# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:58:05 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)methylamino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](NC(=O)N[C@@H](CCCC(=O)NCc1ccc(F)cc1)C(O)=O)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
 9TB  9TB  '(2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)methylamino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid'  ligand  52  31  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9TB
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
 9TB  OAA  O  OC    -1  -0.635    7.8034   1.0797  -3.0178
 9TB  CAW  C  C      0   0.409    7.1752   1.7351  -2.1586
 9TB  OAF  O  O      0  -0.610    7.1950   2.9745  -2.0214
 9TB  CAP  C  CH2    0  -0.576    6.3069   0.9146  -1.1887
 9TB  CAS  C  CH2    0  -0.438    5.5776   1.7142  -0.1218
 9TB  CBE  C  CH1    0  -0.186    4.7654   0.8505   0.8451
 9TB  CAY  C  C      0   0.402    4.2254   1.7108   2.0138
 9TB  OAH  O  OC    -1  -0.624    5.0885   2.1212   2.8181
 9TB  OAC  O  O      0  -0.604    3.0049   1.9512   2.0420
 9TB  NAV  N  NH1    0  -0.664    3.7252   0.1570   0.1191
 9TB  CBA  C  C      0   0.737    3.0102  -0.8283   0.7280
 9TB  OAE  O  O      0  -0.565    3.4001  -1.3945   1.7456
 9TB  N    N  NH1    0  -0.668    1.8256  -1.1401   0.1270
 9TB  CA   C  CH1    0  -0.193    1.2051  -2.4200   0.3826
 9TB  C    C  C      0   0.404    2.0168  -3.6210  -0.1679
 9TB  OXT  O  OC    -1  -0.622    1.6055  -4.7458   0.1856
 9TB  O    O  O      0  -0.597    2.9876  -3.3759  -0.9048
 9TB  CB   C  CH2    0  -0.451   -0.2108  -2.4215  -0.1929
 9TB  CAN  C  CH2    0  -0.411   -1.1413  -1.4159   0.4721
 9TB  CAO  C  CH2    0  -0.559   -2.5400  -1.4415  -0.1437
 9TB  CAZ  C  C      0   0.555   -3.4796  -0.4986   0.5737
 9TB  OAD  O  O      0  -0.510   -3.7419  -0.6349   1.7628
 9TB  NAT  N  NH1    0  -0.619   -3.9779   0.4998  -0.1756
 9TB  CAQ  C  CH2    0  -0.395   -4.8915   1.5072   0.3195
 9TB  CBC  C  CR6    0   0.116   -6.3354   1.1797   0.0319
 9TB  CAL  C  CR16   0  -0.287   -7.0246   1.8372  -0.9810
 9TB  CAJ  C  CR16   0  -0.398   -8.3473   1.5272  -1.2720
 9TB  CBB  C  CR6    0   0.514   -8.9697   0.5445  -0.5300
 9TB  FAI  F  F      0  -0.317  -10.2489   0.2347  -0.8013
 9TB  CAK  C  CR16   0  -0.398   -8.3198  -0.1307   0.4869
 9TB  CAM  C  CR16   0  -0.275   -7.0006   0.1951   0.7613
 9TB  H2   H  HCH2   0   0.223    5.5926   0.3317  -1.7793
 9TB  H3   H  HCH2   0   0.214    6.9473   0.1662  -0.7062
 9TB  H4   H  HCH2   0   0.221    6.2979   2.2852   0.4650
 9TB  H5   H  HCH2   0   0.204    4.9163   2.4520  -0.5897
 9TB  H6   H  HCH1   0   0.218    5.4388   0.1007   1.2697
 9TB  H8   H  HNH1   0   0.365    3.2218   0.7297  -0.5423
 9TB  H9   H  HNH1   0   0.365    1.7144  -0.8103  -0.8207
 9TB  H10  H  HCH1   0   0.227    1.1227  -2.5486   1.4656
 9TB  H12  H  HCH2   0   0.216   -0.1654  -2.2290  -1.2719
 9TB  H13  H  HCH2   0   0.233   -0.6197  -3.4263  -0.0758
 9TB  H14  H  HCH2   0   0.225   -1.2098  -1.6399   1.5396
 9TB  H15  H  HCH2   0   0.231   -0.7281  -0.4081   0.3876
 9TB  H16  H  HCH2   0   0.244   -2.4790  -1.2054  -1.2087
 9TB  H17  H  HCH2   0   0.256   -2.9562  -2.4498  -0.0654
 9TB  H18  H  HNH1   0   0.401   -3.7498   0.5261  -1.1558
 9TB  H19  H  HCH2   0   0.266   -4.7318   1.6180   1.3913
 9TB  H20  H  HCH2   0   0.271   -4.6284   2.4586  -0.1434
 9TB  H21  H  HCR6   0   0.264   -6.5284   2.6087  -1.5574
 9TB  H22  H  HCR6   0   0.279   -8.8803   2.0419  -2.0605
 9TB  H23  H  HCR6   0   0.278   -8.8356  -0.8930   1.0560
 9TB  H24  H  HCR6   0   0.263   -6.4834  -0.3240   1.5584

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
 9TB  OAC  CAY  deloc     1.244  0.020  1.244
 9TB  OAF  CAW  deloc     1.247  0.020  1.247
 9TB  OAH  CAY  deloc     1.249  0.020  1.249
 9TB  CAY  CBE  single    1.548  0.020  1.548
 9TB  CAW  OAA  deloc     1.250  0.020  1.250
 9TB  CAW  CAP  single    1.539  0.020  1.539
 9TB  CAP  CAS  single    1.520  0.020  1.520
 9TB  CAS  CBE  single    1.530  0.020  1.530
 9TB  CBE  NAV  single    1.446  0.020  1.446
 9TB  OAE  CBA  double    1.228  0.020  1.228
 9TB  NAV  CBA  single    1.361  0.020  1.361
 9TB  CBA  N    single    1.364  0.020  1.364
 9TB  CAO  CAN  single    1.529  0.020  1.529
 9TB  CAO  CAZ  single    1.512  0.020  1.512
 9TB  CB   CAN  single    1.523  0.020  1.523
 9TB  CB   CA   single    1.528  0.020  1.528
 9TB  N    CA   single    1.445  0.020  1.445
 9TB  OAD  CAZ  double    1.225  0.020  1.225
 9TB  CAZ  NAT  single    1.344  0.020  1.344
 9TB  CA   C    single    1.551  0.020  1.551
 9TB  NAT  CAQ  single    1.447  0.020  1.447
 9TB  C    O    deloc     1.243  0.020  1.243
 9TB  C    OXT  deloc     1.249  0.020  1.249
 9TB  CAQ  CBC  single    1.508  0.020  1.508
 9TB  CBC  CAM  aromatic  1.394  0.020  1.394
 9TB  CBC  CAL  aromatic  1.390  0.020  1.390
 9TB  CAM  CAK  aromatic  1.386  0.020  1.386
 9TB  CAL  CAJ  aromatic  1.389  0.020  1.389
 9TB  CAK  CBB  aromatic  1.383  0.020  1.383
 9TB  CAJ  CBB  aromatic  1.380  0.020  1.380
 9TB  CBB  FAI  single    1.344  0.020  1.344
 9TB  CAP  H2   single    0.970  0.020  1.090
 9TB  CAP  H3   single    0.970  0.020  1.090
 9TB  CAS  H4   single    0.970  0.020  1.090
 9TB  CAS  H5   single    0.970  0.020  1.090
 9TB  CBE  H6   single    0.970  0.020  1.090
 9TB  NAV  H8   single    0.890  0.020  1.040
 9TB  N    H9   single    0.890  0.020  1.040
 9TB  CA   H10  single    0.970  0.020  1.090
 9TB  CB   H12  single    0.970  0.020  1.090
 9TB  CB   H13  single    0.970  0.020  1.090
 9TB  CAN  H14  single    0.970  0.020  1.090
 9TB  CAN  H15  single    0.970  0.020  1.090
 9TB  CAO  H16  single    0.970  0.020  1.090
 9TB  CAO  H17  single    0.970  0.020  1.090
 9TB  NAT  H18  single    0.860  0.020  1.020
 9TB  CAQ  H19  single    0.970  0.020  1.090
 9TB  CAQ  H20  single    0.970  0.020  1.090
 9TB  CAL  H21  single    0.930  0.020  1.080
 9TB  CAJ  H22  single    0.930  0.020  1.080
 9TB  CAK  H23  single    0.930  0.020  1.080
 9TB  CAM  H24  single    0.930  0.020  1.080

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
 9TB  CAP  CAW  OAF  118.00  3.000
 9TB  CAP  CAW  OAA  115.93  3.000
 9TB  OAF  CAW  OAA  126.06  3.000
 9TB  H3   CAP  H2   104.77  3.000
 9TB  H3   CAP  CAS  109.29  3.000
 9TB  H2   CAP  CAS  110.23  3.000
 9TB  H3   CAP  CAW  108.16  3.000
 9TB  H2   CAP  CAW  108.18  3.000
 9TB  CAS  CAP  CAW  115.64  3.000
 9TB  H5   CAS  H4   106.01  3.000
 9TB  H5   CAS  CBE  109.25  3.000
 9TB  H4   CAS  CBE  107.83  3.000
 9TB  H5   CAS  CAP  110.13  3.000
 9TB  H4   CAS  CAP  109.65  3.000
 9TB  CBE  CAS  CAP  113.67  3.000
 9TB  H6   CBE  NAV  108.01  3.000
 9TB  H6   CBE  CAY  107.61  3.000
 9TB  NAV  CBE  CAY  113.24  3.000
 9TB  H6   CBE  CAS  107.80  3.000
 9TB  NAV  CBE  CAS  109.60  3.000
 9TB  CAY  CBE  CAS  110.39  3.000
 9TB  OAC  CAY  OAH  126.85  3.000
 9TB  OAH  CAY  CBE  115.31  3.000
 9TB  OAC  CAY  CBE  117.81  3.000
 9TB  H8   NAV  CBA  116.22  3.000
 9TB  H8   NAV  CBE  114.57  3.000
 9TB  CBA  NAV  CBE  120.04  3.000
 9TB  N    CBA  OAE  122.36  3.000
 9TB  N    CBA  NAV  115.12  3.000
 9TB  OAE  CBA  NAV  122.52  3.000
 9TB  H9   N    CA   114.08  3.000
 9TB  H9   N    CBA  115.74  3.000
 9TB  CA   N    CBA  119.82  3.000
 9TB  H10  CA   CB   107.63  3.000
 9TB  H10  CA   C    107.46  3.000
 9TB  CB   CA   C    110.52  3.000
 9TB  H10  CA   N    108.15  3.000
 9TB  C    CA   N    113.48  3.000
 9TB  CB   CA   N    109.39  3.000
 9TB  O    C    OXT  127.06  3.000
 9TB  OXT  C    CA   115.13  3.000
 9TB  O    C    CA   117.81  3.000
 9TB  H13  CB   H12  106.42  3.000
 9TB  H13  CB   CAN  109.40  3.000
 9TB  H12  CB   CAN  109.81  3.000
 9TB  H13  CB   CA   107.92  3.000
 9TB  H12  CB   CA   109.38  3.000
 9TB  CAN  CB   CA   113.64  3.000
 9TB  H15  CAN  H14  106.76  3.000
 9TB  H15  CAN  CAO  109.29  3.000
 9TB  H14  CAN  CAO  109.44  3.000
 9TB  H15  CAN  CB   110.13  3.000
 9TB  H14  CAN  CB   109.24  3.000
 9TB  CAO  CAN  CB   111.85  3.000
 9TB  H17  CAO  H16  106.88  3.000
 9TB  H17  CAO  CAZ  107.73  3.000
 9TB  H16  CAO  CAZ  111.25  3.000
 9TB  H17  CAO  CAN  109.56  3.000
 9TB  H16  CAO  CAN  109.76  3.000
 9TB  CAZ  CAO  CAN  111.53  3.000
 9TB  NAT  CAZ  OAD  122.97  3.000
 9TB  NAT  CAZ  CAO  115.41  3.000
 9TB  OAD  CAZ  CAO  121.61  3.000
 9TB  H18  NAT  CAQ  117.25  3.000
 9TB  H18  NAT  CAZ  118.57  3.000
 9TB  CAQ  NAT  CAZ  124.08  3.000
 9TB  H20  CAQ  H19  107.07  3.000
 9TB  H20  CAQ  CBC  109.85  3.000
 9TB  H19  CAQ  CBC  110.49  3.000
 9TB  H20  CAQ  NAT  108.05  3.000
 9TB  H19  CAQ  NAT  108.36  3.000
 9TB  CBC  CAQ  NAT  112.83  3.000
 9TB  CAM  CBC  CAL  118.59  3.000
 9TB  CAL  CBC  CAQ  120.71  3.000
 9TB  CAM  CBC  CAQ  120.68  3.000
 9TB  H21  CAL  CAJ  118.91  3.000
 9TB  H21  CAL  CBC  119.82  3.000
 9TB  CAJ  CAL  CBC  121.26  3.000
 9TB  H22  CAJ  CBB  120.56  3.000
 9TB  H22  CAJ  CAL  121.03  3.000
 9TB  CBB  CAJ  CAL  118.41  3.000
 9TB  CAK  CBB  FAI  118.90  3.000
 9TB  FAI  CBB  CAJ  119.01  3.000
 9TB  CAK  CBB  CAJ  122.09  3.000
 9TB  H23  CAK  CAM  121.00  3.000
 9TB  H23  CAK  CBB  120.44  3.000
 9TB  CAM  CAK  CBB  118.56  3.000
 9TB  H24  CAM  CAK  119.18  3.000
 9TB  H24  CAM  CBC  119.73  3.000
 9TB  CAK  CAM  CBC  121.09  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
 9TB  CONST_01  CBB  CAK  CAM  CBC     0.00   0.0  0
 9TB  CONST_02  CBB  CAJ  CAL  CBC     0.00   0.0  0
 9TB  CONST_03  CAK  CAM  CBC  CAL     0.00   0.0  0
 9TB  CONST_04  CAK  CBB  CAJ  CAL     0.00   0.0  0
 9TB  CONST_05  CAM  CBC  CAL  CAJ     0.00   0.0  0
 9TB  CONST_06  CAM  CAK  CBB  CAJ     0.00   0.0  0
 9TB  CONST_07  CAK  CAM  CBC  CAQ   180.00   0.0  0
 9TB  CONST_08  CAJ  CAL  CBC  CAQ   180.00   0.0  0
 9TB  CONST_09  FAI  CBB  CAJ  CAL   180.00   0.0  0
 9TB  CONST_10  CAM  CAK  CBB  FAI   180.00   0.0  0
 9TB  CONST_11  H23  CAK  CAM  CBC   180.00   0.0  0
 9TB  CONST_12  H22  CAJ  CAL  CBC   180.00   0.0  0
 9TB  CONST_13  H24  CAM  CBC  CAL   180.00   0.0  0
 9TB  CONST_14  H21  CAL  CAJ  CBB   180.00   0.0  0
 9TB  CONST_17  CAQ  NAT  CAZ  CAO   180.00   0.0  0
 9TB  CONST_18  CAQ  NAT  CAZ  OAD     0.00   0.0  0
 9TB  CONST_23  H18  NAT  CAZ  CAO     0.00   0.0  0
 9TB  Var_01    CAM  CBC  CAQ  NAT    74.68  30.0  2
 9TB  Var_02    CBC  CAQ  NAT  CAZ   -96.21  30.0  3
 9TB  Var_03    CAS  CAP  CAW  OAA   178.30  30.0  3
 9TB  Var_04    CBE  CAS  CAP  CAW  -178.09  30.0  3
 9TB  Var_05    CAO  CAN  CB   CA    179.39  30.0  3
 9TB  Var_06    CAZ  CAO  CAN  CB    176.70  30.0  2
 9TB  Var_07    OAD  CAZ  CAO  CAN   -60.87  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
 9TB  chir_01  CBE  CAY  CAS  NAV  positiv
 9TB  chir_02  CA   N    CB   C    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
 9TB  plan-1  CAQ  0.020
 9TB  plan-1  CBC  0.020
 9TB  plan-1  CAL  0.020
 9TB  plan-1  CAJ  0.020
 9TB  plan-1  CBB  0.020
 9TB  plan-1  FAI  0.020
 9TB  plan-1  CAK  0.020
 9TB  plan-1  CAM  0.020
 9TB  plan-1  H21  0.020
 9TB  plan-1  H22  0.020
 9TB  plan-1  H23  0.020
 9TB  plan-1  H24  0.020
 9TB  plan-2  CA   0.020
 9TB  plan-2  C    0.020
 9TB  plan-2  OXT  0.020
 9TB  plan-2  O    0.020
 9TB  plan-3  CBE  0.020
 9TB  plan-3  NAV  0.020
 9TB  plan-3  CBA  0.020
 9TB  plan-3  OAE  0.020
 9TB  plan-3  N    0.020
 9TB  plan-3  CA   0.020
 9TB  plan-3  H8   0.020
 9TB  plan-3  H9   0.020
 9TB  plan-4  CAO  0.020
 9TB  plan-4  CAZ  0.020
 9TB  plan-4  OAD  0.020
 9TB  plan-4  NAT  0.020
 9TB  plan-4  CAQ  0.020
 9TB  plan-4  H18  0.020
 9TB  plan-5  OAA  0.020
 9TB  plan-5  CAW  0.020
 9TB  plan-5  OAF  0.020
 9TB  plan-5  CAP  0.020
 9TB  plan-6  CBE  0.020
 9TB  plan-6  CAY  0.020
 9TB  plan-6  OAH  0.020
 9TB  plan-6  OAC  0.020

