# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:57:45 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: {(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}(pyrrolidin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCN(C[C@@H]1N(C)c2ncnc3[nH]ccc23)C(=O)N4CCCC4
#
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
 7GV  7GV  {(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}(pyrrolidin-1-yl)methanone  ligand  51  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7GV
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
 7GV  C4   C  CH2   0  -0.320   2.3679  -1.0321   1.5088
 7GV  C7   C  CH1   0  -0.066  -0.2022  -0.2223   0.5145
 7GV  C6   C  CH2   0  -0.296   0.9250   0.7762   0.7985
 7GV  C13  C  CR15  0  -0.019  -5.7077   1.6643  -0.5893
 7GV  N5   N  NT    0  -0.502   2.1876   0.0906   0.5939
 7GV  C19  C  C     0   0.708   3.2641   0.8519   0.1878
 7GV  C2   C  CH1   0  -0.252  -0.1298  -1.4579   1.4242
 7GV  C3   C  CH2   0  -0.435   1.2728  -2.0623   1.2959
 7GV  N8   N  NT    0  -0.493  -1.5154   0.4171   0.5031
 7GV  C10  C  CR6   0   0.508  -2.4544  -0.0058  -0.3722
 7GV  C11  C  CR56  0  -0.079  -3.7395   0.5845  -0.5083
 7GV  C12  C  CR15  0  -0.439  -4.4992   1.6738   0.0378
 7GV  N14  N  NR15  0  -0.656  -5.7436   0.6384  -1.4964
 7GV  C15  C  CR56  0   0.467  -4.5663  -0.0243  -1.4719
 7GV  N16  N  N     0  -0.455  -4.2563  -1.0662  -2.2475
 7GV  C17  C  CR16  0   0.035  -3.0346  -1.5037  -2.0304
 7GV  N18  N  N     0  -0.500  -2.1460  -1.0450  -1.1583
 7GV  O20  O  O     0  -0.530   3.2514   2.0789   0.2160
 7GV  N21  N  NT    0  -0.498   4.3374   0.1607  -0.2745
 7GV  C22  C  CH2   0  -0.278   4.2727  -1.1512  -0.9213
 7GV  C23  C  CH2   0  -0.470   5.3663  -1.0802  -1.9805
 7GV  C24  C  CH2   0  -0.484   6.4038  -0.1763  -1.3242
 7GV  C25  C  CH2   0  -0.252   5.5435   0.8894  -0.6580
 7GV  H1   H  HCH2  0   0.264   3.3426  -1.4898   1.3675
 7GV  H2   H  HCH2  0   0.240   2.3505  -0.6612   2.5426
 7GV  H3   H  HCH1  0   0.261  -0.0276  -0.5729  -0.5028
 7GV  H4   H  HCH2  0   0.265   0.8463   1.6097   0.1029
 7GV  H5   H  HCH2  0   0.222   0.8783   1.1894   1.8132
 7GV  H6   H  HCH3  0   0.271  -1.0609   1.5211   2.2159
 7GV  H7   H  HCH3  0   0.253  -1.9511   2.4260   1.0053
 7GV  H8   H  HCH3  0   0.254  -2.7632   1.2083   2.0050
 7GV  H13  H  HCH1  0   0.244  -0.8420  -2.1887   1.0302
 7GV  H14  H  HCH2  0   0.235   1.3952  -2.4973   0.2996
 7GV  H15  H  HCH2  0   0.236   1.3943  -2.8735   2.0176
 7GV  H16  H  HCR5  0   0.257  -4.2095   2.3857   0.7905
 7GV  H17  H  HNR5  0   0.411  -6.5198   0.4142  -2.0979
 7GV  H18  H  HCR6  0   0.241  -2.7090  -2.3477  -2.6308
 7GV  H19  H  HCH2  0   0.231   4.4860  -1.9595  -0.2158
 7GV  H20  H  HCH2  0   0.249   3.2806  -1.3327  -1.3370
 7GV  H21  H  HCH2  0   0.249   5.7490  -2.0664  -2.2406
 7GV  H22  H  HCH2  0   0.236   4.9840  -0.6159  -2.8924
 7GV  H23  H  HCH2  0   0.236   6.9734  -0.7350  -0.5776
 7GV  H24  H  HCH2  0   0.250   7.1132   0.2565  -2.0287
 7GV  H25  H  HCH2  0   0.226   5.3108   1.6913  -1.3649
 7GV  H26  H  HCH2  0   0.240   6.0261   1.3430   0.2090
 7GV  C9   C  CH3   0  -0.568  -1.8436   1.4441   1.4701
 7GV  C1   C  CH3   0  -0.682  -0.5056  -1.1810   2.8765
 7GV  H9   H  HCR5  0   0.285  -6.5559   2.3156  -0.4600
 7GV  H10  H  HCH3  0   0.238  -1.5471  -0.8715   2.9696
 7GV  H11  H  HCH3  0   0.238  -0.3866  -2.0863   3.4741
 7GV  H12  H  HCH3  0   0.221   0.1100  -0.4068   3.3377

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
 7GV  C23  C24  single    1.524  0.020  1.524
 7GV  C23  C22  single    1.524  0.020  1.524
 7GV  C24  C25  single    1.523  0.020  1.523
 7GV  C25  N21  single    1.460  0.020  1.460
 7GV  C22  N21  single    1.464  0.020  1.464
 7GV  C4   C3   single    1.519  0.020  1.519
 7GV  C4   N5   single    1.459  0.020  1.459
 7GV  N21  C19  single    1.358  0.020  1.358
 7GV  C3   C2   single    1.533  0.020  1.533
 7GV  C19  N5   single    1.380  0.020  1.380
 7GV  C19  O20  double    1.227  0.020  1.227
 7GV  C1   C2   single    1.526  0.020  1.526
 7GV  N5   C6   single    1.451  0.020  1.451
 7GV  C2   C7   single    1.536  0.020  1.536
 7GV  C6   C7   single    1.532  0.020  1.532
 7GV  C7   N8   single    1.461  0.020  1.461
 7GV  N8   C9   single    1.448  0.020  1.448
 7GV  N8   C10  single    1.352  0.020  1.352
 7GV  C12  C13  aromatic  1.362  0.020  1.362
 7GV  C12  C11  aromatic  1.436  0.020  1.436
 7GV  C13  N14  aromatic  1.370  0.020  1.370
 7GV  C10  C11  aromatic  1.421  0.020  1.421
 7GV  C10  N18  aromatic  1.339  0.020  1.339
 7GV  C11  C15  aromatic  1.408  0.020  1.408
 7GV  N18  C17  aromatic  1.327  0.020  1.327
 7GV  N14  C15  aromatic  1.351  0.020  1.351
 7GV  C15  N16  aromatic  1.335  0.020  1.335
 7GV  C17  N16  aromatic  1.316  0.020  1.316
 7GV  C4   H1   single    0.970  0.020  1.090
 7GV  C4   H2   single    0.970  0.020  1.090
 7GV  C7   H3   single    0.970  0.020  1.090
 7GV  C6   H4   single    0.970  0.020  1.090
 7GV  C6   H5   single    0.970  0.020  1.090
 7GV  C9   H6   single    0.970  0.020  1.090
 7GV  C9   H7   single    0.970  0.020  1.090
 7GV  C9   H8   single    0.970  0.020  1.090
 7GV  C13  H9   single    0.930  0.020  1.080
 7GV  C1   H10  single    0.970  0.020  1.090
 7GV  C1   H11  single    0.970  0.020  1.090
 7GV  C1   H12  single    0.970  0.020  1.090
 7GV  C2   H13  single    0.970  0.020  1.090
 7GV  C3   H14  single    0.970  0.020  1.090
 7GV  C3   H15  single    0.970  0.020  1.090
 7GV  C12  H16  single    0.930  0.020  1.080
 7GV  N14  H17  single    0.860  0.020  1.020
 7GV  C17  H18  single    0.930  0.020  1.080
 7GV  C22  H19  single    0.970  0.020  1.090
 7GV  C22  H20  single    0.970  0.020  1.090
 7GV  C23  H21  single    0.970  0.020  1.090
 7GV  C23  H22  single    0.970  0.020  1.090
 7GV  C24  H23  single    0.970  0.020  1.090
 7GV  C24  H24  single    0.970  0.020  1.090
 7GV  C25  H25  single    0.970  0.020  1.090
 7GV  C25  H26  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
 7GV  H2   C4   H1   106.20  3.000
 7GV  H2   C4   C3   110.46  3.000
 7GV  H1   C4   C3   110.06  3.000
 7GV  H2   C4   N5   109.16  3.000
 7GV  H1   C4   N5   110.70  3.000
 7GV  C3   C4   N5   110.17  3.000
 7GV  H3   C7   N8   106.11  3.000
 7GV  H3   C7   C2   106.64  3.000
 7GV  N8   C7   C2   113.52  3.000
 7GV  H3   C7   C6   105.35  3.000
 7GV  N8   C7   C6   112.18  3.000
 7GV  C2   C7   C6   112.32  3.000
 7GV  H5   C6   H4   107.44  3.000
 7GV  H5   C6   N5   110.21  3.000
 7GV  H4   C6   N5   109.55  3.000
 7GV  H5   C6   C7   112.69  3.000
 7GV  H4   C6   C7   109.11  3.000
 7GV  N5   C6   C7   107.82  3.000
 7GV  H9   C13  N14  120.78  3.000
 7GV  H9   C13  C12  129.74  3.000
 7GV  N14  C13  C12  109.48  3.000
 7GV  C19  N5   C6   117.37  3.000
 7GV  C6   N5   C4   112.49  3.000
 7GV  C19  N5   C4   120.83  3.000
 7GV  N21  C19  O20  121.66  3.000
 7GV  O20  C19  N5   122.46  3.000
 7GV  N21  C19  N5   115.86  3.000
 7GV  H13  C2   C3   107.59  3.000
 7GV  H13  C2   C1   107.69  3.000
 7GV  C3   C2   C1   112.13  3.000
 7GV  H13  C2   C7   107.07  3.000
 7GV  C1   C2   C7   113.96  3.000
 7GV  C3   C2   C7   108.10  3.000
 7GV  H15  C3   H14  107.09  3.000
 7GV  H15  C3   C2   109.83  3.000
 7GV  H14  C3   C2   109.60  3.000
 7GV  H15  C3   C4   109.32  3.000
 7GV  H14  C3   C4   108.47  3.000
 7GV  C2   C3   C4   112.38  3.000
 7GV  C10  N8   C9   119.80  3.000
 7GV  C10  N8   C7   119.52  3.000
 7GV  C9   N8   C7   120.59  3.000
 7GV  N18  C10  C11  118.33  3.000
 7GV  N18  C10  N8   117.59  3.000
 7GV  C11  C10  N8   124.09  3.000
 7GV  C15  C11  C12  106.12  3.000
 7GV  C15  C11  C10  114.65  3.000
 7GV  C12  C11  C10  139.23  3.000
 7GV  H16  C12  C11  128.73  3.000
 7GV  H16  C12  C13  124.47  3.000
 7GV  C11  C12  C13  106.80  3.000
 7GV  H17  N14  C15  124.97  3.000
 7GV  H17  N14  C13  125.62  3.000
 7GV  C15  N14  C13  109.42  3.000
 7GV  N16  C15  N14  125.06  3.000
 7GV  N16  C15  C11  126.76  3.000
 7GV  N14  C15  C11  108.18  3.000
 7GV  C17  N16  C15  112.28  3.000
 7GV  H18  C17  N18  115.55  3.000
 7GV  H18  C17  N16  116.47  3.000
 7GV  N18  C17  N16  127.98  3.000
 7GV  C17  N18  C10  119.99  3.000
 7GV  C25  N21  C22  111.57  3.000
 7GV  C22  N21  C19  124.86  3.000
 7GV  C25  N21  C19  119.23  3.000
 7GV  H20  C22  H19  107.47  3.000
 7GV  H20  C22  C23  113.30  3.000
 7GV  H19  C22  C23  110.05  3.000
 7GV  H20  C22  N21  110.95  3.000
 7GV  H19  C22  N21  111.63  3.000
 7GV  C23  C22  N21  103.51  3.000
 7GV  H22  C23  H21  107.96  3.000
 7GV  H22  C23  C24  110.22  3.000
 7GV  H21  C23  C24  113.60  3.000
 7GV  H22  C23  C22  110.42  3.000
 7GV  H21  C23  C22  112.07  3.000
 7GV  C24  C23  C22  102.52  3.000
 7GV  H24  C24  H23  107.79  3.000
 7GV  H24  C24  C25  111.88  3.000
 7GV  H23  C24  C25  110.70  3.000
 7GV  H24  C24  C23  113.60  3.000
 7GV  H23  C24  C23  110.23  3.000
 7GV  C25  C24  C23  102.64  3.000
 7GV  H26  C25  H25  107.63  3.000
 7GV  H26  C25  C24  112.87  3.000
 7GV  H25  C25  C24  110.51  3.000
 7GV  H26  C25  N21  111.35  3.000
 7GV  H25  C25  N21  111.09  3.000
 7GV  C24  C25  N21  103.42  3.000
 7GV  H8   C9   H7   108.69  3.000
 7GV  H8   C9   H6   106.68  3.000
 7GV  H7   C9   H6   107.47  3.000
 7GV  H8   C9   N8   111.44  3.000
 7GV  H7   C9   N8   112.08  3.000
 7GV  H6   C9   N8   110.26  3.000
 7GV  H12  C1   H11  107.19  3.000
 7GV  H12  C1   H10  107.54  3.000
 7GV  H11  C1   H10  107.03  3.000
 7GV  H12  C1   C2   113.09  3.000
 7GV  H11  C1   C2   110.11  3.000
 7GV  H10  C1   C2   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
 7GV  CONST_01  C10  C11  C12  C13  180.00   0.0  0
 7GV  CONST_02  C15  C11  C12  C13    0.00   0.0  0
 7GV  CONST_03  C11  C15  N14  C13    0.00   0.0  0
 7GV  CONST_04  N16  C15  N14  C13  180.00   0.0  0
 7GV  CONST_05  N14  C15  C11  C10  180.00   0.0  0
 7GV  CONST_06  N16  C15  C11  C10    0.00   0.0  0
 7GV  CONST_07  N16  C17  N18  C10    0.00   0.0  0
 7GV  CONST_08  N14  C13  C12  C11    0.00   0.0  0
 7GV  CONST_09  C17  N18  C10  C11    0.00   0.0  0
 7GV  CONST_10  C17  N16  C15  C11    0.00   0.0  0
 7GV  CONST_11  C15  N14  C13  C12    0.00   0.0  0
 7GV  CONST_12  N18  C10  C11  C12  180.00   0.0  0
 7GV  CONST_13  N14  C15  C11  C12    0.00   0.0  0
 7GV  CONST_14  N16  C15  C11  C12  180.00   0.0  0
 7GV  CONST_15  C17  N16  C15  N14  180.00   0.0  0
 7GV  CONST_16  N18  C10  C11  C15    0.00   0.0  0
 7GV  CONST_17  N18  C17  N16  C15    0.00   0.0  0
 7GV  CONST_18  C12  C11  C10  N8     0.00   0.0  0
 7GV  CONST_19  C15  C11  C10  N8   180.00   0.0  0
 7GV  CONST_20  C17  N18  C10  N8   180.00   0.0  0
 7GV  CONST_21  C11  C10  N8   C7   180.00   0.0  0
 7GV  CONST_22  N18  C10  N8   C7     0.00   0.0  0
 7GV  CONST_24  N21  C19  N5   C6   180.00   0.0  0
 7GV  CONST_25  C25  N21  C19  N5   180.00   0.0  0
 7GV  CONST_27  H16  C12  C11  C10    0.00   0.0  0
 7GV  CONST_28  H18  C17  N18  C10  180.00   0.0  0
 7GV  CONST_29  H9   C13  C12  C11  180.00   0.0  0
 7GV  CONST_30  H17  N14  C15  C11  180.00   0.0  0
 7GV  CONST_32  O20  C19  N5   C6     0.00   0.0  0
 7GV  CONST_33  C25  N21  C19  O20    0.00   0.0  0
 7GV  CONST_35  C11  C10  N8   C9     0.00   0.0  0
 7GV  CONST_36  N18  C10  N8   C9   180.00   0.0  0
 7GV  Var_01    C7   C6   N5   C4   -62.13  30.0  1
 7GV  Var_02    C3   C4   N5   C6    61.10  30.0  1
 7GV  Var_03    C2   C3   C4   N5   -55.21  30.0  1
 7GV  Var_04    C23  C24  C25  N21   33.04  30.0  1
 7GV  Var_05    C24  C23  C22  N21   32.33  30.0  1
 7GV  Var_06    C25  C24  C23  C22  -40.53  30.0  1
 7GV  Var_07    C24  C25  N21  C22  -13.22  30.0  1
 7GV  Var_08    C25  N21  C22  C23  -12.10  30.0  1
 7GV  Var_09    H6   C9   N8   C7    -8.02  30.0  3

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
 7GV  chir_01  C7  C2  C6  N8  positiv
 7GV  chir_02  C2  C7  C1  C3  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
 7GV  plan-1  C4   0.020
 7GV  plan-1  C6   0.020
 7GV  plan-1  N5   0.020
 7GV  plan-1  C19  0.020
 7GV  plan-1  O20  0.020
 7GV  plan-1  N21  0.020
 7GV  plan-1  C22  0.020
 7GV  plan-1  C25  0.020
 7GV  plan-2  C13  0.020
 7GV  plan-2  N8   0.020
 7GV  plan-2  C10  0.020
 7GV  plan-2  C11  0.020
 7GV  plan-2  C12  0.020
 7GV  plan-2  N14  0.020
 7GV  plan-2  C15  0.020
 7GV  plan-2  N16  0.020
 7GV  plan-2  C17  0.020
 7GV  plan-2  N18  0.020
 7GV  plan-2  H16  0.020
 7GV  plan-2  H17  0.020
 7GV  plan-2  H18  0.020
 7GV  plan-2  H9   0.020
 7GV  plan-3  C7   0.020
 7GV  plan-3  N8   0.020
 7GV  plan-3  C10  0.020
 7GV  plan-3  C9   0.020

