# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:20:07 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-{5-[2-(3-methylbenzyl)-2H-tetrazol-5-yl]-3-oxo-2,3-dihydro-1,2-oxazol-4-yl}-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Cn2nnc(n2)C3=C(C[C@H](N)C(O)=O)C(=O)NO3)c1
#
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
 5XO  5XO  3-{5-[2-(3-methylbenzyl)-2H-tetrazol-5-yl]-3-oxo-2,3-dihydro-1,2-oxazol-4-yl}-L-alanine  ligand  40  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5XO
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
 5XO  C1    C  CR5    0  -0.209  -2.2220  -0.9795   0.3613
 5XO  C2    C  CR5    0   0.479  -1.0434  -1.0793  -0.2775
 5XO  O3    O  O      0  -0.354  -0.7295  -2.3464  -0.6146
 5XO  N4    N  NR15   0  -0.376  -1.7344  -3.1181  -0.0989
 5XO  C5    C  CR5    0   0.546  -2.7394  -2.3407   0.4188
 5XO  C6    C  CR5    0   0.305  -0.0442  -0.0991  -0.6418
 5XO  N7    N  N      0  -0.330  -0.2026   1.2302  -0.5492
 5XO  N8    N  N      0  -0.041   0.9048   1.7493  -0.9606
 5XO  N9    N  NR5    0  -0.092   1.6836   0.7590  -1.2903
 5XO  N10   N  N      0  -0.240   1.1491  -0.4158  -1.1075
 5XO  C11   C  CH2    0  -0.417   3.0612   0.9477  -1.7243
 5XO  C12   C  CR16   0  -0.299   5.7450   0.2934   1.5413
 5XO  C13   C  CR6    0   0.114   5.5030  -0.7447   0.6436
 5XO  C14   C  CR16   0  -0.338   4.6323  -0.5085  -0.4169
 5XO  C15   C  CR6    0   0.139   4.0157   0.7264  -0.5834
 5XO  C16   C  CR16   0  -0.302   4.2661   1.7492   0.3238
 5XO  C17   C  CR16   0  -0.227   5.1329   1.5288   1.3843
 5XO  O23   O  O      0  -0.477  -3.7985  -2.7647   0.8508
 5XO  C24   C  CH2    0  -0.544  -2.9594   0.2006   0.8781
 5XO  C25   C  CH1    0  -0.217  -4.0332   0.6978  -0.0997
 5XO  C26   C  C      0   0.392  -4.8596   1.8394   0.5519
 5XO  O27   O  O      0  -0.603  -5.0604   2.8628  -0.1298
 5XO  O28   O  OC    -1  -0.617  -5.2823   1.6205   1.7061
 5XO  N29   N  NH2    0  -0.786  -3.4230   1.0073  -1.3802
 5XO  H4    H  HNR5   0   0.435  -1.8581  -3.9846  -0.6060
 5XO  H111  H  HCH2   0   0.312   3.2390   0.2534  -2.5430
 5XO  H112  H  HCH2   0   0.312   3.1243   1.9612  -2.1149
 5XO  H14   H  HCR6   0   0.252   4.4360  -1.3010  -1.1309
 5XO  H16   H  HCR6   0   0.258   3.7937   2.7165   0.2011
 5XO  H17   H  HCR6   0   0.259   5.3386   2.3257   2.0874
 5XO  H241  H  HCH2   0   0.256  -3.4390  -0.0653   1.8193
 5XO  H242  H  HCH2   0   0.247  -2.2592   1.0116   1.0902
 5XO  H25   H  HCH1   0   0.227  -4.7359  -0.1306  -0.2619
 5XO  H292  H  HNH2   0   0.334  -4.1256   1.4358  -1.9701
 5XO  H291  H  HNH2   0   0.330  -2.7277   1.7315  -1.2401
 5XO  H1    H  HCH3   0   0.251   5.6218  -2.6698   1.5880
 5XO  H3    H  HCH3   0   0.245   6.1381  -2.6677  -0.0924
 5XO  H2    H  HCH3   0   0.246   7.1829  -1.9916   1.1576
 5XO  C18   C  CH3    0  -0.722   6.1480  -2.0871   0.8292
 5XO  H12   H  HCR6   0   0.253   6.4259   0.1354   2.3692

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
 5XO  O27  C26   deloc     1.246  0.020  1.246
 5XO  O28  C26   deloc     1.248  0.020  1.248
 5XO  C26  C25   single    1.553  0.020  1.553
 5XO  C25  N29   single    1.452  0.020  1.452
 5XO  C25  C24   single    1.535  0.020  1.535
 5XO  C24  C1    single    1.484  0.020  1.484
 5XO  O23  C5    double    1.220  0.020  1.220
 5XO  C1   C5    single    1.457  0.020  1.457
 5XO  C1   C2    double    1.344  0.020  1.344
 5XO  C5   N4    single    1.372  0.020  1.372
 5XO  N10  N9    aromatic  1.303  0.020  1.303
 5XO  N10  C6    aromatic  1.320  0.020  1.320
 5XO  C11  N9    single    1.457  0.020  1.457
 5XO  C11  C15   single    1.504  0.020  1.504
 5XO  N9   N8    aromatic  1.302  0.020  1.302
 5XO  C2   C6    single    1.446  0.020  1.446
 5XO  C2   O3    single    1.348  0.020  1.348
 5XO  C16  C15   aromatic  1.390  0.020  1.390
 5XO  C16  C17   aromatic  1.387  0.020  1.387
 5XO  C15  C14   aromatic  1.390  0.020  1.390
 5XO  C6   N7    aromatic  1.342  0.020  1.342
 5XO  N4   O3    single    1.368  0.020  1.368
 5XO  C17  C12   aromatic  1.388  0.020  1.388
 5XO  C14  C13   aromatic  1.392  0.020  1.392
 5XO  N8   N7    aromatic  1.290  0.020  1.290
 5XO  C12  C13   aromatic  1.394  0.020  1.394
 5XO  C13  C18   single    1.501  0.020  1.501
 5XO  N4   H4    single    0.890  0.020  1.040
 5XO  C11  H111  single    0.970  0.020  1.090
 5XO  C11  H112  single    0.970  0.020  1.090
 5XO  C12  H12   single    0.930  0.020  1.080
 5XO  C14  H14   single    0.930  0.020  1.080
 5XO  C16  H16   single    0.930  0.020  1.080
 5XO  C17  H17   single    0.930  0.020  1.080
 5XO  C24  H241  single    0.970  0.020  1.090
 5XO  C24  H242  single    0.970  0.020  1.090
 5XO  C25  H25   single    0.970  0.020  1.090
 5XO  N29  H292  single    0.890  0.020  1.040
 5XO  N29  H291  single    0.890  0.020  1.040
 5XO  C18  H1    single    0.970  0.020  1.090
 5XO  C18  H3    single    0.970  0.020  1.090
 5XO  C18  H2    single    0.970  0.020  1.090

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
 5XO  C24   C1   C5    123.54  3.000
 5XO  C5    C1   C2    105.11  3.000
 5XO  C24   C1   C2    131.30  3.000
 5XO  C6    C2   O3    114.40  3.000
 5XO  O3    C2   C1    113.13  3.000
 5XO  C6    C2   C1    132.46  3.000
 5XO  N4    O3   C2    105.36  3.000
 5XO  H4    N4   C5    125.80  3.000
 5XO  H4    N4   O3    112.58  3.000
 5XO  C5    N4   O3    111.15  3.000
 5XO  O23   C5   N4    124.94  3.000
 5XO  N4    C5   C1    104.73  3.000
 5XO  O23   C5   C1    130.30  3.000
 5XO  N10   C6   N7    111.65  3.000
 5XO  N7    C6   C2    124.92  3.000
 5XO  N10   C6   C2    123.44  3.000
 5XO  N8    N7   C6    105.97  3.000
 5XO  N9    N8   N7    106.74  3.000
 5XO  C11   N9   N10   123.12  3.000
 5XO  C11   N9   N8    122.85  3.000
 5XO  N10   N9   N8    113.87  3.000
 5XO  N9    N10  C6    101.77  3.000
 5XO  H112  C11  H111  108.35  3.000
 5XO  H112  C11  C15   111.88  3.000
 5XO  H111  C11  C15   111.91  3.000
 5XO  H112  C11  N9    106.41  3.000
 5XO  H111  C11  N9    107.22  3.000
 5XO  C15   C11  N9    110.80  3.000
 5XO  H12   C12  C17   119.57  3.000
 5XO  H12   C12  C13   119.51  3.000
 5XO  C17   C12  C13   120.91  3.000
 5XO  C18   C13  C14   120.97  3.000
 5XO  C18   C13  C12   120.80  3.000
 5XO  C14   C13  C12   118.22  3.000
 5XO  H14   C14  C15   119.34  3.000
 5XO  H14   C14  C13   119.38  3.000
 5XO  C15   C14  C13   121.28  3.000
 5XO  C16   C15  C14   119.71  3.000
 5XO  C14   C15  C11   120.20  3.000
 5XO  C16   C15  C11   120.08  3.000
 5XO  H16   C16  C17   120.05  3.000
 5XO  H16   C16  C15   120.30  3.000
 5XO  C17   C16  C15   119.64  3.000
 5XO  H17   C17  C16   119.89  3.000
 5XO  H17   C17  C12   119.88  3.000
 5XO  C16   C17  C12   120.23  3.000
 5XO  H242  C24  H241  107.20  3.000
 5XO  H242  C24  C25   109.37  3.000
 5XO  H241  C24  C25   108.75  3.000
 5XO  H242  C24  C1    109.84  3.000
 5XO  H241  C24  C1    108.99  3.000
 5XO  C25   C24  C1    112.53  3.000
 5XO  H25   C25  N29   107.43  3.000
 5XO  H25   C25  C26   106.02  3.000
 5XO  N29   C25  C26   115.92  3.000
 5XO  H25   C25  C24   107.30  3.000
 5XO  N29   C25  C24   109.68  3.000
 5XO  C26   C25  C24   110.07  3.000
 5XO  O28   C26  O27   126.53  3.000
 5XO  O28   C26  C25   116.05  3.000
 5XO  O27   C26  C25   117.39  3.000
 5XO  H291  N29  H292  104.72  3.000
 5XO  H291  N29  C25   108.58  3.000
 5XO  H292  N29  C25   108.20  3.000
 5XO  H2    C18  H3    108.08  3.000
 5XO  H2    C18  H1    107.15  3.000
 5XO  H3    C18  H1    107.41  3.000
 5XO  H2    C18  C13   111.53  3.000
 5XO  H3    C18  C13   111.61  3.000
 5XO  H1    C18  C13   110.86  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
 5XO  CONST_01  N8   N9   N10  C6     0.00   0.0  0
 5XO  CONST_02  N9   N8   N7   C6     0.00   0.0  0
 5XO  CONST_03  N9   N10  C6   N7     0.00   0.0  0
 5XO  CONST_04  N10  N9   N8   N7     0.00   0.0  0
 5XO  CONST_05  N10  C6   N7   N8     0.00   0.0  0
 5XO  CONST_06  C15  C16  C17  C12    0.00   0.0  0
 5XO  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 5XO  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 5XO  CONST_09  C16  C17  C12  C13    0.00   0.0  0
 5XO  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 5XO  CONST_11  C17  C12  C13  C14    0.00   0.0  0
 5XO  CONST_12  N9   N10  C6   C2   180.00   0.0  0
 5XO  CONST_13  N8   N7   C6   C2   180.00   0.0  0
 5XO  CONST_14  O3   N4   C5   C1     0.00   0.0  0
 5XO  CONST_15  C11  N9   N10  C6   180.00   0.0  0
 5XO  CONST_16  C11  N9   N8   N7   180.00   0.0  0
 5XO  CONST_17  C17  C16  C15  C11  180.00   0.0  0
 5XO  CONST_18  C13  C14  C15  C11  180.00   0.0  0
 5XO  CONST_19  C18  C13  C14  C15  180.00   0.0  0
 5XO  CONST_20  C18  C13  C12  C17  180.00   0.0  0
 5XO  CONST_21  O23  C5   N4   O3   180.00   0.0  0
 5XO  CONST_22  H16  C16  C17  C12  180.00   0.0  0
 5XO  CONST_23  H14  C14  C13  C12  180.00   0.0  0
 5XO  CONST_24  H17  C17  C12  C13  180.00   0.0  0
 5XO  CONST_25  H12  C12  C13  C14  180.00   0.0  0
 5XO  Var_01    N10  C6   C2   C1   170.07  30.0  2
 5XO  Var_02    C15  C11  N9   N8    97.81  30.0  1
 5XO  Var_03    C16  C15  C11  N9   -82.42  30.0  2
 5XO  Var_04    C25  C24  C1   C2    96.76  30.0  1
 5XO  Var_05    H1   C18  C13  C12   79.31  30.0  2

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
 5XO  chir_01  C25  C26  N29  C24  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
 5XO  plan-1  C1   0.020
 5XO  plan-1  C2   0.020
 5XO  plan-1  O3   0.020
 5XO  plan-1  N4   0.020
 5XO  plan-1  C5   0.020
 5XO  plan-1  C6   0.020
 5XO  plan-1  O23  0.020
 5XO  plan-1  C24  0.020
 5XO  plan-1  H4   0.020
 5XO  plan-2  C2   0.020
 5XO  plan-2  C6   0.020
 5XO  plan-2  N7   0.020
 5XO  plan-2  N8   0.020
 5XO  plan-2  N9   0.020
 5XO  plan-2  N10  0.020
 5XO  plan-2  C11  0.020
 5XO  plan-3  C11  0.020
 5XO  plan-3  C12  0.020
 5XO  plan-3  C13  0.020
 5XO  plan-3  C14  0.020
 5XO  plan-3  C15  0.020
 5XO  plan-3  C16  0.020
 5XO  plan-3  C17  0.020
 5XO  plan-3  H14  0.020
 5XO  plan-3  H16  0.020
 5XO  plan-3  H17  0.020
 5XO  plan-3  C18  0.020
 5XO  plan-3  H12  0.020
 5XO  plan-4  C25  0.020
 5XO  plan-4  C26  0.020
 5XO  plan-4  O27  0.020
 5XO  plan-4  O28  0.020

