# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:58:47 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (1R)-1-{3-[3-(dimethylcarbamoyl)phenoxy]-4-nitrophenyl}ethyl bis[(aziridin-1-yl)]phosphinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[P](=O)(N1CC1)N2CC2)c3ccc(c(Oc4cccc(c4)C(=O)N(C)C)c3)[N+]([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
 6LG  6LG  '(1R)-1-{3-[3-(dimethylcarbamoyl)phenoxy]-4-nitrophenyl}ethyl bis[(aziridin-1-yl)]phosphinate'  ligand  57  32  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6LG
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
 6LG  C10   C  CR6    0   0.417   0.7856  -1.6572   0.4466
 6LG  C13   C  CH1    0  -0.047  -1.6355   0.3675  -1.6538
 6LG  C17   C  CH2    0  -0.349  -6.0228   0.4965  -1.0782
 6LG  C20   C  CH2    0  -0.355  -2.3773   0.0356   2.0371
 6LG  C21   C  CH2    0  -0.356  -3.6657   0.5389   2.5433
 6LG  C24   C  CR16   0  -0.294  -1.6917  -2.0118  -0.8165
 6LG  C26   C  CR6    0   0.160   0.1195  -2.8866   0.4964
 6LG  O01   O  O      0  -0.487   6.1993   2.3015   0.3014
 6LG  N03   N  NT     0  -0.439   5.0495   1.8039  -1.5806
 6LG  C04   C  CH3    0  -0.525   6.1888   2.0831  -2.4306
 6LG  C05   C  CH3    0  -0.532   3.7904   1.6631  -2.2855
 6LG  C06   C  CR6    0  -0.061   4.0353   1.4322   0.6023
 6LG  C07   C  CR16   0  -0.309   3.4724   0.1735   0.4135
 6LG  C08   C  CR6    0   0.304   2.4736  -0.2544   1.2692
 6LG  O09   O  O2     0  -0.489   1.9523  -1.5183   1.1010
 6LG  C11   C  CR16   0  -0.408   0.1824  -0.6145  -0.2520
 6LG  C12   C  CR6    0   0.122  -1.0377  -0.7848  -0.8845
 6LG  O14   O  O2     0  -0.594  -3.0306   0.4737  -1.3603
 6LG  P15   P  P      0   1.391  -3.5744   1.2624  -0.0629
 6LG  N16   N  NT     0  -0.545  -5.2029   1.4274  -0.3256
 6LG  C18   C  CH2    0  -0.356  -5.7617   1.8548  -1.5963
 6LG  N19   N  NT     0  -0.557  -3.5342   0.1148   1.1551
 6LG  O22   O  O      0  -0.708  -2.8695   2.5441   0.1934
 6LG  C23   C  CH3    0  -0.664  -1.4886   0.1741  -3.1508
 6LG  C25   C  CR16   0  -0.258  -1.1145  -3.0522  -0.1218
 6LG  N27   N  N      1   0.334   0.6838  -4.0247   1.1907
 6LG  O28   O  O      0  -0.371   1.8847  -4.1444   1.2186
 6LG  O29   O  O     -1  -0.382  -0.0884  -4.8111   1.6907
 6LG  C30   C  CR16   0  -0.292   2.0165   0.5422   2.3068
 6LG  C31   C  CR16   0  -0.243   2.5886   1.7925   2.4914
 6LG  C32   C  CR16   0  -0.270   3.6018   2.2336   1.6526
 6LG  H131  H  HCH1   0   0.260  -1.1314   1.2936  -1.3601
 6LG  H172  H  HCH2   0   0.269  -5.5398  -0.3384  -1.5727
 6LG  H171  H  HCH2   0   0.270  -6.9800   0.2677  -0.6267
 6LG  H202  H  HCH2   0   0.261  -1.5789   0.7584   1.9076
 6LG  H201  H  HCH2   0   0.269  -2.0522  -0.9706   2.2712
 6LG  H211  H  HCH2   0   0.271  -4.2965  -0.0971   3.1513
 6LG  H212  H  HCH2   0   0.266  -3.7434   1.5998   2.7557
 6LG  H241  H  HCR6   0   0.274  -2.6500  -2.1611  -1.2939
 6LG  H041  H  HCH3   0   0.247   6.1497   1.4294  -3.3018
 6LG  H043  H  HCH3   0   0.242   6.1825   3.1182  -2.7802
 6LG  H042  H  HCH3   0   0.256   7.1191   1.8986  -1.9027
 6LG  H053  H  HCH3   0   0.259   2.9417   1.7441  -1.6139
 6LG  H051  H  HCH3   0   0.259   3.7010   2.4622  -3.0232
 6LG  H052  H  HCH3   0   0.248   3.7342   0.7085  -2.8114
 6LG  H071  H  HCR6   0   0.290   3.8138  -0.4759  -0.3838
 6LG  H111  H  HCR6   0   0.294   0.6587   0.3568  -0.2858
 6LG  H182  H  HCH2   0   0.268  -5.0974   1.9515  -2.4481
 6LG  H181  H  HCH2   0   0.272  -6.5274   2.6169  -1.5268
 6LG  H231  H  HCH3   0   0.244  -0.4339   0.0911  -3.4123
 6LG  H232  H  HCH3   0   0.242  -1.9940  -0.7330  -3.4835
 6LG  H233  H  HCH3   0   0.253  -1.9032   1.0263  -3.6893
 6LG  H251  H  HCR6   0   0.300  -1.6169  -4.0077  -0.0696
 6LG  H301  H  HCR6   0   0.285   1.2333   0.1875   2.9651
 6LG  H311  H  HCR6   0   0.275   2.2429   2.4234   3.2990
 6LG  H321  H  HCR6   0   0.270   4.0453   3.2074   1.8120
 6LG  C02   C  C      0   0.516   5.1814   1.8944  -0.2442

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
 6LG  C05  N03   single    1.450  0.020  1.450
 6LG  C04  N03   single    1.449  0.020  1.449
 6LG  N03  C02   single    1.346  0.020  1.346
 6LG  C20  C21   single    1.473  0.020  1.473
 6LG  C20  N19   single    1.457  0.020  1.457
 6LG  C02  O01   double    1.225  0.020  1.225
 6LG  C02  C06   single    1.498  0.020  1.498
 6LG  C21  N19   single    1.457  0.020  1.457
 6LG  N19  P15   single    1.674  0.020  1.674
 6LG  C07  C06   aromatic  1.392  0.020  1.392
 6LG  C07  C08   aromatic  1.383  0.020  1.383
 6LG  O22  P15   double    1.485  0.020  1.485
 6LG  C06  C32   aromatic  1.390  0.020  1.390
 6LG  O09  C08   single    1.377  0.020  1.377
 6LG  O09  C10   single    1.345  0.020  1.345
 6LG  C08  C30   aromatic  1.386  0.020  1.386
 6LG  O14  P15   single    1.613  0.020  1.613
 6LG  O14  C13   single    1.430  0.020  1.430
 6LG  P15  N16   single    1.658  0.020  1.658
 6LG  C11  C10   aromatic  1.393  0.020  1.393
 6LG  C11  C12   aromatic  1.385  0.020  1.385
 6LG  C10  C26   aromatic  1.399  0.020  1.399
 6LG  C23  C13   single    1.517  0.020  1.517
 6LG  C32  C31   aromatic  1.387  0.020  1.387
 6LG  O28  N27   double    1.207  0.020  1.207
 6LG  C13  C12   single    1.509  0.020  1.509
 6LG  C12  C24   aromatic  1.392  0.020  1.392
 6LG  C26  N27   single    1.448  0.020  1.448
 6LG  C26  C25   aromatic  1.390  0.020  1.390
 6LG  N27  O29   single    1.210  0.020  1.210
 6LG  C30  C31   aromatic  1.387  0.020  1.387
 6LG  N16  C18   single    1.452  0.020  1.452
 6LG  N16  C17   single    1.451  0.020  1.451
 6LG  C24  C25   aromatic  1.378  0.020  1.378
 6LG  C18  C17   single    1.477  0.020  1.477
 6LG  C13  H131  single    0.970  0.020  1.090
 6LG  C17  H172  single    0.970  0.020  1.090
 6LG  C17  H171  single    0.970  0.020  1.090
 6LG  C20  H202  single    0.970  0.020  1.090
 6LG  C20  H201  single    0.970  0.020  1.090
 6LG  C21  H211  single    0.970  0.020  1.090
 6LG  C21  H212  single    0.970  0.020  1.090
 6LG  C24  H241  single    0.930  0.020  1.080
 6LG  C04  H041  single    0.970  0.020  1.090
 6LG  C04  H043  single    0.970  0.020  1.090
 6LG  C04  H042  single    0.970  0.020  1.090
 6LG  C05  H053  single    0.970  0.020  1.090
 6LG  C05  H051  single    0.970  0.020  1.090
 6LG  C05  H052  single    0.970  0.020  1.090
 6LG  C07  H071  single    0.930  0.020  1.080
 6LG  C11  H111  single    0.930  0.020  1.080
 6LG  C18  H182  single    0.970  0.020  1.090
 6LG  C18  H181  single    0.970  0.020  1.090
 6LG  C23  H231  single    0.970  0.020  1.090
 6LG  C23  H232  single    0.970  0.020  1.090
 6LG  C23  H233  single    0.970  0.020  1.090
 6LG  C25  H251  single    0.930  0.020  1.080
 6LG  C30  H301  single    0.930  0.020  1.080
 6LG  C31  H311  single    0.930  0.020  1.080
 6LG  C32  H321  single    0.930  0.020  1.080

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
 6LG  C11   C10  O09   122.86  3.000
 6LG  C11   C10  C26   118.01  3.000
 6LG  O09   C10  C26   119.11  3.000
 6LG  H131  C13  C23   109.16  3.000
 6LG  H131  C13  O14   109.36  3.000
 6LG  C23   C13  O14   107.86  3.000
 6LG  H131  C13  C12   109.08  3.000
 6LG  C23   C13  C12   111.56  3.000
 6LG  O14   C13  C12   109.79  3.000
 6LG  H171  C17  H172  114.93  3.000
 6LG  H171  C17  C18   119.79  3.000
 6LG  H172  C17  C18   118.00  3.000
 6LG  H171  C17  N16   114.76  3.000
 6LG  H172  C17  N16   118.62  3.000
 6LG  C18   C17  N16    59.47  3.000
 6LG  H201  C20  H202  115.08  3.000
 6LG  H201  C20  N19   114.82  3.000
 6LG  H202  C20  N19   118.43  3.000
 6LG  H201  C20  C21   120.38  3.000
 6LG  H202  C20  C21   117.21  3.000
 6LG  N19   C20  C21    59.66  3.000
 6LG  H212  C21  H211  115.01  3.000
 6LG  H212  C21  N19   118.52  3.000
 6LG  H211  C21  N19   114.62  3.000
 6LG  H212  C21  C20   117.66  3.000
 6LG  H211  C21  C20   120.14  3.000
 6LG  N19   C21  C20    59.62  3.000
 6LG  H241  C24  C25   119.33  3.000
 6LG  H241  C24  C12   121.11  3.000
 6LG  C25   C24  C12   119.56  3.000
 6LG  N27   C26  C25   117.75  3.000
 6LG  C25   C26  C10   120.76  3.000
 6LG  N27   C26  C10   121.49  3.000
 6LG  C05   N03  C04   114.61  3.000
 6LG  C04   N03  C02   119.51  3.000
 6LG  C05   N03  C02   125.06  3.000
 6LG  H042  C04  H043  108.76  3.000
 6LG  H042  C04  H041  108.51  3.000
 6LG  H043  C04  H041  108.20  3.000
 6LG  H042  C04  N03   110.85  3.000
 6LG  H043  C04  N03   111.46  3.000
 6LG  H041  C04  N03   108.98  3.000
 6LG  H052  C05  H051  108.09  3.000
 6LG  H052  C05  H053  108.86  3.000
 6LG  H051  C05  H053  107.44  3.000
 6LG  H052  C05  N03   111.34  3.000
 6LG  H051  C05  N03   109.19  3.000
 6LG  H053  C05  N03   111.78  3.000
 6LG  C32   C06  C07   119.84  3.000
 6LG  C32   C06  C02   119.18  3.000
 6LG  C07   C06  C02   120.79  3.000
 6LG  H071  C07  C08   119.83  3.000
 6LG  H071  C07  C06   120.96  3.000
 6LG  C08   C07  C06   119.21  3.000
 6LG  C30   C08  O09   119.61  3.000
 6LG  C30   C08  C07   121.58  3.000
 6LG  O09   C08  C07   118.79  3.000
 6LG  C08   O09  C10   118.85  3.000
 6LG  H111  C11  C12   118.94  3.000
 6LG  H111  C11  C10   119.80  3.000
 6LG  C12   C11  C10   121.24  3.000
 6LG  C11   C12  C24   120.00  3.000
 6LG  C24   C12  C13   120.79  3.000
 6LG  C11   C12  C13   119.21  3.000
 6LG  P15   O14  C13   122.04  3.000
 6LG  O22   P15  N19   117.05  3.000
 6LG  O22   P15  N16   114.06  3.000
 6LG  N19   P15  N16   101.95  3.000
 6LG  N16   P15  O14   104.62  3.000
 6LG  O22   P15  O14   113.64  3.000
 6LG  N19   P15  O14   104.00  3.000
 6LG  C18   N16  P15   123.08  3.000
 6LG  C18   N16  C17    61.16  3.000
 6LG  P15   N16  C17   124.99  3.000
 6LG  H181  C18  H182  114.90  3.000
 6LG  H181  C18  N16   115.02  3.000
 6LG  H182  C18  N16   118.54  3.000
 6LG  H181  C18  C17   119.99  3.000
 6LG  H182  C18  C17   117.76  3.000
 6LG  N16   C18  C17    59.37  3.000
 6LG  P15   N19  C21   119.43  3.000
 6LG  P15   N19  C20   119.79  3.000
 6LG  C21   N19  C20    60.71  3.000
 6LG  H233  C23  H232  108.86  3.000
 6LG  H233  C23  H231  108.01  3.000
 6LG  H232  C23  H231  108.18  3.000
 6LG  H233  C23  C13   110.55  3.000
 6LG  H232  C23  C13   111.25  3.000
 6LG  H231  C23  C13   109.90  3.000
 6LG  H251  C25  C26   119.77  3.000
 6LG  H251  C25  C24   119.82  3.000
 6LG  C26   C25  C24   120.41  3.000
 6LG  O29   N27  O28   124.11  3.000
 6LG  O29   N27  C26   117.40  3.000
 6LG  O28   N27  C26   118.48  3.000
 6LG  H301  C30  C31   120.84  3.000
 6LG  H301  C30  C08   120.36  3.000
 6LG  C31   C30  C08   118.80  3.000
 6LG  H311  C31  C32   119.96  3.000
 6LG  H311  C31  C30   119.56  3.000
 6LG  C32   C31  C30   120.48  3.000
 6LG  H321  C32  C31   119.77  3.000
 6LG  H321  C32  C06   120.15  3.000
 6LG  C31   C32  C06   120.08  3.000
 6LG  C06   C02  N03   117.73  3.000
 6LG  C06   C02  O01   119.13  3.000
 6LG  N03   C02  O01   123.11  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
 6LG  CONST_01  C24   C12  C11  C10     0.00   0.0  0
 6LG  CONST_02  C24   C25  C26  C10     0.00   0.0  0
 6LG  CONST_03  C12   C11  C10  C26     0.00   0.0  0
 6LG  CONST_04  C12   C24  C25  C26     0.00   0.0  0
 6LG  CONST_05  C30   C08  C07  C06     0.00   0.0  0
 6LG  CONST_06  C30   C31  C32  C06     0.00   0.0  0
 6LG  CONST_07  C31   C32  C06  C07     0.00   0.0  0
 6LG  CONST_08  C31   C30  C08  C07     0.00   0.0  0
 6LG  CONST_09  C32   C06  C07  C08     0.00   0.0  0
 6LG  CONST_10  C32   C31  C30  C08     0.00   0.0  0
 6LG  CONST_11  C25   C26  C10  C11     0.00   0.0  0
 6LG  CONST_12  C25   C24  C12  C11     0.00   0.0  0
 6LG  CONST_13  C13   C12  C11  C10   180.00   0.0  0
 6LG  CONST_14  C25   C24  C12  C13   180.00   0.0  0
 6LG  CONST_15  N27   C26  C25  C24   180.00   0.0  0
 6LG  CONST_16  C08   C07  C06  C02   180.00   0.0  0
 6LG  CONST_17  C31   C32  C06  C02   180.00   0.0  0
 6LG  CONST_18  O09   C08  C07  C06   180.00   0.0  0
 6LG  CONST_19  C31   C30  C08  O09   180.00   0.0  0
 6LG  CONST_20  C12   C11  C10  O09   180.00   0.0  0
 6LG  CONST_21  C25   C26  C10  O09   180.00   0.0  0
 6LG  CONST_22  N27   C26  C10  C11   180.00   0.0  0
 6LG  CONST_23  H251  C25  C26  C10   180.00   0.0  0
 6LG  CONST_24  H111  C11  C12  C24   180.00   0.0  0
 6LG  CONST_25  H241  C24  C25  C26   180.00   0.0  0
 6LG  CONST_26  H311  C31  C32  C06   180.00   0.0  0
 6LG  CONST_27  H321  C32  C06  C07   180.00   0.0  0
 6LG  CONST_28  H301  C30  C08  C07   180.00   0.0  0
 6LG  CONST_29  H071  C07  C08  C30   180.00   0.0  0
 6LG  CONST_34  C06   C02  N03  C04   180.00   0.0  0
 6LG  CONST_37  C04   N03  C02  O01     0.00   0.0  0
 6LG  Var_01    C07   C08  O09  C10   -99.37  30.0  2
 6LG  Var_02    N19   P15  N16  C17   -77.93  30.0  2
 6LG  Var_03    P15   N16  C18  C17   114.99  30.0  1
 6LG  Var_04    P15   N19  C21  C20  -109.73  30.0  1
 6LG  Var_05    N16   P15  N19  C20  -156.48  30.0  3
 6LG  Var_06    C11   C10  O09  C08    10.42  30.0  2
 6LG  Var_07    H172  C17  C18  N16  -108.44  30.0  1
 6LG  Var_08    C07   C06  C02  O01  -126.67  30.0  2
 6LG  Var_09    H053  C05  N03  C02     6.07  30.0  3
 6LG  Var_10    H041  C04  N03  C02   145.39  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
 6LG  chir_01  C13  O14  C23  C12  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
 6LG  plan-1  C06   0.020
 6LG  plan-1  C07   0.020
 6LG  plan-1  C08   0.020
 6LG  plan-1  O09   0.020
 6LG  plan-1  C30   0.020
 6LG  plan-1  C31   0.020
 6LG  plan-1  C32   0.020
 6LG  plan-1  H071  0.020
 6LG  plan-1  H301  0.020
 6LG  plan-1  H311  0.020
 6LG  plan-1  H321  0.020
 6LG  plan-1  C02   0.020
 6LG  plan-2  C10   0.020
 6LG  plan-2  C13   0.020
 6LG  plan-2  C24   0.020
 6LG  plan-2  C26   0.020
 6LG  plan-2  O09   0.020
 6LG  plan-2  C11   0.020
 6LG  plan-2  C12   0.020
 6LG  plan-2  C25   0.020
 6LG  plan-2  N27   0.020
 6LG  plan-2  H241  0.020
 6LG  plan-2  H111  0.020
 6LG  plan-2  H251  0.020
 6LG  plan-3  O01   0.020
 6LG  plan-3  N03   0.020
 6LG  plan-3  C04   0.020
 6LG  plan-3  C05   0.020
 6LG  plan-3  C06   0.020
 6LG  plan-3  C02   0.020
 6LG  plan-4  C26   0.020
 6LG  plan-4  N27   0.020
 6LG  plan-4  O28   0.020
 6LG  plan-4  O29   0.020

