# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 12:06:47 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-methyl-D-phenylalanyl-N-[(trans-4-aminocyclohexyl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NC[C@@H]3CC[C@@H](N)CC3
#
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
 MIN  MIN  N-methyl-D-phenylalanyl-N-[(trans-4-aminocyclohexyl)methyl]-L-prolinamide  peptide  62  28  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MIN
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
 MIN  N13   N  NH1   0  -0.560  -3.1408  -1.7063   0.7180
 MIN  C15   C  CH1   0  -0.207  -2.9410  -0.3695   0.2247
 MIN  C13   C  C     0   0.549  -1.4643  -0.0472  -0.0300
 MIN  O13   O  O     0  -0.502  -0.6955  -0.9181  -0.4219
 MIN  C16   C  CH2   0  -0.540  -3.7029  -0.1601  -1.0954
 MIN  C17   C  CR6   0   0.165  -5.1892  -0.2691  -0.9207
 MIN  C18   C  CR16  0  -0.315  -5.9279   0.8332  -0.4968
 MIN  C22   C  CR16  0  -0.308  -5.8585  -1.4673  -1.1534
 MIN  C19   C  CR16  0  -0.240  -7.3008   0.7444  -0.3099
 MIN  C21   C  CR16  0  -0.244  -7.2322  -1.5610  -0.9735
 MIN  C20   C  CR16  0  -0.274  -7.9583  -0.4555  -0.5491
 MIN  C14   C  CH3   0  -0.528  -2.6153  -1.9211   2.0524
 MIN  N9    N  NT    0  -0.472  -1.0534   1.2161   0.1466
 MIN  C9    C  CH1   0  -0.166   0.3395   1.5602  -0.0752
 MIN  C8    C  C     0   0.563   1.2551   0.7156   0.8033
 MIN  O8    O  O     0  -0.498   0.9804   0.4817   1.9705
 MIN  C10   C  CH2   0  -0.480   0.4124   3.0439   0.3143
 MIN  C11   C  CH2   0  -0.470  -1.0137   3.5402   0.1051
 MIN  C12   C  CH2   0  -0.285  -1.8561   2.3595   0.5648
 MIN  N7    N  NH1   0  -0.646   2.3983   0.3331   0.2243
 MIN  C7    C  CH2   0  -0.221   3.4033  -0.4489   0.9131
 MIN  C4    C  CH1   0  -0.297   4.6507  -0.6306   0.0590
 MIN  C5    C  CH2   0  -0.422   5.3435   0.6943  -0.2619
 MIN  C6    C  CH2   0  -0.432   6.6115   0.4760  -1.0799
 MIN  C1    C  CH1   0  -0.053   7.5833  -0.4588  -0.3695
 MIN  C2    C  CH2   0  -0.433   6.8954  -1.7838  -0.0617
 MIN  C3    C  CH2   0  -0.424   5.6261  -1.5779   0.7568
 MIN  N1    N  NH2   0  -0.806   8.7542  -0.6857  -1.2056
 MIN  HN3   H  HNH1  0   0.342  -2.7208  -2.3674   0.0764
 MIN  H15   H  HCH1  0   0.261  -3.3497   0.3165   0.9737
 MIN  H161  H  HCH2  0   0.263  -3.4529   0.8230  -1.5039
 MIN  H162  H  HCH2  0   0.262  -3.3489  -0.8953  -1.8232
 MIN  H18   H  HCR6  0   0.247  -5.4232   1.7760  -0.3147
 MIN  H22   H  HCR6  0   0.242  -5.3027  -2.3345  -1.4884
 MIN  H19   H  HCR6  0   0.253  -7.8567   1.6140   0.0168
 MIN  H21   H  HCR6  0   0.252  -7.7367  -2.4994  -1.1661
 MIN  H20   H  HCR6  0   0.253  -9.0294  -0.5275  -0.4106
 MIN  H141  H  HCH3  0   0.234  -2.7698  -2.9613   2.3380
 MIN  H142  H  HCH3  0   0.201  -1.5465  -1.6997   2.1698
 MIN  H143  H  HCH3  0   0.223  -3.1603  -1.3020   2.7676
 MIN  H9    H  HCH1  0   0.272   0.5962   1.4299  -1.1321
 MIN  H101  H  HCH2  0   0.250   0.6895   3.1464   1.3655
 MIN  H102  H  HCH2  0   0.265   1.1496   3.5799  -0.2807
 MIN  H111  H  HCH2  0   0.258  -1.2361   4.4484   0.6634
 MIN  H112  H  HCH2  0   0.245  -1.1997   3.7384  -0.9522
 MIN  H121  H  HCH2  0   0.248  -1.9929   2.3674   1.6503
 MIN  H122  H  HCH2  0   0.256  -2.8410   2.3536   0.0988
 MIN  HN7   H  HNH1  0   0.399   2.5002   0.4652  -0.7693
 MIN  H71   H  HCH2  0   0.236   2.9970  -1.4308   1.1788
 MIN  H72   H  HCH2  0   0.229   3.6682   0.0475   1.8508
 MIN  H4    H  HCH1  0   0.226   4.3505  -1.1014  -0.8876
 MIN  H51   H  HCH2  0   0.232   4.6713   1.3646  -0.8031
 MIN  H52   H  HCH2  0   0.212   5.5955   1.2008   0.6774
 MIN  H61   H  HCH2  0   0.228   7.0964   1.4364  -1.2800
 MIN  H62   H  HCH2  0   0.210   6.3553   0.0445  -2.0540
 MIN  H1    H  HCH1  0   0.185   7.8427   0.0088   0.5957
 MIN  H21A  H  HCH2  0   0.210   6.6500  -2.2832  -1.0057
 MIN  H22A  H  HCH2  0   0.228   7.5819  -2.4447   0.4764
 MIN  H31   H  HCH2  0   0.233   5.1416  -2.5402   0.9432
 MIN  H32   H  HCH2  0   0.213   5.8852  -1.1669   1.7395
 MIN  HN11  H  HNH2  0   0.339   9.2380   0.1929  -1.3503
 MIN  HN12  H  HNH2  0   0.339   9.4121  -1.2783  -0.7129

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
 MIN  N1   C1    single    1.457  0.020  1.457
 MIN  N1   HN11  single    0.890  0.020  1.040
 MIN  N1   HN12  single    0.890  0.020  1.040
 MIN  C1   C2    single    1.524  0.020  1.524
 MIN  C1   C6    single    1.524  0.020  1.524
 MIN  C1   H1    single    0.970  0.020  1.090
 MIN  C2   C3    single    1.524  0.020  1.524
 MIN  C2   H21A  single    0.970  0.020  1.090
 MIN  C2   H22A  single    0.970  0.020  1.090
 MIN  C3   C4    single    1.528  0.020  1.528
 MIN  C3   H31   single    0.970  0.020  1.090
 MIN  C3   H32   single    0.970  0.020  1.090
 MIN  C4   C5    single    1.529  0.020  1.529
 MIN  C4   C7    single    1.523  0.020  1.523
 MIN  C4   H4    single    0.970  0.020  1.090
 MIN  C5   C6    single    1.525  0.020  1.525
 MIN  C5   H51   single    0.970  0.020  1.090
 MIN  C5   H52   single    0.970  0.020  1.090
 MIN  C6   H61   single    0.970  0.020  1.090
 MIN  C6   H62   single    0.970  0.020  1.090
 MIN  C7   N7    single    1.448  0.020  1.448
 MIN  C7   H71   single    0.970  0.020  1.090
 MIN  C7   H72   single    0.970  0.020  1.090
 MIN  N7   C8    single    1.337  0.020  1.337
 MIN  N7   HN7   single    0.860  0.020  1.020
 MIN  C8   O8    double    1.222  0.020  1.222
 MIN  C8   C9    single    1.524  0.020  1.524
 MIN  C9   C10   single    1.536  0.020  1.536
 MIN  C9   N9    single    1.452  0.020  1.452
 MIN  C9   H9    single    0.970  0.020  1.090
 MIN  C10  C11   single    1.524  0.020  1.524
 MIN  C10  H101  single    0.970  0.020  1.090
 MIN  C10  H102  single    0.970  0.020  1.090
 MIN  C11  C12   single    1.522  0.020  1.522
 MIN  C11  H111  single    0.970  0.020  1.090
 MIN  C11  H112  single    0.970  0.020  1.090
 MIN  C12  N9    single    1.458  0.020  1.458
 MIN  C12  H121  single    0.970  0.020  1.090
 MIN  C12  H122  single    0.970  0.020  1.090
 MIN  N9   C13   single    1.340  0.020  1.340
 MIN  C13  O13   double    1.226  0.020  1.226
 MIN  C13  C15   single    1.533  0.020  1.533
 MIN  C14  N13   single    1.450  0.020  1.450
 MIN  C14  H141  single    0.970  0.020  1.090
 MIN  C14  H142  single    0.970  0.020  1.090
 MIN  C14  H143  single    0.970  0.020  1.090
 MIN  N13  C15   single    1.439  0.020  1.439
 MIN  N13  HN3   single    0.890  0.020  1.040
 MIN  C15  C16   single    1.539  0.020  1.539
 MIN  C15  H15   single    0.970  0.020  1.090
 MIN  C16  C17   single    1.501  0.020  1.501
 MIN  C16  H161  single    0.970  0.020  1.090
 MIN  C16  H162  single    0.970  0.020  1.090
 MIN  C17  C18   aromatic  1.393  0.020  1.393
 MIN  C17  C22   aromatic  1.392  0.020  1.392
 MIN  C18  C19   aromatic  1.388  0.020  1.388
 MIN  C18  H18   single    0.930  0.020  1.080
 MIN  C19  C20   aromatic  1.389  0.020  1.389
 MIN  C19  H19   single    0.930  0.020  1.080
 MIN  C20  C21   aromatic  1.389  0.020  1.389
 MIN  C20  H20   single    0.930  0.020  1.080
 MIN  C21  C22   aromatic  1.389  0.020  1.389
 MIN  C21  H21   single    0.930  0.020  1.080
 MIN  C22  H22   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
 MIN  HN3   N13  C14   109.64  3.000
 MIN  HN3   N13  C15   109.37  3.000
 MIN  C14   N13  C15   113.75  3.000
 MIN  H15   C15  C16   108.47  3.000
 MIN  H15   C15  C13   109.98  3.000
 MIN  C16   C15  C13   107.81  3.000
 MIN  H15   C15  N13   107.20  3.000
 MIN  C16   C15  N13   110.60  3.000
 MIN  C13   C15  N13   112.72  3.000
 MIN  N9    C13  O13   121.30  3.000
 MIN  O13   C13  C15   120.52  3.000
 MIN  N9    C13  C15   118.15  3.000
 MIN  H162  C16  H161  106.37  3.000
 MIN  H162  C16  C17   110.45  3.000
 MIN  H161  C16  C17   109.59  3.000
 MIN  H162  C16  C15   108.62  3.000
 MIN  H161  C16  C15   109.25  3.000
 MIN  C17   C16  C15   112.38  3.000
 MIN  C22   C17  C18   118.49  3.000
 MIN  C22   C17  C16   121.29  3.000
 MIN  C18   C17  C16   120.21  3.000
 MIN  H18   C18  C19   119.54  3.000
 MIN  H18   C18  C17   119.48  3.000
 MIN  C19   C18  C17   120.98  3.000
 MIN  H22   C22  C21   119.58  3.000
 MIN  H22   C22  C17   119.61  3.000
 MIN  C21   C22  C17   120.80  3.000
 MIN  H19   C19  C20   120.19  3.000
 MIN  H19   C19  C18   119.80  3.000
 MIN  C20   C19  C18   120.01  3.000
 MIN  H21   C21  C20   120.04  3.000
 MIN  H21   C21  C22   119.76  3.000
 MIN  C20   C21  C22   120.20  3.000
 MIN  H20   C20  C21   120.22  3.000
 MIN  H20   C20  C19   120.26  3.000
 MIN  C21   C20  C19   119.52  3.000
 MIN  H143  C14  H142  107.56  3.000
 MIN  H143  C14  H141  107.39  3.000
 MIN  H142  C14  H141  107.61  3.000
 MIN  H143  C14  N13   109.75  3.000
 MIN  H142  C14  N13   114.92  3.000
 MIN  H141  C14  N13   109.33  3.000
 MIN  C12   N9   C9    112.71  3.000
 MIN  C12   N9   C13   127.46  3.000
 MIN  C9    N9   C13   119.83  3.000
 MIN  H9    C9   C10   110.40  3.000
 MIN  H9    C9   C8    110.45  3.000
 MIN  C10   C9   C8    111.14  3.000
 MIN  H9    C9   N9    110.12  3.000
 MIN  C10   C9   N9    103.64  3.000
 MIN  C8    C9   N9    110.91  3.000
 MIN  N7    C8   O8    123.44  3.000
 MIN  O8    C8   C9    121.44  3.000
 MIN  N7    C8   C9    114.99  3.000
 MIN  H102  C10  H101  107.94  3.000
 MIN  H102  C10  C11   113.47  3.000
 MIN  H101  C10  C11   109.81  3.000
 MIN  H102  C10  C9    111.67  3.000
 MIN  H101  C10  C9    110.30  3.000
 MIN  C11   C10  C9    103.61  3.000
 MIN  H112  C11  H111  108.08  3.000
 MIN  H112  C11  C12   109.83  3.000
 MIN  H111  C11  C12   112.28  3.000
 MIN  H112  C11  C10   110.57  3.000
 MIN  H111  C11  C10   113.09  3.000
 MIN  C12   C11  C10   102.93  3.000
 MIN  H122  C12  H121  108.14  3.000
 MIN  H122  C12  C11   112.05  3.000
 MIN  H121  C12  C11   111.31  3.000
 MIN  H122  C12  N9    111.75  3.000
 MIN  H121  C12  N9    111.04  3.000
 MIN  C11   C12  N9    102.54  3.000
 MIN  HN7   N7   C7    118.03  3.000
 MIN  HN7   N7   C8    118.42  3.000
 MIN  C7    N7   C8    122.81  3.000
 MIN  H72   C7   H71   106.79  3.000
 MIN  H72   C7   C4    109.67  3.000
 MIN  H71   C7   C4    109.45  3.000
 MIN  H72   C7   N7    109.33  3.000
 MIN  H71   C7   N7    110.01  3.000
 MIN  C4    C7   N7    111.48  3.000
 MIN  H4    C4   C3    107.58  3.000
 MIN  H4    C4   C5    108.31  3.000
 MIN  C3    C4   C5    110.11  3.000
 MIN  H4    C4   C7    108.08  3.000
 MIN  C5    C4   C7    112.68  3.000
 MIN  C3    C4   C7    109.92  3.000
 MIN  H52   C5   H51   106.40  3.000
 MIN  H52   C5   C6    109.55  3.000
 MIN  H51   C5   C6    109.49  3.000
 MIN  H52   C5   C4    108.94  3.000
 MIN  H51   C5   C4    110.90  3.000
 MIN  C6    C5   C4    111.43  3.000
 MIN  H62   C6   H61   106.66  3.000
 MIN  H62   C6   C1    108.77  3.000
 MIN  H61   C6   C1    109.94  3.000
 MIN  H62   C6   C5    109.81  3.000
 MIN  H61   C6   C5    109.94  3.000
 MIN  C1    C6   C5    111.59  3.000
 MIN  H1    C1   N1    112.28  3.000
 MIN  H1    C1   C2    107.33  3.000
 MIN  N1    C1   C2    110.08  3.000
 MIN  H1    C1   C6    107.31  3.000
 MIN  C2    C1   C6    109.85  3.000
 MIN  N1    C1   C6    109.91  3.000
 MIN  H22A  C2   H21A  106.79  3.000
 MIN  H22A  C2   C3    109.87  3.000
 MIN  H21A  C2   C3    109.74  3.000
 MIN  H22A  C2   C1    109.94  3.000
 MIN  H21A  C2   C1    108.86  3.000
 MIN  C3    C2   C1    111.52  3.000
 MIN  H32   C3   H31   106.37  3.000
 MIN  H32   C3   C2    109.58  3.000
 MIN  H31   C3   C2    109.98  3.000
 MIN  H32   C3   C4    109.13  3.000
 MIN  H31   C3   C4    109.92  3.000
 MIN  C2    C3   C4    111.71  3.000
 MIN  HN12  N1   HN11  105.45  3.000
 MIN  HN12  N1   C1    109.51  3.000
 MIN  HN11  N1   C1    109.31  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
 MIN  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 MIN  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 MIN  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 MIN  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 MIN  CONST_05  C19   C18  C17  C22     0.00   0.0  0
 MIN  CONST_06  C19   C20  C21  C22     0.00   0.0  0
 MIN  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 MIN  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 MIN  CONST_09  H19   C19  C18  C17   180.00   0.0  0
 MIN  CONST_10  H21   C21  C22  C17   180.00   0.0  0
 MIN  CONST_11  H22   C22  C17  C18   180.00   0.0  0
 MIN  CONST_12  H20   C20  C19  C18   180.00   0.0  0
 MIN  CONST_13  H18   C18  C17  C22   180.00   0.0  0
 MIN  CONST_14  C9    N9   C13  C15   180.00   0.0  0
 MIN  CONST_15  C12   N9   C13  C15     0.00   0.0  0
 MIN  CONST_16  C9    N9   C13  O13     0.00   0.0  0
 MIN  CONST_17  C12   N9   C13  O13   180.00   0.0  0
 MIN  CONST_18  C7    N7   C8   C9    180.00   0.0  0
 MIN  CONST_19  HN7   N7   C8   C9      0.00   0.0  0
 MIN  CONST_20  C7    N7   C8   O8      0.00   0.0  0
 MIN  Var_01    C10   C11  C12  N9    -34.99  30.0  1
 MIN  Var_02    C12   C11  C10  C9     37.44  30.0  1
 MIN  Var_03    C11   C12  N9   C9     20.21  30.0  1
 MIN  Var_04    C1    C2   C3   C4     56.36  30.0  1
 MIN  Var_05    C1    C6   C5   C4    -56.73  30.0  1
 MIN  Var_06    C18   C17  C16  C15    84.09  30.0  2
 MIN  Var_07    C4    C7   N7   C8   -174.79  30.0  2
 MIN  Var_08    H141  C14  N13  C15  -177.81  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
 MIN  chir_01  C15  C13  N13  C16  positiv
 MIN  chir_02  C9   N9   C10  C8   negativ
 MIN  chir_03  C4   C3   C5   C7   positiv
 MIN  chir_04  C1   N1   C6   C2   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
 MIN  plan-1  C16  0.020
 MIN  plan-1  C17  0.020
 MIN  plan-1  C18  0.020
 MIN  plan-1  C22  0.020
 MIN  plan-1  C19  0.020
 MIN  plan-1  C21  0.020
 MIN  plan-1  C20  0.020
 MIN  plan-1  H18  0.020
 MIN  plan-1  H22  0.020
 MIN  plan-1  H19  0.020
 MIN  plan-1  H21  0.020
 MIN  plan-1  H20  0.020
 MIN  plan-2  C9   0.020
 MIN  plan-2  C8   0.020
 MIN  plan-2  O8   0.020
 MIN  plan-2  N7   0.020
 MIN  plan-2  C7   0.020
 MIN  plan-2  HN7  0.020
 MIN  plan-3  C15  0.020
 MIN  plan-3  C13  0.020
 MIN  plan-3  O13  0.020
 MIN  plan-3  N9   0.020
 MIN  plan-3  C9   0.020
 MIN  plan-3  C12  0.020

