# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 05:49:09 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2-oxidanyl-propyl]-(phenylmethyl)phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC[C@H](O)C[P](O)(=O)Cc1ccccc1)c2ccc(Cl)c(Cl)c2
#
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
 SGG  SGG  '[(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2-oxidanyl-propyl]-(phenylmethyl)phosphinic acid'  ligand  46  25  .  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_SGG
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
 SGG  C13  C   CR6    0  -0.021  203.9362  146.6213  107.6479
 SGG  C15  C   CH3    0  -0.662  204.5972  141.8122  108.8559
 SGG  C17  C   CH1    0   0.033  201.7501  141.3185  105.4955
 SGG  C20  C   CR6    0   0.153  199.2257  144.1647  105.0191
 SGG  C21  C   CR16   0  -0.300  198.6676  144.8969  103.9696
 SGG  C22  C   CR16   0  -0.241  199.1877  146.1296  103.6008
 SGG  C24  C   CR16   0  -0.237  200.8517  145.9430  105.3154
 SGG  C04  C   CR6    0   0.016  204.8072  145.8471  106.8899
 SGG  C07  C   CR16   0  -0.251  204.7170  144.4648  106.9158
 SGG  C09  C   CR6    0   0.119  203.7486  143.8341  107.6868
 SGG  C11  C   CR16   0  -0.308  202.8799  144.6174  108.4388
 SGG  C12  C   CR16   0  -0.208  202.9718  145.9994  108.4260
 SGG  C14  C   CH1    0  -0.138  203.6709  142.3241  107.7550
 SGG  C18  C   CH2    0  -0.743  200.9926  141.5412  104.1943
 SGG  C19  C   CH2    0  -0.809  198.6893  142.8210  105.3969
 SGG  C23  C   CR16   0  -0.281  200.2866  146.6576  104.2677
 SGG  C25  C   CR16   0  -0.325  200.3227  144.7134  105.6849
 SGG  N05  N   NH1    0  -0.607  204.0592  141.7269  106.4927
 SGG  O06  O   O      0  -0.803  198.6579  141.7939  102.8484
 SGG  O08  O   OP    -1  -0.802  198.6887  140.1480  104.8754
 SGG  O10  O   OH1    0  -0.670  201.8121  139.9292  105.7592
 SGG  P03  P   P      0   1.183  199.1525  141.4380  104.2352
 SGG  CL1  CL  CL     0  -0.102  204.0216  148.3423  107.6088
 SGG  CL2  CL  CL     0  -0.105  206.0082  146.5952  105.9026
 SGG  H1   H   HCH3   0   0.238  204.3350  142.2503  109.8182
 SGG  H2   H   HCH3   0   0.236  204.5178  140.7273  108.9507
 SGG  H3   H   HCH3   0   0.230  205.6355  142.0628  108.6354
 SGG  H4   H   HCH1   0   0.202  201.2220  141.8305  106.3125
 SGG  H5   H   HCR6   0   0.237  197.8121  144.4979  103.4395
 SGG  H6   H   HCR6   0   0.245  198.7349  146.6810  102.7861
 SGG  H7   H   HCR6   0   0.253  201.7040  146.3415  105.8518
 SGG  H8   H   HCR6   0   0.277  205.3986  143.8714  106.3208
 SGG  H9   H   HCR6   0   0.266  202.1142  144.1462  109.0437
 SGG  H10  H   HCR6   0   0.284  202.2869  146.5988  109.0105
 SGG  H11  H   HCH1   0   0.226  202.6413  142.0713  108.0530
 SGG  H12  H   HCH2   0   0.227  203.6382  141.4982  104.4866
 SGG  H13  H   HCH2   0   0.218  203.0541  142.9925  105.1867
 SGG  H14  H   HCH2   0   0.243  201.3502  140.8258  103.4450
 SGG  H15  H   HCH2   0   0.240  201.2444  142.5295  103.7992
 SGG  H16  H   HCH2   0   0.255  197.5949  142.8326  105.3984
 SGG  H17  H   HCH2   0   0.249  199.0014  142.5556  106.4094
 SGG  H18  H   HCR6   0   0.245  200.6942  147.6176  103.9775
 SGG  H19  H   HCR6   0   0.247  200.7673  144.1704  106.5114
 SGG  H20  H   HNH1   0   0.349  204.2573  140.7429  106.6219
 SGG  H23  H   HOH1   0   0.444  202.0373  139.8043  106.6855
 SGG  C16  C   CH2    0  -0.304  203.1564  141.9194  105.3748

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
 SGG  O06  P03  deloc     1.515  0.020  1.515
 SGG  C22  C21  aromatic  1.388  0.020  1.388
 SGG  C22  C23  aromatic  1.390  0.020  1.390
 SGG  C21  C20  aromatic  1.396  0.020  1.396
 SGG  C23  C24  aromatic  1.388  0.020  1.388
 SGG  C18  P03  single    1.843  0.020  1.843
 SGG  C18  C17  single    1.522  0.020  1.522
 SGG  P03  O08  deloc     1.513  0.020  1.513
 SGG  P03  C19  single    1.865  0.020  1.865
 SGG  O10  C17  single    1.415  0.020  1.415
 SGG  C20  C19  single    1.495  0.020  1.495
 SGG  C20  C25  aromatic  1.396  0.020  1.396
 SGG  C24  C25  aromatic  1.389  0.020  1.389
 SGG  C17  C16  single    1.534  0.020  1.534
 SGG  C16  N05  single    1.450  0.020  1.450
 SGG  CL2  C04  single    1.725  0.020  1.725
 SGG  N05  C14  single    1.449  0.020  1.449
 SGG  CL1  C13  single    1.724  0.020  1.724
 SGG  C04  C13  aromatic  1.390  0.020  1.390
 SGG  C04  C07  aromatic  1.386  0.020  1.386
 SGG  C13  C12  aromatic  1.386  0.020  1.386
 SGG  C07  C09  aromatic  1.389  0.020  1.389
 SGG  C12  C11  aromatic  1.385  0.020  1.385
 SGG  C09  C11  aromatic  1.391  0.020  1.391
 SGG  C09  C14  single    1.514  0.020  1.514
 SGG  C14  C15  single    1.527  0.020  1.527
 SGG  C15  H1   single    0.970  0.020  1.090
 SGG  C15  H2   single    0.970  0.020  1.090
 SGG  C15  H3   single    0.970  0.020  1.090
 SGG  C17  H4   single    0.970  0.020  1.090
 SGG  C21  H5   single    0.930  0.020  1.080
 SGG  C22  H6   single    0.930  0.020  1.080
 SGG  C24  H7   single    0.930  0.020  1.080
 SGG  C07  H8   single    0.930  0.020  1.080
 SGG  C11  H9   single    0.930  0.020  1.080
 SGG  C12  H10  single    0.930  0.020  1.080
 SGG  C14  H11  single    0.970  0.020  1.090
 SGG  C16  H12  single    0.970  0.020  1.090
 SGG  C16  H13  single    0.970  0.020  1.090
 SGG  C18  H14  single    0.970  0.020  1.090
 SGG  C18  H15  single    0.970  0.020  1.090
 SGG  C19  H16  single    0.970  0.020  1.090
 SGG  C19  H17  single    0.970  0.020  1.090
 SGG  C23  H18  single    0.930  0.020  1.080
 SGG  C25  H19  single    0.930  0.020  1.080
 SGG  N05  H20  single    0.890  0.020  1.040
 SGG  O10  H23  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
 SGG  CL1  C13  C12  119.67  3.000
 SGG  C12  C13  C04  119.48  3.000
 SGG  CL1  C13  C04  120.84  3.000
 SGG  H3   C15  H2   108.37  3.000
 SGG  H3   C15  H1   108.38  3.000
 SGG  H2   C15  H1   107.78  3.000
 SGG  H3   C15  C14  110.77  3.000
 SGG  H2   C15  C14  110.58  3.000
 SGG  H1   C15  C14  110.85  3.000
 SGG  H4   C17  O10  109.86  3.000
 SGG  H4   C17  C18  109.16  3.000
 SGG  O10  C17  C18  108.95  3.000
 SGG  H4   C17  C16  108.44  3.000
 SGG  O10  C17  C16  111.04  3.000
 SGG  C18  C17  C16  109.37  3.000
 SGG  C25  C20  C19  120.98  3.000
 SGG  C25  C20  C21  117.82  3.000
 SGG  C19  C20  C21  121.19  3.000
 SGG  H5   C21  C22  119.57  3.000
 SGG  H5   C21  C20  119.38  3.000
 SGG  C22  C21  C20  121.05  3.000
 SGG  H6   C22  C23  119.88  3.000
 SGG  H6   C22  C21  119.70  3.000
 SGG  C23  C22  C21  120.42  3.000
 SGG  H7   C24  C25  119.59  3.000
 SGG  H7   C24  C23  120.31  3.000
 SGG  C25  C24  C23  120.10  3.000
 SGG  CL2  C04  C07  119.25  3.000
 SGG  C07  C04  C13  120.30  3.000
 SGG  CL2  C04  C13  120.45  3.000
 SGG  H8   C07  C09  119.69  3.000
 SGG  H8   C07  C04  119.73  3.000
 SGG  C09  C07  C04  120.58  3.000
 SGG  C14  C09  C11  120.37  3.000
 SGG  C14  C09  C07  120.91  3.000
 SGG  C11  C09  C07  118.68  3.000
 SGG  H9   C11  C12  119.08  3.000
 SGG  H9   C11  C09  119.89  3.000
 SGG  C12  C11  C09  121.03  3.000
 SGG  H10  C12  C11  120.39  3.000
 SGG  H10  C12  C13  119.68  3.000
 SGG  C11  C12  C13  119.93  3.000
 SGG  H11  C14  N05  113.05  3.000
 SGG  H11  C14  C09  106.81  3.000
 SGG  N05  C14  C09  110.98  3.000
 SGG  H11  C14  C15  107.16  3.000
 SGG  C09  C14  C15  109.62  3.000
 SGG  N05  C14  C15  109.10  3.000
 SGG  H15  C18  H14  105.53  3.000
 SGG  H15  C18  P03  106.76  3.000
 SGG  H14  C18  P03  107.71  3.000
 SGG  H15  C18  C17  109.06  3.000
 SGG  H14  C18  C17  109.07  3.000
 SGG  P03  C18  C17  118.01  3.000
 SGG  H17  C19  H16  106.68  3.000
 SGG  H17  C19  P03  109.05  3.000
 SGG  H16  C19  P03  104.90  3.000
 SGG  H17  C19  C20  110.49  3.000
 SGG  H16  C19  C20  110.45  3.000
 SGG  P03  C19  C20  114.84  3.000
 SGG  H18  C23  C24  120.36  3.000
 SGG  H18  C23  C22  120.40  3.000
 SGG  C24  C23  C22  119.23  3.000
 SGG  H19  C25  C24  119.34  3.000
 SGG  H19  C25  C20  119.28  3.000
 SGG  C24  C25  C20  121.38  3.000
 SGG  H20  N05  C16  110.45  3.000
 SGG  H20  N05  C14  110.00  3.000
 SGG  C16  N05  C14  116.75  3.000
 SGG  H23  O10  C17  108.50  3.000
 SGG  O08  P03  O06  119.19  3.000
 SGG  O08  P03  C19  107.01  3.000
 SGG  O06  P03  C19  108.36  3.000
 SGG  C19  P03  C18  102.72  3.000
 SGG  O08  P03  C18  111.29  3.000
 SGG  O06  P03  C18  107.01  3.000
 SGG  H13  C16  H12  106.20  3.000
 SGG  H13  C16  N05  108.72  3.000
 SGG  H12  C16  N05  107.49  3.000
 SGG  H13  C16  C17  108.18  3.000
 SGG  H12  C16  C17  108.45  3.000
 SGG  N05  C16  C17  117.27  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
 SGG  CONST_01  C09  C07  C04  C13    0.00   0.0  0
 SGG  CONST_02  C09  C11  C12  C13    0.00   0.0  0
 SGG  CONST_03  C23  C22  C21  C20    0.00   0.0  0
 SGG  CONST_04  C23  C24  C25  C20    0.00   0.0  0
 SGG  CONST_05  C24  C23  C22  C21    0.00   0.0  0
 SGG  CONST_06  C24  C25  C20  C21    0.00   0.0  0
 SGG  CONST_07  C25  C20  C21  C22    0.00   0.0  0
 SGG  CONST_08  C25  C24  C23  C22    0.00   0.0  0
 SGG  CONST_09  C11  C12  C13  C04    0.00   0.0  0
 SGG  CONST_10  C11  C09  C07  C04    0.00   0.0  0
 SGG  CONST_11  C12  C13  C04  C07    0.00   0.0  0
 SGG  CONST_12  C12  C11  C09  C07    0.00   0.0  0
 SGG  CONST_13  C19  C20  C21  C22  180.00   0.0  0
 SGG  CONST_14  C19  C20  C25  C24  180.00   0.0  0
 SGG  CONST_15  C14  C09  C07  C04  180.00   0.0  0
 SGG  CONST_16  CL1  C13  C04  C07  180.00   0.0  0
 SGG  CONST_17  CL2  C04  C07  C09  180.00   0.0  0
 SGG  CONST_18  CL1  C13  C12  C11  180.00   0.0  0
 SGG  CONST_19  CL2  C04  C13  C12  180.00   0.0  0
 SGG  CONST_20  C14  C09  C11  C12  180.00   0.0  0
 SGG  CONST_21  H8   C07  C04  C13  180.00   0.0  0
 SGG  CONST_22  H9   C11  C12  C13  180.00   0.0  0
 SGG  CONST_23  H6   C22  C21  C20  180.00   0.0  0
 SGG  CONST_24  H7   C24  C25  C20  180.00   0.0  0
 SGG  CONST_25  H18  C23  C22  C21  180.00   0.0  0
 SGG  CONST_26  H19  C25  C20  C21  180.00   0.0  0
 SGG  CONST_27  H10  C12  C13  C04  180.00   0.0  0
 SGG  CONST_28  H5   C21  C22  C23  180.00   0.0  0
 SGG  Var_01    P03  C19  C20  C21   75.25  30.0  2
 SGG  Var_02    O06  P03  C19  C20  -57.91  30.0  1
 SGG  Var_03    C14  N05  C16  C17  -63.12  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
 SGG  chir_01  C17  C18  O10  C16  negativ
 SGG  chir_02  C14  N05  C09  C15  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
 SGG  plan-1  C20  0.020
 SGG  plan-1  C21  0.020
 SGG  plan-1  C22  0.020
 SGG  plan-1  C24  0.020
 SGG  plan-1  C19  0.020
 SGG  plan-1  C23  0.020
 SGG  plan-1  C25  0.020
 SGG  plan-1  H5   0.020
 SGG  plan-1  H6   0.020
 SGG  plan-1  H7   0.020
 SGG  plan-1  H18  0.020
 SGG  plan-1  H19  0.020
 SGG  plan-2  C13  0.020
 SGG  plan-2  C04  0.020
 SGG  plan-2  C07  0.020
 SGG  plan-2  C09  0.020
 SGG  plan-2  C11  0.020
 SGG  plan-2  C12  0.020
 SGG  plan-2  C14  0.020
 SGG  plan-2  CL1  0.020
 SGG  plan-2  CL2  0.020
 SGG  plan-2  H8   0.020
 SGG  plan-2  H9   0.020
 SGG  plan-2  H10  0.020

