# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 21:15:44 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3sc(Br)cc3
#
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
 MJK  MJK  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide  ligand  48  26  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MJK
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
 MJK  C4   C   CH2   0  -0.335  58.3849  -14.9743  163.4904
 MJK  C7   C   CR15  0  -0.151  55.0560  -16.5084  164.4174
 MJK  C6   C   CR15  0  -0.227  55.9869  -15.9055  163.5270
 MJK  C9   C   CH2   0  -0.480  62.6020  -16.7609  163.2690
 MJK  C13  C   CR6   0   0.105  63.2768  -19.2563  167.6817
 MJK  C8   C   CR5   0  -0.356  55.6011  -16.7014  165.6475
 MJK  C18  C   CR16  0  -0.308  64.3644  -20.0871  167.4177
 MJK  C16  C   CR16  0  -0.269  65.8221  -18.1833  167.2160
 MJK  C1   C   C     0   0.579  60.9329  -18.6011  165.9181
 MJK  C2   C   CR15  0  -0.174  61.5426  -16.8623  164.3773
 MJK  C3   C   C     0   0.578  60.1470  -16.6317  163.8171
 MJK  C5   C   CR5   0  -0.159  57.1988  -15.6603  164.0971
 MJK  C10  C   CH2   0  -0.468  63.6283  -17.8186  163.6592
 MJK  C11  C   CH2   0  -0.279  62.7646  -18.9409  164.2142
 MJK  C12  C   CH2   0  -0.526  61.9015  -19.8364  167.8546
 MJK  C14  C   CR16  0  -0.287  63.4872  -17.8791  167.7158
 MJK  C15  C   CR16  0  -0.240  64.7478  -17.3453  167.4847
 MJK  C17  C   CR16  0  -0.241  65.6269  -19.5581  167.1861
 MJK  N    N   NH2   0  -0.784  59.8258  -20.5969  166.6582
 MJK  C    C   CH1   0  -0.202  61.1340  -19.9855  166.5217
 MJK  O    O   O     0  -0.479  59.5710  -17.4730  163.1505
 MJK  N1   N   NR5   0  -0.471  61.6909  -18.2147  164.8828
 MJK  N2   N   NH1   0  -0.648  59.6438  -15.4066  164.0431
 MJK  O1   O   O     0  -0.492  60.1017  -17.8443  166.4078
 MJK  S    S   S2    0   0.292  57.2336  -16.1730  165.7406
 MJK  BR   BR  BR    0   0.004  54.7869  -17.4858  167.1262
 MJK  H1   H   HCH2  0   0.288  58.3165  -13.8994  163.6600
 MJK  H2   H   HCH2  0   0.269  58.3623  -15.1268  162.4092
 MJK  H3   H   HCR5  0   0.283  54.0477  -16.7886  164.1490
 MJK  H4   H   HCR5  0   0.269  55.7597  -15.6637  162.4979
 MJK  H5   H   HCH2  0   0.265  63.0158  -15.7563  163.2005
 MJK  H6   H   HCH2  0   0.250  62.1653  -17.0098  162.2997
 MJK  H7   H   HCR6  0   0.248  64.2214  -21.1615  167.3928
 MJK  H8   H   HCR6  0   0.253  66.8056  -17.7686  167.0356
 MJK  H9   H   HCR5  0   0.271  61.7524  -16.1416  165.1748
 MJK  H10  H   HCH2  0   0.254  64.2404  -18.1446  162.8194
 MJK  H11  H   HCH2  0   0.246  64.2913  -17.4438  164.4413
 MJK  H12  H   HCH2  0   0.245  62.3649  -19.5669  163.4112
 MJK  H13  H   HCH2  0   0.262  63.3151  -19.5760  164.9032
 MJK  H14  H   HCH2  0   0.248  61.3067  -19.2175  168.5315
 MJK  H15  H   HCH2  0   0.255  61.9716  -20.8295  168.3059
 MJK  H16  H   HCR6  0   0.246  62.6563  -17.2154  167.9262
 MJK  H17  H   HCR6  0   0.253  64.8907  -16.2726  167.5167
 MJK  H18  H   HCR6  0   0.253  66.4592  -20.2204  166.9844
 MJK  H19  H   HNH2  0   0.352  59.9207  -21.4896  167.1266
 MJK  H20  H   HNH2  0   0.343  59.2437  -20.0202  167.2534
 MJK  H22  H   HCH1  0   0.257  61.7226  -20.6212  165.8575
 MJK  H23  H   HNH1  0   0.410  60.1537  -14.7606  164.6222

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
 MJK  O    C3   double    1.218  0.020  1.218
 MJK  C9   C10  single    1.525  0.020  1.525
 MJK  C9   C2   single    1.536  0.020  1.536
 MJK  C4   N2   single    1.441  0.020  1.441
 MJK  C4   C5   single    1.498  0.020  1.498
 MJK  C10  C11  single    1.521  0.020  1.521
 MJK  C3   N2   single    1.343  0.020  1.343
 MJK  C3   C2   single    1.521  0.020  1.521
 MJK  C11  N1   single    1.459  0.020  1.459
 MJK  C2   N1   single    1.451  0.020  1.451
 MJK  C5   C6   aromatic  1.361  0.020  1.361
 MJK  C5   S    aromatic  1.722  0.020  1.722
 MJK  C6   C7   aromatic  1.422  0.020  1.422
 MJK  N1   C1   single    1.340  0.020  1.340
 MJK  S    C8   aromatic  1.718  0.020  1.718
 MJK  C7   C8   aromatic  1.359  0.020  1.359
 MJK  C1   O1   double    1.226  0.020  1.226
 MJK  C1   C    single    1.524  0.020  1.524
 MJK  C8   BR   single    1.861  0.020  1.861
 MJK  N    C    single    1.450  0.020  1.450
 MJK  C    C12  single    1.545  0.020  1.545
 MJK  C18  C17  aromatic  1.388  0.020  1.388
 MJK  C18  C13  aromatic  1.394  0.020  1.394
 MJK  C17  C16  aromatic  1.389  0.020  1.389
 MJK  C12  C13  single    1.503  0.020  1.503
 MJK  C13  C14  aromatic  1.394  0.020  1.394
 MJK  C16  C15  aromatic  1.389  0.020  1.389
 MJK  C14  C15  aromatic  1.388  0.020  1.388
 MJK  C4   H1   single    0.970  0.020  1.090
 MJK  C4   H2   single    0.970  0.020  1.090
 MJK  C7   H3   single    0.930  0.020  1.080
 MJK  C6   H4   single    0.930  0.020  1.080
 MJK  C9   H5   single    0.970  0.020  1.090
 MJK  C9   H6   single    0.970  0.020  1.090
 MJK  C18  H7   single    0.930  0.020  1.080
 MJK  C16  H8   single    0.930  0.020  1.080
 MJK  C2   H9   single    0.970  0.020  1.090
 MJK  C10  H10  single    0.970  0.020  1.090
 MJK  C10  H11  single    0.970  0.020  1.090
 MJK  C11  H12  single    0.970  0.020  1.090
 MJK  C11  H13  single    0.970  0.020  1.090
 MJK  C12  H14  single    0.970  0.020  1.090
 MJK  C12  H15  single    0.970  0.020  1.090
 MJK  C14  H16  single    0.930  0.020  1.080
 MJK  C15  H17  single    0.930  0.020  1.080
 MJK  C17  H18  single    0.930  0.020  1.080
 MJK  N    H19  single    0.890  0.020  1.040
 MJK  N    H20  single    0.890  0.020  1.040
 MJK  C    H22  single    0.970  0.020  1.090
 MJK  N2   H23  single    0.860  0.020  1.020

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
 MJK  H2   C4   H1   106.88  3.000
 MJK  H2   C4   N2   110.84  3.000
 MJK  H1   C4   N2   106.91  3.000
 MJK  H2   C4   C5   108.69  3.000
 MJK  H1   C4   C5   109.80  3.000
 MJK  N2   C4   C5   113.51  3.000
 MJK  H3   C7   C8   124.21  3.000
 MJK  H3   C7   C6   124.42  3.000
 MJK  C8   C7   C6   111.36  3.000
 MJK  H4   C6   C5   123.04  3.000
 MJK  H4   C6   C7   123.58  3.000
 MJK  C5   C6   C7   113.38  3.000
 MJK  H6   C9   H5   107.85  3.000
 MJK  H6   C9   C10  109.77  3.000
 MJK  H5   C9   C10  113.61  3.000
 MJK  H6   C9   C2   110.46  3.000
 MJK  H5   C9   C2   111.61  3.000
 MJK  C10  C9   C2   103.52  3.000
 MJK  C14  C13  C12  121.13  3.000
 MJK  C14  C13  C18  118.41  3.000
 MJK  C12  C13  C18  120.39  3.000
 MJK  BR   C8   S    120.14  3.000
 MJK  BR   C8   C7   127.11  3.000
 MJK  S    C8   C7   112.73  3.000
 MJK  H7   C18  C17  119.59  3.000
 MJK  H7   C18  C13  119.47  3.000
 MJK  C17  C18  C13  120.94  3.000
 MJK  H8   C16  C17  120.22  3.000
 MJK  H8   C16  C15  120.25  3.000
 MJK  C17  C16  C15  119.52  3.000
 MJK  O1   C1   N1   120.93  3.000
 MJK  O1   C1   C    119.47  3.000
 MJK  N1   C1   C    119.57  3.000
 MJK  H9   C2   N1   109.87  3.000
 MJK  H9   C2   C3   110.12  3.000
 MJK  N1   C2   C3   111.30  3.000
 MJK  H9   C2   C9   110.47  3.000
 MJK  N1   C2   C9   104.02  3.000
 MJK  C3   C2   C9   110.91  3.000
 MJK  N2   C3   O    123.01  3.000
 MJK  N2   C3   C2   114.83  3.000
 MJK  O    C3   C2   122.04  3.000
 MJK  S    C5   C6   111.34  3.000
 MJK  S    C5   C4   120.44  3.000
 MJK  C6   C5   C4   128.13  3.000
 MJK  H11  C10  H10  108.29  3.000
 MJK  H11  C10  C11  109.68  3.000
 MJK  H10  C10  C11  112.31  3.000
 MJK  H11  C10  C9   110.73  3.000
 MJK  H10  C10  C9   112.87  3.000
 MJK  C11  C10  C9   102.89  3.000
 MJK  H13  C11  H12  108.42  3.000
 MJK  H13  C11  N1   111.92  3.000
 MJK  H12  C11  N1   110.64  3.000
 MJK  H13  C11  C10  112.01  3.000
 MJK  H12  C11  C10  111.22  3.000
 MJK  N1   C11  C10  102.59  3.000
 MJK  H15  C12  H14  107.07  3.000
 MJK  H15  C12  C    107.48  3.000
 MJK  H14  C12  C    108.57  3.000
 MJK  H15  C12  C13  109.85  3.000
 MJK  H14  C12  C13  110.53  3.000
 MJK  C    C12  C13  113.12  3.000
 MJK  H16  C14  C15  119.53  3.000
 MJK  H16  C14  C13  119.60  3.000
 MJK  C15  C14  C13  120.87  3.000
 MJK  H17  C15  C14  119.73  3.000
 MJK  H17  C15  C16  120.10  3.000
 MJK  C14  C15  C16  120.17  3.000
 MJK  H18  C17  C16  120.10  3.000
 MJK  H18  C17  C18  119.81  3.000
 MJK  C16  C17  C18  120.09  3.000
 MJK  H20  N    H19  106.50  3.000
 MJK  H20  N    C    109.49  3.000
 MJK  H19  N    C    109.31  3.000
 MJK  H22  C    N    107.34  3.000
 MJK  H22  C    C12  108.25  3.000
 MJK  N    C    C12  114.04  3.000
 MJK  H22  C    C1   111.05  3.000
 MJK  C12  C    C1   108.64  3.000
 MJK  N    C    C1   107.54  3.000
 MJK  C11  N1   C2   112.30  3.000
 MJK  C2   N1   C1   118.69  3.000
 MJK  C11  N1   C1   128.83  3.000
 MJK  H23  N2   C3   119.50  3.000
 MJK  H23  N2   C4   118.08  3.000
 MJK  C3   N2   C4   122.42  3.000
 MJK  C5   S    C8    91.18  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
 MJK  CONST_01  S    C5   C6   C7      0.00   0.0  0
 MJK  CONST_02  C5   S    C8   C7      0.00   0.0  0
 MJK  CONST_03  C8   S    C5   C6      0.00   0.0  0
 MJK  CONST_04  S    C8   C7   C6      0.00   0.0  0
 MJK  CONST_05  C16  C17  C18  C13     0.00   0.0  0
 MJK  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 MJK  CONST_07  C5   C6   C7   C8      0.00   0.0  0
 MJK  CONST_08  C15  C16  C17  C18     0.00   0.0  0
 MJK  CONST_09  C15  C14  C13  C18     0.00   0.0  0
 MJK  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 MJK  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 MJK  CONST_12  C7   C6   C5   C4    180.00   0.0  0
 MJK  CONST_13  C8   S    C5   C4    180.00   0.0  0
 MJK  CONST_14  BR   C8   C7   C6    180.00   0.0  0
 MJK  CONST_15  BR   C8   S    C5    180.00   0.0  0
 MJK  CONST_16  C17  C18  C13  C12   180.00   0.0  0
 MJK  CONST_17  C15  C14  C13  C12   180.00   0.0  0
 MJK  CONST_18  H18  C17  C18  C13   180.00   0.0  0
 MJK  CONST_19  H17  C15  C14  C13   180.00   0.0  0
 MJK  CONST_20  H4   C6   C7   C8    180.00   0.0  0
 MJK  CONST_21  H8   C16  C17  C18   180.00   0.0  0
 MJK  CONST_22  H16  C14  C13  C18   180.00   0.0  0
 MJK  CONST_23  H7   C18  C17  C16   180.00   0.0  0
 MJK  CONST_24  H3   C7   C6   C5    180.00   0.0  0
 MJK  CONST_25  O1   C1   N1   C2      0.00   0.0  0
 MJK  CONST_26  C    C1   N1   C2    180.00   0.0  0
 MJK  CONST_27  O1   C1   N1   C11   180.00   0.0  0
 MJK  CONST_28  C    C1   N1   C11     0.00   0.0  0
 MJK  CONST_29  C2   C3   N2   C4    180.00   0.0  0
 MJK  CONST_30  H23  N2   C3   C2      0.00   0.0  0
 MJK  CONST_31  O    C3   N2   C4      0.00   0.0  0
 MJK  Var_01    N1   C11  C10  C9    -35.74  30.0  1
 MJK  Var_02    C11  C10  C9   C2     37.14  30.0  1
 MJK  Var_03    C10  C11  N1   C2     21.65  30.0  1
 MJK  Var_04    N2   C4   C5   C6   -152.14  30.0  1
 MJK  Var_05    C    C12  C13  C18   -87.69  30.0  1
 MJK  Var_06    C5   C4   N2   C3     69.85  30.0  1

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
 MJK  chir_01  C2  C9  C3   N1  negativ
 MJK  chir_02  C   N   C12  C1  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
 MJK  plan-1  C4   0.020
 MJK  plan-1  C7   0.020
 MJK  plan-1  C6   0.020
 MJK  plan-1  C8   0.020
 MJK  plan-1  C5   0.020
 MJK  plan-1  S    0.020
 MJK  plan-1  BR   0.020
 MJK  plan-1  H3   0.020
 MJK  plan-1  H4   0.020
 MJK  plan-2  C13  0.020
 MJK  plan-2  C18  0.020
 MJK  plan-2  C16  0.020
 MJK  plan-2  C12  0.020
 MJK  plan-2  C14  0.020
 MJK  plan-2  C15  0.020
 MJK  plan-2  C17  0.020
 MJK  plan-2  H7   0.020
 MJK  plan-2  H8   0.020
 MJK  plan-2  H16  0.020
 MJK  plan-2  H17  0.020
 MJK  plan-2  H18  0.020
 MJK  plan-3  C4   0.020
 MJK  plan-3  C2   0.020
 MJK  plan-3  C3   0.020
 MJK  plan-3  O    0.020
 MJK  plan-3  N2   0.020
 MJK  plan-3  H23  0.020
 MJK  plan-4  C1   0.020
 MJK  plan-4  C2   0.020
 MJK  plan-4  C11  0.020
 MJK  plan-4  C    0.020
 MJK  plan-4  N1   0.020
 MJK  plan-4  O1   0.020

