# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 19:19:12 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[[2-methoxy-4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]amino]-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(Nc2ccc(cc2OC)N3CCCC3=O)nc4[nH]cc(C#N)c14
#
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
 G5C  G5C  2-[[2-methoxy-4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]amino]-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  47  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G5C
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
 G5C  C10  C  CH3   0  -0.436   0.0944  35.3723   4.7363
 G5C  C12  C  CR6   0   0.373  -0.6839  38.7637   7.0914
 G5C  C14  C  CH2   0  -0.271  -0.1796  41.2206   7.0753
 G5C  C16  C  CH2   0  -0.585  -1.3673  41.7813   5.0789
 G5C  C19  C  CR16  0  -0.338  -0.8207  38.5895   8.4617
 G5C  C20  C  CR16  0  -0.275  -0.6510  37.3334   9.0247
 G5C  C22  C  CR56  0   0.507   1.3842  32.9448  11.1034
 G5C  C24  C  CR5   0  -0.116   2.6394  33.0390  12.9898
 G5C  N26  N  NS    0  -0.258   3.9752  33.8546  15.0200
 G5C  C27  C  CR15  0   0.030   2.4029  31.7257  12.6661
 G5C  N13  N  NT    0  -0.590  -0.8455  40.0433   6.5265
 G5C  C17  C  C     0   0.522  -1.5228  40.3063   5.3747
 G5C  N21  N  N     0  -0.515   0.6694  33.2573  10.0282
 G5C  C23  C  CR56  0  -0.069   1.9882  33.8352  11.9873
 G5C  C25  C  CSP   0  -0.056   3.3758  33.4760  14.1083
 G5C  C01  C  CH3   0  -0.514   2.1195  37.5868  12.1379
 G5C  C03  C  CR6   0   0.501   1.8079  35.2026  11.6751
 G5C  C05  C  CR6   0   0.569   0.5615  34.5701   9.8487
 G5C  C07  C  CR6   0   0.247  -0.3336  36.2311   8.2439
 G5C  C08  C  CR6   0   0.354  -0.2067  36.4098   6.8547
 G5C  C11  C  CR16  0  -0.437  -0.3757  37.6660   6.2886
 G5C  C15  C  CH2   0  -0.480  -0.9113  42.3781   6.4028
 G5C  N04  N  N     0  -0.521   1.0928  35.5328  10.6040
 G5C  N28  N  NR15  0  -0.666   1.6541  31.6809  11.5364
 G5C  O09  O  O2    0  -0.472   0.0859  35.3017   6.1480
 G5C  O18  O  O     0  -0.470  -2.1312  39.4944   4.7045
 G5C  H1   H  HCH3  0   0.262   0.2695  34.3600   4.3800
 G5C  H2   H  HCH3  0   0.231  -0.8617  35.7234   4.3395
 G5C  H3   H  HCH3  0   0.230   0.8922  36.0200   4.3645
 G5C  H4   H  HCH2  0   0.246   0.8825  41.2031   6.8119
 G5C  H5   H  HCH2  0   0.258  -0.2508  41.2523   8.1609
 G5C  H6   H  HCH2  0   0.273  -0.6077  41.8914   4.2980
 G5C  H7   H  HCH2  0   0.275  -2.2914  42.2056   4.6894
 G5C  H8   H  HCR6  0   0.265  -1.0795  39.4208   9.1035
 G5C  H9   H  HCR6  0   0.264  -0.7758  37.2105  10.0900
 G5C  H10  H  HCR5  0   0.316   2.7268  30.8300  13.1697
 G5C  H11  H  HCH3  0   0.251   2.7155  38.1634  12.8389
 G5C  H12  H  HCH3  0   0.239   2.4250  37.8505  11.1249
 G5C  H13  H  HCH3  0   0.237   1.0723  37.8711  12.2586
 G5C  H14  H  HCR6  0   0.287  -0.2505  37.8022   5.2249
 G5C  H15  H  HCH2  0   0.258  -0.2751  43.2531   6.2895
 G5C  H16  H  HCH2  0   0.251  -1.7761  42.6677   7.0005
 G5C  H17  H  HNH1  0   0.410   2.8734  35.9475  13.2251
 G5C  H18  H  HNH1  0   0.395  -0.4281  34.1796   8.1555
 G5C  H19  H  HNR5  0   0.423   1.3360  30.8348  11.0883
 G5C  N06  N  NH1   0  -0.746  -0.1808  34.9436   8.7655
 G5C  N02  N  NH1   0  -0.661   2.3307  36.1864  12.4133

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
 G5C  O18  C17  double    1.216  0.020  1.216
 G5C  C10  O09  single    1.413  0.020  1.413
 G5C  C16  C17  single    1.512  0.020  1.512
 G5C  C16  C15  single    1.522  0.020  1.522
 G5C  C17  N13  single    1.362  0.020  1.362
 G5C  O09  C08  single    1.346  0.020  1.346
 G5C  C15  C14  single    1.526  0.020  1.526
 G5C  C11  C08  aromatic  1.388  0.020  1.388
 G5C  C11  C12  aromatic  1.394  0.020  1.394
 G5C  N13  C12  single    1.408  0.020  1.408
 G5C  N13  C14  single    1.460  0.020  1.460
 G5C  C08  C07  aromatic  1.406  0.020  1.406
 G5C  C12  C19  aromatic  1.388  0.020  1.388
 G5C  C07  N06  single    1.398  0.020  1.398
 G5C  C07  C20  aromatic  1.387  0.020  1.387
 G5C  C19  C20  aromatic  1.387  0.020  1.387
 G5C  N06  C05  single    1.365  0.020  1.365
 G5C  C05  N21  aromatic  1.329  0.020  1.329
 G5C  C05  N04  aromatic  1.334  0.020  1.334
 G5C  N21  C22  aromatic  1.328  0.020  1.328
 G5C  N04  C03  aromatic  1.329  0.020  1.329
 G5C  C22  N28  aromatic  1.363  0.020  1.363
 G5C  C22  C23  aromatic  1.392  0.020  1.392
 G5C  C03  C23  aromatic  1.414  0.020  1.414
 G5C  C03  N02  single    1.336  0.020  1.336
 G5C  N28  C27  aromatic  1.356  0.020  1.356
 G5C  C23  C24  aromatic  1.436  0.020  1.436
 G5C  C01  N02  single    1.443  0.020  1.443
 G5C  C27  C24  aromatic  1.373  0.020  1.373
 G5C  C24  C25  single    1.409  0.020  1.409
 G5C  C25  N26  triple    1.155  0.020  1.155
 G5C  C10  H1   single    0.970  0.020  1.090
 G5C  C10  H2   single    0.970  0.020  1.090
 G5C  C10  H3   single    0.970  0.020  1.090
 G5C  C14  H4   single    0.970  0.020  1.090
 G5C  C14  H5   single    0.970  0.020  1.090
 G5C  C16  H6   single    0.970  0.020  1.090
 G5C  C16  H7   single    0.970  0.020  1.090
 G5C  C19  H8   single    0.930  0.020  1.080
 G5C  C20  H9   single    0.930  0.020  1.080
 G5C  C27  H10  single    0.930  0.020  1.080
 G5C  C01  H11  single    0.970  0.020  1.090
 G5C  C01  H12  single    0.970  0.020  1.090
 G5C  C01  H13  single    0.970  0.020  1.090
 G5C  C11  H14  single    0.930  0.020  1.080
 G5C  C15  H15  single    0.970  0.020  1.090
 G5C  C15  H16  single    0.970  0.020  1.090
 G5C  N02  H17  single    0.860  0.020  1.020
 G5C  N06  H18  single    0.860  0.020  1.020
 G5C  N28  H19  single    0.860  0.020  1.020

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
 G5C  H3   C10  H2   108.95  3.000
 G5C  H3   C10  H1   108.83  3.000
 G5C  H2   C10  H1   108.72  3.000
 G5C  H3   C10  O09  111.95  3.000
 G5C  H2   C10  O09  111.92  3.000
 G5C  H1   C10  O09  106.37  3.000
 G5C  C11  C12  N13  120.65  3.000
 G5C  N13  C12  C19  119.92  3.000
 G5C  C11  C12  C19  119.43  3.000
 G5C  H5   C14  H4   107.70  3.000
 G5C  H5   C14  C15  112.72  3.000
 G5C  H4   C14  C15  111.80  3.000
 G5C  H5   C14  N13  111.63  3.000
 G5C  H4   C14  N13  109.84  3.000
 G5C  C15  C14  N13  103.14  3.000
 G5C  H7   C16  H6   107.12  3.000
 G5C  H7   C16  C15  114.37  3.000
 G5C  H6   C16  C15  111.91  3.000
 G5C  H7   C16  C17  111.27  3.000
 G5C  H6   C16  C17  108.00  3.000
 G5C  C15  C16  C17  104.07  3.000
 G5C  H8   C19  C20  118.98  3.000
 G5C  H8   C19  C12  120.86  3.000
 G5C  C20  C19  C12  120.15  3.000
 G5C  H9   C20  C07  119.42  3.000
 G5C  H9   C20  C19  119.30  3.000
 G5C  C07  C20  C19  121.27  3.000
 G5C  N28  C22  C23  107.78  3.000
 G5C  C23  C22  N21  126.64  3.000
 G5C  N28  C22  N21  125.58  3.000
 G5C  C25  C24  C23  128.27  3.000
 G5C  C25  C24  C27  125.02  3.000
 G5C  C23  C24  C27  106.71  3.000
 G5C  H10  C27  N28  121.87  3.000
 G5C  H10  C27  C24  129.29  3.000
 G5C  N28  C27  C24  108.85  3.000
 G5C  C17  N13  C14  112.90  3.000
 G5C  C14  N13  C12  121.99  3.000
 G5C  C17  N13  C12  124.88  3.000
 G5C  O18  C17  N13  125.88  3.000
 G5C  N13  C17  C16  107.62  3.000
 G5C  O18  C17  C16  126.50  3.000
 G5C  C05  N21  C22  112.66  3.000
 G5C  C03  C23  C24  138.41  3.000
 G5C  C24  C23  C22  106.58  3.000
 G5C  C03  C23  C22  115.01  3.000
 G5C  N26  C25  C24  180.00  3.000
 G5C  H13  C01  H12  107.96  3.000
 G5C  H13  C01  H11  108.47  3.000
 G5C  H12  C01  H11  108.51  3.000
 G5C  H13  C01  N02  111.84  3.000
 G5C  H12  C01  N02  111.79  3.000
 G5C  H11  C01  N02  108.17  3.000
 G5C  N04  C03  N02  118.20  3.000
 G5C  N02  C03  C23  122.68  3.000
 G5C  N04  C03  C23  119.12  3.000
 G5C  N06  C05  N04  117.93  3.000
 G5C  N04  C05  N21  127.15  3.000
 G5C  N06  C05  N21  114.92  3.000
 G5C  N06  C07  C08  118.41  3.000
 G5C  N06  C07  C20  123.15  3.000
 G5C  C08  C07  C20  118.39  3.000
 G5C  O09  C08  C11  123.86  3.000
 G5C  C11  C08  C07  120.45  3.000
 G5C  O09  C08  C07  115.69  3.000
 G5C  H14  C11  C08  120.12  3.000
 G5C  H14  C11  C12  119.57  3.000
 G5C  C08  C11  C12  120.30  3.000
 G5C  H16  C15  H15  107.90  3.000
 G5C  H16  C15  C16  110.08  3.000
 G5C  H15  C15  C16  113.57  3.000
 G5C  H16  C15  C14  109.90  3.000
 G5C  H15  C15  C14  112.07  3.000
 G5C  C16  C15  C14  103.28  3.000
 G5C  C05  N04  C03  119.42  3.000
 G5C  H19  N28  C27  124.88  3.000
 G5C  H19  N28  C22  125.04  3.000
 G5C  C27  N28  C22  110.08  3.000
 G5C  C08  O09  C10  118.98  3.000
 G5C  H18  N06  C07  116.45  3.000
 G5C  H18  N06  C05  113.95  3.000
 G5C  C07  N06  C05  127.42  3.000
 G5C  H17  N02  C03  118.84  3.000
 G5C  H17  N02  C01  117.64  3.000
 G5C  C03  N02  C01  123.49  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
 G5C  CONST_01  C07  C08  C11  C12     0.00   0.0  0
 G5C  CONST_02  C07  C20  C19  C12     0.00   0.0  0
 G5C  CONST_03  C08  C11  C12  C19     0.00   0.0  0
 G5C  CONST_04  C08  C07  C20  C19     0.00   0.0  0
 G5C  CONST_05  C11  C08  C07  C20     0.00   0.0  0
 G5C  CONST_06  C11  C12  C19  C20     0.00   0.0  0
 G5C  CONST_07  N04  C05  N21  C22     0.00   0.0  0
 G5C  CONST_08  C24  C27  N28  C22     0.00   0.0  0
 G5C  CONST_09  N04  C03  C23  C22     0.00   0.0  0
 G5C  CONST_10  C27  C24  C23  C22     0.00   0.0  0
 G5C  CONST_11  N21  C22  C23  C24   180.00   0.0  0
 G5C  CONST_12  N28  C22  C23  C24     0.00   0.0  0
 G5C  CONST_13  N04  C03  C23  C24   180.00   0.0  0
 G5C  CONST_14  N21  C22  N28  C27   180.00   0.0  0
 G5C  CONST_15  C23  C22  N28  C27     0.00   0.0  0
 G5C  CONST_16  C03  C23  C24  C27   180.00   0.0  0
 G5C  CONST_17  C03  N04  C05  N21     0.00   0.0  0
 G5C  CONST_18  C03  C23  C22  N21     0.00   0.0  0
 G5C  CONST_19  C05  N21  C22  C23     0.00   0.0  0
 G5C  CONST_20  C05  N04  C03  C23     0.00   0.0  0
 G5C  CONST_21  N28  C27  C24  C23     0.00   0.0  0
 G5C  CONST_22  N28  C22  C23  C03   180.00   0.0  0
 G5C  CONST_23  N28  C22  N21  C05   180.00   0.0  0
 G5C  CONST_24  N13  C12  C19  C20   180.00   0.0  0
 G5C  CONST_25  C08  C11  C12  N13   180.00   0.0  0
 G5C  CONST_26  C16  C17  N13  C12   180.00   0.0  0
 G5C  CONST_27  C16  C17  N13  C14     0.00   0.0  0
 G5C  CONST_28  O09  C08  C11  C12   180.00   0.0  0
 G5C  CONST_29  N06  C07  C20  C19   180.00   0.0  0
 G5C  CONST_30  O09  C08  C07  C20   180.00   0.0  0
 G5C  CONST_31  N06  C05  N21  C22   180.00   0.0  0
 G5C  CONST_32  N02  C03  C23  C22   180.00   0.0  0
 G5C  CONST_33  C25  C24  C23  C22   180.00   0.0  0
 G5C  CONST_34  N02  C03  C23  C24     0.00   0.0  0
 G5C  CONST_35  C03  C23  C24  C25     0.00   0.0  0
 G5C  CONST_36  N28  C27  C24  C25   180.00   0.0  0
 G5C  CONST_37  N06  C05  N04  C03   180.00   0.0  0
 G5C  CONST_38  N02  C03  N04  C05   180.00   0.0  0
 G5C  CONST_39  N06  C07  C08  C11   180.00   0.0  0
 G5C  CONST_40  O18  C17  N13  C12     0.00   0.0  0
 G5C  CONST_41  O18  C17  N13  C14   180.00   0.0  0
 G5C  CONST_42  H9   C20  C19  C12   180.00   0.0  0
 G5C  CONST_43  H14  C11  C12  C19   180.00   0.0  0
 G5C  CONST_44  H10  C27  N28  C22   180.00   0.0  0
 G5C  CONST_45  H19  N28  C27  C24   180.00   0.0  0
 G5C  CONST_46  H8   C19  C12  N13     0.00   0.0  0
 G5C  CONST_47  C01  N02  C03  C23   180.00   0.0  0
 G5C  CONST_48  N04  C03  N02  C01     0.00   0.0  0
 G5C  CONST_49  H17  N02  C03  C23     0.00   0.0  0
 G5C  Var_01    C15  C14  N13  C12  -165.87  30.0  1
 G5C  Var_02    C17  C16  C15  C14    28.12  30.0  1
 G5C  Var_03    C11  C12  N13  C14  -131.18  30.0  2
 G5C  Var_04    N13  C14  C15  C16   -28.60  30.0  1
 G5C  Var_05    C15  C16  C17  N13   -17.34  30.0  1
 G5C  Var_06    C05  N06  C07  C20   -48.91  30.0  2
 G5C  Var_07    C07  N06  C05  N21  -171.85  30.0  2
 G5C  Var_08    C11  C08  O09  C10    -6.63  30.0  2
 G5C  Var_09    H11  C01  N02  C03  -175.66  30.0  3
 G5C  Var_10    H1   C10  O09  C08  -175.37  30.0  3

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
 G5C  plan-1  C12  0.020
 G5C  plan-1  C19  0.020
 G5C  plan-1  C20  0.020
 G5C  plan-1  N13  0.020
 G5C  plan-1  C07  0.020
 G5C  plan-1  C08  0.020
 G5C  plan-1  C11  0.020
 G5C  plan-1  O09  0.020
 G5C  plan-1  H8   0.020
 G5C  plan-1  H9   0.020
 G5C  plan-1  H14  0.020
 G5C  plan-1  N06  0.020
 G5C  plan-2  C22  0.020
 G5C  plan-2  C24  0.020
 G5C  plan-2  N26  0.020
 G5C  plan-2  C27  0.020
 G5C  plan-2  N21  0.020
 G5C  plan-2  C23  0.020
 G5C  plan-2  C25  0.020
 G5C  plan-2  C03  0.020
 G5C  plan-2  C05  0.020
 G5C  plan-2  N04  0.020
 G5C  plan-2  N28  0.020
 G5C  plan-2  H10  0.020
 G5C  plan-2  H19  0.020
 G5C  plan-2  N06  0.020
 G5C  plan-2  N02  0.020
 G5C  plan-3  C01  0.020
 G5C  plan-3  C03  0.020
 G5C  plan-3  H17  0.020
 G5C  plan-3  N02  0.020
 G5C  plan-4  C12  0.020
 G5C  plan-4  C14  0.020
 G5C  plan-4  C16  0.020
 G5C  plan-4  N13  0.020
 G5C  plan-4  C17  0.020
 G5C  plan-4  O18  0.020

