# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:56:59 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: D-phenylalanyl-N-[(4-chloropyridin-3-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cnccc3Cl
#
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
 P97  P97  D-phenylalanyl-N-[(4-chloropyridin-3-yl)methyl]-L-prolinamide  peptide  50  27  .  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_P97
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
 P97  N4    N   NH2   0  -0.760   3.6608  -1.7579  -1.2537
 P97  C3    C   CH1   0  -0.214   3.1833  -0.6483  -0.4666
 P97  C5    C   C     0   0.527   1.7364  -0.8107   0.0060
 P97  O7    O   O     0  -0.497   1.2349  -1.9211   0.1362
 P97  C2    C   CH2   0  -0.534   4.0652  -0.4625   0.7828
 P97  C1    C   CR6   0   0.161   5.4750  -0.0801   0.4399
 P97  C8    C   CR16  0  -0.314   5.8230   1.2613   0.2978
 P97  C12   C   CR16  0  -0.297   6.4568  -1.0462   0.2347
 P97  C9    C   CR16  0  -0.242   7.1184   1.6318  -0.0385
 P97  C11   C   CR16  0  -0.245   7.7547  -0.6815  -0.0972
 P97  C10   C   CR16  0  -0.273   8.0899   0.6595  -0.2368
 P97  N6    N   NT    0  -0.457   1.0569   0.3023   0.3323
 P97  C13   C   CH1   0  -0.223  -0.2956   0.1910   0.8344
 P97  C14   C   C     0   0.584  -1.2345  -0.3095  -0.2600
 P97  O15   O   O     0  -0.482  -1.0175  -0.1040  -1.4411
 P97  C19   C   CH2   0  -0.466  -0.6396   1.6293   1.2424
 P97  C20   C   CH2   0  -0.472   0.1726   2.4750   0.2693
 P97  C21   C   CH2   0  -0.277   1.4685   1.6866   0.1133
 P97  N16   N   NH1   0  -0.630  -2.3291  -0.9344   0.2075
 P97  C17   C   CH2   0  -0.365  -3.4138  -1.4053  -0.6207
 P97  C18   C   CR6   0   0.072  -4.7376  -0.8655  -0.1588
 P97  C22   C   CR16  0  -0.098  -5.6878  -1.7117   0.4037
 P97  N23   N   N     0  -0.400  -6.8761  -1.3258   0.8468
 P97  C24   C   CR16  0  -0.062  -7.1791  -0.0388   0.7484
 P97  C25   C   CR16  0  -0.292  -6.3221   0.9082   0.2087
 P97  C26   C   CR6   0   0.025  -5.0888   0.4773  -0.2458
 P97  CL27  CL  CL    0  -0.086  -3.9981   1.6197  -0.9375
 P97  HN4   H   HNH2  0   0.339   3.4948  -2.6258  -0.7584
 P97  HN4A  H   HNH2  0   0.350   3.1320  -1.8222  -2.1147
 P97  H3    H   HCH1  0   0.264   3.2667   0.2510  -1.0831
 P97  H2    H   HCH2  0   0.260   4.0504  -1.3944   1.3559
 P97  H2A   H   HCH2  0   0.262   3.6263   0.3006   1.4293
 P97  H8    H   HCR6  0   0.240   5.0722   2.0281   0.4564
 P97  H12   H   HCR6  0   0.240   6.2046  -2.0937   0.3425
 P97  H9    H   HCR6  0   0.252   7.3695   2.6799  -0.1412
 P97  H11   H   HCR6  0   0.251   8.5063  -1.4462  -0.2468
 P97  H10   H   HCR6  0   0.253   9.1016   0.9448  -0.4946
 P97  H13   H   HCH1  0   0.285  -0.3340  -0.4828   1.6941
 P97  H19   H   HCH2  0   0.256  -1.7096   1.8309   1.2090
 P97  H19A  H   HCH2  0   0.260  -0.3045   1.7963   2.2676
 P97  H20   H   HCH2  0   0.246  -0.3387   2.5501  -0.6909
 P97  H20A  H   HCH2  0   0.258   0.3527   3.4856   0.6323
 P97  H21   H   HCH2  0   0.239   2.2075   1.9954   0.8586
 P97  H21A  H   HCH2  0   0.260   1.9097   1.8251  -0.8735
 P97  HN16  H   HNH1  0   0.403  -2.3960  -1.1132   1.1970
 P97  H17   H   HCH2  0   0.278  -3.2139  -1.1059  -1.6487
 P97  H17A  H   HCH2  0   0.275  -3.4508  -2.4969  -0.6070
 P97  H22   H   HCR6  0   0.272  -5.4569  -2.7687   0.4934
 P97  H24   H   HCR6  0   0.278  -8.1520   0.2669   1.1148
 P97  H25   H   HCR6  0   0.297  -6.6155   1.9467   0.1484

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
 P97  C1   C2    single    1.500  0.020  1.500
 P97  C1   C8    aromatic  1.393  0.020  1.393
 P97  C1   C12   aromatic  1.393  0.020  1.393
 P97  C2   C3    single    1.541  0.020  1.541
 P97  C3   N4    single    1.442  0.020  1.442
 P97  C3   C5    single    1.531  0.020  1.531
 P97  C5   N6    single    1.344  0.020  1.344
 P97  C5   O7    double    1.225  0.020  1.225
 P97  N6   C13   single    1.447  0.020  1.447
 P97  N6   C21   single    1.461  0.020  1.461
 P97  C8   C9    aromatic  1.389  0.020  1.389
 P97  C9   C10   aromatic  1.389  0.020  1.389
 P97  C10  C11   aromatic  1.389  0.020  1.389
 P97  C11  C12   aromatic  1.388  0.020  1.388
 P97  C13  C14   single    1.526  0.020  1.526
 P97  C13  C19   single    1.534  0.020  1.534
 P97  C14  O15   double    1.218  0.020  1.218
 P97  C14  N16   single    1.344  0.020  1.344
 P97  N16  C17   single    1.444  0.020  1.444
 P97  C17  C18   single    1.502  0.020  1.502
 P97  C18  C22   aromatic  1.391  0.020  1.391
 P97  C18  C26   aromatic  1.391  0.020  1.391
 P97  C19  C20   single    1.524  0.020  1.524
 P97  C20  C21   single    1.525  0.020  1.525
 P97  C22  N23   aromatic  1.326  0.020  1.326
 P97  N23  C24   aromatic  1.326  0.020  1.326
 P97  C24  C25   aromatic  1.387  0.020  1.387
 P97  C25  C26   aromatic  1.383  0.020  1.383
 P97  C26  CL27  single    1.724  0.020  1.724
 P97  C2   H2    single    0.970  0.020  1.090
 P97  C2   H2A   single    0.970  0.020  1.090
 P97  C3   H3    single    0.970  0.020  1.090
 P97  N4   HN4   single    0.890  0.020  1.040
 P97  N4   HN4A  single    0.890  0.020  1.040
 P97  C8   H8    single    0.930  0.020  1.080
 P97  C9   H9    single    0.930  0.020  1.080
 P97  C10  H10   single    0.930  0.020  1.080
 P97  C11  H11   single    0.930  0.020  1.080
 P97  C12  H12   single    0.930  0.020  1.080
 P97  C13  H13   single    0.970  0.020  1.090
 P97  N16  HN16  single    0.860  0.020  1.020
 P97  C17  H17   single    0.970  0.020  1.090
 P97  C17  H17A  single    0.970  0.020  1.090
 P97  C19  H19   single    0.970  0.020  1.090
 P97  C19  H19A  single    0.970  0.020  1.090
 P97  C20  H20   single    0.970  0.020  1.090
 P97  C20  H20A  single    0.970  0.020  1.090
 P97  C21  H21   single    0.970  0.020  1.090
 P97  C21  H21A  single    0.970  0.020  1.090
 P97  C22  H22   single    0.930  0.020  1.080
 P97  C24  H24   single    0.930  0.020  1.080
 P97  C25  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
 P97  HN4A  N4   HN4  106.02  3.000
 P97  HN4A  N4   C3   109.88  3.000
 P97  HN4   N4   C3   109.76  3.000
 P97  H3    C3   C2   108.32  3.000
 P97  H3    C3   C5   109.48  3.000
 P97  C2    C3   C5   107.67  3.000
 P97  H3    C3   N4   107.45  3.000
 P97  C5    C3   N4   113.57  3.000
 P97  C2    C3   N4   110.24  3.000
 P97  N6    C5   O7   121.17  3.000
 P97  O7    C5   C3   121.05  3.000
 P97  N6    C5   C3   117.70  3.000
 P97  H2A   C2   H2   106.24  3.000
 P97  H2A   C2   C1   109.56  3.000
 P97  H2    C2   C1   110.46  3.000
 P97  H2A   C2   C3   109.53  3.000
 P97  H2    C2   C3   108.32  3.000
 P97  C1    C2   C3   112.54  3.000
 P97  C12   C1   C8   118.48  3.000
 P97  C12   C1   C2   121.28  3.000
 P97  C8    C1   C2   120.22  3.000
 P97  H8    C8   C9   119.50  3.000
 P97  H8    C8   C1   119.53  3.000
 P97  C9    C8   C1   120.97  3.000
 P97  H12   C12  C11  119.71  3.000
 P97  H12   C12  C1   119.49  3.000
 P97  C11   C12  C1   120.80  3.000
 P97  H9    C9   C10  120.14  3.000
 P97  H9    C9   C8   119.84  3.000
 P97  C10   C9   C8   120.02  3.000
 P97  H11   C11  C10  120.03  3.000
 P97  H11   C11  C12  119.77  3.000
 P97  C10   C11  C12  120.20  3.000
 P97  H10   C10  C11  120.26  3.000
 P97  H10   C10  C9   120.22  3.000
 P97  C11   C10  C9   119.52  3.000
 P97  C21   N6   C13  112.85  3.000
 P97  C21   N6   C5   127.29  3.000
 P97  C13   N6   C5   119.54  3.000
 P97  H13   C13  C19  111.16  3.000
 P97  H13   C13  C14  109.89  3.000
 P97  C19   C13  C14  111.11  3.000
 P97  H13   C13  N6   110.68  3.000
 P97  C19   C13  N6   103.28  3.000
 P97  C14   C13  N6   110.57  3.000
 P97  N16   C14  O15  124.09  3.000
 P97  N16   C14  C13  113.83  3.000
 P97  O15   C14  C13  122.02  3.000
 P97  H19A  C19  H19  107.59  3.000
 P97  H19A  C19  C20  110.57  3.000
 P97  H19   C19  C20  113.65  3.000
 P97  H19A  C19  C13  108.93  3.000
 P97  H19   C19  C13  112.68  3.000
 P97  C20   C19  C13  103.35  3.000
 P97  H20A  C20  H20  107.89  3.000
 P97  H20A  C20  C21  111.93  3.000
 P97  H20   C20  C21  110.12  3.000
 P97  H20A  C20  C19  112.98  3.000
 P97  H20   C20  C19  110.52  3.000
 P97  C21   C20  C19  103.38  3.000
 P97  H21A  C21  H21  107.91  3.000
 P97  H21A  C21  C20  111.78  3.000
 P97  H21   C21  C20  111.00  3.000
 P97  H21A  C21  N6   111.74  3.000
 P97  H21   C21  N6   110.83  3.000
 P97  C20   C21  N6   103.60  3.000
 P97  HN16  N16  C17  117.10  3.000
 P97  HN16  N16  C14  118.55  3.000
 P97  C17   N16  C14  124.33  3.000
 P97  H17A  C17  H17  107.02  3.000
 P97  H17A  C17  C18  108.98  3.000
 P97  H17   C17  C18  110.68  3.000
 P97  H17A  C17  N16  110.14  3.000
 P97  H17   C17  N16  108.30  3.000
 P97  C18   C17  N16  111.62  3.000
 P97  C26   C18  C22  116.11  3.000
 P97  C26   C18  C17  123.38  3.000
 P97  C22   C18  C17  120.51  3.000
 P97  H22   C22  N23  116.51  3.000
 P97  H22   C22  C18  118.71  3.000
 P97  N23   C22  C18  124.78  3.000
 P97  C24   N23  C22  117.55  3.000
 P97  H24   C24  C25  119.59  3.000
 P97  H24   C24  N23  117.00  3.000
 P97  C25   C24  N23  123.41  3.000
 P97  H25   C25  C26  121.54  3.000
 P97  H25   C25  C24  120.67  3.000
 P97  C26   C25  C24  117.78  3.000
 P97  CL27  C26  C25  119.30  3.000
 P97  CL27  C26  C18  120.34  3.000
 P97  C25   C26  C18  120.36  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
 P97  CONST_01  C10   C9   C8   C1      0.00   0.0  0
 P97  CONST_02  C10   C11  C12  C1      0.00   0.0  0
 P97  CONST_03  C11   C12  C1   C8      0.00   0.0  0
 P97  CONST_04  C11   C10  C9   C8      0.00   0.0  0
 P97  CONST_05  C9    C8   C1   C12     0.00   0.0  0
 P97  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 P97  CONST_07  C24   N23  C22  C18     0.00   0.0  0
 P97  CONST_08  C24   C25  C26  C18     0.00   0.0  0
 P97  CONST_09  C25   C26  C18  C22     0.00   0.0  0
 P97  CONST_10  C25   C24  N23  C22     0.00   0.0  0
 P97  CONST_11  C26   C18  C22  N23     0.00   0.0  0
 P97  CONST_12  C26   C25  C24  N23     0.00   0.0  0
 P97  CONST_13  C9    C8   C1   C2    180.00   0.0  0
 P97  CONST_14  C11   C12  C1   C2    180.00   0.0  0
 P97  CONST_15  N23   C22  C18  C17   180.00   0.0  0
 P97  CONST_16  C25   C26  C18  C17   180.00   0.0  0
 P97  CONST_17  CL27  C26  C18  C22   180.00   0.0  0
 P97  CONST_18  CL27  C26  C25  C24   180.00   0.0  0
 P97  CONST_19  H9    C9   C8   C1    180.00   0.0  0
 P97  CONST_20  H11   C11  C12  C1    180.00   0.0  0
 P97  CONST_21  H12   C12  C1   C8    180.00   0.0  0
 P97  CONST_22  H10   C10  C9   C8    180.00   0.0  0
 P97  CONST_23  H8    C8   C1   C12   180.00   0.0  0
 P97  CONST_24  H25   C25  C26  C18   180.00   0.0  0
 P97  CONST_25  H24   C24  N23  C22   180.00   0.0  0
 P97  CONST_26  H22   C22  N23  C24   180.00   0.0  0
 P97  CONST_27  C13   N6   C5   C3    180.00   0.0  0
 P97  CONST_28  C21   N6   C5   C3      0.00   0.0  0
 P97  CONST_29  C13   N6   C5   O7      0.00   0.0  0
 P97  CONST_30  C21   N6   C5   O7    180.00   0.0  0
 P97  CONST_31  C17   N16  C14  C13   180.00   0.0  0
 P97  CONST_32  HN16  N16  C14  C13     0.00   0.0  0
 P97  CONST_33  C17   N16  C14  O15     0.00   0.0  0
 P97  Var_01    C19   C20  C21  N6     29.08  30.0  1
 P97  Var_02    C20   C21  N6   C13   -10.25  30.0  1
 P97  Var_03    C21   C20  C19  C13   -37.00  30.0  1
 P97  Var_04    C8    C1   C2   C3     88.81  30.0  2
 P97  Var_05    C22   C18  C17  N16  -111.43  30.0  2
 P97  Var_06    C18   C17  N16  C14  -125.85  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
 P97  chir_01  C3   C2  N4   C5   negativ
 P97  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
 P97  plan-1  C2    0.020
 P97  plan-1  C1    0.020
 P97  plan-1  C8    0.020
 P97  plan-1  C12   0.020
 P97  plan-1  C9    0.020
 P97  plan-1  C11   0.020
 P97  plan-1  C10   0.020
 P97  plan-1  H8    0.020
 P97  plan-1  H12   0.020
 P97  plan-1  H9    0.020
 P97  plan-1  H11   0.020
 P97  plan-1  H10   0.020
 P97  plan-2  C17   0.020
 P97  plan-2  C18   0.020
 P97  plan-2  C22   0.020
 P97  plan-2  N23   0.020
 P97  plan-2  C24   0.020
 P97  plan-2  C25   0.020
 P97  plan-2  C26   0.020
 P97  plan-2  CL27  0.020
 P97  plan-2  H22   0.020
 P97  plan-2  H24   0.020
 P97  plan-2  H25   0.020
 P97  plan-3  C13   0.020
 P97  plan-3  C14   0.020
 P97  plan-3  O15   0.020
 P97  plan-3  N16   0.020
 P97  plan-3  C17   0.020
 P97  plan-3  HN16  0.020
 P97  plan-4  C3    0.020
 P97  plan-4  C5    0.020
 P97  plan-4  O7    0.020
 P97  plan-4  N6    0.020
 P97  plan-4  C13   0.020
 P97  plan-4  C21   0.020

