# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 17:58:54 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (3-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}oxetan-3-yl)acetic acid
#   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)NCCSC1(COC1)CC(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
 AFY  AFY  '(3-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}oxetan-3-yl)acetic acid'  ligand  59  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AFY
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
 AFY  C10  C  CH2   0  -0.601  -4.6441   0.3862  -0.5414
 AFY  C12  C  C     0  -0.233  -7.1302  -0.9015  -0.7554
 AFY  C13  C  C     0  -0.138  -6.9131  -1.3647  -2.2040
 AFY  C15  C  C     0  -0.141  -8.5887  -0.7420  -1.2090
 AFY  C16  C  CH2   0  -0.585  -6.8271  -1.8990   0.3397
 AFY  C22  C  CT    0  -0.212   4.7023   0.0345   0.6345
 AFY  C17  C  C     0   0.535  -7.4393  -1.5063   1.6554
 AFY  P27  P  P     0   1.458   7.6608  -1.3136  -1.3030
 AFY  O01  O  OH1   0  -0.643   4.5870   2.4172   0.0094
 AFY  C02  C  CH1   0  -0.072   4.2320   1.4718   0.9946
 AFY  C03  C  C     0   0.471   2.7383   1.5517   1.3406
 AFY  N04  N  NH1   0  -0.585   1.9934   2.2942   0.5132
 AFY  C05  C  CH2   0  -0.253   0.5720   2.4821   0.6800
 AFY  C06  C  CH2   0  -0.625  -0.2422   1.3556   0.0386
 AFY  C07  C  C     0   0.610  -1.7226   1.5883   0.2352
 AFY  N08  N  NH1   0  -0.683  -2.4768   1.5101  -0.8749
 AFY  C09  C  CH2   0  -0.216  -3.9086   1.6831  -0.8652
 AFY  S11  S  S2    0   0.003  -6.4237   0.7394  -0.4277
 AFY  O14  O  O     0  -0.479  -8.2217  -0.9325  -2.5803
 AFY  O18  O  OH1   0  -0.505  -6.8059  -2.0547   2.6848
 AFY  O19  O  O     0  -0.463  -8.4170  -0.8111   1.7708
 AFY  O20  O  O     0  -0.473  -2.1954   1.8364   1.3364
 AFY  O21  O  O     0  -0.436   2.2845   0.9982   2.3319
 AFY  C24  C  CH3   0  -0.708   3.9202  -0.5203  -0.5599
 AFY  C25  C  CH2   0  -0.105   6.1931   0.1649   0.2872
 AFY  O26  O  O2    0  -0.569   6.7379  -1.1253  -0.0200
 AFY  O28  O  OH1   0  -0.769   7.9386  -2.8716  -1.1103
 AFY  O29  O  OH1   0  -0.805   6.7144  -1.1371  -2.5817
 AFY  O30  O  O     0  -0.661   8.8254  -0.4183  -1.4320
 AFY  H1   H  HCH2  0   0.247  -4.4722  -0.3463  -1.3324
 AFY  H2   H  HCH2  0   0.315  -4.2807  -0.0306   0.3981
 AFY  H3   H  H     0   0.233  -6.1204  -0.8721  -2.7716
 AFY  H4   H  H     0   0.239  -6.7924  -2.4505  -2.2928
 AFY  H5   H  H     0   0.249  -9.2395  -1.5417  -0.8416
 AFY  H6   H  H     0   0.200  -9.0719   0.2202  -1.0258
 AFY  H7   H  HCH2  0   0.275  -7.2453  -2.8755   0.0672
 AFY  H8   H  HCH2  0   0.271  -5.7532  -2.0584   0.4475
 AFY  H9   H  HOH1  0   0.450   4.4403   2.0511  -0.8698
 AFY  H10  H  HCH1  0   0.246   4.7663   1.7701   1.9032
 AFY  H11  H  HNH1  0   0.361   2.4470   2.7604  -0.2548
 AFY  H12  H  HCH2  0   0.225   0.3375   2.5547   1.7406
 AFY  H13  H  HCH2  0   0.277   0.3135   3.4367   0.2215
 AFY  H14  H  HCH2  0   0.302   0.0122   1.2680  -1.0192
 AFY  H15  H  HCH2  0   0.293   0.0198   0.4092   0.5126
 AFY  H16  H  HNH1  0   0.401  -2.0374   1.2642  -1.7463
 AFY  H17  H  HCH2  0   0.258  -4.2131   2.0432  -1.8472
 AFY  H18  H  HCH2  0   0.219  -4.1672   2.4550  -0.1393
 AFY  H19  H  HOH1  0   0.491  -7.2554  -1.8243   3.5119
 AFY  H20  H  HCH3  0   0.243   3.5109  -1.0900   2.0713
 AFY  H21  H  HCH3  0   0.223   5.0089  -1.8735   1.6066
 AFY  H22  H  HCH3  0   0.250   5.0389  -0.5024   2.7173
 AFY  H23  H  HCH3  0   0.276   2.8555  -0.5948  -0.3333
 AFY  H24  H  HCH3  0   0.236   4.0234   0.0838  -1.4651
 AFY  H25  H  HCH3  0   0.250   4.2582  -1.5261  -0.8074
 AFY  H26  H  HCH2  0   0.255   6.3347   0.8495  -0.5516
 AFY  H27  H  HCH2  0   0.276   6.7464   0.5693   1.1380
 AFY  H28  H  HOH1  0   0.499   8.6366  -3.2165  -1.6824
 AFY  H29  H  HOH1  0   0.472   5.9510  -1.7271  -2.6259
 AFY  C23  C  CH3   0  -0.648   4.5533  -0.9090   1.8284

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
 AFY  O30  P27  double  1.475  0.020  1.475
 AFY  O28  P27  single  1.594  0.020  1.594
 AFY  C25  O26  single  1.434  0.020  1.434
 AFY  C25  C22  single  1.536  0.020  1.536
 AFY  P27  O26  single  1.592  0.020  1.592
 AFY  P27  O29  single  1.601  0.020  1.601
 AFY  C24  C22  single  1.532  0.020  1.532
 AFY  C22  C23  single  1.529  0.020  1.529
 AFY  C22  C02  single  1.555  0.020  1.555
 AFY  C02  O01  single  1.411  0.020  1.411
 AFY  C02  C03  single  1.535  0.020  1.535
 AFY  C03  N04  single  1.338  0.020  1.338
 AFY  C03  O21  double  1.223  0.020  1.223
 AFY  N04  C05  single  1.443  0.020  1.443
 AFY  C05  C06  single  1.531  0.020  1.531
 AFY  O19  C17  double  1.205  0.020  1.205
 AFY  O14  C15  single  1.432  0.020  1.432
 AFY  O14  C13  single  1.429  0.020  1.429
 AFY  C15  C12  single  1.536  0.020  1.536
 AFY  C06  C07  single  1.511  0.020  1.511
 AFY  C17  O18  single  1.327  0.020  1.327
 AFY  C17  C16  single  1.503  0.020  1.503
 AFY  C13  C12  single  1.536  0.020  1.536
 AFY  C12  C16  single  1.512  0.020  1.512
 AFY  C12  S11  single  1.816  0.020  1.816
 AFY  C07  O20  double  1.224  0.020  1.224
 AFY  C07  N08  single  1.344  0.020  1.344
 AFY  C10  S11  single  1.818  0.020  1.818
 AFY  C10  C09  single  1.526  0.020  1.526
 AFY  C09  N08  single  1.442  0.020  1.442
 AFY  C10  H1   single  0.970  0.020  1.090
 AFY  C10  H2   single  0.970  0.020  1.090
 AFY  C13  H3   single  0.970  0.020  1.090
 AFY  C13  H4   single  0.970  0.020  1.090
 AFY  C15  H5   single  0.970  0.020  1.090
 AFY  C15  H6   single  0.970  0.020  1.090
 AFY  C16  H7   single  0.970  0.020  1.090
 AFY  C16  H8   single  0.970  0.020  1.090
 AFY  O01  H9   single  0.850  0.020  0.980
 AFY  C02  H10  single  0.970  0.020  1.090
 AFY  N04  H11  single  0.860  0.020  1.020
 AFY  C05  H12  single  0.970  0.020  1.090
 AFY  C05  H13  single  0.970  0.020  1.090
 AFY  C06  H14  single  0.970  0.020  1.090
 AFY  C06  H15  single  0.970  0.020  1.090
 AFY  N08  H16  single  0.860  0.020  1.020
 AFY  C09  H17  single  0.970  0.020  1.090
 AFY  C09  H18  single  0.970  0.020  1.090
 AFY  O18  H19  single  0.850  0.020  0.980
 AFY  C23  H20  single  0.970  0.020  1.090
 AFY  C23  H21  single  0.970  0.020  1.090
 AFY  C23  H22  single  0.970  0.020  1.090
 AFY  C24  H23  single  0.970  0.020  1.090
 AFY  C24  H24  single  0.970  0.020  1.090
 AFY  C24  H25  single  0.970  0.020  1.090
 AFY  C25  H26  single  0.970  0.020  1.090
 AFY  C25  H27  single  0.970  0.020  1.090
 AFY  O28  H28  single  0.850  0.020  0.980
 AFY  O29  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
 AFY  H2   C10  H1   108.39  3.000
 AFY  H2   C10  S11  110.29  3.000
 AFY  H1   C10  S11  109.26  3.000
 AFY  H2   C10  C09  110.31  3.000
 AFY  H1   C10  C09  109.92  3.000
 AFY  S11  C10  C09  108.67  3.000
 AFY  S11  C12  C16  112.79  3.000
 AFY  S11  C12  C15  109.20  3.000
 AFY  C16  C12  C15  118.22  3.000
 AFY  S11  C12  C13  112.80  3.000
 AFY  C16  C12  C13  117.11  3.000
 AFY  C15  C12  C13   83.51  3.000
 AFY  H4   C13  H3   108.94  3.000
 AFY  H4   C13  O14  112.29  3.000
 AFY  H3   C13  O14  113.04  3.000
 AFY  H4   C13  C12  112.99  3.000
 AFY  H3   C13  C12  117.16  3.000
 AFY  O14  C13  C12   91.59  3.000
 AFY  H6   C15  H5   108.93  3.000
 AFY  H6   C15  O14  113.03  3.000
 AFY  H5   C15  O14  112.12  3.000
 AFY  H6   C15  C12  117.52  3.000
 AFY  H5   C15  C12  112.93  3.000
 AFY  O14  C15  C12   91.47  3.000
 AFY  H8   C16  H7   105.65  3.000
 AFY  H8   C16  C17  110.64  3.000
 AFY  H7   C16  C17  107.14  3.000
 AFY  H8   C16  C12  111.42  3.000
 AFY  H7   C16  C12  109.33  3.000
 AFY  C17  C16  C12  112.33  3.000
 AFY  C25  C22  C24  110.49  3.000
 AFY  C24  C22  C23  109.61  3.000
 AFY  C25  C22  C23  108.87  3.000
 AFY  C23  C22  C02  111.11  3.000
 AFY  C24  C22  C02  111.17  3.000
 AFY  C25  C22  C02  105.51  3.000
 AFY  O19  C17  O18  123.45  3.000
 AFY  O18  C17  C16  112.12  3.000
 AFY  O19  C17  C16  124.39  3.000
 AFY  O30  P27  O29  109.28  3.000
 AFY  O29  P27  O28  107.90  3.000
 AFY  O30  P27  O28  117.80  3.000
 AFY  O29  P27  O26  106.74  3.000
 AFY  O28  P27  O26   96.84  3.000
 AFY  O30  P27  O26  117.17  3.000
 AFY  H9   O01  C02  110.13  3.000
 AFY  H10  C02  C03  105.87  3.000
 AFY  H10  C02  O01  105.90  3.000
 AFY  C03  C02  O01  111.55  3.000
 AFY  H10  C02  C22  107.24  3.000
 AFY  C03  C02  C22  113.24  3.000
 AFY  O01  C02  C22  112.44  3.000
 AFY  O21  C03  N04  123.08  3.000
 AFY  O21  C03  C02  121.35  3.000
 AFY  N04  C03  C02  115.54  3.000
 AFY  H11  N04  C05  118.15  3.000
 AFY  H11  N04  C03  118.55  3.000
 AFY  C05  N04  C03  123.29  3.000
 AFY  H13  C05  H12  107.47  3.000
 AFY  H13  C05  C06  110.01  3.000
 AFY  H12  C05  C06  110.04  3.000
 AFY  H13  C05  N04  107.39  3.000
 AFY  H12  C05  N04  109.47  3.000
 AFY  C06  C05  N04  112.31  3.000
 AFY  H15  C06  H14  107.19  3.000
 AFY  H15  C06  C07  108.21  3.000
 AFY  H14  C06  C07  111.51  3.000
 AFY  H15  C06  C05  109.19  3.000
 AFY  H14  C06  C05  109.95  3.000
 AFY  C07  C06  C05  110.68  3.000
 AFY  O20  C07  N08  122.56  3.000
 AFY  N08  C07  C06  115.67  3.000
 AFY  O20  C07  C06  121.78  3.000
 AFY  H16  N08  C09  117.95  3.000
 AFY  H16  N08  C07  118.96  3.000
 AFY  C09  N08  C07  122.98  3.000
 AFY  H18  C09  H17  107.44  3.000
 AFY  H18  C09  N08  108.95  3.000
 AFY  H17  C09  N08  108.12  3.000
 AFY  H18  C09  C10  110.25  3.000
 AFY  H17  C09  C10  109.73  3.000
 AFY  N08  C09  C10  112.21  3.000
 AFY  C12  S11  C10  101.19  3.000
 AFY  C15  O14  C13   91.30  3.000
 AFY  H19  O18  C17  110.02  3.000
 AFY  H25  C24  H24  107.03  3.000
 AFY  H25  C24  H23  106.67  3.000
 AFY  H24  C24  H23  107.57  3.000
 AFY  H25  C24  C22  110.68  3.000
 AFY  H24  C24  C22  113.41  3.000
 AFY  H23  C24  C22  111.16  3.000
 AFY  H27  C25  H26  107.49  3.000
 AFY  H27  C25  O26  107.91  3.000
 AFY  H26  C25  O26  110.50  3.000
 AFY  H27  C25  C22  110.30  3.000
 AFY  H26  C25  C22  110.66  3.000
 AFY  O26  C25  C22  109.92  3.000
 AFY  C25  O26  P27  119.96  3.000
 AFY  H28  O28  P27  113.77  3.000
 AFY  H29  O29  P27  115.89  3.000
 AFY  H22  C23  H21  108.03  3.000
 AFY  H22  C23  H20  107.88  3.000
 AFY  H21  C23  H20  107.43  3.000
 AFY  H22  C23  C22  111.27  3.000
 AFY  H21  C23  C22  110.28  3.000
 AFY  H20  C23  C22  111.79  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
 AFY  CONST_01  C05  N04  C03  C02   180.00   0.0  0
 AFY  CONST_02  O21  C03  N04  C05     0.00   0.0  0
 AFY  CONST_03  C09  N08  C07  C06   180.00   0.0  0
 AFY  CONST_04  O20  C07  N08  C09     0.00   0.0  0
 AFY  CONST_05  H11  N04  C03  C02     0.00   0.0  0
 AFY  CONST_06  H16  N08  C07  C06     0.00   0.0  0
 AFY  CONST_07  H19  O18  C17  C16   180.00   0.0  0
 AFY  Var_01    H5   C15  O14  C13  -104.16  30.0  1
 AFY  Var_02    O19  C17  C16  C12    25.60  30.0  2
 AFY  Var_03    C09  C10  S11  C12   156.93  30.0  2
 AFY  Var_04    C07  N08  C09  C10   -85.49  30.0  3
 AFY  Var_05    O26  C25  C22  C02   178.11  30.0  1
 AFY  Var_06    C06  C05  N04  C03   -85.43  30.0  3
 AFY  Var_07    C07  C06  C05  N04   179.97  30.0  3
 AFY  Var_08    O20  C07  C06  C05   -50.42  30.0  3
 AFY  Var_09    S11  C10  C09  N08   175.68  30.0  2
 AFY  Var_10    O30  P27  O26  C25    53.76  30.0  1
 AFY  Var_11    H26  C25  O26  P27    11.47  30.0  1
 AFY  Var_12    H23  C24  C22  C02   -61.83  30.0  3
 AFY  Var_13    H20  C23  C22  C02    68.19  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
 AFY  chir_01  C12  C13  C15  S11  positiv
 AFY  chir_02  C02  C22  O01  C03  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
 AFY  plan-1  C02  0.020
 AFY  plan-1  C03  0.020
 AFY  plan-1  N04  0.020
 AFY  plan-1  C05  0.020
 AFY  plan-1  O21  0.020
 AFY  plan-1  H11  0.020
 AFY  plan-2  C06  0.020
 AFY  plan-2  C07  0.020
 AFY  plan-2  N08  0.020
 AFY  plan-2  C09  0.020
 AFY  plan-2  O20  0.020
 AFY  plan-2  H16  0.020
 AFY  plan-3  C16  0.020
 AFY  plan-3  C17  0.020
 AFY  plan-3  O18  0.020
 AFY  plan-3  O19  0.020
 AFY  plan-3  H19  0.020

