# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jul 26 01:05:31 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: ~{N}-[(5~{S})-5-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-6-oxidanylidene-6-(prop-2-ynylamino)hexyl]-2,3-bis(oxidanyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(C(=O)NCCCC[C@H](NC(=O)c2cccc(O)c2O)C(=O)NCC#C)c1O
#
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
 Q62  Q62  ~{N}-[(5~{S})-5-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-6-oxidanylidene-6-(prop-2-ynylamino)hexyl]-2,3-bis(oxidanyl)benzamide  ligand  58  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q62
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
 Q62  C4   C  C     0   0.557  -92.2980  33.7011  126.2053
 Q62  C14  C  CR16  0  -0.353  -84.8724  29.6626  122.2642
 Q62  C5   C  CH1   0  -0.173  -91.6697  33.6218  124.8189
 Q62  C6   C  CH2   0  -0.487  -92.2717  32.4629  124.0136
 Q62  C11  C  CR6   0  -0.107  -87.5423  30.4253  122.4258
 Q62  C7   C  CH2   0  -0.451  -91.8939  31.0640  124.5000
 Q62  C8   C  CH2   0  -0.430  -92.1529  29.9766  123.4619
 Q62  C9   C  CH2   0  -0.314  -91.3004  30.0690  122.1995
 Q62  C10  C  C     0   0.504  -88.9765  30.8557  122.4634
 Q62  C12  C  CR16  0  -0.310  -86.7774  30.7936  121.3202
 Q62  C13  C  CR16  0  -0.250  -85.4524  30.4014  121.2416
 Q62  N1   N  NH1   0  -0.620  -91.6871  33.0386  127.1987
 Q62  N2   N  NH1   0  -0.587  -89.8769  29.8737  122.4075
 Q62  C3   C  CH2   0  -0.439  -92.1907  33.0510  128.5516
 Q62  N3   N  NH1   0  -0.757  -90.2247  33.4706  124.8376
 Q62  C1   C  CSP1  0  -0.492  -91.6551  35.3169  129.8473
 Q62  C2   C  CSP   0   0.244  -91.8999  34.2989  129.2581
 Q62  O1   O  O     0  -0.484  -93.3533  34.2941  126.3603
 Q62  O2   O  O     0  -0.504  -89.2672  32.0518  122.4731
 Q62  C15  C  CR6   0   0.333  -85.6210  29.3228  123.3813
 Q62  O3   O  OH1   0  -0.632  -85.0420  28.6347  124.3807
 Q62  C16  C  CR6   0   0.208  -86.9659  29.7042  123.4610
 Q62  O4   O  OH1   0  -0.677  -87.6614  29.3388  124.5767
 Q62  C17  C  C     0   0.515  -89.4312  34.4843  125.3061
 Q62  O5   O  O     0  -0.429  -89.8808  35.4843  125.8266
 Q62  C18  C  CR6   0  -0.128  -87.9661  34.2363  125.1715
 Q62  C19  C  CR16  0  -0.301  -87.1387  35.3174  124.8574
 Q62  C20  C  CR16  0  -0.256  -85.7749  35.1408  124.7528
 Q62  C21  C  CR16  0  -0.368  -85.2129  33.8920  124.9998
 Q62  C22  C  CR6   0   0.317  -86.0131  32.8167  125.3444
 Q62  O6   O  OH1   0  -0.626  -85.5423  31.5912  125.6395
 Q62  C23  C  CR6   0   0.271  -87.4032  32.9819  125.4088
 Q62  O7   O  OH1   0  -0.665  -88.1140  31.8803  125.7581
 Q62  H2   H  HCH1  0   0.289  -91.9477  34.5554  124.3214
 Q62  H3   H  HCH2  0   0.260  -91.9504  32.6056  122.9798
 Q62  H4   H  HCH2  0   0.263  -93.3575  32.5745  124.0063
 Q62  H5   H  HCH2  0   0.204  -90.8404  31.0160  124.7886
 Q62  H6   H  HCH2  0   0.252  -92.4533  30.8214  125.4060
 Q62  H7   H  HCH2  0   0.234  -93.2005  30.0061  123.1485
 Q62  H8   H  HCH2  0   0.241  -91.9984  28.9981  123.9228
 Q62  H9   H  HCH2  0   0.250  -91.4442  31.0259  121.6995
 Q62  H10  H  HCH2  0   0.268  -91.6259  29.3009  121.4977
 Q62  H11  H  HCR6  0   0.259  -87.2261  31.3662  120.5191
 Q62  H12  H  HCR6  0   0.259  -84.8600  30.6710  120.3773
 Q62  H13  H  HNH1  0   0.401  -90.7988  32.5975  127.0411
 Q62  H14  H  HNH1  0   0.412  -89.5372  28.9251  122.3833
 Q62  H15  H  HCH2  0   0.285  -93.2668  32.8722  128.5518
 Q62  H16  H  HCH2  0   0.298  -91.7343  32.2174  129.0847
 Q62  H17  H  HNH1  0   0.446  -89.8602  32.9901  124.0101
 Q62  H18  H  H     0   0.281  -91.4372  36.2225  130.3653
 Q62  H19  H  HOH1  0   0.467  -85.6927  28.4903  125.0805
 Q62  H20  H  HOH1  0   0.486  -87.8094  30.1289  125.1262
 Q62  H21  H  HCR6  0   0.264  -87.5802  36.2890  124.6808
 Q62  H22  H  HCR6  0   0.265  -85.1359  35.9719  124.4878
 Q62  H23  H  HCR6  0   0.282  -84.1392  33.7587  124.9344
 Q62  H24  H  HOH1  0   0.478  -84.5891  31.5537  125.5044
 Q62  H25  H  HOH1  0   0.479  -89.0619  32.0762  125.7086
 Q62  H1   H  HCR6  0   0.266  -83.8335  29.3631  122.2064

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
 Q62  C13  C12  aromatic  1.384  0.020  1.384
 Q62  C13  C14  aromatic  1.389  0.020  1.389
 Q62  C12  C11  aromatic  1.394  0.020  1.394
 Q62  O2   C10  double    1.231  0.020  1.231
 Q62  C14  C15  aromatic  1.387  0.020  1.387
 Q62  C11  C10  single    1.498  0.020  1.498
 Q62  C11  C16  aromatic  1.387  0.020  1.387
 Q62  C10  N2   single    1.334  0.020  1.334
 Q62  C9   N2   single    1.452  0.020  1.452
 Q62  C9   C8   single    1.526  0.020  1.526
 Q62  C15  C16  aromatic  1.400  0.020  1.400
 Q62  C15  O3   single    1.344  0.020  1.344
 Q62  C16  O4   single    1.365  0.020  1.365
 Q62  C6   C7   single    1.528  0.020  1.528
 Q62  C6   C5   single    1.534  0.020  1.534
 Q62  C8   C7   single    1.526  0.020  1.526
 Q62  C5   N3   single    1.453  0.020  1.453
 Q62  C5   C4   single    1.524  0.020  1.524
 Q62  N3   C17  single    1.370  0.020  1.370
 Q62  O7   C23  single    1.357  0.020  1.357
 Q62  O6   C22  single    1.346  0.020  1.346
 Q62  C23  C22  aromatic  1.401  0.020  1.401
 Q62  C23  C18  aromatic  1.395  0.020  1.395
 Q62  C17  C18  single    1.492  0.020  1.492
 Q62  C17  O5   double    1.214  0.020  1.214
 Q62  C22  C21  aromatic  1.384  0.020  1.384
 Q62  C18  C19  aromatic  1.397  0.020  1.397
 Q62  C21  C20  aromatic  1.392  0.020  1.392
 Q62  C19  C20  aromatic  1.379  0.020  1.379
 Q62  C4   O1   double    1.220  0.020  1.220
 Q62  C4   N1   single    1.341  0.020  1.341
 Q62  N1   C3   single    1.444  0.020  1.444
 Q62  C1   C2   triple    1.201  0.020  1.201
 Q62  C3   C2   single    1.463  0.020  1.463
 Q62  C14  H1   single    0.929  0.020  1.085
 Q62  C5   H2   single    0.939  0.020  1.096
 Q62  C6   H3   single    0.939  0.020  1.096
 Q62  C6   H4   single    0.939  0.020  1.096
 Q62  C7   H5   single    0.939  0.020  1.096
 Q62  C7   H6   single    0.939  0.020  1.096
 Q62  C8   H7   single    0.939  0.020  1.096
 Q62  C8   H8   single    0.939  0.020  1.096
 Q62  C9   H9   single    0.939  0.020  1.096
 Q62  C9   H10  single    0.939  0.020  1.096
 Q62  C12  H11  single    0.929  0.020  1.085
 Q62  C13  H12  single    0.929  0.020  1.085
 Q62  N1   H13  single    0.868  0.020  1.013
 Q62  N2   H14  single    0.868  0.020  1.013
 Q62  C3   H15  single    0.939  0.020  1.096
 Q62  C3   H16  single    0.939  0.020  1.096
 Q62  N3   H17  single    0.868  0.020  1.013
 Q62  C1   H18  single    0.913  0.020  1.066
 Q62  O3   H19  single    0.832  0.020  0.971
 Q62  O4   H20  single    0.832  0.020  0.971
 Q62  C19  H21  single    0.929  0.020  1.085
 Q62  C20  H22  single    0.929  0.020  1.085
 Q62  C21  H23  single    0.929  0.020  1.085
 Q62  O6   H24  single    0.832  0.020  0.971
 Q62  O7   H25  single    0.832  0.020  0.971

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
 Q62  O1   C4   N1   122.67  3.000
 Q62  N1   C4   C5   117.40  3.000
 Q62  O1   C4   C5   119.82  3.000
 Q62  H1   C14  C15  119.55  3.000
 Q62  H1   C14  C13  120.57  3.000
 Q62  C15  C14  C13  119.87  3.000
 Q62  H2   C5   N3   110.33  3.000
 Q62  H2   C5   C6   107.84  3.000
 Q62  N3   C5   C6   108.56  3.000
 Q62  H2   C5   C4   105.34  3.000
 Q62  N3   C5   C4   113.81  3.000
 Q62  C6   C5   C4   110.79  3.000
 Q62  H4   C6   H3   105.84  3.000
 Q62  H4   C6   C7   109.97  3.000
 Q62  H3   C6   C7   110.38  3.000
 Q62  H4   C6   C5   108.45  3.000
 Q62  H3   C6   C5   106.43  3.000
 Q62  C7   C6   C5   115.30  3.000
 Q62  C16  C11  C12  120.09  3.000
 Q62  C16  C11  C10  121.91  3.000
 Q62  C12  C11  C10  117.99  3.000
 Q62  H6   C7   H5   105.35  3.000
 Q62  H6   C7   C8   108.62  3.000
 Q62  H5   C7   C8   108.17  3.000
 Q62  H6   C7   C6   109.93  3.000
 Q62  H5   C7   C6   111.24  3.000
 Q62  C8   C7   C6   113.20  3.000
 Q62  H8   C8   H7   106.28  3.000
 Q62  H8   C8   C9   108.92  3.000
 Q62  H7   C8   C9   107.24  3.000
 Q62  H8   C8   C7   109.11  3.000
 Q62  H7   C8   C7   109.77  3.000
 Q62  C9   C8   C7   115.15  3.000
 Q62  H10  C9   H9   106.51  3.000
 Q62  H10  C9   N2   106.87  3.000
 Q62  H9   C9   N2   108.27  3.000
 Q62  H10  C9   C8   108.84  3.000
 Q62  H9   C9   C8   111.05  3.000
 Q62  N2   C9   C8   114.90  3.000
 Q62  O2   C10  N2   123.81  3.000
 Q62  N2   C10  C11  115.71  3.000
 Q62  O2   C10  C11  120.37  3.000
 Q62  H11  C12  C13  120.33  3.000
 Q62  H11  C12  C11  119.96  3.000
 Q62  C13  C12  C11  119.70  3.000
 Q62  H12  C13  C12  119.93  3.000
 Q62  H12  C13  C14  119.48  3.000
 Q62  C12  C13  C14  120.59  3.000
 Q62  H13  N1   C3   117.35  3.000
 Q62  H13  N1   C4   120.24  3.000
 Q62  C3   N1   C4   122.07  3.000
 Q62  H14  N2   C10  117.81  3.000
 Q62  H14  N2   C9   116.98  3.000
 Q62  C10  N2   C9   124.68  3.000
 Q62  H16  C3   H15  106.72  3.000
 Q62  H16  C3   C2   109.45  3.000
 Q62  H15  C3   C2   109.62  3.000
 Q62  H16  C3   N1   107.80  3.000
 Q62  H15  C3   N1   110.06  3.000
 Q62  C2   C3   N1   112.98  3.000
 Q62  H17  N3   C17  114.67  3.000
 Q62  H17  N3   C5   113.11  3.000
 Q62  C17  N3   C5   120.23  3.000
 Q62  H18  C1   C2   180.00  3.000
 Q62  C1   C2   C3   180.00  3.000
 Q62  C16  C15  O3   120.71  3.000
 Q62  O3   C15  C14  119.45  3.000
 Q62  C16  C15  C14  119.84  3.000
 Q62  H19  O3   C15  108.95  3.000
 Q62  O4   C16  C15  117.59  3.000
 Q62  O4   C16  C11  122.52  3.000
 Q62  C15  C16  C11  119.89  3.000
 Q62  H20  O4   C16  108.76  3.000
 Q62  C18  C17  O5   122.65  3.000
 Q62  O5   C17  N3   122.80  3.000
 Q62  C18  C17  N3   114.51  3.000
 Q62  C23  C18  C19  119.67  3.000
 Q62  C19  C18  C17  118.24  3.000
 Q62  C23  C18  C17  122.03  3.000
 Q62  H21  C19  C20  120.41  3.000
 Q62  H21  C19  C18  119.34  3.000
 Q62  C20  C19  C18  120.24  3.000
 Q62  H22  C20  C21  119.64  3.000
 Q62  H22  C20  C19  120.30  3.000
 Q62  C21  C20  C19  120.05  3.000
 Q62  H23  C21  C22  119.49  3.000
 Q62  H23  C21  C20  119.98  3.000
 Q62  C22  C21  C20  120.53  3.000
 Q62  C23  C22  O6   116.38  3.000
 Q62  C23  C22  C21  119.56  3.000
 Q62  O6   C22  C21  124.05  3.000
 Q62  H24  O6   C22  110.54  3.000
 Q62  O7   C23  C22  115.83  3.000
 Q62  C22  C23  C18  119.90  3.000
 Q62  O7   C23  C18  124.22  3.000
 Q62  H25  O7   C23  109.58  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
 Q62  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 Q62  CONST_02  C11  C16  C15  C14     0.00   0.0  0
 Q62  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 Q62  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 Q62  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 Q62  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 Q62  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 Q62  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 Q62  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 Q62  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 Q62  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 Q62  CONST_12  C23  C18  C19  C20     0.00   0.0  0
 Q62  CONST_13  O4   C16  C15  C14   180.00   0.0  0
 Q62  CONST_14  O3   C15  C16  C11   180.00   0.0  0
 Q62  CONST_15  C13  C12  C11  C10   180.00   0.0  0
 Q62  CONST_16  C15  C16  C11  C10   180.00   0.0  0
 Q62  CONST_17  O4   C16  C11  C12   180.00   0.0  0
 Q62  CONST_18  O3   C15  C14  C13   180.00   0.0  0
 Q62  CONST_19  C22  C23  C18  C17   180.00   0.0  0
 Q62  CONST_20  C20  C19  C18  C17   180.00   0.0  0
 Q62  CONST_21  O6   C22  C23  C18   180.00   0.0  0
 Q62  CONST_22  O7   C23  C18  C19   180.00   0.0  0
 Q62  CONST_23  O6   C22  C21  C20   180.00   0.0  0
 Q62  CONST_24  O7   C23  C22  C21   180.00   0.0  0
 Q62  CONST_25  H11  C12  C13  C14   180.00   0.0  0
 Q62  CONST_26  H12  C13  C12  C11   180.00   0.0  0
 Q62  CONST_27  H1   C14  C13  C12   180.00   0.0  0
 Q62  CONST_28  H22  C20  C19  C18   180.00   0.0  0
 Q62  CONST_29  H23  C21  C20  C19   180.00   0.0  0
 Q62  CONST_30  H21  C19  C20  C21   180.00   0.0  0
 Q62  CONST_31  C18  C17  N3   C5    180.00   0.0  0
 Q62  CONST_32  C9   N2   C10  C11   180.00   0.0  0
 Q62  CONST_33  H14  N2   C10  C11     0.00   0.0  0
 Q62  CONST_35  O5   C17  N3   C5      0.00   0.0  0
 Q62  CONST_36  C3   N1   C4   C5    180.00   0.0  0
 Q62  CONST_37  O2   C10  N2   C9      0.00   0.0  0
 Q62  CONST_38  O1   C4   N1   C3      0.00   0.0  0
 Q62  CONST_39  H13  N1   C4   C5      0.00   0.0  0
 Q62  Var_01    O2   C10  C11  C12   -61.96  30.0  2
 Q62  Var_02    C23  C18  C17  N3    -39.71  30.0  2
 Q62  Var_03    C2   C3   N1   C4    -76.63  30.0  3
 Q62  Var_04    C8   C7   C6   C5   -162.81  30.0  3
 Q62  Var_05    C9   C8   C7   C6     65.28  30.0  1
 Q62  Var_06    N2   C9   C8   C7     65.01  30.0  1
 Q62  Var_07    C10  N2   C9   C8   -101.41  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
 Q62  chir_01  C5  C6  N3  C4  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
 Q62  plan-1  C14  0.020
 Q62  plan-1  C11  0.020
 Q62  plan-1  C10  0.020
 Q62  plan-1  C12  0.020
 Q62  plan-1  C13  0.020
 Q62  plan-1  C15  0.020
 Q62  plan-1  O3   0.020
 Q62  plan-1  C16  0.020
 Q62  plan-1  O4   0.020
 Q62  plan-1  H11  0.020
 Q62  plan-1  H12  0.020
 Q62  plan-1  H1   0.020
 Q62  plan-2  C17  0.020
 Q62  plan-2  C18  0.020
 Q62  plan-2  C19  0.020
 Q62  plan-2  C20  0.020
 Q62  plan-2  C21  0.020
 Q62  plan-2  C22  0.020
 Q62  plan-2  O6   0.020
 Q62  plan-2  C23  0.020
 Q62  plan-2  O7   0.020
 Q62  plan-2  H21  0.020
 Q62  plan-2  H22  0.020
 Q62  plan-2  H23  0.020
 Q62  plan-3  C4   0.020
 Q62  plan-3  C5   0.020
 Q62  plan-3  N1   0.020
 Q62  plan-3  C3   0.020
 Q62  plan-3  O1   0.020
 Q62  plan-3  H13  0.020
 Q62  plan-4  C11  0.020
 Q62  plan-4  C9   0.020
 Q62  plan-4  C10  0.020
 Q62  plan-4  N2   0.020
 Q62  plan-4  O2   0.020
 Q62  plan-4  H14  0.020
 Q62  plan-5  C5   0.020
 Q62  plan-5  N3   0.020
 Q62  plan-5  C17  0.020
 Q62  plan-5  O5   0.020
 Q62  plan-5  C18  0.020
 Q62  plan-5  H17  0.020

