# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:07:21 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2R,3S)-3-{[(benzyloxy)carbonyl]amino}-2-hydroxy-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@H](Cc1ccccc1)NC(=O)OCc2ccccc2)C(O)=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
 KI2  KI2  '(2R,3S)-3-{[(benzyloxy)carbonyl]amino}-2-hydroxy-4-phenylbutanoic acid'  ligand  43  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KI2
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
 KI2  O1    O  O2    0  -0.480  -2.4018  -3.8105   1.1735
 KI2  C2    C  CR16  0  -0.263  -3.3156  -5.5427   5.6708
 KI2  C3    C  CR16  0  -0.240  -3.4924  -6.4983   4.6810
 KI2  C4    C  CR16  0  -0.303  -3.6034  -6.1090   3.3511
 KI2  C5    C  CR6   0   0.077  -3.5465  -4.7655   3.0004
 KI2  C6    C  CR16  0  -0.280  -3.3702  -3.8113   4.0011
 KI2  C7    C  CR16  0  -0.244  -3.2535  -4.1963   5.3276
 KI2  C8    C  C     0   0.771  -2.3579  -3.1461   0.0135
 KI2  O9    O  O     0  -0.502  -3.2946  -3.0535  -0.7484
 KI2  N10   N  NH1   0  -0.664  -1.1229  -2.6335  -0.1906
 KI2  C11   C  CH1   0  -0.109  -0.8735  -1.6147  -1.1837
 KI2  C12   C  CH2   0  -0.532  -0.9063  -0.2091  -0.5638
 KI2  C13   C  CR6   0   0.135  -2.2153   0.0521   0.1258
 KI2  C14   C  CR16  0  -0.291  -3.3229   0.4949  -0.5927
 KI2  C15   C  CR16  0  -0.240  -4.5480   0.6788   0.0317
 KI2  C16   C  CR16  0  -0.268  -4.6859   0.4145   1.3887
 KI2  C17   C  CR16  0  -0.242  -3.5883  -0.0252   2.1157
 KI2  C18   C  CR16  0  -0.310  -2.3624  -0.2012   1.4871
 KI2  C19   C  CH2   0  -0.238  -3.6703  -4.3392   1.5687
 KI2  C21   C  CH1   0  -0.074   0.4692  -1.8887  -1.8810
 KI2  O22   O  OH1   0  -0.658   1.5506  -1.8252  -0.9973
 KI2  C     C  C     0   0.526   0.4613  -3.2850  -2.4759
 KI2  O     O  O     0  -0.426   1.2024  -4.1719  -2.1478
 KI2  OXT   O  OH1   0  -0.593  -0.4726  -3.4013  -3.4095
 KI2  H3    H  HCR6  0   0.258  -3.5414  -7.5481   4.9397
 KI2  H4    H  HCR6  0   0.256  -3.7347  -6.8596   2.5807
 KI2  H6    H  HCR6  0   0.250  -3.3292  -2.7591   3.7429
 KI2  H7    H  HCR6  0   0.258  -3.1186  -3.4466   6.0964
 KI2  H10   H  HNH1  0   0.394  -0.4655  -2.6925   0.5736
 KI2  H11   H  HCH1  0   0.283  -1.6612  -1.6777  -1.9340
 KI2  H121  H  HCH2  0   0.263  -0.7390   0.5254  -1.3559
 KI2  H122  H  HCH2  0   0.254  -0.0906  -0.1004   0.1563
 KI2  H14   H  HCR6  0   0.244  -3.2256   0.6971  -1.6534
 KI2  H15   H  HCR6  0   0.251  -5.3978   1.0286  -0.5406
 KI2  H16   H  HCR6  0   0.252  -5.6416   0.5570   1.8766
 KI2  H17   H  HCR6  0   0.251  -3.6841  -0.2262   3.1756
 KI2  H18   H  HCR6  0   0.248  -1.5074  -0.5350   2.0639
 KI2  H191  H  HCH2  0   0.249  -3.9448  -5.1851   0.9342
 KI2  H192  H  HCH2  0   0.247  -4.4416  -3.5734   1.4606
 KI2  H21   H  HCH1  0   0.277   0.5703  -1.1696  -2.7056
 KI2  H22   H  HOH1  0   0.468   1.7973  -0.9027  -0.8821
 KI2  HXT   H  HOH1  0   0.487  -0.4837  -4.3038  -3.7626
 KI2  H2    H  HCR6  0   0.258  -3.2280  -5.8422   6.7073

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
 KI2  O1   C8    single    1.337  0.020  1.337
 KI2  O1   C19   single    1.430  0.020  1.430
 KI2  C2   C3    aromatic  1.387  0.020  1.387
 KI2  C2   C7    aromatic  1.391  0.020  1.391
 KI2  C2   H2    single    0.930  0.020  1.080
 KI2  C3   C4    aromatic  1.390  0.020  1.390
 KI2  C3   H3    single    0.930  0.020  1.080
 KI2  C4   C5    aromatic  1.390  0.020  1.390
 KI2  C4   H4    single    0.930  0.020  1.080
 KI2  C5   C6    aromatic  1.394  0.020  1.394
 KI2  C5   C19   single    1.499  0.020  1.499
 KI2  C6   C7    aromatic  1.386  0.020  1.386
 KI2  C6   H6    single    0.930  0.020  1.080
 KI2  C7   H7    single    0.930  0.020  1.080
 KI2  C8   O9    double    1.211  0.020  1.211
 KI2  C8   N10   single    1.353  0.020  1.353
 KI2  N10  C11   single    1.445  0.020  1.445
 KI2  N10  H10   single    0.890  0.020  1.040
 KI2  C11  C12   single    1.537  0.020  1.537
 KI2  C11  C21   single    1.538  0.020  1.538
 KI2  C11  H11   single    0.970  0.020  1.090
 KI2  C12  C13   single    1.502  0.020  1.502
 KI2  C12  H121  single    0.970  0.020  1.090
 KI2  C12  H122  single    0.970  0.020  1.090
 KI2  C13  C14   aromatic  1.393  0.020  1.393
 KI2  C13  C18   aromatic  1.392  0.020  1.392
 KI2  C14  C15   aromatic  1.387  0.020  1.387
 KI2  C14  H14   single    0.930  0.020  1.080
 KI2  C15  C16   aromatic  1.389  0.020  1.389
 KI2  C15  H15   single    0.930  0.020  1.080
 KI2  C16  C17   aromatic  1.388  0.020  1.388
 KI2  C16  H16   single    0.930  0.020  1.080
 KI2  C17  C18   aromatic  1.389  0.020  1.389
 KI2  C17  H17   single    0.930  0.020  1.080
 KI2  C18  H18   single    0.930  0.020  1.080
 KI2  C19  H191  single    0.970  0.020  1.090
 KI2  C19  H192  single    0.970  0.020  1.090
 KI2  C21  O22   single    1.398  0.020  1.398
 KI2  C21  C     single    1.518  0.020  1.518
 KI2  C21  H21   single    0.970  0.020  1.090
 KI2  O22  H22   single    0.850  0.020  0.980
 KI2  C    O     double    1.201  0.020  1.201
 KI2  C    OXT   single    1.326  0.020  1.326
 KI2  OXT  HXT   single    0.850  0.020  0.980

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
 KI2  C19   O1   C8    116.90  3.000
 KI2  H2    C2   C7    120.03  3.000
 KI2  H2    C2   C3    120.20  3.000
 KI2  C7    C2   C3    119.77  3.000
 KI2  H3    C3   C4    119.78  3.000
 KI2  H3    C3   C2    120.23  3.000
 KI2  C4    C3   C2    119.99  3.000
 KI2  H4    C4   C5    119.68  3.000
 KI2  H4    C4   C3    119.73  3.000
 KI2  C5    C4   C3    120.59  3.000
 KI2  C19   C5   C6    120.10  3.000
 KI2  C19   C5   C4    120.83  3.000
 KI2  C6    C5   C4    119.06  3.000
 KI2  H6    C6   C7    119.62  3.000
 KI2  H6    C6   C5    119.88  3.000
 KI2  C7    C6   C5    120.50  3.000
 KI2  H7    C7   C6    119.86  3.000
 KI2  H7    C7   C2    120.06  3.000
 KI2  C6    C7   C2    120.08  3.000
 KI2  N10   C8   O9    125.61  3.000
 KI2  N10   C8   O1    110.43  3.000
 KI2  O9    C8   O1    123.94  3.000
 KI2  H10   N10  C11   116.69  3.000
 KI2  H10   N10  C8    117.26  3.000
 KI2  C11   N10  C8    121.92  3.000
 KI2  H11   C11  C21   107.98  3.000
 KI2  H11   C11  C12   108.38  3.000
 KI2  C21   C11  C12   111.39  3.000
 KI2  H11   C11  N10   107.92  3.000
 KI2  C21   C11  N10   109.69  3.000
 KI2  C12   C11  N10   111.35  3.000
 KI2  H122  C12  H121  107.24  3.000
 KI2  H122  C12  C13   109.29  3.000
 KI2  H121  C12  C13   110.43  3.000
 KI2  H122  C12  C11   109.92  3.000
 KI2  H121  C12  C11   108.60  3.000
 KI2  C13   C12  C11   111.27  3.000
 KI2  C18   C13  C14   118.57  3.000
 KI2  C18   C13  C12   120.61  3.000
 KI2  C14   C13  C12   120.76  3.000
 KI2  H14   C14  C15   119.66  3.000
 KI2  H14   C14  C13   119.52  3.000
 KI2  C15   C14  C13   120.82  3.000
 KI2  H15   C15  C16   119.99  3.000
 KI2  H15   C15  C14   119.88  3.000
 KI2  C16   C15  C14   120.13  3.000
 KI2  H16   C16  C17   120.25  3.000
 KI2  H16   C16  C15   120.19  3.000
 KI2  C17   C16  C15   119.56  3.000
 KI2  H17   C17  C18   119.84  3.000
 KI2  H17   C17  C16   120.09  3.000
 KI2  C18   C17  C16   120.07  3.000
 KI2  H18   C18  C17   119.63  3.000
 KI2  H18   C18  C13   119.53  3.000
 KI2  C17   C18  C13   120.84  3.000
 KI2  H192  C19  H191  107.94  3.000
 KI2  H192  C19  C5    110.63  3.000
 KI2  H191  C19  C5    110.82  3.000
 KI2  H192  C19  O1    109.86  3.000
 KI2  H191  C19  O1    110.40  3.000
 KI2  C5    C19  O1    107.21  3.000
 KI2  H21   C21  C     107.96  3.000
 KI2  H21   C21  O22   111.93  3.000
 KI2  C     C21  O22   107.08  3.000
 KI2  H21   C21  C11   107.70  3.000
 KI2  C     C21  C11   109.70  3.000
 KI2  O22   C21  C11   112.38  3.000
 KI2  H22   O22  C21   108.52  3.000
 KI2  OXT   C    O     124.20  3.000
 KI2  OXT   C    C21   111.13  3.000
 KI2  O     C    C21   124.67  3.000
 KI2  HXT   OXT  C     110.27  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
 KI2  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 KI2  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 KI2  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 KI2  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 KI2  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 KI2  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 KI2  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 KI2  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 KI2  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 KI2  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 KI2  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 KI2  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 KI2  CONST_13  C19  C5   C4   C3    180.00   0.0  0
 KI2  CONST_14  C19  C5   C6   C7    180.00   0.0  0
 KI2  CONST_15  C15  C14  C13  C12   180.00   0.0  0
 KI2  CONST_16  C17  C18  C13  C12   180.00   0.0  0
 KI2  CONST_17  H4   C4   C3   C2    180.00   0.0  0
 KI2  CONST_18  H6   C6   C7   C2    180.00   0.0  0
 KI2  CONST_19  H7   C7   C2   C3    180.00   0.0  0
 KI2  CONST_20  H2   C2   C3   C4    180.00   0.0  0
 KI2  CONST_21  H3   C3   C4   C5    180.00   0.0  0
 KI2  CONST_22  H15  C15  C14  C13   180.00   0.0  0
 KI2  CONST_23  H17  C17  C18  C13   180.00   0.0  0
 KI2  CONST_24  H18  C18  C13  C14   180.00   0.0  0
 KI2  CONST_25  H16  C16  C15  C14   180.00   0.0  0
 KI2  CONST_26  H14  C14  C15  C16   180.00   0.0  0
 KI2  CONST_27  HXT  OXT  C    C21   180.00   0.0  0
 KI2  Var_01    C4   C5   C19  O1   -112.35  30.0  2
 KI2  Var_02    C14  C13  C12  C11   -83.84  30.0  2
 KI2  Var_03    C11  N10  C8   O1   -164.85  30.0  2

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
 KI2  chir_01  C11  N10  C12  C21  negativ
 KI2  chir_02  C21  O22  C11  C    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
 KI2  plan-1  C2   0.020
 KI2  plan-1  C3   0.020
 KI2  plan-1  C4   0.020
 KI2  plan-1  C5   0.020
 KI2  plan-1  C6   0.020
 KI2  plan-1  C7   0.020
 KI2  plan-1  C19  0.020
 KI2  plan-1  H3   0.020
 KI2  plan-1  H4   0.020
 KI2  plan-1  H6   0.020
 KI2  plan-1  H7   0.020
 KI2  plan-1  H2   0.020
 KI2  plan-2  C12  0.020
 KI2  plan-2  C13  0.020
 KI2  plan-2  C14  0.020
 KI2  plan-2  C15  0.020
 KI2  plan-2  C16  0.020
 KI2  plan-2  C17  0.020
 KI2  plan-2  C18  0.020
 KI2  plan-2  H14  0.020
 KI2  plan-2  H15  0.020
 KI2  plan-2  H16  0.020
 KI2  plan-2  H17  0.020
 KI2  plan-2  H18  0.020
 KI2  plan-3  C21  0.020
 KI2  plan-3  C    0.020
 KI2  plan-3  O    0.020
 KI2  plan-3  OXT  0.020
 KI2  plan-3  HXT  0.020
 KI2  plan-4  O1   0.020
 KI2  plan-4  C8   0.020
 KI2  plan-4  O9   0.020
 KI2  plan-4  N10  0.020

