# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 00:24:45 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-{3,5-dimethyl-4-[3-(3-methylisoxazol-5-yl)propoxy]phenyl}-5-(trifluoromethyl)-1,2,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CCCOc2c(C)cc(cc2C)c3noc(n3)C(F)(F)F)on1
#
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
 W11  W11  3-{3,5-dimethyl-4-[3-(3-methylisoxazol-5-yl)propoxy]phenyl}-5-(trifluoromethyl)-1,2,4-oxadiazole  ligand  45  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W11
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
 W11  O1    O  O     0  -0.350  -1.1206  -0.3242   6.9638
 W11  N2    N  N     0  -0.188  -0.8891  -0.5087   8.2986
 W11  C3    C  CR5   0   0.255   0.1122   0.2641   8.6073
 W11  CM3   C  CH3   0  -0.734   0.6434   0.3268   9.9942
 W11  C4    C  CR15  0  -0.529   0.5655   0.9798   7.4672
 W11  C5    C  CR5   0   0.470  -0.2515   0.5645   6.4718
 W11  C1C   C  CH2   0  -0.546  -0.3313   0.8908   5.0266
 W11  C2C   C  CH2   0  -0.472  -0.0561  -0.3161   4.1257
 W11  C3C   C  CH2   0  -0.156  -0.0714   0.1021   2.6716
 W11  O1B   O  O2    0  -0.489   0.1813  -1.0493   1.8679
 W11  C1B   C  CR6   0   0.288   0.2855  -0.8003   0.5333
 W11  C2B   C  CR6   0   0.045   1.5391  -0.4842  -0.0007
 W11  CM2   C  CH3   0  -0.720   2.7555  -0.4275   0.8761
 W11  C3B   C  CR16  0  -0.354   1.6323  -0.2503  -1.3642
 W11  C4B   C  CR6   0   0.018   0.5073  -0.3267  -2.1816
 W11  C5B   C  CR16  0  -0.360  -0.7239  -0.6614  -1.6284
 W11  C6B   C  CR6   0   0.041  -0.8535  -0.9032  -0.2669
 W11  CM6   C  CH3   0  -0.717  -2.1748  -1.3041   0.3191
 W11  C2A   C  CR5   0   0.344   0.6102  -0.0696  -3.6130
 W11  N1A   N  N     0  -0.139   1.7246   0.2391  -4.2132
 W11  N3A   N  N     0  -0.436  -0.4599  -0.1232  -4.4670
 W11  C3A   C  CR5   0   0.272   0.0811   0.1688  -5.5891
 W11  CM4   C  CT    0   1.077  -0.6213   0.2721  -6.9139
 W11  O1A   O  O     0  -0.306   1.3743   0.3968  -5.5218
 W11  F1    F  F     0  -0.291   0.2396   0.5384  -7.8861
 W11  F2    F  F     0  -0.292  -1.2420  -0.8687  -7.1914
 W11  F3    F  F     0  -0.293  -1.5323   1.2382  -6.8746
 W11  HM31  H  HCH3  0   0.259   0.5522   1.3372  10.3931
 W11  HM32  H  HCH3  0   0.256   0.1097  -0.3547  10.6534
 W11  HM33  H  HCH3  0   0.258   1.7015   0.0661  10.0108
 W11  H41   H  HCR5  0   0.275   1.3729   1.6902   7.4101
 W11  H1C1  H  HCH2  0   0.272  -1.3182   1.3044   4.7995
 W11  H1C2  H  HCH2  0   0.271   0.3944   1.6804   4.8255
 W11  H2C1  H  HCH2  0   0.249   0.9181  -0.7443   4.3733
 W11  H2C2  H  HCH2  0   0.249  -0.8079  -1.0902   4.2929
 W11  H3C1  H  HCH2  0   0.227  -1.0414   0.5410   2.4106
 W11  H3C2  H  HCH2  0   0.226   0.6911   0.8678   2.4916
 W11  HM21  H  HCH3  0   0.251   2.8645  -1.3392   1.4639
 W11  HM22  H  HCH3  0   0.252   3.6566  -0.3025   0.2782
 W11  HM23  H  HCH3  0   0.249   2.7114   0.4047   1.5803
 W11  H3B   H  HCR6  0   0.258   2.5971  -0.0002  -1.7881
 W11  H5B   H  HCR6  0   0.260  -1.5981  -0.7359  -2.2629
 W11  HM61  H  HCH3  0   0.252  -2.1200  -2.2880   0.7863
 W11  HM62  H  HCH3  0   0.247  -2.5173  -0.6068   1.0845
 W11  HM63  H  HCH3  0   0.250  -2.9413  -1.3432  -0.4529

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
 W11  O1   N2    aromatic  1.367  0.020  1.367
 W11  O1   C5    aromatic  1.337  0.020  1.337
 W11  N2   C3    aromatic  1.302  0.020  1.302
 W11  C3   CM3   single    1.487  0.020  1.487
 W11  C3   C4    aromatic  1.420  0.020  1.420
 W11  CM3  HM31  single    0.970  0.020  1.090
 W11  CM3  HM32  single    0.970  0.020  1.090
 W11  CM3  HM33  single    0.970  0.020  1.090
 W11  C4   C5    aromatic  1.353  0.020  1.353
 W11  C4   H41   single    0.930  0.020  1.080
 W11  C5   C1C   single    1.484  0.020  1.484
 W11  C1C  C2C   single    1.531  0.020  1.531
 W11  C1C  H1C1  single    0.970  0.020  1.090
 W11  C1C  H1C2  single    0.970  0.020  1.090
 W11  C2C  C3C   single    1.513  0.020  1.513
 W11  C2C  H2C1  single    0.970  0.020  1.090
 W11  C2C  H2C2  single    0.970  0.020  1.090
 W11  C3C  O1B   single    1.427  0.020  1.427
 W11  C3C  H3C1  single    0.970  0.020  1.090
 W11  C3C  H3C2  single    0.970  0.020  1.090
 W11  O1B  C1B   single    1.362  0.020  1.362
 W11  C1B  C2B   aromatic  1.399  0.020  1.399
 W11  C1B  C6B   aromatic  1.396  0.020  1.396
 W11  C2B  CM2   single    1.501  0.020  1.501
 W11  C2B  C3B   aromatic  1.387  0.020  1.387
 W11  CM2  HM21  single    0.970  0.020  1.090
 W11  CM2  HM22  single    0.970  0.020  1.090
 W11  CM2  HM23  single    0.970  0.020  1.090
 W11  C3B  C4B   aromatic  1.393  0.020  1.393
 W11  C3B  H3B   single    0.930  0.020  1.080
 W11  C4B  C5B   aromatic  1.391  0.020  1.391
 W11  C4B  C2A   single    1.458  0.020  1.458
 W11  C5B  C6B   aromatic  1.389  0.020  1.389
 W11  C5B  H5B   single    0.930  0.020  1.080
 W11  C6B  CM6   single    1.500  0.020  1.500
 W11  CM6  HM61  single    0.970  0.020  1.090
 W11  CM6  HM62  single    0.970  0.020  1.090
 W11  CM6  HM63  single    0.970  0.020  1.090
 W11  C2A  N1A   aromatic  1.303  0.020  1.303
 W11  C2A  N3A   aromatic  1.370  0.020  1.370
 W11  N1A  O1A   aromatic  1.364  0.020  1.364
 W11  N3A  C3A   aromatic  1.279  0.020  1.279
 W11  C3A  CM4   single    1.503  0.020  1.503
 W11  C3A  O1A   aromatic  1.315  0.020  1.315
 W11  CM4  F1    single    1.326  0.020  1.326
 W11  CM4  F2    single    1.328  0.020  1.328
 W11  CM4  F3    single    1.329  0.020  1.329

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
 W11  C5    O1   N2    109.82  3.000
 W11  C3    N2   O1    106.35  3.000
 W11  C4    C3   CM3   127.85  3.000
 W11  C4    C3   N2    110.75  3.000
 W11  CM3   C3   N2    121.40  3.000
 W11  HM33  CM3  HM32  108.49  3.000
 W11  HM33  CM3  HM31  107.30  3.000
 W11  HM32  CM3  HM31  108.54  3.000
 W11  HM33  CM3  C3    110.55  3.000
 W11  HM32  CM3  C3    111.32  3.000
 W11  HM31  CM3  C3    110.52  3.000
 W11  H41   C4   C5    128.03  3.000
 W11  H41   C4   C3    127.90  3.000
 W11  C5    C4   C3    104.07  3.000
 W11  C1C   C5   C4    132.96  3.000
 W11  C1C   C5   O1    118.02  3.000
 W11  C4    C5   O1    109.01  3.000
 W11  H1C2  C1C  H1C1  106.75  3.000
 W11  H1C2  C1C  C2C   110.03  3.000
 W11  H1C1  C1C  C2C   109.76  3.000
 W11  H1C2  C1C  C5    107.63  3.000
 W11  H1C1  C1C  C5    109.51  3.000
 W11  C2C   C1C  C5    112.96  3.000
 W11  H2C2  C2C  H2C1  107.54  3.000
 W11  H2C2  C2C  C3C   109.64  3.000
 W11  H2C1  C2C  C3C   109.58  3.000
 W11  H2C2  C2C  C1C   110.18  3.000
 W11  H2C1  C2C  C1C   109.62  3.000
 W11  C3C   C2C  C1C   110.23  3.000
 W11  H3C2  C3C  H3C1  107.27  3.000
 W11  H3C2  C3C  O1B   110.38  3.000
 W11  H3C1  C3C  O1B   110.23  3.000
 W11  H3C2  C3C  C2C   110.12  3.000
 W11  H3C1  C3C  C2C   110.39  3.000
 W11  O1B   C3C  C2C   108.45  3.000
 W11  C1B   O1B  C3C   114.71  3.000
 W11  C6B   C1B  C2B   121.95  3.000
 W11  C6B   C1B  O1B   119.08  3.000
 W11  C2B   C1B  O1B   118.95  3.000
 W11  C3B   C2B  CM2   120.91  3.000
 W11  C3B   C2B  C1B   118.28  3.000
 W11  CM2   C2B  C1B   120.79  3.000
 W11  HM23  CM2  HM22  107.48  3.000
 W11  HM23  CM2  HM21  107.09  3.000
 W11  HM22  CM2  HM21  108.02  3.000
 W11  HM23  CM2  C2B   111.91  3.000
 W11  HM22  CM2  C2B   110.76  3.000
 W11  HM21  CM2  C2B   111.38  3.000
 W11  H3B   C3B  C4B   120.17  3.000
 W11  H3B   C3B  C2B   118.93  3.000
 W11  C4B   C3B  C2B   120.90  3.000
 W11  C2A   C4B  C5B   119.70  3.000
 W11  C2A   C4B  C3B   120.63  3.000
 W11  C5B   C4B  C3B   119.66  3.000
 W11  H5B   C5B  C6B   119.16  3.000
 W11  H5B   C5B  C4B   119.89  3.000
 W11  C6B   C5B  C4B   120.96  3.000
 W11  CM6   C6B  C5B   120.77  3.000
 W11  CM6   C6B  C1B   120.97  3.000
 W11  C5B   C6B  C1B   118.23  3.000
 W11  HM63  CM6  HM62  107.43  3.000
 W11  HM63  CM6  HM61  107.87  3.000
 W11  HM62  CM6  HM61  106.97  3.000
 W11  HM63  CM6  C6B   110.66  3.000
 W11  HM62  CM6  C6B   112.33  3.000
 W11  HM61  CM6  C6B   111.36  3.000
 W11  N3A   C2A  N1A   112.96  3.000
 W11  N3A   C2A  C4B   123.36  3.000
 W11  N1A   C2A  C4B   123.67  3.000
 W11  O1A   N1A  C2A   104.46  3.000
 W11  C3A   N3A  C2A   101.97  3.000
 W11  O1A   C3A  CM4   119.52  3.000
 W11  O1A   C3A  N3A   114.24  3.000
 W11  CM4   C3A  N3A   126.24  3.000
 W11  F3    CM4  F2    108.08  3.000
 W11  F3    CM4  F1    108.72  3.000
 W11  F2    CM4  F1    108.84  3.000
 W11  F3    CM4  C3A   110.14  3.000
 W11  F2    CM4  C3A   110.09  3.000
 W11  F1    CM4  C3A   110.90  3.000
 W11  C3A   O1A  N1A   106.36  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
 W11  CONST_01  C4    C3   N2   O1      0.00   0.0  0
 W11  CONST_02  C3    C4   C5   O1      0.00   0.0  0
 W11  CONST_03  C4    C5   O1   N2      0.00   0.0  0
 W11  CONST_04  C5    C4   C3   N2      0.00   0.0  0
 W11  CONST_05  C5    O1   N2   C3      0.00   0.0  0
 W11  CONST_06  C4B   C3B  C2B  C1B     0.00   0.0  0
 W11  CONST_07  C4B   C5B  C6B  C1B     0.00   0.0  0
 W11  CONST_08  C5B   C6B  C1B  C2B     0.00   0.0  0
 W11  CONST_09  C5B   C4B  C3B  C2B     0.00   0.0  0
 W11  CONST_10  C2A   C4B  C3B  C2B   180.00   0.0  0
 W11  CONST_11  C6B   C1B  C2B  C3B     0.00   0.0  0
 W11  CONST_12  C6B   C5B  C4B  C3B     0.00   0.0  0
 W11  CONST_13  N1A   C2A  C4B  C3B     0.00   0.0  0
 W11  CONST_14  N3A   C2A  C4B  C3B   180.00   0.0  0
 W11  CONST_15  O1A   N1A  C2A  C4B   180.00   0.0  0
 W11  CONST_16  C3A   N3A  C2A  C4B   180.00   0.0  0
 W11  CONST_17  N1A   C2A  C4B  C5B   180.00   0.0  0
 W11  CONST_18  N3A   C2A  C4B  C5B     0.00   0.0  0
 W11  CONST_19  C2A   C4B  C5B  C6B   180.00   0.0  0
 W11  CONST_20  C3A   O1A  N1A  C2A     0.00   0.0  0
 W11  CONST_21  O1A   C3A  N3A  C2A     0.00   0.0  0
 W11  CONST_22  C3A   N3A  C2A  N1A     0.00   0.0  0
 W11  CONST_23  N3A   C3A  O1A  N1A     0.00   0.0  0
 W11  CONST_24  O1A   N1A  C2A  N3A     0.00   0.0  0
 W11  CONST_25  CM3   C3   N2   O1    180.00   0.0  0
 W11  CONST_26  C1C   C5   O1   N2    180.00   0.0  0
 W11  CONST_27  C1C   C5   C4   C3    180.00   0.0  0
 W11  CONST_28  C5    C4   C3   CM3   180.00   0.0  0
 W11  CONST_29  C3B   C2B  C1B  O1B   180.00   0.0  0
 W11  CONST_30  C5B   C6B  C1B  O1B   180.00   0.0  0
 W11  CONST_31  CM6   C6B  C1B  C2B   180.00   0.0  0
 W11  CONST_32  C6B   C1B  C2B  CM2   180.00   0.0  0
 W11  CONST_33  C4B   C3B  C2B  CM2   180.00   0.0  0
 W11  CONST_34  CM6   C6B  C5B  C4B   180.00   0.0  0
 W11  CONST_35  CM4   C3A  N3A  C2A   180.00   0.0  0
 W11  CONST_36  CM4   C3A  O1A  N1A   180.00   0.0  0
 W11  CONST_37  H41   C4   C5   O1    180.00   0.0  0
 W11  CONST_38  H3B   C3B  C2B  C1B   180.00   0.0  0
 W11  CONST_39  H5B   C5B  C6B  C1B   180.00   0.0  0
 W11  Var_01    C2C   C1C  C5   O1    -62.62  30.0  2
 W11  Var_02    C2B   C1B  O1B  C3C    89.22  30.0  2
 W11  Var_03    F1    CM4  C3A  N3A  -177.43  30.0  2
 W11  Var_04    HM31  CM3  C3   N2   -119.20  30.0  2
 W11  Var_05    HM21  CM2  C2B  C1B    52.06  30.0  2
 W11  Var_06    HM61  CM6  C6B  C1B   -59.31  30.0  2
 W11  Var_07    C3C   C2C  C1C  C5   -176.63  30.0  3
 W11  Var_08    H3C1  C3C  O1B  C1B    63.27  30.0  1
 W11  Var_09    O1B   C3C  C2C  C1C  -179.70  30.0  3

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
 W11  plan-1  O1   0.020
 W11  plan-1  N2   0.020
 W11  plan-1  C3   0.020
 W11  plan-1  CM3  0.020
 W11  plan-1  C4   0.020
 W11  plan-1  C5   0.020
 W11  plan-1  C1C  0.020
 W11  plan-1  H41  0.020
 W11  plan-2  C4B  0.020
 W11  plan-2  C2A  0.020
 W11  plan-2  N1A  0.020
 W11  plan-2  N3A  0.020
 W11  plan-2  C3A  0.020
 W11  plan-2  CM4  0.020
 W11  plan-2  O1A  0.020
 W11  plan-3  O1B  0.020
 W11  plan-3  C1B  0.020
 W11  plan-3  C2B  0.020
 W11  plan-3  CM2  0.020
 W11  plan-3  C3B  0.020
 W11  plan-3  C4B  0.020
 W11  plan-3  C5B  0.020
 W11  plan-3  C6B  0.020
 W11  plan-3  CM6  0.020
 W11  plan-3  C2A  0.020
 W11  plan-3  H3B  0.020
 W11  plan-3  H5B  0.020

