# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 21:48:28 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)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)NCc3ccc(O)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
 MD8  MD8  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide  ligand  52  27  .  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_MD8
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
 MD8  N    N  NT    0  -0.471  75.1445  -16.7423  93.0641
 MD8  C    C  CR16  0  -0.268  79.1951  -16.8322  95.5216
 MD8  O    O  O     0  -0.496  73.4958  -16.3307  94.5140
 MD8  C1   C  CR16  0  -0.240  78.1377  -15.9577  95.7365
 MD8  C10  C  CH2   0  -0.468  77.1293  -16.4167  91.8980
 MD8  C11  C  CH2   0  -0.480  76.1476  -15.3322  91.4688
 MD8  C12  C  CH1   0  -0.168  75.0565  -15.3877  92.5482
 MD8  C13  C  C     0   0.583  73.6791  -15.1179  91.9562
 MD8  C14  C  CH2   0  -0.394  71.9275  -13.4089  91.6977
 MD8  C15  C  CR6   0   0.099  70.8283  -13.5492  92.7201
 MD8  C16  C  CR16  0  -0.296  70.2585  -12.4349  93.3217
 MD8  C17  C  CR16  0  -0.373  69.2479  -12.5580  94.2674
 MD8  C18  C  CR6   0   0.342  68.7896  -13.8198  94.6295
 MD8  C19  C  CR16  0  -0.327  69.3551  -14.9493  94.0376
 MD8  C2   C  CR16  0  -0.287  76.8534  -16.4490  95.9272
 MD8  C20  C  CR16  0  -0.263  70.3609  -14.8082  93.0988
 MD8  C3   C  CR6   0   0.105  76.6011  -17.8195  95.9043
 MD8  C4   C  CR16  0  -0.307  77.6721  -18.6870  95.6961
 MD8  C5   C  CR16  0  -0.241  78.9583  -18.2005  95.5054
 MD8  C6   C  CH2   0  -0.527  75.2031  -18.3549  96.0345
 MD8  C7   C  CH1   0  -0.204  74.4759  -18.4943  94.6779
 MD8  C8   C  C     0   0.578  74.3297  -17.1083  94.0627
 MD8  C9   C  CH2   0  -0.279  76.2137  -17.5069  92.4323
 MD8  N1   N  NH1   0  -0.622  73.2109  -13.8808  92.1735
 MD8  N2   N  NH2   0  -0.783  73.1498  -19.0745  94.7760
 MD8  O1   O  O     0  -0.501  73.1103  -15.9566  91.2749
 MD8  O2   O  OH1   0  -0.634  67.8101  -14.0090  95.5373
 MD8  H2   H  HCR6  0   0.252  78.3119  -14.8894  95.7568
 MD8  H3   H  HCH2  0   0.254  77.7576  -16.7682  91.0806
 MD8  H4   H  HCH2  0   0.246  77.7784  -16.0575  92.6989
 MD8  H5   H  HCH2  0   0.264  76.5937  -14.3416  91.3988
 MD8  H6   H  HCH2  0   0.249  75.7277  -15.5808  90.4920
 MD8  H7   H  HCH1  0   0.268  75.2739  -14.6712  93.3479
 MD8  H8   H  HCH2  0   0.267  72.0360  -12.3625  91.4095
 MD8  H9   H  HCH2  0   0.261  71.6789  -13.9616  90.7920
 MD8  H10  H  HCR6  0   0.254  70.6036  -11.4430  93.0534
 MD8  H11  H  HCR6  0   0.268  68.8208  -11.6696  94.7194
 MD8  H12  H  HCR6  0   0.260  69.0014  -15.9347  94.3152
 MD8  H13  H  HCR6  0   0.246  76.0365  -15.7563  96.0956
 MD8  H14  H  HCR6  0   0.251  70.7902  -15.6956  92.6520
 MD8  H15  H  HCR6  0   0.248  77.4978  -19.7570  95.6818
 MD8  H16  H  HCR6  0   0.253  79.7761  -18.8916  95.3456
 MD8  H17  H  HCH2  0   0.248  74.6053  -17.7094  96.6834
 MD8  H18  H  HCH2  0   0.255  75.2258  -19.3441  96.4983
 MD8  H19  H  HCH1  0   0.258  75.0696  -19.1474  94.0356
 MD8  H20  H  HCH2  0   0.244  75.8181  -18.1244  91.6206
 MD8  H21  H  HCH2  0   0.262  76.7229  -18.1565  93.1397
 MD8  H22  H  HNH1  0   0.398  73.6990  -13.2939  92.8307
 MD8  H23  H  HNH2  0   0.352  73.2112  -19.9680  95.2484
 MD8  H24  H  HNH2  0   0.343  72.5642  -18.4841  95.3543
 MD8  H26  H  HOH1  0   0.473  67.4991  -13.1618  95.8752
 MD8  H1   H  HCR6  0   0.253  80.1971  -16.4507  95.3727

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
 MD8  O1   C13  double    1.221  0.020  1.221
 MD8  C11  C10  single    1.524  0.020  1.524
 MD8  C11  C12  single    1.536  0.020  1.536
 MD8  C14  N1   single    1.448  0.020  1.448
 MD8  C14  C15  single    1.508  0.020  1.508
 MD8  C10  C9   single    1.521  0.020  1.521
 MD8  C13  N1   single    1.340  0.020  1.340
 MD8  C13  C12  single    1.523  0.020  1.523
 MD8  C12  N    single    1.452  0.020  1.452
 MD8  C9   N    single    1.458  0.020  1.458
 MD8  C15  C20  aromatic  1.395  0.020  1.395
 MD8  C15  C16  aromatic  1.389  0.020  1.389
 MD8  C20  C19  aromatic  1.383  0.020  1.383
 MD8  N    C8   single    1.340  0.020  1.340
 MD8  C16  C17  aromatic  1.390  0.020  1.390
 MD8  C8   O    double    1.226  0.020  1.226
 MD8  C8   C7   single    1.523  0.020  1.523
 MD8  C19  C18  aromatic  1.395  0.020  1.395
 MD8  C17  C18  aromatic  1.390  0.020  1.390
 MD8  C7   N2   single    1.451  0.020  1.451
 MD8  C7   C6   single    1.546  0.020  1.546
 MD8  C18  O2   single    1.349  0.020  1.349
 MD8  C4   C5   aromatic  1.388  0.020  1.388
 MD8  C4   C3   aromatic  1.394  0.020  1.394
 MD8  C5   C    aromatic  1.389  0.020  1.389
 MD8  C6   C3   single    1.503  0.020  1.503
 MD8  C3   C2   aromatic  1.394  0.020  1.394
 MD8  C    C1   aromatic  1.389  0.020  1.389
 MD8  C2   C1   aromatic  1.388  0.020  1.388
 MD8  C    H1   single    0.930  0.020  1.080
 MD8  C1   H2   single    0.930  0.020  1.080
 MD8  C10  H3   single    0.970  0.020  1.090
 MD8  C10  H4   single    0.970  0.020  1.090
 MD8  C11  H5   single    0.970  0.020  1.090
 MD8  C11  H6   single    0.970  0.020  1.090
 MD8  C12  H7   single    0.970  0.020  1.090
 MD8  C14  H8   single    0.970  0.020  1.090
 MD8  C14  H9   single    0.970  0.020  1.090
 MD8  C16  H10  single    0.930  0.020  1.080
 MD8  C17  H11  single    0.930  0.020  1.080
 MD8  C19  H12  single    0.930  0.020  1.080
 MD8  C2   H13  single    0.930  0.020  1.080
 MD8  C20  H14  single    0.930  0.020  1.080
 MD8  C4   H15  single    0.930  0.020  1.080
 MD8  C5   H16  single    0.930  0.020  1.080
 MD8  C6   H17  single    0.970  0.020  1.090
 MD8  C6   H18  single    0.970  0.020  1.090
 MD8  C7   H19  single    0.970  0.020  1.090
 MD8  C9   H20  single    0.970  0.020  1.090
 MD8  C9   H21  single    0.970  0.020  1.090
 MD8  N1   H22  single    0.860  0.020  1.020
 MD8  N2   H23  single    0.890  0.020  1.040
 MD8  N2   H24  single    0.890  0.020  1.040
 MD8  O2   H26  single    0.850  0.020  0.980

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
 MD8  C9   N    C8   128.72  3.000
 MD8  C8   N    C12  118.87  3.000
 MD8  C9   N    C12  112.31  3.000
 MD8  H1   C    C5   120.23  3.000
 MD8  H1   C    C1   120.27  3.000
 MD8  C5   C    C1   119.49  3.000
 MD8  H2   C1   C2   119.70  3.000
 MD8  H2   C1   C    120.11  3.000
 MD8  C2   C1   C    120.18  3.000
 MD8  H4   C10  H3   108.28  3.000
 MD8  H4   C10  C9   109.64  3.000
 MD8  H3   C10  C9   112.31  3.000
 MD8  H4   C10  C11  110.82  3.000
 MD8  H3   C10  C11  112.94  3.000
 MD8  C9   C10  C11  102.78  3.000
 MD8  H6   C11  H5   107.89  3.000
 MD8  H6   C11  C12  110.32  3.000
 MD8  H5   C11  C12  111.67  3.000
 MD8  H6   C11  C10  109.73  3.000
 MD8  H5   C11  C10  113.67  3.000
 MD8  C12  C11  C10  103.53  3.000
 MD8  H7   C12  C13  110.32  3.000
 MD8  H7   C12  C11  110.39  3.000
 MD8  C13  C12  C11  111.27  3.000
 MD8  H7   C12  N    109.80  3.000
 MD8  C13  C12  N    110.99  3.000
 MD8  C11  C12  N    103.91  3.000
 MD8  O1   C13  N1   124.17  3.000
 MD8  N1   C13  C12  114.60  3.000
 MD8  O1   C13  C12  121.09  3.000
 MD8  H9   C14  H8   106.84  3.000
 MD8  H9   C14  N1   108.06  3.000
 MD8  H8   C14  N1   108.14  3.000
 MD8  H9   C14  C15  110.49  3.000
 MD8  H8   C14  C15  109.94  3.000
 MD8  N1   C14  C15  113.15  3.000
 MD8  C20  C15  C16  117.97  3.000
 MD8  C16  C15  C14  121.21  3.000
 MD8  C20  C15  C14  120.81  3.000
 MD8  H10  C16  C17  118.76  3.000
 MD8  H10  C16  C15  119.77  3.000
 MD8  C17  C16  C15  121.47  3.000
 MD8  H11  C17  C18  120.34  3.000
 MD8  H11  C17  C16  119.83  3.000
 MD8  C18  C17  C16  119.83  3.000
 MD8  O2   C18  C19  117.80  3.000
 MD8  O2   C18  C17  122.82  3.000
 MD8  C19  C18  C17  119.38  3.000
 MD8  H12  C19  C20  120.28  3.000
 MD8  H12  C19  C18  119.70  3.000
 MD8  C20  C19  C18  120.01  3.000
 MD8  H13  C2   C3   119.63  3.000
 MD8  H13  C2   C1   119.49  3.000
 MD8  C3   C2   C1   120.88  3.000
 MD8  H14  C20  C19  119.01  3.000
 MD8  H14  C20  C15  119.66  3.000
 MD8  C19  C20  C15  121.32  3.000
 MD8  C6   C3   C4   120.40  3.000
 MD8  C6   C3   C2   121.16  3.000
 MD8  C4   C3   C2   118.38  3.000
 MD8  H15  C4   C5   119.53  3.000
 MD8  H15  C4   C3   119.52  3.000
 MD8  C5   C4   C3   120.95  3.000
 MD8  H16  C5   C4   119.77  3.000
 MD8  H16  C5   C    120.12  3.000
 MD8  C4   C5   C    120.11  3.000
 MD8  H18  C6   H17  107.09  3.000
 MD8  H18  C6   C7   107.50  3.000
 MD8  H17  C6   C7   108.48  3.000
 MD8  H18  C6   C3   109.87  3.000
 MD8  H17  C6   C3   110.47  3.000
 MD8  C7   C6   C3   113.20  3.000
 MD8  H19  C7   N2   107.32  3.000
 MD8  H19  C7   C8   111.03  3.000
 MD8  N2   C7   C8   107.67  3.000
 MD8  H19  C7   C6   108.33  3.000
 MD8  N2   C7   C6   114.00  3.000
 MD8  C8   C7   C6   108.51  3.000
 MD8  C7   C8   O    119.57  3.000
 MD8  C7   C8   N    119.42  3.000
 MD8  O    C8   N    120.97  3.000
 MD8  H21  C9   H20  108.36  3.000
 MD8  H21  C9   C10  112.02  3.000
 MD8  H20  C9   C10  111.21  3.000
 MD8  H21  C9   N    112.01  3.000
 MD8  H20  C9   N    110.63  3.000
 MD8  C10  C9   N    102.58  3.000
 MD8  H22  N1   C14  117.01  3.000
 MD8  H22  N1   C13  118.30  3.000
 MD8  C14  N1   C13  123.86  3.000
 MD8  H24  N2   H23  106.44  3.000
 MD8  H24  N2   C7   109.51  3.000
 MD8  H23  N2   C7   109.21  3.000
 MD8  H26  O2   C18  110.30  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
 MD8  CONST_01  C3   C4   C5   C      0.00   0.0  0
 MD8  CONST_02  C3   C2   C1   C      0.00   0.0  0
 MD8  CONST_03  C4   C5   C    C1     0.00   0.0  0
 MD8  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 MD8  CONST_05  C18  C19  C20  C15    0.00   0.0  0
 MD8  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 MD8  CONST_07  C19  C20  C15  C16    0.00   0.0  0
 MD8  CONST_08  C19  C18  C17  C16    0.00   0.0  0
 MD8  CONST_09  C20  C15  C16  C17    0.00   0.0  0
 MD8  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 MD8  CONST_11  C5   C4   C3   C2     0.00   0.0  0
 MD8  CONST_12  C5   C    C1   C2     0.00   0.0  0
 MD8  CONST_13  C6   C3   C2   C1   180.00   0.0  0
 MD8  CONST_14  C19  C20  C15  C14  180.00   0.0  0
 MD8  CONST_15  C17  C16  C15  C14  180.00   0.0  0
 MD8  CONST_16  O2   C18  C17  C16  180.00   0.0  0
 MD8  CONST_17  O2   C18  C19  C20  180.00   0.0  0
 MD8  CONST_18  C6   C3   C4   C5   180.00   0.0  0
 MD8  CONST_19  H15  C4   C5   C    180.00   0.0  0
 MD8  CONST_20  H13  C2   C1   C    180.00   0.0  0
 MD8  CONST_21  H16  C5   C    C1   180.00   0.0  0
 MD8  CONST_22  H12  C19  C20  C15  180.00   0.0  0
 MD8  CONST_23  H11  C17  C16  C15  180.00   0.0  0
 MD8  CONST_24  H14  C20  C15  C16  180.00   0.0  0
 MD8  CONST_25  H10  C16  C17  C18  180.00   0.0  0
 MD8  CONST_26  H1   C    C1   C2   180.00   0.0  0
 MD8  CONST_27  H2   C1   C2   C3   180.00   0.0  0
 MD8  CONST_28  C12  N    C8   O      0.00   0.0  0
 MD8  CONST_29  C9   N    C8   O    180.00   0.0  0
 MD8  CONST_30  C7   C8   N    C12  180.00   0.0  0
 MD8  CONST_31  C9   N    C8   C7     0.00   0.0  0
 MD8  CONST_32  C14  N1   C13  C12  180.00   0.0  0
 MD8  CONST_33  H22  N1   C13  C12    0.00   0.0  0
 MD8  CONST_34  O1   C13  N1   C14    0.00   0.0  0
 MD8  Var_01    C11  C10  C9   N    -35.88  30.0  1
 MD8  Var_02    C12  N    C9   C10   21.57  30.0  1
 MD8  Var_03    C9   C10  C11  C12   37.49  30.0  1
 MD8  Var_04    N1   C14  C15  C16  110.80  30.0  2
 MD8  Var_05    C7   C6   C3   C2    88.87  30.0  2
 MD8  Var_06    C15  C14  N1   C13   94.49  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
 MD8  chir_01  C12  C11  C13  N   negativ
 MD8  chir_02  C7   N2   C6   C8  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
 MD8  plan-1  C14  0.020
 MD8  plan-1  C15  0.020
 MD8  plan-1  C16  0.020
 MD8  plan-1  C17  0.020
 MD8  plan-1  C18  0.020
 MD8  plan-1  C19  0.020
 MD8  plan-1  C20  0.020
 MD8  plan-1  O2   0.020
 MD8  plan-1  H10  0.020
 MD8  plan-1  H11  0.020
 MD8  plan-1  H12  0.020
 MD8  plan-1  H14  0.020
 MD8  plan-2  C    0.020
 MD8  plan-2  C1   0.020
 MD8  plan-2  C2   0.020
 MD8  plan-2  C3   0.020
 MD8  plan-2  C4   0.020
 MD8  plan-2  C5   0.020
 MD8  plan-2  C6   0.020
 MD8  plan-2  H2   0.020
 MD8  plan-2  H13  0.020
 MD8  plan-2  H15  0.020
 MD8  plan-2  H16  0.020
 MD8  plan-2  H1   0.020
 MD8  plan-3  N    0.020
 MD8  plan-3  O    0.020
 MD8  plan-3  C12  0.020
 MD8  plan-3  C7   0.020
 MD8  plan-3  C8   0.020
 MD8  plan-3  C9   0.020
 MD8  plan-4  C12  0.020
 MD8  plan-4  C13  0.020
 MD8  plan-4  C14  0.020
 MD8  plan-4  N1   0.020
 MD8  plan-4  O1   0.020
 MD8  plan-4  H22  0.020

