FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 74G2K

Calculation Name: 5DSS-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DSS

Chain ID: B

ChEMBL ID:

UniProt ID: A0A158

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1905573.069757
FMO2-HF: Nuclear repulsion 1834554.19428
FMO2-HF: Total energy -71018.875477
FMO2-MP2: Total energy -71225.158349


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:1:LYS)


Summations of interaction energy for fragment #1(B:1:LYS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-176.243-169.2533.775-4.565-6.201-0.042
Interaction energy analysis for fragmet #1(B:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.775 / q_NPA : 1.860
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B3ASP-1-0.881-0.9312.222-101.910-95.5173.757-4.513-5.637-0.040
4B4ALA00.0000.0053.20210.21010.7470.019-0.050-0.506-0.002
5B5GLU-1-0.822-0.9045.210-42.582-42.522-0.001-0.002-0.0580.000
6B6PRO0-0.059-0.0328.716-1.231-1.2310.0000.0000.0000.000
7B7VAL00.0070.01711.8730.5950.5950.0000.0000.0000.000
8B8ILE0-0.0100.00213.9591.7451.7450.0000.0000.0000.000
9B9ASP-1-0.801-0.91617.196-26.825-26.8250.0000.0000.0000.000
10B10THR0-0.048-0.02619.318-0.110-0.1100.0000.0000.0000.000
11B11ASP-1-0.900-0.94921.602-22.489-22.4890.0000.0000.0000.000
12B12GLY0-0.067-0.03121.7740.7380.7380.0000.0000.0000.000
13B13ASN0-0.046-0.03020.654-1.130-1.1300.0000.0000.0000.000
14B14PRO0-0.023-0.00816.069-0.735-0.7350.0000.0000.0000.000
15B15LEU0-0.0070.00517.1071.8071.8070.0000.0000.0000.000
16B16LEU0-0.011-0.01417.504-1.343-1.3430.0000.0000.0000.000
17B17HIS00.0370.01316.461-0.134-0.1340.0000.0000.0000.000
18B18ARG10.8190.90020.98523.49523.4950.0000.0000.0000.000
19B19GLY0-0.015-0.01223.6571.3941.3940.0000.0000.0000.000
20B20LYS10.8740.93824.73519.23819.2380.0000.0000.0000.000
21B21TYR00.0660.03522.0670.2300.2300.0000.0000.0000.000
22B22TYR00.0310.02325.8580.6850.6850.0000.0000.0000.000
23B23ILE0-0.014-0.00621.624-0.767-0.7670.0000.0000.0000.000
24B24MET00.0350.02224.8541.0251.0250.0000.0000.0000.000
25B25PRO0-0.060-0.01124.489-1.109-1.1090.0000.0000.0000.000
26B26SER00.014-0.00622.3860.2940.2940.0000.0000.0000.000
27B27ASN00.0070.00124.4830.8080.8080.0000.0000.0000.000
28B28TRP00.0220.00026.9230.1790.1790.0000.0000.0000.000
29B29GLY00.0710.03426.9010.4860.4860.0000.0000.0000.000
30B30PRO0-0.0230.03027.473-0.333-0.3330.0000.0000.0000.000
31B31PRO00.0490.00830.4310.0580.0580.0000.0000.0000.000
32B32GLY0-0.016-0.00629.879-0.399-0.3990.0000.0000.0000.000
33B33GLY00.0460.02429.7430.6850.6850.0000.0000.0000.000
34B34GLY00.0710.04729.041-0.858-0.8580.0000.0000.0000.000
35B35LEU0-0.040-0.02824.5510.0550.0550.0000.0000.0000.000
36B36ARG10.9390.97129.29718.55718.5570.0000.0000.0000.000
37B37LEU00.0400.03331.120-0.371-0.3710.0000.0000.0000.000
38B38GLY00.011-0.00133.3160.4000.4000.0000.0000.0000.000
39B39LYS10.9240.95735.40114.51714.5170.0000.0000.0000.000
40B40THR00.017-0.02133.649-0.117-0.1170.0000.0000.0000.000
41B41ARG10.7420.85635.90416.72916.7290.0000.0000.0000.000
42B42ASN0-0.003-0.02438.4980.4290.4290.0000.0000.0000.000
43B43LEU00.0200.02139.675-0.346-0.3460.0000.0000.0000.000
44B44ASN00.0180.01238.9680.1870.1870.0000.0000.0000.000
45B45CYS0-0.037-0.01737.672-0.240-0.2400.0000.0000.0000.000
46B46PRO0-0.004-0.00635.724-0.383-0.3830.0000.0000.0000.000
47B47VAL00.0700.08629.985-0.297-0.2970.0000.0000.0000.000
48B48THR0-0.058-0.02730.038-0.648-0.6480.0000.0000.0000.000
49B49VAL00.0260.02526.6980.5580.5580.0000.0000.0000.000
50B50LEU0-0.061-0.02828.877-0.229-0.2290.0000.0000.0000.000
51B51GLN00.023-0.00325.916-0.493-0.4930.0000.0000.0000.000
52B52ASP-1-0.860-0.95229.833-17.197-17.1970.0000.0000.0000.000
53B53TYR0-0.113-0.05332.281-0.533-0.5330.0000.0000.0000.000
54B54ASN0-0.015-0.00735.0280.4670.4670.0000.0000.0000.000
55B55GLU-1-0.847-0.94333.656-17.823-17.8230.0000.0000.0000.000
56B56ALA0-0.049-0.00334.891-0.188-0.1880.0000.0000.0000.000
57B57ILE0-0.043-0.01434.5950.1760.1760.0000.0000.0000.000
58B58ASN00.0250.01030.670-0.019-0.0190.0000.0000.0000.000
59B59GLY0-0.018-0.01930.503-0.673-0.6730.0000.0000.0000.000
60B60LEU0-0.034-0.01231.1700.3920.3920.0000.0000.0000.000
61B61PRO00.001-0.00629.098-0.695-0.6950.0000.0000.0000.000
62B62VAL0-0.036-0.02023.6980.2700.2700.0000.0000.0000.000
63B63LYS10.8610.93124.76722.06622.0660.0000.0000.0000.000
64B64PHE00.0960.03718.2420.0520.0520.0000.0000.0000.000
65B65ASN00.0550.04220.289-0.762-0.7620.0000.0000.0000.000
66B66ILE00.0940.04914.643-0.039-0.0390.0000.0000.0000.000
67B67ARG10.8250.89718.76826.36326.3630.0000.0000.0000.000
68B68GLU-1-0.869-0.91422.012-22.597-22.5970.0000.0000.0000.000
69B69ILE00.0090.00418.9000.1160.1160.0000.0000.0000.000
70B70LEU0-0.021-0.01922.8440.5050.5050.0000.0000.0000.000
71B71PRO00.0100.01717.5100.1890.1890.0000.0000.0000.000
72B72ARG10.9450.95818.24828.78628.7860.0000.0000.0000.000
73B73THR00.003-0.01113.4852.0332.0330.0000.0000.0000.000
74B74ILE0-0.0110.02213.719-1.248-1.2480.0000.0000.0000.000
75B75PHE00.0210.0078.7070.8410.8410.0000.0000.0000.000
76B76THR0-0.034-0.0317.3500.5520.5520.0000.0000.0000.000
77B77ASP-1-0.949-0.9755.572-78.896-78.8960.0000.0000.0000.000
78B78THR0-0.049-0.0287.847-2.324-2.3240.0000.0000.0000.000
79B79GLU-1-0.931-0.94810.649-37.780-37.7800.0000.0000.0000.000
80B80LEU0-0.015-0.02312.8372.0882.0880.0000.0000.0000.000
81B81ASN0-0.055-0.03016.5860.1510.1510.0000.0000.0000.000
82B82ILE00.0010.02419.8690.5510.5510.0000.0000.0000.000
83B83GLU-1-0.816-0.91221.824-21.995-21.9950.0000.0000.0000.000
84B84PHE00.0150.01225.648-0.223-0.2230.0000.0000.0000.000
85B85THR0-0.028-0.03928.5500.0090.0090.0000.0000.0000.000
86B86GLU-1-0.958-0.98030.881-16.503-16.5030.0000.0000.0000.000
87B87LYS10.8390.93033.41017.04517.0450.0000.0000.0000.000
88B88PRO00.0430.01834.6740.4900.4900.0000.0000.0000.000
89B89ASN00.011-0.00837.138-0.321-0.3210.0000.0000.0000.000
90B91ALA00.0340.03933.694-0.036-0.0360.0000.0000.0000.000
91B92GLU-1-0.856-0.92933.239-17.803-17.8030.0000.0000.0000.000
92B93ASN00.0290.00027.7450.5010.5010.0000.0000.0000.000
93B94ARG10.8610.91329.22020.96920.9690.0000.0000.0000.000
94B95ALA0-0.0040.00824.462-0.401-0.4010.0000.0000.0000.000
95B96TRP0-0.058-0.02721.9910.2840.2840.0000.0000.0000.000
96B97SER00.0660.03322.400-1.541-1.5410.0000.0000.0000.000
97B98LEU0-0.010-0.00819.4640.3690.3690.0000.0000.0000.000
98B99PHE00.0080.01723.350-0.156-0.1560.0000.0000.0000.000
99B100LYS10.9190.95324.18421.68721.6870.0000.0000.0000.000
100B101GLY0-0.016-0.02325.3500.7070.7070.0000.0000.0000.000
101B102ASP-1-0.830-0.90326.104-19.030-19.0300.0000.0000.0000.000
102B103ASP-1-0.920-0.95329.878-17.349-17.3490.0000.0000.0000.000
103B104ARG10.9450.95733.20515.90015.9000.0000.0000.0000.000
104B105GLY0-0.018-0.00230.3440.2640.2640.0000.0000.0000.000
105B106HIS0-0.037-0.02528.907-0.518-0.5180.0000.0000.0000.000
106B107LYS10.9690.99822.86323.61823.6180.0000.0000.0000.000
107B108ALA0-0.0020.01121.3800.6260.6260.0000.0000.0000.000
108B109ARG10.8060.90923.22720.12520.1250.0000.0000.0000.000
109B110VAL00.0110.01323.811-0.082-0.0820.0000.0000.0000.000
110B111GLY0-0.011-0.03525.2840.9980.9980.0000.0000.0000.000
111B112ILE0-0.0250.00326.714-0.721-0.7210.0000.0000.0000.000
112B113GLY00.003-0.00229.2320.5920.5920.0000.0000.0000.000
113B114GLY00.0140.00229.495-0.640-0.6400.0000.0000.0000.000
114B115SER00.009-0.00230.941-0.178-0.1780.0000.0000.0000.000
115B116ASN0-0.034-0.02331.956-0.233-0.2330.0000.0000.0000.000
116B117GLY0-0.005-0.01133.7810.5390.5390.0000.0000.0000.000
117B118HIS00.004-0.00936.014-0.406-0.4060.0000.0000.0000.000
118B119PRO0-0.0040.01633.4120.0050.0050.0000.0000.0000.000
119B120GLY00.032-0.00431.272-0.609-0.6090.0000.0000.0000.000
120B121GLY0-0.006-0.01230.7120.5540.5540.0000.0000.0000.000
121B122GLU-1-0.827-0.89828.042-20.752-20.7520.0000.0000.0000.000
122B123MET0-0.0200.01125.429-0.592-0.5920.0000.0000.0000.000
123B124LEU0-0.052-0.04020.6440.0220.0220.0000.0000.0000.000
124B125ARG10.8270.91721.21423.44823.4480.0000.0000.0000.000
125B126GLY00.0780.01717.318-0.641-0.6410.0000.0000.0000.000
126B127GLY0-0.0120.02115.7031.7811.7810.0000.0000.0000.000
127B128PHE0-0.067-0.05614.722-0.757-0.7570.0000.0000.0000.000
128B129TYR00.0650.0388.557-1.860-1.8600.0000.0000.0000.000
129B130GLY0-0.061-0.04711.2193.9073.9070.0000.0000.0000.000
130B131GLU-1-0.723-0.85310.844-42.364-42.3640.0000.0000.0000.000
131B132GLN0-0.080-0.04410.996-3.478-3.4780.0000.0000.0000.000
132B133HIS0-0.0110.0077.693-0.451-0.4510.0000.0000.0000.000
133B134GLY0-0.005-0.01611.9912.9692.9690.0000.0000.0000.000
134B135LEU0-0.028-0.01214.017-0.777-0.7770.0000.0000.0000.000
135B136ARG10.9630.97716.80226.94326.9430.0000.0000.0000.000
136B137ASN00.001-0.02219.4171.2001.2000.0000.0000.0000.000
137B138GLY00.0120.02219.3120.0000.0000.0000.0000.0000.000
138B139THR0-0.041-0.00816.079-1.074-1.0740.0000.0000.0000.000
139B140TYR0-0.068-0.05514.9731.5411.5410.0000.0000.0000.000
140B141LYS10.8870.95612.03041.45341.4530.0000.0000.0000.000
141B142LEU00.0360.02714.417-1.788-1.7880.0000.0000.0000.000
142B143VAL0-0.009-0.01010.4191.4291.4290.0000.0000.0000.000
143B144PHE0-0.007-0.00513.8010.1980.1980.0000.0000.0000.000
144B145CYS0-0.0120.0019.5150.5750.5750.0000.0000.0000.000
145B146ARG10.9290.95513.19032.30532.3050.0000.0000.0000.000
146B147ASP-1-0.834-0.92515.127-31.600-31.6000.0000.0000.0000.000
147B148GLY0-0.036-0.01316.982-0.230-0.2300.0000.0000.0000.000
148B149SER0-0.037-0.04416.2810.8200.8200.0000.0000.0000.000
149B150SER0-0.112-0.05313.8651.3381.3380.0000.0000.0000.000
150B151THR00.0920.0569.075-3.095-3.0950.0000.0000.0000.000
151B153LEU00.0140.01811.232-0.447-0.4470.0000.0000.0000.000
152B154ASP-1-0.763-0.87913.630-40.541-40.5410.0000.0000.0000.000
153B155VAL0-0.035-0.00815.1252.1132.1130.0000.0000.0000.000
154B156GLY00.0260.00718.594-0.316-0.3160.0000.0000.0000.000
155B157ARG10.7410.84721.45024.38324.3830.0000.0000.0000.000
156B158TYR00.0230.01525.2180.2840.2840.0000.0000.0000.000
157B159GLY00.0520.03128.1880.1880.1880.0000.0000.0000.000
158B160ASN0-0.075-0.06831.8590.0330.0330.0000.0000.0000.000
159B161ARG10.9530.97834.56115.90415.9040.0000.0000.0000.000
160B162GLU-1-0.734-0.82035.715-16.293-16.2930.0000.0000.0000.000
161B163GLY00.0750.03634.4650.1740.1740.0000.0000.0000.000
162B164ARG10.8170.90428.72720.16420.1640.0000.0000.0000.000
163B165ARG10.9060.96829.04218.75718.7570.0000.0000.0000.000
164B166LEU00.0540.03123.118-0.151-0.1510.0000.0000.0000.000
165B167GLY00.021-0.00422.9740.8060.8060.0000.0000.0000.000
166B168LEU0-0.0340.00417.254-0.249-0.2490.0000.0000.0000.000
167B169SER0-0.036-0.03618.6251.8741.8740.0000.0000.0000.000
168B170GLU-1-0.965-0.98117.508-28.144-28.1440.0000.0000.0000.000
169B171ALA00.0090.00916.903-1.027-1.0270.0000.0000.0000.000
170B172GLY00.0090.01416.493-1.543-1.5430.0000.0000.0000.000
171B173GLU-1-0.877-0.94417.208-24.179-24.1790.0000.0000.0000.000
172B174LEU0-0.044-0.01518.566-1.141-1.1410.0000.0000.0000.000
173B175GLY00.0690.03818.810-1.706-1.7060.0000.0000.0000.000
174B176VAL0-0.071-0.04618.5381.4421.4420.0000.0000.0000.000
175B177GLY00.0400.04519.873-1.056-1.0560.0000.0000.0000.000
176B178PHE0-0.040-0.02317.1961.1081.1080.0000.0000.0000.000
177B179GLU-1-0.743-0.85422.600-20.450-20.4500.0000.0000.0000.000
178B180LYS10.9210.96024.92122.60722.6070.0000.0000.0000.000
179B181ALA0-0.017-0.00826.3760.8110.8110.0000.0000.0000.000
180B182GLY0-0.021-0.02029.5690.6810.6810.0000.0000.0000.000
181B183GLY0-0.059-0.04029.901-0.510-0.5100.0000.0000.0000.000
182B184GLY00.0190.01230.405-0.174-0.1740.0000.0000.0000.000
183B185ASN-1-0.860-0.90028.023-21.501-21.5010.0000.0000.0000.000