# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:48:52 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CN(CC2(CCCC2)n3ccc4cccnc34)C=C(O)C1=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
 M4H  M4H  '5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid'  ligand  45  26  .  2022-03-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M4H
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
 M4H  C5   C  CR16  0   0.081  107.7861  162.7152  100.4142
 M4H  C6   C  CR6   0  -0.371  108.2052  161.7683   99.5050
 M4H  C7   C  C     0   0.542  108.9701  160.6031   99.9764
 M4H  C3   C  CR16  0  -0.101  106.7648  164.0139   98.7504
 M4H  C2   C  CR6   0   0.187  107.1383  163.1358   97.7953
 M4H  C1   C  CR6   0   0.354  107.8783  161.9166   98.1122
 M4H  C12  C  CH2   0  -0.355  106.5464  164.6724  101.0951
 M4H  C13  C  CT    0   0.108  105.1606  164.2311  101.6103
 M4H  C14  C  CH2   0  -0.490  104.0584  164.4330  100.5634
 M4H  C15  C  CH2   0  -0.458  103.8348  165.9473  100.5364
 M4H  C16  C  CH2   0  -0.463  104.2334  166.4496  101.9429
 M4H  C17  C  CH2   0  -0.433  104.7133  165.2096  102.7078
 M4H  C19  C  CR56  0   0.464  105.9800  162.3881  103.1187
 M4H  C20  C  CR56  0   0.044  105.9041  160.9768  103.1327
 M4H  C21  C  CR15  0  -0.440  105.0945  160.5979  102.0234
 M4H  C22  C  CR15  0   0.001  104.7262  161.7522  101.4027
 M4H  C23  C  CR16  0  -0.223  106.6046  160.3148  104.1379
 M4H  C24  C  CR16  0  -0.350  107.3238  161.0855  105.0336
 M4H  C25  C  CR16  0  -0.092  107.3335  162.4778  104.9011
 M4H  N18  N  NR5   0  -0.543  105.2397  162.8483  102.0595
 M4H  N26  N  N     0  -0.438  106.6759  163.1380  103.9588
 M4H  N4   N  NR6   0  -0.427  107.0806  163.7887  100.0666
 M4H  O10  O  O     0  -0.484  108.1666  161.1551   97.1841
 M4H  O11  O  OH1   0  -0.623  106.8491  163.3431   96.5074
 M4H  O8   O  O     0  -0.438  109.2949  159.6659   99.2879
 M4H  O9   O  OH1   0  -0.603  109.2758  160.6815  101.2703
 M4H  H1   H  HCR6  0   0.325  108.0201  162.6268  101.4645
 M4H  H2   H  HCR6  0   0.319  106.2308  164.9262   98.5249
 M4H  H3   H  HCH2  0   0.304  107.2549  164.6962  101.9217
 M4H  H4   H  HCH2  0   0.300  106.5008  165.6821  100.6882
 M4H  H5   H  HCH2  0   0.266  103.1525  163.9336  100.9164
 M4H  H6   H  HCH2  0   0.263  104.2882  164.0168   99.5811
 M4H  H7   H  HCH2  0   0.238  104.4471  166.4198   99.7656
 M4H  H8   H  HCH2  0   0.253  102.7999  166.1804  100.2904
 M4H  H9   H  HCH2  0   0.240  105.0258  167.1962  101.8758
 M4H  H10  H  HCH2  0   0.248  103.4014  166.9268  102.4593
 M4H  H11  H  HCH2  0   0.251  103.8851  164.7490  103.2508
 M4H  H12  H  HCH2  0   0.259  105.4977  165.4215  103.4325
 M4H  H13  H  HCR5  0   0.253  104.8204  159.6009  101.7191
 M4H  H14  H  HCR5  0   0.296  104.1148  161.8711  100.5242
 M4H  H15  H  HCR6  0   0.264  106.5929  159.2348  104.2149
 M4H  H16  H  HCR6  0   0.263  107.8862  160.6255  105.8344
 M4H  H17  H  HCR6  0   0.256  107.9066  163.0798  105.5968
 M4H  H18  H  HOH1  0   0.467  107.2166  162.5886   96.0171
 M4H  H19  H  HOH1  0   0.484  109.7460  159.8807  101.5434

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
 M4H  O11  C2   single    1.336  0.020  1.336
 M4H  O10  C1   double    1.235  0.020  1.235
 M4H  C2   C1   single    1.461  0.020  1.461
 M4H  C2   C3   double    1.350  0.020  1.350
 M4H  C1   C6   single    1.438  0.020  1.438
 M4H  C3   N4   single    1.372  0.020  1.372
 M4H  O8   C7   double    1.207  0.020  1.207
 M4H  C6   C7   single    1.471  0.020  1.471
 M4H  C6   C5   double    1.378  0.020  1.378
 M4H  N4   C5   single    1.331  0.020  1.331
 M4H  N4   C12  single    1.457  0.020  1.457
 M4H  C7   O9   single    1.332  0.020  1.332
 M4H  C14  C15  single    1.531  0.020  1.531
 M4H  C14  C13  single    1.533  0.020  1.533
 M4H  C15  C16  single    1.546  0.020  1.546
 M4H  C12  C13  single    1.543  0.020  1.543
 M4H  C13  N18  single    1.456  0.020  1.456
 M4H  C13  C17  single    1.537  0.020  1.537
 M4H  C22  N18  aromatic  1.377  0.020  1.377
 M4H  C22  C21  aromatic  1.361  0.020  1.361
 M4H  N18  C19  aromatic  1.372  0.020  1.372
 M4H  C16  C17  single    1.534  0.020  1.534
 M4H  C21  C20  aromatic  1.425  0.020  1.425
 M4H  C19  C20  aromatic  1.413  0.020  1.413
 M4H  C19  N26  aromatic  1.324  0.020  1.324
 M4H  C20  C23  aromatic  1.393  0.020  1.393
 M4H  N26  C25  aromatic  1.325  0.020  1.325
 M4H  C23  C24  aromatic  1.383  0.020  1.383
 M4H  C25  C24  aromatic  1.399  0.020  1.399
 M4H  C5   H1   single    0.930  0.020  1.080
 M4H  C3   H2   single    0.930  0.020  1.080
 M4H  C12  H3   single    0.970  0.020  1.090
 M4H  C12  H4   single    0.970  0.020  1.090
 M4H  C14  H5   single    0.970  0.020  1.090
 M4H  C14  H6   single    0.970  0.020  1.090
 M4H  C15  H7   single    0.970  0.020  1.090
 M4H  C15  H8   single    0.970  0.020  1.090
 M4H  C16  H9   single    0.970  0.020  1.090
 M4H  C16  H10  single    0.970  0.020  1.090
 M4H  C17  H11  single    0.970  0.020  1.090
 M4H  C17  H12  single    0.970  0.020  1.090
 M4H  C21  H13  single    0.930  0.020  1.080
 M4H  C22  H14  single    0.930  0.020  1.080
 M4H  C23  H15  single    0.930  0.020  1.080
 M4H  C24  H16  single    0.930  0.020  1.080
 M4H  C25  H17  single    0.930  0.020  1.080
 M4H  O11  H18  single    0.850  0.020  0.980
 M4H  O9   H19  single    0.850  0.020  0.980

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
 M4H  H1   C5   N4   115.78  3.000
 M4H  H1   C5   C6   121.31  3.000
 M4H  N4   C5   C6   122.90  3.000
 M4H  C1   C6   C7   120.67  3.000
 M4H  C7   C6   C5   119.40  3.000
 M4H  C1   C6   C5   119.93  3.000
 M4H  O9   C7   O8   122.54  3.000
 M4H  O9   C7   C6   112.58  3.000
 M4H  O8   C7   C6   124.88  3.000
 M4H  H2   C3   N4   116.89  3.000
 M4H  H2   C3   C2   122.55  3.000
 M4H  N4   C3   C2   120.54  3.000
 M4H  O11  C2   C1   116.62  3.000
 M4H  C1   C2   C3   121.97  3.000
 M4H  O11  C2   C3   121.41  3.000
 M4H  O10  C1   C2   118.03  3.000
 M4H  C2   C1   C6   114.28  3.000
 M4H  O10  C1   C6   127.68  3.000
 M4H  H4   C12  H3   106.89  3.000
 M4H  H4   C12  N4   108.28  3.000
 M4H  H3   C12  N4   108.09  3.000
 M4H  H4   C12  C13  110.62  3.000
 M4H  H3   C12  C13  109.71  3.000
 M4H  N4   C12  C13  113.04  3.000
 M4H  N18  C13  C17  113.59  3.000
 M4H  C17  C13  C14  101.22  3.000
 M4H  N18  C13  C14  112.01  3.000
 M4H  C17  C13  C12  108.52  3.000
 M4H  N18  C13  C12  109.01  3.000
 M4H  C14  C13  C12  112.33  3.000
 M4H  H6   C14  H5   106.91  3.000
 M4H  H6   C14  C15  113.09  3.000
 M4H  H5   C14  C15  109.67  3.000
 M4H  H6   C14  C13  114.39  3.000
 M4H  H5   C14  C13  108.36  3.000
 M4H  C15  C14  C13  104.31  3.000
 M4H  H8   C15  H7   106.31  3.000
 M4H  H8   C15  C16  112.40  3.000
 M4H  H7   C15  C16  110.92  3.000
 M4H  H8   C15  C14  110.76  3.000
 M4H  H7   C15  C14  111.01  3.000
 M4H  C16  C15  C14  105.53  3.000
 M4H  H10  C16  H9   106.51  3.000
 M4H  H10  C16  C17  110.89  3.000
 M4H  H9   C16  C17  110.90  3.000
 M4H  H10  C16  C15  112.13  3.000
 M4H  H9   C16  C15  110.72  3.000
 M4H  C17  C16  C15  105.77  3.000
 M4H  H12  C17  H11  107.31  3.000
 M4H  H12  C17  C16  113.58  3.000
 M4H  H11  C17  C16  110.58  3.000
 M4H  H12  C17  C13  112.93  3.000
 M4H  H11  C17  C13  107.89  3.000
 M4H  C16  C17  C13  104.45  3.000
 M4H  N26  C19  N18  125.71  3.000
 M4H  N26  C19  C20  125.98  3.000
 M4H  N18  C19  C20  108.28  3.000
 M4H  C23  C20  C21  136.17  3.000
 M4H  C23  C20  C19  117.06  3.000
 M4H  C21  C20  C19  106.76  3.000
 M4H  H13  C21  C22  125.93  3.000
 M4H  H13  C21  C20  127.62  3.000
 M4H  C22  C21  C20  106.46  3.000
 M4H  H14  C22  N18  120.86  3.000
 M4H  H14  C22  C21  128.26  3.000
 M4H  N18  C22  C21  110.88  3.000
 M4H  H15  C23  C24  121.02  3.000
 M4H  H15  C23  C20  121.33  3.000
 M4H  C24  C23  C20  117.64  3.000
 M4H  H16  C24  C25  119.35  3.000
 M4H  H16  C24  C23  120.86  3.000
 M4H  C25  C24  C23  119.79  3.000
 M4H  H17  C25  N26  116.23  3.000
 M4H  H17  C25  C24  119.72  3.000
 M4H  N26  C25  C24  124.05  3.000
 M4H  C22  N18  C19  107.61  3.000
 M4H  C19  N18  C13  125.88  3.000
 M4H  C22  N18  C13  126.04  3.000
 M4H  C25  N26  C19  115.46  3.000
 M4H  C12  N4   C3   119.54  3.000
 M4H  C12  N4   C5   119.94  3.000
 M4H  C3   N4   C5   120.33  3.000
 M4H  H18  O11  C2   106.50  3.000
 M4H  H19  O9   C7   109.68  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
 M4H  CONST_01  C21  C22  N18  C19    0.00   0.0  0
 M4H  CONST_02  C22  C21  C20  C19    0.00   0.0  0
 M4H  CONST_03  C24  C23  C20  C19    0.00   0.0  0
 M4H  CONST_04  C24  C25  N26  C19    0.00   0.0  0
 M4H  CONST_05  N18  C22  C21  C20    0.00   0.0  0
 M4H  CONST_06  C22  N18  C19  C20    0.00   0.0  0
 M4H  CONST_07  C25  N26  C19  C20    0.00   0.0  0
 M4H  CONST_08  C25  C24  C23  C20    0.00   0.0  0
 M4H  CONST_09  N18  C19  C20  C21    0.00   0.0  0
 M4H  CONST_10  N26  C19  C20  C21  180.00   0.0  0
 M4H  CONST_11  C24  C23  C20  C21  180.00   0.0  0
 M4H  CONST_12  N26  C19  N18  C22  180.00   0.0  0
 M4H  CONST_13  C23  C20  C21  C22  180.00   0.0  0
 M4H  CONST_14  N18  C19  C20  C23  180.00   0.0  0
 M4H  CONST_15  N26  C19  C20  C23    0.00   0.0  0
 M4H  CONST_16  N26  C25  C24  C23    0.00   0.0  0
 M4H  CONST_17  N18  C19  N26  C25  180.00   0.0  0
 M4H  CONST_18  C21  C22  N18  C13  180.00   0.0  0
 M4H  CONST_19  C20  C19  N18  C13  180.00   0.0  0
 M4H  CONST_20  N26  C19  N18  C13    0.00   0.0  0
 M4H  CONST_21  H14  C22  N18  C13    0.00   0.0  0
 M4H  CONST_22  H13  C21  C20  C19  180.00   0.0  0
 M4H  CONST_23  H15  C23  C20  C19  180.00   0.0  0
 M4H  CONST_24  H17  C25  N26  C19  180.00   0.0  0
 M4H  CONST_25  H16  C24  C23  C20  180.00   0.0  0
 M4H  CONST_26  H19  O9   C7   C6   180.00   0.0  0
 M4H  Var_01    C16  C15  C14  C13  -27.25  30.0  1
 M4H  Var_02    C15  C16  C17  C13   24.29  30.0  1
 M4H  Var_03    C17  C16  C15  C14    1.78  30.0  1
 M4H  Var_04    C13  C12  N4   C5   -87.33  30.0  3
 M4H  Var_05    O8   C7   C6   C5   173.91  30.0  2

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
 M4H  chir_01  C13  C14  N18  C17  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
 M4H  plan-1  C5   0.020
 M4H  plan-1  C6   0.020
 M4H  plan-1  C7   0.020
 M4H  plan-1  C3   0.020
 M4H  plan-1  C2   0.020
 M4H  plan-1  C1   0.020
 M4H  plan-1  C12  0.020
 M4H  plan-1  N4   0.020
 M4H  plan-1  O10  0.020
 M4H  plan-1  O11  0.020
 M4H  plan-1  H1   0.020
 M4H  plan-1  H2   0.020
 M4H  plan-2  C13  0.020
 M4H  plan-2  C19  0.020
 M4H  plan-2  C20  0.020
 M4H  plan-2  C21  0.020
 M4H  plan-2  C22  0.020
 M4H  plan-2  C23  0.020
 M4H  plan-2  C24  0.020
 M4H  plan-2  C25  0.020
 M4H  plan-2  N18  0.020
 M4H  plan-2  N26  0.020
 M4H  plan-2  H13  0.020
 M4H  plan-2  H14  0.020
 M4H  plan-2  H15  0.020
 M4H  plan-2  H16  0.020
 M4H  plan-2  H17  0.020
 M4H  plan-3  C6   0.020
 M4H  plan-3  C7   0.020
 M4H  plan-3  O8   0.020
 M4H  plan-3  O9   0.020
 M4H  plan-3  H19  0.020

