# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:23:53 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: {(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)NCC(=O)N1CCC[C@H]1COC(=O)Cc2cccc(Cl)c2
#
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
 M18  M18  '{(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate'  ligand  55  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M18
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
 M18  C1    C   CH2   0  -0.692  -2.7791  -0.0719   0.8151
 M18  C2    C   C     0   0.616  -2.3442  -0.7086  -0.4844
 M18  O1    O   O     0  -0.441  -2.7645  -0.4164  -1.5740
 M18  O2    O   O2    0  -0.448  -1.4321  -1.6434  -0.2685
 M18  C3    C   CH2   0  -0.195  -0.8961  -2.3402  -1.3949
 M18  C4    C   CR15  0  -0.086   0.1563  -3.3039  -0.8764
 M18  C5    C   CH2   0  -0.487  -0.4212  -4.4088   0.0213
 M18  C6    C   CH2   0  -0.461   0.6152  -4.5976   1.1228
 M18  C7    C   CH2   0  -0.287   1.1548  -3.1904   1.3272
 M18  N1    N   NR5   0  -0.479   1.1578  -2.6540  -0.0278
 M18  C8    C   C     0   0.537   1.9939  -1.7253  -0.5027
 M18  C9    C   CH2   0  -0.366   2.9712  -1.1287   0.4986
 M18  N2    N   NH1   0  -0.672   3.6983  -0.0673  -0.1324
 M18  C10   C   C     0   0.763   4.7095   0.5657   0.4899
 M18  O3    O   O2    0  -0.505   5.2257   1.5017  -0.3061
 M18  C11   C   CT    0   0.191   6.3572   2.3261   0.0764
 M18  C12   C   CH3   0  -0.671   7.6018   1.4741   0.2947
 M18  C13   C   CH3   0  -0.658   6.5508   3.2241  -1.1397
 M18  C14   C   CH3   0  -0.672   6.0359   3.1783   1.2983
 M18  O4    O   O     0  -0.523   5.0760   0.3055   1.6194
 M18  O5    O   O     0  -0.503   1.9914  -1.3630  -1.6739
 M18  C15   C   CR6   0   0.139  -3.7461   1.0530   0.5998
 M18  C16   C   CR16  0  -0.260  -5.1148   0.8091   0.6087
 M18  C17   C   CR6   0  -0.022  -5.9982   1.8549   0.3931
 M18  CL1   CL  CL    0  -0.131  -7.7038   1.5379   0.4117
 M18  C18   C   CR16  0  -0.229  -5.5512   3.1465   0.1656
 M18  C19   C   CR16  0  -0.246  -4.1837   3.3833   0.1588
 M18  C20   C   CR16  0  -0.285  -3.2876   2.3468   0.3741
 M18  H1    H   HCH2  0   0.307  -3.2197  -0.8513   1.4430
 M18  H1A   H   HCH2  0   0.304  -1.8899   0.2754   1.3476
 M18  H3    H   HCH2  0   0.254  -1.6798  -2.9069  -1.9043
 M18  H3A   H   HCH2  0   0.257  -0.4665  -1.6343  -2.1043
 M18  H4    H   HCR5  0   0.275   0.6457  -3.7392  -1.7522
 M18  H5    H   HCH2  0   0.246  -1.3713  -4.0928   0.4557
 M18  H5A   H   HCH2  0   0.261  -0.6097  -5.3186  -0.5468
 M18  H6    H   HCH2  0   0.255   0.1953  -5.0160   2.0362
 M18  H6A   H   HCH2  0   0.243   1.4211  -5.2542   0.7894
 M18  H7    H   HCH2  0   0.247   0.4977  -2.6028   1.9748
 M18  H7A   H   HCH2  0   0.265   2.1523  -3.1909   1.7643
 M18  H9    H   HCH2  0   0.272   2.4221  -0.7741   1.3770
 M18  H9A   H   HCH2  0   0.276   3.6462  -1.9164   0.8504
 M18  HN2   H   HNH1  0   0.397   3.4641   0.1547  -1.0880
 M18  H12   H   HCH3  0   0.235   7.7806   0.8168  -0.5581
 M18  H12A  H   HCH3  0   0.234   8.4705   2.1260   0.3960
 M18  H12B  H   HCH3  0   0.245   7.5365   0.8668   1.1948
 M18  H13   H   HCH3  0   0.237   5.6681   3.8392  -1.3228
 M18  H13A  H   HCH3  0   0.230   7.3946   3.8933  -0.9742
 M18  H13B  H   HCH3  0   0.237   6.7568   2.6406  -2.0381
 M18  H14   H   HCH3  0   0.246   5.9608   2.5891   2.2090
 M18  H14A  H   HCH3  0   0.233   6.8316   3.9114   1.4386
 M18  H14B  H   HCH3  0   0.234   5.1042   3.7288   1.1585
 M18  H16   H   HCR6  0   0.276  -5.4888  -0.1912   0.7876
 M18  H18   H   HCR6  0   0.280  -6.2528   3.9527   0.0009
 M18  H19   H   HCR6  0   0.268  -3.8200   4.3873  -0.0156
 M18  H20   H   HCR6  0   0.260  -2.2229   2.5449   0.3686

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
 M18  C1   C2    single    1.511  0.020  1.511
 M18  C1   C15   single    1.499  0.020  1.499
 M18  C2   O1    double    1.204  0.020  1.204
 M18  C2   O2    single    1.324  0.020  1.324
 M18  O2   C3    single    1.429  0.020  1.429
 M18  C3   C4    single    1.518  0.020  1.518
 M18  C4   C5    single    1.536  0.020  1.536
 M18  C4   N1    single    1.465  0.020  1.465
 M18  C5   C6    single    1.524  0.020  1.524
 M18  C6   C7    single    1.521  0.020  1.521
 M18  C7   N1    single    1.457  0.020  1.457
 M18  N1   C8    single    1.337  0.020  1.337
 M18  C8   C9    single    1.521  0.020  1.521
 M18  C8   O5    double    1.226  0.020  1.226
 M18  C9   N2    single    1.433  0.020  1.433
 M18  N2   C10   single    1.345  0.020  1.345
 M18  C10  O3    single    1.333  0.020  1.333
 M18  C10  O4    double    1.216  0.020  1.216
 M18  O3   C11   single    1.451  0.020  1.451
 M18  C11  C12   single    1.524  0.020  1.524
 M18  C11  C13   single    1.524  0.020  1.524
 M18  C11  C14   single    1.524  0.020  1.524
 M18  C15  C16   aromatic  1.390  0.020  1.390
 M18  C15  C20   aromatic  1.391  0.020  1.391
 M18  C16  C17   aromatic  1.386  0.020  1.386
 M18  C17  CL1   single    1.735  0.020  1.735
 M18  C17  C18   aromatic  1.386  0.020  1.386
 M18  C18  C19   aromatic  1.388  0.020  1.388
 M18  C19  C20   aromatic  1.387  0.020  1.387
 M18  C1   H1    single    0.970  0.020  1.090
 M18  C1   H1A   single    0.970  0.020  1.090
 M18  C3   H3    single    0.970  0.020  1.090
 M18  C3   H3A   single    0.970  0.020  1.090
 M18  C4   H4    single    0.970  0.020  1.090
 M18  C5   H5    single    0.970  0.020  1.090
 M18  C5   H5A   single    0.970  0.020  1.090
 M18  C6   H6    single    0.970  0.020  1.090
 M18  C6   H6A   single    0.970  0.020  1.090
 M18  C7   H7    single    0.970  0.020  1.090
 M18  C7   H7A   single    0.970  0.020  1.090
 M18  C9   H9    single    0.970  0.020  1.090
 M18  C9   H9A   single    0.970  0.020  1.090
 M18  N2   HN2   single    0.860  0.020  1.020
 M18  C12  H12   single    0.970  0.020  1.090
 M18  C12  H12A  single    0.970  0.020  1.090
 M18  C12  H12B  single    0.970  0.020  1.090
 M18  C13  H13   single    0.970  0.020  1.090
 M18  C13  H13A  single    0.970  0.020  1.090
 M18  C13  H13B  single    0.970  0.020  1.090
 M18  C14  H14   single    0.970  0.020  1.090
 M18  C14  H14A  single    0.970  0.020  1.090
 M18  C14  H14B  single    0.970  0.020  1.090
 M18  C16  H16   single    0.930  0.020  1.080
 M18  C18  H18   single    0.930  0.020  1.080
 M18  C19  H19   single    0.930  0.020  1.080
 M18  C20  H20   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
 M18  H1A   C1   H1    105.93  3.000
 M18  H1A   C1   C15   110.87  3.000
 M18  H1    C1   C15   110.94  3.000
 M18  H1A   C1   C2    108.58  3.000
 M18  H1    C1   C2    108.03  3.000
 M18  C15   C1   C2    112.23  3.000
 M18  O2    C2   O1    124.03  3.000
 M18  O2    C2   C1    110.83  3.000
 M18  O1    C2   C1    125.14  3.000
 M18  C3    O2   C2    118.31  3.000
 M18  H3A   C3   H3    108.38  3.000
 M18  H3A   C3   C4    111.13  3.000
 M18  H3    C3   C4    109.09  3.000
 M18  H3A   C3   O2    110.21  3.000
 M18  H3    C3   O2    110.56  3.000
 M18  C4    C3   O2    107.48  3.000
 M18  H4    C4   N1    109.54  3.000
 M18  H4    C4   C5    110.48  3.000
 M18  N1    C4   C5    103.75  3.000
 M18  H4    C4   C3    106.82  3.000
 M18  N1    C4   C3    112.96  3.000
 M18  C5    C4   C3    113.30  3.000
 M18  H5A   C5   H5    107.38  3.000
 M18  H5A   C5   C6    113.04  3.000
 M18  H5    C5   C6    109.88  3.000
 M18  H5A   C5   C4    111.17  3.000
 M18  H5    C5   C4    110.58  3.000
 M18  C6    C5   C4    104.82  3.000
 M18  H6A   C6   H6    108.05  3.000
 M18  H6A   C6   C7    109.61  3.000
 M18  H6    C6   C7    112.31  3.000
 M18  H6A   C6   C5    110.84  3.000
 M18  H6    C6   C5    113.05  3.000
 M18  C7    C6   C5    102.93  3.000
 M18  H7A   C7   H7    108.23  3.000
 M18  H7A   C7   N1    111.80  3.000
 M18  H7    C7   N1    110.73  3.000
 M18  H7A   C7   C6    112.25  3.000
 M18  H7    C7   C6    111.31  3.000
 M18  N1    C7   C6    102.49  3.000
 M18  C8    N1   C7    125.96  3.000
 M18  C8    N1   C4    122.01  3.000
 M18  C7    N1   C4    111.96  3.000
 M18  O5    C8   C9    120.95  3.000
 M18  O5    C8   N1    122.91  3.000
 M18  C9    C8   N1    116.14  3.000
 M18  H9A   C9   H9    106.51  3.000
 M18  H9A   C9   N2    111.19  3.000
 M18  H9    C9   N2    111.58  3.000
 M18  H9A   C9   C8    108.99  3.000
 M18  H9    C9   C8    109.44  3.000
 M18  N2    C9   C8    109.07  3.000
 M18  HN2   N2   C10   120.61  3.000
 M18  HN2   N2   C9    117.54  3.000
 M18  C10   N2   C9    121.75  3.000
 M18  O4    C10  O3    126.05  3.000
 M18  O4    C10  N2    123.75  3.000
 M18  O3    C10  N2    110.20  3.000
 M18  C11   O3   C10   122.92  3.000
 M18  C14   C11  C13   109.70  3.000
 M18  C14   C11  C12   111.71  3.000
 M18  C13   C11  C12   109.87  3.000
 M18  C14   C11  O3    111.38  3.000
 M18  C13   C11  O3    102.91  3.000
 M18  C12   C11  O3    110.91  3.000
 M18  H12B  C12  H12A  107.74  3.000
 M18  H12B  C12  H12   108.67  3.000
 M18  H12A  C12  H12   107.58  3.000
 M18  H12B  C12  C11   112.43  3.000
 M18  H12A  C12  C11   109.24  3.000
 M18  H12   C12  C11   111.01  3.000
 M18  H13B  C13  H13A  107.90  3.000
 M18  H13B  C13  H13   108.42  3.000
 M18  H13A  C13  H13   107.80  3.000
 M18  H13B  C13  C11   111.47  3.000
 M18  H13A  C13  C11   109.82  3.000
 M18  H13   C13  C11   111.30  3.000
 M18  H14B  C14  H14A  107.46  3.000
 M18  H14B  C14  H14   108.77  3.000
 M18  H14A  C14  H14   107.87  3.000
 M18  H14B  C14  C11   111.07  3.000
 M18  H14A  C14  C11   108.98  3.000
 M18  H14   C14  C11   112.53  3.000
 M18  C20   C15  C16   119.25  3.000
 M18  C20   C15  C1    120.58  3.000
 M18  C16   C15  C1    120.17  3.000
 M18  H16   C16  C17   120.17  3.000
 M18  H16   C16  C15   120.21  3.000
 M18  C17   C16  C15   119.62  3.000
 M18  C18   C17  CL1   119.29  3.000
 M18  C18   C17  C16   121.55  3.000
 M18  CL1   C17  C16   119.15  3.000
 M18  H18   C18  C19   120.75  3.000
 M18  H18   C18  C17   120.71  3.000
 M18  C19   C18  C17   118.54  3.000
 M18  H19   C19  C20   120.09  3.000
 M18  H19   C19  C18   119.36  3.000
 M18  C20   C19  C18   120.55  3.000
 M18  H20   C20  C19   119.85  3.000
 M18  H20   C20  C15   119.66  3.000
 M18  C19   C20  C15   120.49  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
 M18  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 M18  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 M18  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 M18  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 M18  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 M18  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 M18  CONST_07  C17  C16  C15  C1    180.00   0.0  0
 M18  CONST_08  C19  C20  C15  C1    180.00   0.0  0
 M18  CONST_09  CL1  C17  C16  C15   180.00   0.0  0
 M18  CONST_10  C19  C18  C17  CL1   180.00   0.0  0
 M18  CONST_11  H19  C19  C20  C15   180.00   0.0  0
 M18  CONST_12  H20  C20  C15  C16   180.00   0.0  0
 M18  CONST_13  H18  C18  C17  C16   180.00   0.0  0
 M18  CONST_14  H16  C16  C17  C18   180.00   0.0  0
 M18  CONST_15  C9   C8   N1   C4    180.00   0.0  0
 M18  CONST_16  O5   C8   N1   C4      0.00   0.0  0
 M18  CONST_17  C9   C8   N1   C7      0.00   0.0  0
 M18  CONST_18  O5   C8   N1   C7    180.00   0.0  0
 M18  Var_01    C7   C6   C5   C4     34.39  30.0  1
 M18  Var_02    C6   C7   N1   C4     26.28  30.0  1
 M18  Var_03    N1   C7   C6   C5    -36.53  30.0  1
 M18  Var_04    C16  C15  C1   C2     91.78  30.0  2
 M18  Var_05    C4   C3   O2   C2    177.74  30.0  3
 M18  Var_06    C15  C1   C2   O1     -3.88  30.0  2
 M18  Var_07    N2   C9   C8   N1   -174.40  30.0  3
 M18  Var_08    C10  N2   C9   C8   -174.44  30.0  3
 M18  Var_09    O3   C10  N2   C9    179.59  30.0  2
 M18  Var_10    C12  C11  O3   C10    63.01  30.0  3
 M18  Var_11    H12  C12  C11  O3     51.04  30.0  3
 M18  Var_12    H13  C13  C11  O3     61.32  30.0  3
 M18  Var_13    H14  C14  C11  O3     70.96  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
 M18  chir_01  C4  C3  C5  N1  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
 M18  plan-1  C1   0.020
 M18  plan-1  C15  0.020
 M18  plan-1  C16  0.020
 M18  plan-1  C17  0.020
 M18  plan-1  CL1  0.020
 M18  plan-1  C18  0.020
 M18  plan-1  C19  0.020
 M18  plan-1  C20  0.020
 M18  plan-1  H16  0.020
 M18  plan-1  H18  0.020
 M18  plan-1  H19  0.020
 M18  plan-1  H20  0.020
 M18  plan-2  C4   0.020
 M18  plan-2  C7   0.020
 M18  plan-2  N1   0.020
 M18  plan-2  C8   0.020
 M18  plan-2  C9   0.020
 M18  plan-2  O5   0.020
 M18  plan-3  C1   0.020
 M18  plan-3  C2   0.020
 M18  plan-3  O1   0.020
 M18  plan-3  O2   0.020
 M18  plan-4  N2   0.020
 M18  plan-4  C10  0.020
 M18  plan-4  O3   0.020
 M18  plan-4  O4   0.020

