# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:41:54 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)-N-(3-phenylpropanoyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1[nH]c2ccccc2n1)NC(=O)CCc3ccccc3
#
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
 4C0  4C0  3-(1H-benzimidazol-2-yl)-N-(3-phenylpropanoyl)-D-alanine  ligand  43  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4C0
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
 4C0  C1    C  CR16   0  -0.273  -3.9047   3.9710   0.7440
 4C0  C2    C  CR16   0  -0.281  -4.1543   3.7055  -0.6105
 4C0  C3    C  CR16   0  -0.311  -3.9815   2.4386  -1.1436
 4C0  C4    C  CR16   0  -0.339  -3.4736   2.9766   1.6061
 4C0  C5    C  CR56   0   0.133  -3.2928   1.6948   1.0888
 4C0  C6    C  CR56   0   0.335  -3.5488   1.4483  -0.2707
 4C0  N7    N  NR15   0  -0.695  -3.2784   0.1162  -0.4331
 4C0  C8    C  CR5    0   0.464  -2.8837  -0.3762   0.7722
 4C0  N9    N  N      0  -0.480  -2.8790   0.5365   1.7062
 4C0  C10   C  CH2    0  -0.561  -2.4958  -1.8005   0.9484
 4C0  C11   C  CH1    0  -0.234  -1.3149  -2.1954   0.0543
 4C0  N12   N  NH1    0  -0.609  -0.2087  -1.2990   0.2717
 4C0  C13   C  C      0   0.554   0.5440  -0.7847  -0.7103
 4C0  O14   O  O      0  -0.514   0.2859  -0.9166  -1.9014
 4C0  C15   C  CH2    0  -0.564   1.7519   0.0063  -0.2544
 4C0  C16   C  CH2    0  -0.508   3.0330  -0.4991  -0.9260
 4C0  C17   C  C      0   0.131   4.2318   0.3058  -0.5091
 4C0  C18   C  C1     0  -0.316   5.0930  -0.1502   0.4856
 4C0  C19   C  C1     0  -0.239   6.1830   0.6105   0.8902
 4C0  C20   C  C1     0  -0.274   6.4263   1.8455   0.3050
 4C0  C21   C  C1     0  -0.240   5.5732   2.3120  -0.6881
 4C0  C22   C  C1     0  -0.305   4.4869   1.5474  -1.0895
 4C0  C23   C  C      0   0.425  -0.9264  -3.6887   0.2455
 4C0  O24   O  O      0  -0.583   0.2812  -3.9495   0.3553
 4C0  O25   O  OC    -1  -0.608  -1.8827  -4.4873   0.2435
 4C0  H1    H  HCR6   0   0.250  -4.0530   4.9755   1.1188
 4C0  H2    H  HCR6   0   0.253  -4.4887   4.5095  -1.2534
 4C0  H3    H  HCR6   0   0.264  -4.1743   2.2347  -2.1888
 4C0  H4    H  HCR6   0   0.251  -3.2811   3.1845   2.6510
 4C0  H10   H  HCH2   0   0.261  -2.2485  -1.9532   2.0007
 4C0  H10A  H  HCH2   0   0.275  -3.3407  -2.4512   0.7192
 4C0  H11   H  HCH1   0   0.259  -1.6134  -2.0823  -0.9911
 4C0  HN12  H  HNH1   0   0.388   0.1463  -1.2339   1.2126
 4C0  H15   H  HCH2   0   0.267   1.5901   1.0543  -0.5224
 4C0  H15A  H  HCH2   0   0.254   1.8657  -0.0272   0.8310
 4C0  H16   H  HCH2   0   0.251   3.1842  -1.5502  -0.6689
 4C0  H16A  H  HCH2   0   0.252   2.9111  -0.4507  -2.0095
 4C0  H18   H  H      0   0.246   4.9114  -1.1147   0.9456
 4C0  H19   H  H      0   0.253   6.8426   0.2356   1.6626
 4C0  H20   H  H      0   0.253   7.2745   2.4402   0.6190
 4C0  H21   H  H      0   0.253   5.7564   3.2729  -1.1519
 4C0  H22   H  H      0   0.247   3.8297   1.9199  -1.8675
 4C0  HN7   H  HNR5   0   0.417  -3.3607  -0.4097  -1.2886

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
 4C0  C2   C1    aromatic  1.403  0.020  1.403
 4C0  C1   C4    aromatic  1.385  0.020  1.385
 4C0  C1   H1    single    0.930  0.020  1.080
 4C0  C3   C2    aromatic  1.385  0.020  1.385
 4C0  C2   H2    single    0.930  0.020  1.080
 4C0  C3   C6    aromatic  1.389  0.020  1.389
 4C0  C3   H3    single    0.930  0.020  1.080
 4C0  C5   C4    aromatic  1.394  0.020  1.394
 4C0  C4   H4    single    0.930  0.020  1.080
 4C0  C6   C5    aromatic  1.405  0.020  1.405
 4C0  C5   N9    aromatic  1.376  0.020  1.376
 4C0  N7   C6    aromatic  1.369  0.020  1.369
 4C0  N7   C8    aromatic  1.361  0.020  1.361
 4C0  C10  C8    single    1.487  0.020  1.487
 4C0  C8   N9    aromatic  1.306  0.020  1.306
 4C0  C11  C10   single    1.533  0.020  1.533
 4C0  C10  H10   single    0.970  0.020  1.090
 4C0  C10  H10A  single    0.970  0.020  1.090
 4C0  N12  C11   single    1.440  0.020  1.440
 4C0  C11  C23   single    1.555  0.020  1.555
 4C0  C11  H11   single    0.970  0.020  1.090
 4C0  C13  N12   single    1.340  0.020  1.340
 4C0  N12  HN12  single    0.860  0.020  1.020
 4C0  C15  C13   single    1.514  0.020  1.514
 4C0  C13  O14   double    1.226  0.020  1.226
 4C0  C16  C15   single    1.532  0.020  1.532
 4C0  C15  H15   single    0.970  0.020  1.090
 4C0  C15  H15A  single    0.970  0.020  1.090
 4C0  C17  C16   single    1.503  0.020  1.503
 4C0  C16  H16   single    0.970  0.020  1.090
 4C0  C16  H16A  single    0.970  0.020  1.090
 4C0  C18  C17   aromatic  1.392  0.020  1.392
 4C0  C22  C17   aromatic  1.394  0.020  1.394
 4C0  C19  C18   aromatic  1.389  0.020  1.389
 4C0  C18  H18   single    0.930  0.020  1.080
 4C0  C20  C19   aromatic  1.388  0.020  1.388
 4C0  C19  H19   single    0.930  0.020  1.080
 4C0  C20  C21   aromatic  1.390  0.020  1.390
 4C0  C20  H20   single    0.930  0.020  1.080
 4C0  C21  C22   aromatic  1.388  0.020  1.388
 4C0  C21  H21   single    0.930  0.020  1.080
 4C0  C22  H22   single    0.930  0.020  1.080
 4C0  O24  C23   deloc     1.240  0.020  1.240
 4C0  C23  O25   deloc     1.246  0.020  1.246
 4C0  N7   HN7   single    0.860  0.020  1.020

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
 4C0  H1    C1   C4   119.57  3.000
 4C0  H1    C1   C2   119.06  3.000
 4C0  C4    C1   C2   121.37  3.000
 4C0  H2    C2   C3   119.29  3.000
 4C0  H2    C2   C1   119.21  3.000
 4C0  C3    C2   C1   121.50  3.000
 4C0  H3    C3   C6   121.87  3.000
 4C0  H3    C3   C2   121.45  3.000
 4C0  C6    C3   C2   116.68  3.000
 4C0  H4    C4   C5   120.77  3.000
 4C0  H4    C4   C1   121.22  3.000
 4C0  C5    C4   C1   118.01  3.000
 4C0  N9    C5   C6   109.94  3.000
 4C0  N9    C5   C4   130.27  3.000
 4C0  C6    C5   C4   119.78  3.000
 4C0  N7    C6   C5   104.45  3.000
 4C0  N7    C6   C3   132.90  3.000
 4C0  C5    C6   C3   122.65  3.000
 4C0  HN7   N7   C8   125.94  3.000
 4C0  HN7   N7   C6   126.33  3.000
 4C0  C8    N7   C6   107.73  3.000
 4C0  C10   C8   N9   125.73  3.000
 4C0  N9    C8   N7   112.44  3.000
 4C0  C10   C8   N7   121.83  3.000
 4C0  C8    N9   C5   105.45  3.000
 4C0  H10A  C10  H10  107.13  3.000
 4C0  H10A  C10  C11  108.69  3.000
 4C0  H10   C10  C11  110.59  3.000
 4C0  H10A  C10  C8   110.15  3.000
 4C0  H10   C10  C8   107.90  3.000
 4C0  C11   C10  C8   112.25  3.000
 4C0  H11   C11  C23  106.57  3.000
 4C0  H11   C11  N12  106.84  3.000
 4C0  C23   C11  N12  112.78  3.000
 4C0  H11   C11  C10  108.71  3.000
 4C0  C23   C11  C10  111.60  3.000
 4C0  N12   C11  C10  110.08  3.000
 4C0  HN12  N12  C13  117.48  3.000
 4C0  HN12  N12  C11  116.86  3.000
 4C0  C13   N12  C11  124.04  3.000
 4C0  C15   C13  O14  121.11  3.000
 4C0  O14   C13  N12  123.54  3.000
 4C0  C15   C13  N12  115.34  3.000
 4C0  H15A  C15  H15  106.76  3.000
 4C0  H15A  C15  C16  109.78  3.000
 4C0  H15   C15  C16  109.41  3.000
 4C0  H15A  C15  C13  111.50  3.000
 4C0  H15   C15  C13  107.99  3.000
 4C0  C16   C15  C13  111.27  3.000
 4C0  H16A  C16  H16  106.97  3.000
 4C0  H16A  C16  C17  109.92  3.000
 4C0  H16   C16  C17  109.85  3.000
 4C0  H16A  C16  C15  109.09  3.000
 4C0  H16   C16  C15  109.26  3.000
 4C0  C17   C16  C15  111.63  3.000
 4C0  C22   C17  C18  118.42  3.000
 4C0  C22   C17  C16  120.49  3.000
 4C0  C18   C17  C16  121.07  3.000
 4C0  H18   C18  C19  119.67  3.000
 4C0  H18   C18  C17  119.41  3.000
 4C0  C19   C18  C17  120.93  3.000
 4C0  H19   C19  C20  120.14  3.000
 4C0  H19   C19  C18  119.74  3.000
 4C0  C20   C19  C18  120.12  3.000
 4C0  H20   C20  C21  120.26  3.000
 4C0  H20   C20  C19  120.25  3.000
 4C0  C21   C20  C19  119.49  3.000
 4C0  H21   C21  C22  119.84  3.000
 4C0  H21   C21  C20  120.01  3.000
 4C0  C22   C21  C20  120.15  3.000
 4C0  H22   C22  C21  119.51  3.000
 4C0  H22   C22  C17  119.59  3.000
 4C0  C21   C22  C17  120.90  3.000
 4C0  O25   C23  O24  127.78  3.000
 4C0  O25   C23  C11  115.06  3.000
 4C0  O24   C23  C11  117.14  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
 4C0  CONST_01  C6    C3   C2   C1     0.00   0.0  0
 4C0  CONST_02  C6    C5   C4   C1     0.00   0.0  0
 4C0  CONST_03  N9    C5   C4   C1   180.00   0.0  0
 4C0  CONST_04  C5    C4   C1   C2     0.00   0.0  0
 4C0  CONST_05  C5    C6   C3   C2     0.00   0.0  0
 4C0  CONST_06  N7    C6   C3   C2   180.00   0.0  0
 4C0  CONST_07  C4    C1   C2   C3     0.00   0.0  0
 4C0  CONST_08  C4    C5   C6   C3     0.00   0.0  0
 4C0  CONST_09  N9    C5   C6   C3   180.00   0.0  0
 4C0  CONST_10  C8    N7   C6   C3   180.00   0.0  0
 4C0  CONST_11  N7    C6   C5   C4   180.00   0.0  0
 4C0  CONST_12  C8    N9   C5   C4   180.00   0.0  0
 4C0  CONST_13  C8    N7   C6   C5     0.00   0.0  0
 4C0  CONST_14  N7    C8   N9   C5     0.00   0.0  0
 4C0  CONST_15  C8    N9   C5   C6     0.00   0.0  0
 4C0  CONST_16  N9    C8   N7   C6     0.00   0.0  0
 4C0  CONST_17  N9    C5   C6   N7     0.00   0.0  0
 4C0  CONST_18  C20   C19  C18  C17    0.00   0.0  0
 4C0  CONST_19  C20   C21  C22  C17    0.00   0.0  0
 4C0  CONST_20  C21   C22  C17  C18    0.00   0.0  0
 4C0  CONST_21  C21   C20  C19  C18    0.00   0.0  0
 4C0  CONST_22  C22   C17  C18  C19    0.00   0.0  0
 4C0  CONST_23  C22   C21  C20  C19    0.00   0.0  0
 4C0  CONST_24  C10   C8   N9   C5   180.00   0.0  0
 4C0  CONST_25  C10   C8   N7   C6   180.00   0.0  0
 4C0  CONST_26  C19   C18  C17  C16  180.00   0.0  0
 4C0  CONST_27  C21   C22  C17  C16  180.00   0.0  0
 4C0  CONST_28  H3    C3   C2   C1   180.00   0.0  0
 4C0  CONST_29  H4    C4   C1   C2   180.00   0.0  0
 4C0  CONST_30  H1    C1   C2   C3   180.00   0.0  0
 4C0  CONST_31  HN7   N7   C6   C3     0.00   0.0  0
 4C0  CONST_32  H2    C2   C1   C4   180.00   0.0  0
 4C0  CONST_33  H19   C19  C18  C17  180.00   0.0  0
 4C0  CONST_34  H21   C21  C22  C17  180.00   0.0  0
 4C0  CONST_35  H22   C22  C17  C18  180.00   0.0  0
 4C0  CONST_36  H20   C20  C19  C18  180.00   0.0  0
 4C0  CONST_37  H18   C18  C19  C20  180.00   0.0  0
 4C0  CONST_38  C15   C13  N12  C11  180.00   0.0  0
 4C0  CONST_39  O14   C13  N12  C11    0.00   0.0  0
 4C0  CONST_40  HN12  N12  C13  O14  180.00   0.0  0
 4C0  Var_01    C11   C10  C8   N7    59.45  30.0  3
 4C0  Var_02    C18   C17  C16  C15   98.80  30.0  2
 4C0  Var_03    C17   C16  C15  C13  178.38  30.0  2
 4C0  Var_04    C16   C15  C13  N12  127.18  30.0  1

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
 4C0  chir_01  C11  C10  N12  C23  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
 4C0  plan-1  C16   0.020
 4C0  plan-1  C17   0.020
 4C0  plan-1  C18   0.020
 4C0  plan-1  C19   0.020
 4C0  plan-1  C20   0.020
 4C0  plan-1  C21   0.020
 4C0  plan-1  C22   0.020
 4C0  plan-1  H18   0.020
 4C0  plan-1  H19   0.020
 4C0  plan-1  H20   0.020
 4C0  plan-1  H21   0.020
 4C0  plan-1  H22   0.020
 4C0  plan-2  C1    0.020
 4C0  plan-2  C2    0.020
 4C0  plan-2  C3    0.020
 4C0  plan-2  C4    0.020
 4C0  plan-2  C5    0.020
 4C0  plan-2  C6    0.020
 4C0  plan-2  N7    0.020
 4C0  plan-2  C8    0.020
 4C0  plan-2  N9    0.020
 4C0  plan-2  C10   0.020
 4C0  plan-2  H1    0.020
 4C0  plan-2  H2    0.020
 4C0  plan-2  H3    0.020
 4C0  plan-2  H4    0.020
 4C0  plan-2  HN7   0.020
 4C0  plan-3  C11   0.020
 4C0  plan-3  N12   0.020
 4C0  plan-3  C13   0.020
 4C0  plan-3  O14   0.020
 4C0  plan-3  C15   0.020
 4C0  plan-3  HN12  0.020
 4C0  plan-4  C11   0.020
 4C0  plan-4  C23   0.020
 4C0  plan-4  O24   0.020
 4C0  plan-4  O25   0.020

