# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:12:29 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cccnc3
#
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
 99P  99P  D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide  peptide  50  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_99P
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
 99P  N4   N  NH2   0  -0.781   3.0287   1.6398   1.2246
 99P  C3   C  CH1   0  -0.220   2.6659   0.4748   0.4501
 99P  C5   C  C     0   0.563   1.2255   0.6181  -0.0175
 99P  O7   O  O     0  -0.500   0.7639   1.7175  -0.2981
 99P  C2   C  CH2   0  -0.540   3.5284   0.2269  -0.8143
 99P  C1   C  CR6   0   0.138   4.9750   0.0258  -0.4727
 99P  C8   C  CR16  0  -0.319   5.8677   1.0959  -0.4654
 99P  C12  C  CR16  0  -0.304   5.4458  -1.2347  -0.1080
 99P  C9   C  CR16  0  -0.241   7.1972   0.9119  -0.1067
 99P  C11  C  CR16  0  -0.240   6.7729  -1.4235   0.2507
 99P  C10  C  CR16  0  -0.270   7.6538  -0.3487   0.2529
 99P  N6   N  NT    0  -0.462   0.5129  -0.5059  -0.1965
 99P  C13  C  CH1   0  -0.219  -0.8150  -0.4239  -0.7653
 99P  C14  C  C     0   0.580  -1.7823   0.2370   0.2109
 99P  O15  O  O     0  -0.491  -1.6547   0.1255   1.4198
 99P  C19  C  CH2   0  -0.469  -1.1891  -1.8938  -0.9984
 99P  C20  C  CH2   0  -0.474  -0.4313  -2.6353   0.0970
 99P  C21  C  CH2   0  -0.277   0.8758  -1.8592   0.2170
 99P  N16  N  NH1   0  -0.625  -2.7973   0.8885  -0.3789
 99P  C17  C  CH2   0  -0.388  -3.9029   1.4833   0.3369
 99P  C18  C  CR6   0   0.033  -5.1439   0.6328   0.2898
 99P  C22  C  CR16  0  -0.105  -6.2954   1.0874  -0.3400
 99P  N23  N  N     0  -0.401  -7.4218   0.3884  -0.4274
 99P  C24  C  CR16  0  -0.069  -7.4439  -0.8193   0.1200
 99P  C25  C  CR16  0  -0.317  -6.3518  -1.3761   0.7732
 99P  C26  C  CR16  0  -0.179  -5.1846  -0.6372   0.8578
 99P  H4   H  HNH2  0   0.356   3.9703   1.5308   1.5794
 99P  H5   H  HNH2  0   0.342   3.0362   2.4641   0.6364
 99P  H3   H  HCH1  0   0.266   2.7702  -0.3940   1.1042
 99P  H1   H  HCH2  0   0.258   3.1507  -0.6470  -1.3517
 99P  H2   H  HCH2  0   0.260   3.4130   1.0839  -1.4834
 99P  H7   H  HCR6  0   0.250   5.5221   2.0817  -0.7542
 99P  H11  H  HCR6  0   0.244   4.7665  -2.0799  -0.1103
 99P  H8   H  HCR6  0   0.255   7.8770   1.7541  -0.1101
 99P  H10  H  HCR6  0   0.255   7.1213  -2.4108   0.5256
 99P  H9   H  HCR6  0   0.255   8.6900  -0.4948   0.5291
 99P  H12  H  HCH1  0   0.286  -0.7975   0.1330  -1.7051
 99P  H16  H  HCH2  0   0.261  -2.2658  -2.0623  -0.9746
 99P  H17  H  HCH2  0   0.262  -0.8315  -2.1972  -1.9839
 99P  H18  H  HCH2  0   0.248  -0.9818  -2.5998   1.0374
 99P  H19  H  HCH2  0   0.259  -0.2589  -3.6823  -0.1472
 99P  H20  H  HCH2  0   0.242   1.6407  -2.2762  -0.4438
 99P  H21  H  HCH2  0   0.261   1.2649  -1.8747   1.2348
 99P  H13  H  HNH1  0   0.405  -2.8290   0.9240  -1.3854
 99P  H14  H  HCH2  0   0.274  -3.5933   1.6482   1.3683
 99P  H15  H  HCH2  0   0.275  -4.1115   2.4636  -0.0936
 99P  H22  H  HCR6  0   0.260  -6.3026   2.0721  -0.7991
 99P  H23  H  HCR6  0   0.265  -8.3721  -1.3744   0.0383
 99P  H24  H  HCR6  0   0.272  -6.4222  -2.3643   1.2065
 99P  H25  H  HCR6  0   0.268  -4.3179  -1.0407   1.3672

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
 99P  O15  C14  double    1.221  0.020  1.221
 99P  C19  C20  single    1.524  0.020  1.524
 99P  C19  C13  single    1.535  0.020  1.535
 99P  C17  N16  single    1.445  0.020  1.445
 99P  C17  C18  single    1.505  0.020  1.505
 99P  C20  C21  single    1.525  0.020  1.525
 99P  C14  N16  single    1.343  0.020  1.343
 99P  C14  C13  single    1.525  0.020  1.525
 99P  C21  N6   single    1.461  0.020  1.461
 99P  C13  N6   single    1.447  0.020  1.447
 99P  C18  C26  aromatic  1.392  0.020  1.392
 99P  C18  C22  aromatic  1.389  0.020  1.389
 99P  C26  C25  aromatic  1.384  0.020  1.384
 99P  N6   C5   single    1.343  0.020  1.343
 99P  C22  N23  aromatic  1.329  0.020  1.329
 99P  C25  C24  aromatic  1.389  0.020  1.389
 99P  C5   O7   double    1.225  0.020  1.225
 99P  C5   C3   single    1.521  0.020  1.521
 99P  N23  C24  aromatic  1.326  0.020  1.326
 99P  N4   C3   single    1.445  0.020  1.445
 99P  C3   C2   single    1.550  0.020  1.550
 99P  C8   C9   aromatic  1.389  0.020  1.389
 99P  C8   C1   aromatic  1.394  0.020  1.394
 99P  C9   C10  aromatic  1.388  0.020  1.388
 99P  C2   C1   single    1.500  0.020  1.500
 99P  C1   C12  aromatic  1.394  0.020  1.394
 99P  C10  C11  aromatic  1.390  0.020  1.390
 99P  C12  C11  aromatic  1.388  0.020  1.388
 99P  C2   H1   single    0.970  0.020  1.090
 99P  C2   H2   single    0.970  0.020  1.090
 99P  C3   H3   single    0.970  0.020  1.090
 99P  N4   H4   single    0.890  0.020  1.040
 99P  N4   H5   single    0.890  0.020  1.040
 99P  C8   H7   single    0.930  0.020  1.080
 99P  C9   H8   single    0.930  0.020  1.080
 99P  C10  H9   single    0.930  0.020  1.080
 99P  C11  H10  single    0.930  0.020  1.080
 99P  C12  H11  single    0.930  0.020  1.080
 99P  C13  H12  single    0.970  0.020  1.090
 99P  N16  H13  single    0.860  0.020  1.020
 99P  C17  H14  single    0.970  0.020  1.090
 99P  C17  H15  single    0.970  0.020  1.090
 99P  C19  H16  single    0.970  0.020  1.090
 99P  C19  H17  single    0.970  0.020  1.090
 99P  C20  H18  single    0.970  0.020  1.090
 99P  C20  H19  single    0.970  0.020  1.090
 99P  C21  H20  single    0.970  0.020  1.090
 99P  C21  H21  single    0.970  0.020  1.090
 99P  C22  H22  single    0.930  0.020  1.080
 99P  C24  H23  single    0.930  0.020  1.080
 99P  C25  H24  single    0.930  0.020  1.080
 99P  C26  H25  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
 99P  H5   N4   H4   106.52  3.000
 99P  H5   N4   C3   110.28  3.000
 99P  H4   N4   C3   109.55  3.000
 99P  H3   C3   C2   107.94  3.000
 99P  H3   C3   C5   110.45  3.000
 99P  C2   C3   C5   106.93  3.000
 99P  H3   C3   N4   107.23  3.000
 99P  C2   C3   N4   115.23  3.000
 99P  C5   C3   N4   109.06  3.000
 99P  N6   C5   O7   121.38  3.000
 99P  O7   C5   C3   120.78  3.000
 99P  N6   C5   C3   117.69  3.000
 99P  H2   C2   H1   106.82  3.000
 99P  H2   C2   C1   110.26  3.000
 99P  H1   C2   C1   109.75  3.000
 99P  H2   C2   C3   108.36  3.000
 99P  H1   C2   C3   109.67  3.000
 99P  C1   C2   C3   111.85  3.000
 99P  C12  C1   C8   118.46  3.000
 99P  C12  C1   C2   120.43  3.000
 99P  C8   C1   C2   121.07  3.000
 99P  H7   C8   C9   119.63  3.000
 99P  H7   C8   C1   119.53  3.000
 99P  C9   C8   C1   120.84  3.000
 99P  H11  C12  C11  119.58  3.000
 99P  H11  C12  C1   119.51  3.000
 99P  C11  C12  C1   120.91  3.000
 99P  H8   C9   C10  120.05  3.000
 99P  H8   C9   C8   119.82  3.000
 99P  C10  C9   C8   120.13  3.000
 99P  H10  C11  C10  120.06  3.000
 99P  H10  C11  C12  119.84  3.000
 99P  C10  C11  C12  120.09  3.000
 99P  H9   C10  C11  120.19  3.000
 99P  H9   C10  C9   120.24  3.000
 99P  C11  C10  C9   119.57  3.000
 99P  C21  N6   C13  113.06  3.000
 99P  C13  N6   C5   119.47  3.000
 99P  C21  N6   C5   127.29  3.000
 99P  H12  C13  C19  111.19  3.000
 99P  H12  C13  C14  109.87  3.000
 99P  C19  C13  C14  110.96  3.000
 99P  H12  C13  N6   110.63  3.000
 99P  C14  C13  N6   110.80  3.000
 99P  C19  C13  N6   103.25  3.000
 99P  N16  C14  O15  123.95  3.000
 99P  N16  C14  C13  114.12  3.000
 99P  O15  C14  C13  121.87  3.000
 99P  H17  C19  H16  107.49  3.000
 99P  H17  C19  C20  110.54  3.000
 99P  H16  C19  C20  113.58  3.000
 99P  H17  C19  C13  108.88  3.000
 99P  H16  C19  C13  112.67  3.000
 99P  C20  C19  C13  103.62  3.000
 99P  H19  C20  H18  107.74  3.000
 99P  H19  C20  C21  111.79  3.000
 99P  H18  C20  C21  110.39  3.000
 99P  H19  C20  C19  112.66  3.000
 99P  H18  C20  C19  110.67  3.000
 99P  C21  C20  C19  103.60  3.000
 99P  H21  C21  H20  108.01  3.000
 99P  H21  C21  C20  111.86  3.000
 99P  H20  C21  C20  110.98  3.000
 99P  H21  C21  N6   111.48  3.000
 99P  H20  C21  N6   110.86  3.000
 99P  C20  C21  N6   103.67  3.000
 99P  H13  N16  C17  117.14  3.000
 99P  H13  N16  C14  118.67  3.000
 99P  C17  N16  C14  124.09  3.000
 99P  H15  C17  H14  106.97  3.000
 99P  H15  C17  C18  109.74  3.000
 99P  H14  C17  C18  110.45  3.000
 99P  H15  C17  N16  108.71  3.000
 99P  H14  C17  N16  108.29  3.000
 99P  C18  C17  N16  112.50  3.000
 99P  C26  C18  C22  117.35  3.000
 99P  C22  C18  C17  120.85  3.000
 99P  C26  C18  C17  121.80  3.000
 99P  H22  C22  N23  116.32  3.000
 99P  H22  C22  C18  119.58  3.000
 99P  N23  C22  C18  124.09  3.000
 99P  C24  N23  C22  117.78  3.000
 99P  H23  C24  C25  120.21  3.000
 99P  H23  C24  N23  116.69  3.000
 99P  C25  C24  N23  123.10  3.000
 99P  H24  C25  C26  121.21  3.000
 99P  H24  C25  C24  120.24  3.000
 99P  C26  C25  C24  118.55  3.000
 99P  H25  C26  C25  120.32  3.000
 99P  H25  C26  C18  120.55  3.000
 99P  C25  C26  C18  119.13  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
 99P  CONST_01  C10  C9   C8   C1      0.00   0.0  0
 99P  CONST_02  C10  C11  C12  C1      0.00   0.0  0
 99P  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 99P  CONST_04  C11  C12  C1   C8      0.00   0.0  0
 99P  CONST_05  C9   C8   C1   C12     0.00   0.0  0
 99P  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 99P  CONST_07  C24  C25  C26  C18     0.00   0.0  0
 99P  CONST_08  C24  N23  C22  C18     0.00   0.0  0
 99P  CONST_09  C25  C26  C18  C22     0.00   0.0  0
 99P  CONST_10  C25  C24  N23  C22     0.00   0.0  0
 99P  CONST_11  C26  C18  C22  N23     0.00   0.0  0
 99P  CONST_12  C26  C25  C24  N23     0.00   0.0  0
 99P  CONST_13  C9   C8   C1   C2    180.00   0.0  0
 99P  CONST_14  C11  C12  C1   C2    180.00   0.0  0
 99P  CONST_15  C25  C26  C18  C17   180.00   0.0  0
 99P  CONST_16  N23  C22  C18  C17   180.00   0.0  0
 99P  CONST_17  H8   C9   C8   C1    180.00   0.0  0
 99P  CONST_18  H10  C11  C12  C1    180.00   0.0  0
 99P  CONST_19  H9   C10  C9   C8    180.00   0.0  0
 99P  CONST_20  H11  C12  C1   C8    180.00   0.0  0
 99P  CONST_21  H7   C8   C1   C12   180.00   0.0  0
 99P  CONST_22  H24  C25  C26  C18   180.00   0.0  0
 99P  CONST_23  H25  C26  C18  C22   180.00   0.0  0
 99P  CONST_24  H23  C24  N23  C22   180.00   0.0  0
 99P  CONST_25  H22  C22  N23  C24   180.00   0.0  0
 99P  CONST_26  C21  N6   C5   C3      0.00   0.0  0
 99P  CONST_27  C13  N6   C5   C3    180.00   0.0  0
 99P  CONST_28  C21  N6   C5   O7    180.00   0.0  0
 99P  CONST_29  C13  N6   C5   O7      0.00   0.0  0
 99P  CONST_30  C17  N16  C14  C13   180.00   0.0  0
 99P  CONST_31  H13  N16  C14  C13     0.00   0.0  0
 99P  CONST_32  C17  N16  C14  O15     0.00   0.0  0
 99P  Var_01    C19  C20  C21  N6     28.12  30.0  1
 99P  Var_02    C21  C20  C19  C13   -36.05  30.0  1
 99P  Var_03    C20  C21  N6   C13    -9.67  30.0  1
 99P  Var_04    C8   C1   C2   C3    -92.68  30.0  2
 99P  Var_05    C26  C18  C17  N16    63.30  30.0  2
 99P  Var_06    C18  C17  N16  C14  -101.18  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
 99P  chir_01  C3   C5  N4   C2   positiv
 99P  chir_02  C13  N6  C14  C19  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
 99P  plan-1  C2   0.020
 99P  plan-1  C1   0.020
 99P  plan-1  C8   0.020
 99P  plan-1  C12  0.020
 99P  plan-1  C9   0.020
 99P  plan-1  C11  0.020
 99P  plan-1  C10  0.020
 99P  plan-1  H7   0.020
 99P  plan-1  H11  0.020
 99P  plan-1  H8   0.020
 99P  plan-1  H10  0.020
 99P  plan-1  H9   0.020
 99P  plan-2  C17  0.020
 99P  plan-2  C18  0.020
 99P  plan-2  C22  0.020
 99P  plan-2  N23  0.020
 99P  plan-2  C24  0.020
 99P  plan-2  C25  0.020
 99P  plan-2  C26  0.020
 99P  plan-2  H22  0.020
 99P  plan-2  H23  0.020
 99P  plan-2  H24  0.020
 99P  plan-2  H25  0.020
 99P  plan-3  C13  0.020
 99P  plan-3  C14  0.020
 99P  plan-3  O15  0.020
 99P  plan-3  N16  0.020
 99P  plan-3  C17  0.020
 99P  plan-3  H13  0.020
 99P  plan-4  C3   0.020
 99P  plan-4  C5   0.020
 99P  plan-4  O7   0.020
 99P  plan-4  N6   0.020
 99P  plan-4  C13  0.020
 99P  plan-4  C21  0.020

