# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:22:07 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2S)-2-{[(R)-hydroxy(4-iodobenzyl)phosphoryl]methyl}pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](C[P@](O)(=O)Cc1ccc(I)cc1)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
 24I  24I  '(2S)-2-{[(R)-hydroxy(4-iodobenzyl)phosphoryl]methyl}pentanedioic acid'  ligand  34  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_24I
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
 24I  O5    O  O      0  -0.611   7.9929   1.6634   0.7360
 24I  C14   C  C      0   0.408   7.9657   0.9199  -0.2650
 24I  O6    O  OC    -1  -0.637   8.9412   0.6362  -0.9944
 24I  C13   C  CH2    0  -0.587   6.6182   0.2946  -0.6695
 24I  C12   C  CH2    0  -0.385   5.4790   0.4707   0.3215
 24I  C10   C  CH1    0  -0.319   4.1318  -0.0576  -0.1791
 24I  C9    C  C      0   0.419   4.2161  -1.5687  -0.4614
 24I  O4    O  OC    -1  -0.631   4.0818  -1.9503  -1.6422
 24I  O3    O  O      0  -0.630   4.4529  -2.3036   0.5218
 24I  C7    C  CH2    0  -0.689   3.0317   0.2621   0.8346
 24I  P1    P  P      0   1.185   1.3395  -0.0540   0.2031
 24I  O1    O  O      0  -0.818   1.1130   0.7694  -1.0497
 24I  O2    O  OP    -1  -0.809   1.0489  -1.5394   0.1648
 24I  C6    C  CH2    0  -0.784   0.2989   0.6891   1.5566
 24I  C8    C  CR6    0   0.152  -1.1430   0.5208   1.2224
 24I  C5    C  CR16   0  -0.294  -1.8454  -0.6169   1.6163
 24I  C3    C  CR16   0  -0.216  -3.1774  -0.8021   1.2728
 24I  C4    C  CR16   0  -0.291  -1.8112   1.4626   0.4413
 24I  C2    C  CR16   0  -0.216  -3.1427   1.2975   0.0864
 24I  C1    C  CR6    0  -0.241  -3.8176   0.1610   0.5069
 24I  I     I  I      0   0.028  -5.8408  -0.1027  -0.0188
 24I  H131  H  HCH2   0   0.212   6.3264   0.7243  -1.6365
 24I  H132  H  HCH2   0   0.215   6.7859  -0.7676  -0.8739
 24I  H121  H  HCH2   0   0.190   5.7253  -0.0230   1.2663
 24I  H122  H  HCH2   0   0.194   5.3704   1.5328   0.5573
 24I  H10   H  HCH1   0   0.182   3.8919   0.4585  -1.1151
 24I  H7C1  H  HCH2   0   0.219   3.2004  -0.3107   1.7507
 24I  H7C2  H  HCH2   0   0.216   3.0919   1.3208   1.1125
 24I  H6C1  H  HCH2   0   0.249   0.5415   0.1964   2.5010
 24I  H6C2  H  HCH2   0   0.249   0.5538   1.7462   1.6619
 24I  H5    H  HCR6   0   0.249  -1.3491  -1.3725   2.2125
 24I  H3    H  HCR6   0   0.271  -3.6968  -1.6918   1.6030
 24I  HA    H  HCR6   0   0.249  -1.2883   2.3502   0.1086
 24I  H2    H  HCR6   0   0.271  -3.6351   2.0518  -0.5126

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
 24I  O5   C14   deloc     1.247  0.020  1.247
 24I  C14  O6    deloc     1.251  0.020  1.251
 24I  C14  C13   single    1.540  0.020  1.540
 24I  C13  C12   single    1.520  0.020  1.520
 24I  C13  H131  single    0.970  0.020  1.090
 24I  C13  H132  single    0.970  0.020  1.090
 24I  C12  C10   single    1.531  0.020  1.531
 24I  C12  H121  single    0.970  0.020  1.090
 24I  C12  H122  single    0.970  0.020  1.090
 24I  C10  C9    single    1.540  0.020  1.540
 24I  C10  C7    single    1.530  0.020  1.530
 24I  C10  H10   single    0.970  0.020  1.090
 24I  C9   O4    deloc     1.248  0.020  1.248
 24I  C9   O3    deloc     1.250  0.020  1.250
 24I  C7   P1    single    1.834  0.020  1.834
 24I  C7   H7C1  single    0.970  0.020  1.090
 24I  C7   H7C2  single    0.970  0.020  1.090
 24I  P1   O1    deloc     1.516  0.020  1.516
 24I  P1   O2    deloc     1.514  0.020  1.514
 24I  P1   C6    single    1.862  0.020  1.862
 24I  C6   C8    single    1.490  0.020  1.490
 24I  C6   H6C1  single    0.970  0.020  1.090
 24I  C6   H6C2  single    0.970  0.020  1.090
 24I  C8   C5    aromatic  1.394  0.020  1.394
 24I  C8   C4    aromatic  1.394  0.020  1.394
 24I  C5   C3    aromatic  1.388  0.020  1.388
 24I  C5   H5    single    0.930  0.020  1.080
 24I  C3   C1    aromatic  1.387  0.020  1.387
 24I  C3   H3    single    0.930  0.020  1.080
 24I  C4   C2    aromatic  1.388  0.020  1.388
 24I  C4   HA    single    0.930  0.020  1.080
 24I  C2   C1    aromatic  1.387  0.020  1.387
 24I  C2   H2    single    0.930  0.020  1.080
 24I  C1   I     single    2.107  0.020  2.107

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
 24I  C13   C14  O6    115.93  3.000
 24I  C13   C14  O5    118.17  3.000
 24I  O6    C14  O5    125.89  3.000
 24I  H132  C13  H131  104.84  3.000
 24I  H132  C13  C12   110.43  3.000
 24I  H131  C13  C12   109.25  3.000
 24I  H132  C13  C14   108.00  3.000
 24I  H131  C13  C14   107.76  3.000
 24I  C12   C13  C14   115.95  3.000
 24I  H122  C12  H121  105.93  3.000
 24I  H122  C12  C10   108.56  3.000
 24I  H121  C12  C10   108.95  3.000
 24I  H122  C12  C13   109.12  3.000
 24I  H121  C12  C13   109.99  3.000
 24I  C10   C12  C13   113.97  3.000
 24I  H10   C10  C7    108.07  3.000
 24I  H10   C10  C9    108.53  3.000
 24I  C7    C10  C9    111.47  3.000
 24I  H10   C10  C12   108.03  3.000
 24I  C7    C10  C12   110.12  3.000
 24I  C9    C10  C12   110.51  3.000
 24I  O3    C9   O4    125.78  3.000
 24I  O3    C9   C10   116.31  3.000
 24I  O4    C9   C10   117.88  3.000
 24I  H7C2  C7   H7C1  106.56  3.000
 24I  H7C2  C7   P1    107.73  3.000
 24I  H7C1  C7   P1    109.91  3.000
 24I  H7C2  C7   C10   109.29  3.000
 24I  H7C1  C7   C10   109.55  3.000
 24I  P1    C7   C10   113.54  3.000
 24I  C6    P1   O2    107.62  3.000
 24I  C6    P1   O1    107.48  3.000
 24I  O2    P1   O1    118.90  3.000
 24I  C6    P1   C7    101.34  3.000
 24I  O2    P1   C7    110.79  3.000
 24I  O1    P1   C7    109.20  3.000
 24I  H6C2  C6   H6C1  107.54  3.000
 24I  H6C2  C6   C8    110.90  3.000
 24I  H6C1  C6   C8    110.97  3.000
 24I  H6C2  C6   P1    109.02  3.000
 24I  H6C1  C6   P1    108.92  3.000
 24I  C8    C6   P1    109.44  3.000
 24I  C4    C8   C5    117.92  3.000
 24I  C4    C8   C6    120.88  3.000
 24I  C5    C8   C6    121.10  3.000
 24I  H5    C5   C3    118.88  3.000
 24I  H5    C5   C8    119.61  3.000
 24I  C3    C5   C8    121.50  3.000
 24I  H3    C3   C1    121.19  3.000
 24I  H3    C3   C5    119.67  3.000
 24I  C1    C3   C5    119.14  3.000
 24I  HA    C4   C2    118.84  3.000
 24I  HA    C4   C8    119.64  3.000
 24I  C2    C4   C8    121.52  3.000
 24I  H2    C2   C1    121.18  3.000
 24I  H2    C2   C4    119.69  3.000
 24I  C1    C2   C4    119.13  3.000
 24I  I     C1   C2    119.61  3.000
 24I  I     C1   C3    119.61  3.000
 24I  C2    C1   C3    120.78  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
 24I  CONST_01  C1   C3   C5   C8      0.00   0.0  0
 24I  CONST_02  C1   C2   C4   C8      0.00   0.0  0
 24I  CONST_03  C2   C4   C8   C5      0.00   0.0  0
 24I  CONST_04  C2   C1   C3   C5      0.00   0.0  0
 24I  CONST_05  C4   C8   C5   C3      0.00   0.0  0
 24I  CONST_06  C4   C2   C1   C3      0.00   0.0  0
 24I  CONST_07  C3   C5   C8   C6    180.00   0.0  0
 24I  CONST_08  C2   C4   C8   C6    180.00   0.0  0
 24I  CONST_09  I    C1   C3   C5    180.00   0.0  0
 24I  CONST_10  I    C1   C2   C4    180.00   0.0  0
 24I  CONST_11  H3   C3   C5   C8    180.00   0.0  0
 24I  CONST_12  H2   C2   C4   C8    180.00   0.0  0
 24I  CONST_13  HA   C4   C8   C5    180.00   0.0  0
 24I  CONST_14  H5   C5   C8   C4    180.00   0.0  0
 24I  Var_01    C5   C8   C6   P1     89.24  30.0  2
 24I  Var_02    C8   C6   P1   C7   -179.69  30.0  3
 24I  Var_03    C12  C13  C14  O5     -9.20  30.0  3
 24I  Var_04    C10  C12  C13  C14   174.83  30.0  3
 24I  Var_05    O1   P1   C7   C10   -58.07  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
 24I  chir_01  C10  C12  C9  C7  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
 24I  plan-1  C6   0.020
 24I  plan-1  C8   0.020
 24I  plan-1  C5   0.020
 24I  plan-1  C3   0.020
 24I  plan-1  C4   0.020
 24I  plan-1  C2   0.020
 24I  plan-1  C1   0.020
 24I  plan-1  I    0.020
 24I  plan-1  H5   0.020
 24I  plan-1  H3   0.020
 24I  plan-1  HA   0.020
 24I  plan-1  H2   0.020
 24I  plan-2  O5   0.020
 24I  plan-2  C14  0.020
 24I  plan-2  O6   0.020
 24I  plan-2  C13  0.020
 24I  plan-3  C10  0.020
 24I  plan-3  C9   0.020
 24I  plan-3  O4   0.020
 24I  plan-3  O3   0.020

