# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 00:24:07 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-[(2R)-2-aminobutanoyl]-N-(3-chlorobenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](N)C(=O)N1CCC[C@H]1C(=O)NCc2cccc(Cl)c2
#
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
 19U  19U  1-[(2R)-2-aminobutanoyl]-N-(3-chlorobenzyl)-L-prolinamide  peptide  44  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_19U
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
 19U  N     N   NH2   0  -0.784  -5.0490   1.6686  -1.0216
 19U  C15   C   CH1   0  -0.230  -4.7817   0.4008  -0.3683
 19U  C14   C   C     0   0.578  -3.3043   0.3541  -0.0059
 19U  O32   O   O     0  -0.506  -2.7120   1.3655   0.3528
 19U  C1    C   CH2   0  -0.433  -5.6053   0.1299   0.9033
 19U  C17   C   CH3   0  -0.674  -7.1024   0.0663   0.6381
 19U  N1    N   NT    0  -0.478  -2.6844  -0.8361  -0.0431
 19U  C12   C   CH1   0  -0.166  -1.2743  -0.9274   0.2844
 19U  C7    C   C     0   0.563  -0.4344  -0.0406  -0.6254
 19U  O22   O   O     0  -0.493  -0.7113   0.1202  -1.8029
 19U  C2    C   CH2   0  -0.481  -0.9371  -2.4090   0.0467
 19U  C3    C   CH2   0  -0.468  -2.2806  -3.1123   0.1958
 19U  C4    C   CH2   0  -0.284  -3.2505  -2.1226  -0.4307
 19U  N23   N   NH1   0  -0.635   0.6705   0.4540  -0.0502
 19U  C24   C   CH2   0  -0.323   1.6574   1.2300  -0.7728
 19U  C25   C   CR6   0   0.059   2.9898   1.1486  -0.0797
 19U  C26   C   CR16  0  -0.288   3.4926   2.2249   0.6404
 19U  C27   C   CR16  0  -0.246   4.7182   2.1262   1.2870
 19U  C28   C   CR16  0  -0.224   5.4548   0.9537   1.2251
 19U  C29   C   CR6   0  -0.023   4.9429  -0.1163   0.5049
 19U  C30   C   CR16  0  -0.241   3.7235  -0.0335  -0.1441
 19U  CL21  CL  CL    0  -0.129   5.8533  -1.5897   0.4104
 19U  HN    H   HNH2  0   0.352  -6.0136   1.6932  -1.3252
 19U  HNA   H   HNH2  0   0.341  -4.9373   2.4272  -0.3597
 19U  H15   H   HCH1  0   0.253  -5.0070  -0.3841  -1.0962
 19U  H1    H   HCH2  0   0.227  -5.2839  -0.8122   1.3572
 19U  H1A   H   HCH2  0   0.231  -5.3875   0.9127   1.6363
 19U  H17   H   HCH3  0   0.224  -7.3380  -0.6864  -0.1167
 19U  H17A  H   HCH3  0   0.238  -7.6450  -0.1951   1.5465
 19U  H17B  H   HCH3  0   0.220  -7.4989   1.0214   0.2919
 19U  H12   H   HCH1  0   0.276  -1.1105  -0.6604   1.3337
 19U  H2    H   HCH2  0   0.251  -0.5578  -2.5558  -0.9670
 19U  H2A   H   HCH2  0   0.266  -0.1785  -2.7661   0.7409
 19U  H3    H   HCH2  0   0.257  -2.3072  -4.0845  -0.2942
 19U  H3A   H   HCH2  0   0.245  -2.5261  -3.2565   1.2497
 19U  H4    H   HCH2  0   0.257  -4.2639  -2.2511  -0.0542
 19U  H4A   H   HCH2  0   0.247  -3.2754  -2.2279  -1.5193
 19U  HN23  H   HNH1  0   0.404   0.7991   0.3354   0.9420
 19U  H24   H   HCH2  0   0.264   1.7413   0.8293  -1.7838
 19U  H24A  H   HCH2  0   0.259   1.3439   2.2733  -0.8664
 19U  H26   H   HCR6  0   0.262   2.9273   3.1471   0.6928
 19U  H27   H   HCR6  0   0.270   5.1050   2.9680   1.8456
 19U  H28   H   HCR6  0   0.281   6.4093   0.8744   1.7272
 19U  H30   H   HCR6  0   0.277   3.3434  -0.8807  -0.7016

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
 19U  N1   C4    single    1.458  0.020  1.458
 19U  N1   C14   single    1.342  0.020  1.342
 19U  N1   C12   single    1.451  0.020  1.451
 19U  C4   C3    single    1.521  0.020  1.521
 19U  C7   C12   single    1.523  0.020  1.523
 19U  C7   N23   single    1.340  0.020  1.340
 19U  C7   O22   double    1.220  0.020  1.220
 19U  C15  C1    single    1.539  0.020  1.539
 19U  C15  N     single    1.451  0.020  1.451
 19U  C15  C14   single    1.522  0.020  1.522
 19U  C17  C1    single    1.522  0.020  1.522
 19U  C24  N23   single    1.449  0.020  1.449
 19U  C24  C25   single    1.504  0.020  1.504
 19U  C26  C25   aromatic  1.389  0.020  1.389
 19U  C26  C27   aromatic  1.389  0.020  1.389
 19U  C28  C29   aromatic  1.388  0.020  1.388
 19U  C28  C27   aromatic  1.386  0.020  1.386
 19U  C14  O32   double    1.226  0.020  1.226
 19U  C3   C2    single    1.524  0.020  1.524
 19U  C2   C12   single    1.538  0.020  1.538
 19U  C25  C30   aromatic  1.393  0.020  1.393
 19U  C30  C29   aromatic  1.384  0.020  1.384
 19U  C29  CL21  single    1.735  0.020  1.735
 19U  C4   H4    single    0.970  0.020  1.090
 19U  C4   H4A   single    0.970  0.020  1.090
 19U  C15  H15   single    0.970  0.020  1.090
 19U  C17  H17   single    0.970  0.020  1.090
 19U  C17  H17A  single    0.970  0.020  1.090
 19U  C17  H17B  single    0.970  0.020  1.090
 19U  C24  H24   single    0.970  0.020  1.090
 19U  C24  H24A  single    0.970  0.020  1.090
 19U  C26  H26   single    0.930  0.020  1.080
 19U  C28  H28   single    0.930  0.020  1.080
 19U  C1   H1    single    0.970  0.020  1.090
 19U  C1   H1A   single    0.970  0.020  1.090
 19U  N    HN    single    0.890  0.020  1.040
 19U  N    HNA   single    0.890  0.020  1.040
 19U  C3   H3    single    0.970  0.020  1.090
 19U  C3   H3A   single    0.970  0.020  1.090
 19U  C2   H2    single    0.970  0.020  1.090
 19U  C2   H2A   single    0.970  0.020  1.090
 19U  C12  H12   single    0.970  0.020  1.090
 19U  N23  HN23  single    0.860  0.020  1.020
 19U  C30  H30   single    0.930  0.020  1.080
 19U  C27  H27   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
 19U  HNA   N    HN    106.44  3.000
 19U  HNA   N    C15   109.86  3.000
 19U  HN    N    C15   109.39  3.000
 19U  H15   C15  C1    108.26  3.000
 19U  H15   C15  C14   109.66  3.000
 19U  C1    C15  C14   108.50  3.000
 19U  H15   C15  N     106.82  3.000
 19U  C14   C15  N     108.23  3.000
 19U  C1    C15  N     115.29  3.000
 19U  N1    C14  O32   121.10  3.000
 19U  O32   C14  C15   120.90  3.000
 19U  N1    C14  C15   117.95  3.000
 19U  H1A   C1   H1    106.24  3.000
 19U  H1A   C1   C17   110.02  3.000
 19U  H1    C1   C17   108.99  3.000
 19U  H1A   C1   C15   108.73  3.000
 19U  H1    C1   C15   109.70  3.000
 19U  C17   C1   C15   112.94  3.000
 19U  H17B  C17  H17A  107.07  3.000
 19U  H17B  C17  H17   107.81  3.000
 19U  H17A  C17  H17   107.66  3.000
 19U  H17B  C17  C1    112.12  3.000
 19U  H17A  C17  C1    110.76  3.000
 19U  H17   C17  C1    111.20  3.000
 19U  C4    N1   C12   112.46  3.000
 19U  C12   N1   C14   119.89  3.000
 19U  C4    N1   C14   127.62  3.000
 19U  H12   C12  C2    110.50  3.000
 19U  H12   C12  C7    110.36  3.000
 19U  C2    C12  C7    110.34  3.000
 19U  H12   C12  N1    110.27  3.000
 19U  C2    C12  N1    103.82  3.000
 19U  C7    C12  N1    111.38  3.000
 19U  N23   C7   O22   123.54  3.000
 19U  O22   C7   C12   121.88  3.000
 19U  N23   C7   C12   114.40  3.000
 19U  H2A   C2   H2    107.80  3.000
 19U  H2A   C2   C3    113.62  3.000
 19U  H2    C2   C3    109.57  3.000
 19U  H2A   C2   C12   111.73  3.000
 19U  H2    C2   C12   110.43  3.000
 19U  C3    C2   C12   103.66  3.000
 19U  H3A   C3   H3    108.11  3.000
 19U  H3A   C3   C4    109.89  3.000
 19U  H3    C3   C4    112.34  3.000
 19U  H3A   C3   C2    110.71  3.000
 19U  H3    C3   C2    112.93  3.000
 19U  C4    C3   C2    102.81  3.000
 19U  H4A   C4   H4    108.15  3.000
 19U  H4A   C4   C3    111.21  3.000
 19U  H4    C4   C3    111.99  3.000
 19U  H4A   C4   N1    111.00  3.000
 19U  H4    C4   N1    111.94  3.000
 19U  C3    C4   N1    102.54  3.000
 19U  HN23  N23  C24   117.87  3.000
 19U  HN23  N23  C7    118.97  3.000
 19U  C24   N23  C7    123.04  3.000
 19U  H24A  C24  H24   107.05  3.000
 19U  H24A  C24  C25   110.19  3.000
 19U  H24   C24  C25   109.82  3.000
 19U  H24A  C24  N23   111.01  3.000
 19U  H24   C24  N23   108.54  3.000
 19U  C25   C24  N23   110.16  3.000
 19U  C30   C25  C26   119.40  3.000
 19U  C30   C25  C24   119.42  3.000
 19U  C26   C25  C24   121.17  3.000
 19U  H26   C26  C27   119.90  3.000
 19U  H26   C26  C25   119.73  3.000
 19U  C27   C26  C25   120.36  3.000
 19U  H27   C27  C28   119.43  3.000
 19U  H27   C27  C26   120.03  3.000
 19U  C28   C27  C26   120.54  3.000
 19U  H28   C28  C29   120.67  3.000
 19U  H28   C28  C27   120.69  3.000
 19U  C29   C28  C27   118.64  3.000
 19U  CL21  C29  C30   119.20  3.000
 19U  CL21  C29  C28   119.31  3.000
 19U  C30   C29  C28   121.49  3.000
 19U  H30   C30  C29   120.26  3.000
 19U  H30   C30  C25   120.19  3.000
 19U  C29   C30  C25   119.56  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
 19U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 19U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 19U  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 19U  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 19U  CONST_05  C30   C25  C26  C27     0.00   0.0  0
 19U  CONST_06  C30   C29  C28  C27     0.00   0.0  0
 19U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 19U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 19U  CONST_09  CL21  C29  C30  C25   180.00   0.0  0
 19U  CONST_10  CL21  C29  C28  C27   180.00   0.0  0
 19U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 19U  CONST_12  H30   C30  C25  C26   180.00   0.0  0
 19U  CONST_13  H28   C28  C27  C26   180.00   0.0  0
 19U  CONST_14  H26   C26  C27  C28   180.00   0.0  0
 19U  CONST_15  C4    N1   C14  C15     0.00   0.0  0
 19U  CONST_16  C12   N1   C14  C15   180.00   0.0  0
 19U  CONST_17  C4    N1   C14  O32   180.00   0.0  0
 19U  CONST_18  C12   N1   C14  O32     0.00   0.0  0
 19U  CONST_19  C24   N23  C7   C12   180.00   0.0  0
 19U  CONST_20  HN23  N23  C7   C12     0.00   0.0  0
 19U  CONST_21  C24   N23  C7   O22     0.00   0.0  0
 19U  Var_01    C2    C3   C4   N1    -35.83  30.0  1
 19U  Var_02    C3    C4   N1   C12    21.92  30.0  1
 19U  Var_03    C4    C3   C2   C12    37.13  30.0  1
 19U  Var_04    C26   C25  C24  N23  -106.24  30.0  2
 19U  Var_05    C25   C24  N23  C7   -156.23  30.0  2
 19U  Var_06    H17   C17  C1   C15    56.38  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
 19U  chir_01  C15  C1  N   C14  negativ
 19U  chir_02  C12  N1  C2  C7   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
 19U  plan-1  C24   0.020
 19U  plan-1  C25   0.020
 19U  plan-1  C26   0.020
 19U  plan-1  C27   0.020
 19U  plan-1  C28   0.020
 19U  plan-1  C29   0.020
 19U  plan-1  C30   0.020
 19U  plan-1  CL21  0.020
 19U  plan-1  H26   0.020
 19U  plan-1  H27   0.020
 19U  plan-1  H28   0.020
 19U  plan-1  H30   0.020
 19U  plan-2  C12   0.020
 19U  plan-2  C7    0.020
 19U  plan-2  O22   0.020
 19U  plan-2  N23   0.020
 19U  plan-2  C24   0.020
 19U  plan-2  HN23  0.020
 19U  plan-3  C15   0.020
 19U  plan-3  C14   0.020
 19U  plan-3  O32   0.020
 19U  plan-3  N1    0.020
 19U  plan-3  C12   0.020
 19U  plan-3  C4    0.020

