# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:03:25 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-{4-[(2R)-2-(5-methyl-1,2,4-oxadiazol-3-yl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(n1)[C@H]2CN(CCO2)c3ncnc4[nH]cc(c5cccc(c5)C#N)c34
#
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
 3JB  3JB  3-{4-[(2R)-2-(5-methyl-1,2,4-oxadiazol-3-yl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile  ligand  46  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3JB
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
 3JB  N3   N  NR15  0  -0.660   3.9493   0.6363  -1.8377
 3JB  C4   C  CH2   0  -0.318  -0.0830   2.6897   2.0063
 3JB  N2   N  NT    0  -0.508   0.4416   1.8024   0.9849
 3JB  C7   C  CR16  0  -0.280   1.4544  -1.4107   1.3608
 3JB  C6   C  CR15  0  -0.035   3.2509  -0.5113  -1.5822
 3JB  C9   C  CR16  0  -0.254  -0.1659  -3.1847   1.2847
 3JB  C8   C  CR16  0  -0.238   0.6829  -2.3632   2.0089
 3JB  N5   N  N     0  -0.449  -2.5579  -0.7281  -0.8796
 3JB  C16  C  CR5   0   0.288  -2.7398  -0.0544   0.2898
 3JB  C02  C  CR6   0   0.442   1.6353   2.0943   0.3788
 3JB  N    N  N     0  -0.469   2.1488   3.3108   0.5240
 3JB  C04  C  CR16  0   0.037   3.2518   3.6324  -0.1527
 3JB  N1   N  N     0  -0.439   3.9142   2.8861  -1.0124
 3JB  C2   C  CH2   0  -0.327  -0.6230   1.2399   0.1681
 3JB  C03  C  CH1   0  -0.002  -1.5948   0.4931   1.0725
 3JB  O    O  O2    0  -0.489  -2.1004   1.3335   2.0752
 3JB  C05  C  CH2   0  -0.195  -1.0628   1.8982   2.8544
 3JB  C1   C  CR56  0   0.493   3.4353   1.6463  -1.0983
 3JB  C3   C  CR56  0  -0.072   2.3351   1.1418  -0.3867
 3JB  C5   C  CR5   0  -0.047   2.2524  -0.2600  -0.6823
 3JB  C01  C  CR6   0   0.007   1.4114  -1.2711  -0.0288
 3JB  C10  C  CR6   0   0.040  -0.2223  -3.0404  -0.0996
 3JB  C06  C  CR16  0  -0.277   0.5648  -2.0967  -0.7572
 3JB  C11  C  CSP   0   0.059  -1.1285  -3.8419  -0.8567
 3JB  N02  N  NS    0  -0.260  -1.8645  -4.4865  -1.4656
 3JB  N4   N  N     0  -0.153  -3.9773   0.0384   0.6605
 3JB  O1   O  O     0  -0.326  -4.6568  -0.6221  -0.3303
 3JB  C14  C  CR5   0   0.515  -3.7642  -1.0519  -1.2117
 3JB  C    C  CH3   0  -0.766  -4.2202  -1.8170  -2.3907
 3JB  H1   H  HNR5  0   0.419   4.7612   0.7026  -2.4309
 3JB  H2   H  HCH2  0   0.265   0.7275   3.0487   2.6383
 3JB  H3   H  HCH2  0   0.232  -0.5786   3.5649   1.5670
 3JB  H4   H  HCR6  0   0.264   2.1089  -0.7713   1.9387
 3JB  H5   H  HCR5  0   0.299   3.5441  -1.4467  -2.0306
 3JB  H6   H  HCR6  0   0.282  -0.7816  -3.9207   1.7836
 3JB  H7   H  HCR6  0   0.276   0.7371  -2.4610   3.0846
 3JB  H8   H  HCR6  0   0.252   3.6269   4.6373   0.0077
 3JB  H9   H  HCH2  0   0.259  -1.1535   2.0443  -0.3614
 3JB  H10  H  HCH2  0   0.289  -0.2229   0.5666  -0.5833
 3JB  H11  H  HCH1  0   0.259  -1.0563  -0.3594   1.5146
 3JB  H12  H  HCH2  0   0.214  -0.5218   1.1109   3.3965
 3JB  H13  H  HCH2  0   0.253  -1.5370   2.5513   3.5867
 3JB  H14  H  HCR6  0   0.275   0.4927  -1.9881  -1.8311
 3JB  H15  H  HCH3  0   0.278  -5.2896  -1.7065  -2.5501
 3JB  H16  H  HCH3  0   0.281  -3.6888  -1.4776  -3.2774
 3JB  H17  H  HCH3  0   0.285  -3.9943  -2.8750  -2.2551

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
 3JB  C04  N1   aromatic  1.317  0.020  1.317
 3JB  C04  N    aromatic  1.333  0.020  1.333
 3JB  N1   C1   aromatic  1.332  0.020  1.332
 3JB  N    C02  aromatic  1.328  0.020  1.328
 3JB  C1   N3   aromatic  1.353  0.020  1.353
 3JB  C1   C3   aromatic  1.404  0.020  1.404
 3JB  O1   N4   aromatic  1.371  0.020  1.371
 3JB  O1   C14  aromatic  1.326  0.020  1.326
 3JB  N4   C16  aromatic  1.295  0.020  1.295
 3JB  N3   C6   aromatic  1.367  0.020  1.367
 3JB  C02  C3   aromatic  1.408  0.020  1.408
 3JB  C02  N2   single    1.370  0.020  1.370
 3JB  C2   C03  single    1.523  0.020  1.523
 3JB  C2   N2   single    1.455  0.020  1.455
 3JB  C3   C5   aromatic  1.435  0.020  1.435
 3JB  C14  C    single    1.478  0.020  1.478
 3JB  C14  N5   aromatic  1.292  0.020  1.292
 3JB  C16  C03  single    1.491  0.020  1.491
 3JB  C16  N5   aromatic  1.362  0.020  1.362
 3JB  C6   C5   aromatic  1.367  0.020  1.367
 3JB  C03  O    single    1.403  0.020  1.403
 3JB  N2   C4   single    1.451  0.020  1.451
 3JB  C5   C01  single    1.469  0.020  1.469
 3JB  C7   C8   aromatic  1.387  0.020  1.387
 3JB  C7   C01  aromatic  1.397  0.020  1.397
 3JB  C8   C9   aromatic  1.386  0.020  1.386
 3JB  C01  C06  aromatic  1.389  0.020  1.389
 3JB  O    C05  single    1.415  0.020  1.415
 3JB  C4   C05  single    1.518  0.020  1.518
 3JB  C9   C10  aromatic  1.393  0.020  1.393
 3JB  C06  C10  aromatic  1.394  0.020  1.394
 3JB  C10  C11  single    1.427  0.020  1.427
 3JB  C11  N02  triple    1.152  0.020  1.152
 3JB  N3   H1   single    0.860  0.020  1.020
 3JB  C4   H2   single    0.970  0.020  1.090
 3JB  C4   H3   single    0.970  0.020  1.090
 3JB  C7   H4   single    0.930  0.020  1.080
 3JB  C6   H5   single    0.930  0.020  1.080
 3JB  C9   H6   single    0.930  0.020  1.080
 3JB  C8   H7   single    0.930  0.020  1.080
 3JB  C04  H8   single    0.930  0.020  1.080
 3JB  C2   H9   single    0.970  0.020  1.090
 3JB  C2   H10  single    0.970  0.020  1.090
 3JB  C03  H11  single    0.970  0.020  1.090
 3JB  C05  H12  single    0.970  0.020  1.090
 3JB  C05  H13  single    0.970  0.020  1.090
 3JB  C06  H14  single    0.930  0.020  1.080
 3JB  C    H15  single    0.970  0.020  1.090
 3JB  C    H16  single    0.970  0.020  1.090
 3JB  C    H17  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
 3JB  H1   N3   C1   125.35  3.000
 3JB  H1   N3   C6   125.22  3.000
 3JB  C1   N3   C6   109.29  3.000
 3JB  H3   C4   H2   107.78  3.000
 3JB  H3   C4   C05  110.36  3.000
 3JB  H2   C4   C05  109.15  3.000
 3JB  H3   C4   N2   111.66  3.000
 3JB  H2   C4   N2   109.95  3.000
 3JB  C05  C4   N2   107.92  3.000
 3JB  C2   N2   C02  118.13  3.000
 3JB  C2   N2   C4   111.53  3.000
 3JB  C02  N2   C4   119.74  3.000
 3JB  H4   C7   C01  119.39  3.000
 3JB  H4   C7   C8   119.52  3.000
 3JB  C01  C7   C8   121.09  3.000
 3JB  H5   C6   C5   129.18  3.000
 3JB  H5   C6   N3   120.77  3.000
 3JB  C5   C6   N3   109.98  3.000
 3JB  H6   C9   C10  120.39  3.000
 3JB  H6   C9   C8   120.74  3.000
 3JB  C10  C9   C8   118.87  3.000
 3JB  H7   C8   C9   119.79  3.000
 3JB  H7   C8   C7   119.95  3.000
 3JB  C9   C8   C7   120.25  3.000
 3JB  C14  N5   C16  102.70  3.000
 3JB  N4   C16  C03  123.86  3.000
 3JB  C03  C16  N5   121.99  3.000
 3JB  N4   C16  N5   114.13  3.000
 3JB  C3   C02  N    119.12  3.000
 3JB  C3   C02  N2   121.96  3.000
 3JB  N    C02  N2   118.92  3.000
 3JB  C04  N    C02  119.02  3.000
 3JB  H8   C04  N1   116.59  3.000
 3JB  H8   C04  N    115.75  3.000
 3JB  N1   C04  N    127.64  3.000
 3JB  C1   N1   C04  112.87  3.000
 3JB  H10  C2   H9   107.35  3.000
 3JB  H10  C2   C03  110.00  3.000
 3JB  H9   C2   C03  109.68  3.000
 3JB  H10  C2   N2   111.02  3.000
 3JB  H9   C2   N2   109.92  3.000
 3JB  C03  C2   N2   108.85  3.000
 3JB  H11  C03  O    110.69  3.000
 3JB  H11  C03  C2   107.82  3.000
 3JB  O    C03  C2   111.14  3.000
 3JB  H11  C03  C16  107.58  3.000
 3JB  O    C03  C16  108.57  3.000
 3JB  C2   C03  C16  110.99  3.000
 3JB  C05  O    C03  111.61  3.000
 3JB  H13  C05  H12  108.19  3.000
 3JB  H13  C05  O    106.86  3.000
 3JB  H12  C05  O    110.29  3.000
 3JB  H13  C05  C4   110.11  3.000
 3JB  H12  C05  C4   109.36  3.000
 3JB  O    C05  C4   111.93  3.000
 3JB  C3   C1   N1   125.70  3.000
 3JB  C3   C1   N3   107.84  3.000
 3JB  N1   C1   N3   126.41  3.000
 3JB  C5   C3   C1   106.96  3.000
 3JB  C5   C3   C02  138.08  3.000
 3JB  C1   C3   C02  114.95  3.000
 3JB  C01  C5   C3   127.87  3.000
 3JB  C01  C5   C6   125.76  3.000
 3JB  C3   C5   C6   105.84  3.000
 3JB  C06  C01  C5   121.67  3.000
 3JB  C06  C01  C7   118.75  3.000
 3JB  C5   C01  C7   119.58  3.000
 3JB  C11  C10  C06  119.25  3.000
 3JB  C11  C10  C9   119.65  3.000
 3JB  C06  C10  C9   121.07  3.000
 3JB  H14  C06  C10  119.92  3.000
 3JB  H14  C06  C01  120.10  3.000
 3JB  C10  C06  C01  119.96  3.000
 3JB  N02  C11  C10  180.00  3.000
 3JB  O1   N4   C16  103.43  3.000
 3JB  C14  O1   N4   107.63  3.000
 3JB  C    C14  O1   119.38  3.000
 3JB  C    C14  N5   128.52  3.000
 3JB  O1   C14  N5   112.10  3.000
 3JB  H17  C    H16  107.63  3.000
 3JB  H17  C    H15  108.71  3.000
 3JB  H16  C    H15  109.23  3.000
 3JB  H17  C    C14  109.83  3.000
 3JB  H16  C    C14  109.76  3.000
 3JB  H15  C    C14  111.59  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
 3JB  CONST_01  C04  N1   C1   N3    180.00   0.0  0
 3JB  CONST_02  C02  C3   C1   N3    180.00   0.0  0
 3JB  CONST_03  C5   C3   C1   N3      0.00   0.0  0
 3JB  CONST_04  C3   C5   C6   N3      0.00   0.0  0
 3JB  CONST_05  C01  C5   C6   N3    180.00   0.0  0
 3JB  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 3JB  CONST_09  C10  C06  C01  C7      0.00   0.0  0
 3JB  CONST_10  N1   C1   N3   C6    180.00   0.0  0
 3JB  CONST_11  C3   C1   N3   C6      0.00   0.0  0
 3JB  CONST_12  C1   C3   C5   C6      0.00   0.0  0
 3JB  CONST_13  C02  C3   C5   C6    180.00   0.0  0
 3JB  CONST_15  C01  C7   C8   C9      0.00   0.0  0
 3JB  CONST_16  C01  C06  C10  C9      0.00   0.0  0
 3JB  CONST_17  C5   C01  C7   C8    180.00   0.0  0
 3JB  CONST_18  C06  C01  C7   C8      0.00   0.0  0
 3JB  CONST_19  C06  C10  C9   C8      0.00   0.0  0
 3JB  CONST_20  N4   O1   C14  N5      0.00   0.0  0
 3JB  CONST_21  O1   N4   C16  N5      0.00   0.0  0
 3JB  CONST_22  C14  O1   N4   C16     0.00   0.0  0
 3JB  CONST_23  O1   C14  N5   C16     0.00   0.0  0
 3JB  CONST_24  N1   C04  N    C02     0.00   0.0  0
 3JB  CONST_25  N1   C1   C3   C02     0.00   0.0  0
 3JB  CONST_26  C01  C5   C3   C02     0.00   0.0  0
 3JB  CONST_27  C1   N1   C04  N       0.00   0.0  0
 3JB  CONST_28  C1   C3   C02  N       0.00   0.0  0
 3JB  CONST_29  C5   C3   C02  N     180.00   0.0  0
 3JB  CONST_30  C3   C1   N1   C04     0.00   0.0  0
 3JB  CONST_31  C3   C02  N    C04     0.00   0.0  0
 3JB  CONST_32  C5   C3   C1   N1    180.00   0.0  0
 3JB  CONST_33  C5   C6   N3   C1      0.00   0.0  0
 3JB  CONST_34  C01  C5   C3   C1    180.00   0.0  0
 3JB  CONST_36  C10  C06  C01  C5    180.00   0.0  0
 3JB  CONST_37  C14  N5   C16  N4      0.00   0.0  0
 3JB  CONST_38  C04  N    C02  N2    180.00   0.0  0
 3JB  CONST_39  C1   C3   C02  N2    180.00   0.0  0
 3JB  CONST_40  C5   C3   C02  N2      0.00   0.0  0
 3JB  CONST_41  O1   N4   C16  C03   180.00   0.0  0
 3JB  CONST_42  C14  N5   C16  C03   180.00   0.0  0
 3JB  CONST_43  C11  C10  C9   C8    180.00   0.0  0
 3JB  CONST_44  C    C14  N5   C16   180.00   0.0  0
 3JB  CONST_45  C11  C10  C06  C01   180.00   0.0  0
 3JB  CONST_46  C    C14  O1   N4    180.00   0.0  0
 3JB  CONST_47  H6   C9   C8   C7    180.00   0.0  0
 3JB  CONST_48  H14  C06  C01  C7    180.00   0.0  0
 3JB  CONST_49  H4   C7   C8   C9    180.00   0.0  0
 3JB  CONST_50  H8   C04  N    C02   180.00   0.0  0
 3JB  CONST_51  H1   N3   C1   N1      0.00   0.0  0
 3JB  CONST_52  H5   C6   N3   C1    180.00   0.0  0
 3JB  CONST_53  H7   C8   C7   C01   180.00   0.0  0
 3JB  Var_01    N    C02  N2   C4    -14.16  30.0  2
 3JB  Var_02    C03  C2   N2   C4    -57.94  30.0  1
 3JB  Var_03    O    C05  C4   N2    -56.95  30.0  1
 3JB  Var_04    C05  C4   N2   C02  -158.29  30.0  1
 3JB  Var_05    H15  C    C14  N5   -164.61  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
 3JB  chir_01  C03  C2  C16  O  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
 3JB  plan-1  N5   0.020
 3JB  plan-1  C16  0.020
 3JB  plan-1  C03  0.020
 3JB  plan-1  N4   0.020
 3JB  plan-1  O1   0.020
 3JB  plan-1  C14  0.020
 3JB  plan-1  C    0.020
 3JB  plan-2  C7   0.020
 3JB  plan-2  C9   0.020
 3JB  plan-2  C8   0.020
 3JB  plan-2  C5   0.020
 3JB  plan-2  C01  0.020
 3JB  plan-2  C10  0.020
 3JB  plan-2  C06  0.020
 3JB  plan-2  C11  0.020
 3JB  plan-2  N02  0.020
 3JB  plan-2  H4   0.020
 3JB  plan-2  H6   0.020
 3JB  plan-2  H7   0.020
 3JB  plan-2  H14  0.020
 3JB  plan-3  N3   0.020
 3JB  plan-3  N2   0.020
 3JB  plan-3  C6   0.020
 3JB  plan-3  C02  0.020
 3JB  plan-3  N    0.020
 3JB  plan-3  C04  0.020
 3JB  plan-3  N1   0.020
 3JB  plan-3  C1   0.020
 3JB  plan-3  C3   0.020
 3JB  plan-3  C5   0.020
 3JB  plan-3  C01  0.020
 3JB  plan-3  H1   0.020
 3JB  plan-3  H5   0.020
 3JB  plan-3  H8   0.020

