# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:11:13 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-[(2S)-2-(3-methoxyphenyl)pyrrolidin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)[C@@H]2CCCN2C(C)=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
 GZY  GZY  1-[(2S)-2-(3-methoxyphenyl)pyrrolidin-1-yl]ethan-1-one  ligand  33  16  .  2021-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GZY
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
 GZY  C4   C  CH2   0  -0.471   1.4344   2.1586   0.0293
 GZY  C5   C  CH1   0  -0.114   1.0195   0.7530   0.4899
 GZY  C6   C  CR6   0   0.193  -0.2916   0.3228  -0.1176
 GZY  C7   C  CR16  0  -0.326  -0.3765  -0.0434  -1.4612
 GZY  C8   C  CR16  0  -0.230  -1.6069  -0.3610  -2.0060
 GZY  C10  C  CR6   0   0.399  -2.6866   0.0534   0.0963
 GZY  O    O  O     0  -0.501   1.2726  -1.9428   0.9568
 GZY  C    C  CH3   0  -0.795   3.4205  -2.1376  -0.0852
 GZY  N    N  NT    0  -0.473   2.1555  -0.0715   0.0868
 GZY  C3   C  CH2   0  -0.472   2.9558   2.1181   0.0614
 GZY  C2   C  CH2   0  -0.272   3.2595   0.7171  -0.4503
 GZY  C12  C  CR16  0  -0.427  -1.4421   0.3673   0.6490
 GZY  O1   O  O2    0  -0.474  -3.7407   0.1335   0.9324
 GZY  C11  C  CH3   0  -0.436  -5.0248  -0.1758   0.4303
 GZY  C9   C  CR16  0  -0.400  -2.7703  -0.3170  -1.2422
 GZY  H1   H  HCH2  0   0.243   1.0886   2.3312  -0.9926
 GZY  H2   H  HCH2  0   0.261   0.9988   2.9320   0.6604
 GZY  H3   H  HCH1  0   0.259   0.9235   0.7335   1.5812
 GZY  H4   H  HCR6  0   0.243   0.5143  -0.0810  -2.0762
 GZY  H5   H  HCR6  0   0.255  -1.6760  -0.6481  -3.0476
 GZY  H6   H  HCH3  0   0.266   3.2513  -3.2074   0.0103
 GZY  H7   H  HCH3  0   0.259   3.6825  -1.9120  -1.1191
 GZY  H8   H  HCH3  0   0.267   4.2809  -1.8734   0.5330
 GZY  H9   H  HCH2  0   0.254   3.4197   2.8923  -0.5480
 GZY  H10  H  HCH2  0   0.241   3.3209   2.2306   1.0845
 GZY  H11  H  HCH2  0   0.259   4.2230   0.3481  -0.1018
 GZY  H12  H  HCH2  0   0.240   3.2647   0.6899  -1.5445
 GZY  H13  H  HCR6  0   0.251  -1.3834   0.6452   1.6956
 GZY  H14  H  HCH3  0   0.227  -5.3170   0.4894  -0.3866
 GZY  H15  H  HCH3  0   0.227  -5.0904  -1.2097   0.0809
 GZY  H16  H  HCH3  0   0.258  -5.7204  -0.0406   1.2548
 GZY  H17  H  HCR6  0   0.275  -3.7146  -0.5711  -1.7035
 GZY  C1   C  C     0   0.516   2.1912  -1.3881   0.3662

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
 GZY  O1   C10  single    1.348  0.020  1.348
 GZY  O1   C11  single    1.413  0.020  1.413
 GZY  C9   C10  aromatic  1.391  0.020  1.391
 GZY  C9   C8   aromatic  1.392  0.020  1.392
 GZY  C10  C12  aromatic  1.397  0.020  1.397
 GZY  C8   C7   aromatic  1.383  0.020  1.383
 GZY  C3   C4   single    1.522  0.020  1.522
 GZY  C3   C2   single    1.522  0.020  1.522
 GZY  C12  C6   aromatic  1.383  0.020  1.383
 GZY  C7   C6   aromatic  1.395  0.020  1.395
 GZY  C4   C5   single    1.536  0.020  1.536
 GZY  C6   C5   single    1.508  0.020  1.508
 GZY  C2   N    single    1.459  0.020  1.459
 GZY  C5   N    single    1.460  0.020  1.460
 GZY  N    C1   single    1.346  0.020  1.346
 GZY  C1   O    double    1.225  0.020  1.225
 GZY  C1   C    single    1.509  0.020  1.509
 GZY  C4   H1   single    0.970  0.020  1.090
 GZY  C4   H2   single    0.970  0.020  1.090
 GZY  C5   H3   single    0.970  0.020  1.090
 GZY  C7   H4   single    0.930  0.020  1.080
 GZY  C8   H5   single    0.930  0.020  1.080
 GZY  C    H6   single    0.970  0.020  1.090
 GZY  C    H7   single    0.970  0.020  1.090
 GZY  C    H8   single    0.970  0.020  1.090
 GZY  C3   H9   single    0.970  0.020  1.090
 GZY  C3   H10  single    0.970  0.020  1.090
 GZY  C2   H11  single    0.970  0.020  1.090
 GZY  C2   H12  single    0.970  0.020  1.090
 GZY  C12  H13  single    0.930  0.020  1.080
 GZY  C11  H14  single    0.970  0.020  1.090
 GZY  C11  H15  single    0.970  0.020  1.090
 GZY  C11  H16  single    0.970  0.020  1.090
 GZY  C9   H17  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
 GZY  H2   C4   H1   107.66  3.000
 GZY  H2   C4   C3   113.98  3.000
 GZY  H1   C4   C3   109.89  3.000
 GZY  H2   C4   C5   111.59  3.000
 GZY  H1   C4   C5   109.85  3.000
 GZY  C3   C4   C5   103.84  3.000
 GZY  H3   C5   N    109.45  3.000
 GZY  H3   C5   C6   108.67  3.000
 GZY  N    C5   C6   113.84  3.000
 GZY  H3   C5   C4   109.79  3.000
 GZY  N    C5   C4   102.92  3.000
 GZY  C6   C5   C4   112.03  3.000
 GZY  C12  C6   C7   119.45  3.000
 GZY  C7   C6   C5   121.05  3.000
 GZY  C12  C6   C5   119.39  3.000
 GZY  H4   C7   C8   120.01  3.000
 GZY  H4   C7   C6   120.39  3.000
 GZY  C8   C7   C6   119.59  3.000
 GZY  H5   C8   C9   118.87  3.000
 GZY  H5   C8   C7   119.79  3.000
 GZY  C9   C8   C7   121.34  3.000
 GZY  C9   C10  O1   124.43  3.000
 GZY  C9   C10  C12  119.60  3.000
 GZY  O1   C10  C12  115.97  3.000
 GZY  H8   C    H7   107.31  3.000
 GZY  H8   C    H6   108.12  3.000
 GZY  H7   C    H6   108.92  3.000
 GZY  H8   C    C1   110.63  3.000
 GZY  H7   C    C1   112.13  3.000
 GZY  H6   C    C1   109.61  3.000
 GZY  C2   N    C1   125.79  3.000
 GZY  C1   N    C5   121.02  3.000
 GZY  C2   N    C5   112.65  3.000
 GZY  H10  C3   H9   107.97  3.000
 GZY  H10  C3   C2   110.06  3.000
 GZY  H9   C3   C2   112.41  3.000
 GZY  H10  C3   C4   110.55  3.000
 GZY  H9   C3   C4   113.27  3.000
 GZY  C2   C3   C4   102.53  3.000
 GZY  H12  C2   H11  107.89  3.000
 GZY  H12  C2   C3   111.10  3.000
 GZY  H11  C2   C3   112.39  3.000
 GZY  H12  C2   N    110.98  3.000
 GZY  H11  C2   N    111.62  3.000
 GZY  C3   C2   N    102.87  3.000
 GZY  H13  C12  C10  119.18  3.000
 GZY  H13  C12  C6   119.87  3.000
 GZY  C10  C12  C6   120.95  3.000
 GZY  C11  O1   C10  118.51  3.000
 GZY  H16  C11  H15  108.76  3.000
 GZY  H16  C11  H14  108.66  3.000
 GZY  H15  C11  H14  108.70  3.000
 GZY  H16  C11  O1   106.54  3.000
 GZY  H15  C11  O1   112.03  3.000
 GZY  H14  C11  O1   112.04  3.000
 GZY  H17  C9   C10  121.71  3.000
 GZY  H17  C9   C8   119.22  3.000
 GZY  C10  C9   C8   119.07  3.000
 GZY  N    C1   C    116.44  3.000
 GZY  C    C1   O    122.02  3.000
 GZY  N    C1   O    121.54  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
 GZY  CONST_01  C9   C10  C12  C6      0.00   0.0  0
 GZY  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 GZY  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 GZY  CONST_04  C10  C12  C6   C7      0.00   0.0  0
 GZY  CONST_05  C12  C10  C9   C8      0.00   0.0  0
 GZY  CONST_06  C12  C6   C7   C8      0.00   0.0  0
 GZY  CONST_07  C10  C12  C6   C5    180.00   0.0  0
 GZY  CONST_08  C8   C7   C6   C5    180.00   0.0  0
 GZY  CONST_09  O1   C10  C12  C6    180.00   0.0  0
 GZY  CONST_10  O1   C10  C9   C8    180.00   0.0  0
 GZY  CONST_11  H13  C12  C6   C5      0.00   0.0  0
 GZY  CONST_12  H4   C7   C6   C5      0.00   0.0  0
 GZY  CONST_13  H5   C8   C7   C6    180.00   0.0  0
 GZY  CONST_14  H17  C9   C8   C7    180.00   0.0  0
 GZY  CONST_15  O    C1   N    C5      0.00   0.0  0
 GZY  CONST_16  C    C1   N    C5    180.00   0.0  0
 GZY  CONST_17  C2   N    C1   O     180.00   0.0  0
 GZY  CONST_18  C2   N    C1   C       0.00   0.0  0
 GZY  Var_01    N    C2   C3   C4    -34.71  30.0  1
 GZY  Var_02    C2   C3   C4   C5     38.74  30.0  1
 GZY  Var_03    C3   C2   N    C5     18.47  30.0  1
 GZY  Var_04    C9   C10  O1   C11    -0.04  30.0  2
 GZY  Var_05    H14  C11  O1   C10   -60.80  30.0  3
 GZY  Var_06    H6   C    C1   N    -168.59  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
 GZY  chir_01  C5  C4  C6  N  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
 GZY  plan-1  C5   0.020
 GZY  plan-1  C6   0.020
 GZY  plan-1  C7   0.020
 GZY  plan-1  C8   0.020
 GZY  plan-1  C10  0.020
 GZY  plan-1  C12  0.020
 GZY  plan-1  O1   0.020
 GZY  plan-1  C9   0.020
 GZY  plan-1  H4   0.020
 GZY  plan-1  H5   0.020
 GZY  plan-1  H13  0.020
 GZY  plan-1  H17  0.020
 GZY  plan-2  C5   0.020
 GZY  plan-2  O    0.020
 GZY  plan-2  C    0.020
 GZY  plan-2  N    0.020
 GZY  plan-2  C2   0.020
 GZY  plan-2  C1   0.020

