# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:02:27 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-methyl-5-(5-{4-[(4S)-4-methyl-4,5-dihydro-1,3-oxazol-2-yl]phenoxy}pentyl)isoxazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1COC(=N1)c2ccc(OCCCCCc3onc(C)c3)cc2
#
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
 W56  W56  3-methyl-5-(5-{4-[(4S)-4-methyl-4,5-dihydro-1,3-oxazol-2-yl]phenoxy}pentyl)isoxazole  ligand  48  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W56
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
 W56  O1    O  O     0  -0.351  -0.3627  -0.9270   -7.1399
 W56  N2    N  N     0  -0.189  -0.7862  -0.6724   -8.4145
 W56  C3    C  CR5   0   0.255  -0.2340   0.4531   -8.7660
 W56  C31   C  CH3   0  -0.734  -0.4708   1.0450  -10.1090
 W56  C4    C  CR15  0  -0.531   0.5720   0.9676   -7.7162
 W56  C5    C  CR5   0   0.468   0.4479   0.0530   -6.7260
 W56  C1C   C  CH2   0  -0.535   1.0060  -0.0355   -5.3538
 W56  C2C   C  CH2   0  -0.424  -0.0610  -0.0004   -4.2578
 W56  C3C   C  CH2   0  -0.433   0.5564  -0.0660   -2.8671
 W56  C4C   C  CH2   0  -0.458  -0.4973  -0.0269   -1.7675
 W56  C5C   C  CH2   0  -0.174   0.1295  -0.1123   -0.3922
 W56  O1B   O  O2    0  -0.470  -0.9145  -0.0449    0.5708
 W56  C1B   C  CR6   0   0.396  -0.6137  -0.0841    1.8755
 W56  C2B   C  CR16  0  -0.337  -1.6894   0.0174    2.7620
 W56  C3B   C  CR16  0  -0.262  -1.4766  -0.0135    4.1252
 W56  C4B   C  CR6   0  -0.035  -0.1859  -0.1449    4.6433
 W56  C5B   C  CR16  0  -0.259   0.8799  -0.2447    3.7534
 W56  C6B   C  CR16  0  -0.368   0.6797  -0.2169    2.3836
 W56  C2A   C  CR5   0   0.493   0.0653  -0.1757    6.0844
 W56  N3A   N  N     0  -0.442   1.1967  -0.3098    6.6394
 W56  C4A   C  CR15  0  -0.173   0.9877  -0.2356    8.0813
 W56  CM1   C  CH3   0  -0.665   1.7119   0.9613    8.6778
 W56  C5A   C  CH2   0  -0.199  -0.5462  -0.1608    8.2282
 W56  O1A   O  O     0  -0.483  -1.0140  -0.0479    6.8772
 W56  H311  H  HCH3  0   0.258  -0.9056   2.0405  -10.0184
 W56  H312  H  HCH3  0   0.258   0.4688   1.1499  -10.6517
 W56  H313  H  HCH3  0   0.255  -1.1439   0.4269  -10.6998
 W56  H4    H  HCR5  0   0.273   1.1495   1.8767   -7.7093
 W56  H1C1  H  HCH2  0   0.264   1.6992   0.7972   -5.2237
 W56  H1C2  H  HCH2  0   0.264   1.5979  -0.9514   -5.2606
 W56  H2C1  H  HCH2  0   0.233  -0.7550  -0.8352   -4.3865
 W56  H2C2  H  HCH2  0   0.233  -0.6522   0.9149   -4.3549
 W56  H3C1  H  HCH2  0   0.225   1.2543   0.7675   -2.7384
 W56  H3C2  H  HCH2  0   0.225   1.1517  -0.9809   -2.7778
 W56  H4C1  H  HCH2  0   0.233  -1.1978  -0.8562   -1.8999
 W56  H4C2  H  HCH2  0   0.233  -1.0765   0.8977   -1.8467
 W56  H5C1  H  HCH2  0   0.226   0.8377   0.7106   -0.2413
 W56  H5C2  H  HCH2  0   0.226   0.6858  -1.0508   -0.2863
 W56  H2B   H  HCR6  0   0.267  -2.6932   0.1235    2.3703
 W56  H3B   H  HCR6  0   0.261  -2.3300   0.0667    4.7845
 W56  H5B   H  HCR6  0   0.261   1.8869  -0.3467    4.1360
 W56  H6B   H  HCR6  0   0.285   1.5375  -0.2976    1.7307
 W56  H4A   H  HCR5  0   0.249   1.3744  -1.1456    8.5478
 W56  HM11  H  HCH3  0   0.237   2.7830   0.9041    8.4845
 W56  HM12  H  HCH3  0   0.225   1.3375   1.8957    8.2562
 W56  HM13  H  HCH3  0   0.233   1.5670   0.9957    9.7584
 W56  H5A1  H  HCH2  0   0.246  -0.9773  -1.0575    8.6752
 W56  H5A2  H  HCH2  0   0.242  -0.8852   0.7102    8.7915

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
 W56  O1   N2    aromatic  1.367  0.020  1.367
 W56  O1   C5    aromatic  1.337  0.020  1.337
 W56  N2   C3    aromatic  1.302  0.020  1.302
 W56  C3   C31   single    1.487  0.020  1.487
 W56  C3   C4    aromatic  1.420  0.020  1.420
 W56  C31  H311  single    0.970  0.020  1.090
 W56  C31  H312  single    0.970  0.020  1.090
 W56  C31  H313  single    0.970  0.020  1.090
 W56  C4   C5    aromatic  1.354  0.020  1.354
 W56  C4   H4    single    0.930  0.020  1.080
 W56  C5   C1C   single    1.484  0.020  1.484
 W56  C1C  C2C   single    1.530  0.020  1.530
 W56  C1C  H1C1  single    0.970  0.020  1.090
 W56  C1C  H1C2  single    0.970  0.020  1.090
 W56  C2C  C3C   single    1.523  0.020  1.523
 W56  C2C  H2C1  single    0.970  0.020  1.090
 W56  C2C  H2C2  single    0.970  0.020  1.090
 W56  C3C  C4C   single    1.523  0.020  1.523
 W56  C3C  H3C1  single    0.970  0.020  1.090
 W56  C3C  H3C2  single    0.970  0.020  1.090
 W56  C4C  C5C   single    1.514  0.020  1.514
 W56  C4C  H4C1  single    0.970  0.020  1.090
 W56  C4C  H4C2  single    0.970  0.020  1.090
 W56  C5C  O1B   single    1.422  0.020  1.422
 W56  C5C  H5C1  single    0.970  0.020  1.090
 W56  C5C  H5C2  single    0.970  0.020  1.090
 W56  O1B  C1B   single    1.340  0.020  1.340
 W56  C1B  C2B   aromatic  1.398  0.020  1.398
 W56  C1B  C6B   aromatic  1.396  0.020  1.396
 W56  C2B  C3B   aromatic  1.380  0.020  1.380
 W56  C2B  H2B   single    0.930  0.020  1.080
 W56  C3B  C4B   aromatic  1.397  0.020  1.397
 W56  C3B  H3B   single    0.930  0.020  1.080
 W56  C4B  C5B   aromatic  1.392  0.020  1.392
 W56  C4B  C2A   single    1.463  0.020  1.463
 W56  C5B  C6B   aromatic  1.385  0.020  1.385
 W56  C5B  H5B   single    0.930  0.020  1.080
 W56  C6B  H6B   single    0.930  0.020  1.080
 W56  C2A  N3A   double    1.267  0.020  1.267
 W56  C2A  O1A   single    1.345  0.020  1.345
 W56  N3A  C4A   single    1.459  0.020  1.459
 W56  C4A  CM1   single    1.521  0.020  1.521
 W56  C4A  C5A   single    1.543  0.020  1.543
 W56  C4A  H4A   single    0.970  0.020  1.090
 W56  CM1  HM11  single    0.970  0.020  1.090
 W56  CM1  HM12  single    0.970  0.020  1.090
 W56  CM1  HM13  single    0.970  0.020  1.090
 W56  C5A  O1A   single    1.434  0.020  1.434
 W56  C5A  H5A1  single    0.970  0.020  1.090
 W56  C5A  H5A2  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
 W56  C5    O1   N2    109.87  3.000
 W56  C3    N2   O1    106.34  3.000
 W56  C4    C3   C31   127.88  3.000
 W56  C4    C3   N2    110.75  3.000
 W56  C31   C3   N2    121.37  3.000
 W56  H313  C31  H312  108.51  3.000
 W56  H313  C31  H311  108.49  3.000
 W56  H312  C31  H311  107.30  3.000
 W56  H313  C31  C3    111.27  3.000
 W56  H312  C31  C3    110.53  3.000
 W56  H311  C31  C3    110.61  3.000
 W56  H4    C4   C5    127.93  3.000
 W56  H4    C4   C3    127.95  3.000
 W56  C5    C4   C3    104.12  3.000
 W56  C1C   C5   C4    133.02  3.000
 W56  C1C   C5   O1    118.06  3.000
 W56  C4    C5   O1    108.92  3.000
 W56  H1C2  C1C  H1C1  106.55  3.000
 W56  H1C2  C1C  C2C   109.59  3.000
 W56  H1C1  C1C  C2C   109.88  3.000
 W56  H1C2  C1C  C5    109.39  3.000
 W56  H1C1  C1C  C5    107.68  3.000
 W56  C2C   C1C  C5    113.50  3.000
 W56  H2C2  C2C  H2C1  106.58  3.000
 W56  H2C2  C2C  C3C   109.64  3.000
 W56  H2C1  C2C  C3C   109.39  3.000
 W56  H2C2  C2C  C1C   109.42  3.000
 W56  H2C1  C2C  C1C   109.93  3.000
 W56  C3C   C2C  C1C   111.74  3.000
 W56  H3C2  C3C  H3C1  106.25  3.000
 W56  H3C2  C3C  C4C   109.79  3.000
 W56  H3C1  C3C  C4C   109.67  3.000
 W56  H3C2  C3C  C2C   109.32  3.000
 W56  H3C1  C3C  C2C   109.45  3.000
 W56  C4C   C3C  C2C   112.18  3.000
 W56  H4C2  C4C  H4C1  107.03  3.000
 W56  H4C2  C4C  C5C   109.43  3.000
 W56  H4C1  C4C  C5C   109.42  3.000
 W56  H4C2  C4C  C3C   109.62  3.000
 W56  H4C1  C4C  C3C   109.64  3.000
 W56  C5C   C4C  C3C   111.59  3.000
 W56  H5C2  C5C  H5C1  107.56  3.000
 W56  H5C2  C5C  O1B   110.35  3.000
 W56  H5C1  C5C  O1B   110.22  3.000
 W56  H5C2  C5C  C4C   110.25  3.000
 W56  H5C1  C5C  C4C   110.50  3.000
 W56  O1B   C5C  C4C   107.97  3.000
 W56  C1B   O1B  C5C   119.56  3.000
 W56  C6B   C1B  C2B   119.29  3.000
 W56  C6B   C1B  O1B   124.43  3.000
 W56  C2B   C1B  O1B   116.29  3.000
 W56  H2B   C2B  C3B   120.17  3.000
 W56  H2B   C2B  C1B   119.42  3.000
 W56  C3B   C2B  C1B   120.41  3.000
 W56  H3B   C3B  C4B   120.66  3.000
 W56  H3B   C3B  C2B   118.62  3.000
 W56  C4B   C3B  C2B   120.73  3.000
 W56  C2A   C4B  C5B   119.78  3.000
 W56  C2A   C4B  C3B   121.73  3.000
 W56  C5B   C4B  C3B   118.49  3.000
 W56  H5B   C5B  C6B   119.10  3.000
 W56  H5B   C5B  C4B   119.55  3.000
 W56  C6B   C5B  C4B   121.35  3.000
 W56  H6B   C6B  C5B   118.77  3.000
 W56  H6B   C6B  C1B   121.50  3.000
 W56  C5B   C6B  C1B   119.73  3.000
 W56  O1A   C2A  N3A   117.92  3.000
 W56  O1A   C2A  C4B   116.15  3.000
 W56  N3A   C2A  C4B   125.93  3.000
 W56  C4A   N3A  C2A   107.43  3.000
 W56  H4A   C4A  C5A   110.58  3.000
 W56  H4A   C4A  CM1   108.62  3.000
 W56  C5A   C4A  CM1   113.45  3.000
 W56  H4A   C4A  N3A   109.19  3.000
 W56  C5A   C4A  N3A   103.83  3.000
 W56  CM1   C4A  N3A   111.07  3.000
 W56  HM13  CM1  HM12  108.07  3.000
 W56  HM13  CM1  HM11  107.93  3.000
 W56  HM12  CM1  HM11  108.28  3.000
 W56  HM13  CM1  C4A   110.49  3.000
 W56  HM12  CM1  C4A   111.04  3.000
 W56  HM11  CM1  C4A   110.92  3.000
 W56  H5A2  C5A  H5A1  108.77  3.000
 W56  H5A2  C5A  O1A   108.79  3.000
 W56  H5A1  C5A  O1A   108.77  3.000
 W56  H5A2  C5A  C4A   113.37  3.000
 W56  H5A1  C5A  C4A   113.09  3.000
 W56  O1A   C5A  C4A   103.79  3.000
 W56  C5A   O1A  C2A   106.62  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
 W56  CONST_01  C4    C3   N2   O1      0.00   0.0  0
 W56  CONST_02  C3    C4   C5   O1      0.00   0.0  0
 W56  CONST_03  C4    C5   O1   N2      0.00   0.0  0
 W56  CONST_04  C5    C4   C3   N2      0.00   0.0  0
 W56  CONST_05  C5    O1   N2   C3      0.00   0.0  0
 W56  CONST_06  C4B   C3B  C2B  C1B     0.00   0.0  0
 W56  CONST_07  C4B   C5B  C6B  C1B     0.00   0.0  0
 W56  CONST_08  C5B   C6B  C1B  C2B     0.00   0.0  0
 W56  CONST_09  C5B   C4B  C3B  C2B     0.00   0.0  0
 W56  CONST_10  C6B   C1B  C2B  C3B     0.00   0.0  0
 W56  CONST_11  C6B   C5B  C4B  C3B     0.00   0.0  0
 W56  CONST_12  C2A   C4B  C3B  C2B   180.00   0.0  0
 W56  CONST_13  C2A   C4B  C5B  C6B   180.00   0.0  0
 W56  CONST_14  C31   C3   N2   O1    180.00   0.0  0
 W56  CONST_15  C1C   C5   O1   N2    180.00   0.0  0
 W56  CONST_16  C1C   C5   C4   C3    180.00   0.0  0
 W56  CONST_17  C5    C4   C3   C31   180.00   0.0  0
 W56  CONST_18  C3B   C2B  C1B  O1B   180.00   0.0  0
 W56  CONST_19  C5B   C6B  C1B  O1B   180.00   0.0  0
 W56  CONST_20  H4    C4   C5   O1    180.00   0.0  0
 W56  CONST_21  H3B   C3B  C2B  C1B   180.00   0.0  0
 W56  CONST_22  H5B   C5B  C6B  C1B   180.00   0.0  0
 W56  CONST_23  H6B   C6B  C1B  C2B   180.00   0.0  0
 W56  CONST_24  H2B   C2B  C3B  C4B   180.00   0.0  0
 W56  Var_01    N3A   C2A  C4B  C3B   178.97  30.0  2
 W56  Var_02    C4A   C5A  O1A  C2A     5.31  30.0  1
 W56  Var_03    C2C   C1C  C5   O1    -62.66  30.0  2
 W56  Var_04    C2B   C1B  O1B  C5C   178.60  30.0  2
 W56  Var_05    H311  C31  C3   N2    121.24  30.0  2
 W56  Var_06    C3C   C2C  C1C  C5   -178.88  30.0  3
 W56  Var_07    H5C1  C5C  O1B  C1B   -58.41  30.0  1
 W56  Var_08    C4C   C3C  C2C  C1C   179.80  30.0  3
 W56  Var_09    C5C   C4C  C3C  C2C   179.20  30.0  3
 W56  Var_10    O1B   C5C  C4C  C3C   178.96  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
 W56  chir_01  C4A  N3A  CM1  C5A  negativ

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
 W56  plan-1  O1   0.020
 W56  plan-1  N2   0.020
 W56  plan-1  C3   0.020
 W56  plan-1  C31  0.020
 W56  plan-1  C4   0.020
 W56  plan-1  C5   0.020
 W56  plan-1  C1C  0.020
 W56  plan-1  H4   0.020
 W56  plan-2  O1B  0.020
 W56  plan-2  C1B  0.020
 W56  plan-2  C2B  0.020
 W56  plan-2  C3B  0.020
 W56  plan-2  C4B  0.020
 W56  plan-2  C5B  0.020
 W56  plan-2  C6B  0.020
 W56  plan-2  C2A  0.020
 W56  plan-2  H2B  0.020
 W56  plan-2  H3B  0.020
 W56  plan-2  H5B  0.020
 W56  plan-2  H6B  0.020

