# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:10:24 2021
#   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  47  25  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.019  203.1511  146.2240  107.7835
 SGG  C15  C   CH3   0  -0.653  204.9121  141.6414  108.7987
 SGG  C17  C   CH1   0  -0.002  201.8664  141.4780  105.5498
 SGG  C20  C   CR6   0   0.113  199.4018  144.5555  104.9370
 SGG  C21  C   CR16  0  -0.284  198.6220  145.1887  103.9709
 SGG  C22  C   CR16  0  -0.242  199.0524  146.3657  103.3751
 SGG  C24  C   CR16  0  -0.226  201.0607  146.2991  104.6863
 SGG  C04  C   CR6   0   0.011  204.1461  145.6747  106.9823
 SGG  C07  C   CR16  0  -0.253  204.3653  144.3062  106.9780
 SGG  C09  C   CR6   0   0.107  203.5815  143.4663  107.7592
 SGG  C11  C   CR16  0  -0.312  202.5865  144.0246  108.5550
 SGG  C12  C   CR16  0  -0.204  202.3748  145.3931  108.5763
 SGG  C14  C   CH1   0  -0.151  203.8228  141.9753  107.7827
 SGG  C18  C   CH2   0  -0.759  201.1089  141.7833  104.2636
 SGG  C19  C   CH2   0  -0.802  198.9540  143.2634  105.5569
 SGG  C23  C   CR16  0  -0.268  200.2748  146.9237  103.7280
 SGG  C25  C   CR16  0  -0.296  200.6252  145.1244  105.2847
 SGG  N05  N   NH1   0  -0.603  204.2304  141.4761  106.4823
 SGG  O06  O   O     0  -0.710  198.5445  141.9180  103.1772
 SGG  O08  O   OH1   0  -0.781  198.9454  140.5422  105.3374
 SGG  O10  O   OH1   0  -0.672  201.5696  140.1308  105.9011
 SGG  P03  P   P     0   1.258  199.3030  141.8469  104.4594
 SGG  CL1  CL  CL    0  -0.094  202.8576  147.9212  107.7849
 SGG  CL2  CL  CL    0  -0.095  205.1051  146.6864  105.9677
 SGG  H1   H   HCH3  0   0.239  204.6344  141.9896  109.7930
 SGG  H2   H   HCH3  0   0.239  205.0696  140.5626  108.8532
 SGG  H3   H   HCH3  0   0.233  205.8543  142.1129  108.5169
 SGG  H4   H   HCH1  0   0.223  201.5107  142.1488  106.3442
 SGG  H5   H   HCR6  0   0.252  197.6676  144.7619  103.6890
 SGG  H6   H   HCR6  0   0.257  198.4318  146.8482  102.6311
 SGG  H7   H   HCR6  0   0.236  202.0128  146.7295  104.9706
 SGG  H8   H   HCR6  0   0.290  205.1452  143.8906  106.3526
 SGG  H9   H   HCR6  0   0.270  201.9625  143.3839  109.1661
 SGG  H10  H   HCR6  0   0.290  201.5959  145.8172  109.1952
 SGG  H11  H   HCH1  0   0.218  202.8918  141.5111  108.1467
 SGG  H12  H   HCH2  0   0.255  203.7160  141.0980  104.5241
 SGG  H13  H   HCH2  0   0.226  203.4724  142.7555  105.0194
 SGG  H14  H   HCH2  0   0.303  201.3390  141.0326  103.5012
 SGG  H15  H   HCH2  0   0.294  201.4263  142.7471  103.8586
 SGG  H16  H   HCH2  0   0.308  197.8752  143.2589  105.7338
 SGG  H17  H   HCH2  0   0.291  199.4322  143.0995  106.5254
 SGG  H18  H   HCR6  0   0.257  200.6094  147.8414  103.2621
 SGG  H19  H   HCR6  0   0.239  201.2445  144.6518  106.0387
 SGG  H20  H   HNH1  0   0.362  204.4612  140.4947  106.5551
 SGG  H22  H   HOH1  0   0.486  199.7577  140.1303  105.7039
 SGG  H23  H   HOH1  0   0.471  201.8449  139.9656  106.8092
 SGG  C16  C   CH2   0  -0.296  203.3606  141.7183  105.3504

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  double    1.491  0.020  1.491
 SGG  C22  C21  aromatic  1.388  0.020  1.388
 SGG  C22  C23  aromatic  1.389  0.020  1.389
 SGG  C21  C20  aromatic  1.394  0.020  1.394
 SGG  C23  C24  aromatic  1.388  0.020  1.388
 SGG  C18  P03  single    1.818  0.020  1.818
 SGG  C18  C17  single    1.524  0.020  1.524
 SGG  P03  O08  single    1.613  0.020  1.613
 SGG  P03  C19  single    1.826  0.020  1.826
 SGG  O10  C17  single    1.424  0.020  1.424
 SGG  C20  C19  single    1.501  0.020  1.501
 SGG  C20  C25  aromatic  1.393  0.020  1.393
 SGG  C24  C25  aromatic  1.388  0.020  1.388
 SGG  C17  C16  single    1.526  0.020  1.526
 SGG  C16  N05  single    1.448  0.020  1.448
 SGG  CL2  C04  single    1.724  0.020  1.724
 SGG  N05  C14  single    1.451  0.020  1.451
 SGG  CL1  C13  single    1.722  0.020  1.722
 SGG  C04  C13  aromatic  1.391  0.020  1.391
 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    1.510  0.020  1.510
 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  O08  H22  single    0.850  0.020  0.980
 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  119.65  3.000
 SGG  C12  C13  C04  119.57  3.000
 SGG  CL1  C13  C04  120.77  3.000
 SGG  H3   C15  H2   108.39  3.000
 SGG  H3   C15  H1   108.54  3.000
 SGG  H2   C15  H1   107.88  3.000
 SGG  H3   C15  C14  110.49  3.000
 SGG  H2   C15  C14  110.63  3.000
 SGG  H1   C15  C14  110.83  3.000
 SGG  H4   C17  O10  109.38  3.000
 SGG  H4   C17  C18  109.09  3.000
 SGG  O10  C17  C18  107.11  3.000
 SGG  H4   C17  C16  108.38  3.000
 SGG  O10  C17  C16  112.66  3.000
 SGG  C18  C17  C16  110.17  3.000
 SGG  C25  C20  C19  120.68  3.000
 SGG  C25  C20  C21  118.61  3.000
 SGG  C19  C20  C21  120.69  3.000
 SGG  H5   C21  C22  119.74  3.000
 SGG  H5   C21  C20  119.64  3.000
 SGG  C22  C21  C20  120.62  3.000
 SGG  H6   C22  C23  120.00  3.000
 SGG  H6   C22  C21  119.69  3.000
 SGG  C23  C22  C21  120.31  3.000
 SGG  H7   C24  C25  119.93  3.000
 SGG  H7   C24  C23  120.02  3.000
 SGG  C25  C24  C23  120.05  3.000
 SGG  CL2  C04  C07  119.31  3.000
 SGG  C07  C04  C13  120.34  3.000
 SGG  CL2  C04  C13  120.35  3.000
 SGG  H8   C07  C09  119.94  3.000
 SGG  H8   C07  C04  119.66  3.000
 SGG  C09  C07  C04  120.39  3.000
 SGG  C14  C09  C11  120.10  3.000
 SGG  C14  C09  C07  121.03  3.000
 SGG  C11  C09  C07  118.85  3.000
 SGG  H9   C11  C12  119.19  3.000
 SGG  H9   C11  C09  119.83  3.000
 SGG  C12  C11  C09  120.98  3.000
 SGG  H10  C12  C11  120.43  3.000
 SGG  H10  C12  C13  119.71  3.000
 SGG  C11  C12  C13  119.86  3.000
 SGG  H11  C14  N05  112.84  3.000
 SGG  H11  C14  C09  106.62  3.000
 SGG  N05  C14  C09  111.74  3.000
 SGG  H11  C14  C15  106.91  3.000
 SGG  C09  C14  C15  109.89  3.000
 SGG  N05  C14  C15  108.70  3.000
 SGG  H15  C18  H14  106.61  3.000
 SGG  H15  C18  P03  107.32  3.000
 SGG  H14  C18  P03  107.93  3.000
 SGG  H15  C18  C17  110.20  3.000
 SGG  H14  C18  C17  110.25  3.000
 SGG  P03  C18  C17  114.21  3.000
 SGG  H17  C19  H16  106.74  3.000
 SGG  H17  C19  P03  109.44  3.000
 SGG  H16  C19  P03  106.42  3.000
 SGG  H17  C19  C20  111.39  3.000
 SGG  H16  C19  C20  111.38  3.000
 SGG  P03  C19  C20  111.25  3.000
 SGG  H18  C23  C24  120.25  3.000
 SGG  H18  C23  C22  120.22  3.000
 SGG  C24  C23  C22  119.53  3.000
 SGG  H19  C25  C24  119.30  3.000
 SGG  H19  C25  C20  119.81  3.000
 SGG  C24  C25  C20  120.88  3.000
 SGG  H20  N05  C16  110.85  3.000
 SGG  H20  N05  C14  109.49  3.000
 SGG  C16  N05  C14  118.31  3.000
 SGG  H22  O08  P03  111.05  3.000
 SGG  H23  O10  C17  109.59  3.000
 SGG  O08  P03  O06  113.19  3.000
 SGG  O08  P03  C19  104.96  3.000
 SGG  O06  P03  C19  112.50  3.000
 SGG  C19  P03  C18  106.37  3.000
 SGG  O08  P03  C18  104.51  3.000
 SGG  O06  P03  C18  114.48  3.000
 SGG  H13  C16  H12  106.03  3.000
 SGG  H13  C16  N05  109.49  3.000
 SGG  H12  C16  N05  107.51  3.000
 SGG  H13  C16  C17  106.77  3.000
 SGG  H12  C16  C17  109.14  3.000
 SGG  N05  C16  C17  117.35  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
 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   79.78  30.0  2
 SGG  Var_02    O06  P03  C19  C20  -63.59  30.0  1
 SGG  Var_03    C14  N05  C16  C17  -44.71  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
 SGG  chir_03  P03  C18  O08  C19  both

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

