N25     0.00   0.0  0
 VS0  CONST_42  C2   C6   C15  C19   180.00   0.0  0
 VS0  CONST_43  C3   C7   C15  C19   180.00   0.0  0
 VS0  CONST_44  C4   C8   C16  N29   180.00   0.0  0
 VS0  CONST_45  C5   C9   C16  N29   180.00   0.0  0
 VS0  CONST_46  N28  C18  C12  C14     0.00   0.0  0
 VS0  CONST_47  C17  C12  C18  N28   180.00   0.0  0
 VS0  CONST_48  C11  N26  C18  N28   180.00   0.0  0
 VS0  CONST_49  H2   C2   C6   C15   180.00   0.0  0
 VS0  CONST_50  H4   C3   C7   C15   180.00   0.0  0
 VS0  CONST_51  H3   C1   C2   C6    180.00   0.0  0
 VS0  CONST_52  H5   C7   C15  C6    180.00   0.0  0
 VS0  CONST_53  H1   C6   C2   C1    180.00   0.0  0
 VS0  CONST_54  H8   C4   C8   C16   180.00   0.0  0
 VS0  CONST_55  H9   C5   C9   C16   180.00   0.0  0
 VS0  CONST_56  H10  C9   C16  C8    180.00   0.0  0
 VS0  CONST_57  H7   C8   C4   C13   180.00   0.0  0
 VS0  CONST_58  H14  C10  C14  C13     0.00   0.0  0
 VS0  CONST_59  H13  C11  N26  C18   180.00   0.0  0
 VS0  CONST_60  C16  N29  C19  C15   180.00   0.0  0
 VS0  CONST_63  H6   N29  C16  C8    180.00   0.0  0
 VS0  CONST_65  H12  N28  C18  C12   180.00   0.0  0
 VS0  CONST_66  C16  N29  C19  O30     0.00   0.0  0
 VS0  Var_01    C20  C21  C23  C24    32.72  30.0  1
 VS0  Var_02    C21  C20  C22  C24    35.84  30.0  1
 VS0  Var_03    C22  C20  C21  C23   -42.41  30.0  1
 VS0  Var_04    C6   C15  C19  O30  -151.15  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
 VS0  chir_01  C24  C23  N27  C22  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
 VS0  plan-1  C19  0.020
 VS0  plan-1  C15  0.020
 VS0  plan-1  C6   0.020
 VS0  plan-1  C2   0.020
 VS0  plan-1  C1   0.020
 VS0  plan-1  C3   0.020
 VS0  plan-1  C7   0.020
 VS0  plan-1  H1   0.020
 VS0  plan-1  H2   0.020
 VS0  plan-1  H3   0.020
 VS0  plan-1  H4   0.020
 VS0  plan-1  H5   0.020
 VS0  plan-2  N29  0.020
 VS0  plan-2  C16  0.020
 VS0  plan-2  C8   0.020
 VS0  plan-2  C4   0.020
 VS0  plan-2  C13  0.020
 VS0  plan-2  C5   0.020
 VS0  plan-2  C9   0.020
 VS0  plan-2  C14  0.020
 VS0  plan-2  H7   0.020
 VS0  plan-2  H8   0.020
 VS0  plan-2  H9   0.020
 VS0  plan-2  H10  0.020
 VS0  plan-3  C13  0.020
 VS0  plan-3  C14  0.020
 VS0  plan-3  C12  0.020
 VS0  plan-3  C18  0.020
 VS0  plan-3  N28  0.020
 VS0  plan-3  N26  0.020
 VS0  plan-3  C11  0.020
 VS0  plan-3  N25  0.020
 VS0  plan-3  C17  0.020
 VS0  plan-3  N27  0.020
 VS0  plan-3  C10  0.020
 VS0  plan-3  C24  0.020
 VS0  plan-3  H13  0.020
 VS0  plan-3  H14  0.020
 VS0  plan-4  C18  0.020
 VS0  plan-4  N28  0.020
 VS0  plan-4  H11  0.020
 VS0  plan-4  H12  0.020
 VS0  plan-5  O30  0.020
 VS0  plan-5  C19  0.020
 VS0  plan-5  C15  0.020
 VS0  plan-5  N29  0.020
 VS0  plan-5  C16  0.020
 VS0  plan-5  H6   0.020

