# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:38:35 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[3-(1H-benzimidazol-1-yl)propanoyl]glycyl-L-alanyl-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](C)NC(=O)CNC(=O)CCn1cnc2ccccc12)C(N)=O
#
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
 N31  N31  N-[3-(1H-benzimidazol-1-yl)propanoyl]glycyl-L-alanyl-L-alaninamide  peptide  52  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N31
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
 N31  C1   C  CR16  0  -0.305  -5.8102  -1.7241  -0.1977
 N31  C2   C  CR16  0  -0.323  -8.3071  -0.9064  -1.2985
 N31  C3   C  CR16  0  -0.273  -7.8093  -2.1795  -1.5073
 N31  C4   C  CR16  0  -0.276  -6.5797  -2.5826  -0.9631
 N31  C5   C  CR56  0   0.125  -7.5468  -0.0249  -0.5300
 N31  C6   C  CH2   0  -0.598  -3.4120   0.8624   0.4082
 N31  N1   N  NR5   0  -0.510  -5.8418   0.6410   0.6975
 N31  C8   C  CR56  0   0.338  -6.3166  -0.4440   0.0044
 N31  C9   C  CR15  0   0.107  -6.7652   1.6241   0.5474
 N31  N2   N  N     0  -0.470  -7.7964   1.2783  -0.1681
 N31  C10  C  C     0   0.578  -2.0975   1.0922   1.1235
 N31  O1   O  O     0  -0.501  -2.0293   1.6915   2.1882
 N31  N3   N  NH1   0  -0.648  -1.0172   0.6239   0.4863
 N31  C11  C  CH2   0  -0.372   0.3180   0.8399   0.9683
 N31  C12  C  C     0   0.531   1.3189   0.3368  -0.0590
 N31  O3   O  O     0  -0.491   0.9743  -0.3187  -1.0316
 N31  N4   N  NH1   0  -0.639   2.5883   0.6568   0.2122
 N31  C13  C  CH1   0  -0.203   3.6965   0.2754  -0.6297
 N31  C14  C  C     0   0.561   4.9586   0.2532   0.2271
 N31  O5   O  O     0  -0.491   5.0590   0.9305   1.2404
 N31  C15  C  CH3   0  -0.648   3.8855   1.2394  -1.8039
 N31  N5   N  NH1   0  -0.637   5.9399  -0.5143  -0.2559
 N31  C16  C  CH1   0  -0.199   7.2478  -0.6061   0.3458
 N31  C17  C  C     0   0.522   8.2412  -1.0039  -0.7441
 N31  O7   O  O     0  -0.484   7.8743  -1.5477  -1.7754
 N31  C18  C  CH3   0  -0.651   7.2855  -1.6272   1.4850
 N31  N6   N  NH2   0  -0.797   9.5187  -0.7445  -0.4546
 N31  H1   H  HCR6  0   0.269  -4.8634  -2.0428   0.2187
 N31  H2   H  HCR6  0   0.255  -9.2570  -0.5994  -1.7171
 N31  H3   H  HCR6  0   0.253  -8.3755  -2.8827  -2.1038
 N31  H4   H  HCR6  0   0.256  -6.2256  -3.5884  -1.1472
 N31  H5   H  HCH2  0   0.273  -3.3561  -0.0232  -0.2280
 N31  H6   H  HCH2  0   0.274  -4.4526  -0.1121   2.0404
 N31  H7   H  HCH2  0   0.279  -4.6216   1.6328   2.0232
 N31  H8   H  HCR5  0   0.289  -6.6218   2.5933   1.0042
 N31  H9   H  HCH2  0   0.291  -3.5788   1.7132  -0.2598
 N31  H11  H  HNH1  0   0.403  -1.1174   0.1085  -0.3753
 N31  H13  H  HCH2  0   0.276   0.4963   1.9004   1.1646
 N31  H14  H  HCH2  0   0.283   0.4946   0.3121   1.9117
 N31  H16  H  HNH1  0   0.405   2.7983   1.2403   1.0094
 N31  H18  H  HCH1  0   0.281   3.5086  -0.7275  -1.0189
 N31  H19  H  HCH3  0   0.238   4.0878   2.2494  -1.4469
 N31  H20  H  HCH3  0   0.240   4.7132   0.9255  -2.4393
 N31  H21  H  HCH3  0   0.252   2.9848   1.2617  -2.4150
 N31  H23  H  HNH1  0   0.403   5.7772  -1.0832  -1.0740
 N31  H25  H  HCH1  0   0.282   7.5229   0.3762   0.7363
 N31  H26  H  HCH3  0   0.238   7.0383  -2.6242   1.1198
 N31  H27  H  HCH3  0   0.242   8.2709  -1.6656   1.9486
 N31  H28  H  HCH3  0   0.252   6.5658  -1.3531   2.2548
 N31  H30  H  HNH2  0   0.414   9.7914  -0.2786   0.3938
 N31  H31  H  HNH2  0   0.408  10.2527  -1.0257  -1.0845
 N31  C7   C  CH2   0  -0.302  -4.5747   0.7522   1.3856

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
 N31  C1   C4   aromatic  1.384  0.020  1.384
 N31  C1   C8   aromatic  1.391  0.020  1.391
 N31  C1   H1   single    0.930  0.020  1.080
 N31  C2   C3   aromatic  1.383  0.020  1.383
 N31  C2   C5   aromatic  1.395  0.020  1.395
 N31  C2   H2   single    0.930  0.020  1.080
 N31  C3   C4   aromatic  1.404  0.020  1.404
 N31  C3   H3   single    0.930  0.020  1.080
 N31  C4   H4   single    0.930  0.020  1.080
 N31  C5   C8   aromatic  1.405  0.020  1.405
 N31  C5   N2   aromatic  1.375  0.020  1.375
 N31  C6   C7   single    1.523  0.020  1.523
 N31  C6   C10  single    1.514  0.020  1.514
 N31  C6   H5   single    0.970  0.020  1.090
 N31  C7   N1   single    1.446  0.020  1.446
 N31  C7   H6   single    0.970  0.020  1.090
 N31  C7   H7   single    0.970  0.020  1.090
 N31  N1   C8   aromatic  1.372  0.020  1.372
 N31  N1   C9   aromatic  1.357  0.020  1.357
 N31  C9   N2   aromatic  1.302  0.020  1.302
 N31  C9   H8   aromatic  0.930  0.020  1.080
 N31  C10  O1   double    1.224  0.020  1.224
 N31  C6   H9   single    0.970  0.020  1.090
 N31  N3   C11  single    1.436  0.020  1.436
 N31  N3   H11  single    0.860  0.020  1.020
 N31  C11  C12  single    1.520  0.020  1.520
 N31  C11  H13  single    0.970  0.020  1.090
 N31  C11  H14  single    0.970  0.020  1.090
 N31  C12  O3   double    1.222  0.020  1.222
 N31  N4   C13  single    1.443  0.020  1.443
 N31  N4   H16  single    0.860  0.020  1.020
 N31  C13  C14  single    1.526  0.020  1.526
 N31  C13  C15  single    1.531  0.020  1.531
 N31  C13  H18  single    0.970  0.020  1.090
 N31  C14  O5   double    1.223  0.020  1.223
 N31  C15  H19  single    0.970  0.020  1.090
 N31  C15  H20  single    0.970  0.020  1.090
 N31  C15  H21  single    0.970  0.020  1.090
 N31  N5   C16  single    1.443  0.020  1.443
 N31  N5   H23  single    0.860  0.020  1.020
 N31  C16  C17  single    1.527  0.020  1.527
 N31  C16  C18  single    1.530  0.020  1.530
 N31  C16  H25  single    0.970  0.020  1.090
 N31  C17  O7   double    1.222  0.020  1.222
 N31  C18  H26  single    0.970  0.020  1.090
 N31  C18  H27  single    0.970  0.020  1.090
 N31  C18  H28  single    0.970  0.020  1.090
 N31  N6   H30  single    0.860  0.020  1.020
 N31  N6   H31  single    0.860  0.020  1.020
 N31  C10  N3   single    1.339  0.020  1.339
 N31  C12  N4   single    1.337  0.020  1.337
 N31  C14  N5   single    1.336  0.020  1.336
 N31  C17  N6   single    1.335  0.020  1.335

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
 N31  H1   C1   C8   122.23  3.000
 N31  H1   C1   C4   121.10  3.000
 N31  C8   C1   C4   116.66  3.000
 N31  H2   C2   C5   120.81  3.000
 N31  H2   C2   C3   121.24  3.000
 N31  C5   C2   C3   117.95  3.000
 N31  H3   C3   C4   119.04  3.000
 N31  H3   C3   C2   119.55  3.000
 N31  C4   C3   C2   121.41  3.000
 N31  H4   C4   C3   119.18  3.000
 N31  H4   C4   C1   119.27  3.000
 N31  C3   C4   C1   121.56  3.000
 N31  N2   C5   C8   109.96  3.000
 N31  N2   C5   C2   130.15  3.000
 N31  C8   C5   C2   119.88  3.000
 N31  H9   C6   H5   106.42  3.000
 N31  H9   C6   C10  107.62  3.000
 N31  H5   C6   C10  110.73  3.000
 N31  H9   C6   C7   109.36  3.000
 N31  H5   C6   C7   110.75  3.000
 N31  C10  C6   C7   111.75  3.000
 N31  C9   N1   C8   106.35  3.000
 N31  C9   N1   C7   126.37  3.000
 N31  C8   N1   C7   127.18  3.000
 N31  N1   C8   C5   105.02  3.000
 N31  N1   C8   C1   132.44  3.000
 N31  C5   C8   C1   122.53  3.000
 N31  H8   C9   N2   125.13  3.000
 N31  H8   C9   N1   120.83  3.000
 N31  N2   C9   N1   114.04  3.000
 N31  C9   N2   C5   104.63  3.000
 N31  N3   C10  O1   122.72  3.000
 N31  N3   C10  C6   115.00  3.000
 N31  O1   C10  C6   122.26  3.000
 N31  H11  N3   C11  117.12  3.000
 N31  H11  N3   C10  120.33  3.000
 N31  C11  N3   C10  122.54  3.000
 N31  H14  C11  H13  106.65  3.000
 N31  H14  C11  C12  108.45  3.000
 N31  H13  C11  C12  109.58  3.000
 N31  H14  C11  N3   111.51  3.000
 N31  H13  C11  N3   110.97  3.000
 N31  C12  C11  N3   109.61  3.000
 N31  N4   C12  O3   123.88  3.000
 N31  N4   C12  C11  114.14  3.000
 N31  O3   C12  C11  121.98  3.000
 N31  H16  N4   C13  116.97  3.000
 N31  H16  N4   C12  119.72  3.000
 N31  C13  N4   C12  123.20  3.000
 N31  H18  C13  C15  109.04  3.000
 N31  H18  C13  C14  109.21  3.000
 N31  C15  C13  C14  109.74  3.000
 N31  H18  C13  N4   108.58  3.000
 N31  C15  C13  N4   112.08  3.000
 N31  C14  C13  N4   108.15  3.000
 N31  N5   C14  O5   123.87  3.000
 N31  N5   C14  C13  114.39  3.000
 N31  O5   C14  C13  121.68  3.000
 N31  H21  C15  H20  107.88  3.000
 N31  H21  C15  H19  108.57  3.000
 N31  H20  C15  H19  108.48  3.000
 N31  H21  C15  C13  109.95  3.000
 N31  H20  C15  C13  111.08  3.000
 N31  H19  C15  C13  110.80  3.000
 N31  H23  N5   C16  116.63  3.000
 N31  H23  N5   C14  119.88  3.000
 N31  C16  N5   C14  123.48  3.000
 N31  H25  C16  C18  109.13  3.000
 N31  H25  C16  C17  108.99  3.000
 N31  C18  C16  C17  109.97  3.000
 N31  H25  C16  N5   108.67  3.000
 N31  C18  C16  N5   112.04  3.000
 N31  C17  C16  N5   107.98  3.000
 N31  N6   C17  O7   123.81  3.000
 N31  N6   C17  C16  114.64  3.000
 N31  O7   C17  C16  121.52  3.000
 N31  H28  C18  H27  107.81  3.000
 N31  H28  C18  H26  108.49  3.000
 N31  H27  C18  H26  108.38  3.000
 N31  H28  C18  C16  110.00  3.000
 N31  H27  C18  C16  111.25  3.000
 N31  H26  C18  C16  110.81  3.000
 N31  H31  N6   H30  117.35  3.000
 N31  H31  N6   C17  120.49  3.000
 N31  H30  N6   C17  122.16  3.000
 N31  H7   C7   H6   107.11  3.000
 N31  H7   C7   N1   107.65  3.000
 N31  H6   C7   N1   108.82  3.000
 N31  H7   C7   C6   110.51  3.000
 N31  H6   C7   C6   110.92  3.000
 N31  N1   C7   C6   111.66  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
 N31  CONST_01  C2   C3   C4   C1      0.00   0.0  0
 N31  CONST_02  C2   C5   C8   C1      0.00   0.0  0
 N31  CONST_03  N2   C5   C8   C1    180.00   0.0  0
 N31  CONST_04  C9   N1   C8   C1    180.00   0.0  0
 N31  CONST_05  N1   C8   C5   C2    180.00   0.0  0
 N31  CONST_06  C9   N2   C5   C2    180.00   0.0  0
 N31  CONST_07  C8   C5   C2   C3      0.00   0.0  0
 N31  CONST_08  N2   C5   C2   C3    180.00   0.0  0
 N31  CONST_09  C8   C1   C4   C3      0.00   0.0  0
 N31  CONST_10  C5   C8   C1   C4      0.00   0.0  0
 N31  CONST_11  N1   C8   C1   C4    180.00   0.0  0
 N31  CONST_12  C5   C2   C3   C4      0.00   0.0  0
 N31  CONST_13  C9   N1   C8   C5      0.00   0.0  0
 N31  CONST_14  N1   C9   N2   C5      0.00   0.0  0
 N31  CONST_15  N2   C5   C8   N1      0.00   0.0  0
 N31  CONST_16  C9   N2   C5   C8      0.00   0.0  0
 N31  CONST_17  N2   C9   N1   C8      0.00   0.0  0
 N31  CONST_18  C7   N1   C8   C1      0.00   0.0  0
 N31  CONST_19  C7   N1   C8   C5    180.00   0.0  0
 N31  CONST_20  N2   C9   N1   C7    180.00   0.0  0
 N31  CONST_21  H8   C9   N2   C5    180.00   0.0  0
 N31  CONST_22  H3   C3   C4   C1    180.00   0.0  0
 N31  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 N31  CONST_24  H1   C1   C4   C3    180.00   0.0  0
 N31  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 N31  CONST_26  C11  N3   C10  C6    180.00   0.0  0
 N31  CONST_27  C11  N3   C10  O1      0.00   0.0  0
 N31  CONST_28  C13  N4   C12  C11   180.00   0.0  0
 N31  CONST_29  C13  N4   C12  O3      0.00   0.0  0
 N31  CONST_30  C16  N5   C14  C13   180.00   0.0  0
 N31  CONST_31  C16  N5   C14  O5      0.00   0.0  0
 N31  CONST_32  H11  N3   C10  C6      0.00   0.0  0
 N31  CONST_33  H16  N4   C12  C11     0.00   0.0  0
 N31  CONST_34  H23  N5   C14  C13     0.00   0.0  0
 N31  CONST_35  H30  N6   C17  C16     0.00   0.0  0
 N31  CONST_36  H31  N6   C17  C16   180.00   0.0  0
 N31  Var_01    C8   N1   C7   C6     72.24  30.0  2
 N31  Var_02    C10  C6   C7   N1    175.35  30.0  2
 N31  Var_03    O1   C10  C6   C7    -30.28  30.0  3
 N31  Var_04    C12  C11  N3   C10  -173.06  30.0  3
 N31  Var_05    O3   C12  C11  N3     -9.69  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
 N31  chir_01  C13  N4  C14  C15  positiv
 N31  chir_02  C16  N5  C17  C18  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
 N31  plan-1  C1   0.020
 N31  plan-1  C2   0.020
 N31  plan-1  C3   0.020
 N31  plan-1  C4   0.020
 N31  plan-1  C5   0.020
 N31  plan-1  N1   0.020
 N31  plan-1  C8   0.020
 N31  plan-1  C9   0.020
 N31  plan-1  N2   0.020
 N31  plan-1  H1   0.020
 N31  plan-1  H2   0.020
 N31  plan-1  H3   0.020
 N31  plan-1  H4   0.020
 N31  plan-1  H8   0.020
 N31  plan-1  C7   0.020
 N31  plan-2  C6   0.020
 N31  plan-2  C10  0.020
 N31  plan-2  O1   0.020
 N31  plan-2  N3   0.020
 N31  plan-2  C11  0.020
 N31  plan-2  H11  0.020
 N31  plan-3  C11  0.020
 N31  plan-3  C12  0.020
 N31  plan-3  O3   0.020
 N31  plan-3  N4   0.020
 N31  plan-3  C13  0.020
 N31  plan-3  H16  0.020
 N31  plan-4  C13  0.020
 N31  plan-4  C14  0.020
 N31  plan-4  O5   0.020
 N31  plan-4  N5   0.020
 N31  plan-4  C16  0.020
 N31  plan-4  H23  0.020
 N31  plan-5  C16  0.020
 N31  plan-5  C17  0.020
 N31  plan-5  O7   0.020
 N31  plan-5  N6   0.020
 N31  plan-5  H30  0.020
 N31  plan-5  H31  0.020

