# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:10:49 2021
#   Inital geometry file: a 160 line input string
#   Ligand name: (3~{Z},5~{E},8~{S},9~{E},11~{E},14~{S},16~{R},17~{Z},19~{E},24~{R})-24-methyl-8,14,16-tris(oxidanyl)-1-oxacyclotetracosa-3,5,9,11,17,19-hexaen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCC\C=C\C=C/[C@H](O)C[C@@H](O)C\C=C\C=C\[C@@H](O)C\C=C\C=C/C(=O)O1
#
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
 D9F  D9F  (3~{Z},5~{E},8~{S},9~{E},11~{E},14~{S},16~{R},17~{Z},19~{E},24~{R})-24-methyl-8,14,16-tris(oxidanyl)-1-oxacyclotetracosa-3,5,9,11,17,19-hexaen-2-one  ligand  63  29  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D9F
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
 D9F  C02  C  C     0   0.580  11.0848  82.5814  105.7862
 D9F  C03  C  C1    0  -0.402   9.9772  83.4868  105.4514
 D9F  C04  C  C1    0  -0.182   9.8919  84.8242  105.5773
 D9F  C05  C  C1    0  -0.260  10.8286  85.7941  106.1021
 D9F  C06  C  C1    0  -0.176  10.4706  87.0770  106.2486
 D9F  C07  C  CH2   0  -0.531  11.3228  88.1184  106.8948
 D9F  C08  C  CH1   0  -0.005  11.0003  89.5536  106.4567
 D9F  C10  C  C1    0  -0.247  11.3766  89.8020  105.0317
 D9F  C11  C  C1    0  -0.264  10.5550  90.1663  104.0466
 D9F  C12  C  C1    0  -0.258  11.0099  90.5235  102.7006
 D9F  C13  C  C1    0  -0.201  12.0995  91.2538  102.4563
 D9F  C14  C  CH2   0  -0.532  12.6149  91.6453  101.1120
 D9F  C15  C  CH1   0   0.067  14.0792  91.2213  100.9283
 D9F  C17  C  CH2   0  -0.454  14.1974  89.7083  100.7648
 D9F  C18  C  CH1   0  -0.008  15.4651  89.0759  101.3351
 D9F  C20  C  C1    0  -0.286  15.4842  89.1675  102.8369
 D9F  C21  C  C1    0  -0.225  15.0989  88.2102  103.6894
 D9F  C22  C  C1    0  -0.264  14.6316  86.8837  103.3258
 D9F  C23  C  C1    0  -0.204  14.2024  85.9695  104.2019
 D9F  C24  C  CH2   0  -0.491  13.7502  84.6003  103.8120
 D9F  C25  C  CH2   0  -0.447  14.6192  83.4785  104.3978
 D9F  C26  C  CH2   0  -0.444  14.5707  83.2793  105.9146
 D9F  C27  C  CH1   0   0.015  13.3992  82.4490  106.4143
 D9F  C28  C  CH3   0  -0.673  13.4825  82.1407  107.8968
 D9F  O01  O  O     0  -0.473  10.9755  81.3764  105.7123
 D9F  O09  O  OH1   0  -0.661   9.6429  89.8623  106.6536
 D9F  O16  O  OH1   0  -0.672  14.6471  91.8302   99.7866
 D9F  O19  O  OH1   0  -0.668  16.5910  89.7167  100.7704
 D9F  O29  O  O2    0  -0.472  12.1981  83.1999  106.1520
 D9F  H1   H  H     0   0.267   9.1096  82.9683  105.0634
 D9F  H2   H  H     0   0.264   8.9450  85.2516  105.2593
 D9F  H3   H  H     0   0.258  11.8125  85.4761  106.4165
 D9F  H4   H  H     0   0.258   9.4740  87.3816  105.9408
 D9F  H5   H  HCH2  0   0.254  12.3842  87.9118  106.7322
 D9F  H6   H  HCH2  0   0.268  11.1766  88.0595  107.9809
 D9F  H7   H  HCH1  0   0.236  11.6380  90.2116  107.0675
 D9F  H8   H  H     0   0.255  12.4370  89.6902  104.8194
 D9F  H9   H  H     0   0.246   9.4856  90.2200  104.2235
 D9F  H10  H  H     0   0.239  10.3863  90.2030  101.8693
 D9F  H11  H  H     0   0.235  12.6735  91.6209  103.3046
 D9F  H12  H  HCH2  0   0.244  12.5609  92.7371  101.0194
 D9F  H13  H  HCH2  0   0.235  11.9963  91.2246  100.3136
 D9F  H14  H  HCH1  0   0.200  14.6213  91.5381  101.8320
 D9F  H15  H  HCH2  0   0.239  14.1082  89.4664   99.7004
 D9F  H16  H  HCH2  0   0.247  13.3546  89.2213  101.2602
 D9F  H17  H  HCH1  0   0.223  15.4497  88.0191  101.0369
 D9F  H18  H  H     0   0.245  15.8136  90.1173  103.2478
 D9F  H19  H  H     0   0.239  15.1344  88.4286  104.7531
 D9F  H20  H  H     0   0.239  14.6347  86.6145  102.2736
 D9F  H21  H  H     0   0.234  14.1845  86.2235  105.2600
 D9F  H22  H  HCH2  0   0.241  12.7071  84.4633  104.1037
 D9F  H23  H  HCH2  0   0.238  13.7763  84.5177  102.7223
 D9F  H24  H  HCH2  0   0.231  14.3447  82.5376  103.9109
 D9F  H25  H  HCH2  0   0.233  15.6544  83.6730  104.1065
 D9F  H26  H  HCH2  0   0.243  15.4743  82.7449  106.2193
 D9F  H27  H  HCH2  0   0.232  14.6038  84.2355  106.4461
 D9F  H28  H  HCH1  0   0.237  13.3650  81.5147  105.8483
 D9F  H29  H  HCH3  0   0.241  12.6338  81.5415  108.2270
 D9F  H30  H  HCH3  0   0.236  14.3887  81.5719  108.1060
 D9F  H31  H  HCH3  0   0.231  13.5116  83.0552  108.4909
 D9F  H32  H  HOH1  0   0.456   9.4430  89.7640  107.5900
 D9F  H33  H  HOH1  0   0.444  14.6220  92.7836   99.9148
 D9F  H34  H  HOH1  0   0.446  17.3791  89.2852  101.1149

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
 D9F  O19  C18  single  1.413  0.020  1.413
 D9F  C18  C17  single  1.527  0.020  1.527
 D9F  C18  C20  single  1.505  0.020  1.505
 D9F  C17  C15  single  1.526  0.020  1.526
 D9F  C20  C21  double  1.338  0.020  1.338
 D9F  O16  C15  single  1.413  0.020  1.413
 D9F  C14  C15  single  1.535  0.020  1.535
 D9F  C14  C13  single  1.492  0.020  1.492
 D9F  C21  C22  single  1.453  0.020  1.453
 D9F  C22  C23  double  1.337  0.020  1.337
 D9F  C13  C12  double  1.334  0.020  1.334
 D9F  C12  C11  single  1.465  0.020  1.465
 D9F  C23  C24  single  1.494  0.020  1.494
 D9F  C24  C25  single  1.535  0.020  1.535
 D9F  C25  C26  single  1.531  0.020  1.531
 D9F  C11  C10  double  1.333  0.020  1.333
 D9F  C10  C08  single  1.495  0.020  1.495
 D9F  O01  C02  double  1.212  0.020  1.212
 D9F  C26  C27  single  1.520  0.020  1.520
 D9F  C03  C02  single  1.469  0.020  1.469
 D9F  C03  C04  double  1.346  0.020  1.346
 D9F  C27  O29  single  1.441  0.020  1.441
 D9F  C27  C28  single  1.517  0.020  1.517
 D9F  C02  O29  single  1.325  0.020  1.325
 D9F  C04  C05  single  1.447  0.020  1.447
 D9F  O09  C08  single  1.406  0.020  1.406
 D9F  C08  C07  single  1.535  0.020  1.535
 D9F  C06  C05  double  1.340  0.020  1.340
 D9F  C06  C07  single  1.493  0.020  1.493
 D9F  C03  H1   single  0.930  0.020  1.080
 D9F  C04  H2   single  0.930  0.020  1.080
 D9F  C05  H3   single  0.930  0.020  1.080
 D9F  C06  H4   single  0.930  0.020  1.080
 D9F  C07  H5   single  0.970  0.020  1.090
 D9F  C07  H6   single  0.970  0.020  1.090
 D9F  C08  H7   single  0.970  0.020  1.090
 D9F  C10  H8   single  0.930  0.020  1.080
 D9F  C11  H9   single  0.930  0.020  1.080
 D9F  C12  H10  single  0.930  0.020  1.080
 D9F  C13  H11  single  0.930  0.020  1.080
 D9F  C14  H12  single  0.970  0.020  1.090
 D9F  C14  H13  single  0.970  0.020  1.090
 D9F  C15  H14  single  0.970  0.020  1.090
 D9F  C17  H15  single  0.970  0.020  1.090
 D9F  C17  H16  single  0.970  0.020  1.090
 D9F  C18  H17  single  0.970  0.020  1.090
 D9F  C20  H18  single  0.930  0.020  1.080
 D9F  C21  H19  single  0.930  0.020  1.080
 D9F  C22  H20  single  0.930  0.020  1.080
 D9F  C23  H21  single  0.930  0.020  1.080
 D9F  C24  H22  single  0.970  0.020  1.090
 D9F  C24  H23  single  0.970  0.020  1.090
 D9F  C25  H24  single  0.970  0.020  1.090
 D9F  C25  H25  single  0.970  0.020  1.090
 D9F  C26  H26  single  0.970  0.020  1.090
 D9F  C26  H27  single  0.970  0.020  1.090
 D9F  C27  H28  single  0.970  0.020  1.090
 D9F  C28  H29  single  0.970  0.020  1.090
 D9F  C28  H30  single  0.970  0.020  1.090
 D9F  C28  H31  single  0.970  0.020  1.090
 D9F  O09  H32  single  0.850  0.020  0.980
 D9F  O16  H33  single  0.850  0.020  0.980
 D9F  O19  H34  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
 D9F  O29  C02  O01  123.82  3.000
 D9F  O29  C02  C03  114.12  3.000
 D9F  O01  C02  C03  122.06  3.000
 D9F  H1   C03  C04  117.30  3.000
 D9F  H1   C03  C02  113.00  3.000
 D9F  C04  C03  C02  129.70  3.000
 D9F  H2   C04  C05  114.00  3.000
 D9F  H2   C04  C03  114.75  3.000
 D9F  C05  C04  C03  131.22  3.000
 D9F  H3   C05  C06  119.55  3.000
 D9F  H3   C05  C04  119.84  3.000
 D9F  C06  C05  C04  120.56  3.000
 D9F  H4   C06  C07  116.79  3.000
 D9F  H4   C06  C05  118.84  3.000
 D9F  C07  C06  C05  124.24  3.000
 D9F  H6   C07  H5   105.45  3.000
 D9F  H6   C07  C08  107.73  3.000
 D9F  H5   C07  C08  109.77  3.000
 D9F  H6   C07  C06  108.35  3.000
 D9F  H5   C07  C06  110.98  3.000
 D9F  C08  C07  C06  114.13  3.000
 D9F  H7   C08  O09  110.50  3.000
 D9F  H7   C08  C10  106.48  3.000
 D9F  O09  C08  C10  109.88  3.000
 D9F  H7   C08  C07  106.19  3.000
 D9F  O09  C08  C07  111.61  3.000
 D9F  C10  C08  C07  112.00  3.000
 D9F  H8   C10  C11  118.99  3.000
 D9F  H8   C10  C08  114.50  3.000
 D9F  C11  C10  C08  126.49  3.000
 D9F  H9   C11  C12  116.34  3.000
 D9F  H9   C11  C10  120.01  3.000
 D9F  C12  C11  C10  123.65  3.000
 D9F  H10  C12  C13  119.31  3.000
 D9F  H10  C12  C11  116.90  3.000
 D9F  C13  C12  C11  123.73  3.000
 D9F  H11  C13  C14  115.57  3.000
 D9F  H11  C13  C12  118.22  3.000
 D9F  C14  C13  C12  126.21  3.000
 D9F  H13  C14  H12  107.05  3.000
 D9F  H13  C14  C15  110.23  3.000
 D9F  H12  C14  C15  108.16  3.000
 D9F  H13  C14  C13  111.18  3.000
 D9F  H12  C14  C13  108.67  3.000
 D9F  C15  C14  C13  111.39  3.000
 D9F  H14  C15  O16  109.97  3.000
 D9F  H14  C15  C17  109.58  3.000
 D9F  O16  C15  C17  108.02  3.000
 D9F  H14  C15  C14  106.99  3.000
 D9F  O16  C15  C14  111.16  3.000
 D9F  C17  C15  C14  111.12  3.000
 D9F  H16  C17  H15  106.23  3.000
 D9F  H16  C17  C18  106.65  3.000
 D9F  H15  C17  C18  109.83  3.000
 D9F  H16  C17  C15  109.49  3.000
 D9F  H15  C17  C15  108.47  3.000
 D9F  C18  C17  C15  115.76  3.000
 D9F  H17  C18  O19  109.82  3.000
 D9F  H17  C18  C20  109.25  3.000
 D9F  O19  C18  C20  111.17  3.000
 D9F  H17  C18  C17  106.58  3.000
 D9F  C20  C18  C17  110.98  3.000
 D9F  O19  C18  C17  108.93  3.000
 D9F  H18  C20  C21  118.15  3.000
 D9F  H18  C20  C18  115.77  3.000
 D9F  C21  C20  C18  126.05  3.000
 D9F  H19  C21  C22  116.04  3.000
 D9F  H19  C21  C20  118.06  3.000
 D9F  C22  C21  C20  125.90  3.000
 D9F  H20  C22  C23  117.79  3.000
 D9F  H20  C22  C21  117.89  3.000
 D9F  C23  C22  C21  124.31  3.000
 D9F  H21  C23  C24  117.57  3.000
 D9F  H21  C23  C22  118.87  3.000
 D9F  C24  C23  C22  123.56  3.000
 D9F  H23  C24  H22  106.24  3.000
 D9F  H23  C24  C25  108.16  3.000
 D9F  H22  C24  C25  110.31  3.000
 D9F  H23  C24  C23  108.80  3.000
 D9F  H22  C24  C23  109.54  3.000
 D9F  C25  C24  C23  113.50  3.000
 D9F  H25  C25  H24  105.78  3.000
 D9F  H25  C25  C26  108.51  3.000
 D9F  H24  C25  C26  108.73  3.000
 D9F  H25  C25  C24  107.72  3.000
 D9F  H24  C25  C24  108.45  3.000
 D9F  C26  C25  C24  117.09  3.000
 D9F  H27  C26  H26  105.47  3.000
 D9F  H27  C26  C27  109.93  3.000
 D9F  H26  C26  C27  106.17  3.000
 D9F  H27  C26  C25  111.50  3.000
 D9F  H26  C26  C25  108.28  3.000
 D9F  C27  C26  C25  114.91  3.000
 D9F  H28  C27  O29  108.98  3.000
 D9F  H28  C27  C28  109.52  3.000
 D9F  O29  C27  C28  109.25  3.000
 D9F  H28  C27  C26  108.71  3.000
 D9F  C28  C27  C26  112.95  3.000
 D9F  O29  C27  C26  107.34  3.000
 D9F  H31  C28  H30  108.10  3.000
 D9F  H31  C28  H29  108.46  3.000
 D9F  H30  C28  H29  107.59  3.000
 D9F  H31  C28  C27  111.31  3.000
 D9F  H30  C28  C27  109.84  3.000
 D9F  H29  C28  C27  111.42  3.000
 D9F  H32  O09  C08  108.32  3.000
 D9F  H33  O16  C15  107.99  3.000
 D9F  H34  O19  C18  107.82  3.000
 D9F  C27  O29  C02  120.50  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
 D9F  Var_01  C05  C04  C03  C02    -1.64   0.0  0
 D9F  Var_02  C07  C06  C05  C04   174.16   0.0  0
 D9F  Var_03  C12  C11  C10  C08   173.65   0.0  0
 D9F  Var_04  C14  C13  C12  C11   179.77   0.0  0
 D9F  Var_05  C22  C21  C20  C18     2.24   0.0  0
 D9F  Var_06  C24  C23  C22  C21  -178.77   0.0  0
 D9F  Var_07  C06  C05  C04  C03  -173.39  30.0  1
 D9F  Var_08  O29  C02  C03  C04    -6.74  30.0  1
 D9F  Var_09  C08  C07  C06  C05   156.18  30.0  1
 D9F  Var_10  C13  C12  C11  C10   -40.56  30.0  1
 D9F  Var_11  C15  C14  C13  C12  -125.30  30.0  1
 D9F  Var_12  C23  C22  C21  C20  -177.15  30.0  1
 D9F  Var_13  C25  C24  C23  C22   117.05  30.0  1
 D9F  Var_14  C26  C25  C24  C23    67.58  30.0  1
 D9F  Var_15  C27  C26  C25  C24    82.64  30.0  1
 D9F  Var_16  H4   C06  C05  C04    -1.68   0.0  0
 D9F  Var_17  H1   C03  C04  C05   177.19   0.0  0
 D9F  Var_18  H8   C10  C11  C12    -4.61   0.0  0
 D9F  Var_19  H10  C12  C13  C14    -3.07   0.0  0
 D9F  Var_20  H18  C20  C21  C22  -179.93   0.0  0
 D9F  Var_21  H20  C22  C23  C24     0.97   0.0  0

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
 D9F  chir_01  C08  C10  O09  C07  negativ
 D9F  chir_02  C15  O16  C17  C14  positiv
 D9F  chir_03  C18  O19  C20  C17  negativ
 D9F  chir_04  C27  C26  O29  C28  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
 D9F  plan-1  C18  0.020
 D9F  plan-1  C20  0.020
 D9F  plan-1  C21  0.020
 D9F  plan-1  C22  0.020
 D9F  plan-1  H18  0.020
 D9F  plan-1  H19  0.020
 D9F  plan-2  C21  0.020
 D9F  plan-2  C22  0.020
 D9F  plan-2  C23  0.020
 D9F  plan-2  C24  0.020
 D9F  plan-2  H20  0.020
 D9F  plan-2  H21  0.020
 D9F  plan-3  C11  0.020
 D9F  plan-3  C12  0.020
 D9F  plan-3  C13  0.020
 D9F  plan-3  C14  0.020
 D9F  plan-3  H10  0.020
 D9F  plan-3  H11  0.020
 D9F  plan-4  C08  0.020
 D9F  plan-4  C10  0.020
 D9F  plan-4  C11  0.020
 D9F  plan-4  C12  0.020
 D9F  plan-4  H8   0.020
 D9F  plan-4  H9   0.020
 D9F  plan-5  C02  0.020
 D9F  plan-5  C03  0.020
 D9F  plan-5  O01  0.020
 D9F  plan-5  O29  0.020
 D9F  plan-6  C02  0.020
 D9F  plan-6  C03  0.020
 D9F  plan-6  C04  0.020
 D9F  plan-6  C05  0.020
 D9F  plan-6  H1   0.020
 D9F  plan-6  H2   0.020
 D9F  plan-7  C04  0.020
 D9F  plan-7  C05  0.020
 D9F  plan-7  C06  0.020
 D9F  plan-7  C07  0.020
 D9F  plan-7  H3   0.020
 D9F  plan-7  H4   0.020

