# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:43:59 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CC[C@H]2CCN([C@H]2C1)c3ncnc4[nH]ccc34
#
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
 7KV  7KV  1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one  ligand  43  22  .  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_7KV
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
 7KV  N3   N  NR15  0  -0.657   3.7268   2.0608   0.4594
 7KV  C4   C  CR56  0   0.466   3.6278   0.7642   0.0885
 7KV  N2   N  N     0  -0.455   4.6535  -0.0234  -0.2479
 7KV  C7   C  CH2   0  -0.494  -0.8916  -3.1442  -0.4528
 7KV  C6   C  CR15  0  -0.453   1.5477   1.5806   0.5115
 7KV  C9   C  CH1   0  -0.260  -1.2906  -2.1109   0.5978
 7KV  C13  C  CH2   0  -0.430  -2.7828  -1.8194   0.7240
 7KV  C8   C  CH2   0  -0.257   0.6062  -2.9142  -0.6243
 7KV  N5   N  NT    0  -0.447  -2.4845   0.2312  -0.5545
 7KV  C16  C  CH3   0  -0.652  -4.4701   3.0841   0.9108
 7KV  N1   N  N     0  -0.498   3.0298  -1.7231  -0.6054
 7KV  C1   C  CR16  0   0.035   4.2655  -1.2348  -0.5839
 7KV  C2   C  CR6   0   0.489   2.0039  -0.9375  -0.2522
 7KV  C3   C  CR56  0  -0.077   2.2682   0.4075   0.1124
 7KV  C5   C  CR15  0  -0.019   2.4757   2.5582   0.7114
 7KV  N4   N  NT    0  -0.493   0.7872  -1.5065  -0.2701
 7KV  C10  C  CH1   0  -0.094  -0.4460  -0.8948   0.1901
 7KV  C11  C  CH2   0  -0.327  -1.1249  -0.0956  -0.9296
 7KV  C12  C  CH2   0  -0.342  -3.3123  -0.9542  -0.4119
 7KV  O1   O  O     0  -0.499  -1.9653   2.3562  -0.0122
 7KV  C15  C  CH2   0  -0.591  -4.2055   1.6607   0.4520
 7KV  H1   H  HNR5  0   0.411   4.5888   2.5758   0.5375
 7KV  H2   H  HCH2  0   0.260  -1.1104  -4.1635  -0.1363
 7KV  H3   H  HCH2  0   0.241  -1.4212  -2.9772  -1.3941
 7KV  H4   H  HCR5  0   0.263   0.4850   1.7187   0.6185
 7KV  H5   H  HCH1  0   0.263  -0.9243  -2.4553   1.5699
 7KV  H6   H  HCH2  0   0.247  -3.3419  -2.7572   0.7640
 7KV  H7   H  HCH2  0   0.239  -2.9726  -1.3051   1.6703
 7KV  H8   H  HCH2  0   0.238   1.1862  -3.5503   0.0488
 7KV  H9   H  HCH2  0   0.245   0.9522  -3.1143  -1.6388
 7KV  H10  H  HCH3  0   0.227  -4.3308   3.8010   0.1027
 7KV  H11  H  HCH3  0   0.231  -5.4997   3.1706   1.2572
 7KV  H12  H  HCH3  0   0.227  -3.8186   3.3753   1.7336
 7KV  H13  H  HCR6  0   0.241   5.0469  -1.9281  -0.8795
 7KV  H14  H  HCR5  0   0.285   2.3413   3.5837   1.0129
 7KV  H15  H  HCH1  0   0.270  -0.2640  -0.2482   1.0510
 7KV  H16  H  HCH2  0   0.259  -1.1559  -0.6999  -1.8412
 7KV  H17  H  HCH2  0   0.277  -0.5707   0.8085  -1.1691
 7KV  H18  H  HCH2  0   0.253  -3.2895  -1.4983  -1.3602
 7KV  H19  H  HCH2  0   0.279  -4.3508  -0.6869  -0.2366
 7KV  H20  H  HCH2  0   0.264  -4.4004   0.9649   1.2733
 7KV  H21  H  HCH2  0   0.267  -4.9125   1.3894  -0.3366
 7KV  C14  C  C     0   0.564  -2.7884   1.4502  -0.0482

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
 7KV  C16  C15  single    1.519  0.020  1.519
 7KV  C15  C14  single    1.517  0.020  1.517
 7KV  C12  N5   single    1.453  0.020  1.453
 7KV  C12  C13  single    1.523  0.020  1.523
 7KV  N5   C14  single    1.355  0.020  1.355
 7KV  N5   C11  single    1.448  0.020  1.448
 7KV  C14  O1   double    1.225  0.020  1.225
 7KV  C11  C10  single    1.534  0.020  1.534
 7KV  C7   C8   single    1.525  0.020  1.525
 7KV  C7   C9   single    1.527  0.020  1.527
 7KV  C13  C9   single    1.526  0.020  1.526
 7KV  C8   N4   single    1.463  0.020  1.463
 7KV  C9   C10  single    1.536  0.020  1.536
 7KV  C10  N4   single    1.451  0.020  1.451
 7KV  N4   C2   single    1.343  0.020  1.343
 7KV  C6   C5   aromatic  1.363  0.020  1.363
 7KV  C6   C3   aromatic  1.433  0.020  1.433
 7KV  C2   C3   aromatic  1.418  0.020  1.418
 7KV  C2   N1   aromatic  1.339  0.020  1.339
 7KV  C5   N3   aromatic  1.370  0.020  1.370
 7KV  C3   C4   aromatic  1.406  0.020  1.406
 7KV  N1   C1   aromatic  1.329  0.020  1.329
 7KV  N3   C4   aromatic  1.352  0.020  1.352
 7KV  C4   N2   aromatic  1.336  0.020  1.336
 7KV  C1   N2   aromatic  1.316  0.020  1.316
 7KV  N3   H1   single    0.860  0.020  1.020
 7KV  C7   H2   single    0.970  0.020  1.090
 7KV  C7   H3   single    0.970  0.020  1.090
 7KV  C6   H4   single    0.930  0.020  1.080
 7KV  C9   H5   single    0.970  0.020  1.090
 7KV  C13  H6   single    0.970  0.020  1.090
 7KV  C13  H7   single    0.970  0.020  1.090
 7KV  C8   H8   single    0.970  0.020  1.090
 7KV  C8   H9   single    0.970  0.020  1.090
 7KV  C16  H10  single    0.970  0.020  1.090
 7KV  C16  H11  single    0.970  0.020  1.090
 7KV  C16  H12  single    0.970  0.020  1.090
 7KV  C1   H13  single    0.930  0.020  1.080
 7KV  C5   H14  single    0.930  0.020  1.080
 7KV  C10  H15  single    0.970  0.020  1.090
 7KV  C11  H16  single    0.970  0.020  1.090
 7KV  C11  H17  single    0.970  0.020  1.090
 7KV  C12  H18  single    0.970  0.020  1.090
 7KV  C12  H19  single    0.970  0.020  1.090
 7KV  C15  H20  single    0.970  0.020  1.090
 7KV  C15  H21  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
 7KV  H1   N3   C5   125.58  3.000
 7KV  H1   N3   C4   125.04  3.000
 7KV  C5   N3   C4   109.38  3.000
 7KV  C3   C4   N2   126.66  3.000
 7KV  N2   C4   N3   125.31  3.000
 7KV  C3   C4   N3   108.03  3.000
 7KV  C1   N2   C4   112.37  3.000
 7KV  H3   C7   H2   107.20  3.000
 7KV  H3   C7   C8   110.86  3.000
 7KV  H2   C7   C8   111.78  3.000
 7KV  H3   C7   C9   111.26  3.000
 7KV  H2   C7   C9   112.39  3.000
 7KV  C8   C7   C9   103.42  3.000
 7KV  H4   C6   C5   124.43  3.000
 7KV  H4   C6   C3   128.95  3.000
 7KV  C5   C6   C3   106.60  3.000
 7KV  H5   C9   C10  107.52  3.000
 7KV  H5   C9   C13  108.30  3.000
 7KV  C10  C9   C13  114.11  3.000
 7KV  H5   C9   C7   108.11  3.000
 7KV  C10  C9   C7   102.10  3.000
 7KV  C13  C9   C7   116.22  3.000
 7KV  H7   C13  H6   106.45  3.000
 7KV  H7   C13  C12  108.54  3.000
 7KV  H6   C13  C12  109.70  3.000
 7KV  H7   C13  C9   109.34  3.000
 7KV  H6   C13  C9   109.85  3.000
 7KV  C12  C13  C9   112.76  3.000
 7KV  H9   C8   H8   107.32  3.000
 7KV  H9   C8   N4   111.26  3.000
 7KV  H8   C8   N4   110.20  3.000
 7KV  H9   C8   C7   112.87  3.000
 7KV  H8   C8   C7   111.36  3.000
 7KV  N4   C8   C7   103.85  3.000
 7KV  C14  N5   C12  124.73  3.000
 7KV  C14  N5   C11  120.71  3.000
 7KV  C12  N5   C11  112.11  3.000
 7KV  H12  C16  H11  107.69  3.000
 7KV  H12  C16  H10  107.94  3.000
 7KV  H11  C16  H10  107.72  3.000
 7KV  H12  C16  C15  112.00  3.000
 7KV  H11  C16  C15  109.58  3.000
 7KV  H10  C16  C15  111.75  3.000
 7KV  C2   N1   C1   119.50  3.000
 7KV  H13  C1   N1   115.49  3.000
 7KV  H13  C1   N2   116.44  3.000
 7KV  N1   C1   N2   128.08  3.000
 7KV  N4   C2   C3   125.02  3.000
 7KV  C3   C2   N1   118.76  3.000
 7KV  N4   C2   N1   116.22  3.000
 7KV  C2   C3   C6   138.94  3.000
 7KV  C2   C3   C4   114.61  3.000
 7KV  C6   C3   C4   106.45  3.000
 7KV  H14  C5   C6   129.72  3.000
 7KV  H14  C5   N3   120.74  3.000
 7KV  C6   C5   N3   109.55  3.000
 7KV  C10  N4   C2   125.93  3.000
 7KV  C2   N4   C8   121.53  3.000
 7KV  C10  N4   C8   112.16  3.000
 7KV  H15  C10  C11  109.92  3.000
 7KV  H15  C10  N4   110.97  3.000
 7KV  C11  C10  N4   111.36  3.000
 7KV  H15  C10  C9   110.56  3.000
 7KV  N4   C10  C9   102.57  3.000
 7KV  C11  C10  C9   111.28  3.000
 7KV  H17  C11  H16  106.87  3.000
 7KV  H17  C11  C10  111.62  3.000
 7KV  H16  C11  C10  109.45  3.000
 7KV  H17  C11  N5   110.37  3.000
 7KV  H16  C11  N5   108.29  3.000
 7KV  C10  C11  N5   110.13  3.000
 7KV  H19  C12  H18  106.39  3.000
 7KV  H19  C12  N5   111.08  3.000
 7KV  H18  C12  N5   107.99  3.000
 7KV  H19  C12  C13  110.60  3.000
 7KV  H18  C12  C13  110.91  3.000
 7KV  N5   C12  C13  109.79  3.000
 7KV  H21  C15  H20  105.57  3.000
 7KV  H21  C15  C14  109.37  3.000
 7KV  H20  C15  C14  109.01  3.000
 7KV  H21  C15  C16  109.74  3.000
 7KV  H20  C15  C16  109.77  3.000
 7KV  C14  C15  C16  113.10  3.000
 7KV  C15  C14  O1   121.03  3.000
 7KV  O1   C14  N5   121.73  3.000
 7KV  C15  C14  N5   117.23  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
 7KV  CONST_01  C3   C6   C5   N3      0.00   0.0  0
 7KV  CONST_02  C6   C3   C4   N3      0.00   0.0  0
 7KV  CONST_03  C2   C3   C4   N3    180.00   0.0  0
 7KV  CONST_04  C1   N2   C4   N3    180.00   0.0  0
 7KV  CONST_05  C5   C6   C3   C4      0.00   0.0  0
 7KV  CONST_06  N1   C2   C3   C4      0.00   0.0  0
 7KV  CONST_07  C6   C5   N3   C4      0.00   0.0  0
 7KV  CONST_08  N1   C1   N2   C4      0.00   0.0  0
 7KV  CONST_09  C6   C3   C4   N2    180.00   0.0  0
 7KV  CONST_10  C2   C3   C4   N2      0.00   0.0  0
 7KV  CONST_11  C5   N3   C4   N2    180.00   0.0  0
 7KV  CONST_12  C2   N1   C1   N2      0.00   0.0  0
 7KV  CONST_13  N1   C2   C3   C6    180.00   0.0  0
 7KV  CONST_14  C3   C2   N1   C1      0.00   0.0  0
 7KV  CONST_15  C3   C4   N2   C1      0.00   0.0  0
 7KV  CONST_16  C5   C6   C3   C2    180.00   0.0  0
 7KV  CONST_17  C5   N3   C4   C3      0.00   0.0  0
 7KV  CONST_18  N4   C2   C3   C4    180.00   0.0  0
 7KV  CONST_19  N4   C2   C3   C6      0.00   0.0  0
 7KV  CONST_20  N4   C2   N1   C1    180.00   0.0  0
 7KV  CONST_21  H4   C6   C5   N3    180.00   0.0  0
 7KV  CONST_22  H14  C5   N3   C4    180.00   0.0  0
 7KV  CONST_23  H13  C1   N2   C4    180.00   0.0  0
 7KV  CONST_24  H1   N3   C4   N2      0.00   0.0  0
 7KV  CONST_25  C15  C14  N5   C11   180.00   0.0  0
 7KV  CONST_26  O1   C14  N5   C11     0.00   0.0  0
 7KV  CONST_27  C15  C14  N5   C12     0.00   0.0  0
 7KV  CONST_28  O1   C14  N5   C12   180.00   0.0  0
 7KV  Var_01    C10  N4   C8   C7      4.12  30.0  1
 7KV  Var_02    N4   C8   C7   C9    -27.04  30.0  1
 7KV  Var_03    N5   C12  C13  C9    -51.46  30.0  1
 7KV  Var_04    C11  N5   C12  C13    63.50  30.0  1
 7KV  Var_05    C3   C2   N4   C8   -178.28  30.0  2
 7KV  Var_06    C12  N5   C11  C10   -64.54  30.0  1
 7KV  Var_07    C16  C15  C14  N5   -176.07  30.0  1
 7KV  Var_08    H10  C16  C15  C14    60.70  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
 7KV  chir_01  C9   C7  C13  C10  positiv
 7KV  chir_02  C10  N4  C9   C11  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
 7KV  plan-1  N3   0.020
 7KV  plan-1  C4   0.020
 7KV  plan-1  N2   0.020
 7KV  plan-1  C6   0.020
 7KV  plan-1  N1   0.020
 7KV  plan-1  C1   0.020
 7KV  plan-1  C2   0.020
 7KV  plan-1  C3   0.020
 7KV  plan-1  C5   0.020
 7KV  plan-1  N4   0.020
 7KV  plan-1  H1   0.020
 7KV  plan-1  H4   0.020
 7KV  plan-1  H13  0.020
 7KV  plan-1  H14  0.020
 7KV  plan-2  N5   0.020
 7KV  plan-2  C11  0.020
 7KV  plan-2  C12  0.020
 7KV  plan-2  O1   0.020
 7KV  plan-2  C15  0.020
 7KV  plan-2  C14  0.020

