Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LZJK9

Calculation Name: 3QKS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKS

Chain ID: B

ChEMBL ID:

UniProt ID: Q8U1N9

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1629136.193515
FMO2-HF: Nuclear repulsion 1558526.412994
FMO2-HF: Total energy -70609.780521
FMO2-MP2: Total energy -70820.017388


3D Structure
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:704:ALA)


Summations of interaction energy for fragment #1(B:704:ALA)
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.
-1.431.5251.816-1.814-2.9540
Interaction energy analysis for fragmet #1(B:704:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.015
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].
3B706LYS10.9170.9363.584-0.4240.871-0.003-0.563-0.7280.003
4B707GLU-1-0.870-0.9272.162-4.746-3.6421.819-1.145-1.778-0.003
5B708ASN00.0330.0203.9170.7361.1980.001-0.100-0.3620.000
6B709ARG10.9250.9565.3891.1491.243-0.001-0.006-0.0860.000
7B710GLU-1-0.867-0.9497.312-0.396-0.3960.0000.0000.0000.000
8B711ARG10.8640.9297.9030.9470.9470.0000.0000.0000.000
9B712VAL00.0270.0059.5680.2150.2150.0000.0000.0000.000
10B713LYS10.8920.95011.6180.6340.6340.0000.0000.0000.000
11B714LYS10.8880.94512.5270.5790.5790.0000.0000.0000.000
12B715GLU-1-0.816-0.89613.869-0.351-0.3510.0000.0000.0000.000
13B716ILE00.0060.00615.6180.0550.0550.0000.0000.0000.000
14B717LYS10.9530.97917.2250.3600.3600.0000.0000.0000.000
15B718ASP-1-0.906-0.95417.668-0.349-0.3490.0000.0000.0000.000
16B719LEU0-0.001-0.00318.8720.0310.0310.0000.0000.0000.000
17B720GLU-1-0.914-0.95421.758-0.154-0.1540.0000.0000.0000.000
18B721LYS10.9320.98321.5450.2680.2680.0000.0000.0000.000
19B722ALA0-0.030-0.02024.1430.0160.0160.0000.0000.0000.000
20B723LYS10.9170.96025.7650.1380.1380.0000.0000.0000.000
21B724ASP-1-0.852-0.92027.644-0.134-0.1340.0000.0000.0000.000
22B725PHE0-0.029-0.01328.7740.0110.0110.0000.0000.0000.000
23B726THR0-0.062-0.04929.1660.0110.0110.0000.0000.0000.000
24B727GLU-1-0.919-0.95331.542-0.096-0.0960.0000.0000.0000.000
25B728GLU-1-0.912-0.96132.453-0.108-0.1080.0000.0000.0000.000
26B729LEU0-0.066-0.03034.2470.0080.0080.0000.0000.0000.000
27B730ILE00.0180.00634.6590.0070.0070.0000.0000.0000.000
28B731GLU-1-0.895-0.94237.553-0.060-0.0600.0000.0000.0000.000
29B732LYS10.9330.96639.2870.0840.0840.0000.0000.0000.000
30B733VAL00.0150.00738.9750.0050.0050.0000.0000.0000.000
31B734LYS10.9250.96841.6900.0590.0590.0000.0000.0000.000
32B735LYS10.9510.96143.1490.0680.0680.0000.0000.0000.000
33B736TYR00.0060.00144.3330.0020.0020.0000.0000.0000.000
34B737LYS10.9430.96644.1190.0520.0520.0000.0000.0000.000
35B738ALA0-0.029-0.00147.4080.0020.0020.0000.0000.0000.000
36B739LEU00.0660.02949.0400.0020.0020.0000.0000.0000.000
37B740ALA0-0.0090.00049.2210.0020.0020.0000.0000.0000.000
38B741ARG10.8960.95451.2020.0370.0370.0000.0000.0000.000
39B742GLU-1-0.918-0.96653.297-0.037-0.0370.0000.0000.0000.000
40B743ALA00.0110.02154.2520.0020.0020.0000.0000.0000.000
41B744ALA0-0.0030.00554.5710.0010.0010.0000.0000.0000.000
42B745LEU0-0.023-0.02756.5200.0020.0020.0000.0000.0000.000
43B746SER00.0070.00259.0700.0010.0010.0000.0000.0000.000
44B747LYS10.9771.00159.2500.0310.0310.0000.0000.0000.000
45B748ILE0-0.014-0.01958.7940.0010.0010.0000.0000.0000.000
46B749GLY00.0170.00062.3480.0010.0010.0000.0000.0000.000
47B750GLU-1-0.936-0.95663.398-0.028-0.0280.0000.0000.0000.000
48B751LEU0-0.046-0.02562.3330.0010.0010.0000.0000.0000.000
49B752ALA00.010-0.00166.3530.0010.0010.0000.0000.0000.000
50B753SER0-0.038-0.02868.2040.0010.0010.0000.0000.0000.000
51B754GLU-1-0.902-0.95669.966-0.019-0.0190.0000.0000.0000.000
52B755ILE00.0460.04068.0420.0010.0010.0000.0000.0000.000
53B756PHE0-0.024-0.02772.0590.0010.0010.0000.0000.0000.000
54B757ALA00.0230.02873.8890.0010.0010.0000.0000.0000.000
55B758GLU-1-0.809-0.90374.148-0.018-0.0180.0000.0000.0000.000
56B759PHE0-0.072-0.05172.8920.0010.0010.0000.0000.0000.000
57B760THR0-0.111-0.06977.5650.0010.0010.0000.0000.0000.000
58B761GLU-1-0.920-0.95779.859-0.014-0.0140.0000.0000.0000.000
59B762GLY0-0.014-0.00879.5220.0000.0000.0000.0000.0000.000
60B763LYS10.7900.90680.5040.0150.0150.0000.0000.0000.000
61B764TYR0-0.030-0.03476.1310.0000.0000.0000.0000.0000.000
62B765SER00.0220.00775.5160.0000.0000.0000.0000.0000.000
63B766GLU-1-0.904-0.94870.000-0.025-0.0250.0000.0000.0000.000
64B767VAL0-0.034-0.01668.0900.0010.0010.0000.0000.0000.000
65B768VAL0-0.027-0.01266.159-0.001-0.0010.0000.0000.0000.000
66B769VAL00.0140.00361.7120.0010.0010.0000.0000.0000.000
67B770ARG10.8290.89861.5180.0260.0260.0000.0000.0000.000
68B771ALA0-0.005-0.00356.6170.0010.0010.0000.0000.0000.000
69B772GLU-1-0.871-0.94057.810-0.029-0.0290.0000.0000.0000.000
70B773GLU-1-0.897-0.96252.513-0.038-0.0380.0000.0000.0000.000
71B774ASN0-0.038-0.02554.9520.0010.0010.0000.0000.0000.000
72B775LYS10.8760.94956.2300.0280.0280.0000.0000.0000.000
73B776VAL00.0260.01059.083-0.001-0.0010.0000.0000.0000.000
74B777ARG10.8580.94761.2430.0270.0270.0000.0000.0000.000
75B778LEU00.0360.00964.4830.0000.0000.0000.0000.0000.000
76B779PHE0-0.043-0.02666.6880.0010.0010.0000.0000.0000.000
77B780VAL00.0440.03770.3290.0000.0000.0000.0000.0000.000
78B781VAL00.0110.02072.4440.0000.0000.0000.0000.0000.000
79B782TRP0-0.006-0.00574.9520.0000.0000.0000.0000.0000.000
80B783GLU-1-0.929-0.98078.669-0.017-0.0170.0000.0000.0000.000
81B784GLY00.0050.00777.0410.0000.0000.0000.0000.0000.000
82B785LYS10.9040.94975.4640.0180.0180.0000.0000.0000.000
83B786GLU-1-0.764-0.86469.081-0.024-0.0240.0000.0000.0000.000
84B787ARG10.8840.95673.2920.0180.0180.0000.0000.0000.000
85B788PRO00.0190.01972.1500.0000.0000.0000.0000.0000.000
86B789LEU00.1150.03569.6150.0010.0010.0000.0000.0000.000
87B790THR0-0.075-0.03373.7970.0000.0000.0000.0000.0000.000
88B791PHE00.0000.00376.5040.0010.0010.0000.0000.0000.000
89B792LEU0-0.0220.00974.9750.0000.0000.0000.0000.0000.000
90B793SER00.0180.00978.8570.0000.0000.0000.0000.0000.000
91B794GLY00.021-0.01079.2580.0000.0000.0000.0000.0000.000
92B795GLY00.0650.01278.4850.0000.0000.0000.0000.0000.000
93B796GLU-1-0.838-0.93078.241-0.016-0.0160.0000.0000.0000.000
94B797ARG10.8880.95774.9220.0150.0150.0000.0000.0000.000
95B798ILE0-0.0050.00973.663-0.001-0.0010.0000.0000.0000.000
96B799ALA00.0350.03173.5460.0000.0000.0000.0000.0000.000
97B800LEU00.0260.01270.767-0.001-0.0010.0000.0000.0000.000
98B801GLY0-0.025-0.01269.405-0.001-0.0010.0000.0000.0000.000
99B802LEU00.0060.00468.648-0.001-0.0010.0000.0000.0000.000
100B803ALA00.0440.01469.1660.0000.0000.0000.0000.0000.000
101B804PHE0-0.001-0.00462.276-0.001-0.0010.0000.0000.0000.000
102B805ARG10.8970.94961.0050.0210.0210.0000.0000.0000.000
103B806LEU00.0250.00264.394-0.001-0.0010.0000.0000.0000.000
104B807ALA00.0450.03464.623-0.001-0.0010.0000.0000.0000.000
105B808MET0-0.068-0.03560.542-0.001-0.0010.0000.0000.0000.000
106B809SER0-0.024-0.01260.238-0.001-0.0010.0000.0000.0000.000
107B810LEU00.0390.02961.010-0.001-0.0010.0000.0000.0000.000
108B811TYR0-0.051-0.01653.978-0.001-0.0010.0000.0000.0000.000
109B812LEU0-0.079-0.04354.646-0.001-0.0010.0000.0000.0000.000
110B813ALA0-0.009-0.00856.546-0.001-0.0010.0000.0000.0000.000
111B814GLY0-0.0210.00058.9250.0000.0000.0000.0000.0000.000
112B815GLU-1-0.953-0.99060.581-0.022-0.0220.0000.0000.0000.000
113B816ILE0-0.034-0.02963.3550.0000.0000.0000.0000.0000.000
114B817SER00.0260.02564.0420.0010.0010.0000.0000.0000.000
115B818LEU0-0.002-0.00964.2920.0010.0010.0000.0000.0000.000
116B819LEU0-0.022-0.00465.576-0.001-0.0010.0000.0000.0000.000
117B820ILE00.0020.00064.8760.0010.0010.0000.0000.0000.000
118B821LEU0-0.048-0.03367.095-0.001-0.0010.0000.0000.0000.000
119B822ASP-1-0.914-0.96567.747-0.013-0.0130.0000.0000.0000.000
120B823GLU-1-0.879-0.94869.616-0.012-0.0120.0000.0000.0000.000
121B824PRO0-0.032-0.00972.2490.0000.0000.0000.0000.0000.000
122B825THR0-0.047-0.05473.2230.0000.0000.0000.0000.0000.000
123B826PRO00.0170.04172.8650.0010.0010.0000.0000.0000.000
124B827TYR0-0.053-0.05673.7490.0000.0000.0000.0000.0000.000
125B828LEU00.0570.01579.0770.0000.0000.0000.0000.0000.000
126B829ASP-1-0.846-0.89481.728-0.012-0.0120.0000.0000.0000.000
127B830GLU-1-0.763-0.89983.594-0.011-0.0110.0000.0000.0000.000
128B831GLU-1-0.887-0.92782.727-0.013-0.0130.0000.0000.0000.000
129B832ARG10.8130.88577.0330.0130.0130.0000.0000.0000.000
130B833ARG10.7470.85580.6360.0110.0110.0000.0000.0000.000
131B834ARG10.9450.97181.7980.0100.0100.0000.0000.0000.000
132B835LYS10.9430.97880.7390.0140.0140.0000.0000.0000.000
133B836LEU0-0.012-0.00275.4610.0000.0000.0000.0000.0000.000
134B837ILE00.077-0.00278.801-0.001-0.0010.0000.0000.0000.000
135B838THR0-0.0240.01580.5230.0000.0000.0000.0000.0000.000
136B839ILE0-0.059-0.02576.1360.0000.0000.0000.0000.0000.000
137B840MET0-0.099-0.03874.8660.0000.0000.0000.0000.0000.000
138B841GLU-1-0.927-0.96777.779-0.013-0.0130.0000.0000.0000.000
139B842ARG10.9160.97479.6830.0140.0140.0000.0000.0000.000
140B843TYR0-0.038-0.02669.8860.0000.0000.0000.0000.0000.000
141B844LEU00.011-0.00872.5660.0000.0000.0000.0000.0000.000
142B845LYS10.9120.97774.7650.0130.0130.0000.0000.0000.000
143B846LYS10.8100.91673.6960.0180.0180.0000.0000.0000.000
144B847ILE0-0.060-0.01569.397-0.001-0.0010.0000.0000.0000.000
145B848PRO0-0.0300.00069.1860.0010.0010.0000.0000.0000.000
146B849GLN00.003-0.00469.3980.0000.0000.0000.0000.0000.000
147B850VAL00.0330.01470.136-0.001-0.0010.0000.0000.0000.000
148B851ILE0-0.047-0.02368.6910.0010.0010.0000.0000.0000.000
149B852LEU00.0090.00371.036-0.001-0.0010.0000.0000.0000.000
150B853VAL0-0.0090.00270.4110.0010.0010.0000.0000.0000.000
151B854SER00.0400.02573.2530.0000.0000.0000.0000.0000.000
152B855HIS0-0.0010.01076.0300.0010.0010.0000.0000.0000.000
153B856ASP-1-0.742-0.84378.986-0.011-0.0110.0000.0000.0000.000
154B857GLU-1-0.719-0.85180.925-0.009-0.0090.0000.0000.0000.000
155B858GLU-1-0.898-0.92783.415-0.011-0.0110.0000.0000.0000.000
156B859LEU00.0080.00177.6870.0000.0000.0000.0000.0000.000
157B860LYS10.7570.85381.8040.0090.0090.0000.0000.0000.000
158B861ASP-1-0.891-0.94083.673-0.010-0.0100.0000.0000.0000.000
159B862ALA0-0.046-0.00781.0030.0000.0000.0000.0000.0000.000
160B863ALA0-0.042-0.01279.7810.0000.0000.0000.0000.0000.000
161B864ASP-1-0.878-0.94379.233-0.012-0.0120.0000.0000.0000.000
162B865HIS10.7850.86578.1140.0110.0110.0000.0000.0000.000
163B866VAL00.0660.05179.4050.0000.0000.0000.0000.0000.000
164B867ILE0-0.005-0.01576.2850.0000.0000.0000.0000.0000.000
165B868ARG10.8450.91378.9020.0080.0080.0000.0000.0000.000
166B869ILE00.002-0.00274.6890.0000.0000.0000.0000.0000.000
167B870SER00.0070.01078.8630.0000.0000.0000.0000.0000.000
168B871LEU00.007-0.00476.3000.0000.0000.0000.0000.0000.000
169B872GLU-1-0.911-0.95580.088-0.005-0.0050.0000.0000.0000.000
170B873ASN0-0.049-0.03081.3270.0000.0000.0000.0000.0000.000
171B874GLY0-0.0030.00578.7760.0000.0000.0000.0000.0000.000
172B875SER0-0.036-0.01076.0850.0000.0000.0000.0000.0000.000
173B876SER00.013-0.00874.1960.0000.0000.0000.0000.0000.000
174B877LYS10.9560.99876.9670.0060.0060.0000.0000.0000.000
175B878VAL00.001-0.01476.2450.0000.0000.0000.0000.0000.000
176B879GLU-1-0.922-0.96379.488-0.007-0.0070.0000.0000.0000.000
177B880VAL0-0.042-0.02679.9760.0000.0000.0000.0000.0000.000
178B881VAL00.0130.01582.4570.0000.0000.0000.0000.0000.000
179B882SER00.0310.02781.8030.0000.0000.0000.0000.0000.000