# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:47:59 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(c3ccc(Oc4ccccc4)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
 B43  B43  7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  50  28  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B43
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
 B43  N1    N  NH2   0  -0.824   1.3454   3.5729  -0.0612
 B43  C1    C  CR6   0   0.394   2.3750   2.7283   0.1231
 B43  N4    N  N     0  -0.475   3.5737   3.2647   0.3664
 B43  C23   C  CR16  0   0.040   4.6177   2.4549   0.5256
 B43  N3    N  N     0  -0.462   4.6426   1.1407   0.4551
 B43  C22   C  CR56  0   0.510   3.4388   0.6110   0.2271
 B43  C2    C  CR56  0  -0.116   2.2408   1.3247   0.0843
 B43  N2    N  NR5   0  -0.519   3.1707  -0.7111   0.0859
 B43  C17   C  CH1   0  -0.098   4.1358  -1.7927   0.1762
 B43  C21   C  CH2   0  -0.471   3.7195  -2.9033   1.1745
 B43  C20   C  CH2   0  -0.446   3.5551  -4.1719   0.3345
 B43  C19   C  CH2   0  -0.449   4.5544  -3.9731  -0.8018
 B43  C18   C  CH2   0  -0.454   4.3554  -2.5067  -1.1724
 B43  C16   C  CR15  0  -0.049   1.8273  -0.8565  -0.1435
 B43  C3    C  CR5   0  -0.016   1.2036   0.3617  -0.1445
 B43  C4    C  CR6   0   0.018  -0.2405   0.5655  -0.2911
 B43  C15   C  CR16  0  -0.311  -0.9547  -0.0846  -1.2996
 B43  C14   C  CR16  0  -0.286  -2.3280   0.0631  -1.4140
 B43  C7    C  CR6   0   0.289  -3.0034   0.8806  -0.5198
 B43  C6    C  CR16  0  -0.286  -2.3180   1.5398   0.4883
 B43  C5    C  CR16  0  -0.341  -0.9453   1.3788   0.5989
 B43  O     O  O2    0  -0.514  -4.3558   1.0718  -0.6496
 B43  C8    C  CR6   0   0.364  -5.2116   0.1602  -0.1059
 B43  C13   C  CR16  0  -0.343  -4.7976  -0.9351   0.6433
 B43  C12   C  CR16  0  -0.246  -5.7523  -1.8032   1.1613
 B43  C11   C  CR16  0  -0.274  -7.1049  -1.5906   0.9427
 B43  C10   C  CR16  0  -0.246  -7.5047  -0.4892   0.1941
 B43  C9    C  CR16  0  -0.328  -6.5673   0.3853  -0.3309
 B43  HN1   H  HNH2  0   0.407   0.4851   3.2488  -0.4675
 B43  HN1A  H  HNH2  0   0.396   1.5518   4.5516  -0.1721
 B43  H23   H  HCR6  0   0.246   5.5648   2.9456   0.7262
 B43  H17   H  HCH1  0   0.276   5.0629  -1.3272   0.5066
 B43  H21   H  HCH2  0   0.251   4.5183  -3.0413   1.9047
 B43  H21A  H  HCH2  0   0.250   2.8221  -2.6403   1.7353
 B43  H20   H  HCH2  0   0.239   3.7261  -5.0823   0.9098
 B43  H20A  H  HCH2  0   0.224   2.5417  -4.2328  -0.0739
 B43  H19   H  HCH2  0   0.225   5.5725  -4.1430  -0.4400
 B43  H19A  H  HCH2  0   0.239   4.3910  -4.6458  -1.6445
 B43  H18   H  HCH2  0   0.239   3.4606  -2.4085  -1.7928
 B43  H18A  H  HCH2  0   0.249   5.1857  -2.0765  -1.7331
 B43  H16   H  HCR5  0   0.298   1.3882  -1.8354  -0.2628
 B43  H15   H  HCR6  0   0.257  -0.4271  -0.7053  -2.0128
 B43  H14   H  HCR6  0   0.276  -2.8678  -0.4427  -2.2046
 B43  H6    H  HCR6  0   0.274  -2.8531   2.1683   1.1891
 B43  H5    H  HCR6  0   0.270  -0.4222   1.8708   1.4095
 B43  H13   H  HCR6  0   0.278  -3.7494  -1.1258   0.8299
 B43  H12   H  HCR6  0   0.261  -5.4240  -2.6557   1.7419
 B43  H11   H  HCR6  0   0.255  -7.8395  -2.2728   1.3494
 B43  H10   H  HCR6  0   0.260  -8.5562  -0.3063   0.0147
 B43  H9    H  HCR6  0   0.268  -6.8799   1.2443  -0.9114

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
 B43  C1   N1    single    1.344  0.020  1.344
 B43  N1   HN1   single    0.890  0.020  1.040
 B43  N1   HN1A  single    0.890  0.020  1.040
 B43  N4   C1    aromatic  1.336  0.020  1.336
 B43  C1   C2    aromatic  1.411  0.020  1.411
 B43  C23  N4    aromatic  1.331  0.020  1.331
 B43  C23  N3    aromatic  1.316  0.020  1.316
 B43  C23  H23   single    0.930  0.020  1.080
 B43  N3   C22   aromatic  1.335  0.020  1.335
 B43  C22  N2    aromatic  1.356  0.020  1.356
 B43  C22  C2    aromatic  1.402  0.020  1.402
 B43  C2   C3    aromatic  1.434  0.020  1.434
 B43  C17  N2    single    1.452  0.020  1.452
 B43  N2   C16   aromatic  1.371  0.020  1.371
 B43  C21  C17   single    1.550  0.020  1.550
 B43  C17  C18   single    1.542  0.020  1.542
 B43  C17  H17   single    0.970  0.020  1.090
 B43  C20  C21   single    1.530  0.020  1.530
 B43  C21  H21   single    0.970  0.020  1.090
 B43  C21  H21A  single    0.970  0.020  1.090
 B43  C20  C19   single    1.526  0.020  1.526
 B43  C20  H20   single    0.970  0.020  1.090
 B43  C20  H20A  single    0.970  0.020  1.090
 B43  C19  C18   single    1.526  0.020  1.526
 B43  C19  H19   single    0.970  0.020  1.090
 B43  C19  H19A  single    0.970  0.020  1.090
 B43  C18  H18   single    0.970  0.020  1.090
 B43  C18  H18A  single    0.970  0.020  1.090
 B43  C16  C3    aromatic  1.369  0.020  1.369
 B43  C16  H16   single    0.930  0.020  1.080
 B43  C3   C4    single    1.466  0.020  1.466
 B43  C4   C15   aromatic  1.396  0.020  1.396
 B43  C4   C5    aromatic  1.397  0.020  1.397
 B43  C15  C14   aromatic  1.386  0.020  1.386
 B43  C15  H15   single    0.930  0.020  1.080
 B43  C14  C7    aromatic  1.387  0.020  1.387
 B43  C14  H14   single    0.930  0.020  1.080
 B43  C6   C7    aromatic  1.386  0.020  1.386
 B43  C7   O     single    1.372  0.020  1.372
 B43  C5   C6    aromatic  1.387  0.020  1.387
 B43  C6   H6    single    0.930  0.020  1.080
 B43  C5   H5    single    0.930  0.020  1.080
 B43  O    C8    single    1.363  0.020  1.363
 B43  C13  C8    aromatic  1.390  0.020  1.390
 B43  C8   C9    aromatic  1.393  0.020  1.393
 B43  C13  C12   aromatic  1.390  0.020  1.390
 B43  C13  H13   single    0.930  0.020  1.080
 B43  C12  C11   aromatic  1.387  0.020  1.387
 B43  C12  H12   single    0.930  0.020  1.080
 B43  C11  C10   aromatic  1.390  0.020  1.390
 B43  C11  H11   single    0.930  0.020  1.080
 B43  C9   C10   aromatic  1.385  0.020  1.385
 B43  C10  H10   single    0.930  0.020  1.080
 B43  C9   H9    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
 B43  HN1A  N1   HN1  116.40  3.000
 B43  HN1A  N1   C1   117.97  3.000
 B43  HN1   N1   C1   120.56  3.000
 B43  C2    C1   N4   119.35  3.000
 B43  C2    C1   N1   123.27  3.000
 B43  N4    C1   N1   117.38  3.000
 B43  C23   N4   C1   118.78  3.000
 B43  H23   C23  N3   116.41  3.000
 B43  H23   C23  N4   115.56  3.000
 B43  N3    C23  N4   128.02  3.000
 B43  C22   N3   C23  112.85  3.000
 B43  N2    C22  C2   108.47  3.000
 B43  C2    C22  N3   125.88  3.000
 B43  N2    C22  N3   125.65  3.000
 B43  C3    C2   C22  107.01  3.000
 B43  C3    C2   C1   137.86  3.000
 B43  C22   C2   C1   115.00  3.000
 B43  C16   N2   C17  125.64  3.000
 B43  C16   N2   C22  108.34  3.000
 B43  C17   N2   C22  126.02  3.000
 B43  H17   C17  C18  110.02  3.000
 B43  H17   C17  C21  109.85  3.000
 B43  C18   C17  C21  105.65  3.000
 B43  H17   C17  N2   105.44  3.000
 B43  C18   C17  N2   112.65  3.000
 B43  C21   C17  N2   113.27  3.000
 B43  H21A  C21  H21  106.79  3.000
 B43  H21A  C21  C20  113.19  3.000
 B43  H21   C21  C20  109.95  3.000
 B43  H21A  C21  C17  112.30  3.000
 B43  H21   C21  C17  108.96  3.000
 B43  C20   C21  C17  105.62  3.000
 B43  H20A  C20  H20  107.20  3.000
 B43  H20A  C20  C19  109.61  3.000
 B43  H20   C20  C19  113.50  3.000
 B43  H20A  C20  C21  110.52  3.000
 B43  H20   C20  C21  112.69  3.000
 B43  C19   C20  C21  103.32  3.000
 B43  H19A  C19  H19  107.41  3.000
 B43  H19A  C19  C18  112.69  3.000
 B43  H19   C19  C18  110.56  3.000
 B43  H19A  C19  C20  113.38  3.000
 B43  H19   C19  C20  110.05  3.000
 B43  C18   C19  C20  102.75  3.000
 B43  H18A  C18  H18  107.22  3.000
 B43  H18A  C18  C19  113.88  3.000
 B43  H18   C18  C19  109.33  3.000
 B43  H18A  C18  C17  112.06  3.000
 B43  H18   C18  C17  109.77  3.000
 B43  C19   C18  C17  104.55  3.000
 B43  H16   C16  C3   128.44  3.000
 B43  H16   C16  N2   120.89  3.000
 B43  C3    C16  N2   110.64  3.000
 B43  C4    C3   C16  124.95  3.000
 B43  C4    C3   C2   129.45  3.000
 B43  C16   C3   C2   105.54  3.000
 B43  C5    C4   C15  118.25  3.000
 B43  C5    C4   C3   120.96  3.000
 B43  C15   C4   C3   120.76  3.000
 B43  H15   C15  C14  119.31  3.000
 B43  H15   C15  C4   119.56  3.000
 B43  C14   C15  C4   121.12  3.000
 B43  H14   C14  C7   120.22  3.000
 B43  H14   C14  C15  120.30  3.000
 B43  C7    C14  C15  119.48  3.000
 B43  O     C7   C6   119.34  3.000
 B43  O     C7   C14  120.07  3.000
 B43  C6    C7   C14  120.56  3.000
 B43  H6    C6   C5   120.34  3.000
 B43  H6    C6   C7   120.16  3.000
 B43  C5    C6   C7   119.50  3.000
 B43  H5    C5   C6   119.02  3.000
 B43  H5    C5   C4   119.86  3.000
 B43  C6    C5   C4   121.09  3.000
 B43  C8    O    C7   119.20  3.000
 B43  C9    C8   C13  120.29  3.000
 B43  C9    C8   O    116.01  3.000
 B43  C13   C8   O    123.70  3.000
 B43  H13   C13  C12  119.41  3.000
 B43  H13   C13  C8   121.37  3.000
 B43  C12   C13  C8   119.22  3.000
 B43  H12   C12  C11  120.08  3.000
 B43  H12   C12  C13  118.90  3.000
 B43  C11   C12  C13  121.02  3.000
 B43  H11   C11  C10  120.44  3.000
 B43  H11   C11  C12  120.43  3.000
 B43  C10   C11  C12  119.13  3.000
 B43  H10   C10  C9   119.21  3.000
 B43  H10   C10  C11  120.16  3.000
 B43  C9    C10  C11  120.63  3.000
 B43  H9    C9   C10  120.57  3.000
 B43  H9    C9   C8   119.73  3.000
 B43  C10   C9   C8   119.70  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
 B43  CONST_01  N3    C23  N4   C1     0.00   0.0  0
 B43  CONST_02  N3    C22  C2   C1     0.00   0.0  0
 B43  CONST_03  N2    C22  C2   C1   180.00   0.0  0
 B43  CONST_04  C16   C3   C2   C1   180.00   0.0  0
 B43  CONST_05  C4    C3   C2   C1     0.00   0.0  0
 B43  CONST_06  C22   C2   C1   N4     0.00   0.0  0
 B43  CONST_07  C3    C2   C1   N4   180.00   0.0  0
 B43  CONST_08  C22   N3   C23  N4     0.00   0.0  0
 B43  CONST_09  C2    C1   N4   C23    0.00   0.0  0
 B43  CONST_10  N2    C22  N3   C23  180.00   0.0  0
 B43  CONST_11  C2    C22  N3   C23    0.00   0.0  0
 B43  CONST_12  C16   N2   C22  N3   180.00   0.0  0
 B43  CONST_13  C3    C2   C22  N3   180.00   0.0  0
 B43  CONST_14  C3    C16  N2   C22    0.00   0.0  0
 B43  CONST_15  C16   C3   C2   C22    0.00   0.0  0
 B43  CONST_16  C4    C3   C2   C22  180.00   0.0  0
 B43  CONST_17  C16   N2   C22  C2     0.00   0.0  0
 B43  CONST_18  N2    C16  C3   C2     0.00   0.0  0
 B43  CONST_21  C3    C2   C22  N2     0.00   0.0  0
 B43  CONST_22  C4    C3   C16  N2   180.00   0.0  0
 B43  CONST_25  C14   C15  C4   C3   180.00   0.0  0
 B43  CONST_26  C6    C5   C4   C3   180.00   0.0  0
 B43  CONST_27  C7    C14  C15  C4     0.00   0.0  0
 B43  CONST_28  C7    C6   C5   C4     0.00   0.0  0
 B43  CONST_29  C6    C5   C4   C15    0.00   0.0  0
 B43  CONST_30  C6    C7   C14  C15    0.00   0.0  0
 B43  CONST_31  C5    C4   C15  C14    0.00   0.0  0
 B43  CONST_32  C5    C6   C7   C14    0.00   0.0  0
 B43  CONST_33  C11   C12  C13  C8     0.00   0.0  0
 B43  CONST_34  C11   C10  C9   C8     0.00   0.0  0
 B43  CONST_35  C10   C9   C8   C13    0.00   0.0  0
 B43  CONST_36  C10   C11  C12  C13    0.00   0.0  0
 B43  CONST_37  C9    C8   C13  C12    0.00   0.0  0
 B43  CONST_38  C9    C10  C11  C12    0.00   0.0  0
 B43  CONST_39  C17   N2   C22  N3     0.00   0.0  0
 B43  CONST_40  C17   N2   C22  C2   180.00   0.0  0
 B43  CONST_41  C3    C16  N2   C17  180.00   0.0  0
 B43  CONST_42  C23   N4   C1   N1   180.00   0.0  0
 B43  CONST_43  C22   C2   C1   N1   180.00   0.0  0
 B43  CONST_44  C3    C2   C1   N1     0.00   0.0  0
 B43  CONST_45  O     C7   C14  C15  180.00   0.0  0
 B43  CONST_46  O     C7   C6   C5   180.00   0.0  0
 B43  CONST_47  C12   C13  C8   O    180.00   0.0  0
 B43  CONST_48  C10   C9   C8   O    180.00   0.0  0
 B43  CONST_49  H23   C23  N4   C1   180.00   0.0  0
 B43  CONST_50  H16   C16  N2   C22  180.00   0.0  0
 B43  CONST_51  H15   C15  C4   C3     0.00   0.0  0
 B43  CONST_52  H5    C5   C4   C3     0.00   0.0  0
 B43  CONST_53  H14   C14  C15  C4   180.00   0.0  0
 B43  CONST_54  H6    C6   C5   C4   180.00   0.0  0
 B43  CONST_55  H12   C12  C13  C8   180.00   0.0  0
 B43  CONST_56  H10   C10  C9   C8   180.00   0.0  0
 B43  CONST_57  H9    C9   C8   C13  180.00   0.0  0
 B43  CONST_58  H11   C11  C12  C13  180.00   0.0  0
 B43  CONST_59  H13   C13  C12  C11  180.00   0.0  0
 B43  CONST_61  HN1A  N1   C1   N4     0.00   0.0  0
 B43  Var_01    C19   C20  C21  C17   30.12  30.0  1
 B43  Var_02    C20   C19  C18  C17   38.42  30.0  1
 B43  Var_03    C18   C19  C20  C21  -42.45  30.0  1
 B43  Var_04    C13   C8   O    C7     3.43  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
 B43  chir_01  C17  N2  C21  C18  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
 B43  plan-1  C3    0.020
 B43  plan-1  C4    0.020
 B43  plan-1  C15   0.020
 B43  plan-1  C14   0.020
 B43  plan-1  C7    0.020
 B43  plan-1  C6    0.020
 B43  plan-1  C5    0.020
 B43  plan-1  O     0.020
 B43  plan-1  H15   0.020
 B43  plan-1  H14   0.020
 B43  plan-1  H6    0.020
 B43  plan-1  H5    0.020
 B43  plan-2  O     0.020
 B43  plan-2  C8    0.020
 B43  plan-2  C13   0.020
 B43  plan-2  C12   0.020
 B43  plan-2  C11   0.020
 B43  plan-2  C10   0.020
 B43  plan-2  C9    0.020
 B43  plan-2  H13   0.020
 B43  plan-2  H12   0.020
 B43  plan-2  H11   0.020
 B43  plan-2  H10   0.020
 B43  plan-2  H9    0.020
 B43  plan-3  N1    0.020
 B43  plan-3  C1    0.020
 B43  plan-3  N4    0.020
 B43  plan-3  C23   0.020
 B43  plan-3  N3    0.020
 B43  plan-3  C22   0.020
 B43  plan-3  C2    0.020
 B43  plan-3  N2    0.020
 B43  plan-3  C17   0.020
 B43  plan-3  C16   0.020
 B43  plan-3  C3    0.020
 B43  plan-3  C4    0.020
 B43  plan-3  H23   0.020
 B43  plan-3  H16   0.020
 B43  plan-4  N1    0.020
 B43  plan-4  C1    0.020
 B43  plan-4  HN1   0.020
 B43  plan-4  HN1A  0.020

