# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:49:36 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S,3S)-2-(1,3-benzodioxol-5-ylmethyl)-3-benzylbutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccccc1)[C@H](Cc2ccc3OCOc3c2)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
 BYS  BYS  '(2S,3S)-2-(1,3-benzodioxol-5-ylmethyl)-3-benzylbutanedioic acid'  ligand  43  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYS
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
 BYS  C1    C  CH1   0  -0.343   0.3286  -0.1341   1.6250
 BYS  C2    C  C     0   0.555   1.4520   0.6053   2.3137
 BYS  O3    O  O     0  -0.445   1.8076   1.7155   1.9968
 BYS  O4    O  OH1   0  -0.575   1.9809  -0.0730   3.3174
 BYS  C5    C  CH2   0  -0.531  -1.0096   0.3597   2.2132
 BYS  C6    C  CR6   0   0.141  -1.1366   0.1116   3.6908
 BYS  C7    C  CR16  0  -0.307  -0.9567   1.1418   4.6086
 BYS  C8    C  CR16  0  -0.240  -1.0506   0.9020   5.9738
 BYS  C9    C  CR16  0  -0.271  -1.3259  -0.3762   6.4391
 BYS  C10   C  CR16  0  -0.239  -1.5092  -1.4121   5.5307
 BYS  C11   C  CR16  0  -0.307  -1.4153  -1.1673   4.1686
 BYS  C12   C  CH1   0  -0.348   0.3760   0.1108   0.1085
 BYS  C13   C  C     0   0.555   1.7921  -0.0162  -0.4028
 BYS  O14   O  O     0  -0.443   2.5571  -0.8740  -0.0316
 BYS  O15   O  OH1   0  -0.575   2.0964   0.8895  -1.3167
 BYS  C16   C  CH2   0  -0.520  -0.4983  -0.9207  -0.6353
 BYS  C17   C  CR6   0   0.111  -0.4363  -0.7886  -2.1320
 BYS  C18   C  CR16  0  -0.388  -1.0665   0.3011  -2.7571
 BYS  C19   C  CR56  0   0.314  -0.9501   0.4015  -4.1188
 BYS  O20   O  O     0  -0.487  -1.4797   1.3357  -4.9474
 BYS  C21   C  CH2   0   0.067  -0.8883   1.1075  -6.2193
 BYS  O22   O  O     0  -0.486  -0.3216  -0.1945  -6.1829
 BYS  C23   C  CR56  0   0.285  -0.2457  -0.5284  -4.8696
 BYS  C24   C  CR16  0  -0.330   0.3710  -1.6042  -4.2858
 BYS  C25   C  CR16  0  -0.323   0.2620  -1.7151  -2.8929
 BYS  HC11  H  HCH1  0   0.284   0.4300  -1.2040   1.8244
 BYS  HXT1  H  HOH1  0   0.481   2.6590   0.4607   3.7599
 BYS  HC51  H  HCH2  0   0.264  -1.1197   1.4255   1.9992
 BYS  HC52  H  HCH2  0   0.277  -1.8223  -0.1478   1.6910
 BYS  HC71  H  HCR6  0   0.249  -0.7414   2.1436   4.2552
 BYS  HC81  H  HCR6  0   0.254  -0.9106   1.7158   6.6738
 BYS  HC91  H  HCR6  0   0.254  -1.4004  -0.5647   7.5023
 BYS  H101  H  HCR6  0   0.254  -1.7298  -2.4113   5.8840
 BYS  H111  H  HCR6  0   0.247  -1.5604  -1.9810   3.4667
 BYS  H121  H  HCH1  0   0.284   0.0056   1.1153  -0.1108
 BYS  HXT2  H  HOH1  0   0.480   2.9948   0.7378  -1.6480
 BYS  H161  H  HCH2  0   0.262  -0.1866  -1.9242  -0.3376
 BYS  H162  H  HCH2  0   0.275  -1.5312  -0.8014  -0.3016
 BYS  H181  H  HCR6  0   0.266  -1.6230   1.0320  -2.1833
 BYS  H211  H  HCH2  0   0.231  -0.1037   1.8503  -6.4030
 BYS  H212  H  HCH2  0   0.246  -1.6509   1.1575  -6.9953
 BYS  H241  H  HCR6  0   0.272   0.9133  -2.3382  -4.8664
 BYS  H251  H  HCR6  0   0.253   0.7411  -2.5519  -2.4004

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
 BYS  C1   C2    single    1.511  0.020  1.511
 BYS  C1   C5    single    1.543  0.020  1.543
 BYS  C1   C12   single    1.537  0.020  1.537
 BYS  C1   HC11  single    0.970  0.020  1.090
 BYS  C2   O3    double    1.208  0.020  1.208
 BYS  C2   O4    single    1.322  0.020  1.322
 BYS  O4   HXT1  single    0.850  0.020  0.980
 BYS  C5   C6    single    1.504  0.020  1.504
 BYS  C5   HC51  single    0.970  0.020  1.090
 BYS  C5   HC52  single    0.970  0.020  1.090
 BYS  C6   C7    aromatic  1.391  0.020  1.391
 BYS  C6   C11   aromatic  1.393  0.020  1.393
 BYS  C7   C8    aromatic  1.389  0.020  1.389
 BYS  C7   HC71  single    0.930  0.020  1.080
 BYS  C8   C9    aromatic  1.388  0.020  1.388
 BYS  C8   HC81  single    0.930  0.020  1.080
 BYS  C9   C10   aromatic  1.390  0.020  1.390
 BYS  C9   HC91  single    0.930  0.020  1.080
 BYS  C10  C11   aromatic  1.387  0.020  1.387
 BYS  C10  H101  single    0.930  0.020  1.080
 BYS  C11  H111  single    0.930  0.020  1.080
 BYS  C12  C13   single    1.511  0.020  1.511
 BYS  C12  C16   single    1.543  0.020  1.543
 BYS  C12  H121  single    0.970  0.020  1.090
 BYS  C13  O14   double    1.208  0.020  1.208
 BYS  C13  O15   single    1.322  0.020  1.322
 BYS  O15  HXT2  single    0.850  0.020  0.980
 BYS  C16  C17   single    1.504  0.020  1.504
 BYS  C16  H161  single    0.970  0.020  1.090
 BYS  C16  H162  single    0.970  0.020  1.090
 BYS  C17  C18   aromatic  1.405  0.020  1.405
 BYS  C17  C25   aromatic  1.387  0.020  1.387
 BYS  C18  C19   aromatic  1.370  0.020  1.370
 BYS  C18  H181  single    0.930  0.020  1.080
 BYS  C19  O20   single    1.356  0.020  1.356
 BYS  C19  C23   aromatic  1.387  0.020  1.387
 BYS  O20  C21   single    1.421  0.020  1.421
 BYS  C21  O22   single    1.420  0.020  1.420
 BYS  C21  H211  single    0.970  0.020  1.090
 BYS  C21  H212  single    0.970  0.020  1.090
 BYS  O22  C23   single    1.357  0.020  1.357
 BYS  C23  C24   aromatic  1.371  0.020  1.371
 BYS  C24  C25   aromatic  1.402  0.020  1.402
 BYS  C24  H241  single    0.930  0.020  1.080
 BYS  C25  H251  single    0.930  0.020  1.080

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
 BYS  HC11  C1   C12   109.46  3.000
 BYS  HC11  C1   C5    108.92  3.000
 BYS  C12   C1   C5    110.61  3.000
 BYS  HC11  C1   C2    109.07  3.000
 BYS  C12   C1   C2    110.42  3.000
 BYS  C5    C1   C2    108.33  3.000
 BYS  O4    C2   O3    123.57  3.000
 BYS  O4    C2   C1    113.12  3.000
 BYS  O3    C2   C1    123.30  3.000
 BYS  HXT1  O4   C2    110.11  3.000
 BYS  HC52  C5   HC51  106.55  3.000
 BYS  HC52  C5   C6    109.31  3.000
 BYS  HC51  C5   C6    110.18  3.000
 BYS  HC52  C5   C1    108.34  3.000
 BYS  HC51  C5   C1    108.96  3.000
 BYS  C6    C5   C1    113.27  3.000
 BYS  C11   C6   C7    118.63  3.000
 BYS  C11   C6   C5    120.35  3.000
 BYS  C7    C6   C5    121.00  3.000
 BYS  HC71  C7   C8    119.56  3.000
 BYS  HC71  C7   C6    119.66  3.000
 BYS  C8    C7   C6    120.78  3.000
 BYS  HC81  C8   C9    120.08  3.000
 BYS  HC81  C8   C7    119.80  3.000
 BYS  C9    C8   C7    120.12  3.000
 BYS  HC91  C9   C10   120.20  3.000
 BYS  HC91  C9   C8    120.23  3.000
 BYS  C10   C9   C8    119.57  3.000
 BYS  H101  C10  C11   119.81  3.000
 BYS  H101  C10  C9    120.10  3.000
 BYS  C11   C10  C9    120.09  3.000
 BYS  H111  C11  C10   119.61  3.000
 BYS  H111  C11  C6    119.57  3.000
 BYS  C10   C11  C6    120.81  3.000
 BYS  H121  C12  C16   109.00  3.000
 BYS  H121  C12  C13   109.09  3.000
 BYS  C16   C12  C13   108.16  3.000
 BYS  H121  C12  C1    109.51  3.000
 BYS  C16   C12  C1    110.59  3.000
 BYS  C13   C12  C1    110.45  3.000
 BYS  O15   C13  O14   123.59  3.000
 BYS  O15   C13  C12   113.08  3.000
 BYS  O14   C13  C12   123.32  3.000
 BYS  HXT2  O15  C13   110.02  3.000
 BYS  H162  C16  H161  106.68  3.000
 BYS  H162  C16  C17   109.49  3.000
 BYS  H161  C16  C17   109.89  3.000
 BYS  H162  C16  C12   108.39  3.000
 BYS  H161  C16  C12   108.72  3.000
 BYS  C17   C16  C12   113.43  3.000
 BYS  C25   C17  C18   119.97  3.000
 BYS  C25   C17  C16   120.53  3.000
 BYS  C18   C17  C16   119.49  3.000
 BYS  H181  C18  C19   121.37  3.000
 BYS  H181  C18  C17   121.20  3.000
 BYS  C19   C18  C17   117.43  3.000
 BYS  C23   C19  O20   109.23  3.000
 BYS  C23   C19  C18   122.12  3.000
 BYS  O20   C19  C18   128.64  3.000
 BYS  C21   O20  C19   105.88  3.000
 BYS  H212  C21  H211  110.53  3.000
 BYS  H212  C21  O22   109.86  3.000
 BYS  H211  C21  O22   109.87  3.000
 BYS  H212  C21  O20   109.81  3.000
 BYS  H211  C21  O20   109.82  3.000
 BYS  O22   C21  O20   106.88  3.000
 BYS  C23   O22  C21   105.82  3.000
 BYS  C24   C23  O22   129.09  3.000
 BYS  C24   C23  C19   121.61  3.000
 BYS  O22   C23  C19   109.29  3.000
 BYS  H241  C24  C25   121.25  3.000
 BYS  H241  C24  C23   121.98  3.000
 BYS  C25   C24  C23   116.77  3.000
 BYS  H251  C25  C24   118.60  3.000
 BYS  H251  C25  C17   119.30  3.000
 BYS  C24   C25  C17   122.10  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
 BYS  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 BYS  CONST_02  C9    C10  C11  C6      0.00   0.0  0
 BYS  CONST_03  C10   C11  C6   C7      0.00   0.0  0
 BYS  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 BYS  CONST_05  C11   C6   C7   C8      0.00   0.0  0
 BYS  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 BYS  CONST_07  C23   C19  C18  C17     0.00   0.0  0
 BYS  CONST_08  C23   C24  C25  C17     0.00   0.0  0
 BYS  CONST_09  C24   C25  C17  C18     0.00   0.0  0
 BYS  CONST_10  C24   C23  C19  C18     0.00   0.0  0
 BYS  CONST_11  C25   C17  C18  C19     0.00   0.0  0
 BYS  CONST_12  C25   C24  C23  C19     0.00   0.0  0
 BYS  CONST_13  C8    C7   C6   C5    180.00   0.0  0
 BYS  CONST_14  C10   C11  C6   C5    180.00   0.0  0
 BYS  CONST_15  C19   C18  C17  C16   180.00   0.0  0
 BYS  CONST_16  C24   C25  C17  C16   180.00   0.0  0
 BYS  CONST_17  HC81  C8   C7   C6    180.00   0.0  0
 BYS  CONST_18  H101  C10  C11  C6    180.00   0.0  0
 BYS  CONST_19  H111  C11  C6   C7    180.00   0.0  0
 BYS  CONST_20  HC91  C9   C8   C7    180.00   0.0  0
 BYS  CONST_21  HC71  C7   C8   C9    180.00   0.0  0
 BYS  CONST_22  H241  C24  C25  C17   180.00   0.0  0
 BYS  CONST_23  H251  C25  C17  C18   180.00   0.0  0
 BYS  CONST_24  H181  C18  C19  O20     0.00   0.0  0
 BYS  CONST_25  HXT1  O4   C2   C1    180.00   0.0  0
 BYS  CONST_26  HXT2  O15  C13  C12   180.00   0.0  0
 BYS  Var_01    O22   C21  O20  C19    16.57  30.0  1
 BYS  Var_02    C23   C19  O20  C21   -10.34  30.0  1
 BYS  Var_03    C24   C23  O22  C21  -171.19  30.0  1
 BYS  Var_04    C7    C6   C5   C1    102.68  30.0  2
 BYS  Var_05    C18   C17  C16  C12   -72.10  30.0  2

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
 BYS  chir_01  C1   C2  C5   C12  negativ
 BYS  chir_02  C12  C1  C13  C16  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
 BYS  plan-1  C5    0.020
 BYS  plan-1  C6    0.020
 BYS  plan-1  C7    0.020
 BYS  plan-1  C8    0.020
 BYS  plan-1  C9    0.020
 BYS  plan-1  C10   0.020
 BYS  plan-1  C11   0.020
 BYS  plan-1  HC71  0.020
 BYS  plan-1  HC81  0.020
 BYS  plan-1  HC91  0.020
 BYS  plan-1  H101  0.020
 BYS  plan-1  H111  0.020
 BYS  plan-2  C16   0.020
 BYS  plan-2  C17   0.020
 BYS  plan-2  C18   0.020
 BYS  plan-2  C19   0.020
 BYS  plan-2  O20   0.020
 BYS  plan-2  O22   0.020
 BYS  plan-2  C23   0.020
 BYS  plan-2  C24   0.020
 BYS  plan-2  C25   0.020
 BYS  plan-2  H181  0.020
 BYS  plan-2  H241  0.020
 BYS  plan-2  H251  0.020
 BYS  plan-3  C1    0.020
 BYS  plan-3  C2    0.020
 BYS  plan-3  O3    0.020
 BYS  plan-3  O4    0.020
 BYS  plan-3  HXT1  0.020
 BYS  plan-4  C12   0.020
 BYS  plan-4  C13   0.020
 BYS  plan-4  O14   0.020
 BYS  plan-4  O15   0.020
 BYS  plan-4  HXT2  0.020

