# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:56:51 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-[(1-methylpyridinium-2-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccccc1CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3
#
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
 B04  B04  D-phenylalanyl-N-[(1-methylpyridinium-2-yl)methyl]-L-prolinamide  peptide  54  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_B04
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
 B04  N4    N  NH2   0  -0.762   3.2616  -1.8299  -1.1180
 B04  C3    C  CH1   0  -0.213   2.8549  -0.6207  -0.4464
 B04  C5    C  C     0   0.530   1.3957  -0.6382   0.0144
 B04  O7    O  O     0  -0.496   0.8180  -1.6928   0.2500
 B04  C2    C  CH2   0  -0.533   3.7314  -0.3781   0.7983
 B04  C1    C  CR6   0   0.160   5.1690  -0.1259   0.4499
 B04  C8    C  CR16  0  -0.315   5.6144   1.1715   0.2067
 B04  C12   C  CR16  0  -0.298   6.0808  -1.1729   0.3391
 B04  C9    C  CR16  0  -0.241   6.9363   1.4203  -0.1384
 B04  C11   C  CR16  0  -0.245   7.4045  -0.9298  -0.0016
 B04  C10   C  CR16  0  -0.273   7.8368   0.3682  -0.2434
 B04  N6    N  NT    0  -0.459   0.7872   0.5439   0.2141
 B04  C13   C  CH1   0  -0.218  -0.5598   0.5667   0.7400
 B04  C14   C  C     0   0.583  -1.5395  -0.0077  -0.2776
 B04  O15   O  O     0  -0.469  -1.3706   0.0988  -1.4782
 B04  C19   C  CH2   0  -0.478  -0.8163   2.0598   0.9850
 B04  C20   C  CH2   0  -0.471   0.0391   2.7478  -0.0724
 B04  C21   C  CH2   0  -0.277   1.2837   1.8704  -0.1424
 B04  N16   N  NH1   0  -0.638  -2.6326  -0.5773   0.2747
 B04  C17   C  CH2   0  -0.389  -3.6539  -1.2426  -0.4916
 B04  C18   C  CR6   0   0.437  -5.0358  -0.7721  -0.1324
 B04  C22   C  CR16  0  -0.358  -5.9260  -1.6296   0.4843
 B04  C23   C  CR16  0  -0.079  -7.2004  -1.2052   0.8198
 B04  C24   C  CR16  0  -0.337  -7.5712   0.0971   0.5311
 B04  C25   C  CR16  0   0.072  -6.6603   0.9200  -0.0845
 B04  N26   N  NR6   1  -0.453  -5.4304   0.4906  -0.4072
 B04  C27   C  CH3   0  -0.553  -4.5233   1.4530  -1.0457
 B04  HN4   H  HNH2  0   0.340   3.0234  -2.6344  -0.5503
 B04  HN4A  H  HNH2  0   0.351   2.7447  -1.9353  -1.9821
 B04  H3    H  HCH1  0   0.265   3.0106   0.2090  -1.1411
 B04  H2    H  HCH2  0   0.260   3.6435  -1.2483   1.4548
 B04  H2A   H  HCH2  0   0.262   3.3393   0.4731   1.3592
 B04  H8    H  HCR6  0   0.242   4.9197   2.0001   0.2928
 B04  H12   H  HCR6  0   0.241   5.7530  -2.1873   0.5280
 B04  H9    H  HCR6  0   0.252   7.2636   2.4360  -0.3198
 B04  H11   H  HCR6  0   0.252   8.1006  -1.7553  -0.0782
 B04  H10   H  HCR6  0   0.253   8.8693   0.5592  -0.5063
 B04  H13   H  HCH1  0   0.290  -0.6211  -0.0019   1.6711
 B04  H19   H  HCH2  0   0.265  -1.8728   2.3233   0.9355
 B04  H19A  H  HCH2  0   0.266  -0.4649   2.3150   1.9860
 B04  H20   H  HCH2  0   0.249  -0.4719   2.7574  -1.0355
 B04  H20A  H  HCH2  0   0.261   0.2825   3.7766   0.1873
 B04  H21   H  HCH2  0   0.242   2.0403   2.2080   0.5717
 B04  H21A  H  HCH2  0   0.262   1.7321   1.8761  -1.1353
 B04  HN16  H  HNH1  0   0.415  -2.6419  -0.7277   1.2719
 B04  H17   H  HCH2  0   0.310  -3.4597  -1.0971  -1.5546
 B04  H17A  H  HCH2  0   0.311  -3.6187  -2.3181  -0.3142
 B04  H22   H  HCR6  0   0.316  -5.6066  -2.6383   0.7022
 B04  H23   H  HCR6  0   0.315  -7.8917  -1.8827   1.3008
 B04  H24   H  HCR6  0   0.317  -8.5509   0.4807   0.7714
 B04  H25   H  HCR6  0   0.349  -6.8928   1.9430  -0.3379
 B04  H27   H  HCH3  0   0.290  -3.9390   0.9721  -1.8219
 B04  H27A  H  HCH3  0   0.301  -5.1166   2.2400  -1.4971
 B04  H27B  H  HCH3  0   0.294  -3.8671   1.8859  -0.2958

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
 B04  C1   C2    single    1.501  0.020  1.501
 B04  C1   C8    aromatic  1.393  0.020  1.393
 B04  C1   C12   aromatic  1.393  0.020  1.393
 B04  C2   C3    single    1.542  0.020  1.542
 B04  C3   N4    single    1.442  0.020  1.442
 B04  C3   C5    single    1.530  0.020  1.530
 B04  C5   N6    single    1.344  0.020  1.344
 B04  C5   O7    double    1.225  0.020  1.225
 B04  N6   C13   single    1.446  0.020  1.446
 B04  N6   C21   single    1.460  0.020  1.460
 B04  C8   C9    aromatic  1.389  0.020  1.389
 B04  C9   C10   aromatic  1.389  0.020  1.389
 B04  C10  C11   aromatic  1.389  0.020  1.389
 B04  C11  C12   aromatic  1.388  0.020  1.388
 B04  C13  C14   single    1.525  0.020  1.525
 B04  C13  C19   single    1.535  0.020  1.535
 B04  C14  O15   double    1.217  0.020  1.217
 B04  C14  N16   single    1.351  0.020  1.351
 B04  N16  C17   single    1.440  0.020  1.440
 B04  C17  C18   single    1.503  0.020  1.503
 B04  C18  C22   aromatic  1.381  0.020  1.381
 B04  C18  N26   aromatic  1.351  0.020  1.351
 B04  C19  C20   single    1.524  0.020  1.524
 B04  C20  C21   single    1.524  0.020  1.524
 B04  C22  C23   aromatic  1.384  0.020  1.384
 B04  C23  C24   aromatic  1.384  0.020  1.384
 B04  C24  C25   aromatic  1.373  0.020  1.373
 B04  C25  N26   aromatic  1.342  0.020  1.342
 B04  N26  C27   single    1.469  0.020  1.469
 B04  C2   H2    single    0.970  0.020  1.090
 B04  C2   H2A   single    0.970  0.020  1.090
 B04  C3   H3    single    0.970  0.020  1.090
 B04  N4   HN4   single    0.890  0.020  1.040
 B04  N4   HN4A  single    0.890  0.020  1.040
 B04  C8   H8    single    0.930  0.020  1.080
 B04  C9   H9    single    0.930  0.020  1.080
 B04  C10  H10   single    0.930  0.020  1.080
 B04  C11  H11   single    0.930  0.020  1.080
 B04  C12  H12   single    0.930  0.020  1.080
 B04  C13  H13   single    0.970  0.020  1.090
 B04  N16  HN16  single    0.860  0.020  1.020
 B04  C17  H17   single    0.970  0.020  1.090
 B04  C17  H17A  single    0.970  0.020  1.090
 B04  C19  H19   single    0.970  0.020  1.090
 B04  C19  H19A  single    0.970  0.020  1.090
 B04  C20  H20   single    0.970  0.020  1.090
 B04  C20  H20A  single    0.970  0.020  1.090
 B04  C21  H21   single    0.970  0.020  1.090
 B04  C21  H21A  single    0.970  0.020  1.090
 B04  C22  H22   single    0.930  0.020  1.080
 B04  C23  H23   single    0.930  0.020  1.080
 B04  C24  H24   single    0.930  0.020  1.080
 B04  C25  H25   single    0.930  0.020  1.080
 B04  C27  H27   single    0.970  0.020  1.090
 B04  C27  H27A  single    0.970  0.020  1.090
 B04  C27  H27B  single    0.970  0.020  1.090

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
 B04  HN4A  N4   HN4   106.00  3.000
 B04  HN4A  N4   C3    109.93  3.000
 B04  HN4   N4   C3    109.80  3.000
 B04  H3    C3   C2    108.22  3.000
 B04  H3    C3   C5    109.62  3.000
 B04  C2    C3   C5    107.51  3.000
 B04  H3    C3   N4    107.48  3.000
 B04  C5    C3   N4    113.56  3.000
 B04  C2    C3   N4    110.35  3.000
 B04  N6    C5   O7    120.98  3.000
 B04  O7    C5   C3    121.15  3.000
 B04  N6    C5   C3    117.79  3.000
 B04  H2A   C2   H2    106.44  3.000
 B04  H2A   C2   C1    109.41  3.000
 B04  H2    C2   C1    110.49  3.000
 B04  H2A   C2   C3    109.46  3.000
 B04  H2    C2   C3    108.29  3.000
 B04  C1    C2   C3    112.56  3.000
 B04  C12   C1   C8    118.48  3.000
 B04  C12   C1   C2    121.29  3.000
 B04  C8    C1   C2    120.22  3.000
 B04  H8    C8   C9    119.51  3.000
 B04  H8    C8   C1    119.53  3.000
 B04  C9    C8   C1    120.97  3.000
 B04  H12   C12  C11   119.70  3.000
 B04  H12   C12  C1    119.49  3.000
 B04  C11   C12  C1    120.80  3.000
 B04  H9    C9   C10   120.14  3.000
 B04  H9    C9   C8    119.84  3.000
 B04  C10   C9   C8    120.02  3.000
 B04  H11   C11  C10   120.01  3.000
 B04  H11   C11  C12   119.80  3.000
 B04  C10   C11  C12   120.20  3.000
 B04  H10   C10  C11   120.26  3.000
 B04  H10   C10  C9    120.22  3.000
 B04  C11   C10  C9    119.53  3.000
 B04  C21   N6   C13   113.02  3.000
 B04  C21   N6   C5    127.48  3.000
 B04  C13   N6   C5    119.30  3.000
 B04  H13   C13  C19   111.15  3.000
 B04  H13   C13  C14   109.67  3.000
 B04  C19   C13  C14   111.45  3.000
 B04  H13   C13  N6    110.73  3.000
 B04  C19   C13  N6    103.24  3.000
 B04  C14   C13  N6    110.48  3.000
 B04  N16   C14  O15   123.55  3.000
 B04  N16   C14  C13   113.95  3.000
 B04  O15   C14  C13   122.42  3.000
 B04  H19A  C19  H19   107.29  3.000
 B04  H19A  C19  C20   110.50  3.000
 B04  H19   C19  C20   113.79  3.000
 B04  H19A  C19  C13   108.68  3.000
 B04  H19   C19  C13   112.95  3.000
 B04  C20   C19  C13   103.57  3.000
 B04  H20A  C20  H20   107.89  3.000
 B04  H20A  C20  C21   111.86  3.000
 B04  H20   C20  C21   110.32  3.000
 B04  H20A  C20  C19   112.74  3.000
 B04  H20   C20  C19   110.72  3.000
 B04  C21   C20  C19   103.31  3.000
 B04  H21A  C21  H21   107.98  3.000
 B04  H21A  C21  C20   112.01  3.000
 B04  H21   C21  C20   110.92  3.000
 B04  H21A  C21  N6    111.54  3.000
 B04  H21   C21  N6    110.86  3.000
 B04  C20   C21  N6    103.53  3.000
 B04  HN16  N16  C17   116.80  3.000
 B04  HN16  N16  C14   118.34  3.000
 B04  C17   N16  C14   123.45  3.000
 B04  H17A  C17  H17   106.52  3.000
 B04  H17A  C17  C18   107.43  3.000
 B04  H17   C17  C18   110.79  3.000
 B04  H17A  C17  N16   110.25  3.000
 B04  H17   C17  N16   109.32  3.000
 B04  C18   C17  N16   112.35  3.000
 B04  N26   C18  C22   118.86  3.000
 B04  N26   C18  C17   120.82  3.000
 B04  C22   C18  C17   120.32  3.000
 B04  H22   C22  C23   120.63  3.000
 B04  H22   C22  C18   118.63  3.000
 B04  C23   C22  C18   120.74  3.000
 B04  H23   C23  C24   120.73  3.000
 B04  H23   C23  C22   120.30  3.000
 B04  C24   C23  C22   118.97  3.000
 B04  H24   C24  C25   119.27  3.000
 B04  H24   C24  C23   122.08  3.000
 B04  C25   C24  C23   118.66  3.000
 B04  H25   C25  N26   116.37  3.000
 B04  H25   C25  C24   122.04  3.000
 B04  N26   C25  C24   121.59  3.000
 B04  C27   N26  C25   117.45  3.000
 B04  C27   N26  C18   121.36  3.000
 B04  C25   N26  C18   121.18  3.000
 B04  H27B  C27  H27A  109.19  3.000
 B04  H27B  C27  H27   110.21  3.000
 B04  H27A  C27  H27   108.60  3.000
 B04  H27B  C27  N26   109.51  3.000
 B04  H27A  C27  N26   108.59  3.000
 B04  H27   C27  N26   110.70  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
 B04  CONST_01  C10   C9   C8   C1      0.00   0.0  0
 B04  CONST_02  C10   C11  C12  C1      0.00   0.0  0
 B04  CONST_03  C11   C12  C1   C8      0.00   0.0  0
 B04  CONST_04  C11   C10  C9   C8      0.00   0.0  0
 B04  CONST_05  C9    C8   C1   C12     0.00   0.0  0
 B04  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 B04  CONST_07  C24   C23  C22  C18     0.00   0.0  0
 B04  CONST_08  C24   C25  N26  C18     0.00   0.0  0
 B04  CONST_09  C25   N26  C18  C22     0.00   0.0  0
 B04  CONST_10  C25   C24  C23  C22     0.00   0.0  0
 B04  CONST_11  N26   C18  C22  C23     0.00   0.0  0
 B04  CONST_12  N26   C25  C24  C23     0.00   0.0  0
 B04  CONST_13  C9    C8   C1   C2    180.00   0.0  0
 B04  CONST_14  C11   C12  C1   C2    180.00   0.0  0
 B04  CONST_15  C23   C22  C18  C17   180.00   0.0  0
 B04  CONST_16  C25   N26  C18  C17   180.00   0.0  0
 B04  CONST_17  C27   N26  C18  C22   180.00   0.0  0
 B04  CONST_18  C27   N26  C25  C24   180.00   0.0  0
 B04  CONST_19  H9    C9   C8   C1    180.00   0.0  0
 B04  CONST_20  H11   C11  C12  C1    180.00   0.0  0
 B04  CONST_21  H12   C12  C1   C8    180.00   0.0  0
 B04  CONST_22  H10   C10  C9   C8    180.00   0.0  0
 B04  CONST_23  H8    C8   C1   C12   180.00   0.0  0
 B04  CONST_24  H23   C23  C22  C18   180.00   0.0  0
 B04  CONST_25  H25   C25  N26  C18   180.00   0.0  0
 B04  CONST_26  H24   C24  C23  C22   180.00   0.0  0
 B04  CONST_27  H22   C22  C23  C24   180.00   0.0  0
 B04  CONST_28  C13   N6   C5   C3    180.00   0.0  0
 B04  CONST_29  C21   N6   C5   C3      0.00   0.0  0
 B04  CONST_30  C13   N6   C5   O7      0.00   0.0  0
 B04  CONST_31  C21   N6   C5   O7    180.00   0.0  0
 B04  CONST_32  C17   N16  C14  C13   180.00   0.0  0
 B04  CONST_33  HN16  N16  C14  C13     0.00   0.0  0
 B04  CONST_34  C17   N16  C14  O15     0.00   0.0  0
 B04  Var_01    C19   C20  C21  N6     29.44  30.0  1
 B04  Var_02    C20   C21  N6   C13   -11.21  30.0  1
 B04  Var_03    C21   C20  C19  C13   -36.77  30.0  1
 B04  Var_04    C8    C1   C2   C3     89.59  30.0  2
 B04  Var_05    C22   C18  C17  N16  -113.19  30.0  2
 B04  Var_06    H27   C27  N26  C18    40.16  30.0  2
 B04  Var_07    C18   C17  N16  C14  -130.38  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
 B04  chir_01  C3   C2  N4   C5   negativ
 B04  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
 B04  plan-1  C2    0.020
 B04  plan-1  C1    0.020
 B04  plan-1  C8    0.020
 B04  plan-1  C12   0.020
 B04  plan-1  C9    0.020
 B04  plan-1  C11   0.020
 B04  plan-1  C10   0.020
 B04  plan-1  H8    0.020
 B04  plan-1  H12   0.020
 B04  plan-1  H9    0.020
 B04  plan-1  H11   0.020
 B04  plan-1  H10   0.020
 B04  plan-2  C17   0.020
 B04  plan-2  C18   0.020
 B04  plan-2  C22   0.020
 B04  plan-2  C23   0.020
 B04  plan-2  C24   0.020
 B04  plan-2  C25   0.020
 B04  plan-2  N26   0.020
 B04  plan-2  C27   0.020
 B04  plan-2  H22   0.020
 B04  plan-2  H23   0.020
 B04  plan-2  H24   0.020
 B04  plan-2  H25   0.020
 B04  plan-3  C13   0.020
 B04  plan-3  C14   0.020
 B04  plan-3  O15   0.020
 B04  plan-3  N16   0.020
 B04  plan-3  C17   0.020
 B04  plan-3  HN16  0.020
 B04  plan-4  C3    0.020
 B04  plan-4  C5    0.020
 B04  plan-4  O7    0.020
 B04  plan-4  N6    0.020
 B04  plan-4  C13   0.020
 B04  plan-4  C21   0.020

