# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:42:21 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2~{R},3~{S})-2-methyl-2-(4-methylpent-3-enyl)-3-oxidanyl-3,4-dihydrochromene-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC[C@@]1(C)Oc2ccc(cc2C[C@@H]1O)C(O)=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
 XIA  XIA  '(2~{R},3~{S})-2-methyl-2-(4-methylpent-3-enyl)-3-oxidanyl-3,4-dihydrochromene-6-carboxylic acid'  ligand  42  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XIA
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
 XIA  O39  O  O      0  -0.598   5.8779  -0.3044   0.3446
 XIA  C11  C  C      0   0.392   5.2241   0.7361   0.1296
 XIA  O13  O  OC    -1  -0.599   5.6877   1.8836  -0.0247
 XIA  C6   C  CR6    0  -0.105   3.7145   0.5918   0.0442
 XIA  C5   C  CR16   0  -0.354   3.0989  -0.6370   0.2513
 XIA  C4   C  CR6    0   0.017   1.7201  -0.8026   0.1766
 XIA  C7   C  CH2    0  -0.540   1.0734  -2.1395   0.3991
 XIA  C8   C  CH1    0   0.067  -0.4235  -1.9971   0.6367
 XIA  O16  O  OH1    0  -0.671  -1.0926  -3.2300   0.5361
 XIA  C9   C  CT     0   0.180  -1.0437  -1.0255  -0.3811
 XIA  C15  C  CH3    0  -0.684  -0.8364  -1.4897  -1.8191
 XIA  O10  O  O2     0  -0.497  -0.4150   0.2503  -0.1961
 XIA  C3   C  CR6    0   0.354   0.9324   0.3085  -0.1211
 XIA  C2   C  CR16   0  -0.349   1.5268   1.5523  -0.3297
 XIA  C1   C  CR16   0  -0.293   2.9002   1.6873  -0.2425
 XIA  C17  C  CH2    0  -0.430  -2.5234  -0.8028  -0.0624
 XIA  C18  C  CH2    0  -0.498  -3.1974   0.3482  -0.8167
 XIA  C19  C  C1     0  -0.253  -4.6674   0.3793  -0.5309
 XIA  C21  C  C      0   0.078  -5.3519   1.2922   0.1633
 XIA  C23  C  CH3    0  -0.721  -4.7516   2.5106   0.7999
 XIA  C22  C  CH3    0  -0.705  -6.8334   1.1548   0.3667
 XIA  H2   H  HCR6   0   0.236   3.7108  -1.5013   0.4826
 XIA  H3   H  HCH2   0   0.254   1.2413  -2.7898  -0.4656
 XIA  H4   H  HCH2   0   0.262   1.5369  -2.6412   1.2533
 XIA  H5   H  HCH1   0   0.219  -0.5808  -1.5546   1.6328
 XIA  H6   H  HOH1   0   0.456  -0.7279  -3.8249   1.1985
 XIA  H7   H  HCH3   0   0.246  -1.3073  -0.8044  -2.5235
 XIA  H8   H  HCH3   0   0.242   0.2198  -1.5499  -2.0850
 XIA  H9   H  HCH3   0   0.241  -1.2717  -2.4760  -1.9746
 XIA  H10  H  HCR6   0   0.250   0.9022   2.4075  -0.5590
 XIA  H11  H  HCR6   0   0.240   3.3492   2.6574  -0.4090
 XIA  H12  H  HCH2   0   0.238  -3.0580  -1.7315  -0.2724
 XIA  H13  H  HCH2   0   0.231  -2.6310  -0.6234   1.0124
 XIA  H14  H  HCH2   0   0.238  -2.7239   1.2940  -0.5559
 XIA  H15  H  HCH2   0   0.232  -3.0570   0.2197  -1.8942
 XIA  H16  H  H      0   0.220  -5.2257  -0.4657  -0.9290
 XIA  H17  H  HCH3   0   0.234  -5.2155   3.4186   0.4061
 XIA  H18  H  HCH3   0   0.235  -4.9387   2.5108   1.8767
 XIA  H19  H  HCH3   0   0.239  -3.6772   2.5962   0.6517
 XIA  H20  H  HCH3   0   0.235  -7.2347   0.2696  -0.1261
 XIA  H21  H  HCH3   0   0.230  -7.0780   1.0909   1.4305
 XIA  H22  H  HCH3   0   0.229  -7.3648   2.0283  -0.0203

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
 XIA  C15  C9   single    1.525  0.020  1.525
 XIA  C9   C17  single    1.530  0.020  1.530
 XIA  C9   O10  single    1.434  0.020  1.434
 XIA  C9   C8   single    1.538  0.020  1.538
 XIA  C17  C18  single    1.532  0.020  1.532
 XIA  O16  C8   single    1.406  0.020  1.406
 XIA  O10  C3   single    1.351  0.020  1.351
 XIA  C7   C8   single    1.522  0.020  1.522
 XIA  C7   C4   single    1.502  0.020  1.502
 XIA  C3   C4   aromatic  1.394  0.020  1.394
 XIA  C3   C2   aromatic  1.394  0.020  1.394
 XIA  C4   C5   aromatic  1.391  0.020  1.391
 XIA  C19  C18  single    1.498  0.020  1.498
 XIA  C19  C21  double    1.336  0.020  1.336
 XIA  C2   C1   aromatic  1.383  0.020  1.383
 XIA  C5   C6   aromatic  1.390  0.020  1.390
 XIA  C22  C21  single    1.502  0.020  1.502
 XIA  C1   C6   aromatic  1.395  0.020  1.395
 XIA  C21  C23  single    1.500  0.020  1.500
 XIA  C6   C11  single    1.519  0.020  1.519
 XIA  C11  O39  deloc     1.248  0.020  1.248
 XIA  C11  O13  deloc     1.247  0.020  1.247
 XIA  C5   H2   single    0.930  0.020  1.080
 XIA  C7   H3   single    0.970  0.020  1.090
 XIA  C7   H4   single    0.970  0.020  1.090
 XIA  C8   H5   single    0.970  0.020  1.090
 XIA  O16  H6   single    0.850  0.020  0.980
 XIA  C15  H7   single    0.970  0.020  1.090
 XIA  C15  H8   single    0.970  0.020  1.090
 XIA  C15  H9   single    0.970  0.020  1.090
 XIA  C2   H10  single    0.930  0.020  1.080
 XIA  C1   H11  single    0.930  0.020  1.080
 XIA  C17  H12  single    0.970  0.020  1.090
 XIA  C17  H13  single    0.970  0.020  1.090
 XIA  C18  H14  single    0.970  0.020  1.090
 XIA  C18  H15  single    0.970  0.020  1.090
 XIA  C19  H16  single    0.930  0.020  1.080
 XIA  C23  H17  single    0.970  0.020  1.090
 XIA  C23  H18  single    0.970  0.020  1.090
 XIA  C23  H19  single    0.970  0.020  1.090
 XIA  C22  H20  single    0.970  0.020  1.090
 XIA  C22  H21  single    0.970  0.020  1.090
 XIA  C22  H22  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
 XIA  C6   C11  O13  116.74  3.000
 XIA  O13  C11  O39  126.44  3.000
 XIA  C6   C11  O39  116.82  3.000
 XIA  C1   C6   C5   117.80  3.000
 XIA  C1   C6   C11  121.14  3.000
 XIA  C5   C6   C11  121.05  3.000
 XIA  H2   C5   C4   118.44  3.000
 XIA  H2   C5   C6   119.12  3.000
 XIA  C4   C5   C6   122.44  3.000
 XIA  C3   C4   C7   119.86  3.000
 XIA  C3   C4   C5   118.47  3.000
 XIA  C7   C4   C5   121.67  3.000
 XIA  H4   C7   H3   106.22  3.000
 XIA  H4   C7   C8   109.74  3.000
 XIA  H3   C7   C8   109.25  3.000
 XIA  H4   C7   C4   109.97  3.000
 XIA  H3   C7   C4   110.23  3.000
 XIA  C8   C7   C4   111.30  3.000
 XIA  H5   C8   C9   106.69  3.000
 XIA  H5   C8   O16  110.43  3.000
 XIA  C9   C8   O16  108.34  3.000
 XIA  H5   C8   C7   108.62  3.000
 XIA  O16  C8   C7   112.01  3.000
 XIA  C9   C8   C7   110.63  3.000
 XIA  H6   O16  C8   108.21  3.000
 XIA  C17  C9   O10  105.52  3.000
 XIA  O10  C9   C15  109.44  3.000
 XIA  C17  C9   C15  111.85  3.000
 XIA  O10  C9   C8   107.45  3.000
 XIA  C17  C9   C8   110.13  3.000
 XIA  C15  C9   C8   112.14  3.000
 XIA  H9   C15  H8   107.58  3.000
 XIA  H9   C15  H7   107.73  3.000
 XIA  H8   C15  H7   107.19  3.000
 XIA  H9   C15  C9   110.85  3.000
 XIA  H8   C15  C9   112.22  3.000
 XIA  H7   C15  C9   111.06  3.000
 XIA  C3   O10  C9   118.87  3.000
 XIA  C2   C3   O10  117.10  3.000
 XIA  C2   C3   C4   120.14  3.000
 XIA  O10  C3   C4   122.76  3.000
 XIA  H10  C2   C1   120.59  3.000
 XIA  H10  C2   C3   119.33  3.000
 XIA  C1   C2   C3   120.07  3.000
 XIA  H11  C1   C2   119.34  3.000
 XIA  H11  C1   C6   119.58  3.000
 XIA  C2   C1   C6   121.08  3.000
 XIA  H13  C17  H12  106.26  3.000
 XIA  H13  C17  C18  108.48  3.000
 XIA  H12  C17  C18  109.20  3.000
 XIA  H13  C17  C9   108.87  3.000
 XIA  H12  C17  C9   108.04  3.000
 XIA  C18  C17  C9   115.61  3.000
 XIA  H15  C18  H14  106.38  3.000
 XIA  H15  C18  C19  108.44  3.000
 XIA  H14  C18  C19  111.28  3.000
 XIA  H15  C18  C17  109.88  3.000
 XIA  H14  C18  C17  110.06  3.000
 XIA  C19  C18  C17  110.69  3.000
 XIA  H16  C19  C21  117.26  3.000
 XIA  H16  C19  C18  114.68  3.000
 XIA  C21  C19  C18  128.05  3.000
 XIA  C22  C21  C23  114.31  3.000
 XIA  C23  C21  C19  124.80  3.000
 XIA  C22  C21  C19  120.90  3.000
 XIA  H19  C23  H18  107.66  3.000
 XIA  H19  C23  H17  107.74  3.000
 XIA  H18  C23  H17  106.39  3.000
 XIA  H19  C23  C21  113.66  3.000
 XIA  H18  C23  C21  110.47  3.000
 XIA  H17  C23  C21  110.61  3.000
 XIA  H22  C22  H21  106.39  3.000
 XIA  H22  C22  H20  108.06  3.000
 XIA  H21  C22  H20  108.07  3.000
 XIA  H22  C22  C21  111.01  3.000
 XIA  H21  C22  C21  110.97  3.000
 XIA  H20  C22  C21  112.11  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
 XIA  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 XIA  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 XIA  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 XIA  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 XIA  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 XIA  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 XIA  CONST_07  C4   C5   C6   C11   180.00   0.0  0
 XIA  CONST_08  C2   C1   C6   C11   180.00   0.0  0
 XIA  CONST_09  H10  C2   C1   C6    180.00   0.0  0
 XIA  CONST_10  H11  C1   C6   C5    180.00   0.0  0
 XIA  CONST_11  H2   C5   C4   C7      0.00   0.0  0
 XIA  Var_01    C8   C7   C4   C5    164.64  30.0  1
 XIA  Var_02    C2   C3   O10  C9    161.94  30.0  1
 XIA  Var_03    C5   C6   C11  O39     2.52  30.0  2
 XIA  Var_04    C19  C18  C17  C9    174.17  30.0  3
 XIA  Var_05    C22  C21  C19  C18  -179.23   0.0  2
 XIA  Var_06    C21  C19  C18  C17   111.10  30.0  2
 XIA  Var_07    H20  C22  C21  C19    -1.27  30.0  3
 XIA  Var_08    H17  C23  C21  C19   121.11  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
 XIA  chir_01  C8  C9   O16  C7  negativ
 XIA  chir_02  C9  O10  C17  C8  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
 XIA  plan-1  O39  0.020
 XIA  plan-1  C11  0.020
 XIA  plan-1  O13  0.020
 XIA  plan-1  C6   0.020
 XIA  plan-2  C11  0.020
 XIA  plan-2  C6   0.020
 XIA  plan-2  C5   0.020
 XIA  plan-2  C4   0.020
 XIA  plan-2  C7   0.020
 XIA  plan-2  O10  0.020
 XIA  plan-2  C3   0.020
 XIA  plan-2  C2   0.020
 XIA  plan-2  C1   0.020
 XIA  plan-2  H2   0.020
 XIA  plan-2  H10  0.020
 XIA  plan-2  H11  0.020
 XIA  plan-3  C18  0.020
 XIA  plan-3  C19  0.020
 XIA  plan-3  C21  0.020
 XIA  plan-3  C23  0.020
 XIA  plan-3  C22  0.020
 XIA  plan-3  H16  0.020

