# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:52:31 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2~{S})-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)CCCCCn2ccnc2
#
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
 IC6  IC6  '(2~{S})-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid'  ligand  46  24  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IC6
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
 IC6  C1   C  CR15   0   0.093   0.3713  -0.7199  21.7888
 IC6  C3   C  CR15   0  -0.218  -0.2991  -0.3491  19.8064
 IC6  C4   C  CR15   0  -0.107  -0.5766  -1.6614  20.0649
 IC6  C7   C  CH2    0  -0.438   0.9639  -4.0739  21.6126
 IC6  C8   C  CH2    0  -0.433   0.8812  -5.4535  22.2571
 IC6  C09  C  CH2    0  -0.426   1.0842  -5.4519  23.7675
 IC6  C10  C  CH2    0  -0.564   1.0607  -6.8653  24.3381
 IC6  C11  C  C      0   0.570   1.2181  -6.8906  25.8466
 IC6  C13  C  CH1    0  -0.207   2.4177  -8.0461  27.6907
 IC6  C14  C  C      0   0.420   1.1705  -8.1076  28.6215
 IC6  C17  C  CH2    0  -0.486   3.5856  -7.1631  28.1626
 IC6  C18  C  CR6    0   0.149   3.4249  -5.6841  27.9600
 IC6  C19  C  CR16   0  -0.304   2.8835  -4.8646  28.9488
 IC6  C20  C  CR16   0  -0.243   2.7429  -3.4987  28.7463
 IC6  C21  C  CR16   0  -0.276   3.1371  -2.9242  27.5439
 IC6  C22  C  CR16   0  -0.244   3.6859  -3.7277  26.5535
 IC6  C23  C  CR16   0  -0.310   3.8342  -5.0922  26.7662
 IC6  N2   N  N      0  -0.455   0.2940   0.2306  20.8916
 IC6  N5   N  NR5    0  -0.396  -0.1462  -1.8832  21.3424
 IC6  N12  N  NH1    0  -0.637   2.0820  -7.8121  26.3025
 IC6  O24  O  O      0  -0.499   0.5818  -6.1327  26.5645
 IC6  H1   H  HCR5   0   0.274   0.7869  -0.6257  22.7817
 IC6  H2   H  HCR5   0   0.245  -0.5013   0.2035  18.9016
 IC6  H3   H  HCR5   0   0.284  -1.0368  -2.4341  19.4712
 IC6  H6   H  HCH2   0   0.241   0.9264  -4.1855  20.5260
 IC6  H7   H  HCH2   0   0.230   1.9252  -3.6085  21.8490
 IC6  H8   H  HCH2   0   0.220  -0.0868  -5.9073  22.0187
 IC6  H9   H  HCH2   0   0.231   1.6373  -6.0948  21.7958
 IC6  H10  H  HCH2   0   0.224   2.0418  -4.9772  24.0045
 IC6  H11  H  HCH2   0   0.229   0.3123  -4.8549  24.2570
 IC6  H12  H  HCH2   0   0.254   0.1007  -7.3347  24.0980
 IC6  H13  H  HCH2   0   0.240   1.8273  -7.4722  23.8499
 IC6  H14  H  HCH1   0   0.249   2.8091  -9.0698  27.7115
 IC6  H15  H  HCH2   0   0.236   3.7675  -7.3820  29.2148
 IC6  H16  H  HCH2   0   0.229   4.4789  -7.4871  27.6208
 IC6  H17  H  HCR6   0   0.238   2.5604  -5.3098  29.8803
 IC6  H18  H  HCR6   0   0.243   2.3231  -2.8795  29.5294
 IC6  H19  H  HCR6   0   0.245   3.0251  -1.8593  27.3842
 IC6  H20  H  HCR6   0   0.243   4.0065  -3.2911  25.6156
 IC6  H21  H  HCR6   0   0.238   4.2768  -5.7065  25.9904
 IC6  H22  H  HNH1   0   0.387   2.5839  -8.3525  25.6180
 IC6  C6   C  CH2    0  -0.295  -0.1647  -3.1486  22.0505
 IC6  O15  O  OC    -1  -0.589   1.2952  -7.6172  29.7592
 IC6  H4   H  HCH2   0   0.264  -0.1022  -2.9266  23.1155
 IC6  H5   H  HCH2   0   0.257  -1.1321  -3.6233  21.8776
 IC6  O16  O  O      0  -0.606   0.1939  -8.7308  28.1711

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
 IC6  C3   N2   aromatic  1.366  0.020  1.366
 IC6  C3   C4   aromatic  1.366  0.020  1.366
 IC6  N2   C1   aromatic  1.309  0.020  1.309
 IC6  C4   N5   aromatic  1.366  0.020  1.366
 IC6  C1   N5   aromatic  1.349  0.020  1.349
 IC6  N5   C6   single    1.450  0.020  1.450
 IC6  C6   C7   single    1.524  0.020  1.524
 IC6  C7   C8   single    1.525  0.020  1.525
 IC6  C8   C09  single    1.524  0.020  1.524
 IC6  C09  C10  single    1.524  0.020  1.524
 IC6  C10  C11  single    1.517  0.020  1.517
 IC6  C11  N12  single    1.343  0.020  1.343
 IC6  C11  O24  double    1.223  0.020  1.223
 IC6  N12  C13  single    1.447  0.020  1.447
 IC6  C23  C22  aromatic  1.389  0.020  1.389
 IC6  C23  C18  aromatic  1.394  0.020  1.394
 IC6  C13  C17  single    1.538  0.020  1.538
 IC6  C13  C14  single    1.557  0.020  1.557
 IC6  C17  C18  single    1.501  0.020  1.501
 IC6  C22  C21  aromatic  1.388  0.020  1.388
 IC6  C18  C19  aromatic  1.394  0.020  1.394
 IC6  O16  C14  deloc     1.243  0.020  1.243
 IC6  C14  O15  deloc     1.245  0.020  1.245
 IC6  C21  C20  aromatic  1.390  0.020  1.390
 IC6  C19  C20  aromatic  1.388  0.020  1.388
 IC6  C1   H1   single    0.930  0.020  1.080
 IC6  C3   H2   single    0.930  0.020  1.080
 IC6  C4   H3   single    0.930  0.020  1.080
 IC6  C6   H4   single    0.970  0.020  1.090
 IC6  C6   H5   single    0.970  0.020  1.090
 IC6  C7   H6   single    0.970  0.020  1.090
 IC6  C7   H7   single    0.970  0.020  1.090
 IC6  C8   H8   single    0.970  0.020  1.090
 IC6  C8   H9   single    0.970  0.020  1.090
 IC6  C09  H10  single    0.970  0.020  1.090
 IC6  C09  H11  single    0.970  0.020  1.090
 IC6  C10  H12  single    0.970  0.020  1.090
 IC6  C10  H13  single    0.970  0.020  1.090
 IC6  C13  H14  single    0.970  0.020  1.090
 IC6  C17  H15  single    0.970  0.020  1.090
 IC6  C17  H16  single    0.970  0.020  1.090
 IC6  C19  H17  single    0.930  0.020  1.080
 IC6  C20  H18  single    0.930  0.020  1.080
 IC6  C21  H19  single    0.930  0.020  1.080
 IC6  C22  H20  single    0.930  0.020  1.080
 IC6  C23  H21  single    0.930  0.020  1.080
 IC6  N12  H22  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
 IC6  H1   C1   N5   121.79  3.000
 IC6  H1   C1   N2   126.09  3.000
 IC6  N5   C1   N2   112.12  3.000
 IC6  H2   C3   N2   122.01  3.000
 IC6  H2   C3   C4   127.76  3.000
 IC6  N2   C3   C4   110.22  3.000
 IC6  H3   C4   N5   122.22  3.000
 IC6  H3   C4   C3   132.18  3.000
 IC6  N5   C4   C3   105.60  3.000
 IC6  H7   C7   H6   106.76  3.000
 IC6  H7   C7   C8   109.96  3.000
 IC6  H6   C7   C8   109.02  3.000
 IC6  H7   C7   C6   109.29  3.000
 IC6  H6   C7   C6   108.80  3.000
 IC6  C8   C7   C6   112.82  3.000
 IC6  H9   C8   H8   106.04  3.000
 IC6  H9   C8   C09  109.06  3.000
 IC6  H8   C8   C09  109.50  3.000
 IC6  H9   C8   C7   108.35  3.000
 IC6  H8   C8   C7   109.31  3.000
 IC6  C09  C8   C7   114.25  3.000
 IC6  H11  C09  H10  106.52  3.000
 IC6  H11  C09  C10  109.17  3.000
 IC6  H10  C09  C10  109.54  3.000
 IC6  H11  C09  C8   110.54  3.000
 IC6  H10  C09  C8   109.36  3.000
 IC6  C10  C09  C8   111.58  3.000
 IC6  H13  C10  H12  106.20  3.000
 IC6  H13  C10  C11  111.23  3.000
 IC6  H12  C10  C11  107.57  3.000
 IC6  H13  C10  C09  109.69  3.000
 IC6  H12  C10  C09  109.20  3.000
 IC6  C11  C10  C09  112.71  3.000
 IC6  O24  C11  N12  124.12  3.000
 IC6  O24  C11  C10  121.30  3.000
 IC6  N12  C11  C10  114.57  3.000
 IC6  H14  C13  N12  104.59  3.000
 IC6  H14  C13  C17  105.02  3.000
 IC6  N12  C13  C17  112.18  3.000
 IC6  H14  C13  C14  103.75  3.000
 IC6  C17  C13  C14  116.57  3.000
 IC6  N12  C13  C14  113.19  3.000
 IC6  O16  C14  O15  127.39  3.000
 IC6  O15  C14  C13  116.76  3.000
 IC6  O16  C14  C13  115.62  3.000
 IC6  H16  C17  H15  106.40  3.000
 IC6  H16  C17  C18  108.19  3.000
 IC6  H15  C17  C18  110.24  3.000
 IC6  H16  C17  C13  107.34  3.000
 IC6  H15  C17  C13  107.91  3.000
 IC6  C18  C17  C13  116.28  3.000
 IC6  C23  C18  C19  118.16  3.000
 IC6  C19  C18  C17  121.67  3.000
 IC6  C23  C18  C17  120.16  3.000
 IC6  H17  C19  C20  120.02  3.000
 IC6  H17  C19  C18  119.01  3.000
 IC6  C20  C19  C18  120.96  3.000
 IC6  H18  C20  C21  119.95  3.000
 IC6  H18  C20  C19  119.76  3.000
 IC6  C21  C20  C19  120.29  3.000
 IC6  H19  C21  C22  120.33  3.000
 IC6  H19  C21  C20  120.32  3.000
 IC6  C22  C21  C20  119.35  3.000
 IC6  H20  C22  C23  119.80  3.000
 IC6  H20  C22  C21  120.10  3.000
 IC6  C23  C22  C21  120.10  3.000
 IC6  H21  C23  C22  119.39  3.000
 IC6  H21  C23  C18  119.48  3.000
 IC6  C22  C23  C18  121.13  3.000
 IC6  C3   N2   C1   105.18  3.000
 IC6  C6   N5   C4   126.46  3.000
 IC6  C6   N5   C1   126.56  3.000
 IC6  C4   N5   C1   106.88  3.000
 IC6  H22  N12  C13  116.74  3.000
 IC6  H22  N12  C11  117.29  3.000
 IC6  C13  N12  C11  125.86  3.000
 IC6  H5   C6   H4   107.11  3.000
 IC6  H5   C6   N5   108.26  3.000
 IC6  H4   C6   N5   107.38  3.000
 IC6  H5   C6   C7   110.30  3.000
 IC6  H4   C6   C7   111.23  3.000
 IC6  N5   C6   C7   112.35  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
 IC6  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 IC6  CONST_02  C3   C4   N5   C1      0.00   0.0  0
 IC6  CONST_03  N5   C1   N2   C3      0.00   0.0  0
 IC6  CONST_04  N2   C1   N5   C4      0.00   0.0  0
 IC6  CONST_05  C21  C22  C23  C18     0.00   0.0  0
 IC6  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 IC6  CONST_07  C22  C23  C18  C19     0.00   0.0  0
 IC6  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 IC6  CONST_09  C23  C22  C21  C20     0.00   0.0  0
 IC6  CONST_10  C23  C18  C19  C20     0.00   0.0  0
 IC6  CONST_11  N5   C4   C3   N2      0.00   0.0  0
 IC6  CONST_12  C6   N5   C4   C3    180.00   0.0  0
 IC6  CONST_13  N2   C1   N5   C6    180.00   0.0  0
 IC6  CONST_14  C22  C23  C18  C17   180.00   0.0  0
 IC6  CONST_15  C20  C19  C18  C17   180.00   0.0  0
 IC6  CONST_16  H2   C3   N2   C1    180.00   0.0  0
 IC6  CONST_17  H3   C4   N5   C1    180.00   0.0  0
 IC6  CONST_18  H1   C1   N2   C3    180.00   0.0  0
 IC6  CONST_19  H20  C22  C23  C18   180.00   0.0  0
 IC6  CONST_20  H18  C20  C19  C18   180.00   0.0  0
 IC6  CONST_21  H21  C23  C18  C19   180.00   0.0  0
 IC6  CONST_22  H19  C21  C20  C19   180.00   0.0  0
 IC6  CONST_23  H17  C19  C20  C21   180.00   0.0  0
 IC6  CONST_24  C13  N12  C11  C10   180.00   0.0  0
 IC6  CONST_25  O24  C11  N12  C13     0.00   0.0  0
 IC6  CONST_26  H22  N12  C11  C10     0.00   0.0  0
 IC6  Var_01    C7   C6   N5   C1    -98.37  30.0  2
 IC6  Var_02    C23  C18  C17  C13   -88.63  30.0  2
 IC6  Var_03    N5   C6   C7   C8   -174.81  30.0  1
 IC6  Var_04    C09  C8   C7   C6    -65.68  30.0  3
 IC6  Var_05    C10  C09  C8   C7   -177.08  30.0  3
 IC6  Var_06    C11  C10  C09  C8   -178.25  30.0  3
 IC6  Var_07    N12  C11  C10  C09  -134.97  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
 IC6  chir_01  C13  N12  C17  C14  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
 IC6  plan-1  C1   0.020
 IC6  plan-1  C3   0.020
 IC6  plan-1  C4   0.020
 IC6  plan-1  N2   0.020
 IC6  plan-1  N5   0.020
 IC6  plan-1  H1   0.020
 IC6  plan-1  H2   0.020
 IC6  plan-1  H3   0.020
 IC6  plan-1  C6   0.020
 IC6  plan-2  C17  0.020
 IC6  plan-2  C18  0.020
 IC6  plan-2  C19  0.020
 IC6  plan-2  C20  0.020
 IC6  plan-2  C21  0.020
 IC6  plan-2  C22  0.020
 IC6  plan-2  C23  0.020
 IC6  plan-2  H17  0.020
 IC6  plan-2  H18  0.020
 IC6  plan-2  H19  0.020
 IC6  plan-2  H20  0.020
 IC6  plan-2  H21  0.020
 IC6  plan-3  C10  0.020
 IC6  plan-3  C11  0.020
 IC6  plan-3  C13  0.020
 IC6  plan-3  N12  0.020
 IC6  plan-3  O24  0.020
 IC6  plan-3  H22  0.020
 IC6  plan-4  C13  0.020
 IC6  plan-4  C14  0.020
 IC6  plan-4  O15  0.020
 IC6  plan-4  O16  0.020

