# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:08:35 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 1-cyclopentyl-N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-1H-pyrrolo[3,2-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1CCN(CC1)c2nccc(Nc3cc4n(ccc4cn3)C5CCCC5)n2
#
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
 3QS  3QS  1-cyclopentyl-N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-1H-pyrrolo[3,2-c]pyridin-6-amine  ligand  57  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3QS
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
 3QS  C4   C  CH2   0  -0.457   5.9200   0.1266  -0.0325
 3QS  C5   C  CH2   0  -0.311   5.0636  -0.6477   0.9652
 3QS  C11  C  CR16  0  -0.019   2.7785  -3.7029  -0.5066
 3QS  C7   C  CH2   0  -0.315   3.1862   0.8558   0.6082
 3QS  C8   C  CH2   0  -0.473   3.9930   1.6704  -0.3975
 3QS  C9   C  CR6   0   0.627   2.9376  -1.5363   0.1107
 3QS  C12  C  CR16  0  -0.473   1.4763  -3.5404  -0.9122
 3QS  C13  C  CR6   0   0.533   0.9517  -2.2442  -0.7481
 3QS  C3   C  CH1   0   0.031   5.4948   1.5868  -0.1229
 3QS  O2   O  O2    0  -0.492   5.8591   2.1985   1.0996
 3QS  N6   N  NT    0  -0.492   3.6562  -0.5175   0.6432
 3QS  N10  N  N     0  -0.505   3.5319  -2.7299  -0.0035
 3QS  N14  N  N     0  -0.499   1.6740  -1.2678  -0.2327
 3QS  N15  N  NH1   0  -0.754  -0.3373  -1.9948  -1.1100
 3QS  C16  C  CR6   0   0.456  -1.0088  -0.7672  -1.0253
 3QS  C17  C  CR16  0  -0.447  -2.2833  -0.7507  -0.4825
 3QS  C18  C  CR56  0   0.485  -2.9392   0.4773  -0.4902
 3QS  C19  C  CR56  0  -0.045  -2.2988   1.6272  -1.0016
 3QS  C20  C  CR15  0  -0.432  -3.2180   2.7115  -0.8614
 3QS  C21  C  CR15  0  -0.026  -4.3367   2.1884  -0.2890
 3QS  N22  N  NR5   0  -0.544  -4.1732   0.8419  -0.0539
 3QS  C23  C  CH1   0  -0.097  -5.1860  -0.0377   0.5014
 3QS  C24  C  CH2   0  -0.472  -5.8358   0.5061   1.8002
 3QS  C25  C  CH2   0  -0.446  -7.3260   0.6579   1.4866
 3QS  C26  C  CH2   0  -0.449  -7.5787  -0.4134   0.4287
 3QS  C27  C  CH2   0  -0.452  -6.3528  -0.2977  -0.4711
 3QS  C28  C  CR16  0  -0.143  -1.0103   1.4711  -1.5070
 3QS  N29  N  N     0  -0.418  -0.3929   0.3060  -1.5339
 3QS  H1   H  HCH2  0   0.240   6.9733   0.0581   0.2504
 3QS  H2   H  HCH2  0   0.233   5.8257  -0.3290  -1.0216
 3QS  H3   H  HCH2  0   0.264   5.3384  -1.6978   0.9732
 3QS  H4   H  HCH2  0   0.235   5.2239  -0.2611   1.9757
 3QS  H5   H  HCR6  0   0.258   3.2528  -4.6752  -0.5962
 3QS  H6   H  HCH2  0   0.231   3.2843   1.2851   1.6101
 3QS  H7   H  HCH2  0   0.279   2.1318   0.8673   0.3472
 3QS  H8   H  HCH2  0   0.236   3.8060   1.2875  -1.4047
 3QS  H9   H  HCH2  0   0.243   3.6454   2.7065  -0.3965
 3QS  H10  H  HCR6  0   0.266   0.8994  -4.3542  -1.3272
 3QS  H11  H  HCH1  0   0.222   6.0352   2.0736  -0.9487
 3QS  H12  H  HCH3  0   0.205   4.6911   3.9332   1.1148
 3QS  H13  H  HCH3  0   0.233   6.2008   3.9606   2.0318
 3QS  H14  H  HCH3  0   0.201   6.2392   4.0654   0.2637
 3QS  H15  H  HNH1  0   0.409  -0.9137  -2.8057  -1.2698
 3QS  H16  H  HCR6  0   0.279  -2.7250  -1.6528  -0.0798
 3QS  H17  H  HCR5  0   0.253  -3.0679   3.7407  -1.1449
 3QS  H18  H  HCR5  0   0.291  -5.2584   2.6813  -0.0200
 3QS  H19  H  HCH1  0   0.274  -4.6820  -0.9770   0.7245
 3QS  H20  H  HCH2  0   0.252  -5.6951  -0.2231   2.5992
 3QS  H21  H  HCH2  0   0.251  -5.3708   1.4332   2.1361
 3QS  H22  H  HCH2  0   0.239  -7.9542   0.5467   2.3709
 3QS  H23  H  HCH2  0   0.224  -7.5323   1.6473   1.0684
 3QS  H24  H  HCH2  0   0.226  -7.6137  -1.4004   0.8986
 3QS  H25  H  HCH2  0   0.239  -8.5146  -0.2761  -0.1137
 3QS  H26  H  HCH2  0   0.238  -6.4700   0.5569  -1.1432
 3QS  H27  H  HCH2  0   0.249  -6.1808  -1.1757  -1.0946
 3QS  H28  H  HCR6  0   0.255  -0.4714   2.3180  -1.9208
 3QS  C1   C  CH3   0  -0.399   5.7333   3.5968   1.1169

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
 3QS  C12  C11  aromatic  1.374  0.020  1.374
 3QS  C12  C13  aromatic  1.408  0.020  1.408
 3QS  C11  N10  aromatic  1.329  0.020  1.329
 3QS  N15  C13  single    1.362  0.020  1.362
 3QS  N15  C16  single    1.402  0.020  1.402
 3QS  N29  C16  aromatic  1.338  0.020  1.338
 3QS  N29  C28  aromatic  1.319  0.020  1.319
 3QS  C13  N14  aromatic  1.319  0.020  1.319
 3QS  C16  C17  aromatic  1.385  0.020  1.385
 3QS  C28  C19  aromatic  1.393  0.020  1.393
 3QS  N10  C9   aromatic  1.338  0.020  1.338
 3QS  N14  C9   aromatic  1.337  0.020  1.337
 3QS  C17  C18  aromatic  1.392  0.020  1.392
 3QS  C19  C18  aromatic  1.412  0.020  1.412
 3QS  C19  C20  aromatic  1.428  0.020  1.428
 3QS  C9   N6   single    1.356  0.020  1.356
 3QS  C18  N22  aromatic  1.359  0.020  1.359
 3QS  C20  C21  aromatic  1.361  0.020  1.361
 3QS  C5   N6   single    1.450  0.020  1.450
 3QS  C5   C4   single    1.526  0.020  1.526
 3QS  N6   C7   single    1.452  0.020  1.452
 3QS  C4   C3   single    1.523  0.020  1.523
 3QS  N22  C21  aromatic  1.377  0.020  1.377
 3QS  N22  C23  single    1.452  0.020  1.452
 3QS  C8   C7   single    1.525  0.020  1.525
 3QS  C8   C3   single    1.529  0.020  1.529
 3QS  C23  C27  single    1.541  0.020  1.541
 3QS  C23  C24  single    1.551  0.020  1.551
 3QS  C3   O2   single    1.415  0.020  1.415
 3QS  C27  C26  single    1.525  0.020  1.525
 3QS  O2   C1   single    1.404  0.020  1.404
 3QS  C24  C25  single    1.530  0.020  1.530
 3QS  C26  C25  single    1.527  0.020  1.527
 3QS  C4   H1   single    0.970  0.020  1.090
 3QS  C4   H2   single    0.970  0.020  1.090
 3QS  C5   H3   single    0.970  0.020  1.090
 3QS  C5   H4   single    0.970  0.020  1.090
 3QS  C11  H5   single    0.930  0.020  1.080
 3QS  C7   H6   single    0.970  0.020  1.090
 3QS  C7   H7   single    0.970  0.020  1.090
 3QS  C8   H8   single    0.970  0.020  1.090
 3QS  C8   H9   single    0.970  0.020  1.090
 3QS  C12  H10  single    0.930  0.020  1.080
 3QS  C3   H11  single    0.970  0.020  1.090
 3QS  C1   H12  single    0.970  0.020  1.090
 3QS  C1   H13  single    0.970  0.020  1.090
 3QS  C1   H14  single    0.970  0.020  1.090
 3QS  N15  H15  single    0.860  0.020  1.020
 3QS  C17  H16  single    0.930  0.020  1.080
 3QS  C20  H17  single    0.930  0.020  1.080
 3QS  C21  H18  single    0.930  0.020  1.080
 3QS  C23  H19  single    0.970  0.020  1.090
 3QS  C24  H20  single    0.970  0.020  1.090
 3QS  C24  H21  single    0.970  0.020  1.090
 3QS  C25  H22  single    0.970  0.020  1.090
 3QS  C25  H23  single    0.970  0.020  1.090
 3QS  C26  H24  single    0.970  0.020  1.090
 3QS  C26  H25  single    0.970  0.020  1.090
 3QS  C27  H26  single    0.970  0.020  1.090
 3QS  C27  H27  single    0.970  0.020  1.090
 3QS  C28  H28  single    0.930  0.020  1.080

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
 3QS  H2   C4   H1   106.93  3.000
 3QS  H2   C4   C3   108.77  3.000
 3QS  H1   C4   C3   110.15  3.000
 3QS  H2   C4   C5   109.38  3.000
 3QS  H1   C4   C5   109.87  3.000
 3QS  C3   C4   C5   111.63  3.000
 3QS  H4   C5   H3   107.34  3.000
 3QS  H4   C5   N6   108.41  3.000
 3QS  H3   C5   N6   109.53  3.000
 3QS  H4   C5   C4   110.03  3.000
 3QS  H3   C5   C4   110.71  3.000
 3QS  N6   C5   C4   110.74  3.000
 3QS  H5   C11  N10  116.06  3.000
 3QS  H5   C11  C12  119.72  3.000
 3QS  N10  C11  C12  124.22  3.000
 3QS  H7   C7   H6   107.62  3.000
 3QS  H7   C7   N6   109.27  3.000
 3QS  H6   C7   N6   108.66  3.000
 3QS  H7   C7   C8   110.46  3.000
 3QS  H6   C7   C8   110.29  3.000
 3QS  N6   C7   C8   110.48  3.000
 3QS  H9   C8   H8   106.16  3.000
 3QS  H9   C8   C3   111.35  3.000
 3QS  H8   C8   C3   108.31  3.000
 3QS  H9   C8   C7   109.73  3.000
 3QS  H8   C8   C7   109.26  3.000
 3QS  C3   C8   C7   111.84  3.000
 3QS  N14  C9   N10  125.24  3.000
 3QS  N14  C9   N6   116.81  3.000
 3QS  N10  C9   N6   117.94  3.000
 3QS  H10  C12  C13  122.63  3.000
 3QS  H10  C12  C11  122.04  3.000
 3QS  C13  C12  C11  115.33  3.000
 3QS  N15  C13  N14  119.11  3.000
 3QS  N14  C13  C12  121.52  3.000
 3QS  N15  C13  C12  119.36  3.000
 3QS  H11  C3   O2   109.31  3.000
 3QS  H11  C3   C8   108.87  3.000
 3QS  O2   C3   C8   112.61  3.000
 3QS  H11  C3   C4   109.36  3.000
 3QS  O2   C3   C4   106.94  3.000
 3QS  C8   C3   C4   109.71  3.000
 3QS  C1   O2   C3   114.72  3.000
 3QS  C9   N6   C7   121.99  3.000
 3QS  C7   N6   C5   113.87  3.000
 3QS  C9   N6   C5   122.30  3.000
 3QS  C9   N10  C11  115.69  3.000
 3QS  C13  N14  C9   117.99  3.000
 3QS  H15  N15  C16  116.12  3.000
 3QS  H15  N15  C13  115.86  3.000
 3QS  C16  N15  C13  126.71  3.000
 3QS  N29  C16  C17  124.26  3.000
 3QS  C17  C16  N15  118.34  3.000
 3QS  N29  C16  N15  117.32  3.000
 3QS  H16  C17  C18  123.03  3.000
 3QS  H16  C17  C16  120.75  3.000
 3QS  C18  C17  C16  116.21  3.000
 3QS  N22  C18  C19  108.04  3.000
 3QS  N22  C18  C17  131.51  3.000
 3QS  C19  C18  C17  120.44  3.000
 3QS  C28  C19  C20  135.72  3.000
 3QS  C20  C19  C18  106.90  3.000
 3QS  C28  C19  C18  117.37  3.000
 3QS  H17  C20  C21  126.30  3.000
 3QS  H17  C20  C19  127.54  3.000
 3QS  C21  C20  C19  106.17  3.000
 3QS  H18  C21  N22  120.37  3.000
 3QS  H18  C21  C20  129.13  3.000
 3QS  N22  C21  C20  110.50  3.000
 3QS  C23  N22  C21  125.11  3.000
 3QS  C23  N22  C18  126.43  3.000
 3QS  C21  N22  C18  108.39  3.000
 3QS  H19  C23  C27  109.52  3.000
 3QS  H19  C23  C24  108.95  3.000
 3QS  C27  C23  C24  105.69  3.000
 3QS  H19  C23  N22  106.15  3.000
 3QS  C24  C23  N22  113.59  3.000
 3QS  C27  C23  N22  112.90  3.000
 3QS  H21  C24  H20  106.73  3.000
 3QS  H21  C24  C25  113.21  3.000
 3QS  H20  C24  C25  110.00  3.000
 3QS  H21  C24  C23  112.18  3.000
 3QS  H20  C24  C23  108.97  3.000
 3QS  C25  C24  C23  105.74  3.000
 3QS  H23  C25  H22  107.08  3.000
 3QS  H23  C25  C26  109.79  3.000
 3QS  H22  C25  C26  113.27  3.000
 3QS  H23  C25  C24  110.59  3.000
 3QS  H22  C25  C24  112.62  3.000
 3QS  C26  C25  C24  103.50  3.000
 3QS  H25  C26  H24  107.45  3.000
 3QS  H25  C26  C27  112.76  3.000
 3QS  H24  C26  C27  110.35  3.000
 3QS  H25  C26  C25  113.48  3.000
 3QS  H24  C26  C25  109.93  3.000
 3QS  C27  C26  C25  102.86  3.000
 3QS  H27  C27  H26  107.14  3.000
 3QS  H27  C27  C26  113.77  3.000
 3QS  H26  C27  C26  109.62  3.000
 3QS  H27  C27  C23  112.16  3.000
 3QS  H26  C27  C23  109.71  3.000
 3QS  C26  C27  C23  104.42  3.000
 3QS  H28  C28  N29  116.68  3.000
 3QS  H28  C28  C19  120.67  3.000
 3QS  N29  C28  C19  122.64  3.000
 3QS  C28  N29  C16  119.04  3.000
 3QS  H14  C1   H13  108.21  3.000
 3QS  H14  C1   H12  107.82  3.000
 3QS  H13  C1   H12  107.89  3.000
 3QS  H14  C1   O2   112.00  3.000
 3QS  H13  C1   O2   107.72  3.000
 3QS  H12  C1   O2   113.03  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
 3QS  CONST_01  N14  C13  C12  C11     0.00   0.0  0
 3QS  CONST_02  N14  C9   N10  C11     0.00   0.0  0
 3QS  CONST_03  C12  C11  N10  C9      0.00   0.0  0
 3QS  CONST_04  C12  C13  N14  C9      0.00   0.0  0
 3QS  CONST_05  N10  C11  C12  C13     0.00   0.0  0
 3QS  CONST_06  N10  C9   N14  C13     0.00   0.0  0
 3QS  CONST_07  C19  C28  N29  C16     0.00   0.0  0
 3QS  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 3QS  CONST_09  N22  C18  C17  C16   180.00   0.0  0
 3QS  CONST_10  C28  N29  C16  C17     0.00   0.0  0
 3QS  CONST_11  C28  C19  C18  C17     0.00   0.0  0
 3QS  CONST_12  C20  C19  C18  C17   180.00   0.0  0
 3QS  CONST_13  C21  N22  C18  C17   180.00   0.0  0
 3QS  CONST_14  N29  C16  C17  C18     0.00   0.0  0
 3QS  CONST_15  N29  C28  C19  C18     0.00   0.0  0
 3QS  CONST_16  C21  C20  C19  C18     0.00   0.0  0
 3QS  CONST_17  C20  C21  N22  C18     0.00   0.0  0
 3QS  CONST_18  C21  N22  C18  C19     0.00   0.0  0
 3QS  CONST_19  N22  C21  C20  C19     0.00   0.0  0
 3QS  CONST_20  N29  C28  C19  C20   180.00   0.0  0
 3QS  CONST_21  N22  C18  C19  C20     0.00   0.0  0
 3QS  CONST_22  C28  C19  C20  C21   180.00   0.0  0
 3QS  CONST_23  C28  C19  C18  N22   180.00   0.0  0
 3QS  CONST_24  N6   C9   N10  C11   180.00   0.0  0
 3QS  CONST_25  N6   C9   N14  C13   180.00   0.0  0
 3QS  CONST_26  C23  N22  C18  C17     0.00   0.0  0
 3QS  CONST_27  C23  N22  C18  C19   180.00   0.0  0
 3QS  CONST_28  C23  N22  C21  C20   180.00   0.0  0
 3QS  CONST_29  N15  C13  C12  C11   180.00   0.0  0
 3QS  CONST_30  N15  C13  N14  C9    180.00   0.0  0
 3QS  CONST_31  C28  N29  C16  N15   180.00   0.0  0
 3QS  CONST_32  C18  C17  C16  N15   180.00   0.0  0
 3QS  CONST_33  H5   C11  N10  C9    180.00   0.0  0
 3QS  CONST_34  H10  C12  C11  N10   180.00   0.0  0
 3QS  CONST_35  H28  C28  N29  C16   180.00   0.0  0
 3QS  CONST_36  H17  C20  C19  C18   180.00   0.0  0
 3QS  CONST_37  H18  C21  N22  C18   180.00   0.0  0
 3QS  CONST_38  H16  C17  C18  C19   180.00   0.0  0
 3QS  Var_01    C9   N6   C5   C4    107.13  30.0  1
 3QS  Var_02    N10  C9   N6   C5      6.07  30.0  1
 3QS  Var_03    C8   C7   N6   C5     57.47  30.0  1
 3QS  Var_04    N6   C5   C4   C3     54.84  30.0  1
 3QS  Var_05    N6   C7   C8   C3    -54.56  30.0  1
 3QS  Var_06    C25  C26  C27  C23    38.74  30.0  1
 3QS  Var_07    C26  C25  C24  C23    28.77  30.0  1
 3QS  Var_08    C27  C26  C25  C24   -41.84  30.0  1
 3QS  Var_09    C16  N15  C13  C12  -179.39  30.0  2
 3QS  Var_10    N29  C16  N15  C13    49.54  30.0  2
 3QS  Var_11    H12  C1   O2   C3     70.62  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
 3QS  chir_01  C3   C4   C8   O2   negativ
 3QS  chir_02  C23  N22  C27  C24  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
 3QS  plan-1  C11  0.020
 3QS  plan-1  C9   0.020
 3QS  plan-1  C12  0.020
 3QS  plan-1  C13  0.020
 3QS  plan-1  N6   0.020
 3QS  plan-1  N10  0.020
 3QS  plan-1  N14  0.020
 3QS  plan-1  N15  0.020
 3QS  plan-1  H5   0.020
 3QS  plan-1  H10  0.020
 3QS  plan-2  N15  0.020
 3QS  plan-2  C16  0.020
 3QS  plan-2  C17  0.020
 3QS  plan-2  C18  0.020
 3QS  plan-2  C19  0.020
 3QS  plan-2  C20  0.020
 3QS  plan-2  C21  0.020
 3QS  plan-2  N22  0.020
 3QS  plan-2  C23  0.020
 3QS  plan-2  C28  0.020
 3QS  plan-2  N29  0.020
 3QS  plan-2  H16  0.020
 3QS  plan-2  H17  0.020
 3QS  plan-2  H18  0.020
 3QS  plan-2  H28  0.020

