# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:34:03 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: methyl (2~{S})-2-(4-methoxypyridin-2-yl)propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](C)c1cc(OC)ccn1
#
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
 SQV  SQV  'methyl (2~{S})-2-(4-methoxypyridin-2-yl)propanoate'  ligand  27  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SQV
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
 SQV  C4   C  CR6   0   0.319  33.9324  87.5318   1.6595
 SQV  C5   C  CR16  0  -0.438  33.9437  88.4051   2.7302
 SQV  C6   C  CR6   0   0.475  33.0137  88.2358   3.7587
 SQV  C7   C  CH3   0  -0.441  32.1257  88.9742   5.8242
 SQV  C8   C  CR16  0  -0.444  32.1079  87.1839   3.6563
 SQV  N    N  N     0  -0.432  33.0645  86.5254   1.5553
 SQV  C    C  CH3   0  -0.648  34.2465  87.6602  -0.8383
 SQV  O    O  O2    0  -0.451  36.8527  86.6852  -0.3577
 SQV  C1   C  CH1   0  -0.489  34.9230  87.6942   0.5348
 SQV  C2   C  C     0   0.633  36.0160  86.6505   0.6681
 SQV  C3   C  CH3   0  -0.424  37.9447  85.7652  -0.3532
 SQV  C9   C  CR16  0  -0.084  32.1878  86.3719   2.5342
 SQV  O1   O  O     0  -0.442  36.1366  85.8949   1.5987
 SQV  O2   O  O2    0  -0.458  33.0638  89.1056   4.7688
 SQV  H1   H  HCR6  0   0.274  34.6621  89.2139   2.7782
 SQV  H2   H  HCH3  0   0.265  32.3409  89.7739   6.5275
 SQV  H3   H  HCH3  0   0.236  31.0994  89.0820   5.4666
 SQV  H4   H  HCH3  0   0.236  32.2263  88.0151   6.3370
 SQV  H5   H  HCR6  0   0.288  31.3539  86.9822   4.4038
 SQV  H6   H  HCH3  0   0.242  33.4520  88.4047  -0.8753
 SQV  H7   H  HCH3  0   0.245  34.9536  87.8907  -1.6324
 SQV  H8   H  HCH3  0   0.237  33.8031  86.6862  -1.0383
 SQV  H9   H  HCH1  0   0.304  35.4170  88.6665   0.6449
 SQV  H10  H  HCH3  0   0.252  38.4993  85.9561  -1.2671
 SQV  H11  H  HCH3  0   0.240  38.5970  85.9241   0.5051
 SQV  H12  H  HCH3  0   0.240  37.5941  84.7335  -0.3526
 SQV  H13  H  HCR6  0   0.263  31.4892  85.5483   2.4332

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
 SQV  C   C1   single    1.531  0.020  1.531
 SQV  C3  O    single    1.428  0.020  1.428
 SQV  O   C2   single    1.324  0.020  1.324
 SQV  C2  C1   single    1.517  0.020  1.517
 SQV  C2  O1   double    1.205  0.020  1.205
 SQV  C1  C4   single    1.508  0.020  1.508
 SQV  C4  N    aromatic  1.333  0.020  1.333
 SQV  C4  C5   aromatic  1.382  0.020  1.382
 SQV  N   C9   aromatic  1.323  0.020  1.323
 SQV  C5  C6   aromatic  1.397  0.020  1.397
 SQV  C9  C8   aromatic  1.387  0.020  1.387
 SQV  C6  C8   aromatic  1.392  0.020  1.392
 SQV  C6  O2   single    1.334  0.020  1.334
 SQV  O2  C7   single    1.418  0.020  1.418
 SQV  C5  H1   single    0.930  0.020  1.080
 SQV  C7  H2   single    0.970  0.020  1.090
 SQV  C7  H3   single    0.970  0.020  1.090
 SQV  C7  H4   single    0.970  0.020  1.090
 SQV  C8  H5   single    0.930  0.020  1.080
 SQV  C   H6   single    0.970  0.020  1.090
 SQV  C   H7   single    0.970  0.020  1.090
 SQV  C   H8   single    0.970  0.020  1.090
 SQV  C1  H9   single    0.970  0.020  1.090
 SQV  C3  H10  single    0.970  0.020  1.090
 SQV  C3  H11  single    0.970  0.020  1.090
 SQV  C3  H12  single    0.970  0.020  1.090
 SQV  C9  H13  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
 SQV  C1   C4  N    116.79  3.000
 SQV  N    C4  C5   122.89  3.000
 SQV  C1   C4  C5   120.31  3.000
 SQV  H1   C5  C6   119.97  3.000
 SQV  H1   C5  C4   120.79  3.000
 SQV  C6   C5  C4   119.24  3.000
 SQV  O2   C6  C8   124.96  3.000
 SQV  O2   C6  C5   116.96  3.000
 SQV  C8   C6  C5   118.08  3.000
 SQV  H4   C7  H3   109.09  3.000
 SQV  H4   C7  H2   108.92  3.000
 SQV  H3   C7  H2   108.99  3.000
 SQV  H4   C7  O2   111.71  3.000
 SQV  H3   C7  O2   111.64  3.000
 SQV  H2   C7  O2   106.40  3.000
 SQV  H5   C8  C9   119.37  3.000
 SQV  H5   C8  C6   122.97  3.000
 SQV  C9   C8  C6   117.66  3.000
 SQV  C9   N   C4   117.46  3.000
 SQV  H8   C   H7   108.67  3.000
 SQV  H8   C   H6   107.95  3.000
 SQV  H7   C   H6   107.72  3.000
 SQV  H8   C   C1   111.38  3.000
 SQV  H7   C   C1   111.26  3.000
 SQV  H6   C   C1   109.73  3.000
 SQV  C3   O   C2   117.63  3.000
 SQV  H9   C1  C2   106.06  3.000
 SQV  H9   C1  C    107.99  3.000
 SQV  C2   C1  C    112.45  3.000
 SQV  H9   C1  C4   108.46  3.000
 SQV  C2   C1  C4   109.50  3.000
 SQV  C    C1  C4   112.11  3.000
 SQV  O1   C2  C1   124.85  3.000
 SQV  O1   C2  O    123.48  3.000
 SQV  C1   C2  O    111.66  3.000
 SQV  H12  C3  H11  109.29  3.000
 SQV  H12  C3  H10  109.34  3.000
 SQV  H11  C3  H10  109.36  3.000
 SQV  H12  C3  O    111.35  3.000
 SQV  H11  C3  O    111.49  3.000
 SQV  H10  C3  O    105.94  3.000
 SQV  H13  C9  N    116.48  3.000
 SQV  H13  C9  C8   118.86  3.000
 SQV  N    C9  C8   124.66  3.000
 SQV  C7   O2  C6   118.57  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
 SQV  CONST_01  C8   C9  N   C4     0.00   0.0  0
 SQV  CONST_02  C8   C6  C5  C4     0.00   0.0  0
 SQV  CONST_03  C9   N   C4  C5     0.00   0.0  0
 SQV  CONST_04  C9   C8  C6  C5     0.00   0.0  0
 SQV  CONST_05  N    C4  C5  C6     0.00   0.0  0
 SQV  CONST_06  N    C9  C8  C6     0.00   0.0  0
 SQV  CONST_07  O2   C6  C5  C4   180.00   0.0  0
 SQV  CONST_08  C1   C4  C5  C6   180.00   0.0  0
 SQV  CONST_09  C9   N   C4  C1   180.00   0.0  0
 SQV  CONST_10  O2   C6  C8  C9   180.00   0.0  0
 SQV  CONST_11  H13  C9  N   C4   180.00   0.0  0
 SQV  CONST_12  H5   C8  C6  C5   180.00   0.0  0
 SQV  CONST_13  H1   C5  C6  C8   180.00   0.0  0
 SQV  Var_01    C8   C6  O2  C7    -0.54  30.0  1
 SQV  Var_02    H2   C7  O2  C6  -179.84  30.0  3
 SQV  Var_03    O1   C2  O   C3     0.55  30.0  3
 SQV  Var_04    H10  C3  O   C2   179.99  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
 SQV  chir_01  C1  C  C2  C4  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
 SQV  plan-1  C4   0.020
 SQV  plan-1  C5   0.020
 SQV  plan-1  C6   0.020
 SQV  plan-1  C8   0.020
 SQV  plan-1  N    0.020
 SQV  plan-1  C1   0.020
 SQV  plan-1  C9   0.020
 SQV  plan-1  O2   0.020
 SQV  plan-1  H1   0.020
 SQV  plan-1  H5   0.020
 SQV  plan-1  H13  0.020
 SQV  plan-2  O    0.020
 SQV  plan-2  C1   0.020
 SQV  plan-2  C2   0.020
 SQV  plan-2  O1   0.020

