# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 27 22:27:55 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (4R)-4-{[(2S)-2-{[(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoyl]amino}propanoyl]amino}-5-amino-5-oxopentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@@H](C)O[C@H]1[C@H](O)[C@@H](CO)O[C@@H](O)[C@@H]1NC(C)=O)C(=O)N[C@H](CCC(O)=O)C(N)=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
 3LT  3LT  '(4R)-4-{[(2S)-2-{[(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoyl]amino}propanoyl]amino}-5-amino-5-oxopentanoic acid (non-preferred name)'  ligand  65  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3LT
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
 3LT  CAA  C  CH1    0   0.307   4.4049   1.5215  -0.0874
 3LT  CAJ  C  CH1    0  -0.149   3.3803   0.4277  -0.3988
 3LT  CAI  C  CH1    0   0.030   3.7510  -0.8529   0.3550
 3LT  CAG  C  CH1    0   0.012   5.2143  -1.2273   0.1396
 3LT  CAD  C  CH1    0  -0.021   6.1151  -0.0124   0.3906
 3LT  CAE  C  CH2    0  -0.160   7.5616  -0.3087   0.0612
 3LT  CAN  C  CH3    0  -0.786  -0.0757   1.9515  -0.2942
 3LT  CAP  C  CH1    0  -0.074   1.7737  -2.1920   0.6251
 3LT  CAR  C  C      0   0.558   0.5941  -1.8252  -0.2736
 3LT  CAQ  C  CH3    0  -0.666   1.6979  -3.6727   0.9748
 3LT  OAB  O  OH1    0  -0.647   4.1217   2.6322  -0.8482
 3LT  OAO  O  O2     0  -0.486   2.9772  -1.9489  -0.0529
 3LT  OAH  O  OH1    0  -0.666   5.5333  -2.2729   1.0257
 3LT  OAC  O  O2     0  -0.496   5.6940   1.0667  -0.4146
 3LT  OAF  O  OH1    0  -0.669   8.3442   0.8099   0.4027
 3LT  OAM  O  O      0  -0.492   1.3340   1.3583  -2.1332
 3LT  OAS  O  O      0  -0.493   0.6550  -1.9261  -1.4874
 3LT  NAK  N  NH1    0  -0.641   2.0516   0.8550  -0.0446
 3LT  NAT  N  NH1    0  -0.647  -0.5159  -1.4558   0.3843
 3LT  CAU  C  CH1    0  -0.201  -1.7715  -1.2110  -0.2791
 3LT  CAW  C  C      0   0.564  -2.6342  -0.3450   0.6292
 3LT  CAV  C  CH3    0  -0.646  -2.5178  -2.5099  -0.6019
 3LT  OAX  O  O      0  -0.490  -2.4541  -0.2961   1.8379
 3LT  C    C  C      0   0.522  -3.9951   2.3551   1.2701
 3LT  N    N  NH1    0  -0.631  -3.6379   0.2903   0.0156
 3LT  CA   C  CH1    0  -0.189  -4.6149   1.0613   0.7410
 3LT  CB   C  CH2    0  -0.449  -5.8053   1.3902  -0.1637
 3LT  CD   C  C      0   0.419  -7.7869   0.4248  -1.5084
 3LT  CG   C  CH2    0  -0.585  -6.5614   0.1507  -0.6160
 3LT  OE2  O  O      0  -0.605  -8.0041   1.6032  -1.8502
 3LT  OE1  O  OC    -1  -0.628  -8.4637  -0.5765  -1.8199
 3LT  H1   H  HCH1   0   0.183   4.3678   1.7502   0.9935
 3LT  H2   H  HCH1   0   0.271   3.4007   0.2290  -1.4726
 3LT  H3   H  HCH1   0   0.221   3.6153  -0.6691   1.4342
 3LT  H4   H  HCH1   0   0.231   5.3399  -1.5382  -0.9072
 3LT  H5   H  HCH1   0   0.220   6.0439   0.2588   1.4575
 3LT  H6   H  HCH2   0   0.207   7.8658  -1.1995   0.6214
 3LT  H7   H  HCH2   0   0.198   7.6429  -0.5546  -1.0072
 3LT  H8   H  HCH3   0   0.273   0.0777   3.0228  -0.1495
 3LT  H9   H  HCH3   0   0.255  -0.9348   1.8347  -0.9498
 3LT  H10  H  HCH3   0   0.244  -0.3116   1.5208   0.6765
 3LT  H11  H  HCH1   0   0.235   1.7258  -1.6090   1.5535
 3LT  H12  H  HCH3   0   0.238   1.7499  -4.2885   0.0761
 3LT  H13  H  HCH3   0   0.248   2.5259  -3.9424   1.6297
 3LT  H14  H  HCH3   0   0.233   0.7669  -3.9040   1.4920
 3LT  H15  H  HOH1   0   0.464   4.5670   3.3979  -0.4700
 3LT  H16  H  HOH1   0   0.461   6.0331  -2.9431   0.5543
 3LT  H17  H  HOH1   0   0.457   9.2667   0.5828   0.2567
 3LT  H18  H  HNH1   0   0.396   1.8611   0.9966   0.9362
 3LT  H19  H  HNH1   0   0.397  -0.5113  -1.3975   1.3919
 3LT  H20  H  HCH1   0   0.275  -1.5742  -0.6768  -1.2124
 3LT  H22  H  HCH3   0   0.238  -3.4361  -2.3093  -1.1532
 3LT  H23  H  HCH3   0   0.252  -1.8927  -3.1565  -1.2155
 3LT  H24  H  HCH3   0   0.237  -2.7770  -3.0452   0.3120
 3LT  H26  H  HNH1   0   0.407  -3.6705   0.3006  -0.9918
 3LT  H28  H  HNH2   0   0.402  -4.2397   3.6680   2.8208
 3LT  H29  H  HNH2   0   0.408  -5.2194   2.2590   2.9206
 3LT  H30  H  HCH1   0   0.267  -4.9718   0.4638   1.5859
 3LT  H31  H  HCH2   0   0.245  -6.4784   2.0497   0.3869
 3LT  H32  H  HCH2   0   0.235  -5.4521   1.9620  -1.0260
 3LT  H33  H  HCH2   0   0.228  -5.8967  -0.5283  -1.1609
 3LT  H34  H  HCH2   0   0.228  -6.8928  -0.4174   0.2600
 3LT  O    O  O      0  -0.474  -3.1284   2.9536   0.6551
 3LT  CAL  C  C      0   0.528   1.1587   1.3611  -0.9262
 3LT  NBH  N  NH2    0  -0.800  -4.5248   2.7881   2.4222

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
 3LT  NBH  C    single  1.340  0.020  1.340
 3LT  OAX  CAW  double  1.223  0.020  1.223
 3LT  C    O    double  1.220  0.020  1.220
 3LT  C    CA   single  1.529  0.020  1.529
 3LT  N    CA   single  1.441  0.020  1.441
 3LT  N    CAW  single  1.337  0.020  1.337
 3LT  CA   CB   single  1.531  0.020  1.531
 3LT  CAW  CAU  single  1.523  0.020  1.523
 3LT  CAQ  CAP  single  1.523  0.020  1.523
 3LT  OAS  CAR  double  1.220  0.020  1.220
 3LT  CAR  NAT  single  1.342  0.020  1.342
 3LT  CAR  CAP  single  1.528  0.020  1.528
 3LT  CAU  NAT  single  1.441  0.020  1.441
 3LT  CAU  CAV  single  1.532  0.020  1.532
 3LT  CB   CG   single  1.521  0.020  1.521
 3LT  CAP  OAO  single  1.403  0.020  1.403
 3LT  CG   CD   single  1.541  0.020  1.541
 3LT  OAO  CAI  single  1.402  0.020  1.402
 3LT  OAH  CAG  single  1.407  0.020  1.407
 3LT  CD   OE2  deloc   1.246  0.020  1.246
 3LT  CD   OE1  deloc   1.248  0.020  1.248
 3LT  CAI  CAG  single  1.526  0.020  1.526
 3LT  CAI  CAJ  single  1.532  0.020  1.532
 3LT  CAN  CAL  single  1.507  0.020  1.507
 3LT  CAG  CAD  single  1.533  0.020  1.533
 3LT  CAL  NAK  single  1.353  0.020  1.353
 3LT  CAL  OAM  double  1.220  0.020  1.220
 3LT  NAK  CAJ  single  1.440  0.020  1.440
 3LT  CAJ  CAA  single  1.531  0.020  1.531
 3LT  CAD  CAE  single  1.513  0.020  1.513
 3LT  CAD  OAC  single  1.411  0.020  1.411
 3LT  CAE  OAF  single  1.407  0.020  1.407
 3LT  CAA  OAC  single  1.406  0.020  1.406
 3LT  CAA  OAB  single  1.376  0.020  1.376
 3LT  CAA  H1   single  0.970  0.020  1.090
 3LT  CAJ  H2   single  0.970  0.020  1.090
 3LT  CAI  H3   single  0.970  0.020  1.090
 3LT  CAG  H4   single  0.970  0.020  1.090
 3LT  CAD  H5   single  0.970  0.020  1.090
 3LT  CAE  H6   single  0.970  0.020  1.090
 3LT  CAE  H7   single  0.970  0.020  1.090
 3LT  CAN  H8   single  0.970  0.020  1.090
 3LT  CAN  H9   single  0.970  0.020  1.090
 3LT  CAN  H10  single  0.970  0.020  1.090
 3LT  CAP  H11  single  0.970  0.020  1.090
 3LT  CAQ  H12  single  0.970  0.020  1.090
 3LT  CAQ  H13  single  0.970  0.020  1.090
 3LT  CAQ  H14  single  0.970  0.020  1.090
 3LT  OAB  H15  single  0.850  0.020  0.980
 3LT  OAH  H16  single  0.850  0.020  0.980
 3LT  OAF  H17  single  0.850  0.020  0.980
 3LT  NAK  H18  single  0.860  0.020  1.020
 3LT  NAT  H19  single  0.860  0.020  1.020
 3LT  CAU  H20  single  0.970  0.020  1.090
 3LT  CAV  H22  single  0.970  0.020  1.090
 3LT  CAV  H23  single  0.970  0.020  1.090
 3LT  CAV  H24  single  0.970  0.020  1.090
 3LT  N    H26  single  0.860  0.020  1.020
 3LT  NBH  H28  single  0.860  0.020  1.020
 3LT  NBH  H29  single  0.860  0.020  1.020
 3LT  CA   H30  single  0.970  0.020  1.090
 3LT  CB   H31  single  0.970  0.020  1.090
 3LT  CB   H32  single  0.970  0.020  1.090
 3LT  CG   H33  single  0.970  0.020  1.090
 3LT  CG   H34  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
 3LT  H1   CAA  OAC  108.98  3.000
 3LT  H1   CAA  OAB  111.52  3.000
 3LT  OAC  CAA  OAB  108.74  3.000
 3LT  H1   CAA  CAJ  108.92  3.000
 3LT  OAB  CAA  CAJ  109.06  3.000
 3LT  OAC  CAA  CAJ  109.60  3.000
 3LT  H2   CAJ  NAK  108.25  3.000
 3LT  H2   CAJ  CAI  109.10  3.000
 3LT  NAK  CAJ  CAI  110.51  3.000
 3LT  H2   CAJ  CAA  108.51  3.000
 3LT  NAK  CAJ  CAA  110.83  3.000
 3LT  CAI  CAJ  CAA  109.59  3.000
 3LT  H3   CAI  OAO  110.30  3.000
 3LT  H3   CAI  CAG  107.28  3.000
 3LT  OAO  CAI  CAG  107.24  3.000
 3LT  H3   CAI  CAJ  108.20  3.000
 3LT  CAG  CAI  CAJ  111.58  3.000
 3LT  OAO  CAI  CAJ  112.14  3.000
 3LT  H4   CAG  OAH  111.32  3.000
 3LT  H4   CAG  CAD  108.24  3.000
 3LT  OAH  CAG  CAD  110.64  3.000
 3LT  H4   CAG  CAI  108.27  3.000
 3LT  CAD  CAG  CAI  110.24  3.000
 3LT  OAH  CAG  CAI  108.11  3.000
 3LT  H5   CAD  OAC  110.17  3.000
 3LT  H5   CAD  CAE  108.69  3.000
 3LT  OAC  CAD  CAE  108.12  3.000
 3LT  H5   CAD  CAG  108.37  3.000
 3LT  OAC  CAD  CAG  109.71  3.000
 3LT  CAE  CAD  CAG  111.77  3.000
 3LT  H7   CAE  H6   107.13  3.000
 3LT  H7   CAE  OAF  111.87  3.000
 3LT  H6   CAE  OAF  111.58  3.000
 3LT  H7   CAE  CAD  109.03  3.000
 3LT  H6   CAE  CAD  108.27  3.000
 3LT  OAF  CAE  CAD  108.86  3.000
 3LT  H10  CAN  H9   108.92  3.000
 3LT  H10  CAN  H8   107.50  3.000
 3LT  H9   CAN  H8   107.24  3.000
 3LT  H10  CAN  CAL  113.37  3.000
 3LT  H9   CAN  CAL  110.63  3.000
 3LT  H8   CAN  CAL  108.96  3.000
 3LT  H11  CAP  OAO  110.75  3.000
 3LT  H11  CAP  CAQ  108.66  3.000
 3LT  OAO  CAP  CAQ  108.79  3.000
 3LT  H11  CAP  CAR  109.66  3.000
 3LT  OAO  CAP  CAR  109.67  3.000
 3LT  CAQ  CAP  CAR  109.27  3.000
 3LT  NAT  CAR  OAS  123.50  3.000
 3LT  NAT  CAR  CAP  114.60  3.000
 3LT  OAS  CAR  CAP  121.81  3.000
 3LT  H14  CAQ  H13  108.14  3.000
 3LT  H14  CAQ  H12  108.18  3.000
 3LT  H13  CAQ  H12  108.62  3.000
 3LT  H14  CAQ  CAP  110.96  3.000
 3LT  H13  CAQ  CAP  109.92  3.000
 3LT  H12  CAQ  CAP  110.93  3.000
 3LT  H15  OAB  CAA  109.25  3.000
 3LT  CAP  OAO  CAI  117.93  3.000
 3LT  H16  OAH  CAG  109.13  3.000
 3LT  CAD  OAC  CAA  112.85  3.000
 3LT  H17  OAF  CAE  108.01  3.000
 3LT  H18  NAK  CAL  117.15  3.000
 3LT  H18  NAK  CAJ  117.06  3.000
 3LT  CAL  NAK  CAJ  124.03  3.000
 3LT  H19  NAT  CAU  116.99  3.000
 3LT  H19  NAT  CAR  120.10  3.000
 3LT  CAU  NAT  CAR  122.80  3.000
 3LT  H20  CAU  CAV  108.80  3.000
 3LT  H20  CAU  CAW  109.48  3.000
 3LT  CAV  CAU  CAW  109.38  3.000
 3LT  H20  CAU  NAT  108.59  3.000
 3LT  CAV  CAU  NAT  112.17  3.000
 3LT  CAW  CAU  NAT  108.40  3.000
 3LT  N    CAW  OAX  123.03  3.000
 3LT  N    CAW  CAU  114.94  3.000
 3LT  OAX  CAW  CAU  121.92  3.000
 3LT  H24  CAV  H23  108.50  3.000
 3LT  H24  CAV  H22  108.31  3.000
 3LT  H23  CAV  H22  107.94  3.000
 3LT  H24  CAV  CAU  110.81  3.000
 3LT  H23  CAV  CAU  110.02  3.000
 3LT  H22  CAV  CAU  111.15  3.000
 3LT  CA   C    NBH  114.25  3.000
 3LT  CA   C    O    121.92  3.000
 3LT  NBH  C    O    123.77  3.000
 3LT  H26  N    CA   118.41  3.000
 3LT  H26  N    CAW  119.20  3.000
 3LT  CA   N    CAW  122.16  3.000
 3LT  H30  CA   CB   108.65  3.000
 3LT  H30  CA   N    108.52  3.000
 3LT  CB   CA   N    110.16  3.000
 3LT  H30  CA   C    109.08  3.000
 3LT  CB   CA   C    109.75  3.000
 3LT  N    CA   C    110.63  3.000
 3LT  H32  CB   H31  106.32  3.000
 3LT  H32  CB   CG   110.63  3.000
 3LT  H31  CB   CG   109.63  3.000
 3LT  H32  CB   CA   109.10  3.000
 3LT  H31  CB   CA   108.14  3.000
 3LT  CG   CB   CA   112.79  3.000
 3LT  OE1  CD   OE2  126.57  3.000
 3LT  OE1  CD   CG   115.67  3.000
 3LT  OE2  CD   CG   117.76  3.000
 3LT  H34  CG   H33  105.06  3.000
 3LT  H34  CG   CD   108.35  3.000
 3LT  H33  CG   CD   107.76  3.000
 3LT  H34  CG   CB   109.59  3.000
 3LT  H33  CG   CB   110.58  3.000
 3LT  CD   CG   CB   115.01  3.000
 3LT  NAK  CAL  OAM  123.31  3.000
 3LT  OAM  CAL  CAN  122.24  3.000
 3LT  NAK  CAL  CAN  114.44  3.000
 3LT  H29  NBH  H28  117.33  3.000
 3LT  H29  NBH  C    121.95  3.000
 3LT  H28  NBH  C    120.72  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
 3LT  CONST_01  CAN  CAL  NAK  CAJ  180.00   0.0  0
 3LT  CONST_02  OAM  CAL  NAK  CAJ    0.00   0.0  0
 3LT  CONST_03  CAU  NAT  CAR  CAP  180.00   0.0  0
 3LT  CONST_04  CAU  NAT  CAR  OAS    0.00   0.0  0
 3LT  CONST_05  CA   N    CAW  CAU  180.00   0.0  0
 3LT  CONST_06  CA   N    CAW  OAX    0.00   0.0  0
 3LT  CONST_07  H18  NAK  CAL  CAN    0.00   0.0  0
 3LT  CONST_08  H19  NAT  CAR  CAP    0.00   0.0  0
 3LT  CONST_09  H26  N    CAW  CAU    0.00   0.0  0
 3LT  CONST_10  H28  NBH  C    O      0.00   0.0  0
 3LT  CONST_11  H29  NBH  C    O    180.00   0.0  0
 3LT  Var_01    CD   CG   CB   CA   178.89  30.0  3
 3LT  Var_02    OE2  CD   CG   CB     4.44  30.0  3
 3LT  Var_03    H8   CAN  CAL  OAM  -85.68  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
 3LT  chir_01  CAA  CAJ  OAC  OAB  negativ
 3LT  chir_02  CAJ  NAK  CAI  CAA  positiv
 3LT  chir_03  CAI  OAO  CAG  CAJ  negativ
 3LT  chir_04  CAG  OAH  CAI  CAD  negativ
 3LT  chir_05  CAD  OAC  CAG  CAE  negativ
 3LT  chir_06  CAP  OAO  CAQ  CAR  positiv
 3LT  chir_07  CAU  NAT  CAW  CAV  positiv
 3LT  chir_08  CA   N    CB   C    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
 3LT  plan-1  CAP  0.020
 3LT  plan-1  CAR  0.020
 3LT  plan-1  OAS  0.020
 3LT  plan-1  NAT  0.020
 3LT  plan-1  CAU  0.020
 3LT  plan-1  H19  0.020
 3LT  plan-2  CAU  0.020
 3LT  plan-2  CAW  0.020
 3LT  plan-2  OAX  0.020
 3LT  plan-2  N    0.020
 3LT  plan-2  CA   0.020
 3LT  plan-2  H26  0.020
 3LT  plan-3  C    0.020
 3LT  plan-3  CA   0.020
 3LT  plan-3  H28  0.020
 3LT  plan-3  H29  0.020
 3LT  plan-3  O    0.020
 3LT  plan-3  NBH  0.020
 3LT  plan-4  CAJ  0.020
 3LT  plan-4  CAN  0.020
 3LT  plan-4  OAM  0.020
 3LT  plan-4  NAK  0.020
 3LT  plan-4  H18  0.020
 3LT  plan-4  CAL  0.020
 3LT  plan-5  CD   0.020
 3LT  plan-5  CG   0.020
 3LT  plan-5  OE2  0.020
 3LT  plan-5  OE1  0.020

