# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:49:41 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-(but-3-en-1-yl)-4-[3-(morpholine-4-carbonyl)phenyl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CCCN1C=C(c2cccc(c2)C(=O)N3CCOCC3)c4cc[nH]c4C1=O
#
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
 G9Y  G9Y  6-(but-3-en-1-yl)-4-[3-(morpholine-4-carbonyl)phenyl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one  ligand  51  28  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9Y
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
 G9Y  C4   C  CH2   0  -0.321   3.7125   1.6007   0.8740
 G9Y  C14  C  CR6   0   0.530   3.9924  -0.5967  -0.1509
 G9Y  C6   C  CR16  0  -0.028   1.8673   0.0205   0.8461
 G9Y  C7   C  CR6   0  -0.102   1.2348  -1.1435   0.5514
 G9Y  C8   C  CR56  0   0.173   2.0117  -2.1279  -0.1377
 G9Y  C9   C  CR15  0  -0.458   1.7549  -3.4224  -0.6570
 G9Y  C10  C  CR15  0  -0.011   2.9209  -3.8449  -1.2519
 G9Y  C13  C  CR56  0   0.140   3.3334  -1.8273  -0.4509
 G9Y  C3   C  CH2   0  -0.496   3.5558   2.6052  -0.2669
 G9Y  C29  C  CH2   0  -0.330  -3.2700   0.5795  -1.3956
 G9Y  C19  C  CR16  0  -0.286  -2.8281  -1.7113   1.7459
 G9Y  C18  C  CR16  0  -0.232  -1.9074  -2.7389   1.8890
 G9Y  N5   N  NR6   0  -0.532   3.1748   0.2876   0.5295
 G9Y  C2   C  C1    0  -0.162   4.0227   3.9639   0.1493
 G9Y  O23  O  O     0  -0.485  -3.9270   1.0317   2.1217
 G9Y  C16  C  CR6   0   0.079  -0.1704  -1.3531   0.9366
 G9Y  N24  N  NT    0  -0.457  -3.6278   1.1740  -0.1177
 G9Y  C28  C  CH2   0  -0.175  -4.5284   0.3480  -2.2180
 G9Y  C25  C  CH2   0  -0.330  -4.4495   2.3648  -0.2609
 G9Y  C20  C  CR6   0  -0.056  -2.4308  -0.5103   1.1688
 G9Y  C17  C  CR16  0  -0.321  -0.5899  -2.5617   1.4950
 G9Y  N11  N  NR15  0  -0.644   3.8637  -2.8834  -1.1247
 G9Y  C26  C  CH2   0  -0.184  -5.6606   2.0628  -1.1254
 G9Y  C22  C  C     0   0.510  -3.4037   0.6252   1.0924
 G9Y  O27  O  O2    0  -0.481  -5.2773   1.5312  -2.3751
 G9Y  C21  C  CR16  0  -0.327  -1.1119  -0.3386   0.7655
 G9Y  H1   H  HCH2  0   0.272   4.7610   1.4924   1.1436
 G9Y  H2   H  HCH2  0   0.266   3.1853   1.9496   1.7621
 G9Y  H3   H  HCR6  0   0.296   1.3645   0.8098   1.3876
 G9Y  H4   H  HCR5  0   0.256   0.8343  -3.9817  -0.6163
 G9Y  H5   H  HCR5  0   0.288   3.1390  -4.7701  -1.7600
 G9Y  H6   H  HCH2  0   0.250   4.1120   2.2620  -1.1410
 G9Y  H7   H  HCH2  0   0.248   2.4991   2.6517  -0.5492
 G9Y  H9   H  HCH2  0   0.278  -2.7617  -0.3710  -1.2533
 G9Y  H10  H  HCR6  0   0.263  -3.8524  -1.8507   2.0670
 G9Y  H11  H  HCR6  0   0.263  -2.2152  -3.6805   2.3241
 G9Y  H15  H  H     0   0.247   3.4645   4.4343   0.9547
 G9Y  H16  H  HCH2  0   0.247  -4.2545  -0.0029  -3.2137
 G9Y  H17  H  HCH2  0   0.209  -5.1342  -0.4332  -1.7367
 G9Y  H18  H  HCH2  0   0.270  -4.7646   2.7200   0.7167
 G9Y  H19  H  HCH2  0   0.253  -3.8462   3.1496  -0.7283
 G9Y  H20  H  HCR6  0   0.261   0.1230  -3.3623   1.6452
 G9Y  H12  H  HNR5  0   0.416   4.8043  -2.9351  -1.4811
 G9Y  H21  H  HCH2  0   0.211  -6.3240   1.3653  -0.5956
 G9Y  H22  H  HCH2  0   0.245  -6.2175   2.9811  -1.3164
 G9Y  H23  H  HCR6  0   0.263  -0.8079   0.5943   0.3050
 G9Y  O15  O  O     0  -0.513   5.1530  -0.3235  -0.4504
 G9Y  C1   C  C2    0  -0.530   5.0571   4.6049  -0.3816
 G9Y  H8   H  HCH2  0   0.252  -2.5877   1.2479  -1.9294
 G9Y  H13  H  H     0   0.235   5.6436   4.1752  -1.1858
 G9Y  H14  H  H     0   0.239   5.3532   5.5866  -0.0358

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
 G9Y  C4   N5   single    1.460  0.020  1.460
 G9Y  C4   C3   single    1.528  0.020  1.528
 G9Y  N5   C14  single    1.383  0.020  1.383
 G9Y  N5   C6   single    1.372  0.020  1.372
 G9Y  O15  C14  double    1.229  0.020  1.229
 G9Y  C28  O27  single    1.409  0.020  1.409
 G9Y  C28  C29  single    1.521  0.020  1.521
 G9Y  C1   C2   double    1.328  0.020  1.328
 G9Y  C2   C3   single    1.496  0.020  1.496
 G9Y  C14  C13  single    1.428  0.020  1.428
 G9Y  C6   C7   double    1.357  0.020  1.357
 G9Y  C13  C8   aromatic  1.391  0.020  1.391
 G9Y  C13  N11  aromatic  1.360  0.020  1.360
 G9Y  O27  C26  single    1.411  0.020  1.411
 G9Y  C29  N24  single    1.454  0.020  1.454
 G9Y  C7   C8   single    1.431  0.020  1.431
 G9Y  C7   C16  single    1.472  0.020  1.472
 G9Y  C17  C16  aromatic  1.396  0.020  1.396
 G9Y  C17  C18  aromatic  1.387  0.020  1.387
 G9Y  C8   C9   aromatic  1.418  0.020  1.418
 G9Y  N11  C10  aromatic  1.353  0.020  1.353
 G9Y  C16  C21  aromatic  1.395  0.020  1.395
 G9Y  C18  C19  aromatic  1.387  0.020  1.387
 G9Y  C10  C9   aromatic  1.376  0.020  1.376
 G9Y  C21  C20  aromatic  1.390  0.020  1.390
 G9Y  C19  C20  aromatic  1.390  0.020  1.390
 G9Y  C26  C25  single    1.518  0.020  1.518
 G9Y  C20  C22  single    1.497  0.020  1.497
 G9Y  N24  C22  single    1.347  0.020  1.347
 G9Y  N24  C25  single    1.454  0.020  1.454
 G9Y  C22  O23  double    1.224  0.020  1.224
 G9Y  C4   H1   single    0.970  0.020  1.090
 G9Y  C4   H2   single    0.970  0.020  1.090
 G9Y  C6   H3   single    0.930  0.020  1.080
 G9Y  C9   H4   single    0.930  0.020  1.080
 G9Y  C10  H5   single    0.930  0.020  1.080
 G9Y  C3   H6   single    0.970  0.020  1.090
 G9Y  C3   H7   single    0.970  0.020  1.090
 G9Y  C29  H8   single    0.970  0.020  1.090
 G9Y  C29  H9   single    0.970  0.020  1.090
 G9Y  C19  H10  single    0.930  0.020  1.080
 G9Y  C18  H11  single    0.930  0.020  1.080
 G9Y  C1   H13  single    0.930  0.020  1.080
 G9Y  C1   H14  single    0.930  0.020  1.080
 G9Y  C2   H15  single    0.930  0.020  1.080
 G9Y  C28  H16  single    0.970  0.020  1.090
 G9Y  C28  H17  single    0.970  0.020  1.090
 G9Y  C25  H18  single    0.970  0.020  1.090
 G9Y  C25  H19  single    0.970  0.020  1.090
 G9Y  C17  H20  single    0.930  0.020  1.080
 G9Y  N11  H12  single    0.860  0.020  1.020
 G9Y  C26  H21  single    0.970  0.020  1.090
 G9Y  C26  H22  single    0.970  0.020  1.090
 G9Y  C21  H23  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
 G9Y  H2   C4   H1   107.22  3.000
 G9Y  H2   C4   N5   107.58  3.000
 G9Y  H1   C4   N5   108.90  3.000
 G9Y  H2   C4   C3   110.38  3.000
 G9Y  H1   C4   C3   110.44  3.000
 G9Y  N5   C4   C3   112.16  3.000
 G9Y  O15  C14  N5   122.40  3.000
 G9Y  O15  C14  C13  125.18  3.000
 G9Y  N5   C14  C13  112.43  3.000
 G9Y  H3   C6   N5   114.63  3.000
 G9Y  H3   C6   C7   121.21  3.000
 G9Y  N5   C6   C7   124.14  3.000
 G9Y  C16  C7   C8   123.11  3.000
 G9Y  C16  C7   C6   120.68  3.000
 G9Y  C8   C7   C6   116.21  3.000
 G9Y  C13  C8   C9   106.67  3.000
 G9Y  C9   C8   C7   134.91  3.000
 G9Y  C13  C8   C7   118.39  3.000
 G9Y  H4   C9   C10  125.52  3.000
 G9Y  H4   C9   C8   127.91  3.000
 G9Y  C10  C9   C8   106.57  3.000
 G9Y  H5   C10  N11  120.90  3.000
 G9Y  H5   C10  C9   129.72  3.000
 G9Y  N11  C10  C9   109.38  3.000
 G9Y  N11  C13  C8   108.31  3.000
 G9Y  N11  C13  C14  126.39  3.000
 G9Y  C8   C13  C14  125.27  3.000
 G9Y  H7   C3   H6   107.38  3.000
 G9Y  H7   C3   C2   109.54  3.000
 G9Y  H6   C3   C2   110.45  3.000
 G9Y  H7   C3   C4   108.63  3.000
 G9Y  H6   C3   C4   109.82  3.000
 G9Y  C2   C3   C4   110.94  3.000
 G9Y  H9   C29  H8   107.84  3.000
 G9Y  H9   C29  C28  108.93  3.000
 G9Y  H8   C29  C28  110.19  3.000
 G9Y  H9   C29  N24  110.94  3.000
 G9Y  H8   C29  N24  109.42  3.000
 G9Y  C28  C29  N24  109.50  3.000
 G9Y  H10  C19  C20  120.32  3.000
 G9Y  H10  C19  C18  120.14  3.000
 G9Y  C20  C19  C18  119.54  3.000
 G9Y  H11  C18  C17  119.72  3.000
 G9Y  H11  C18  C19  119.83  3.000
 G9Y  C17  C18  C19  120.45  3.000
 G9Y  C6   N5   C14  123.54  3.000
 G9Y  C6   N5   C4   118.15  3.000
 G9Y  C14  N5   C4   118.25  3.000
 G9Y  H15  C2   C1   119.17  3.000
 G9Y  H15  C2   C3   116.04  3.000
 G9Y  C1   C2   C3   124.79  3.000
 G9Y  C21  C16  C17  118.43  3.000
 G9Y  C21  C16  C7   120.58  3.000
 G9Y  C17  C16  C7   120.99  3.000
 G9Y  C22  N24  C25  121.07  3.000
 G9Y  C25  N24  C29  112.79  3.000
 G9Y  C22  N24  C29  125.58  3.000
 G9Y  H17  C28  H16  108.02  3.000
 G9Y  H17  C28  O27  110.64  3.000
 G9Y  H16  C28  O27  107.56  3.000
 G9Y  H17  C28  C29  109.11  3.000
 G9Y  H16  C28  C29  109.56  3.000
 G9Y  O27  C28  C29  111.85  3.000
 G9Y  H19  C25  H18  108.02  3.000
 G9Y  H19  C25  C26  109.82  3.000
 G9Y  H18  C25  C26  110.24  3.000
 G9Y  H19  C25  N24  108.53  3.000
 G9Y  H18  C25  N24  110.05  3.000
 G9Y  C26  C25  N24  110.12  3.000
 G9Y  C21  C20  C22  120.54  3.000
 G9Y  C22  C20  C19  119.37  3.000
 G9Y  C21  C20  C19  119.89  3.000
 G9Y  H20  C17  C16  119.87  3.000
 G9Y  H20  C17  C18  119.46  3.000
 G9Y  C16  C17  C18  120.65  3.000
 G9Y  H12  N11  C13  125.39  3.000
 G9Y  H12  N11  C10  125.53  3.000
 G9Y  C13  N11  C10  109.07  3.000
 G9Y  H22  C26  H21  108.09  3.000
 G9Y  H22  C26  O27  107.51  3.000
 G9Y  H21  C26  O27  110.60  3.000
 G9Y  H22  C26  C25  109.84  3.000
 G9Y  H21  C26  C25  109.47  3.000
 G9Y  O27  C26  C25  111.26  3.000
 G9Y  C20  C22  N24  117.56  3.000
 G9Y  N24  C22  O23  123.28  3.000
 G9Y  C20  C22  O23  119.13  3.000
 G9Y  C26  O27  C28  111.22  3.000
 G9Y  H23  C21  C20  119.73  3.000
 G9Y  H23  C21  C16  119.26  3.000
 G9Y  C20  C21  C16  121.01  3.000
 G9Y  H14  C1   H13  116.65  3.000
 G9Y  H14  C1   C2   121.56  3.000
 G9Y  H13  C1   C2   121.79  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
 G9Y  CONST_01  C10  N11  C13  C8      0.00   0.0  0
 G9Y  CONST_02  N11  C10  C9   C8      0.00   0.0  0
 G9Y  CONST_03  N11  C13  C8   C9      0.00   0.0  0
 G9Y  CONST_04  C13  N11  C10  C9      0.00   0.0  0
 G9Y  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 G9Y  CONST_06  C16  C17  C18  C19     0.00   0.0  0
 G9Y  CONST_07  C16  C21  C20  C19     0.00   0.0  0
 G9Y  CONST_08  C21  C16  C17  C18     0.00   0.0  0
 G9Y  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 G9Y  CONST_10  C17  C16  C21  C20     0.00   0.0  0
 G9Y  CONST_11  C17  C18  C19  C20     0.00   0.0  0
 G9Y  CONST_12  C18  C17  C16  C7    180.00   0.0  0
 G9Y  CONST_13  C20  C21  C16  C7    180.00   0.0  0
 G9Y  CONST_14  C13  C14  N5   C6      0.00   0.0  0
 G9Y  CONST_15  C22  C20  C19  C18   180.00   0.0  0
 G9Y  CONST_16  C22  C20  C21  C16   180.00   0.0  0
 G9Y  CONST_18  C20  C22  N24  C25   180.00   0.0  0
 G9Y  CONST_19  C13  C14  N5   C4    180.00   0.0  0
 G9Y  CONST_20  O15  C14  N5   C6    180.00   0.0  0
 G9Y  CONST_21  H12  N11  C13  C14     0.00   0.0  0
 G9Y  CONST_22  H4   C9   C8   C7      0.00   0.0  0
 G9Y  CONST_23  H20  C17  C16  C7      0.00   0.0  0
 G9Y  CONST_24  H23  C21  C16  C7      0.00   0.0  0
 G9Y  CONST_25  H5   C10  C9   C8    180.00   0.0  0
 G9Y  CONST_26  H11  C18  C17  C16   180.00   0.0  0
 G9Y  CONST_27  H10  C19  C18  C17   180.00   0.0  0
 G9Y  CONST_28  O23  C22  N24  C29   180.00   0.0  0
 G9Y  CONST_29  C25  N24  C22  O23     0.00   0.0  0
 G9Y  CONST_30  O15  C14  N5   C4      0.00   0.0  0
 G9Y  CONST_31  H13  C1   C2   C3      0.00   0.0  0
 G9Y  CONST_32  H14  C1   C2   C3    180.00   0.0  0
 G9Y  Var_01    C17  C16  C7   C6   -136.31  30.0  2
 G9Y  Var_02    C26  C25  N24  C29    53.19  30.0  1
 G9Y  Var_03    O27  C28  C29  N24    55.12  30.0  1
 G9Y  Var_04    O27  C26  C25  N24   -55.19  30.0  1
 G9Y  Var_05    C25  C26  O27  C28    58.68  30.0  1
 G9Y  Var_06    C25  N24  C29  C28   -52.79  30.0  1
 G9Y  Var_07    N24  C22  C20  C19  -125.63  30.0  2
 G9Y  Var_08    C3   C4   N5   C14    85.43  30.0  2
 G9Y  Var_09    C2   C3   C4   N5    175.84  30.0  3
 G9Y  Var_10    C1   C2   C3   C4    115.66  30.0  1

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
 G9Y  plan-1  C7   0.020
 G9Y  plan-1  C19  0.020
 G9Y  plan-1  C18  0.020
 G9Y  plan-1  C16  0.020
 G9Y  plan-1  C20  0.020
 G9Y  plan-1  C17  0.020
 G9Y  plan-1  C22  0.020
 G9Y  plan-1  C21  0.020
 G9Y  plan-1  H10  0.020
 G9Y  plan-1  H11  0.020
 G9Y  plan-1  H20  0.020
 G9Y  plan-1  H23  0.020
 G9Y  plan-2  C4   0.020
 G9Y  plan-2  C14  0.020
 G9Y  plan-2  C6   0.020
 G9Y  plan-2  C7   0.020
 G9Y  plan-2  C8   0.020
 G9Y  plan-2  C9   0.020
 G9Y  plan-2  C10  0.020
 G9Y  plan-2  C13  0.020
 G9Y  plan-2  N5   0.020
 G9Y  plan-2  C16  0.020
 G9Y  plan-2  N11  0.020
 G9Y  plan-2  H3   0.020
 G9Y  plan-2  H4   0.020
 G9Y  plan-2  H5   0.020
 G9Y  plan-2  H12  0.020
 G9Y  plan-2  O15  0.020
 G9Y  plan-3  C29  0.020
 G9Y  plan-3  O23  0.020
 G9Y  plan-3  N24  0.020
 G9Y  plan-3  C25  0.020
 G9Y  plan-3  C20  0.020
 G9Y  plan-3  C22  0.020
 G9Y  plan-4  C3   0.020
 G9Y  plan-4  C2   0.020
 G9Y  plan-4  H15  0.020
 G9Y  plan-4  C1   0.020
 G9Y  plan-4  H13  0.020
 G9Y  plan-4  H14  0.020

