# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:50:48 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2~{S})-3-[5-[2-[[3-(aminomethyl)phenyl]methyl]-1,2,3,4-tetrazol-5-yl]-3-oxidanyl-1,2-oxazol-4-yl]-2-azanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(Cn2nnc(n2)c3onc(O)c3C[C@H](N)C(O)=O)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
 5XP  5XP  '(2~{S})-3-[5-[2-[[3-(aminomethyl)phenyl]methyl]-1,2,3,4-tetrazol-5-yl]-3-oxidanyl-1,2-oxazol-4-yl]-2-azanyl-propanoic acid'  ligand  42  26  .  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_5XP
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
 5XP  C1    C  CR5    0  -0.159  -2.4988   1.1468  -0.0913
 5XP  C2    C  CR5    0   0.434  -1.3086   1.0780   0.5510
 5XP  O3    O  O      0  -0.356  -1.0405   2.2277   1.1788
 5XP  N4    N  N      0  -0.198  -2.0626   3.1074   0.9719
 5XP  C5    C  CR5    0   0.438  -2.9193   2.4713   0.2284
 5XP  C6    C  CR5    0   0.309  -0.3192   0.0325   0.6745
 5XP  N7    N  N      0  -0.331  -0.4149  -1.1798   0.1056
 5XP  N8    N  N      0  -0.043   0.6503  -1.8211   0.4513
 5XP  N9    N  NR5    0  -0.092   1.3459  -1.0165   1.2007
 5XP  N10   N  N      0  -0.250   0.7972   0.1554   1.3689
 5XP  C11   C  CH2    0  -0.417   2.6611  -1.3696   1.7188
 5XP  C12   C  CR16   0  -0.291   5.6664  -0.5833  -1.2268
 5XP  C13   C  CR6    0   0.111   5.2264   0.4534  -0.4055
 5XP  C14   C  CR16   0  -0.342   4.2540   0.1773   0.5486
 5XP  C15   C  CR6    0   0.138   3.7329  -1.1042   0.6979
 5XP  C16   C  CR16   0  -0.305   4.1854  -2.1283  -0.1240
 5XP  C17   C  CR16   0  -0.227   5.1521  -1.8633  -1.0849
 5XP  O23   O  OH1    0  -0.597  -4.0399   3.0837  -0.1336
 5XP  C24   C  CH2    0  -0.571  -3.2681   0.1431  -0.8728
 5XP  C25   C  CH1    0  -0.206  -4.2623  -0.6397  -0.0022
 5XP  C26   C  C      0   0.390  -5.1565  -1.5352  -0.9023
 5XP  O27   O  OC    -1  -0.616  -5.7325  -0.9540  -1.8452
 5XP  O28   O  O      0  -0.599  -5.2441  -2.7412  -0.6060
 5XP  N29   N  NH2    0  -0.780  -3.5498  -1.3131   1.0656
 5XP  N1    N  NH2    0  -0.793   6.0823   2.2065  -1.8948
 5XP  H112  H  HCH2   0   0.311   2.8065  -0.7843   2.6244
 5XP  H111  H  HCH2   0   0.312   2.6221  -2.4214   1.9948
 5XP  H12   H  HCR6   0   0.252   6.4154  -0.3833  -1.9819
 5XP  H14   H  HCR6   0   0.252   3.8957   0.9766   1.1890
 5XP  H16   H  HCR6   0   0.258   3.7860  -3.1295  -0.0162
 5XP  H17   H  HCR6   0   0.257   5.5056  -2.6605  -1.7260
 5XP  H242  H  HCH2   0   0.255  -3.8157   0.6384  -1.6772
 5XP  H241  H  HCH2   0   0.264  -2.5820  -0.5525  -1.3603
 5XP  H25   H  HCH1   0   0.223  -4.9352   0.0902   0.4686
 5XP  H291  H  HNH2   0   0.336  -4.2140  -1.8642   1.5949
 5XP  H292  H  HNH2   0   0.330  -2.9177  -1.9919   0.6581
 5XP  H1    H  HCH2   0   0.216   5.1516   2.5402   0.0127
 5XP  H26   H  HCH2   0   0.243   6.7588   1.8559   0.0280
 5XP  H2    H  HNH2   0   0.344   5.2087   2.3624  -2.3820
 5XP  H4    H  HNH2   0   0.354   6.5743   3.0902  -1.9131
 5XP  H3    H  HOH1   0   0.490  -4.5535   2.5327  -0.7357
 5XP  C39   C  CH2    0  -0.339   5.8106   1.8391  -0.5169

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
 5XP  C39  C13   single    1.508  0.020  1.508
 5XP  C39  N1    single    1.452  0.020  1.452
 5XP  C12  C13   aromatic  1.394  0.020  1.394
 5XP  C12  C17   aromatic  1.387  0.020  1.387
 5XP  C13  C14   aromatic  1.390  0.020  1.390
 5XP  C17  C16   aromatic  1.389  0.020  1.389
 5XP  N7   N8    aromatic  1.291  0.020  1.291
 5XP  N7   C6    aromatic  1.343  0.020  1.343
 5XP  N8   N9    aromatic  1.301  0.020  1.301
 5XP  C14  C15   aromatic  1.391  0.020  1.391
 5XP  C16  C15   aromatic  1.389  0.020  1.389
 5XP  O3   N4    aromatic  1.364  0.020  1.364
 5XP  O3   C2    aromatic  1.337  0.020  1.337
 5XP  C15  C11   single    1.504  0.020  1.504
 5XP  N4   C5    aromatic  1.300  0.020  1.300
 5XP  C6   C2    single    1.445  0.020  1.445
 5XP  C6   N10   aromatic  1.320  0.020  1.320
 5XP  N9   C11   single    1.457  0.020  1.457
 5XP  N9   N10   aromatic  1.305  0.020  1.305
 5XP  C2   C1    aromatic  1.354  0.020  1.354
 5XP  C5   C1    aromatic  1.426  0.020  1.426
 5XP  C5   O23   single    1.327  0.020  1.327
 5XP  C1   C24   single    1.487  0.020  1.487
 5XP  C24  C25   single    1.536  0.020  1.536
 5XP  N29  C25   single    1.450  0.020  1.450
 5XP  C25  C26   single    1.553  0.020  1.553
 5XP  C26  O28   deloc     1.245  0.020  1.245
 5XP  C26  O27   deloc     1.248  0.020  1.248
 5XP  C11  H112  single    0.970  0.020  1.090
 5XP  C11  H111  single    0.970  0.020  1.090
 5XP  C12  H12   single    0.930  0.020  1.080
 5XP  C14  H14   single    0.930  0.020  1.080
 5XP  C16  H16   single    0.930  0.020  1.080
 5XP  C17  H17   single    0.930  0.020  1.080
 5XP  C24  H242  single    0.970  0.020  1.090
 5XP  C24  H241  single    0.970  0.020  1.090
 5XP  C25  H25   single    0.970  0.020  1.090
 5XP  N29  H291  single    0.890  0.020  1.040
 5XP  N29  H292  single    0.890  0.020  1.040
 5XP  C39  H1    single    0.970  0.020  1.090
 5XP  C39  H26   single    0.970  0.020  1.090
 5XP  N1   H2    single    0.890  0.020  1.040
 5XP  N1   H4    single    0.890  0.020  1.040
 5XP  O23  H3    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
 5XP  C24   C1   C5    126.33  3.000
 5XP  C24   C1   C2    132.05  3.000
 5XP  C5    C1   C2    101.54  3.000
 5XP  C6    C2   O3    116.41  3.000
 5XP  C6    C2   C1    132.78  3.000
 5XP  O3    C2   C1    110.80  3.000
 5XP  N4    O3   C2    109.46  3.000
 5XP  C5    N4   O3    105.35  3.000
 5XP  O23   C5   N4    119.11  3.000
 5XP  O23   C5   C1    128.05  3.000
 5XP  N4    C5   C1    112.85  3.000
 5XP  N10   C6   N7    111.54  3.000
 5XP  N10   C6   C2    123.82  3.000
 5XP  N7    C6   C2    124.64  3.000
 5XP  N8    N7   C6    106.05  3.000
 5XP  N9    N8   N7    106.75  3.000
 5XP  C11   N9   N10   123.46  3.000
 5XP  N10   N9   N8    113.88  3.000
 5XP  C11   N9   N8    122.52  3.000
 5XP  N9    N10  C6    101.78  3.000
 5XP  H111  C11  H112  108.29  3.000
 5XP  H111  C11  C15   111.62  3.000
 5XP  H112  C11  C15   112.01  3.000
 5XP  H111  C11  N9    106.98  3.000
 5XP  H112  C11  N9    106.63  3.000
 5XP  C15   C11  N9    111.05  3.000
 5XP  H12   C12  C17   119.91  3.000
 5XP  H12   C12  C13   119.48  3.000
 5XP  C17   C12  C13   120.61  3.000
 5XP  C39   C13  C14   120.28  3.000
 5XP  C14   C13  C12   118.52  3.000
 5XP  C39   C13  C12   121.18  3.000
 5XP  H14   C14  C15   119.44  3.000
 5XP  H14   C14  C13   119.33  3.000
 5XP  C15   C14  C13   121.24  3.000
 5XP  C16   C15  C14   119.57  3.000
 5XP  C16   C15  C11   120.25  3.000
 5XP  C14   C15  C11   120.15  3.000
 5XP  H16   C16  C17   120.13  3.000
 5XP  H16   C16  C15   120.16  3.000
 5XP  C17   C16  C15   119.71  3.000
 5XP  H17   C17  C16   119.78  3.000
 5XP  H17   C17  C12   119.88  3.000
 5XP  C16   C17  C12   120.35  3.000
 5XP  H3    O23  C5    110.88  3.000
 5XP  H241  C24  H242  105.97  3.000
 5XP  H241  C24  C25   109.58  3.000
 5XP  H242  C24  C25   108.91  3.000
 5XP  H241  C24  C1    109.86  3.000
 5XP  H242  C24  C1    109.91  3.000
 5XP  C25   C24  C1    112.40  3.000
 5XP  H25   C25  N29   107.10  3.000
 5XP  H25   C25  C26   106.19  3.000
 5XP  N29   C25  C26   116.24  3.000
 5XP  H25   C25  C24   107.50  3.000
 5XP  C26   C25  C24   109.76  3.000
 5XP  N29   C25  C24   109.64  3.000
 5XP  O28   C26  O27   126.75  3.000
 5XP  O27   C26  C25   115.78  3.000
 5XP  O28   C26  C25   117.46  3.000
 5XP  H292  N29  H291  104.77  3.000
 5XP  H292  N29  C25   108.77  3.000
 5XP  H291  N29  C25   108.39  3.000
 5XP  H4    N1   H2    106.05  3.000
 5XP  H4    N1   C39   109.22  3.000
 5XP  H2    N1   C39   109.52  3.000
 5XP  H26   C39  H1    105.68  3.000
 5XP  H26   C39  N1    107.86  3.000
 5XP  H1    C39  N1    114.11  3.000
 5XP  H26   C39  C13   108.25  3.000
 5XP  H1    C39  C13   108.58  3.000
 5XP  N1    C39  C13   112.03  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
 5XP  CONST_01  N4   O3   C2   C1     0.00   0.0  0
 5XP  CONST_02  N7   C6   C2   C1     0.00   0.0  0
 5XP  CONST_03  N10  C6   C2   C1   180.00   0.0  0
 5XP  CONST_04  O3   N4   C5   C1     0.00   0.0  0
 5XP  CONST_05  C5   N4   O3   C2     0.00   0.0  0
 5XP  CONST_06  N8   N7   C6   C2   180.00   0.0  0
 5XP  CONST_07  N9   N10  C6   C2   180.00   0.0  0
 5XP  CONST_08  N4   C5   C1   C2     0.00   0.0  0
 5XP  CONST_09  N7   C6   C2   O3   180.00   0.0  0
 5XP  CONST_10  N10  C6   C2   O3     0.00   0.0  0
 5XP  CONST_11  C5   C1   C2   O3     0.00   0.0  0
 5XP  CONST_12  C6   C2   O3   N4   180.00   0.0  0
 5XP  CONST_13  C6   C2   C1   C5   180.00   0.0  0
 5XP  CONST_14  N9   N8   N7   C6     0.00   0.0  0
 5XP  CONST_15  N8   N9   N10  C6     0.00   0.0  0
 5XP  CONST_16  N10  N9   N8   N7     0.00   0.0  0
 5XP  CONST_17  N9   N10  C6   N7     0.00   0.0  0
 5XP  CONST_18  N10  C6   N7   N8     0.00   0.0  0
 5XP  CONST_19  C15  C14  C13  C12    0.00   0.0  0
 5XP  CONST_20  C15  C16  C17  C12    0.00   0.0  0
 5XP  CONST_21  C16  C17  C12  C13    0.00   0.0  0
 5XP  CONST_22  C16  C15  C14  C13    0.00   0.0  0
 5XP  CONST_23  C17  C12  C13  C14    0.00   0.0  0
 5XP  CONST_24  C17  C16  C15  C14    0.00   0.0  0
 5XP  CONST_25  O23  C5   C1   C2   180.00   0.0  0
 5XP  CONST_26  O23  C5   N4   O3   180.00   0.0  0
 5XP  CONST_27  C24  C1   C2   O3   180.00   0.0  0
 5XP  CONST_28  C24  C1   C5   N4   180.00   0.0  0
 5XP  CONST_29  C24  C1   C2   C6     0.00   0.0  0
 5XP  CONST_30  C11  N9   N10  C6   180.00   0.0  0
 5XP  CONST_31  C11  N9   N8   N7   180.00   0.0  0
 5XP  CONST_32  C13  C14  C15  C11  180.00   0.0  0
 5XP  CONST_33  C17  C16  C15  C11  180.00   0.0  0
 5XP  CONST_34  C39  C13  C14  C15  180.00   0.0  0
 5XP  CONST_35  C39  C13  C12  C17  180.00   0.0  0
 5XP  CONST_36  H14  C14  C13  C12  180.00   0.0  0
 5XP  CONST_37  H16  C16  C17  C12  180.00   0.0  0
 5XP  CONST_38  H17  C17  C12  C13  180.00   0.0  0
 5XP  CONST_39  H12  C12  C13  C14  180.00   0.0  0
 5XP  Var_01    C15  C11  N9   N8    83.15  30.0  2
 5XP  Var_02    C14  C15  C11  N9    82.62  30.0  3
 5XP  Var_03    C25  C24  C1   C2    91.58  30.0  2
 5XP  Var_04    N1   C39  C13  C12   38.07  30.0  1
 5XP  Var_05    H2   N1   C39  C13   71.13  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
 5XP  chir_01  C25  C24  N29  C26  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
 5XP  plan-1  C1   0.020
 5XP  plan-1  C2   0.020
 5XP  plan-1  O3   0.020
 5XP  plan-1  N4   0.020
 5XP  plan-1  C5   0.020
 5XP  plan-1  C6   0.020
 5XP  plan-1  O23  0.020
 5XP  plan-1  C24  0.020
 5XP  plan-2  C2   0.020
 5XP  plan-2  C6   0.020
 5XP  plan-2  N7   0.020
 5XP  plan-2  N8   0.020
 5XP  plan-2  N9   0.020
 5XP  plan-2  N10  0.020
 5XP  plan-2  C11  0.020
 5XP  plan-3  C11  0.020
 5XP  plan-3  C12  0.020
 5XP  plan-3  C13  0.020
 5XP  plan-3  C14  0.020
 5XP  plan-3  C15  0.020
 5XP  plan-3  C16  0.020
 5XP  plan-3  C17  0.020
 5XP  plan-3  H12  0.020
 5XP  plan-3  H14  0.020
 5XP  plan-3  H16  0.020
 5XP  plan-3  H17  0.020
 5XP  plan-3  C39  0.020
 5XP  plan-4  C25  0.020
 5XP  plan-4  C26  0.020
 5XP  plan-4  O27  0.020
 5XP  plan-4  O28  0.020

