# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 23:04:23 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: N-{2-[(2-aminoethyl)sulfanyl]ethyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCSCCN
#
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
 XAG  XAG  "N-{2-[(2-aminoethyl)sulfanyl]ethyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide"  ligand  53  25  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XAG
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
 XAG  C01  C  CH3   0  -0.647  -56.0246  22.0616  -2.3906
 XAG  C02  C  CT    0  -0.171  -55.6031  22.2155  -0.9280
 XAG  C03  C  CH2   0  -0.133  -54.1253  22.6199  -0.8651
 XAG  C09  C  CH1   0  -0.032  -55.6891  20.8491  -0.2014
 XAG  C10  C  C     0   0.500  -57.1033  20.2558  -0.2127
 XAG  C12  C  CH2   0  -0.278  -59.1485  19.9502   1.1055
 XAG  C13  C  CH2   0  -0.585  -59.1384  18.5173   1.6338
 XAG  C14  C  C     0   0.560  -60.5364  18.0144   1.9261
 XAG  C16  C  CH2   0  -0.276  -62.0067  16.0481   1.8971
 XAG  C17  C  CH2   0  -0.568  -63.0050  16.2865   0.7688
 XAG  C19  C  CH2   0  -0.546  -64.1069  13.7216   0.6155
 XAG  C20  C  CH2   0  -0.274  -65.3175  12.8113   0.7593
 XAG  C25  C  CH3   0  -0.657  -56.4726  23.2734  -0.2459
 XAG  N11  N  NH1   0  -0.619  -57.8166  20.4671   0.9013
 XAG  N15  N  NH1   0  -0.633  -60.7452  16.7129   1.6634
 XAG  N21  N  NH2   0  -0.793  -64.9436  11.4455   0.4290
 XAG  O04  O  O2    0  -0.588  -53.9392  23.8405  -1.5907
 XAG  O07  O  OH1   0  -0.744  -52.8109  25.2301   0.1076
 XAG  O08  O  O     0  -0.691  -52.6088  25.8168  -2.4458
 XAG  O22  O  O     0  -0.496  -61.4013  18.7428   2.3937
 XAG  O23  O  O     0  -0.489  -57.5267  19.6385  -1.1806
 XAG  O24  O  OH1   0  -0.660  -55.2078  21.0125   1.1127
 XAG  P05  P  P     0   1.457  -52.6617  24.7679  -1.4123
 XAG  S18  S  S2    0  -0.041  -64.5765  15.4264   1.0355
 XAG  O1   O  OH1   0  -0.747  -51.3838  23.8058  -1.3270
 XAG  H1   H  HCH3  0   0.239  -57.0805  21.8154  -2.4824
 XAG  H2   H  HCH3  0   0.237  -55.8654  22.9921  -2.9337
 XAG  H3   H  HCH3  0   0.227  -55.4519  21.2791  -2.8922
 XAG  H4   H  HCH2  0   0.239  -53.5079  21.8395  -1.3208
 XAG  H5   H  HCH2  0   0.248  -53.8102  22.7456   0.1713
 XAG  H6   H  HCH1  0   0.252  -55.0642  20.1394  -0.7612
 XAG  H7   H  HCH2  0   0.256  -59.6519  20.6048   1.8142
 XAG  H8   H  HCH2  0   0.250  -59.7026  20.0042   0.1682
 XAG  H9   H  HCH2  0   0.260  -58.6244  17.8621   0.9282
 XAG  H10  H  HCH2  0   0.275  -58.5681  18.4817   2.5672
 XAG  H11  H  HCH2  0   0.247  -62.4328  16.3859   2.8419
 XAG  H12  H  HCH2  0   0.259  -61.7998  14.9835   2.0006
 XAG  H13  H  HCH2  0   0.269  -62.5864  15.9827  -0.1929
 XAG  H14  H  HCH2  0   0.282  -63.2474  17.3476   0.7009
 XAG  H15  H  HCH2  0   0.258  -63.7349  13.7026  -0.4120
 XAG  H16  H  HCH2  0   0.260  -63.3086  13.3747   1.2726
 XAG  H17  H  HCH2  0   0.229  -65.6581  12.8325   1.7968
 XAG  H18  H  HCH2  0   0.204  -66.1416  13.2063   0.1497
 XAG  H19  H  HCH3  0   0.234  -56.1994  23.4202   0.7994
 XAG  H20  H  HCH3  0   0.239  -56.3729  24.2339  -0.7510
 XAG  H21  H  HCH3  0   0.235  -57.5277  23.0016  -0.2847
 XAG  H22  H  HNH1  0   0.401  -57.3588  20.9259   1.6731
 XAG  H23  H  HNH1  0   0.402  -60.0068  16.1800   1.2341
 XAG  H24  H  HNH2  0   0.350  -65.7153  10.8261   0.6400
 XAG  H25  H  HNH2  0   0.342  -64.7951  11.3687  -0.5697
 XAG  H27  H  HOH1  0   0.498  -52.1315  25.8444   0.4178
 XAG  H28  H  HOH1  0   0.463  -54.9662  20.1500   1.4661
 XAG  H29  H  HOH1  0   0.495  -50.9885  23.5934  -2.1835

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
 XAG  C01  C02  single  1.530  0.020  1.530
 XAG  O23  C10  double  1.224  0.020  1.224
 XAG  O08  P05  double  1.474  0.020  1.474
 XAG  O04  P05  single  1.589  0.020  1.589
 XAG  O04  C03  single  1.432  0.020  1.432
 XAG  C02  C03  single  1.533  0.020  1.533
 XAG  C02  C25  single  1.530  0.020  1.530
 XAG  C02  C09  single  1.550  0.020  1.550
 XAG  P05  O07  single  1.596  0.020  1.596
 XAG  C10  C09  single  1.534  0.020  1.534
 XAG  C10  N11  single  1.340  0.020  1.340
 XAG  C09  O24  single  1.409  0.020  1.409
 XAG  C17  S18  single  1.811  0.020  1.811
 XAG  C17  C16  single  1.525  0.020  1.525
 XAG  C19  S18  single  1.818  0.020  1.818
 XAG  C19  C20  single  1.521  0.020  1.521
 XAG  C12  N11  single  1.443  0.020  1.443
 XAG  C12  C13  single  1.527  0.020  1.527
 XAG  C13  C14  single  1.514  0.020  1.514
 XAG  N15  C14  single  1.344  0.020  1.344
 XAG  N15  C16  single  1.445  0.020  1.445
 XAG  C14  O22  double  1.224  0.020  1.224
 XAG  N21  C20  single  1.454  0.020  1.454
 XAG  P05  O1   single  1.602  0.020  1.602
 XAG  C01  H1   single  0.970  0.020  1.090
 XAG  C01  H2   single  0.970  0.020  1.090
 XAG  C01  H3   single  0.970  0.020  1.090
 XAG  C03  H4   single  0.970  0.020  1.090
 XAG  C03  H5   single  0.970  0.020  1.090
 XAG  C09  H6   single  0.970  0.020  1.090
 XAG  C12  H7   single  0.970  0.020  1.090
 XAG  C12  H8   single  0.970  0.020  1.090
 XAG  C13  H9   single  0.970  0.020  1.090
 XAG  C13  H10  single  0.970  0.020  1.090
 XAG  C16  H11  single  0.970  0.020  1.090
 XAG  C16  H12  single  0.970  0.020  1.090
 XAG  C17  H13  single  0.970  0.020  1.090
 XAG  C17  H14  single  0.970  0.020  1.090
 XAG  C19  H15  single  0.970  0.020  1.090
 XAG  C19  H16  single  0.970  0.020  1.090
 XAG  C20  H17  single  0.970  0.020  1.090
 XAG  C20  H18  single  0.970  0.020  1.090
 XAG  C25  H19  single  0.970  0.020  1.090
 XAG  C25  H20  single  0.970  0.020  1.090
 XAG  C25  H21  single  0.970  0.020  1.090
 XAG  N11  H22  single  0.860  0.020  1.020
 XAG  N15  H23  single  0.860  0.020  1.020
 XAG  N21  H24  single  0.890  0.020  1.040
 XAG  N21  H25  single  0.890  0.020  1.040
 XAG  O07  H27  single  0.850  0.020  0.980
 XAG  O24  H28  single  0.850  0.020  0.980
 XAG  O1   H29  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
 XAG  H3   C01  H2   107.85  3.000
 XAG  H3   C01  H1   107.94  3.000
 XAG  H2   C01  H1   107.04  3.000
 XAG  H3   C01  C02  111.52  3.000
 XAG  H2   C01  C02  110.52  3.000
 XAG  H1   C01  C02  111.76  3.000
 XAG  C25  C02  C09  111.66  3.000
 XAG  C09  C02  C03  105.47  3.000
 XAG  C25  C02  C03  110.31  3.000
 XAG  C09  C02  C01  110.13  3.000
 XAG  C25  C02  C01  109.83  3.000
 XAG  C03  C02  C01  109.35  3.000
 XAG  H5   C03  H4   108.36  3.000
 XAG  H5   C03  O04  110.22  3.000
 XAG  H4   C03  O04  108.87  3.000
 XAG  H5   C03  C02  110.36  3.000
 XAG  H4   C03  C02  109.78  3.000
 XAG  O04  C03  C02  109.22  3.000
 XAG  H6   C09  O24  110.84  3.000
 XAG  H6   C09  C10  105.71  3.000
 XAG  O24  C09  C10  111.51  3.000
 XAG  H6   C09  C02  107.40  3.000
 XAG  O24  C09  C02  108.42  3.000
 XAG  C10  C09  C02  112.88  3.000
 XAG  O23  C10  N11  123.59  3.000
 XAG  N11  C10  C09  115.08  3.000
 XAG  O23  C10  C09  121.33  3.000
 XAG  H8   C12  H7   107.16  3.000
 XAG  H8   C12  N11  109.25  3.000
 XAG  H7   C12  N11  107.67  3.000
 XAG  H8   C12  C13  110.32  3.000
 XAG  H7   C12  C13  110.01  3.000
 XAG  N11  C12  C13  112.26  3.000
 XAG  H10  C13  H9   106.65  3.000
 XAG  H10  C13  C14  107.80  3.000
 XAG  H9   C13  C14  111.11  3.000
 XAG  H10  C13  C12  109.21  3.000
 XAG  H9   C13  C12  110.04  3.000
 XAG  C14  C13  C12  111.86  3.000
 XAG  O22  C14  N15  122.78  3.000
 XAG  O22  C14  C13  121.91  3.000
 XAG  N15  C14  C13  115.29  3.000
 XAG  H12  C16  H11  107.14  3.000
 XAG  H12  C16  N15  107.41  3.000
 XAG  H11  C16  N15  109.81  3.000
 XAG  H12  C16  C17  110.32  3.000
 XAG  H11  C16  C17  109.68  3.000
 XAG  N15  C16  C17  112.32  3.000
 XAG  H14  C17  H13  107.52  3.000
 XAG  H14  C17  S18  106.16  3.000
 XAG  H13  C17  S18  109.28  3.000
 XAG  H14  C17  C16  110.10  3.000
 XAG  H13  C17  C16  110.92  3.000
 XAG  S18  C17  C16  112.63  3.000
 XAG  H16  C19  H15  108.17  3.000
 XAG  H16  C19  S18  110.38  3.000
 XAG  H15  C19  S18  108.76  3.000
 XAG  H16  C19  C20  109.58  3.000
 XAG  H15  C19  C20  110.44  3.000
 XAG  S18  C19  C20  109.50  3.000
 XAG  H18  C20  H17  106.63  3.000
 XAG  H18  C20  N21  113.87  3.000
 XAG  H17  C20  N21  108.32  3.000
 XAG  H18  C20  C19  109.23  3.000
 XAG  H17  C20  C19  109.04  3.000
 XAG  N21  C20  C19  109.63  3.000
 XAG  H21  C25  H20  106.96  3.000
 XAG  H21  C25  H19  108.07  3.000
 XAG  H20  C25  H19  107.62  3.000
 XAG  H21  C25  C02  111.21  3.000
 XAG  H20  C25  C02  110.54  3.000
 XAG  H19  C25  C02  112.22  3.000
 XAG  H22  N11  C12  118.29  3.000
 XAG  H22  N11  C10  117.83  3.000
 XAG  C12  N11  C10  123.54  3.000
 XAG  H23  N15  C16  117.76  3.000
 XAG  H23  N15  C14  118.82  3.000
 XAG  C16  N15  C14  123.33  3.000
 XAG  H25  N21  H24  105.72  3.000
 XAG  H25  N21  C20  109.45  3.000
 XAG  H24  N21  C20  109.36  3.000
 XAG  P05  O04  C03  123.03  3.000
 XAG  H27  O07  P05  115.08  3.000
 XAG  H28  O24  C09  108.91  3.000
 XAG  O1   P05  O08  115.87  3.000
 XAG  O1   P05  O07  101.41  3.000
 XAG  O08  P05  O07  117.73  3.000
 XAG  O1   P05  O04  107.27  3.000
 XAG  O07  P05  O04  101.59  3.000
 XAG  O08  P05  O04  111.45  3.000
 XAG  C19  S18  C17  100.79  3.000
 XAG  H29  O1   P05  114.26  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
 XAG  CONST_01  C12  N11  C10  C09   180.00   0.0  0
 XAG  CONST_02  O23  C10  N11  C12     0.00   0.0  0
 XAG  CONST_03  C16  N15  C14  C13   180.00   0.0  0
 XAG  CONST_04  O22  C14  N15  C16     0.00   0.0  0
 XAG  CONST_05  H22  N11  C10  C09     0.00   0.0  0
 XAG  CONST_06  H23  N15  C14  C13     0.00   0.0  0
 XAG  CONST_07  H23  N15  C14  O22   180.00   0.0  0
 XAG  CONST_08  H22  N11  C10  O23   180.00   0.0  0
 XAG  Var_01    O04  C03  C02  C01    58.01  30.0  3
 XAG  Var_02    P05  O04  C03  C02   162.28  30.0  1
 XAG  Var_03    O08  P05  O04  C03   169.58  30.0  3
 XAG  Var_04    O07  P05  O04  C03   -64.21  30.0  3
 XAG  Var_05    O1   P05  O04  C03    41.77  30.0  3
 XAG  Var_06    O04  C03  C02  C09   176.42  30.0  3
 XAG  Var_07    C13  C12  N11  C10    84.56  30.0  1
 XAG  Var_08    N15  C14  C13  C12   144.23  30.0  3
 XAG  Var_09    O22  C14  C13  C12   -37.17  30.0  3
 XAG  Var_10    N11  C12  C13  C14   176.46  30.0  1
 XAG  Var_11    C17  C16  N15  C14    81.53  30.0  3
 XAG  Var_12    C19  S18  C17  C16   -76.17  30.0  3
 XAG  Var_13    C20  C19  S18  C17  -179.29  30.0  1
 XAG  Var_14    O04  C03  C02  C25   -62.86  30.0  3
 XAG  Var_15    S18  C17  C16  N15   178.72  30.0  2
 XAG  Var_16    S18  C19  C20  N21  -179.77  30.0  1
 XAG  Var_17    H4   C03  C02  C01   -61.29  30.0  3
 XAG  Var_18    H5   C03  C02  C01   179.34  30.0  3
 XAG  Var_19    H19  C25  C02  C01  -179.56  30.0  3
 XAG  Var_20    H20  C25  C02  C01   -59.42  30.0  3
 XAG  Var_21    H21  C25  C02  C01    59.25  30.0  3
 XAG  Var_22    H1   C01  C02  C03  -177.59  30.0  3
 XAG  Var_23    H2   C01  C02  C03   -58.49  30.0  3
 XAG  Var_24    H3   C01  C02  C03    61.47  30.0  3
 XAG  Var_25    H19  C25  C02  C03   -58.97  30.0  3
 XAG  Var_26    H20  C25  C02  C03    61.18  30.0  3
 XAG  Var_27    H21  C25  C02  C03   179.84  30.0  3
 XAG  Var_28    H1   C01  C02  C09    66.95  30.0  3
 XAG  Var_29    H2   C01  C02  C09  -173.95  30.0  3
 XAG  Var_30    H3   C01  C02  C09   -53.98  30.0  3
 XAG  Var_31    H4   C03  C02  C09    57.12  30.0  3
 XAG  Var_32    H5   C03  C02  C09   -62.26  30.0  3
 XAG  Var_33    H19  C25  C02  C09    57.97  30.0  3
 XAG  Var_34    H20  C25  C02  C09   178.11  30.0  3
 XAG  Var_35    H21  C25  C02  C09   -63.22  30.0  3
 XAG  Var_36    H7   C12  N11  C10  -154.21  30.0  1
 XAG  Var_37    H8   C12  N11  C10   -38.15  30.0  1
 XAG  Var_38    H22  N11  C12  C13   -88.57  30.0  3
 XAG  Var_39    H7   C12  C13  C14    56.58  30.0  1
 XAG  Var_40    H8   C12  C13  C14   -61.44  30.0  1
 XAG  Var_41    H11  C16  N15  C14   -40.81  30.0  3
 XAG  Var_42    H12  C16  N15  C14  -156.99  30.0  3
 XAG  Var_43    H15  C19  S18  C17   -58.52  30.0  1
 XAG  Var_44    H16  C19  S18  C17    60.00  30.0  1
 XAG  Var_45    H23  N15  C16  C17   -94.94  30.0  1
 XAG  Var_46    H13  C17  S18  C19    47.59  30.0  1
 XAG  Var_47    H14  C17  S18  C19   163.28  30.0  1
 XAG  Var_48    H24  N21  C20  C19   172.74  30.0  3
 XAG  Var_49    H25  N21  C20  C19   -71.87  30.0  3
 XAG  Var_50    H1   C01  C02  C25   -56.42  30.0  3
 XAG  Var_51    H2   C01  C02  C25    62.68  30.0  3
 XAG  Var_52    H3   C01  C02  C25  -177.35  30.0  3
 XAG  Var_53    H4   C03  C02  C25   177.83  30.0  3
 XAG  Var_54    H5   C03  C02  C25    58.46  30.0  3
 XAG  Var_55    H9   C13  C12  N11   -59.53  30.0  3
 XAG  Var_56    H10  C13  C12  N11    57.21  30.0  3
 XAG  Var_57    H9   C13  C14  N15    20.82  30.0  1
 XAG  Var_58    H10  C13  C14  N15   -95.70  30.0  1
 XAG  Var_59    H13  C17  C16  N15    55.87  30.0  2
 XAG  Var_60    H14  C17  C16  N15   -63.01  30.0  2
 XAG  Var_61    H15  C19  C20  N21    60.49  30.0  1
 XAG  Var_62    H16  C19  C20  N21   -58.58  30.0  1
 XAG  Var_63    H9   C13  C14  O22  -160.58  30.0  1
 XAG  Var_64    H10  C13  C14  O22    82.90  30.0  1
 XAG  Var_65    H4   C03  O04  P05   -77.85  30.0  3
 XAG  Var_66    H5   C03  O04  P05    40.87  30.0  3
 XAG  Var_67    H11  C16  C17  S18   -58.88  30.0  3
 XAG  Var_68    H12  C16  C17  S18    58.92  30.0  3
 XAG  Var_69    H17  C20  C19  S18   -61.35  30.0  3
 XAG  Var_70    H18  C20  C19  S18    54.83  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
 XAG  chir_01  C09  C02  C10  O24  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
 XAG  plan-1  C09  0.020
 XAG  plan-1  C10  0.020
 XAG  plan-1  C12  0.020
 XAG  plan-1  N11  0.020
 XAG  plan-1  O23  0.020
 XAG  plan-1  H22  0.020
 XAG  plan-2  C13  0.020
 XAG  plan-2  C14  0.020
 XAG  plan-2  C16  0.020
 XAG  plan-2  N15  0.020
 XAG  plan-2  O22  0.020
 XAG  plan-2  H23  0.020

