# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:56:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-[5-tert-butyl-3-(phosphonomethoxy)isoxazol-4-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1onc(OC[P](O)(O)=O)c1C[C@H](N)C(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
 AT1  AT1  3-[5-tert-butyl-3-(phosphonomethoxy)isoxazol-4-yl]-L-alanine  ligand  40  21  .  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_AT1
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
 AT1  N    N  NH2   0  -0.786  -2.0654  -0.8970   0.3507
 AT1  C    C  CH2   0  -0.584  -0.7315   0.8027   1.6942
 AT1  O    O  OH1   0  -0.594  -2.6259   0.0296   3.7612
 AT1  C1   C  CH1   0  -0.202  -1.6741  -0.4314   1.6573
 AT1  C2   C  C     0   0.544  -2.9131  -0.1153   2.4726
 AT1  O1   O  O     0  -0.431  -4.0202   0.0169   2.0194
 AT1  O2   O  O     0  -0.350   2.5077   0.0668   0.1345
 AT1  N1   N  N     0  -0.243   1.8153   0.4985  -0.9596
 AT1  C4   C  CH2   0  -0.506  -0.1163   1.3984  -2.6599
 AT1  C5   C  CR5   0   0.507   0.6381   0.8166  -0.5034
 AT1  C6   C  CR5   0  -0.191   0.5051   0.5902   0.8904
 AT1  C7   C  CR5   0   0.525   1.7412   0.1242   1.2285
 AT1  C9   C  CH3   0  -0.647   1.4894  -1.1880   3.3344
 AT1  C10  C  CH3   0  -0.632   2.6142   1.0542   3.3340
 AT1  C11  C  CH3   0  -0.642   3.7409  -0.9300   2.3086
 AT1  P    P  P     0   1.345  -0.5575  -0.1882  -3.4509
 AT1  O4   O  O     0  -0.700  -1.9798  -0.5862  -3.3602
 AT1  O5   O  OH1   0  -0.739   0.0087   0.0995  -4.9212
 AT1  O6   O  OH1   0  -0.747   0.3689  -1.3078  -2.7741
 AT1  H2   H  HNH2  0   0.348  -2.4217  -0.1429  -0.2218
 AT1  H3   H  HNH2  0   0.356  -1.2706  -1.2902  -0.1343
 AT1  H5   H  HCH2  0   0.270  -0.4728   1.0457   2.7247
 AT1  H6   H  HCH2  0   0.276  -1.2682   1.6713   1.3030
 AT1  H1   H  HOH1  0   0.483  -3.4226   0.2750   4.2554
 AT1  H4   H  HCH1  0   0.284  -1.1582  -1.2566   2.1558
 AT1  H7   H  HCH2  0   0.318  -0.7938   2.1658  -3.0341
 AT1  H8   H  HCH2  0   0.294   0.9046   1.7049  -2.9001
 AT1  H11  H  HCH3  0   0.248   1.9970  -1.4735   4.2566
 AT1  H12  H  HCH3  0   0.234   0.5460  -0.7250   3.6203
 AT1  H13  H  HCH3  0   0.241   1.2688  -2.0990   2.7767
 AT1  H14  H  HCH3  0   0.238   1.6749   1.5665   3.5466
 AT1  H15  H  HCH3  0   0.240   3.0880   0.8220   4.2893
 AT1  H16  H  HCH3  0   0.239   3.2631   1.7467   2.7963
 AT1  H17  H  HCH3  0   0.238   3.6379  -1.8522   1.7350
 AT1  H18  H  HCH3  0   0.239   4.4584  -0.2864   1.7997
 AT1  H19  H  HCH3  0   0.240   4.1665  -1.1950   3.2771
 AT1  H9   H  HOH1  0   0.500  -0.3386  -0.4875  -5.6072
 AT1  H10  H  HOH1  0   0.487   1.2561  -1.0107  -2.5147
 AT1  O3   O  O2    0  -0.462  -0.3337   1.3154  -1.2581
 AT1  C3   C  CT    0  -0.242   2.3919  -0.2406   2.5364

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
 AT1  N    C1   single    1.441  0.020  1.441
 AT1  N    H2   single    0.890  0.020  1.040
 AT1  N    H3   single    0.890  0.020  1.040
 AT1  C    C1   single    1.553  0.020  1.553
 AT1  C    C6   single    1.490  0.020  1.490
 AT1  C    H5   single    0.970  0.020  1.090
 AT1  C    H6   single    0.970  0.020  1.090
 AT1  O    C2   single    1.328  0.020  1.328
 AT1  O    H1   single    0.850  0.020  0.980
 AT1  C1   C2   single    1.517  0.020  1.517
 AT1  C1   H4   single    0.970  0.020  1.090
 AT1  C2   O1   double    1.204  0.020  1.204
 AT1  O2   N1   aromatic  1.365  0.020  1.365
 AT1  O2   C7   aromatic  1.337  0.020  1.337
 AT1  O3   C4   single    1.421  0.020  1.421
 AT1  O3   C5   single    1.328  0.020  1.328
 AT1  N1   C5   aromatic  1.302  0.020  1.302
 AT1  C3   C7   single    1.506  0.020  1.506
 AT1  C3   C9   single    1.533  0.020  1.533
 AT1  C3   C10  single    1.537  0.020  1.537
 AT1  C3   C11  single    1.532  0.020  1.532
 AT1  C4   P    single    1.827  0.020  1.827
 AT1  C4   H7   single    0.970  0.020  1.090
 AT1  C4   H8   single    0.970  0.020  1.090
 AT1  C5   C6   aromatic  1.418  0.020  1.418
 AT1  C6   C7   aromatic  1.364  0.020  1.364
 AT1  C9   H11  single    0.970  0.020  1.090
 AT1  C9   H12  single    0.970  0.020  1.090
 AT1  C9   H13  single    0.970  0.020  1.090
 AT1  C10  H14  single    0.970  0.020  1.090
 AT1  C10  H15  single    0.970  0.020  1.090
 AT1  C10  H16  single    0.970  0.020  1.090
 AT1  C11  H17  single    0.970  0.020  1.090
 AT1  C11  H18  single    0.970  0.020  1.090
 AT1  C11  H19  single    0.970  0.020  1.090
 AT1  P    O4   double    1.480  0.020  1.480
 AT1  P    O5   single    1.602  0.020  1.602
 AT1  P    O6   single    1.603  0.020  1.603
 AT1  O5   H9   single    0.850  0.020  0.980
 AT1  O6   H10  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
 AT1  H3   N    H2   107.18  3.000
 AT1  H3   N    C1   110.31  3.000
 AT1  H2   N    C1   111.58  3.000
 AT1  H6   C    H5   106.12  3.000
 AT1  H6   C    C6   109.12  3.000
 AT1  H5   C    C6   110.17  3.000
 AT1  H6   C    C1   108.95  3.000
 AT1  H5   C    C1   110.10  3.000
 AT1  C6   C    C1   112.18  3.000
 AT1  H1   O    C2   110.16  3.000
 AT1  H4   C1   C2   107.32  3.000
 AT1  H4   C1   C    107.60  3.000
 AT1  C2   C1   C    108.50  3.000
 AT1  H4   C1   N    107.31  3.000
 AT1  C2   C1   N    109.44  3.000
 AT1  C    C1   N    116.30  3.000
 AT1  O1   C2   C1   124.89  3.000
 AT1  O1   C2   O    123.52  3.000
 AT1  C1   C2   O    111.57  3.000
 AT1  C7   O2   N1   110.58  3.000
 AT1  C5   N1   O2   104.78  3.000
 AT1  H8   C4   H7   107.92  3.000
 AT1  H8   C4   P    111.97  3.000
 AT1  H7   C4   P    108.23  3.000
 AT1  H8   C4   O3   112.10  3.000
 AT1  H7   C4   O3   106.54  3.000
 AT1  P    C4   O3   109.84  3.000
 AT1  C6   C5   N1   112.96  3.000
 AT1  C6   C5   O3   123.36  3.000
 AT1  N1   C5   O3   123.67  3.000
 AT1  C7   C6   C5   102.31  3.000
 AT1  C7   C6   C    131.85  3.000
 AT1  C5   C6   C    125.81  3.000
 AT1  C6   C7   C3   133.63  3.000
 AT1  C6   C7   O2   109.36  3.000
 AT1  C3   C7   O2   116.91  3.000
 AT1  H13  C9   H12  108.31  3.000
 AT1  H13  C9   H11  107.93  3.000
 AT1  H12  C9   H11  107.01  3.000
 AT1  H13  C9   C3   111.66  3.000
 AT1  H12  C9   C3   112.58  3.000
 AT1  H11  C9   C3   109.15  3.000
 AT1  H16  C10  H15  107.96  3.000
 AT1  H16  C10  H14  108.06  3.000
 AT1  H15  C10  H14  107.65  3.000
 AT1  H16  C10  C3   111.41  3.000
 AT1  H15  C10  C3   109.75  3.000
 AT1  H14  C10  C3   111.86  3.000
 AT1  H19  C11  H18  107.53  3.000
 AT1  H19  C11  H17  107.36  3.000
 AT1  H18  C11  H17  108.41  3.000
 AT1  H19  C11  C3   108.72  3.000
 AT1  H18  C11  C3   112.54  3.000
 AT1  H17  C11  C3   112.05  3.000
 AT1  O6   P    O5   107.98  3.000
 AT1  O6   P    O4   109.99  3.000
 AT1  O5   P    O4   116.38  3.000
 AT1  O6   P    C4   106.51  3.000
 AT1  O5   P    C4    98.98  3.000
 AT1  O4   P    C4   116.05  3.000
 AT1  H9   O5   P    114.52  3.000
 AT1  H10  O6   P    115.29  3.000
 AT1  C5   O3   C4   118.08  3.000
 AT1  C11  C3   C10  109.21  3.000
 AT1  C11  C3   C9   108.53  3.000
 AT1  C10  C3   C9   109.62  3.000
 AT1  C11  C3   C7   111.13  3.000
 AT1  C10  C3   C7   108.01  3.000
 AT1  C9   C3   C7   110.33  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
 AT1  CONST_01  C6   C5   N1  O2     0.00   0.0  0
 AT1  CONST_02  C5   C6   C7  O2     0.00   0.0  0
 AT1  CONST_03  C6   C7   O2  N1     0.00   0.0  0
 AT1  CONST_04  C7   C6   C5  N1     0.00   0.0  0
 AT1  CONST_05  C7   O2   N1  C5     0.00   0.0  0
 AT1  CONST_06  N1   C5   C6  C    180.00   0.0  0
 AT1  CONST_07  O2   C7   C6  C    180.00   0.0  0
 AT1  CONST_08  O3   C5   N1  O2   180.00   0.0  0
 AT1  CONST_09  C7   C6   C5  O3   180.00   0.0  0
 AT1  CONST_10  C3   C7   O2  N1   180.00   0.0  0
 AT1  CONST_11  C5   C6   C7  C3   180.00   0.0  0
 AT1  CONST_12  H1   O    C2  C1   180.00   0.0  0
 AT1  Var_01    C5   C6   C   C1    85.37  30.0  2
 AT1  Var_02    C9   C3   C7  O2  -133.90  30.0  2
 AT1  Var_03    C6   C5   O3  C4  -175.16  30.0  2
 AT1  Var_04    P    C4   O3  C5    85.63  30.0  3
 AT1  Var_05    H11  C9   C3  C7   177.57  30.0  3
 AT1  Var_06    H14  C10  C3  C7    60.72  30.0  3
 AT1  Var_07    H17  C11  C3  C7   -60.32  30.0  3
 AT1  Var_08    O4   P    C4  O3    63.86  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
 AT1  chir_01  C1  N  C  C2  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
 AT1  plan-1  C   0.020
 AT1  plan-1  O2  0.020
 AT1  plan-1  N1  0.020
 AT1  plan-1  C5  0.020
 AT1  plan-1  C6  0.020
 AT1  plan-1  C7  0.020
 AT1  plan-1  O3  0.020
 AT1  plan-1  C3  0.020
 AT1  plan-2  O   0.020
 AT1  plan-2  C1  0.020
 AT1  plan-2  C2  0.020
 AT1  plan-2  O1  0.020
 AT1  plan-2  H1  0.020

