# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:53:02 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]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)NCCc3c[nH]cn3
#
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
 MJH  MJH  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]pyrrolidine-2-carboxamide  ligand  51  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_MJH
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
 MJH  N2   N  NH1   0  -0.629  59.0630  -15.4474  163.9946
 MJH  C2   C  CH1   0  -0.175  61.0294  -16.7353  164.4999
 MJH  O1   O  O     0  -0.495  59.5262  -18.2946  166.1048
 MJH  C3   C  C     0   0.574  59.6989  -16.6053  163.7700
 MJH  C4   C  CH2   0  -0.301  57.8243  -15.0492  163.3638
 MJH  C5   C  CH2   0  -0.529  56.8110  -14.5144  164.3650
 MJH  C6   C  CR5   0   0.127  56.3230  -15.5206  165.3550
 MJH  C7   C  CR15  0  -0.095  56.5722  -16.8642  165.4244
 MJH  C8   C  CR15  0   0.077  55.2410  -16.2506  167.0494
 MJH  C9   C  CH2   0  -0.478  62.1917  -16.2832  163.6004
 MJH  C10  C  CH2   0  -0.468  63.3243  -17.2282  163.9817
 MJH  C11  C  CH2   0  -0.279  62.6026  -18.5461  164.2120
 MJH  C12  C  CH2   0  -0.523  61.4238  -20.2052  167.4892
 MJH  C13  C  CR6   0   0.105  62.6368  -19.3379  167.6756
 MJH  C14  C  CR16  0  -0.285  62.5110  -17.9908  168.0104
 MJH  C15  C  CR16  0  -0.241  63.6289  -17.1738  168.1103
 MJH  C16  C  CR16  0  -0.269  64.8958  -17.6931  167.8777
 MJH  C17  C  CR16  0  -0.241  65.0354  -19.0356  167.5505
 MJH  C18  C  CR16  0  -0.310  63.9142  -19.8487  167.4525
 MJH  N    N  NH2   0  -0.782  59.7506  -21.0656  165.8208
 MJH  C    C  CH1   0  -0.208  60.9136  -20.2242  166.0308
 MJH  O    O  O     0  -0.501  59.3071  -17.4669  162.9979
 MJH  N1   N  NT    0  -0.471  61.3407  -18.1183  164.8068
 MJH  N3   N  NR15  0  -0.573  55.8728  -17.3085  166.5096
 MJH  N4   N  N     0  -0.467  55.4897  -15.1540  166.3800
 MJH  H1   H  HNH1  0   0.396  59.4710  -14.8022  164.6527
 MJH  H2   H  HCH1  0   0.270  61.0131  -16.1440  165.4221
 MJH  H3   H  HCH2  0   0.256  58.0188  -14.2781  162.6140
 MJH  H4   H  HCH2  0   0.249  57.4198  -15.9098  162.8329
 MJH  H5   H  HCH2  0   0.241  57.2366  -13.6558  164.8952
 MJH  H6   H  HCH2  0   0.252  55.9656  -14.1145  163.7975
 MJH  H7   H  HCR5  0   0.277  57.1814  -17.5247  164.8333
 MJH  H8   H  HCR5  0   0.273  54.6172  -16.3327  167.9260
 MJH  H9   H  HCH2  0   0.264  62.4316  -15.2324  163.7536
 MJH  H10  H  HCH2  0   0.249  61.9360  -16.4181  162.5470
 MJH  H11  H  HCH2  0   0.255  64.0925  -17.3039  163.2134
 MJH  H12  H  HCH2  0   0.245  63.8001  -16.9045  164.9100
 MJH  H13  H  HCH2  0   0.244  62.4266  -19.0733  163.2699
 MJH  H14  H  HCH2  0   0.261  63.1611  -19.2017  164.8747
 MJH  H15  H  HCH2  0   0.246  60.6098  -19.8673  168.1359
 MJH  H16  H  HCH2  0   0.255  61.6524  -21.2362  167.7706
 MJH  H17  H  HCR6  0   0.245  61.5272  -17.5763  168.1967
 MJH  H18  H  HCR6  0   0.252  63.5094  -16.1299  168.3711
 MJH  H19  H  HCR6  0   0.253  65.7682  -17.0572  167.9568
 MJH  H20  H  HCR6  0   0.253  66.0188  -19.4517  167.3724
 MJH  H21  H  HCR6  0   0.249  64.0334  -20.8961  167.1979
 MJH  H22  H  HNH2  0   0.352  59.9704  -22.0131  166.1020
 MJH  H23  H  HNH2  0   0.342  58.9948  -20.7568  166.4207
 MJH  H25  H  HCH1  0   0.257  61.7121  -20.6126  165.3965
 MJH  H26  H  HNR5  0   0.415  55.8428  -18.2562  166.8489
 MJH  C1   C  C     0   0.584  60.5372  -18.8028  165.6327

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
 MJH  O    C3   double    1.221  0.020  1.221
 MJH  C9   C10  single    1.524  0.020  1.524
 MJH  C9   C2   single    1.538  0.020  1.538
 MJH  C4   N2   single    1.446  0.020  1.446
 MJH  C4   C5   single    1.522  0.020  1.522
 MJH  C10  C11  single    1.520  0.020  1.520
 MJH  C3   N2   single    1.340  0.020  1.340
 MJH  C3   C2   single    1.523  0.020  1.523
 MJH  C11  N1   single    1.459  0.020  1.459
 MJH  C2   N1   single    1.450  0.020  1.450
 MJH  C5   C6   single    1.494  0.020  1.494
 MJH  N1   C1   single    1.340  0.020  1.340
 MJH  C7   C6   aromatic  1.368  0.020  1.368
 MJH  C7   N3   aromatic  1.365  0.020  1.365
 MJH  C6   N4   aromatic  1.371  0.020  1.371
 MJH  N3   C8   aromatic  1.345  0.020  1.345
 MJH  C1   O1   double    1.226  0.020  1.226
 MJH  C1   C    single    1.523  0.020  1.523
 MJH  N4   C8   aromatic  1.309  0.020  1.309
 MJH  N    C    single    1.451  0.020  1.451
 MJH  C    C12  single    1.545  0.020  1.545
 MJH  C18  C17  aromatic  1.388  0.020  1.388
 MJH  C18  C13  aromatic  1.394  0.020  1.394
 MJH  C17  C16  aromatic  1.389  0.020  1.389
 MJH  C12  C13  single    1.503  0.020  1.503
 MJH  C13  C14  aromatic  1.394  0.020  1.394
 MJH  C16  C15  aromatic  1.389  0.020  1.389
 MJH  C14  C15  aromatic  1.388  0.020  1.388
 MJH  N2   H1   single    0.860  0.020  1.020
 MJH  C2   H2   single    0.970  0.020  1.090
 MJH  C4   H3   single    0.970  0.020  1.090
 MJH  C4   H4   single    0.970  0.020  1.090
 MJH  C5   H5   single    0.970  0.020  1.090
 MJH  C5   H6   single    0.970  0.020  1.090
 MJH  C7   H7   single    0.930  0.020  1.080
 MJH  C8   H8   single    0.930  0.020  1.080
 MJH  C9   H9   single    0.970  0.020  1.090
 MJH  C9   H10  single    0.970  0.020  1.090
 MJH  C10  H11  single    0.970  0.020  1.090
 MJH  C10  H12  single    0.970  0.020  1.090
 MJH  C11  H13  single    0.970  0.020  1.090
 MJH  C11  H14  single    0.970  0.020  1.090
 MJH  C12  H15  single    0.970  0.020  1.090
 MJH  C12  H16  single    0.970  0.020  1.090
 MJH  C14  H17  single    0.930  0.020  1.080
 MJH  C15  H18  single    0.930  0.020  1.080
 MJH  C16  H19  single    0.930  0.020  1.080
 MJH  C17  H20  single    0.930  0.020  1.080
 MJH  C18  H21  single    0.930  0.020  1.080
 MJH  N    H22  single    0.890  0.020  1.040
 MJH  N    H23  single    0.890  0.020  1.040
 MJH  C    H25  single    0.970  0.020  1.090
 MJH  N3   H26  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
 MJH  H1   N2   C4   117.09  3.000
 MJH  H1   N2   C3   118.07  3.000
 MJH  C4   N2   C3   124.85  3.000
 MJH  H2   C2   N1   109.86  3.000
 MJH  H2   C2   C9   110.18  3.000
 MJH  N1   C2   C9   104.00  3.000
 MJH  H2   C2   C3   110.14  3.000
 MJH  N1   C2   C3   111.73  3.000
 MJH  C9   C2   C3   110.78  3.000
 MJH  O    C3   C2   121.53  3.000
 MJH  C2   C3   N2   114.08  3.000
 MJH  O    C3   N2   124.28  3.000
 MJH  H4   C4   H3   106.81  3.000
 MJH  H4   C4   C5   110.56  3.000
 MJH  H3   C4   C5   108.78  3.000
 MJH  H4   C4   N2   108.25  3.000
 MJH  H3   C4   N2   109.94  3.000
 MJH  C5   C4   N2   112.35  3.000
 MJH  H6   C5   H5   105.36  3.000
 MJH  H6   C5   C6   109.73  3.000
 MJH  H5   C5   C6   109.53  3.000
 MJH  H6   C5   C4   107.56  3.000
 MJH  H5   C5   C4   109.60  3.000
 MJH  C6   C5   C4   114.64  3.000
 MJH  N4   C6   C7   109.60  3.000
 MJH  N4   C6   C5   120.93  3.000
 MJH  C7   C6   C5   129.47  3.000
 MJH  H7   C7   N3   121.81  3.000
 MJH  H7   C7   C6   132.71  3.000
 MJH  N3   C7   C6   105.46  3.000
 MJH  H8   C8   N4   126.10  3.000
 MJH  H8   C8   N3   122.52  3.000
 MJH  N4   C8   N3   111.38  3.000
 MJH  H10  C9   H9   107.85  3.000
 MJH  H10  C9   C10  109.80  3.000
 MJH  H9   C9   C10  113.56  3.000
 MJH  H10  C9   C2   110.54  3.000
 MJH  H9   C9   C2   111.60  3.000
 MJH  C10  C9   C2   103.48  3.000
 MJH  H12  C10  H11  108.24  3.000
 MJH  H12  C10  C11  109.57  3.000
 MJH  H11  C10  C11  112.42  3.000
 MJH  H12  C10  C9   110.65  3.000
 MJH  H11  C10  C9   113.01  3.000
 MJH  C11  C10  C9   102.87  3.000
 MJH  H14  C11  H13  108.49  3.000
 MJH  H14  C11  N1   111.89  3.000
 MJH  H13  C11  N1   110.68  3.000
 MJH  H14  C11  C10  111.81  3.000
 MJH  H13  C11  C10  111.33  3.000
 MJH  N1   C11  C10  102.60  3.000
 MJH  H16  C12  H15  107.16  3.000
 MJH  H16  C12  C    107.49  3.000
 MJH  H15  C12  C    108.44  3.000
 MJH  H16  C12  C13  110.10  3.000
 MJH  H15  C12  C13  110.44  3.000
 MJH  C    C12  C13  113.00  3.000
 MJH  C18  C13  C14  118.39  3.000
 MJH  C14  C13  C12  120.98  3.000
 MJH  C18  C13  C12  120.55  3.000
 MJH  H17  C14  C15  119.58  3.000
 MJH  H17  C14  C13  119.53  3.000
 MJH  C15  C14  C13  120.89  3.000
 MJH  H18  C15  C16  120.10  3.000
 MJH  H18  C15  C14  119.73  3.000
 MJH  C16  C15  C14  120.17  3.000
 MJH  H19  C16  C17  120.27  3.000
 MJH  H19  C16  C15  120.22  3.000
 MJH  C17  C16  C15  119.51  3.000
 MJH  H20  C17  C18  119.79  3.000
 MJH  H20  C17  C16  120.11  3.000
 MJH  C18  C17  C16  120.10  3.000
 MJH  H21  C18  C17  119.57  3.000
 MJH  H21  C18  C13  119.49  3.000
 MJH  C17  C18  C13  120.94  3.000
 MJH  H23  N    H22  106.43  3.000
 MJH  H23  N    C    109.61  3.000
 MJH  H22  N    C    109.18  3.000
 MJH  H25  C    N    107.22  3.000
 MJH  H25  C    C12  108.14  3.000
 MJH  N    C    C12  114.11  3.000
 MJH  H25  C    C1   111.16  3.000
 MJH  C12  C    C1   108.47  3.000
 MJH  N    C    C1   107.77  3.000
 MJH  C11  N1   C1   128.31  3.000
 MJH  C1   N1   C2   119.26  3.000
 MJH  C11  N1   C2   112.26  3.000
 MJH  H26  N3   C8   126.22  3.000
 MJH  H26  N3   C7   126.11  3.000
 MJH  C8   N3   C7   107.67  3.000
 MJH  C8   N4   C6   105.89  3.000
 MJH  N1   C1   C    119.31  3.000
 MJH  C    C1   O1   119.33  3.000
 MJH  N1   C1   O1   121.33  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
 MJH  CONST_01  C8   N3   C7   C6     0.00   0.0  0
 MJH  CONST_02  N3   C8   N4   C6     0.00   0.0  0
 MJH  CONST_03  C8   N4   C6   C7     0.00   0.0  0
 MJH  CONST_04  N4   C8   N3   C7     0.00   0.0  0
 MJH  CONST_05  C16  C17  C18  C13    0.00   0.0  0
 MJH  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 MJH  CONST_07  C17  C18  C13  C14    0.00   0.0  0
 MJH  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 MJH  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 MJH  CONST_10  C18  C13  C14  C15    0.00   0.0  0
 MJH  CONST_11  N4   C6   C7   N3     0.00   0.0  0
 MJH  CONST_12  N3   C7   C6   C5   180.00   0.0  0
 MJH  CONST_13  C8   N4   C6   C5   180.00   0.0  0
 MJH  CONST_14  C17  C18  C13  C12  180.00   0.0  0
 MJH  CONST_15  C15  C14  C13  C12  180.00   0.0  0
 MJH  CONST_16  H26  N3   C7   C6   180.00   0.0  0
 MJH  CONST_17  H8   C8   N4   C6   180.00   0.0  0
 MJH  CONST_18  H7   C7   N3   C8   180.00   0.0  0
 MJH  CONST_19  H20  C17  C18  C13  180.00   0.0  0
 MJH  CONST_20  H18  C15  C14  C13  180.00   0.0  0
 MJH  CONST_21  H21  C18  C13  C14  180.00   0.0  0
 MJH  CONST_22  H19  C16  C15  C14  180.00   0.0  0
 MJH  CONST_23  H17  C14  C15  C16  180.00   0.0  0
 MJH  CONST_24  O1   C1   N1   C2     0.00   0.0  0
 MJH  CONST_25  C    C1   N1   C2   180.00   0.0  0
 MJH  CONST_26  C11  N1   C1   O1   180.00   0.0  0
 MJH  CONST_27  C    C1   N1   C11    0.00   0.0  0
 MJH  CONST_28  C4   N2   C3   C2   180.00   0.0  0
 MJH  CONST_29  H1   N2   C3   C2     0.00   0.0  0
 MJH  CONST_30  O    C3   N2   C4     0.00   0.0  0
 MJH  Var_01    C11  C10  C9   C2    37.28  30.0  1
 MJH  Var_02    C10  C11  N1   C2    21.64  30.0  1
 MJH  Var_03    N1   C11  C10  C9   -35.83  30.0  1
 MJH  Var_04    C7   C6   C5   C4    -5.77  30.0  2
 MJH  Var_05    C    C12  C13  C14   90.55  30.0  2
 MJH  Var_06    C6   C5   C4   N2   -65.15  30.0  3
 MJH  Var_07    C5   C4   N2   C3   132.50  30.0  2

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
 MJH  chir_01  C2  C9  C3   N1  negativ
 MJH  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
 MJH  plan-1  C5   0.020
 MJH  plan-1  C6   0.020
 MJH  plan-1  C7   0.020
 MJH  plan-1  C8   0.020
 MJH  plan-1  N3   0.020
 MJH  plan-1  N4   0.020
 MJH  plan-1  H7   0.020
 MJH  plan-1  H8   0.020
 MJH  plan-1  H26  0.020
 MJH  plan-2  C12  0.020
 MJH  plan-2  C13  0.020
 MJH  plan-2  C14  0.020
 MJH  plan-2  C15  0.020
 MJH  plan-2  C16  0.020
 MJH  plan-2  C17  0.020
 MJH  plan-2  C18  0.020
 MJH  plan-2  H17  0.020
 MJH  plan-2  H18  0.020
 MJH  plan-2  H19  0.020
 MJH  plan-2  H20  0.020
 MJH  plan-2  H21  0.020
 MJH  plan-3  C2   0.020
 MJH  plan-3  O1   0.020
 MJH  plan-3  C11  0.020
 MJH  plan-3  C    0.020
 MJH  plan-3  N1   0.020
 MJH  plan-3  C1   0.020
 MJH  plan-4  N2   0.020
 MJH  plan-4  C2   0.020
 MJH  plan-4  C3   0.020
 MJH  plan-4  C4   0.020
 MJH  plan-4  O    0.020
 MJH  plan-4  H1   0.020

