# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:21:19 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: D-phenylalanyl-N-[2-(pyridin-4-ylamino)ethyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCCNc3ccncc3
#
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
 PPX  PPX  D-phenylalanyl-N-[2-(pyridin-4-ylamino)ethyl]-L-prolinamide  peptide  55  28  .  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_PPX
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
 PPX  N1    N  NH2   0  -0.762   2.0584   1.6497  -0.3513
 PPX  C2    C  CH1   0  -0.214   2.4556   0.2987  -0.0366
 PPX  C10   C  C     0   0.540   1.2725  -0.6689   0.0572
 PPX  O11   O  O     0  -0.496   0.2733  -0.5075  -0.6345
 PPX  C3    C  CH2   0  -0.538   3.4174  -0.2350  -1.1134
 PPX  C4    C  CR6   0   0.168   4.6840   0.5656  -1.1966
 PPX  C5    C  CR16  0  -0.314   5.7373   0.3033  -0.3233
 PPX  C6    C  CR16  0  -0.308   4.8308   1.5937  -2.1234
 PPX  C7    C  CR16  0  -0.241   6.9084   1.0474  -0.3721
 PPX  C8    C  CR16  0  -0.245   6.0013   2.3387  -2.1803
 PPX  C9    C  CR16  0  -0.273   7.0441   2.0694  -1.3031
 PPX  N12   N  NT    0  -0.476   1.3787  -1.7148   0.8914
 PPX  C14   C  CH1   0  -0.163   0.2729  -2.6470   1.0296
 PPX  C17   C  C     0   0.566  -1.0090  -1.9092   1.3946
 PPX  O18   O  O     0  -0.491  -1.0119  -1.0187   2.2286
 PPX  C15   C  CH2   0  -0.478   0.7237  -3.5786   2.1631
 PPX  C16   C  CH2   0  -0.472   2.2449  -3.4978   2.1079
 PPX  C13   C  CH2   0  -0.284   2.4953  -2.0355   1.7727
 PPX  N19   N  NH1   0  -0.634  -2.1177  -2.3709   0.7958
 PPX  C20   C  CH2   0  -0.329  -3.4104  -1.7621   0.9784
 PPX  C30   C  CH2   0  -0.263  -3.6043  -0.5672   0.0503
 PPX  N27   N  NH1   0  -0.691  -4.9005   0.0221   0.2778
 PPX  C21   C  CR6   0   0.472  -5.3319   1.1430  -0.3424
 PPX  C22   C  CR16  0  -0.415  -6.6572   1.5883  -0.1850
 PPX  C23   C  CR16  0  -0.073  -7.0599   2.7464  -0.8120
 PPX  N24   N  N     0  -0.441  -6.2750   3.5045  -1.5796
 PPX  C25   C  CR16  0  -0.076  -5.0248   3.0790  -1.7287
 PPX  C26   C  CR16  0  -0.417  -4.5034   1.9337  -1.1548
 PPX  HN11  H  HNH2  0   0.340   1.4885   1.6525  -1.1889
 PPX  HN12  H  HNH2  0   0.351   1.4739   2.0190   0.3881
 PPX  H2    H  HCH1  0   0.265   2.9866   0.3274   0.9192
 PPX  H31   H  HCH2  0   0.261   3.6584  -1.2806  -0.9028
 PPX  H32   H  HCH2  0   0.261   2.8978  -0.2265  -2.0760
 PPX  H5    H  HCR6  0   0.245   5.6420  -0.4980   0.4013
 PPX  H6    H  HCR6  0   0.241   4.0247   1.8101  -2.8140
 PPX  H7    H  HCR6  0   0.252   7.7168   0.8252   0.3129
 PPX  H8    H  HCR6  0   0.252   6.0981   3.1321  -2.9104
 PPX  H9    H  HCR6  0   0.252   7.9573   2.6488  -1.3474
 PPX  H14   H  HCH1  0   0.273   0.1393  -3.2131   0.1018
 PPX  H151  H  HCH2  0   0.251   0.3678  -3.2046   3.1252
 PPX  H152  H  HCH2  0   0.265   0.3384  -4.5883   2.0320
 PPX  H161  H  HCH2  0   0.245   2.6338  -4.1345   1.3108
 PPX  H162  H  HCH2  0   0.258   2.7209  -3.7965   3.0406
 PPX  H131  H  HCH2  0   0.256   3.4554  -1.8862   1.2801
 PPX  H132  H  HCH2  0   0.248   2.4753  -1.4119   2.6714
 PPX  H19   H  HNH1  0   0.403  -2.0210  -3.0469   0.0559
 PPX  H201  H  HCH2  0   0.264  -4.1731  -2.5174   0.7824
 PPX  H202  H  HCH2  0   0.257  -3.5216  -1.4487   2.0165
 PPX  H301  H  HCH2  0   0.242  -2.8210   0.1678   0.2505
 PPX  H302  H  HCH2  0   0.231  -3.4836  -0.8914  -0.9906
 PPX  H27   H  HNH1  0   0.392  -5.6066  -0.5637   0.6942
 PPX  H22   H  HCR6  0   0.267  -7.3569   1.0322   0.4264
 PPX  H23   H  HCR6  0   0.254  -8.0836   3.0840  -0.6873
 PPX  H25   H  HCR6  0   0.254  -4.3806   3.6873  -2.3556
 PPX  H26   H  HCR6  0   0.269  -3.4724   1.6706  -1.3465

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
 PPX  N1   C2    single    1.443  0.020  1.443
 PPX  N1   HN11  single    0.890  0.020  1.040
 PPX  N1   HN12  single    0.890  0.020  1.040
 PPX  C2   C3    single    1.539  0.020  1.539
 PPX  C2   C10   single    1.531  0.020  1.531
 PPX  C2   H2    single    0.970  0.020  1.090
 PPX  C3   C4    single    1.501  0.020  1.501
 PPX  C3   H31   single    0.970  0.020  1.090
 PPX  C3   H32   single    0.970  0.020  1.090
 PPX  C4   C5    aromatic  1.393  0.020  1.393
 PPX  C4   C6    aromatic  1.392  0.020  1.392
 PPX  C5   C7    aromatic  1.388  0.020  1.388
 PPX  C5   H5    single    0.930  0.020  1.080
 PPX  C6   C8    aromatic  1.389  0.020  1.389
 PPX  C6   H6    single    0.930  0.020  1.080
 PPX  C7   C9    aromatic  1.389  0.020  1.389
 PPX  C7   H7    single    0.930  0.020  1.080
 PPX  C8   C9    aromatic  1.389  0.020  1.389
 PPX  C8   H8    single    0.930  0.020  1.080
 PPX  C9   H9    single    0.930  0.020  1.080
 PPX  C10  O11   double    1.226  0.020  1.226
 PPX  C10  N12   single    1.342  0.020  1.342
 PPX  N12  C13   single    1.458  0.020  1.458
 PPX  N12  C14   single    1.453  0.020  1.453
 PPX  C13  C16   single    1.521  0.020  1.521
 PPX  C13  H131  single    0.970  0.020  1.090
 PPX  C13  H132  single    0.970  0.020  1.090
 PPX  C14  C15   single    1.535  0.020  1.535
 PPX  C14  C17   single    1.523  0.020  1.523
 PPX  C14  H14   single    0.970  0.020  1.090
 PPX  C15  C16   single    1.524  0.020  1.524
 PPX  C15  H151  single    0.970  0.020  1.090
 PPX  C15  H152  single    0.970  0.020  1.090
 PPX  C16  H161  single    0.970  0.020  1.090
 PPX  C16  H162  single    0.970  0.020  1.090
 PPX  C17  O18   double    1.220  0.020  1.220
 PPX  C17  N19   single    1.342  0.020  1.342
 PPX  N19  C20   single    1.441  0.020  1.441
 PPX  N19  H19   single    0.860  0.020  1.020
 PPX  C20  C30   single    1.525  0.020  1.525
 PPX  C20  H201  single    0.970  0.020  1.090
 PPX  C20  H202  single    0.970  0.020  1.090
 PPX  C30  N27   single    1.442  0.020  1.442
 PPX  C30  H301  single    0.970  0.020  1.090
 PPX  C30  H302  single    0.970  0.020  1.090
 PPX  N27  C21   single    1.352  0.020  1.352
 PPX  N27  H27   single    0.860  0.020  1.020
 PPX  C21  C22   aromatic  1.407  0.020  1.407
 PPX  C21  C26   aromatic  1.404  0.020  1.404
 PPX  C22  C23   aromatic  1.377  0.020  1.377
 PPX  C22  H22   single    0.930  0.020  1.080
 PPX  C23  N24   aromatic  1.334  0.020  1.334
 PPX  C23  H23   single    0.930  0.020  1.080
 PPX  N24  C25   aromatic  1.329  0.020  1.329
 PPX  C25  C26   aromatic  1.383  0.020  1.383
 PPX  C25  H25   single    0.930  0.020  1.080
 PPX  C26  H26   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
 PPX  HN12  N1   HN11  106.14  3.000
 PPX  HN12  N1   C2    109.95  3.000
 PPX  HN11  N1   C2    109.74  3.000
 PPX  H2    C2   C3    108.49  3.000
 PPX  H2    C2   C10   109.76  3.000
 PPX  C3    C2   C10   107.85  3.000
 PPX  H2    C2   N1    107.43  3.000
 PPX  C10   C2   N1    113.10  3.000
 PPX  C3    C2   N1    110.13  3.000
 PPX  N12   C10  O11   121.19  3.000
 PPX  N12   C10  C2    117.99  3.000
 PPX  O11   C10  C2    120.80  3.000
 PPX  H32   C3   H31   106.35  3.000
 PPX  H32   C3   C4    110.36  3.000
 PPX  H31   C3   C4    109.56  3.000
 PPX  H32   C3   C2    108.43  3.000
 PPX  H31   C3   C2    109.55  3.000
 PPX  C4    C3   C2    112.41  3.000
 PPX  C6    C4   C5    118.47  3.000
 PPX  C6    C4   C3    121.33  3.000
 PPX  C5    C4   C3    120.19  3.000
 PPX  H5    C5   C7    119.58  3.000
 PPX  H5    C5   C4    119.44  3.000
 PPX  C7    C5   C4    120.98  3.000
 PPX  H6    C6   C8    119.60  3.000
 PPX  H6    C6   C4    119.58  3.000
 PPX  C8    C6   C4    120.82  3.000
 PPX  H7    C7   C9    120.14  3.000
 PPX  H7    C7   C5    119.84  3.000
 PPX  C9    C7   C5    120.02  3.000
 PPX  H8    C8   C9    120.06  3.000
 PPX  H8    C8   C6    119.75  3.000
 PPX  C9    C8   C6    120.19  3.000
 PPX  H9    C9   C8    120.25  3.000
 PPX  H9    C9   C7    120.25  3.000
 PPX  C8    C9   C7    119.51  3.000
 PPX  C13   N12  C14   112.59  3.000
 PPX  C14   N12  C10   119.93  3.000
 PPX  C13   N12  C10   127.42  3.000
 PPX  H14   C14  C15   110.35  3.000
 PPX  H14   C14  C17   110.53  3.000
 PPX  C15   C14  C17   111.36  3.000
 PPX  H14   C14  N12   110.12  3.000
 PPX  C17   C14  N12   110.64  3.000
 PPX  C15   C14  N12   103.66  3.000
 PPX  N19   C17  O18   123.65  3.000
 PPX  N19   C17  C14   114.94  3.000
 PPX  O18   C17  C14   121.29  3.000
 PPX  H152  C15  H151  107.97  3.000
 PPX  H152  C15  C16   113.45  3.000
 PPX  H151  C15  C16   109.82  3.000
 PPX  H152  C15  C14   111.72  3.000
 PPX  H151  C15  C14   110.30  3.000
 PPX  C16   C15  C14   103.54  3.000
 PPX  H162  C16  H161  108.04  3.000
 PPX  H162  C16  C13   112.36  3.000
 PPX  H161  C16  C13   109.95  3.000
 PPX  H162  C16  C15   112.99  3.000
 PPX  H161  C16  C15   110.54  3.000
 PPX  C13   C16  C15   102.90  3.000
 PPX  H132  C13  H131  108.03  3.000
 PPX  H132  C13  C16   111.34  3.000
 PPX  H131  C13  C16   112.12  3.000
 PPX  H132  C13  N12   110.92  3.000
 PPX  H131  C13  N12   111.80  3.000
 PPX  C16   C13  N12   102.62  3.000
 PPX  H19   N19  C20   117.58  3.000
 PPX  H19   N19  C17   118.66  3.000
 PPX  C20   N19  C17   122.65  3.000
 PPX  H202  C20  H201  107.38  3.000
 PPX  H202  C20  C30   109.95  3.000
 PPX  H201  C20  C30   110.13  3.000
 PPX  H202  C20  N19   109.50  3.000
 PPX  H201  C20  N19   108.18  3.000
 PPX  C30   C20  N19   111.60  3.000
 PPX  H302  C30  H301  107.09  3.000
 PPX  H302  C30  N27   111.68  3.000
 PPX  H301  C30  N27   109.91  3.000
 PPX  H302  C30  C20   109.38  3.000
 PPX  H301  C30  C20   108.93  3.000
 PPX  N27   C30  C20   109.78  3.000
 PPX  H27   N27  C21   116.62  3.000
 PPX  H27   N27  C30   117.23  3.000
 PPX  C21   N27  C30   123.60  3.000
 PPX  C26   C21  C22   116.25  3.000
 PPX  C26   C21  N27   122.96  3.000
 PPX  C22   C21  N27   120.78  3.000
 PPX  H22   C22  C23   120.00  3.000
 PPX  H22   C22  C21   120.62  3.000
 PPX  C23   C22  C21   119.39  3.000
 PPX  H23   C23  N24   116.38  3.000
 PPX  H23   C23  C22   119.03  3.000
 PPX  N24   C23  C22   124.59  3.000
 PPX  C25   N24  C23   115.85  3.000
 PPX  H25   C25  C26   118.69  3.000
 PPX  H25   C25  N24   116.34  3.000
 PPX  C26   C25  N24   124.97  3.000
 PPX  H26   C26  C25   119.17  3.000
 PPX  H26   C26  C21   121.89  3.000
 PPX  C25   C26  C21   118.94  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
 PPX  CONST_01  C9   C7   C5   C4      0.00   0.0  0
 PPX  CONST_02  C9   C8   C6   C4      0.00   0.0  0
 PPX  CONST_03  C8   C6   C4   C5      0.00   0.0  0
 PPX  CONST_04  C8   C9   C7   C5      0.00   0.0  0
 PPX  CONST_05  C7   C5   C4   C6      0.00   0.0  0
 PPX  CONST_06  C7   C9   C8   C6      0.00   0.0  0
 PPX  CONST_07  N24  C23  C22  C21     0.00   0.0  0
 PPX  CONST_08  N24  C25  C26  C21     0.00   0.0  0
 PPX  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 PPX  CONST_10  C25  N24  C23  C22     0.00   0.0  0
 PPX  CONST_11  C26  C21  C22  C23     0.00   0.0  0
 PPX  CONST_12  C26  C25  N24  C23     0.00   0.0  0
 PPX  CONST_13  C7   C5   C4   C3    180.00   0.0  0
 PPX  CONST_14  C8   C6   C4   C3    180.00   0.0  0
 PPX  CONST_15  C23  C22  C21  N27   180.00   0.0  0
 PPX  CONST_16  C25  C26  C21  N27   180.00   0.0  0
 PPX  CONST_17  H7   C7   C5   C4    180.00   0.0  0
 PPX  CONST_18  H8   C8   C6   C4    180.00   0.0  0
 PPX  CONST_19  H6   C6   C4   C5    180.00   0.0  0
 PPX  CONST_20  H9   C9   C7   C5    180.00   0.0  0
 PPX  CONST_21  H5   C5   C4   C6    180.00   0.0  0
 PPX  CONST_22  H23  C23  C22  C21   180.00   0.0  0
 PPX  CONST_23  H25  C25  C26  C21   180.00   0.0  0
 PPX  CONST_24  H26  C26  C21  C22   180.00   0.0  0
 PPX  CONST_25  H22  C22  C23  N24   180.00   0.0  0
 PPX  CONST_26  C13  N12  C10  C2      0.00   0.0  0
 PPX  CONST_27  C14  N12  C10  C2    180.00   0.0  0
 PPX  CONST_28  C13  N12  C10  O11   180.00   0.0  0
 PPX  CONST_29  C14  N12  C10  O11     0.00   0.0  0
 PPX  CONST_30  C22  C21  N27  C30   180.00   0.0  0
 PPX  CONST_31  C26  C21  N27  C30     0.00   0.0  0
 PPX  CONST_32  H27  N27  C21  C22     0.00   0.0  0
 PPX  CONST_33  C20  N19  C17  C14   180.00   0.0  0
 PPX  CONST_34  H19  N19  C17  C14     0.00   0.0  0
 PPX  CONST_35  C20  N19  C17  O18     0.00   0.0  0
 PPX  Var_01    C15  C16  C13  N12   -34.98  30.0  1
 PPX  Var_02    C16  C13  N12  C14    19.91  30.0  1
 PPX  Var_03    C13  C16  C15  C14    37.66  30.0  1
 PPX  Var_04    C5   C4   C3   C2     83.35  30.0  2
 PPX  Var_05    C21  N27  C30  C20   176.19  30.0  3
 PPX  Var_06    C30  C20  N19  C17    83.29  30.0  3
 PPX  Var_07    N27  C30  C20  N19  -179.23  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
 PPX  chir_01  C2   N1   C3   C10  positiv
 PPX  chir_02  C14  N12  C15  C17  negativ

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
 PPX  plan-1  C3   0.020
 PPX  plan-1  C4   0.020
 PPX  plan-1  C5   0.020
 PPX  plan-1  C6   0.020
 PPX  plan-1  C7   0.020
 PPX  plan-1  C8   0.020
 PPX  plan-1  C9   0.020
 PPX  plan-1  H5   0.020
 PPX  plan-1  H6   0.020
 PPX  plan-1  H7   0.020
 PPX  plan-1  H8   0.020
 PPX  plan-1  H9   0.020
 PPX  plan-2  N27  0.020
 PPX  plan-2  C21  0.020
 PPX  plan-2  C22  0.020
 PPX  plan-2  C23  0.020
 PPX  plan-2  N24  0.020
 PPX  plan-2  C25  0.020
 PPX  plan-2  C26  0.020
 PPX  plan-2  H22  0.020
 PPX  plan-2  H23  0.020
 PPX  plan-2  H25  0.020
 PPX  plan-2  H26  0.020
 PPX  plan-3  C14  0.020
 PPX  plan-3  C17  0.020
 PPX  plan-3  O18  0.020
 PPX  plan-3  N19  0.020
 PPX  plan-3  C20  0.020
 PPX  plan-3  H19  0.020
 PPX  plan-4  C30  0.020
 PPX  plan-4  N27  0.020
 PPX  plan-4  C21  0.020
 PPX  plan-4  H27  0.020
 PPX  plan-5  C2   0.020
 PPX  plan-5  C10  0.020
 PPX  plan-5  O11  0.020
 PPX  plan-5  N12  0.020
 PPX  plan-5  C14  0.020
 PPX  plan-5  C13  0.020

