# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 10:38:49 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: N-{2-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]ethyl}-N~2~-phenylglycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCNC(=O)CNc1ccccc1)c2ncnc3[nH]ccc23
#
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
 0BG  0BG  "N-{2-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]ethyl}-N~2~-phenylglycinamide"  ligand  44  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0BG
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
 0BG  N1   N  N     0  -0.450  18.4295  4.9097  -0.0613
 0BG  N3   N  NT    0  -0.474  21.7701  7.1104   1.0424
 0BG  C4   C  CR56  0  -0.074  19.7326  5.9291   1.7471
 0BG  C5   C  CR6   0   0.489  20.6646  6.3817   0.7775
 0BG  C6   C  CH3   0  -0.522  22.7045  7.4020  -0.0284
 0BG  C10  C  C     0   0.530  22.7081  7.8356   5.4792
 0BG  C13  C  CR16  0  -0.347  22.2869  7.1925   9.7077
 0BG  C15  C  CR16  0  -0.293  23.4803  5.1292  10.0829
 0BG  C17  C  CR16  0  -0.339  23.9925  6.5037   8.1599
 0BG  C1   C  CR56  0   0.465  18.6464  5.2060   1.2225
 0BG  C11  C  CH2   0  -0.456  23.3024  8.7937   6.5136
 0BG  C12  C  CR6   0   0.367  23.0244  7.4407   8.5404
 0BG  C14  C  CR16  0  -0.242  22.5141  6.0556  10.4620
 0BG  C16  C  CR16  0  -0.242  24.2118  5.3685   8.9289
 0BG  C18  C  CH2   0  -0.340  22.0155  7.7677   2.3078
 0BG  C19  C  CR16  0   0.034  19.3811  5.3648  -0.8468
 0BG  C2   C  CR15  0  -0.019  18.4063  5.2656   3.4292
 0BG  C3   C  CR15  0  -0.458  19.5585  5.9452   3.1699
 0BG  C9   C  CH2   0  -0.299  22.9864  6.9796   3.1908
 0BG  N2   N  NR15  0  -0.658  17.8575  4.8274   2.2534
 0BG  N4   N  NH1   0  -0.628  23.4172  7.7348   4.3436
 0BG  N5   N  NH1   0  -0.666  22.8062  8.6050   7.8392
 0BG  N6   N  N     0  -0.494  20.4573  6.0654  -0.5061
 0BG  O1   O  O     0  -0.474  21.6643  7.2372   5.6833
 0BG  H1   H  HCH3  0   0.245  23.6228  7.7887   0.4084
 0BG  H2   H  HCH3  0   0.246  22.9508  6.5070  -0.5955
 0BG  H3   H  HCH3  0   0.237  22.3144  8.1485  -0.7236
 0BG  H5   H  HCR6  0   0.242  23.6552  4.2404  10.6742
 0BG  H6   H  HCR6  0   0.257  24.5841  6.6453   7.2643
 0BG  H7   H  HCH2  0   0.266  24.3948  8.7396   6.4935
 0BG  H8   H  HCH2  0   0.304  23.0542  9.8109   6.2011
 0BG  H9   H  HCR6  0   0.248  21.9267  5.8916  11.3570
 0BG  H10  H  HCR6  0   0.248  24.9667  4.6605   8.6101
 0BG  H11  H  HCH2  0   0.270  22.4421  8.7519   2.1010
 0BG  H12  H  HCH2  0   0.266  21.0780  7.9524   2.8286
 0BG  H13  H  HCR6  0   0.240  19.2789  5.1491  -1.9060
 0BG  H14  H  HCR5  0   0.283  17.9290  5.0550   4.3721
 0BG  H15  H  HCR5  0   0.272  20.1928  6.3792   3.9247
 0BG  H16  H  HCH2  0   0.254  22.5331  6.0417   3.5126
 0BG  H17  H  HCH2  0   0.263  23.8751  6.7217   2.6136
 0BG  H18  H  HNR5  0   0.409  17.0127  4.2859   2.1643
 0BG  H19  H  HNH1  0   0.406  24.2508  8.2928   4.2466
 0BG  H20  H  HNH1  0   0.383  21.9295  9.0606   8.0332
 0BG  H4   H  HCR6  0   0.252  21.5304  7.9045  10.0187

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
 0BG  C19  N6   aromatic  1.329  0.020  1.329
 0BG  C19  N1   aromatic  1.315  0.020  1.315
 0BG  N6   C5   aromatic  1.338  0.020  1.338
 0BG  N1   C1   aromatic  1.335  0.020  1.335
 0BG  C6   N3   single    1.451  0.020  1.451
 0BG  C5   N3   single    1.350  0.020  1.350
 0BG  C5   C4   aromatic  1.419  0.020  1.419
 0BG  N3   C18  single    1.447  0.020  1.447
 0BG  C1   C4   aromatic  1.406  0.020  1.406
 0BG  C1   N2   aromatic  1.352  0.020  1.352
 0BG  C4   C3   aromatic  1.434  0.020  1.434
 0BG  N2   C2   aromatic  1.370  0.020  1.370
 0BG  C18  C9   single    1.531  0.020  1.531
 0BG  C3   C2   aromatic  1.363  0.020  1.363
 0BG  C9   N4   single    1.444  0.020  1.444
 0BG  N4   C10  single    1.343  0.020  1.343
 0BG  C10  O1   double    1.220  0.020  1.220
 0BG  C10  C11  single    1.530  0.020  1.530
 0BG  C11  N5   single    1.428  0.020  1.428
 0BG  N5   C12  single    1.377  0.020  1.377
 0BG  C17  C12  aromatic  1.400  0.020  1.400
 0BG  C17  C16  aromatic  1.389  0.020  1.389
 0BG  C12  C13  aromatic  1.403  0.020  1.403
 0BG  C16  C15  aromatic  1.387  0.020  1.387
 0BG  C13  C14  aromatic  1.383  0.020  1.383
 0BG  C15  C14  aromatic  1.391  0.020  1.391
 0BG  C6   H1   single    0.970  0.020  1.090
 0BG  C6   H2   single    0.970  0.020  1.090
 0BG  C6   H3   single    0.970  0.020  1.090
 0BG  C13  H4   single    0.930  0.020  1.080
 0BG  C15  H5   single    0.930  0.020  1.080
 0BG  C17  H6   single    0.930  0.020  1.080
 0BG  C11  H7   single    0.970  0.020  1.090
 0BG  C11  H8   single    0.970  0.020  1.090
 0BG  C14  H9   single    0.930  0.020  1.080
 0BG  C16  H10  single    0.930  0.020  1.080
 0BG  C18  H11  single    0.970  0.020  1.090
 0BG  C18  H12  single    0.970  0.020  1.090
 0BG  C19  H13  single    0.930  0.020  1.080
 0BG  C2   H14  single    0.930  0.020  1.080
 0BG  C3   H15  single    0.930  0.020  1.080
 0BG  C9   H16  single    0.970  0.020  1.090
 0BG  C9   H17  single    0.970  0.020  1.090
 0BG  N2   H18  single    0.860  0.020  1.020
 0BG  N4   H19  single    0.860  0.020  1.020
 0BG  N5   H20  single    0.890  0.020  1.040

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
 0BG  C19  N1   C1   112.33  3.000
 0BG  C18  N3   C6   116.42  3.000
 0BG  C18  N3   C5   123.75  3.000
 0BG  C6   N3   C5   119.40  3.000
 0BG  C3   C4   C1   106.40  3.000
 0BG  C3   C4   C5   138.97  3.000
 0BG  C1   C4   C5   114.61  3.000
 0BG  N6   C5   C4   118.57  3.000
 0BG  C4   C5   N3   125.16  3.000
 0BG  N6   C5   N3   116.27  3.000
 0BG  H3   C6   H2   108.14  3.000
 0BG  H3   C6   H1   108.31  3.000
 0BG  H2   C6   H1   108.10  3.000
 0BG  H3   C6   N3   112.16  3.000
 0BG  H2   C6   N3   111.42  3.000
 0BG  H1   C6   N3   108.58  3.000
 0BG  O1   C10  N4   123.81  3.000
 0BG  O1   C10  C11  121.75  3.000
 0BG  N4   C10  C11  114.44  3.000
 0BG  H4   C13  C14  119.86  3.000
 0BG  H4   C13  C12  119.29  3.000
 0BG  C14  C13  C12  120.85  3.000
 0BG  H5   C15  C16  120.75  3.000
 0BG  H5   C15  C14  120.70  3.000
 0BG  C16  C15  C14  118.56  3.000
 0BG  H6   C17  C16  118.61  3.000
 0BG  H6   C17  C12  121.01  3.000
 0BG  C16  C17  C12  120.38  3.000
 0BG  N2   C1   C4   108.07  3.000
 0BG  N2   C1   N1   125.18  3.000
 0BG  C4   C1   N1   126.74  3.000
 0BG  H8   C11  H7   105.52  3.000
 0BG  H8   C11  N5   108.03  3.000
 0BG  H7   C11  N5   110.95  3.000
 0BG  H8   C11  C10  107.54  3.000
 0BG  H7   C11  C10  110.15  3.000
 0BG  N5   C11  C10  114.20  3.000
 0BG  N5   C12  C17  122.50  3.000
 0BG  C17  C12  C13  118.12  3.000
 0BG  N5   C12  C13  119.35  3.000
 0BG  H9   C14  C15  120.07  3.000
 0BG  H9   C14  C13  119.08  3.000
 0BG  C15  C14  C13  120.85  3.000
 0BG  H10  C16  C17  118.78  3.000
 0BG  H10  C16  C15  119.98  3.000
 0BG  C17  C16  C15  121.24  3.000
 0BG  H12  C18  H11  105.91  3.000
 0BG  H12  C18  C9   110.96  3.000
 0BG  H11  C18  C9   108.99  3.000
 0BG  H12  C18  N3   110.46  3.000
 0BG  H11  C18  N3   108.06  3.000
 0BG  C9   C18  N3   112.22  3.000
 0BG  H13  C19  N6   115.54  3.000
 0BG  H13  C19  N1   116.48  3.000
 0BG  N6   C19  N1   127.98  3.000
 0BG  H14  C2   N2   120.74  3.000
 0BG  H14  C2   C3   129.68  3.000
 0BG  N2   C2   C3   109.58  3.000
 0BG  H15  C3   C2   124.44  3.000
 0BG  H15  C3   C4   128.94  3.000
 0BG  C2   C3   C4   106.61  3.000
 0BG  H17  C9   H16  106.95  3.000
 0BG  H17  C9   N4   107.64  3.000
 0BG  H16  C9   N4   109.78  3.000
 0BG  H17  C9   C18  109.47  3.000
 0BG  H16  C9   C18  110.46  3.000
 0BG  N4   C9   C18  112.36  3.000
 0BG  H18  N2   C2   125.72  3.000
 0BG  H18  N2   C1   124.92  3.000
 0BG  C2   N2   C1   109.34  3.000
 0BG  H19  N4   C9   117.36  3.000
 0BG  H19  N4   C10  118.47  3.000
 0BG  C9   N4   C10  123.84  3.000
 0BG  H20  N5   C12  115.00  3.000
 0BG  H20  N5   C11  114.94  3.000
 0BG  C12  N5   C11  121.97  3.000
 0BG  C19  N6   C5   119.75  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
 0BG  CONST_01  C5   N6   C19  N1      0.00   0.0  0
 0BG  CONST_02  C5   C4   C1   N1      0.00   0.0  0
 0BG  CONST_03  C3   C4   C1   N1    180.00   0.0  0
 0BG  CONST_04  C2   N2   C1   N1    180.00   0.0  0
 0BG  CONST_05  C19  N6   C5   C4      0.00   0.0  0
 0BG  CONST_06  C19  N1   C1   C4      0.00   0.0  0
 0BG  CONST_07  C2   N2   C1   C4      0.00   0.0  0
 0BG  CONST_08  N2   C2   C3   C4      0.00   0.0  0
 0BG  CONST_09  N2   C1   C4   C5    180.00   0.0  0
 0BG  CONST_10  C2   C3   C4   C5    180.00   0.0  0
 0BG  CONST_11  C16  C17  C12  C13     0.00   0.0  0
 0BG  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 0BG  CONST_13  C12  C17  C16  C15     0.00   0.0  0
 0BG  CONST_14  C12  C13  C14  C15     0.00   0.0  0
 0BG  CONST_15  C14  C13  C12  C17     0.00   0.0  0
 0BG  CONST_16  C14  C15  C16  C17     0.00   0.0  0
 0BG  CONST_17  N6   C19  N1   C1      0.00   0.0  0
 0BG  CONST_18  N6   C5   C4   C1      0.00   0.0  0
 0BG  CONST_19  C2   C3   C4   C1      0.00   0.0  0
 0BG  CONST_20  C3   C2   N2   C1      0.00   0.0  0
 0BG  CONST_21  N2   C1   N1   C19   180.00   0.0  0
 0BG  CONST_22  N6   C5   C4   C3    180.00   0.0  0
 0BG  CONST_23  N2   C1   C4   C3      0.00   0.0  0
 0BG  CONST_24  C19  N6   C5   N3    180.00   0.0  0
 0BG  CONST_25  C1   C4   C5   N3    180.00   0.0  0
 0BG  CONST_26  C3   C4   C5   N3      0.00   0.0  0
 0BG  CONST_27  N5   C12  C13  C14   180.00   0.0  0
 0BG  CONST_28  N5   C12  C17  C16   180.00   0.0  0
 0BG  CONST_29  H18  N2   C1   N1      0.00   0.0  0
 0BG  CONST_30  H18  N2   C1   C4    180.00   0.0  0
 0BG  CONST_31  H14  C2   C3   C4    180.00   0.0  0
 0BG  CONST_32  H13  C19  N6   C5    180.00   0.0  0
 0BG  CONST_33  H15  C3   C4   C5      0.00   0.0  0
 0BG  CONST_34  H6   C17  C12  C13   180.00   0.0  0
 0BG  CONST_35  H5   C15  C14  C13   180.00   0.0  0
 0BG  CONST_36  H6   C17  C16  C15   180.00   0.0  0
 0BG  CONST_37  H4   C13  C14  C15   180.00   0.0  0
 0BG  CONST_38  H4   C13  C12  C17   180.00   0.0  0
 0BG  CONST_39  H5   C15  C16  C17   180.00   0.0  0
 0BG  CONST_40  H13  C19  N1   C1    180.00   0.0  0
 0BG  CONST_41  H15  C3   C4   C1    180.00   0.0  0
 0BG  CONST_42  H14  C2   N2   C1    180.00   0.0  0
 0BG  CONST_43  H10  C16  C17  C12   180.00   0.0  0
 0BG  CONST_44  H9   C14  C13  C12   180.00   0.0  0
 0BG  CONST_45  H10  C16  C15  C14   180.00   0.0  0
 0BG  CONST_46  H9   C14  C15  C16   180.00   0.0  0
 0BG  CONST_47  H18  N2   C2   C3    180.00   0.0  0
 0BG  CONST_48  H15  C3   C2   N2    180.00   0.0  0
 0BG  CONST_49  C6   N3   C5   C4    180.00   0.0  0
 0BG  CONST_50  C18  N3   C5   C4      0.00   0.0  0
 0BG  CONST_51  N6   C5   N3   C6      0.00   0.0  0
 0BG  CONST_52  C11  N5   C12  C13   180.00   0.0  0
 0BG  CONST_54  N6   C5   N3   C18   180.00   0.0  0
 0BG  CONST_57  C9   N4   C10  C11   180.00   0.0  0
 0BG  CONST_58  O1   C10  N4   C9      0.00   0.0  0
 0BG  CONST_59  H19  N4   C10  C11     0.00   0.0  0
 0BG  CONST_60  H19  N4   C10  O1    180.00   0.0  0
 0BG  Var_01    C9   C18  N3   C5    100.82  30.0  3
 0BG  Var_02    C12  N5   C11  C10    63.87  30.0  3
 0BG  Var_03    H1   C6   N3   C5   -167.17  30.0  3
 0BG  Var_04    H2   C6   N3   C5    -48.23  30.0  3
 0BG  Var_05    H3   C6   N3   C5     73.17  30.0  3
 0BG  Var_06    H11  C18  N3   C5   -138.99  30.0  3
 0BG  Var_07    H12  C18  N3   C5    -23.57  30.0  3
 0BG  Var_08    H7   C11  N5   C12   -61.33  30.0  1
 0BG  Var_09    H8   C11  N5   C12  -176.54  30.0  1
 0BG  Var_10    N4   C9   C18  N3    169.79  30.0  3
 0BG  Var_11    C9   C18  N3   C6    -86.72  30.0  3
 0BG  Var_12    C18  C9   N4   C10    82.70  30.0  2
 0BG  Var_13    N5   C11  C10  N4   -161.88  30.0  3
 0BG  Var_14    O1   C10  C11  N5     19.09  30.0  2
 0BG  Var_15    H16  C9   C18  N3    -67.25  30.0  3
 0BG  Var_16    H17  C9   C18  N3     50.26  30.0  3
 0BG  Var_17    H11  C18  N3   C6     33.47  30.0  3
 0BG  Var_18    H12  C18  N3   C6    148.90  30.0  3
 0BG  Var_19    H16  C9   N4   C10   -40.63  30.0  2
 0BG  Var_20    H17  C9   N4   C10  -156.71  30.0  2
 0BG  Var_21    H20  N5   C11  C10   -83.23  30.0  3
 0BG  Var_22    H1   C6   N3   C18    20.02  30.0  3
 0BG  Var_23    H2   C6   N3   C18   138.96  30.0  3
 0BG  Var_24    H3   C6   N3   C18   -99.64  30.0  3
 0BG  Var_25    H19  N4   C9   C18   -90.64  30.0  3
 0BG  Var_26    H11  C18  C9   N4     50.15  30.0  2
 0BG  Var_27    H12  C18  C9   N4    -66.10  30.0  2
 0BG  Var_28    H7   C11  C10  N4    -36.26  30.0  3
 0BG  Var_29    H8   C11  C10  N4     78.26  30.0  3
 0BG  Var_30    H7   C11  C10  O1    144.71  30.0  3
 0BG  Var_31    H8   C11  C10  O1   -100.77  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
 0BG  plan-1  C13  0.020
 0BG  plan-1  C15  0.020
 0BG  plan-1  C17  0.020
 0BG  plan-1  C12  0.020
 0BG  plan-1  C14  0.020
 0BG  plan-1  C16  0.020
 0BG  plan-1  N5   0.020
 0BG  plan-1  H5   0.020
 0BG  plan-1  H6   0.020
 0BG  plan-1  H9   0.020
 0BG  plan-1  H10  0.020
 0BG  plan-1  H4   0.020
 0BG  plan-2  N1   0.020
 0BG  plan-2  N3   0.020
 0BG  plan-2  C4   0.020
 0BG  plan-2  C5   0.020
 0BG  plan-2  C1   0.020
 0BG  plan-2  C19  0.020
 0BG  plan-2  C2   0.020
 0BG  plan-2  C3   0.020
 0BG  plan-2  N2   0.020
 0BG  plan-2  N6   0.020
 0BG  plan-2  H13  0.020
 0BG  plan-2  H14  0.020
 0BG  plan-2  H15  0.020
 0BG  plan-2  H18  0.020
 0BG  plan-3  C10  0.020
 0BG  plan-3  C11  0.020
 0BG  plan-3  C9   0.020
 0BG  plan-3  N4   0.020
 0BG  plan-3  O1   0.020
 0BG  plan-3  H19  0.020
 0BG  plan-4  N3   0.020
 0BG  plan-4  C5   0.020
 0BG  plan-4  C6   0.020
 0BG  plan-4  C18  0.020
 0BG  plan-5  C11  0.020
 0BG  plan-5  C12  0.020
 0BG  plan-5  N5   0.020
 0BG  plan-5  H20  0.020

