# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 22:26:34 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC1CCCCC1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3
#
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
 64U  64U  "3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide"  peptide  57  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_64U
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
 64U  C11   C   CH1   0  -0.236  -5.6639   0.2502   0.0657
 64U  C12   C   CH2   0  -0.430  -5.7997  -0.8616  -0.9760
 64U  C13   C   CH2   0  -0.426  -7.2539  -1.1133  -1.3635
 64U  C16   C   CH2   0  -0.430  -8.1198  -1.4018  -0.1430
 64U  C17   C   CH2   0  -0.432  -8.0065  -0.2802   0.8837
 64U  C18   C   CH2   0  -0.410  -6.5530  -0.0390   1.2768
 64U  N     N   NH2   0  -0.783  -3.5285   2.0411  -1.3161
 64U  C15   C   CH1   0  -0.254  -3.2275   0.8153  -0.6021
 64U  C1    C   CH2   0  -0.425  -4.2192   0.4510   0.5194
 64U  C14   C   C     0   0.580  -1.8462   0.9337   0.0250
 64U  O32   O   O     0  -0.503  -1.4156   2.0127   0.4148
 64U  N1    N   NR5   0  -0.477  -1.1452  -0.1988   0.2012
 64U  C5    C   CR15  0  -0.173   0.1470  -0.1531   0.8560
 64U  C7    C   C     0   0.547   1.1329   0.7098   0.0824
 64U  O22   O   O     0  -0.480   1.1115   0.7760  -1.1348
 64U  C2    C   CH2   0  -0.490   0.6192  -1.6198   0.8505
 64U  C3    C   CH2   0  -0.463  -0.6702  -2.4180   0.6941
 64U  C4    C   CH2   0  -0.283  -1.5022  -1.5453  -0.2310
 64U  N23   N   NH1   0  -0.639   2.0683   1.3013   0.8461
 64U  C24   C   CH2   0  -0.328   3.1948   2.0130   0.3076
 64U  C25   C   CR6   0   0.075   4.4637   1.1975   0.1951
 64U  C26   C   CR16  0  -0.281   5.6628   1.8540  -0.0768
 64U  C27   C   CR16  0  -0.247   6.8425   1.1415  -0.2133
 64U  C28   C   CR16  0  -0.231   6.8536  -0.2415  -0.0771
 64U  C29   C   CR6   0  -0.019   5.6588  -0.8831   0.1956
 64U  C30   C   CR16  0  -0.257   4.4679  -0.1834   0.3328
 64U  CL21  CL  CL    0  -0.131   5.6410  -2.6090   0.3768
 64U  H11   H   HCH1  0   0.205  -6.0210   1.1860  -0.3856
 64U  H12   H   HCH2  0   0.229  -5.2290  -0.6178  -1.8763
 64U  H12A  H   HCH2  0   0.208  -5.3631  -1.7845  -0.5728
 64U  H13   H   HCH2  0   0.208  -7.6452  -0.2317  -1.8829
 64U  H13A  H   HCH2  0   0.226  -7.3116  -1.9411  -2.0743
 64U  H16   H   HCH2  0   0.225  -9.1614  -1.5408  -0.4429
 64U  H16A  H   HCH2  0   0.207  -7.7990  -2.3453   0.3126
 64U  H17   H   HCH2  0   0.208  -8.4262   0.6396   0.4617
 64U  H17A  H   HCH2  0   0.225  -8.6007  -0.5135   1.7708
 64U  H18   H   HCH2  0   0.205  -6.1680  -0.9256   1.7949
 64U  H18A  H   HCH2  0   0.225  -6.4827   0.7892   1.9873
 64U  HNA   H   HNH2  0   0.341  -3.6157   2.8104  -0.6629
 64U  H15   H   HCH1  0   0.261  -3.2115   0.0135  -1.3439
 64U  H1    H   HCH2  0   0.236  -4.1853   1.2446   1.2749
 64U  H1A   H   HCH2  0   0.223  -3.8864  -0.4626   1.0248
 64U  H5    H   HCR5  0   0.282   0.0381   0.2131   1.8816
 64U  H2    H   HCH2  0   0.251   1.2763  -1.8085  -0.0019
 64U  H2A   H   HCH2  0   0.268   1.1672  -1.8675   1.7580
 64U  H3    H   HCH2  0   0.259  -0.5044  -3.4154   0.2899
 64U  H3A   H   HCH2  0   0.246  -1.1722  -2.5223   1.6580
 64U  H4    H   HCH2  0   0.253  -2.5686  -1.7331  -0.1244
 64U  H4A   H   HCH2  0   0.250  -1.2284  -1.7016  -1.2781
 64U  HN23  H   HNH1  0   0.408   2.0196   1.1890   1.8463
 64U  H24   H   HCH2  0   0.275   2.9239   2.3896  -0.6796
 64U  H24A  H   HCH2  0   0.277   3.3851   2.8882   0.9305
 64U  H26   H   HCR6  0   0.258   5.6729   2.9326  -0.1779
 64U  H27   H   HCR6  0   0.268   7.7676   1.6616  -0.4239
 64U  H28   H   HCR6  0   0.279   7.7732  -0.8013  -0.1778
 64U  H30   H   HCR6  0   0.265   3.5577  -0.7217   0.5597
 64U  HN    H   HNH2  0   0.352  -4.4308   1.9477  -1.7658

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
 64U  C1   C15   single    1.541  0.020  1.541
 64U  C1   C11   single    1.528  0.020  1.528
 64U  N    C15   single    1.450  0.020  1.450
 64U  C15  C14   single    1.522  0.020  1.522
 64U  C14  O32   double    1.225  0.020  1.225
 64U  C14  N1    single    1.344  0.020  1.344
 64U  N1   C4    single    1.459  0.020  1.459
 64U  N1   C5    single    1.449  0.020  1.449
 64U  C4   C3    single    1.520  0.020  1.520
 64U  C3   C2    single    1.525  0.020  1.525
 64U  C2   C5    single    1.541  0.020  1.541
 64U  C5   C7    single    1.522  0.020  1.522
 64U  C7   N23   single    1.345  0.020  1.345
 64U  C7   O22   double    1.219  0.020  1.219
 64U  N23  C24   single    1.437  0.020  1.437
 64U  C24  C25   single    1.513  0.020  1.513
 64U  C25  C30   aromatic  1.388  0.020  1.388
 64U  C25  C26   aromatic  1.394  0.020  1.394
 64U  C30  C29   aromatic  1.388  0.020  1.388
 64U  C29  C28   aromatic  1.383  0.020  1.383
 64U  C29  CL21  single    1.736  0.020  1.736
 64U  C28  C27   aromatic  1.390  0.020  1.390
 64U  C27  C26   aromatic  1.385  0.020  1.385
 64U  C11  C12   single    1.530  0.020  1.530
 64U  C11  C18   single    1.530  0.020  1.530
 64U  C12  C13   single    1.526  0.020  1.526
 64U  C13  C16   single    1.524  0.020  1.524
 64U  C16  C17   single    1.525  0.020  1.525
 64U  C17  C18   single    1.525  0.020  1.525
 64U  C1   H1    single    0.970  0.020  1.090
 64U  C1   H1A   single    0.970  0.020  1.090
 64U  N    HN    single    0.890  0.020  1.040
 64U  N    HNA   single    0.890  0.020  1.040
 64U  C15  H15   single    0.970  0.020  1.090
 64U  C4   H4    single    0.970  0.020  1.090
 64U  C4   H4A   single    0.970  0.020  1.090
 64U  C3   H3    single    0.970  0.020  1.090
 64U  C3   H3A   single    0.970  0.020  1.090
 64U  C2   H2    single    0.970  0.020  1.090
 64U  C2   H2A   single    0.970  0.020  1.090
 64U  C5   H5    single    0.970  0.020  1.090
 64U  N23  HN23  single    0.860  0.020  1.020
 64U  C24  H24   single    0.970  0.020  1.090
 64U  C24  H24A  single    0.970  0.020  1.090
 64U  C30  H30   single    0.930  0.020  1.080
 64U  C28  H28   single    0.930  0.020  1.080
 64U  C27  H27   single    0.930  0.020  1.080
 64U  C26  H26   single    0.930  0.020  1.080
 64U  C11  H11   single    0.970  0.020  1.090
 64U  C12  H12   single    0.970  0.020  1.090
 64U  C12  H12A  single    0.970  0.020  1.090
 64U  C13  H13   single    0.970  0.020  1.090
 64U  C13  H13A  single    0.970  0.020  1.090
 64U  C16  H16   single    0.970  0.020  1.090
 64U  C16  H16A  single    0.970  0.020  1.090
 64U  C17  H17   single    0.970  0.020  1.090
 64U  C17  H17A  single    0.970  0.020  1.090
 64U  C18  H18   single    0.970  0.020  1.090
 64U  C18  H18A  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
 64U  H11   C11  C1   108.51  3.000
 64U  H11   C11  C18  107.30  3.000
 64U  C1    C11  C18  109.83  3.000
 64U  H11   C11  C12  108.10  3.000
 64U  C18   C11  C12  110.49  3.000
 64U  C1    C11  C12  112.44  3.000
 64U  H12A  C12  H12  106.40  3.000
 64U  H12A  C12  C13  109.49  3.000
 64U  H12   C12  C13  108.97  3.000
 64U  H12A  C12  C11  109.01  3.000
 64U  H12   C12  C11  110.63  3.000
 64U  C13   C12  C11  112.18  3.000
 64U  H13A  C13  H13  106.40  3.000
 64U  H13A  C13  C16  110.35  3.000
 64U  H13   C13  C16  109.21  3.000
 64U  H13A  C13  C12  109.91  3.000
 64U  H13   C13  C12  109.15  3.000
 64U  C16   C13  C12  111.67  3.000
 64U  H16A  C16  H16  106.48  3.000
 64U  H16A  C16  C17  109.37  3.000
 64U  H16   C16  C17  110.44  3.000
 64U  H16A  C16  C13  109.24  3.000
 64U  H16   C16  C13  110.23  3.000
 64U  C17   C16  C13  110.97  3.000
 64U  H17A  C17  H17  106.48  3.000
 64U  H17A  C17  C18  110.05  3.000
 64U  H17   C17  C18  109.37  3.000
 64U  H17A  C17  C16  110.43  3.000
 64U  H17   C17  C16  109.25  3.000
 64U  C18   C17  C16  111.15  3.000
 64U  H18A  C18  H18  106.42  3.000
 64U  H18A  C18  C17  110.40  3.000
 64U  H18   C18  C17  109.19  3.000
 64U  H18A  C18  C11  109.50  3.000
 64U  H18   C18  C11  108.83  3.000
 64U  C17   C18  C11  112.32  3.000
 64U  HNA   N    HN   106.25  3.000
 64U  HNA   N    C15  110.02  3.000
 64U  HN    N    C15  109.01  3.000
 64U  H15   C15  C14  108.89  3.000
 64U  H15   C15  C1   109.28  3.000
 64U  C14   C15  C1   107.62  3.000
 64U  H15   C15  N    106.81  3.000
 64U  C14   C15  N    109.00  3.000
 64U  C1    C15  N    115.12  3.000
 64U  H1A   C1   H1   106.04  3.000
 64U  H1A   C1   C15  109.71  3.000
 64U  H1    C1   C15  108.09  3.000
 64U  H1A   C1   C11  108.34  3.000
 64U  H1    C1   C11  109.22  3.000
 64U  C15   C1   C11  115.06  3.000
 64U  N1    C14  O32  121.14  3.000
 64U  N1    C14  C15  117.52  3.000
 64U  O32   C14  C15  121.24  3.000
 64U  C4    N1   C5   112.41  3.000
 64U  C5    N1   C14  119.86  3.000
 64U  C4    N1   C14  127.71  3.000
 64U  H5    C5   C2   110.63  3.000
 64U  H5    C5   C7   110.55  3.000
 64U  C2    C5   C7   109.84  3.000
 64U  H5    C5   N1   110.20  3.000
 64U  C7    C5   N1   111.46  3.000
 64U  C2    C5   N1   103.99  3.000
 64U  N23   C7   O22  123.73  3.000
 64U  O22   C7   C5   121.80  3.000
 64U  N23   C7   C5   114.30  3.000
 64U  H2A   C2   H2   107.96  3.000
 64U  H2A   C2   C3   113.08  3.000
 64U  H2    C2   C3   109.76  3.000
 64U  H2A   C2   C5   111.58  3.000
 64U  H2    C2   C5   110.58  3.000
 64U  C3    C2   C5   103.86  3.000
 64U  H3A   C3   H3   108.07  3.000
 64U  H3A   C3   C4   109.91  3.000
 64U  H3    C3   C4   112.54  3.000
 64U  H3A   C3   C2   110.39  3.000
 64U  H3    C3   C2   112.89  3.000
 64U  C4    C3   C2   102.99  3.000
 64U  H4A   C4   H4   108.33  3.000
 64U  H4A   C4   C3   111.33  3.000
 64U  H4    C4   C3   112.20  3.000
 64U  H4A   C4   N1   110.76  3.000
 64U  H4    C4   N1   111.73  3.000
 64U  C3    C4   N1   102.46  3.000
 64U  HN23  N23  C24  117.71  3.000
 64U  HN23  N23  C7   118.75  3.000
 64U  C24   N23  C7   123.39  3.000
 64U  H24A  C24  H24  106.45  3.000
 64U  H24A  C24  C25  109.18  3.000
 64U  H24   C24  C25  109.10  3.000
 64U  H24A  C24  N23  108.67  3.000
 64U  H24   C24  N23  108.39  3.000
 64U  C25   C24  N23  114.73  3.000
 64U  C30   C25  C26  119.04  3.000
 64U  C26   C25  C24  118.83  3.000
 64U  C30   C25  C24  122.12  3.000
 64U  H26   C26  C27  119.67  3.000
 64U  H26   C26  C25  119.68  3.000
 64U  C27   C26  C25  120.65  3.000
 64U  H27   C27  C28  119.38  3.000
 64U  H27   C27  C26  120.01  3.000
 64U  C28   C27  C26  120.60  3.000
 64U  H28   C28  C29  120.85  3.000
 64U  H28   C28  C27  120.85  3.000
 64U  C29   C28  C27  118.29  3.000
 64U  CL21  C29  C30  118.83  3.000
 64U  CL21  C29  C28  119.39  3.000
 64U  C30   C29  C28  121.79  3.000
 64U  H30   C30  C29  119.47  3.000
 64U  H30   C30  C25  120.89  3.000
 64U  C29   C30  C25  119.63  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
 64U  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 64U  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 64U  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 64U  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 64U  CONST_05  C30   C29  C28  C27     0.00   0.0  0
 64U  CONST_06  C30   C25  C26  C27     0.00   0.0  0
 64U  CONST_07  C29   C30  C25  C24   180.00   0.0  0
 64U  CONST_08  C27   C26  C25  C24   180.00   0.0  0
 64U  CONST_09  CL21  C29  C30  C25   180.00   0.0  0
 64U  CONST_10  CL21  C29  C28  C27   180.00   0.0  0
 64U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 64U  CONST_12  H30   C30  C25  C26   180.00   0.0  0
 64U  CONST_13  H28   C28  C27  C26   180.00   0.0  0
 64U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 64U  CONST_15  H26   C26  C27  C28   180.00   0.0  0
 64U  CONST_16  H27   C27  C28  C29   180.00   0.0  0
 64U  CONST_17  H26   C26  C25  C30   180.00   0.0  0
 64U  CONST_18  H28   C28  C29  C30   180.00   0.0  0
 64U  CONST_19  C4    N1   C14  C15     0.00   0.0  0
 64U  CONST_20  C5    N1   C14  C15   180.00   0.0  0
 64U  CONST_21  C4    N1   C14  O32   180.00   0.0  0
 64U  CONST_22  C5    N1   C14  O32     0.00   0.0  0
 64U  CONST_23  C24   N23  C7   C5    180.00   0.0  0
 64U  CONST_24  HN23  N23  C7   C5      0.00   0.0  0
 64U  CONST_25  C24   N23  C7   O22     0.00   0.0  0
 64U  CONST_26  HN23  N23  C7   O22   180.00   0.0  0
 64U  Var_01    C16   C13  C12  C11   -54.74  30.0  1
 64U  Var_02    C16   C17  C18  C11    55.58  30.0  1
 64U  Var_03    C17   C16  C13  C12    55.19  30.0  1
 64U  Var_04    C18   C17  C16  C13   -55.43  30.0  1
 64U  Var_05    C2    C3   C4   N1    -36.05  30.0  1
 64U  Var_06    C3    C4   N1   C5     23.59  30.0  1
 64U  Var_07    C4    C3   C2   C5     35.93  30.0  1
 64U  Var_08    C3    C4   N1   C14  -158.26  30.0  1
 64U  Var_09    H13   C13  C12  C11    66.11  30.0  1
 64U  Var_10    H13A  C13  C12  C11  -177.55  30.0  1
 64U  Var_11    H17   C17  C18  C11   -65.13  30.0  1
 64U  Var_12    H17A  C17  C18  C11   178.23  30.0  1
 64U  Var_13    H16   C16  C13  C12   177.86  30.0  1
 64U  Var_14    H16A  C16  C13  C12   -65.47  30.0  1
 64U  Var_15    H17   C17  C16  C13    65.35  30.0  1
 64U  Var_16    H17A  C17  C16  C13  -177.86  30.0  1
 64U  Var_17    H12   C12  C13  C16  -177.59  30.0  1
 64U  Var_18    H12A  C12  C13  C16    66.42  30.0  1
 64U  Var_19    H18   C18  C17  C16   -65.24  30.0  1
 64U  Var_20    H18A  C18  C17  C16   178.10  30.0  1
 64U  Var_21    H13   C13  C16  C17   -65.63  30.0  1
 64U  Var_22    H13A  C13  C16  C17   177.75  30.0  1
 64U  Var_23    H16   C16  C17  C18  -177.98  30.0  1
 64U  Var_24    H16A  C16  C17  C18    65.15  30.0  1
 64U  Var_25    H3    C3   C4   N1   -157.91  30.0  1
 64U  Var_26    H3A   C3   C4   N1     81.58  30.0  1
 64U  Var_27    H4    C4   N1   C5    143.90  30.0  1
 64U  Var_28    H4A   C4   N1   C5    -95.23  30.0  1
 64U  Var_29    H3    C3   C2   C5    157.56  30.0  1
 64U  Var_30    H3A   C3   C2   C5    -81.37  30.0  1
 64U  Var_31    H4    C4   C3   C2   -156.03  30.0  1
 64U  Var_32    H4A   C4   C3   C2     82.38  30.0  1
 64U  Var_33    H2    C2   C3   C4    -82.33  30.0  1
 64U  Var_34    H2A   C2   C3   C4    157.06  30.0  1
 64U  Var_35    C30   C25  C24  N23    12.83  30.0  2
 64U  Var_36    C26   C25  C24  N23  -168.21  30.0  2
 64U  Var_37    H4    C4   N1   C14   -37.96  30.0  1
 64U  Var_38    H4A   C4   N1   C14    82.91  30.0  1
 64U  Var_39    H24   C24  C25  C26    69.99  30.0  2
 64U  Var_40    H24A  C24  C25  C26   -45.97  30.0  2
 64U  Var_41    H24   C24  C25  C30  -108.97  30.0  2
 64U  Var_42    H24A  C24  C25  C30   135.07  30.0  2
 64U  Var_43    C25   C24  N23  C7    -95.60  30.0  3
 64U  Var_44    HN23  N23  C24  C25    79.95  30.0  2
 64U  Var_45    H24   C24  N23  C7     26.59  30.0  3
 64U  Var_46    H24A  C24  N23  C7    141.89  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
 64U  chir_01  C11  C1  C12  C18  negativ
 64U  chir_02  C15  N   C14  C1   negativ
 64U  chir_03  C5   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
 64U  plan-1  C15   0.020
 64U  plan-1  C14   0.020
 64U  plan-1  O32   0.020
 64U  plan-1  N1    0.020
 64U  plan-1  C5    0.020
 64U  plan-1  C4    0.020
 64U  plan-2  C24   0.020
 64U  plan-2  C25   0.020
 64U  plan-2  C26   0.020
 64U  plan-2  C27   0.020
 64U  plan-2  C28   0.020
 64U  plan-2  C29   0.020
 64U  plan-2  C30   0.020
 64U  plan-2  CL21  0.020
 64U  plan-2  H26   0.020
 64U  plan-2  H27   0.020
 64U  plan-2  H28   0.020
 64U  plan-2  H30   0.020
 64U  plan-3  C5    0.020
 64U  plan-3  C7    0.020
 64U  plan-3  O22   0.020
 64U  plan-3  N23   0.020
 64U  plan-3  C24   0.020
 64U  plan-3  HN23  0.020

