# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:56:11 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Cc2noc(n2)[C@H]3CC[C@@H](C3)Nc4ncnc5[nH]ncc45)cc1
#
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
 5SL  5SL  ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  49  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5SL
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
 5SL  N3   N  NH1   0  -0.671   3.2807  -0.3016  -0.1420
 5SL  C4   C  CR16  0  -0.288  -5.9454  -1.1947  -0.8472
 5SL  N2   N  N     0  -0.150  -2.9050  -0.5197   2.4447
 5SL  C7   C  CR16  0  -0.280  -7.0518   1.1818   0.0251
 5SL  C6   C  CR16  0  -0.275  -6.2757   0.4201   0.8835
 5SL  C9   C  CR5   0   0.328  -3.4517  -1.0561   1.3995
 5SL  C13  C  CH2   0  -0.461   1.4184   1.3062  -0.6071
 5SL  C20  C  CR16  0   0.057   5.8600   1.8769   0.8487
 5SL  C8   C  CH2   0  -0.626  -4.8420  -1.5872   1.3886
 5SL  N5   N  NR15  0  -0.512   7.8026  -0.4193  -0.9424
 5SL  C18  C  CR15  0  -0.128   6.0062  -1.4815  -1.3475
 5SL  C16  C  CR6   0   0.537   4.4942   0.2368  -0.0023
 5SL  C19  C  CR56  0   0.534   6.8530   0.3042  -0.3257
 5SL  C2   C  CR6   0   0.086  -7.2892   0.7714  -1.2871
 5SL  C3   C  CR16  0  -0.292  -6.7239  -0.4287  -1.7065
 5SL  C5   C  CR6   0   0.106  -5.7133  -0.7809   0.4579
 5SL  N1   N  N     0  -0.445  -2.6411  -1.0676   0.3009
 5SL  C10  C  CR5   0   0.549  -1.5626  -0.5029   0.7330
 5SL  O1   O  O     0  -0.333  -1.6563  -0.1509   2.0093
 5SL  C11  C  CH1   0  -0.392  -0.3204  -0.2072  -0.0161
 5SL  C12  C  CH2   0  -0.437  -0.0459   1.2958  -0.1979
 5SL  C14  C  CH1   0  -0.053   2.0598   0.2948   0.3506
 5SL  C15  C  CH2   0  -0.463   0.9714  -0.7688   0.6171
 5SL  C17  C  CR56  0  -0.218   5.6480  -0.3574  -0.5656
 5SL  N4   N  N     0  -0.237   7.2983  -1.4972  -1.5605
 5SL  N6   N  N     0  -0.458   7.0071   1.4304   0.3813
 5SL  N7   N  N     0  -0.495   4.6385   1.3630   0.6986
 5SL  H1   H  HNH1  0   0.402   3.1903  -1.0979  -0.7539
 5SL  H3   H  HCR6  0   0.247  -7.4833   2.1102   0.3808
 5SL  H4   H  HCR6  0   0.249  -6.1083   0.7622   1.8985
 5SL  H5   H  HCH2  0   0.237   1.5231   0.9588  -1.6390
 5SL  H6   H  HCH2  0   0.253   1.8811   2.2904  -0.5381
 5SL  H7   H  HCR6  0   0.253   5.9061   2.7898   1.4337
 5SL  H8   H  HCH2  0   0.288  -4.8112  -2.6305   1.0686
 5SL  H9   H  HCH2  0   0.286  -5.2377  -1.5694   2.4045
 5SL  H10  H  HNR5  0   0.419   8.7927  -0.2334  -0.9775
 5SL  H11  H  HCR5  0   0.270   5.3779  -2.2598  -1.7534
 5SL  H12  H  HCH3  0   0.247  -7.6285   2.5548  -2.4409
 5SL  H13  H  HCH3  0   0.243  -8.3169   1.1001  -3.1529
 5SL  H14  H  HCH3  0   0.245  -9.0868   1.8576  -1.7608
 5SL  H15  H  HCR6  0   0.247  -6.8921  -0.7746  -2.7197
 5SL  H16  H  HCH1  0   0.296  -0.4577  -0.6476  -1.0051
 5SL  H17  H  HCH2  0   0.244  -0.1804   1.8343   0.7436
 5SL  H18  H  HCH2  0   0.263  -0.7070   1.7477  -0.9367
 5SL  H19  H  HCH1  0   0.270   2.3026   0.8027   1.2834
 5SL  H20  H  HCH2  0   0.266   0.8670  -0.9400   1.6879
 5SL  H21  H  HCH2  0   0.265   1.2244  -1.7314   0.1717
 5SL  H2   H  HCR6  0   0.248  -5.5186  -2.1261  -1.1993
 5SL  C1   C  CH3   0  -0.724  -8.1242   1.6102  -2.2102

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
 5SL  C11  C12  single    1.539  0.020  1.539
 5SL  C11  C15  single    1.544  0.020  1.544
 5SL  C11  C10  single    1.480  0.020  1.480
 5SL  C13  C12  single    1.520  0.020  1.520
 5SL  C13  C14  single    1.533  0.020  1.533
 5SL  C1   C2   single    1.501  0.020  1.501
 5SL  C18  N4   aromatic  1.310  0.020  1.310
 5SL  C18  C17  aromatic  1.415  0.020  1.415
 5SL  C15  C14  single    1.545  0.020  1.545
 5SL  N4   N5   aromatic  1.341  0.020  1.341
 5SL  N3   C14  single    1.445  0.020  1.445
 5SL  N3   C16  single    1.335  0.020  1.335
 5SL  C2   C7   aromatic  1.395  0.020  1.395
 5SL  C2   C3   aromatic  1.391  0.020  1.391
 5SL  C10  O1   aromatic  1.327  0.020  1.327
 5SL  C10  N1   aromatic  1.292  0.020  1.292
 5SL  O1   N2   aromatic  1.373  0.020  1.373
 5SL  C17  C16  aromatic  1.415  0.020  1.415
 5SL  C17  C19  aromatic  1.395  0.020  1.395
 5SL  C7   C6   aromatic  1.385  0.020  1.385
 5SL  C3   C4   aromatic  1.390  0.020  1.390
 5SL  C16  N7   aromatic  1.334  0.020  1.334
 5SL  N1   C9   aromatic  1.365  0.020  1.365
 5SL  N5   C19  aromatic  1.344  0.020  1.344
 5SL  C6   C5   aromatic  1.393  0.020  1.393
 5SL  C4   C5   aromatic  1.389  0.020  1.389
 5SL  N2   C9   aromatic  1.296  0.020  1.296
 5SL  C19  N6   aromatic  1.339  0.020  1.339
 5SL  C9   C8   single    1.488  0.020  1.488
 5SL  C5   C8   single    1.508  0.020  1.508
 5SL  N7   C20  aromatic  1.334  0.020  1.334
 5SL  N6   C20  aromatic  1.317  0.020  1.317
 5SL  N3   H1   single    0.860  0.020  1.020
 5SL  C4   H2   single    0.930  0.020  1.080
 5SL  C7   H3   single    0.930  0.020  1.080
 5SL  C6   H4   single    0.930  0.020  1.080
 5SL  C13  H5   single    0.970  0.020  1.090
 5SL  C13  H6   single    0.970  0.020  1.090
 5SL  C20  H7   single    0.930  0.020  1.080
 5SL  C8   H8   single    0.970  0.020  1.090
 5SL  C8   H9   single    0.970  0.020  1.090
 5SL  N5   H10  single    0.860  0.020  1.020
 5SL  C18  H11  single    0.930  0.020  1.080
 5SL  C1   H12  single    0.970  0.020  1.090
 5SL  C1   H13  single    0.970  0.020  1.090
 5SL  C1   H14  single    0.970  0.020  1.090
 5SL  C3   H15  single    0.930  0.020  1.080
 5SL  C11  H16  single    0.970  0.020  1.090
 5SL  C12  H17  single    0.970  0.020  1.090
 5SL  C12  H18  single    0.970  0.020  1.090
 5SL  C14  H19  single    0.970  0.020  1.090
 5SL  C15  H20  single    0.970  0.020  1.090
 5SL  C15  H21  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
 5SL  H1   N3   C14  117.19  3.000
 5SL  H1   N3   C16  117.62  3.000
 5SL  C14  N3   C16  124.46  3.000
 5SL  H2   C4   C5   119.72  3.000
 5SL  H2   C4   C3   119.58  3.000
 5SL  C5   C4   C3   120.70  3.000
 5SL  O1   N2   C9   103.84  3.000
 5SL  H3   C7   C2   119.53  3.000
 5SL  H3   C7   C6   119.38  3.000
 5SL  C2   C7   C6   121.08  3.000
 5SL  H4   C6   C5   119.72  3.000
 5SL  H4   C6   C7   119.55  3.000
 5SL  C5   C6   C7   120.73  3.000
 5SL  N1   C9   C8   123.07  3.000
 5SL  C8   C9   N2   123.21  3.000
 5SL  N1   C9   N2   113.70  3.000
 5SL  H6   C13  H5   107.81  3.000
 5SL  H6   C13  C14  112.24  3.000
 5SL  H5   C13  C14  109.85  3.000
 5SL  H6   C13  C12  113.45  3.000
 5SL  H5   C13  C12  110.12  3.000
 5SL  C14  C13  C12  103.31  3.000
 5SL  H7   C20  N7   115.07  3.000
 5SL  H7   C20  N6   116.08  3.000
 5SL  N7   C20  N6   128.85  3.000
 5SL  H9   C8   H8   107.39  3.000
 5SL  H9   C8   C5   110.89  3.000
 5SL  H8   C8   C5   110.26  3.000
 5SL  H9   C8   C9   109.05  3.000
 5SL  H8   C8   C9   108.47  3.000
 5SL  C5   C8   C9   110.69  3.000
 5SL  H10  N5   N4   120.11  3.000
 5SL  H10  N5   C19  127.65  3.000
 5SL  N4   N5   C19  112.24  3.000
 5SL  H11  C18  N4   120.29  3.000
 5SL  H11  C18  C17  129.28  3.000
 5SL  N4   C18  C17  110.43  3.000
 5SL  N7   C16  C17  118.39  3.000
 5SL  N7   C16  N3   119.59  3.000
 5SL  C17  C16  N3   122.02  3.000
 5SL  N6   C19  C17  126.09  3.000
 5SL  N6   C19  N5   127.88  3.000
 5SL  C17  C19  N5   106.03  3.000
 5SL  C3   C2   C1   121.51  3.000
 5SL  C3   C2   C7   117.92  3.000
 5SL  C1   C2   C7   120.57  3.000
 5SL  H15  C3   C2   119.61  3.000
 5SL  H15  C3   C4   119.28  3.000
 5SL  C2   C3   C4   121.11  3.000
 5SL  C8   C5   C6   120.37  3.000
 5SL  C8   C5   C4   121.15  3.000
 5SL  C6   C5   C4   118.46  3.000
 5SL  C10  N1   C9   102.88  3.000
 5SL  C11  C10  O1   119.53  3.000
 5SL  O1   C10  N1   112.25  3.000
 5SL  C11  C10  N1   128.22  3.000
 5SL  C10  O1   N2   107.34  3.000
 5SL  H16  C11  C15  109.27  3.000
 5SL  H16  C11  C12  108.03  3.000
 5SL  C15  C11  C12  104.74  3.000
 5SL  H16  C11  C10  105.81  3.000
 5SL  C15  C11  C10  114.95  3.000
 5SL  C12  C11  C10  113.87  3.000
 5SL  H18  C12  H17  107.76  3.000
 5SL  H18  C12  C11  112.15  3.000
 5SL  H17  C12  C11  110.95  3.000
 5SL  H18  C12  C13  113.52  3.000
 5SL  H17  C12  C13  110.31  3.000
 5SL  C11  C12  C13  102.14  3.000
 5SL  H19  C14  C15  109.28  3.000
 5SL  H19  C14  C13  108.69  3.000
 5SL  C15  C14  C13  105.49  3.000
 5SL  H19  C14  N3   107.21  3.000
 5SL  C15  C14  N3   111.71  3.000
 5SL  C13  C14  N3   114.37  3.000
 5SL  H21  C15  H20  106.56  3.000
 5SL  H21  C15  C14  111.95  3.000
 5SL  H20  C15  C14  110.20  3.000
 5SL  H21  C15  C11  110.35  3.000
 5SL  H20  C15  C11  112.33  3.000
 5SL  C14  C15  C11  105.56  3.000
 5SL  C19  C17  C16  115.89  3.000
 5SL  C19  C17  C18  104.66  3.000
 5SL  C16  C17  C18  139.45  3.000
 5SL  C18  N4   N5   106.65  3.000
 5SL  C19  N6   C20  111.87  3.000
 5SL  C16  N7   C20  118.91  3.000
 5SL  H14  C1   H13  107.87  3.000
 5SL  H14  C1   H12  106.95  3.000
 5SL  H13  C1   H12  107.62  3.000
 5SL  H14  C1   C2   111.37  3.000
 5SL  H13  C1   C2   111.66  3.000
 5SL  H12  C1   C2   111.16  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
 5SL  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 5SL  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 5SL  CONST_03  N1   C10  O1   N2     0.00   0.0  0
 5SL  CONST_04  C10  N1   C9   N2     0.00   0.0  0
 5SL  CONST_05  C3   C2   C7   C6     0.00   0.0  0
 5SL  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 5SL  CONST_07  O1   C10  N1   C9     0.00   0.0  0
 5SL  CONST_08  C10  O1   N2   C9     0.00   0.0  0
 5SL  CONST_09  C17  C16  N7   C20    0.00   0.0  0
 5SL  CONST_10  C17  C19  N6   C20    0.00   0.0  0
 5SL  CONST_11  N5   C19  N6   C20  180.00   0.0  0
 5SL  CONST_12  C17  C18  N4   N5     0.00   0.0  0
 5SL  CONST_13  C18  C17  C19  N5     0.00   0.0  0
 5SL  CONST_14  C16  C17  C19  N5   180.00   0.0  0
 5SL  CONST_15  C19  N5   N4   C18    0.00   0.0  0
 5SL  CONST_16  N7   C16  C17  C18  180.00   0.0  0
 5SL  CONST_17  N6   C19  C17  C18  180.00   0.0  0
 5SL  CONST_18  N4   C18  C17  C16  180.00   0.0  0
 5SL  CONST_19  N6   C19  C17  C16    0.00   0.0  0
 5SL  CONST_20  N6   C20  N7   C16    0.00   0.0  0
 5SL  CONST_21  N4   C18  C17  C19    0.00   0.0  0
 5SL  CONST_22  N7   C16  C17  C19    0.00   0.0  0
 5SL  CONST_23  N7   C20  N6   C19    0.00   0.0  0
 5SL  CONST_24  C5   C6   C7   C2     0.00   0.0  0
 5SL  CONST_25  C5   C4   C3   C2     0.00   0.0  0
 5SL  CONST_26  O1   N2   C9   N1     0.00   0.0  0
 5SL  CONST_27  N4   N5   C19  C17    0.00   0.0  0
 5SL  CONST_28  N6   C19  N5   N4   180.00   0.0  0
 5SL  CONST_29  C11  C10  O1   N2   180.00   0.0  0
 5SL  CONST_30  C11  C10  N1   C9   180.00   0.0  0
 5SL  CONST_31  C18  C17  C16  N3     0.00   0.0  0
 5SL  CONST_32  C19  C17  C16  N3   180.00   0.0  0
 5SL  CONST_33  C20  N7   C16  N3   180.00   0.0  0
 5SL  CONST_34  C1   C2   C3   C4   180.00   0.0  0
 5SL  CONST_35  C8   C5   C6   C7   180.00   0.0  0
 5SL  CONST_36  C1   C2   C7   C6   180.00   0.0  0
 5SL  CONST_37  C10  N1   C9   C8   180.00   0.0  0
 5SL  CONST_38  O1   N2   C9   C8   180.00   0.0  0
 5SL  CONST_39  C3   C4   C5   C8   180.00   0.0  0
 5SL  CONST_40  C17  C16  N3   C14  180.00   0.0  0
 5SL  CONST_41  N7   C16  N3   C14    0.00   0.0  0
 5SL  CONST_42  H4   C6   C5   C4   180.00   0.0  0
 5SL  CONST_43  H15  C3   C2   C7   180.00   0.0  0
 5SL  CONST_44  H2   C4   C5   C6   180.00   0.0  0
 5SL  CONST_45  H11  C18  N4   N5   180.00   0.0  0
 5SL  CONST_46  H10  N5   N4   C18  180.00   0.0  0
 5SL  CONST_47  H7   C20  N7   C16  180.00   0.0  0
 5SL  CONST_48  H3   C7   C2   C3   180.00   0.0  0
 5SL  CONST_49  H1   N3   C16  C17    0.00   0.0  0
 5SL  Var_01    C14  C13  C12  C11  -43.34  30.0  1
 5SL  Var_02    C9   C8   C5   C4    96.21  30.0  2
 5SL  Var_03    C5   C8   C9   N2   114.66  30.0  2
 5SL  Var_04    H12  C1   C2   C7    66.77  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
 5SL  chir_01  C11  C12  C15  C10  negativ
 5SL  chir_02  C14  N3   C13  C15  negativ

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
 5SL  plan-1  N2   0.020
 5SL  plan-1  C9   0.020
 5SL  plan-1  C8   0.020
 5SL  plan-1  N1   0.020
 5SL  plan-1  C10  0.020
 5SL  plan-1  O1   0.020
 5SL  plan-1  C11  0.020
 5SL  plan-2  C4   0.020
 5SL  plan-2  C7   0.020
 5SL  plan-2  C6   0.020
 5SL  plan-2  C8   0.020
 5SL  plan-2  C2   0.020
 5SL  plan-2  C3   0.020
 5SL  plan-2  C5   0.020
 5SL  plan-2  H3   0.020
 5SL  plan-2  H4   0.020
 5SL  plan-2  H15  0.020
 5SL  plan-2  H2   0.020
 5SL  plan-2  C1   0.020
 5SL  plan-3  N3   0.020
 5SL  plan-3  C20  0.020
 5SL  plan-3  N5   0.020
 5SL  plan-3  C18  0.020
 5SL  plan-3  C16  0.020
 5SL  plan-3  C19  0.020
 5SL  plan-3  C17  0.020
 5SL  plan-3  N4   0.020
 5SL  plan-3  N6   0.020
 5SL  plan-3  N7   0.020
 5SL  plan-3  H7   0.020
 5SL  plan-3  H10  0.020
 5SL  plan-3  H11  0.020
 5SL  plan-4  N3   0.020
 5SL  plan-4  C16  0.020
 5SL  plan-4  C14  0.020
 5SL  plan-4  H1   0.020

