# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:08:10 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: methyl (2~{R})-3-(4-bromophenyl)-2-pyridin-4-yl-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1ccc(Br)cc1)c2ccncc2
#
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
 SQY  SQY  'methyl (2~{R})-3-(4-bromophenyl)-2-pyridin-4-yl-propanoate'  ligand  33  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SQY
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
 SQY  C4   C   CR6   0   0.138  49.7211  117.8497  32.8276
 SQY  C5   C   CR16  0  -0.288  50.1432  119.0109  33.4661
 SQY  C6   C   CR16  0  -0.211  51.3615  119.6010  33.1602
 SQY  C7   C   CR6   0  -0.126  52.1687  119.0162  32.1969
 SQY  C8   C   CR16  0  -0.213  51.7766  117.8570  31.5438
 SQY  C10  C   CR6   0   0.237  47.1598  119.1595  32.0603
 SQY  C13  C   CR16  0  -0.057  47.4654  121.3034  31.0458
 SQY  N    N   N     0  -0.409  46.9288  121.9469  32.0750
 SQY  C    C   C     0   0.622  46.0063  116.9742  32.3075
 SQY  O    O   O     0  -0.435  45.7640  116.2171  33.2121
 SQY  C1   C   CH3   0  -0.427  43.8205  116.7574  31.4583
 SQY  C11  C   CR16  0  -0.360  46.5966  119.8309  33.1402
 SQY  C12  C   CR16  0  -0.058  46.5042  121.2125  33.0978
 SQY  C14  C   CR16  0  -0.372  47.6020  119.9241  30.9910
 SQY  C2   C   CH1   0  -0.462  47.3393  117.6620  32.0801
 SQY  C3   C   CH2   0  -0.506  48.3815  117.2378  33.1250
 SQY  C9   C   CR16  0  -0.303  50.5546  117.2853  31.8658
 SQY  BR   BR  BR    0  -0.054  53.8311  119.8078  31.7688
 SQY  H1   H   HCR6  0   0.258  49.5155  119.4697  34.2197
 SQY  H2   H   HCR6  0   0.277  51.6649  120.5050  33.6709
 SQY  H3   H   HCR6  0   0.278  52.4073  117.3950  30.7961
 SQY  H4   H   HCR6  0   0.265  47.8081  121.9130  30.2168
 SQY  H5   H   HCH3  0   0.254  43.2665  117.1734  30.6223
 SQY  H6   H   HCH3  0   0.242  43.8463  115.6716  31.3707
 SQY  H7   H   HCH3  0   0.242  43.3299  117.0334  32.3913
 SQY  H8   H   HCR6  0   0.272  46.2343  119.3003  34.0124
 SQY  H9   H   HCR6  0   0.266  46.0675  121.7491  33.9328
 SQY  H10  H   HCR6  0   0.269  48.0524  119.4581  30.1244
 SQY  H11  H   HCH1  0   0.311  47.6921  117.3510  31.0905
 SQY  H12  H   HCH2  0   0.263  48.0465  117.5277  34.1230
 SQY  H13  H   HCH2  0   0.273  48.4639  116.1497  33.1199
 SQY  H14  H   HCR6  0   0.261  50.2530  116.3775  31.3565
 SQY  O1   O   O2    0  -0.446  45.1331  117.3171  31.3758

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
 SQY  O1   C1   single    1.429  0.020  1.429
 SQY  O1   C    single    1.322  0.020  1.322
 SQY  BR   C7   single    1.890  0.020  1.890
 SQY  C14  C13  aromatic  1.387  0.020  1.387
 SQY  C14  C10  aromatic  1.387  0.020  1.387
 SQY  C13  N    aromatic  1.327  0.020  1.327
 SQY  C8   C9   aromatic  1.387  0.020  1.387
 SQY  C8   C7   aromatic  1.387  0.020  1.387
 SQY  C9   C4   aromatic  1.392  0.020  1.392
 SQY  C7   C6   aromatic  1.386  0.020  1.386
 SQY  C2   C10  single    1.508  0.020  1.508
 SQY  C2   C    single    1.517  0.020  1.517
 SQY  C2   C3   single    1.536  0.020  1.536
 SQY  N    C12  aromatic  1.329  0.020  1.329
 SQY  C10  C11  aromatic  1.391  0.020  1.391
 SQY  C    O    double    1.204  0.020  1.204
 SQY  C4   C3   single    1.502  0.020  1.502
 SQY  C4   C5   aromatic  1.391  0.020  1.391
 SQY  C12  C11  aromatic  1.385  0.020  1.385
 SQY  C6   C5   aromatic  1.388  0.020  1.388
 SQY  C5   H1   single    0.930  0.020  1.080
 SQY  C6   H2   single    0.930  0.020  1.080
 SQY  C8   H3   single    0.930  0.020  1.080
 SQY  C13  H4   single    0.930  0.020  1.080
 SQY  C1   H5   single    0.970  0.020  1.090
 SQY  C1   H6   single    0.970  0.020  1.090
 SQY  C1   H7   single    0.970  0.020  1.090
 SQY  C11  H8   single    0.930  0.020  1.080
 SQY  C12  H9   single    0.930  0.020  1.080
 SQY  C14  H10  single    0.930  0.020  1.080
 SQY  C2   H11  single    0.970  0.020  1.090
 SQY  C3   H12  single    0.970  0.020  1.090
 SQY  C3   H13  single    0.970  0.020  1.090
 SQY  C9   H14  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
 SQY  C9   C4   C3   120.36  3.000
 SQY  C3   C4   C5   121.31  3.000
 SQY  C9   C4   C5   118.29  3.000
 SQY  H1   C5   C6   118.83  3.000
 SQY  H1   C5   C4   119.82  3.000
 SQY  C6   C5   C4   121.35  3.000
 SQY  H2   C6   C7   121.15  3.000
 SQY  H2   C6   C5   119.83  3.000
 SQY  C7   C6   C5   119.01  3.000
 SQY  BR   C7   C8   119.47  3.000
 SQY  C8   C7   C6   121.01  3.000
 SQY  BR   C7   C6   119.53  3.000
 SQY  H3   C8   C9   119.87  3.000
 SQY  H3   C8   C7   121.16  3.000
 SQY  C9   C8   C7   118.96  3.000
 SQY  C2   C10  C14  121.30  3.000
 SQY  C2   C10  C11  121.15  3.000
 SQY  C14  C10  C11  117.49  3.000
 SQY  H4   C13  C14  119.84  3.000
 SQY  H4   C13  N    116.61  3.000
 SQY  C14  C13  N    123.54  3.000
 SQY  C12  N    C13  117.27  3.000
 SQY  O1   C    C2   110.92  3.000
 SQY  C2   C    O    125.06  3.000
 SQY  O1   C    O    124.02  3.000
 SQY  H7   C1   H6   109.38  3.000
 SQY  H7   C1   H5   109.43  3.000
 SQY  H6   C1   H5   109.38  3.000
 SQY  H7   C1   O1   111.33  3.000
 SQY  H6   C1   O1   111.34  3.000
 SQY  H5   C1   O1   105.91  3.000
 SQY  H8   C11  C12  119.39  3.000
 SQY  H8   C11  C10  121.61  3.000
 SQY  C12  C11  C10  119.00  3.000
 SQY  H9   C12  C11  119.79  3.000
 SQY  H9   C12  N    116.61  3.000
 SQY  C11  C12  N    123.60  3.000
 SQY  H10  C14  C13  120.05  3.000
 SQY  H10  C14  C10  120.85  3.000
 SQY  C13  C14  C10  119.10  3.000
 SQY  H11  C2   C3   108.52  3.000
 SQY  H11  C2   C    106.83  3.000
 SQY  C3   C2   C    111.66  3.000
 SQY  H11  C2   C10  107.96  3.000
 SQY  C3   C2   C10  111.35  3.000
 SQY  C    C2   C10  110.33  3.000
 SQY  H13  C3   H12  106.99  3.000
 SQY  H13  C3   C2   108.87  3.000
 SQY  H12  C3   C2   109.90  3.000
 SQY  H13  C3   C4   109.75  3.000
 SQY  H12  C3   C4   110.27  3.000
 SQY  C2   C3   C4   110.97  3.000
 SQY  H14  C9   C8   118.78  3.000
 SQY  H14  C9   C4   119.84  3.000
 SQY  C8   C9   C4   121.38  3.000
 SQY  C1   O1   C    117.66  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
 SQY  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 SQY  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 SQY  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 SQY  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 SQY  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 SQY  CONST_06  C9   C4   C5   C6      0.00   0.0  0
 SQY  CONST_07  N    C13  C14  C10     0.00   0.0  0
 SQY  CONST_08  N    C12  C11  C10     0.00   0.0  0
 SQY  CONST_09  C11  C10  C14  C13     0.00   0.0  0
 SQY  CONST_10  C11  C12  N    C13     0.00   0.0  0
 SQY  CONST_11  C14  C13  N    C12     0.00   0.0  0
 SQY  CONST_12  C14  C10  C11  C12     0.00   0.0  0
 SQY  CONST_13  BR   C7   C6   C5    180.00   0.0  0
 SQY  CONST_14  C3   C4   C5   C6    180.00   0.0  0
 SQY  CONST_15  C3   C4   C9   C8    180.00   0.0  0
 SQY  CONST_16  C2   C10  C14  C13   180.00   0.0  0
 SQY  CONST_17  C2   C10  C11  C12   180.00   0.0  0
 SQY  CONST_18  BR   C7   C8   C9    180.00   0.0  0
 SQY  CONST_19  H3   C8   C9   C4    180.00   0.0  0
 SQY  CONST_20  H2   C6   C5   C4    180.00   0.0  0
 SQY  CONST_21  H14  C9   C4   C5    180.00   0.0  0
 SQY  CONST_22  H1   C5   C6   C7    180.00   0.0  0
 SQY  CONST_23  H4   C13  C14  C10   180.00   0.0  0
 SQY  CONST_24  H9   C12  C11  C10   180.00   0.0  0
 SQY  CONST_25  H10  C14  C13  N     180.00   0.0  0
 SQY  CONST_26  H8   C11  C12  N     180.00   0.0  0
 SQY  Var_01    C2   C3   C4   C5     97.32  30.0  2
 SQY  Var_02    C2   C    O1   C1   -179.52  30.0  3
 SQY  Var_03    H5   C1   O1   C     179.12  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
 SQY  chir_01  C2  C10  C  C3  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
 SQY  plan-1  C4   0.020
 SQY  plan-1  C5   0.020
 SQY  plan-1  C6   0.020
 SQY  plan-1  C7   0.020
 SQY  plan-1  C8   0.020
 SQY  plan-1  C3   0.020
 SQY  plan-1  C9   0.020
 SQY  plan-1  BR   0.020
 SQY  plan-1  H1   0.020
 SQY  plan-1  H2   0.020
 SQY  plan-1  H3   0.020
 SQY  plan-1  H14  0.020
 SQY  plan-2  C10  0.020
 SQY  plan-2  C13  0.020
 SQY  plan-2  N    0.020
 SQY  plan-2  C11  0.020
 SQY  plan-2  C12  0.020
 SQY  plan-2  C14  0.020
 SQY  plan-2  C2   0.020
 SQY  plan-2  H4   0.020
 SQY  plan-2  H8   0.020
 SQY  plan-2  H9   0.020
 SQY  plan-2  H10  0.020
 SQY  plan-3  C    0.020
 SQY  plan-3  O    0.020
 SQY  plan-3  C2   0.020
 SQY  plan-3  O1   0.020

