# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 19:18:04 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(methylsulfonyl)-N-phenyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N(c1ccccc1)[S](C)(=O)=O)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
 NZ3  NZ3  N-(methylsulfonyl)-N-phenyl-D-alanine  ligand  29  16  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NZ3
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
 NZ3  C01  C  CH3   0  -0.685   0.1390  -2.0605  -1.6182
 NZ3  C02  C  CH1   0  -0.206   1.0341  -1.1600  -0.7697
 NZ3  C03  C  C     0   0.565   1.5104  -1.9015   0.4719
 NZ3  O04  O  OH1   0  -0.590   2.3724  -2.8540   0.1489
 NZ3  O05  O  O     0  -0.429   1.1485  -1.6757   1.5964
 NZ3  N06  N  N     0  -0.701   0.3581   0.0821  -0.4163
 NZ3  C07  C  CR6   0   0.283  -1.0608   0.1808  -0.3211
 NZ3  C08  C  CR16  0  -0.252  -1.7774   0.6702  -1.4073
 NZ3  C09  C  CR16  0  -0.260  -3.1611   0.7636  -1.3451
 NZ3  C10  C  CR16  0  -0.244  -3.8312   0.3661  -0.1967
 NZ3  C11  C  CR16  0  -0.259  -3.1145  -0.1228   0.8887
 NZ3  C12  C  CR16  0  -0.239  -1.7317  -0.2138   0.8315
 NZ3  S13  S  S     0   1.331   1.2585   1.3298   0.1983
 NZ3  C14  C  CH3   0  -0.781   1.2434   2.5569  -1.0853
 NZ3  O15  O  OS    0  -0.650   0.5802   1.8958   1.3524
 NZ3  O16  O  OS    0  -0.661   2.6213   0.8329   0.3381
 NZ3  H1   H  HCH3  0   0.269   0.6935  -2.9468  -1.9192
 NZ3  H2   H  HCH3  0   0.250  -0.7532  -2.3795  -1.0819
 NZ3  H3   H  HCH3  0   0.263  -0.1675  -1.5364  -2.5215
 NZ3  H4   H  HCH1  0   0.303   1.9127  -0.9227  -1.3737
 NZ3  H5   H  HOH1  0   0.486   2.6431  -3.3443   0.9396
 NZ3  H6   H  HCR6  0   0.268  -1.2517   0.9706  -2.3048
 NZ3  H7   H  HCR6  0   0.263  -3.7116   1.1435  -2.1956
 NZ3  H8   H  HCR6  0   0.263  -4.9100   0.4351  -0.1469
 NZ3  H9   H  HCR6  0   0.263  -3.6341  -0.4346   1.7852
 NZ3  H10  H  HCR6  0   0.267  -1.1740  -0.5972   1.6733
 NZ3  H11  H  HCH3  0   0.289   0.2202   2.8750  -1.2710
 NZ3  H12  H  HCH3  0   0.305   1.8346   3.4052  -0.7438
 NZ3  H13  H  HCH3  0   0.292   1.6786   2.1358  -1.9881

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
 NZ3  C01  C02  single    1.527  0.020  1.527
 NZ3  C02  N06  single    1.458  0.020  1.458
 NZ3  C02  C03  single    1.523  0.020  1.523
 NZ3  O05  C03  double    1.203  0.020  1.203
 NZ3  O15  S13  double    1.453  0.020  1.453
 NZ3  O16  S13  double    1.457  0.020  1.457
 NZ3  C12  C11  aromatic  1.387  0.020  1.387
 NZ3  C12  C07  aromatic  1.391  0.020  1.391
 NZ3  N06  S13  single    1.657  0.020  1.657
 NZ3  N06  C07  single    1.425  0.020  1.425
 NZ3  C03  O04  single    1.325  0.020  1.325
 NZ3  S13  C14  single    1.776  0.020  1.776
 NZ3  C11  C10  aromatic  1.390  0.020  1.390
 NZ3  C07  C08  aromatic  1.390  0.020  1.390
 NZ3  C10  C09  aromatic  1.388  0.020  1.388
 NZ3  C08  C09  aromatic  1.388  0.020  1.388
 NZ3  C01  H1   single    0.970  0.020  1.090
 NZ3  C01  H2   single    0.970  0.020  1.090
 NZ3  C01  H3   single    0.970  0.020  1.090
 NZ3  C02  H4   single    0.970  0.020  1.090
 NZ3  O04  H5   single    0.850  0.020  0.980
 NZ3  C08  H6   single    0.930  0.020  1.080
 NZ3  C09  H7   single    0.930  0.020  1.080
 NZ3  C10  H8   single    0.930  0.020  1.080
 NZ3  C11  H9   single    0.930  0.020  1.080
 NZ3  C12  H10  single    0.930  0.020  1.080
 NZ3  C14  H11  single    0.970  0.020  1.090
 NZ3  C14  H12  single    0.970  0.020  1.090
 NZ3  C14  H13  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
 NZ3  H3   C01  H2   108.61  3.000
 NZ3  H3   C01  H1   107.83  3.000
 NZ3  H2   C01  H1   108.37  3.000
 NZ3  H3   C01  C02  110.01  3.000
 NZ3  H2   C01  C02  112.30  3.000
 NZ3  H1   C01  C02  109.60  3.000
 NZ3  H4   C02  N06  108.78  3.000
 NZ3  H4   C02  C03  107.76  3.000
 NZ3  N06  C02  C03  111.25  3.000
 NZ3  H4   C02  C01  107.00  3.000
 NZ3  C03  C02  C01  110.44  3.000
 NZ3  N06  C02  C01  111.43  3.000
 NZ3  O05  C03  O04  123.97  3.000
 NZ3  O04  C03  C02  110.79  3.000
 NZ3  O05  C03  C02  125.23  3.000
 NZ3  H5   O04  C03  110.28  3.000
 NZ3  S13  N06  C07  117.65  3.000
 NZ3  C07  N06  C02  122.46  3.000
 NZ3  S13  N06  C02  118.66  3.000
 NZ3  C12  C07  C08  119.91  3.000
 NZ3  C08  C07  N06  119.03  3.000
 NZ3  C12  C07  N06  121.05  3.000
 NZ3  H6   C08  C09  120.16  3.000
 NZ3  H6   C08  C07  119.67  3.000
 NZ3  C09  C08  C07  120.17  3.000
 NZ3  H7   C09  C10  120.36  3.000
 NZ3  H7   C09  C08  119.71  3.000
 NZ3  C10  C09  C08  119.94  3.000
 NZ3  H8   C10  C11  120.05  3.000
 NZ3  H8   C10  C09  120.08  3.000
 NZ3  C11  C10  C09  119.88  3.000
 NZ3  H9   C11  C12  119.61  3.000
 NZ3  H9   C11  C10  120.05  3.000
 NZ3  C12  C11  C10  120.33  3.000
 NZ3  H10  C12  C11  120.39  3.000
 NZ3  H10  C12  C07  119.84  3.000
 NZ3  C11  C12  C07  119.77  3.000
 NZ3  O16  S13  O15  119.54  3.000
 NZ3  O16  S13  C14  108.24  3.000
 NZ3  O15  S13  C14  107.51  3.000
 NZ3  C14  S13  N06  104.33  3.000
 NZ3  O16  S13  N06  106.68  3.000
 NZ3  O15  S13  N06  109.52  3.000
 NZ3  H13  C14  H12  110.17  3.000
 NZ3  H13  C14  H11  110.38  3.000
 NZ3  H12  C14  H11  109.67  3.000
 NZ3  H13  C14  S13  109.22  3.000
 NZ3  H12  C14  S13  107.87  3.000
 NZ3  H11  C14  S13  109.48  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
 NZ3  CONST_01  C10  C11  C12  C07    0.00   0.0  0
 NZ3  CONST_02  C10  C09  C08  C07    0.00   0.0  0
 NZ3  CONST_03  C11  C12  C07  C08    0.00   0.0  0
 NZ3  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 NZ3  CONST_05  C12  C11  C10  C09    0.00   0.0  0
 NZ3  CONST_06  C12  C07  C08  C09    0.00   0.0  0
 NZ3  CONST_07  C11  C12  C07  N06  180.00   0.0  0
 NZ3  CONST_08  C09  C08  C07  N06  180.00   0.0  0
 NZ3  CONST_09  H9   C11  C12  C07  180.00   0.0  0
 NZ3  CONST_10  H7   C09  C08  C07  180.00   0.0  0
 NZ3  CONST_11  H10  C12  C07  C08  180.00   0.0  0
 NZ3  CONST_12  H8   C10  C09  C08  180.00   0.0  0
 NZ3  CONST_13  H6   C08  C09  C10  180.00   0.0  0
 NZ3  CONST_18  H5   O04  C03  C02  180.00   0.0  0
 NZ3  Var_01    O15  S13  N06  C07   33.08  30.0  3
 NZ3  Var_02    H11  C14  S13  N06   61.42  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
 NZ3  chir_01  C02  C01  N06  C03  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
 NZ3  plan-1  N06  0.020
 NZ3  plan-1  C07  0.020
 NZ3  plan-1  C08  0.020
 NZ3  plan-1  C09  0.020
 NZ3  plan-1  C10  0.020
 NZ3  plan-1  C11  0.020
 NZ3  plan-1  C12  0.020
 NZ3  plan-1  H6   0.020
 NZ3  plan-1  H7   0.020
 NZ3  plan-1  H8   0.020
 NZ3  plan-1  H9   0.020
 NZ3  plan-1  H10  0.020
 NZ3  plan-2  C02  0.020
 NZ3  plan-2  N06  0.020
 NZ3  plan-2  C07  0.020
 NZ3  plan-2  S13  0.020
 NZ3  plan-3  C02  0.020
 NZ3  plan-3  C03  0.020
 NZ3  plan-3  O04  0.020
 NZ3  plan-3  O05  0.020
 NZ3  plan-3  H5   0.020

