# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:52:47 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-azanyl-7-methyl-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCCN1c2n(C)c3ncnc(N)c3c2C#N
#
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
 TWH  TWH  4-azanyl-7-methyl-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  35  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TWH
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
 TWH  C1   C  CH3   0  -0.664  5.4250  -4.7445  14.0427
 TWH  N1   N  NR5   0  -0.537  4.6436  -5.9734  16.0525
 TWH  C2   C  CR15  0  -0.079  5.6210  -5.9400  14.9557
 TWH  N2   N  NS    0  -0.282  8.0467  -3.9368  16.7324
 TWH  C3   C  CH2   0  -0.456  5.3845  -7.2810  14.2695
 TWH  N3   N  NH2   0  -0.837  6.5896  -1.6677  19.2426
 TWH  C4   C  CH2   0  -0.472  5.0286  -8.2044  15.4240
 TWH  N4   N  N     0  -0.464  4.4955  -1.7714  20.1780
 TWH  C5   C  CH2   0  -0.287  4.1260  -7.3309  16.2853
 TWH  N5   N  N     0  -0.459  2.8135  -3.3093  19.5009
 TWH  C6   C  CR5   0   0.659  4.6116  -5.0208  17.0075
 TWH  N6   N  NR5   0  -0.572  3.4771  -4.7982  17.7472
 TWH  C7   C  CR5   0  -0.170  5.5905  -4.1119  17.4223
 TWH  C8   C  CSP   0  -0.049  6.9293  -4.0442  17.0171
 TWH  C9   C  CR56  0  -0.036  4.9993  -3.3131  18.4608
 TWH  C10  C  CR6   0   0.424  5.3813  -2.2506  19.2968
 TWH  C11  C  CR16  0   0.039  3.2851  -2.3108  20.2273
 TWH  C12  C  CR56  0   0.498  3.7042  -3.7791  18.6353
 TWH  C13  C  CH3   0  -0.550  2.1679  -5.3647  17.4994
 TWH  H1   H  HCH3  0   0.238  5.5766  -3.7953  14.5568
 TWH  H2   H  HCH3  0   0.238  6.1391  -4.7870  13.2196
 TWH  H3   H  HCH3  0   0.229  4.4188  -4.7475  13.6216
 TWH  H4   H  HCR5  0   0.248  6.6417  -5.9367  15.3537
 TWH  H5   H  HCH2  0   0.235  4.5470  -7.2003  13.5709
 TWH  H6   H  HCH2  0   0.255  6.2608  -7.6032  13.7084
 TWH  H7   H  HNH2  0   0.398  6.8317  -0.9899  19.9453
 TWH  H8   H  HNH2  0   0.409  7.3443  -2.0653  18.7116
 TWH  H9   H  HCH2  0   0.255  4.5276  -9.1194  15.1104
 TWH  H10  H  HCH2  0   0.240  5.9276  -8.4852  15.9766
 TWH  H11  H  HCH2  0   0.241  3.0880  -7.4227  15.9596
 TWH  H12  H  HCH2  0   0.255  4.1729  -7.5939  17.3433
 TWH  H13  H  HCR6  0   0.247  2.6042  -1.8793  20.9533
 TWH  H14  H  HCH3  0   0.279  1.4260  -4.7194  17.9605
 TWH  H15  H  HCH3  0   0.265  1.9781  -5.4056  16.4291
 TWH  H16  H  HCH3  0   0.261  2.0689  -6.3624  17.9225

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
 TWH  C1   C2   single    1.517  0.020  1.517
 TWH  C3   C2   single    1.525  0.020  1.525
 TWH  C3   C4   single    1.521  0.020  1.521
 TWH  C2   N1   single    1.470  0.020  1.470
 TWH  C4   C5   single    1.523  0.020  1.523
 TWH  N1   C5   single    1.471  0.020  1.471
 TWH  N1   C6   single    1.349  0.020  1.349
 TWH  N2   C8   triple    1.158  0.020  1.158
 TWH  C8   C7   single    1.400  0.020  1.400
 TWH  C6   C7   aromatic  1.399  0.020  1.399
 TWH  C6   N6   aromatic  1.372  0.020  1.372
 TWH  C7   C9   aromatic  1.437  0.020  1.437
 TWH  C13  N6   single    1.448  0.020  1.448
 TWH  N6   C12  aromatic  1.371  0.020  1.371
 TWH  C9   C12  aromatic  1.387  0.020  1.387
 TWH  C9   C10  aromatic  1.405  0.020  1.405
 TWH  C12  N5   aromatic  1.328  0.020  1.328
 TWH  N3   C10  single    1.343  0.020  1.343
 TWH  C10  N4   aromatic  1.338  0.020  1.338
 TWH  N5   C11  aromatic  1.322  0.020  1.322
 TWH  N4   C11  aromatic  1.326  0.020  1.326
 TWH  C1   H1   single    0.970  0.020  1.090
 TWH  C1   H2   single    0.970  0.020  1.090
 TWH  C1   H3   single    0.970  0.020  1.090
 TWH  C2   H4   single    0.970  0.020  1.090
 TWH  C3   H5   single    0.970  0.020  1.090
 TWH  C3   H6   single    0.970  0.020  1.090
 TWH  N3   H7   single    0.860  0.020  1.020
 TWH  N3   H8   single    0.860  0.020  1.020
 TWH  C4   H9   single    0.970  0.020  1.090
 TWH  C4   H10  single    0.970  0.020  1.090
 TWH  C5   H11  single    0.970  0.020  1.090
 TWH  C5   H12  single    0.970  0.020  1.090
 TWH  C11  H13  single    0.930  0.020  1.080
 TWH  C13  H14  single    0.970  0.020  1.090
 TWH  C13  H15  single    0.970  0.020  1.090
 TWH  C13  H16  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
 TWH  H3   C1   H2   108.21  3.000
 TWH  H3   C1   H1   108.22  3.000
 TWH  H2   C1   H1   107.39  3.000
 TWH  H3   C1   C2   110.45  3.000
 TWH  H2   C1   C2   109.81  3.000
 TWH  H1   C1   C2   112.61  3.000
 TWH  C6   N1   C5   122.08  3.000
 TWH  C6   N1   C2   121.87  3.000
 TWH  C5   N1   C2   111.90  3.000
 TWH  H4   C2   C3   108.10  3.000
 TWH  H4   C2   N1   110.40  3.000
 TWH  C3   C2   N1   102.28  3.000
 TWH  H4   C2   C1   109.67  3.000
 TWH  N1   C2   C1   112.40  3.000
 TWH  C3   C2   C1   113.72  3.000
 TWH  H6   C3   H5   107.99  3.000
 TWH  H6   C3   C4   113.57  3.000
 TWH  H5   C3   C4   110.52  3.000
 TWH  H6   C3   C2   111.54  3.000
 TWH  H5   C3   C2   109.96  3.000
 TWH  C4   C3   C2   103.22  3.000
 TWH  H8   N3   H7   117.07  3.000
 TWH  H8   N3   C10  121.70  3.000
 TWH  H7   N3   C10  118.74  3.000
 TWH  H10  C4   H9   107.96  3.000
 TWH  H10  C4   C5   110.44  3.000
 TWH  H9   C4   C5   111.84  3.000
 TWH  H10  C4   C3   110.35  3.000
 TWH  H9   C4   C3   113.53  3.000
 TWH  C5   C4   C3   102.70  3.000
 TWH  C11  N4   C10  118.88  3.000
 TWH  H12  C5   H11  108.05  3.000
 TWH  H12  C5   C4   112.62  3.000
 TWH  H11  C5   C4   110.28  3.000
 TWH  H12  C5   N1   111.14  3.000
 TWH  H11  C5   N1   111.39  3.000
 TWH  C4   C5   N1   103.37  3.000
 TWH  C12  N5   C11  112.72  3.000
 TWH  C7   C6   N6   108.25  3.000
 TWH  N6   C6   N1   121.04  3.000
 TWH  C7   C6   N1   130.70  3.000
 TWH  C13  N6   C12  123.47  3.000
 TWH  C12  N6   C6   109.44  3.000
 TWH  C13  N6   C6   126.28  3.000
 TWH  C9   C7   C8   125.12  3.000
 TWH  C9   C7   C6   106.71  3.000
 TWH  C8   C7   C6   127.93  3.000
 TWH  C7   C8   N2   180.00  3.000
 TWH  C12  C9   C10  115.66  3.000
 TWH  C10  C9   C7   137.59  3.000
 TWH  C12  C9   C7   106.75  3.000
 TWH  C9   C10  N4   118.86  3.000
 TWH  N4   C10  N3   117.83  3.000
 TWH  C9   C10  N3   123.30  3.000
 TWH  H13  C11  N5   116.38  3.000
 TWH  H13  C11  N4   115.84  3.000
 TWH  N5   C11  N4   127.78  3.000
 TWH  C9   C12  N6   108.84  3.000
 TWH  C9   C12  N5   126.10  3.000
 TWH  N6   C12  N5   125.05  3.000
 TWH  H16  C13  H15  109.40  3.000
 TWH  H16  C13  H14  108.51  3.000
 TWH  H15  C13  H14  108.71  3.000
 TWH  H16  C13  N6   111.99  3.000
 TWH  H15  C13  N6   109.93  3.000
 TWH  H14  C13  N6   108.21  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
 TWH  CONST_01  C7   C9   C10  N4    180.00   0.0  0
 TWH  CONST_02  C12  C9   C10  N4      0.00   0.0  0
 TWH  CONST_03  C12  N5   C11  N4      0.00   0.0  0
 TWH  CONST_04  C6   N6   C12  N5    180.00   0.0  0
 TWH  CONST_05  C7   C9   C12  N5    180.00   0.0  0
 TWH  CONST_06  C10  C9   C12  N5      0.00   0.0  0
 TWH  CONST_07  C10  N4   C11  N5      0.00   0.0  0
 TWH  CONST_08  C12  C9   C7   C6      0.00   0.0  0
 TWH  CONST_09  C10  C9   C7   C6    180.00   0.0  0
 TWH  CONST_10  C9   C12  N6   C6      0.00   0.0  0
 TWH  CONST_11  C9   C7   C6   N6      0.00   0.0  0
 TWH  CONST_12  C7   C9   C12  N6      0.00   0.0  0
 TWH  CONST_13  C10  C9   C12  N6    180.00   0.0  0
 TWH  CONST_14  C11  N5   C12  N6    180.00   0.0  0
 TWH  CONST_15  C12  N6   C6   C7      0.00   0.0  0
 TWH  CONST_16  C11  N5   C12  C9      0.00   0.0  0
 TWH  CONST_17  C11  N4   C10  C9      0.00   0.0  0
 TWH  CONST_18  C9   C7   C6   N1    180.00   0.0  0
 TWH  CONST_19  C12  N6   C6   N1    180.00   0.0  0
 TWH  CONST_20  C8   C7   C6   N1      0.00   0.0  0
 TWH  CONST_21  C13  N6   C6   N1      0.00   0.0  0
 TWH  CONST_22  C7   C9   C10  N3      0.00   0.0  0
 TWH  CONST_23  C12  C9   C10  N3    180.00   0.0  0
 TWH  CONST_24  C11  N4   C10  N3    180.00   0.0  0
 TWH  CONST_25  C13  N6   C12  N5      0.00   0.0  0
 TWH  CONST_26  C8   C7   C6   N6    180.00   0.0  0
 TWH  CONST_27  C13  N6   C6   C7    180.00   0.0  0
 TWH  CONST_28  C12  C9   C7   C8    180.00   0.0  0
 TWH  CONST_29  C10  C9   C7   C8      0.00   0.0  0
 TWH  CONST_30  C13  N6   C12  C9    180.00   0.0  0
 TWH  CONST_31  H13  C11  N4   C10   180.00   0.0  0
 TWH  CONST_32  H7   N3   C10  N4      0.00   0.0  0
 TWH  CONST_33  H8   N3   C10  N4    180.00   0.0  0
 TWH  Var_01    C3   C4   C5   N1    -31.00  30.0  1
 TWH  Var_02    C5   C4   C3   C2     40.96  30.0  1
 TWH  Var_03    C4   C5   N1   C2      9.80  30.0  1
 TWH  Var_04    C7   C6   N1   C2    -20.46  30.0  2
 TWH  Var_05    H14  C13  N6   C6   -157.01  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
 TWH  chir_01  C2  C1  C3  N1  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
 TWH  plan-1  N1   0.020
 TWH  plan-1  N2   0.020
 TWH  plan-1  N3   0.020
 TWH  plan-1  N4   0.020
 TWH  plan-1  N5   0.020
 TWH  plan-1  C6   0.020
 TWH  plan-1  N6   0.020
 TWH  plan-1  C7   0.020
 TWH  plan-1  C8   0.020
 TWH  plan-1  C9   0.020
 TWH  plan-1  C10  0.020
 TWH  plan-1  C11  0.020
 TWH  plan-1  C12  0.020
 TWH  plan-1  C13  0.020
 TWH  plan-1  H13  0.020
 TWH  plan-2  N3   0.020
 TWH  plan-2  C10  0.020
 TWH  plan-2  H7   0.020
 TWH  plan-2  H8   0.020

