# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:50:05 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (1-{6-[6-(cyclopentylamino)-1H-indazol-1-yl]pyrazin-2-yl}-1H-pyrrol-3-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1ccn(c1)c2cncc(n2)n3ncc4ccc(NC5CCCC5)cc34
#
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
 ATK  ATK  '(1-{6-[6-(cyclopentylamino)-1H-indazol-1-yl]pyrazin-2-yl}-1H-pyrrol-3-yl)acetic acid'  ligand  51  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ATK
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
 ATK  N1    N  N      0  -0.344   2.1060  -3.8677   0.5218
 ATK  N4    N  N      0  -0.464   0.5570  -1.6129   0.3438
 ATK  C11   C  CR16   0  -0.148   0.8026  -3.9713   0.3472
 ATK  C12   C  CR6    0   0.474   0.0201  -2.8136   0.2612
 ATK  N13   N  N      0  -0.520  -1.3502  -2.8875   0.0847
 ATK  C14   C  CR6    0   0.516   1.8643  -1.5239   0.5199
 ATK  C15   C  CR16   0  -0.158   2.6569  -2.6690   0.6138
 ATK  N15   N  NR5    0  -0.554   2.3967  -0.2477   0.6155
 ATK  C17   C  CR6    0   0.472  -2.2604  -1.8871  -0.1819
 ATK  C18   C  CR6    0  -0.166  -3.5073  -2.5305  -0.2426
 ATK  N20   N  N      0  -0.255  -1.9549  -4.1010   0.1834
 ATK  C28   C  C1     0  -0.056  -3.2241  -3.9028  -0.0048
 ATK  C35   C  CR15   0  -0.117   3.7394   0.0765   0.6735
 ATK  C36   C  CR5    0   0.103   3.8622   1.4302   0.7740
 ATK  C37   C  CR15   0  -0.408   2.5332   1.9579   0.7838
 ATK  C38   C  CR15   0  -0.029   1.6636   0.9165   0.6889
 ATK  C44   C  CR16   0  -0.306  -4.6563  -1.7815  -0.5043
 ATK  N44   N  NH1    0  -0.695  -3.1689   1.5567  -0.9058
 ATK  C45   C  CR16   0  -0.348  -4.5431  -0.4275  -0.7037
 ATK  C46   C  CR6    0   0.423  -3.2790   0.2216  -0.6567
 ATK  C47   C  CR16   0  -0.433  -2.1240  -0.5201  -0.3862
 ATK  C48   C  CR15   0  -0.126  -4.2725   2.4977  -0.8683
 ATK  C57   C  CH2    0  -0.468  -3.7436   3.9013  -1.1581
 ATK  C58   C  CH2    0  -0.463  -3.1728   4.4011   0.1837
 ATK  C59   C  CH2    0  -0.449  -3.8275   3.5194   1.2714
 ATK  C60   C  CH2    0  -0.445  -4.8659   2.6680   0.5346
 ATK  O61   O  O      0  -0.597   4.6063   3.1998  -1.2380
 ATK  O63   O  OC    -1  -0.627   6.5262   3.7445  -0.2458
 ATK  C66   C  CH2    0  -0.714   5.1294   2.2026   0.8776
 ATK  C68   C  C      0   0.421   5.4411   3.1330  -0.3192
 ATK  H11   H  HCR6   0   0.287   0.3722  -4.9596   0.2752
 ATK  H15   H  HCR6   0   0.287   3.7270  -2.6249   0.7648
 ATK  H28   H  H      0   0.280  -3.9176  -4.7299   0.0320
 ATK  H35   H  HCR5   0   0.286   4.5078  -0.6765   0.6285
 ATK  H37   H  HCR5   0   0.242   2.2578   2.9979   0.8632
 ATK  H38   H  HCR5   0   0.276   0.5884   0.9005   0.6812
 ATK  H44   H  HCR6   0   0.260  -5.6273  -2.2573  -0.5536
 ATK  HN44  H  HNH1   0   0.379  -2.2488   1.9481  -0.7800
 ATK  H45   H  HCR6   0   0.272  -5.4341   0.1486  -0.9109
 ATK  H47   H  HCR6   0   0.275  -1.1605  -0.0367  -0.3489
 ATK  H48   H  HCR5   0   0.251  -5.0270   2.2006  -1.6017
 ATK  H57   H  HCH2   0   0.246  -3.0173   3.9168  -1.9727
 ATK  H57A  H  HCH2   0   0.248  -4.5837   4.5244  -1.4692
 ATK  H58   H  HCH2   0   0.233  -2.0853   4.3118   0.2105
 ATK  H58A  H  HCH2   0   0.238  -3.3966   5.4579   0.3293
 ATK  H59   H  HCH2   0   0.228  -3.0827   2.8764   1.7435
 ATK  H59A  H  HCH2   0   0.236  -4.2790   4.1093   2.0693
 ATK  H60   H  HCH2   0   0.231  -5.8140   3.2060   0.4475
 ATK  H60A  H  HCH2   0   0.242  -5.0790   1.7209   1.0333
 ATK  H66   H  HCH2   0   0.241   5.1126   2.8216   1.7816
 ATK  H66A  H  HCH2   0   0.242   5.9723   1.5179   1.0118

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
 ATK  N1   C11   aromatic  1.319  0.020  1.319
 ATK  N1   C15   aromatic  1.322  0.020  1.322
 ATK  N4   C12   aromatic  1.318  0.020  1.318
 ATK  N4   C14   aromatic  1.322  0.020  1.322
 ATK  C11  C12   aromatic  1.400  0.020  1.400
 ATK  C12  N13   single    1.384  0.020  1.384
 ATK  N13  C17   aromatic  1.379  0.020  1.379
 ATK  N13  N20   aromatic  1.359  0.020  1.359
 ATK  C14  C15   aromatic  1.396  0.020  1.396
 ATK  C14  N15   single    1.386  0.020  1.386
 ATK  N15  C35   aromatic  1.383  0.020  1.383
 ATK  N15  C38   aromatic  1.378  0.020  1.378
 ATK  C17  C18   aromatic  1.404  0.020  1.404
 ATK  C17  C47   aromatic  1.389  0.020  1.389
 ATK  C18  C28   aromatic  1.421  0.020  1.421
 ATK  C18  C44   aromatic  1.396  0.020  1.396
 ATK  N20  C28   aromatic  1.298  0.020  1.298
 ATK  C35  C36   aromatic  1.363  0.020  1.363
 ATK  C36  C37   aromatic  1.430  0.020  1.430
 ATK  C36  C66   single    1.488  0.020  1.488
 ATK  C37  C38   aromatic  1.360  0.020  1.360
 ATK  C44  C45   aromatic  1.373  0.020  1.373
 ATK  N44  C46   single    1.363  0.020  1.363
 ATK  N44  C48   single    1.451  0.020  1.451
 ATK  C45  C46   aromatic  1.422  0.020  1.422
 ATK  C46  C47   aromatic  1.399  0.020  1.399
 ATK  C48  C57   single    1.528  0.020  1.528
 ATK  C48  C60   single    1.533  0.020  1.533
 ATK  C57  C58   single    1.541  0.020  1.541
 ATK  C58  C59   single    1.546  0.020  1.546
 ATK  C59  C60   single    1.532  0.020  1.532
 ATK  O61  C68   deloc     1.243  0.020  1.243
 ATK  O63  C68   deloc     1.248  0.020  1.248
 ATK  C66  C68   single    1.548  0.020  1.548
 ATK  C11  H11   single    0.930  0.020  1.080
 ATK  C15  H15   single    0.930  0.020  1.080
 ATK  C28  H28   single    0.930  0.020  1.080
 ATK  C35  H35   single    0.930  0.020  1.080
 ATK  C37  H37   single    0.930  0.020  1.080
 ATK  C38  H38   single    0.930  0.020  1.080
 ATK  C44  H44   single    0.930  0.020  1.080
 ATK  N44  HN44  single    0.890  0.020  1.040
 ATK  C45  H45   single    0.930  0.020  1.080
 ATK  C47  H47   single    0.930  0.020  1.080
 ATK  C48  H48   single    0.970  0.020  1.090
 ATK  C57  H57   single    0.970  0.020  1.090
 ATK  C57  H57A  single    0.970  0.020  1.090
 ATK  C58  H58   single    0.970  0.020  1.090
 ATK  C58  H58A  single    0.970  0.020  1.090
 ATK  C59  H59   single    0.970  0.020  1.090
 ATK  C59  H59A  single    0.970  0.020  1.090
 ATK  C60  H60   single    0.970  0.020  1.090
 ATK  C60  H60A  single    0.970  0.020  1.090
 ATK  C66  H66   single    0.970  0.020  1.090
 ATK  C66  H66A  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
 ATK  C15   N1   C11  119.47  3.000
 ATK  C14   N4   C12  118.20  3.000
 ATK  H11   C11  C12  121.99  3.000
 ATK  H11   C11  N1   118.31  3.000
 ATK  C12   C11  N1   119.70  3.000
 ATK  N13   C12  C11  121.15  3.000
 ATK  N13   C12  N4   117.40  3.000
 ATK  C11   C12  N4   121.46  3.000
 ATK  N20   N13  C17  111.60  3.000
 ATK  N20   N13  C12  118.62  3.000
 ATK  C17   N13  C12  129.78  3.000
 ATK  N15   C14  C15  122.18  3.000
 ATK  N15   C14  N4   116.80  3.000
 ATK  C15   C14  N4   121.02  3.000
 ATK  H15   C15  C14  122.53  3.000
 ATK  H15   C15  N1   117.31  3.000
 ATK  C14   C15  N1   120.16  3.000
 ATK  C38   N15  C35  108.45  3.000
 ATK  C38   N15  C14  125.26  3.000
 ATK  C35   N15  C14  126.29  3.000
 ATK  C47   C17  C18  122.12  3.000
 ATK  C47   C17  N13  132.68  3.000
 ATK  C18   C17  N13  105.19  3.000
 ATK  C44   C18  C28  135.50  3.000
 ATK  C44   C18  C17  119.54  3.000
 ATK  C28   C18  C17  104.97  3.000
 ATK  C28   N20  N13  106.74  3.000
 ATK  H28   C28  N20  120.39  3.000
 ATK  H28   C28  C18  128.11  3.000
 ATK  N20   C28  C18  111.50  3.000
 ATK  H35   C35  C36  129.30  3.000
 ATK  H35   C35  N15  121.82  3.000
 ATK  C36   C35  N15  108.87  3.000
 ATK  C66   C36  C37  126.84  3.000
 ATK  C66   C36  C35  126.69  3.000
 ATK  C37   C36  C35  106.46  3.000
 ATK  H37   C37  C38  125.46  3.000
 ATK  H37   C37  C36  126.41  3.000
 ATK  C38   C37  C36  108.13  3.000
 ATK  H38   C38  C37  130.63  3.000
 ATK  H38   C38  N15  121.27  3.000
 ATK  C37   C38  N15  108.09  3.000
 ATK  H44   C44  C45  120.05  3.000
 ATK  H44   C44  C18  120.73  3.000
 ATK  C45   C44  C18  119.22  3.000
 ATK  HN44  N44  C48  116.06  3.000
 ATK  HN44  N44  C46  115.57  3.000
 ATK  C48   N44  C46  124.70  3.000
 ATK  H45   C45  C46  119.73  3.000
 ATK  H45   C45  C44  119.03  3.000
 ATK  C46   C45  C44  121.24  3.000
 ATK  C47   C46  C45  119.89  3.000
 ATK  C47   C46  N44  119.21  3.000
 ATK  C45   C46  N44  120.87  3.000
 ATK  H47   C47  C46  120.43  3.000
 ATK  H47   C47  C17  121.59  3.000
 ATK  C46   C47  C17  117.98  3.000
 ATK  H48   C48  C60  112.14  3.000
 ATK  H48   C48  C57  111.19  3.000
 ATK  C60   C48  C57  101.86  3.000
 ATK  H48   C48  N44  109.35  3.000
 ATK  C60   C48  N44  112.97  3.000
 ATK  C57   C48  N44  109.13  3.000
 ATK  H57A  C57  H57  106.94  3.000
 ATK  H57A  C57  C58  110.37  3.000
 ATK  H57   C57  C58  113.49  3.000
 ATK  H57A  C57  C48  108.19  3.000
 ATK  H57   C57  C48  112.64  3.000
 ATK  C58   C57  C48  105.13  3.000
 ATK  H58A  C58  H58  106.30  3.000
 ATK  H58A  C58  C59  111.84  3.000
 ATK  H58   C58  C59  110.99  3.000
 ATK  H58A  C58  C57  110.77  3.000
 ATK  H58   C58  C57  111.33  3.000
 ATK  C59   C58  C57  105.71  3.000
 ATK  H59A  C59  H59  106.55  3.000
 ATK  H59A  C59  C60  111.84  3.000
 ATK  H59   C59  C60  110.07  3.000
 ATK  H59A  C59  C58  112.45  3.000
 ATK  H59   C59  C58  110.57  3.000
 ATK  C60   C59  C58  105.41  3.000
 ATK  H60A  C60  H60  107.11  3.000
 ATK  H60A  C60  C59  113.27  3.000
 ATK  H60   C60  C59  110.64  3.000
 ATK  H60A  C60  C48  113.42  3.000
 ATK  H60   C60  C48  108.51  3.000
 ATK  C59   C60  C48  103.86  3.000
 ATK  H66A  C66  H66  105.31  3.000
 ATK  H66A  C66  C68  108.42  3.000
 ATK  H66   C66  C68  107.55  3.000
 ATK  H66A  C66  C36  109.87  3.000
 ATK  H66   C66  C36  109.74  3.000
 ATK  C68   C66  C36  115.46  3.000
 ATK  C66   C68  O63  115.10  3.000
 ATK  C66   C68  O61  117.94  3.000
 ATK  O63   C68  O61  126.95  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
 ATK  CONST_01  N4    C12  C11  N1     0.00   0.0  0
 ATK  CONST_02  N13   C12  C11  N1   180.00   0.0  0
 ATK  CONST_03  N4    C14  C15  N1     0.00   0.0  0
 ATK  CONST_04  N15   C14  C15  N1   180.00   0.0  0
 ATK  CONST_05  C17   N13  C12  N4     0.00   0.0  0
 ATK  CONST_06  N20   N13  C12  N4   180.00   0.0  0
 ATK  CONST_07  C35   N15  C14  N4   180.00   0.0  0
 ATK  CONST_08  C38   N15  C14  N4     0.00   0.0  0
 ATK  CONST_09  C14   C15  N1   C11    0.00   0.0  0
 ATK  CONST_10  C14   N4   C12  C11    0.00   0.0  0
 ATK  CONST_11  C17   N13  C12  C11  180.00   0.0  0
 ATK  CONST_12  N20   N13  C12  C11    0.00   0.0  0
 ATK  CONST_13  C15   C14  N4   C12    0.00   0.0  0
 ATK  CONST_14  N15   C14  N4   C12  180.00   0.0  0
 ATK  CONST_15  C15   N1   C11  C12    0.00   0.0  0
 ATK  CONST_16  C18   C17  N13  C12  180.00   0.0  0
 ATK  CONST_17  C47   C17  N13  C12    0.00   0.0  0
 ATK  CONST_18  C28   N20  N13  C12  180.00   0.0  0
 ATK  CONST_19  C14   N4   C12  N13  180.00   0.0  0
 ATK  CONST_20  C28   C18  C17  N13    0.00   0.0  0
 ATK  CONST_21  C44   C18  C17  N13  180.00   0.0  0
 ATK  CONST_22  C46   C47  C17  N13  180.00   0.0  0
 ATK  CONST_23  C18   C28  N20  N13    0.00   0.0  0
 ATK  CONST_24  C36   C35  N15  C14  180.00   0.0  0
 ATK  CONST_25  C37   C38  N15  C14  180.00   0.0  0
 ATK  CONST_26  C35   N15  C14  C15    0.00   0.0  0
 ATK  CONST_27  C38   N15  C14  C15  180.00   0.0  0
 ATK  CONST_28  C37   C36  C35  N15    0.00   0.0  0
 ATK  CONST_29  C36   C37  C38  N15    0.00   0.0  0
 ATK  CONST_30  C28   N20  N13  C17    0.00   0.0  0
 ATK  CONST_31  N20   C28  C18  C17    0.00   0.0  0
 ATK  CONST_32  C45   C44  C18  C17    0.00   0.0  0
 ATK  CONST_33  C45   C46  C47  C17    0.00   0.0  0
 ATK  CONST_34  N20   N13  C17  C18    0.00   0.0  0
 ATK  CONST_35  C46   C47  C17  C18    0.00   0.0  0
 ATK  CONST_36  C46   C45  C44  C18    0.00   0.0  0
 ATK  CONST_37  C47   C17  N13  N20  180.00   0.0  0
 ATK  CONST_38  C44   C18  C28  N20  180.00   0.0  0
 ATK  CONST_39  C47   C17  C18  C28  180.00   0.0  0
 ATK  CONST_40  C45   C44  C18  C28  180.00   0.0  0
 ATK  CONST_41  C37   C38  N15  C35    0.00   0.0  0
 ATK  CONST_42  C38   C37  C36  C35    0.00   0.0  0
 ATK  CONST_43  C38   N15  C35  C36    0.00   0.0  0
 ATK  CONST_44  C47   C17  C18  C44    0.00   0.0  0
 ATK  CONST_45  C47   C46  C45  C44    0.00   0.0  0
 ATK  CONST_46  C66   C36  C35  N15  180.00   0.0  0
 ATK  CONST_47  N44   C46  C47  C17  180.00   0.0  0
 ATK  CONST_48  C66   C36  C37  C38  180.00   0.0  0
 ATK  CONST_49  N44   C46  C45  C44  180.00   0.0  0
 ATK  CONST_52  H11   C11  C12  N4   180.00   0.0  0
 ATK  CONST_53  H15   C15  C14  N4   180.00   0.0  0
 ATK  CONST_54  H47   C47  C17  N13    0.00   0.0  0
 ATK  CONST_55  H28   C28  N20  N13  180.00   0.0  0
 ATK  CONST_56  H35   C35  N15  C14    0.00   0.0  0
 ATK  CONST_57  H38   C38  N15  C14    0.00   0.0  0
 ATK  CONST_58  H37   C37  C38  N15  180.00   0.0  0
 ATK  CONST_59  H44   C44  C18  C17  180.00   0.0  0
 ATK  CONST_60  H45   C45  C44  C18  180.00   0.0  0
 ATK  CONST_61  HN44  N44  C46  C45  180.00   0.0  0
 ATK  Var_01    C59   C58  C57  C48  -19.70  30.0  1
 ATK  Var_02    C58   C59  C60  C48   30.26  30.0  1
 ATK  Var_03    C60   C59  C58  C57   -6.55  30.0  1
 ATK  Var_04    C68   C66  C36  C35  114.60  30.0  2
 ATK  Var_05    O61   C68  C66  C36    2.35  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
 ATK  chir_01  C48  N44  C57  C60  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
 ATK  plan-1  C14   0.020
 ATK  plan-1  N15   0.020
 ATK  plan-1  C35   0.020
 ATK  plan-1  C36   0.020
 ATK  plan-1  C37   0.020
 ATK  plan-1  C38   0.020
 ATK  plan-1  C66   0.020
 ATK  plan-1  H35   0.020
 ATK  plan-1  H37   0.020
 ATK  plan-1  H38   0.020
 ATK  plan-2  N1    0.020
 ATK  plan-2  N4    0.020
 ATK  plan-2  C11   0.020
 ATK  plan-2  C12   0.020
 ATK  plan-2  N13   0.020
 ATK  plan-2  C14   0.020
 ATK  plan-2  C15   0.020
 ATK  plan-2  N15   0.020
 ATK  plan-2  H11   0.020
 ATK  plan-2  H15   0.020
 ATK  plan-3  C12   0.020
 ATK  plan-3  N13   0.020
 ATK  plan-3  C17   0.020
 ATK  plan-3  C18   0.020
 ATK  plan-3  N20   0.020
 ATK  plan-3  C28   0.020
 ATK  plan-3  C44   0.020
 ATK  plan-3  N44   0.020
 ATK  plan-3  C45   0.020
 ATK  plan-3  C46   0.020
 ATK  plan-3  C47   0.020
 ATK  plan-3  H28   0.020
 ATK  plan-3  H44   0.020
 ATK  plan-3  H45   0.020
 ATK  plan-3  H47   0.020
 ATK  plan-4  N44   0.020
 ATK  plan-4  C46   0.020
 ATK  plan-4  C48   0.020
 ATK  plan-4  HN44  0.020
 ATK  plan-5  O61   0.020
 ATK  plan-5  O63   0.020
 ATK  plan-5  C66   0.020
 ATK  plan-5  C68   0.020

