# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:57:56 2022
#   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  44  26  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.029  107.7393  162.6508  100.3476
 M4H  C6   C  CR6    0  -0.387  108.1679  161.7075   99.4485
 M4H  C7   C  C      0   0.405  108.9718  160.5366  100.0092
 M4H  C3   C  CR16   0  -0.108  106.7201  163.9849   98.7130
 M4H  C2   C  CR6    0   0.163  107.0959  163.1059   97.7583
 M4H  C1   C  CR6    0   0.325  107.8428  161.8869   98.0601
 M4H  C12  C  CH2    0  -0.347  106.5512  164.6356  101.0664
 M4H  C13  C  CT     0   0.124  105.1636  164.2486  101.6205
 M4H  C14  C  CH2    0  -0.488  104.0414  164.4509  100.5944
 M4H  C15  C  CH2    0  -0.459  103.8479  165.9603  100.5578
 M4H  C16  C  CH2    0  -0.443  104.0170  166.3980  102.0215
 M4H  C17  C  CH2    0  -0.439  104.7808  165.2573  102.7264
 M4H  C19  C  CR56   0   0.472  105.9430  162.4034  103.1539
 M4H  C20  C  CR56   0   0.034  105.8350  160.9933  103.1831
 M4H  C21  C  CR15   0  -0.444  105.0190  160.6209  102.0765
 M4H  C22  C  CR15   0   0.006  104.6788  161.7780  101.4440
 M4H  C23  C  CR16   0  -0.227  106.5189  160.3255  104.1961
 M4H  C24  C  CR16   0  -0.349  107.2552  161.0887  105.0845
 M4H  C25  C  CR16   0  -0.093  107.2932  162.4794  104.9398
 M4H  N18  N  NR5    0  -0.544  105.2134  162.8684  102.0908
 M4H  N26  N  N      0  -0.436  106.6521  163.1449  103.9901
 M4H  N4   N  NR6    0  -0.430  107.0361  163.7456  100.0233
 M4H  O10  O  O      0  -0.509  108.1193  161.1583   97.0927
 M4H  O11  O  OH1    0  -0.635  106.8124  163.3080   96.4630
 M4H  O8   O  O      0  -0.575  109.4000  159.6962   99.2014
 M4H  O9   O  OC    -1  -0.596  109.1330  160.5295  101.2486
 M4H  H1   H  HCR6   0   0.300  107.9823  162.5346  101.3939
 M4H  H2   H  HCR6   0   0.307  106.1843  164.8977   98.4910
 M4H  H3   H  HCH2   0   0.294  107.2749  164.6265  101.8806
 M4H  H4   H  HCH2   0   0.291  106.5301  165.6529  100.6755
 M4H  H5   H  HCH2   0   0.260  103.1313  163.9780  100.9745
 M4H  H6   H  HCH2   0   0.262  104.2426  164.0159   99.6145
 M4H  H7   H  HCH2   0   0.236  104.5983  166.4290   99.9178
 M4H  H8   H  HCH2   0   0.248  102.8767  166.2330  100.1459
 M4H  H9   H  HCH2   0   0.238  104.5423  167.3494  102.1003
 M4H  H10  H  HCH2   0   0.238  103.0433  166.5384  102.4913
 M4H  H11  H  HCH2   0   0.253  104.1403  164.7581  103.4541
 M4H  H12  H  HCH2   0   0.251  105.6552  165.6125  103.2697
 M4H  H13  H  HCR5   0   0.251  104.7215  159.6273  101.7826
 M4H  H14  H  HCR5   0   0.294  104.0757  161.9023  100.5601
 M4H  H15  H  HCR6   0   0.262  106.4834  159.2466  104.2823
 M4H  H16  H  HCR6   0   0.261  107.8088  160.6239  105.8887
 M4H  H17  H  HCR6   0   0.253  107.8780  163.0753  105.6312
 M4H  H18  H  HOH1   0   0.454  107.1984  162.5377   96.0058

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    1.341  0.020  1.341
 M4H  O10  C1   double    1.242  0.020  1.242
 M4H  C2   C1   single    1.461  0.020  1.461
 M4H  C2   C3   double    1.351  0.020  1.351
 M4H  C1   C6   single    1.437  0.020  1.437
 M4H  C3   N4   single    1.369  0.020  1.369
 M4H  O8   C7   deloc     1.242  0.020  1.242
 M4H  C6   C7   single    1.527  0.020  1.527
 M4H  C6   C5   double    1.372  0.020  1.372
 M4H  N4   C5   single    1.341  0.020  1.341
 M4H  N4   C12  single    1.454  0.020  1.454
 M4H  C7   O9   deloc     1.250  0.020  1.250
 M4H  C14  C15  single    1.522  0.020  1.522
 M4H  C14  C13  single    1.534  0.020  1.534
 M4H  C15  C16  single    1.537  0.020  1.537
 M4H  C12  C13  single    1.543  0.020  1.543
 M4H  C13  N18  single    1.459  0.020  1.459
 M4H  C13  C17  single    1.545  0.020  1.545
 M4H  C22  N18  aromatic  1.376  0.020  1.376
 M4H  C22  C21  aromatic  1.362  0.020  1.362
 M4H  N18  C19  aromatic  1.371  0.020  1.371
 M4H  C16  C17  single    1.543  0.020  1.543
 M4H  C21  C20  aromatic  1.424  0.020  1.424
 M4H  C19  C20  aromatic  1.414  0.020  1.414
 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

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   116.10  3.000
 M4H  H1   C5   C6   119.37  3.000
 M4H  N4   C5   C6   124.52  3.000
 M4H  C1   C6   C7   124.72  3.000
 M4H  C7   C6   C5   116.81  3.000
 M4H  C1   C6   C5   118.47  3.000
 M4H  O9   C7   O8   126.64  3.000
 M4H  O9   C7   C6   115.87  3.000
 M4H  O8   C7   C6   117.49  3.000
 M4H  H2   C3   N4   117.28  3.000
 M4H  H2   C3   C2   122.81  3.000
 M4H  N4   C3   C2   119.90  3.000
 M4H  O11  C2   C1   115.67  3.000
 M4H  C1   C2   C3   122.62  3.000
 M4H  O11  C2   C3   121.71  3.000
 M4H  O10  C1   C2   116.24  3.000
 M4H  C2   C1   C6   114.79  3.000
 M4H  O10  C1   C6   128.96  3.000
 M4H  H4   C12  H3   106.78  3.000
 M4H  H4   C12  N4   108.69  3.000
 M4H  H3   C12  N4   108.03  3.000
 M4H  H4   C12  C13  110.20  3.000
 M4H  H3   C12  C13  109.07  3.000
 M4H  N4   C12  C13  113.82  3.000
 M4H  N18  C13  C17  113.29  3.000
 M4H  C17  C13  C14  102.21  3.000
 M4H  N18  C13  C14  111.43  3.000
 M4H  C17  C13  C12  108.42  3.000
 M4H  N18  C13  C12  108.80  3.000
 M4H  C14  C13  C12  112.61  3.000
 M4H  H6   C14  H5   107.05  3.000
 M4H  H6   C14  C15  113.41  3.000
 M4H  H5   C14  C15  109.35  3.000
 M4H  H6   C14  C13  114.42  3.000
 M4H  H5   C14  C13  108.61  3.000
 M4H  C15  C14  C13  103.88  3.000
 M4H  H8   C15  H7   106.47  3.000
 M4H  H8   C15  C16  112.76  3.000
 M4H  H7   C15  C16  111.11  3.000
 M4H  H8   C15  C14  111.75  3.000
 M4H  H7   C15  C14  110.63  3.000
 M4H  C16  C15  C14  104.21  3.000
 M4H  H10  C16  H9   106.67  3.000
 M4H  H10  C16  C17  109.90  3.000
 M4H  H9   C16  C17  111.95  3.000
 M4H  H10  C16  C15  110.41  3.000
 M4H  H9   C16  C15  111.75  3.000
 M4H  C17  C16  C15  106.20  3.000
 M4H  H12  C17  H11  106.74  3.000
 M4H  H12  C17  C16  112.59  3.000
 M4H  H11  C17  C16  110.64  3.000
 M4H  H12  C17  C13  111.78  3.000
 M4H  H11  C17  C13  108.93  3.000
 M4H  C16  C17  C13  106.16  3.000
 M4H  N26  C19  N18  125.81  3.000
 M4H  N26  C19  C20  125.90  3.000
 M4H  N18  C19  C20  108.27  3.000
 M4H  C23  C20  C21  136.13  3.000
 M4H  C23  C20  C19  117.10  3.000
 M4H  C21  C20  C19  106.76  3.000
 M4H  H13  C21  C22  125.98  3.000
 M4H  H13  C21  C20  127.65  3.000
 M4H  C22  C21  C20  106.36  3.000
 M4H  H14  C22  N18  120.79  3.000
 M4H  H14  C22  C21  128.24  3.000
 M4H  N18  C22  C21  110.97  3.000
 M4H  H15  C23  C24  121.06  3.000
 M4H  H15  C23  C20  121.30  3.000
 M4H  C24  C23  C20  117.64  3.000
 M4H  H16  C24  C25  119.37  3.000
 M4H  H16  C24  C23  120.86  3.000
 M4H  C25  C24  C23  119.77  3.000
 M4H  H17  C25  N26  116.24  3.000
 M4H  H17  C25  C24  119.68  3.000
 M4H  N26  C25  C24  124.08  3.000
 M4H  C22  N18  C19  107.62  3.000
 M4H  C19  N18  C13  126.09  3.000
 M4H  C22  N18  C13  125.79  3.000
 M4H  C25  N26  C19  115.50  3.000
 M4H  C12  N4   C3   120.17  3.000
 M4H  C12  N4   C5   120.06  3.000
 M4H  C3   N4   C5   119.69  3.000
 M4H  H18  O11  C2   104.48  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  Var_01    C16  C15  C14  C13   -38.27  30.0  1
 M4H  Var_02    C15  C16  C17  C13     5.65  30.0  1
 M4H  Var_03    C17  C16  C15  C14    19.90  30.0  1
 M4H  Var_04    C13  C12  N4   C5    -88.38  30.0  3
 M4H  Var_05    O8   C7   C6   C5   -177.91  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

