# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:52:51 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5Z)-13-chloro-14,16-dihydroxy-1,11-dioxo-3,4,7,8,9,10,11,12-octahydro-1H-2-benzoxacyclotetradecine-6-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)OCC/C=C(/CCCCC(=O)Cc2c1Cl)C=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
 XD6  XD6  (5Z)-13-chloro-14,16-dihydroxy-1,11-dioxo-3,4,7,8,9,10,11,12-octahydro-1H-2-benzoxacyclotetradecine-6-carbaldehyde  ligand  44  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XD6
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
 XD6  C1    C   C     0   0.599  -0.1336   1.3477   0.2074
 XD6  C2    C   CR6   0  -0.264  -1.5385   1.0315  -0.1150
 XD6  C3    C   CR6   0   0.390  -2.5513   1.9900   0.0442
 XD6  C4    C   CR16  0  -0.500  -3.8867   1.6035  -0.0157
 XD6  C5    C   CR6   0   0.466  -4.2243   0.2847  -0.2511
 XD6  C6    C   CR6   0  -0.278  -3.2104  -0.6617  -0.4732
 XD6  C7    C   CR6   0   0.282  -1.8781  -0.3035  -0.4248
 XD6  C8    C   CH2   0  -0.679  -0.7962  -1.2717  -0.8092
 XD6  C9    C   C     0   0.434  -0.0421  -1.8935   0.3533
 XD6  C10   C   CH2   0  -0.553   1.4092  -2.1848   0.0803
 XD6  C11   C   CH2   0  -0.425   2.2851  -2.3619   1.3123
 XD6  C12   C   CH2   0  -0.437   3.7780  -2.3608   0.9713
 XD6  C13   C   CH2   0  -0.490   4.4401  -0.9754   0.9513
 XD6  C14   C   C     0  -0.027   3.8825   0.0367  -0.0155
 XD6  C15   C   C1    0  -0.173   3.2523   1.1447   0.4119
 XD6  C16   C   CH2   0  -0.545   2.7207   2.3039  -0.3760
 XD6  C17   C   CH2   0  -0.205   1.5456   3.0346   0.2679
 XD6  O1    O   O2    0  -0.490   0.2408   2.5758  -0.1450
 XD6  O2    O   O     0  -0.411   0.6122   0.5886   0.7737
 XD6  O3    O   OH1   0  -0.618  -2.3262   3.2833   0.2944
 XD6  O4    O   OH1   0  -0.599  -5.4859  -0.1393  -0.3043
 XD6  CL1   CL  CL    0  -0.101  -3.7055  -2.2807  -0.8329
 XD6  O5    O   O     0  -0.402  -0.6019  -2.1935   1.3811
 XD6  C21   C   C1    0   0.114   4.1024  -0.1849  -1.4439
 XD6  O22   O   O     0  -0.401   4.7523  -1.1045  -1.8982
 XD6  H4    H   HCR6  0   0.296  -4.6600   2.3496   0.1262
 XD6  H3    H   HOH1  0   0.484  -1.3866   3.4935   0.1903
 XD6  HA    H   HOH1  0   0.489  -6.0975   0.5884  -0.1377
 XD6  H81C  H   HCH2  0   0.306  -1.2191  -2.1013  -1.3809
 XD6  H82C  H   HCH2  0   0.284  -0.0979  -0.7833  -1.4889
 XD6  H101  H   HCH2  0   0.272   1.4378  -3.0927  -0.5368
 XD6  H102  H   HCH2  0   0.253   1.8052  -1.3977  -0.5587
 XD6  H111  H   HCH2  0   0.226   2.0778  -1.5655   2.0320
 XD6  H112  H   HCH2  0   0.231   2.0241  -3.2981   1.8094
 XD6  H121  H   HCH2  0   0.234   4.3139  -2.9484   1.7205
 XD6  H122  H   HCH2  0   0.223   3.9470  -2.8701   0.0197
 XD6  H131  H   HCH2  0   0.235   4.3826  -0.5560   1.9592
 XD6  H132  H   HCH2  0   0.240   5.5047  -1.1161   0.7427
 XD6  H15   H   H     0   0.258   3.1751   1.2742   1.4880
 XD6  H161  H   HCH2  0   0.291   3.5262   3.0450  -0.4294
 XD6  H162  H   HCH2  0   0.276   2.4828   2.0588  -1.4116
 XD6  H171  H   HCH2  0   0.257   1.6132   3.0076   1.3576
 XD6  H172  H   HCH2  0   0.273   1.5506   4.0754  -0.0438
 XD6  H21   H   H     0   0.187   3.6461   0.5499  -2.1278

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
 XD6  C1   C2    single    1.476  0.020  1.476
 XD6  C1   O1    single    1.331  0.020  1.331
 XD6  C1   O2    double    1.205  0.020  1.205
 XD6  C2   C3    single    1.404  0.020  1.404
 XD6  C2   C7    aromatic  1.412  0.020  1.412
 XD6  C3   C4    aromatic  1.391  0.020  1.391
 XD6  C3   O3    single    1.336  0.020  1.336
 XD6  C4   C5    aromatic  1.382  0.020  1.382
 XD6  C5   C6    aromatic  1.405  0.020  1.405
 XD6  C5   O4    single    1.332  0.020  1.332
 XD6  C6   C7    single    1.380  0.020  1.380
 XD6  C6   CL1   single    1.731  0.020  1.731
 XD6  C7   C8    single    1.502  0.020  1.502
 XD6  C8   C9    single    1.519  0.020  1.519
 XD6  C9   C10   single    1.505  0.020  1.505
 XD6  C9   O5    double    1.208  0.020  1.208
 XD6  C10  C11   single    1.522  0.020  1.522
 XD6  C11  C12   single    1.531  0.020  1.531
 XD6  C12  C13   single    1.536  0.020  1.536
 XD6  C13  C14   single    1.507  0.020  1.507
 XD6  C14  C15   double    1.344  0.020  1.344
 XD6  C14  C21   single    1.462  0.020  1.462
 XD6  C15  C16   single    1.499  0.020  1.499
 XD6  C16  C17   single    1.526  0.020  1.526
 XD6  C17  O1    single    1.443  0.020  1.443
 XD6  C21  O22   double    1.214  0.020  1.214
 XD6  C21  H21   single    0.930  0.020  1.080
 XD6  C4   H4    single    0.930  0.020  1.080
 XD6  O3   H3    single    0.850  0.020  0.980
 XD6  O4   HA    single    0.850  0.020  0.980
 XD6  C8   H81C  single    0.970  0.020  1.090
 XD6  C8   H82C  single    0.970  0.020  1.090
 XD6  C10  H101  single    0.970  0.020  1.090
 XD6  C10  H102  single    0.970  0.020  1.090
 XD6  C11  H111  single    0.970  0.020  1.090
 XD6  C11  H112  single    0.970  0.020  1.090
 XD6  C12  H121  single    0.970  0.020  1.090
 XD6  C12  H122  single    0.970  0.020  1.090
 XD6  C13  H131  single    0.970  0.020  1.090
 XD6  C13  H132  single    0.970  0.020  1.090
 XD6  C15  H15   single    0.930  0.020  1.080
 XD6  C16  H161  single    0.970  0.020  1.090
 XD6  C16  H162  single    0.970  0.020  1.090
 XD6  C17  H171  single    0.970  0.020  1.090
 XD6  C17  H172  single    0.970  0.020  1.090

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
 XD6  O2    C1   O1    122.09  3.000
 XD6  O2    C1   C2    123.83  3.000
 XD6  O1    C1   C2    114.05  3.000
 XD6  C7    C2   C3    119.81  3.000
 XD6  C7    C2   C1    118.66  3.000
 XD6  C3    C2   C1    121.06  3.000
 XD6  O3    C3   C4    116.01  3.000
 XD6  O3    C3   C2    124.10  3.000
 XD6  C4    C3   C2    119.86  3.000
 XD6  H4    C4   C5    120.34  3.000
 XD6  H4    C4   C3    119.20  3.000
 XD6  C5    C4   C3    120.46  3.000
 XD6  O4    C5   C6    117.57  3.000
 XD6  O4    C5   C4    122.82  3.000
 XD6  C6    C5   C4    119.59  3.000
 XD6  CL1   C6   C7    121.74  3.000
 XD6  CL1   C6   C5    117.17  3.000
 XD6  C7    C6   C5    121.08  3.000
 XD6  C8    C7   C6    121.26  3.000
 XD6  C8    C7   C2    119.50  3.000
 XD6  C6    C7   C2    119.03  3.000
 XD6  H82C  C8   H81C  105.18  3.000
 XD6  H82C  C8   C9    110.04  3.000
 XD6  H81C  C8   C9    106.36  3.000
 XD6  H82C  C8   C7    109.41  3.000
 XD6  H81C  C8   C7    110.15  3.000
 XD6  C9    C8   C7    115.19  3.000
 XD6  O5    C9   C10   123.57  3.000
 XD6  O5    C9   C8    121.52  3.000
 XD6  C10   C9   C8    114.78  3.000
 XD6  H102  C10  H101  104.98  3.000
 XD6  H102  C10  C11   110.49  3.000
 XD6  H101  C10  C11   110.10  3.000
 XD6  H102  C10  C9    108.50  3.000
 XD6  H101  C10  C9    106.68  3.000
 XD6  C11   C10  C9    115.51  3.000
 XD6  H112  C11  H111  106.24  3.000
 XD6  H112  C11  C12   109.59  3.000
 XD6  H111  C11  C12   109.32  3.000
 XD6  H112  C11  C10   109.31  3.000
 XD6  H111  C11  C10   109.81  3.000
 XD6  C12   C11  C10   112.38  3.000
 XD6  H122  C12  H121  105.71  3.000
 XD6  H122  C12  C13   110.03  3.000
 XD6  H121  C12  C13   106.42  3.000
 XD6  H122  C12  C11   110.15  3.000
 XD6  H121  C12  C11   108.96  3.000
 XD6  C13   C12  C11   115.08  3.000
 XD6  H132  C13  H131  106.05  3.000
 XD6  H132  C13  C14   108.92  3.000
 XD6  H131  C13  C14   108.33  3.000
 XD6  H132  C13  C12   107.82  3.000
 XD6  H131  C13  C12   108.15  3.000
 XD6  C14   C13  C12   117.05  3.000
 XD6  C21   C14  C15   120.40  3.000
 XD6  C21   C14  C13   118.00  3.000
 XD6  C15   C14  C13   121.54  3.000
 XD6  H15   C15  C16   113.77  3.000
 XD6  H15   C15  C14   116.51  3.000
 XD6  C16   C15  C14   129.53  3.000
 XD6  H162  C16  H161  105.43  3.000
 XD6  H162  C16  C17   109.89  3.000
 XD6  H161  C16  C17   105.23  3.000
 XD6  H162  C16  C15   113.75  3.000
 XD6  H161  C16  C15   106.73  3.000
 XD6  C17   C16  C15   114.93  3.000
 XD6  H172  C17  H171  108.04  3.000
 XD6  H172  C17  O1    103.10  3.000
 XD6  H171  C17  O1    109.48  3.000
 XD6  H172  C17  C16   109.51  3.000
 XD6  H171  C17  C16   111.19  3.000
 XD6  O1    C17  C16   115.03  3.000
 XD6  C17   O1   C1    118.15  3.000
 XD6  H3    O3   C3    110.70  3.000
 XD6  HA    O4   C5    110.69  3.000
 XD6  H21   C21  O22   119.61  3.000
 XD6  H21   C21  C14   116.27  3.000
 XD6  O22   C21  C14   124.11  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
 XD6  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 XD6  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 XD6  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 XD6  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 XD6  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 XD6  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 XD6  CONST_07  O3   C3   C2   C1      0.00   0.0  0
 XD6  CONST_08  CL1  C6   C7   C2    180.00   0.0  0
 XD6  CONST_09  O4   C5   C4   C3    180.00   0.0  0
 XD6  CONST_10  CL1  C6   C5   C4    180.00   0.0  0
 XD6  CONST_11  O3   C3   C4   C5    180.00   0.0  0
 XD6  CONST_12  O3   C3   C2   C7    180.00   0.0  0
 XD6  CONST_13  O4   C5   C6   C7    180.00   0.0  0
 XD6  CONST_14  CL1  C6   C7   C8      0.00   0.0  0
 XD6  CONST_15  H4   C4   C3   C2    180.00   0.0  0
 XD6  Var_01    C16  C15  C14  C13   175.19   0.0  0
 XD6  Var_02    C16  C17  O1   C1     66.93  30.0  1
 XD6  Var_03    C9   C8   C7   C2     81.98  30.0  1
 XD6  Var_04    O1   C1   C2   C3    -39.07  30.0  1
 XD6  Var_05    C10  C9   C8   C7   -146.79  30.0  1
 XD6  Var_06    C11  C10  C9   C8    160.51  30.0  1
 XD6  Var_07    C12  C11  C10  C9   -167.98  30.0  1
 XD6  Var_08    C13  C12  C11  C10    88.03  30.0  1
 XD6  Var_09    C14  C13  C12  C11   -59.44  30.0  1
 XD6  Var_10    C15  C14  C13  C12   113.23  30.0  1
 XD6  Var_11    C17  C16  C15  C14   152.66  30.0  1
 XD6  Var_12    O1   C17  C16  C15   -93.26  30.0  1
 XD6  Var_13    O22  C21  C14  C13    -3.10  30.0  2

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
 XD6  plan-1  C1   0.020
 XD6  plan-1  C2   0.020
 XD6  plan-1  C3   0.020
 XD6  plan-1  C4   0.020
 XD6  plan-1  C5   0.020
 XD6  plan-1  C6   0.020
 XD6  plan-1  C7   0.020
 XD6  plan-1  C8   0.020
 XD6  plan-1  O3   0.020
 XD6  plan-1  O4   0.020
 XD6  plan-1  CL1  0.020
 XD6  plan-1  H4   0.020
 XD6  plan-2  C8   0.020
 XD6  plan-2  C9   0.020
 XD6  plan-2  C10  0.020
 XD6  plan-2  O5   0.020
 XD6  plan-3  C1   0.020
 XD6  plan-3  C2   0.020
 XD6  plan-3  O1   0.020
 XD6  plan-3  O2   0.020
 XD6  plan-4  C13  0.020
 XD6  plan-4  C14  0.020
 XD6  plan-4  C15  0.020
 XD6  plan-4  C16  0.020
 XD6  plan-4  C21  0.020
 XD6  plan-4  H15  0.020
 XD6  plan-5  C14  0.020
 XD6  plan-5  C21  0.020
 XD6  plan-5  O22  0.020
 XD6  plan-5  H21  0.020

