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: 94G12

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 OptHSide
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 -1630030.225069
FMO2-HF: Nuclear repulsion 1559419.127884
FMO2-HF: Total energy -70611.097185
FMO2-MP2: Total energy -70821.372992


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.
-4.528-0.5841.814-2.343-3.414-0.008
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 : 0.048 / q_NPA : 0.014
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].
3B706LYS10.8750.9223.766-0.7370.685-0.007-0.627-0.7870.003
4B707GLU-1-0.877-0.9422.271-7.013-4.9631.820-1.607-2.263-0.011
5B708ASN00.0310.0203.9620.5811.0530.001-0.109-0.3640.000
6B709ARG10.8580.9155.4440.8610.8610.0000.0000.0000.000
7B710GLU-1-0.780-0.8667.309-0.342-0.3420.0000.0000.0000.000
8B711ARG10.8260.8927.9010.8630.8630.0000.0000.0000.000
9B712VAL00.0370.0119.6440.1990.1990.0000.0000.0000.000
10B713LYS10.8590.91411.6280.5740.5740.0000.0000.0000.000
11B714LYS10.8540.91312.5190.5520.5520.0000.0000.0000.000
12B715GLU-1-0.793-0.87013.864-0.337-0.3370.0000.0000.0000.000
13B716ILE00.0040.00415.6400.0510.0510.0000.0000.0000.000
14B717LYS10.9640.98816.9650.3410.3410.0000.0000.0000.000
15B718ASP-1-0.838-0.89917.692-0.320-0.3200.0000.0000.0000.000
16B719LEU00.0070.00418.9820.0260.0260.0000.0000.0000.000
17B720GLU-1-0.881-0.94021.752-0.122-0.1220.0000.0000.0000.000
18B721LYS10.8530.92421.0630.2570.2570.0000.0000.0000.000
19B722ALA0-0.021-0.01524.1310.0140.0140.0000.0000.0000.000
20B723LYS10.8190.91125.7860.1230.1230.0000.0000.0000.000
21B724ASP-1-0.828-0.90827.627-0.115-0.1150.0000.0000.0000.000
22B725PHE0-0.028-0.01028.7640.0090.0090.0000.0000.0000.000
23B726THR0-0.050-0.05229.1180.0100.0100.0000.0000.0000.000
24B727GLU-1-0.878-0.92431.492-0.079-0.0790.0000.0000.0000.000
25B728GLU-1-0.933-0.96632.843-0.096-0.0960.0000.0000.0000.000
26B729LEU0-0.057-0.02534.3900.0070.0070.0000.0000.0000.000
27B730ILE00.0270.00734.5700.0070.0070.0000.0000.0000.000
28B731GLU-1-0.764-0.86137.582-0.048-0.0480.0000.0000.0000.000
29B732LYS10.9580.98139.3010.0770.0770.0000.0000.0000.000
30B733VAL00.0190.00739.0930.0040.0040.0000.0000.0000.000
31B734LYS10.8340.91041.7090.0530.0530.0000.0000.0000.000
32B735LYS10.8600.91743.0510.0580.0580.0000.0000.0000.000
33B736TYR00.009-0.00144.3530.0020.0020.0000.0000.0000.000
34B737LYS10.9530.97144.0750.0440.0440.0000.0000.0000.000
35B738ALA0-0.0210.00347.4320.0020.0020.0000.0000.0000.000
36B739LEU00.0630.02848.7170.0010.0010.0000.0000.0000.000
37B740ALA0-0.011-0.00249.2100.0010.0010.0000.0000.0000.000
38B741ARG10.8860.94051.2170.0310.0310.0000.0000.0000.000
39B742GLU-1-0.922-0.96853.322-0.032-0.0320.0000.0000.0000.000
40B743ALA00.0110.02054.2210.0010.0010.0000.0000.0000.000
41B744ALA00.0040.00854.5710.0010.0010.0000.0000.0000.000
42B745LEU0-0.014-0.02356.5390.0010.0010.0000.0000.0000.000
43B746SER0-0.006-0.00559.0870.0010.0010.0000.0000.0000.000
44B747LYS10.8140.91159.1810.0270.0270.0000.0000.0000.000
45B748ILE00.005-0.01058.6320.0010.0010.0000.0000.0000.000
46B749GLY00.0260.00162.3710.0010.0010.0000.0000.0000.000
47B750GLU-1-0.820-0.88562.950-0.025-0.0250.0000.0000.0000.000
48B751LEU0-0.024-0.01462.3720.0010.0010.0000.0000.0000.000
49B752ALA00.005-0.00166.3760.0010.0010.0000.0000.0000.000
50B753SER0-0.033-0.03368.2290.0010.0010.0000.0000.0000.000
51B754GLU-1-0.925-0.95769.982-0.017-0.0170.0000.0000.0000.000
52B755ILE00.0260.02467.9760.0010.0010.0000.0000.0000.000
53B756PHE0-0.005-0.01972.0820.0010.0010.0000.0000.0000.000
54B757ALA00.0290.03173.9170.0010.0010.0000.0000.0000.000
55B758GLU-1-0.773-0.86474.583-0.015-0.0150.0000.0000.0000.000
56B759PHE0-0.078-0.05072.9110.0010.0010.0000.0000.0000.000
57B760THR0-0.096-0.06277.6260.0010.0010.0000.0000.0000.000
58B761GLU-1-0.832-0.88979.889-0.012-0.0120.0000.0000.0000.000
59B762GLY0-0.009-0.00579.5390.0000.0000.0000.0000.0000.000
60B763LYS10.7950.90580.5210.0130.0130.0000.0000.0000.000
61B764TYR0-0.038-0.04976.2340.0000.0000.0000.0000.0000.000
62B765SER00.0420.01775.5570.0000.0000.0000.0000.0000.000
63B766GLU-1-0.934-0.96670.166-0.021-0.0210.0000.0000.0000.000
64B767VAL0-0.025-0.01268.0770.0010.0010.0000.0000.0000.000
65B768VAL0-0.045-0.01866.049-0.001-0.0010.0000.0000.0000.000
66B769VAL00.0160.00961.8450.0010.0010.0000.0000.0000.000
67B770ARG10.8010.86061.5150.0220.0220.0000.0000.0000.000
68B771ALA00.0040.00856.6960.0010.0010.0000.0000.0000.000
69B772GLU-1-0.779-0.86257.873-0.024-0.0240.0000.0000.0000.000
70B773GLU-1-0.869-0.92852.437-0.031-0.0310.0000.0000.0000.000
71B774ASN0-0.048-0.03455.0130.0010.0010.0000.0000.0000.000
72B775LYS10.8580.93156.2850.0240.0240.0000.0000.0000.000
73B776VAL00.0210.01159.004-0.001-0.0010.0000.0000.0000.000
74B777ARG10.7750.87261.2870.0220.0220.0000.0000.0000.000
75B778LEU00.0300.00764.5230.0000.0000.0000.0000.0000.000
76B779PHE0-0.046-0.02866.6270.0010.0010.0000.0000.0000.000
77B780VAL00.0490.04170.3620.0000.0000.0000.0000.0000.000
78B781VAL00.0100.01972.3840.0000.0000.0000.0000.0000.000
79B782TRP0-0.051-0.02674.9730.0000.0000.0000.0000.0000.000
80B783GLU-1-0.799-0.91178.690-0.014-0.0140.0000.0000.0000.000
81B784GLY00.0100.00977.0510.0000.0000.0000.0000.0000.000
82B785LYS10.9150.95875.4950.0160.0160.0000.0000.0000.000
83B786GLU-1-0.741-0.82868.929-0.021-0.0210.0000.0000.0000.000
84B787ARG10.7930.89773.3160.0150.0150.0000.0000.0000.000
85B788PRO00.0220.02172.1990.0000.0000.0000.0000.0000.000
86B789LEU00.1220.03869.5890.0010.0010.0000.0000.0000.000
87B790THR0-0.057-0.02873.8410.0000.0000.0000.0000.0000.000
88B791PHE0-0.019-0.00576.5530.0010.0010.0000.0000.0000.000
89B792LEU0-0.0070.01974.9950.0000.0000.0000.0000.0000.000
90B793SER00.002-0.00678.9000.0000.0000.0000.0000.0000.000
91B794GLY00.026-0.00779.3130.0000.0000.0000.0000.0000.000
92B795GLY00.034-0.00378.5380.0000.0000.0000.0000.0000.000
93B796GLU-1-0.814-0.90178.368-0.013-0.0130.0000.0000.0000.000
94B797ARG10.8640.94174.8550.0120.0120.0000.0000.0000.000
95B798ILE00.0060.01173.7110.0000.0000.0000.0000.0000.000
96B799ALA00.0410.03573.5940.0000.0000.0000.0000.0000.000
97B800LEU00.0240.01070.8340.0000.0000.0000.0000.0000.000
98B801GLY0-0.022-0.01169.453-0.001-0.0010.0000.0000.0000.000
99B802LEU00.0070.00368.695-0.001-0.0010.0000.0000.0000.000
100B803ALA00.0390.01669.2080.0000.0000.0000.0000.0000.000
101B804PHE0-0.002-0.00862.219-0.001-0.0010.0000.0000.0000.000
102B805ARG10.8820.93161.5130.0170.0170.0000.0000.0000.000
103B806LEU00.0280.01364.436-0.001-0.0010.0000.0000.0000.000
104B807ALA00.0420.02864.735-0.001-0.0010.0000.0000.0000.000
105B808MET0-0.060-0.02960.488-0.001-0.0010.0000.0000.0000.000
106B809SER0-0.009-0.00460.273-0.001-0.0010.0000.0000.0000.000
107B810LEU00.0330.03061.042-0.001-0.0010.0000.0000.0000.000
108B811TYR0-0.041-0.01454.051-0.001-0.0010.0000.0000.0000.000
109B812LEU0-0.083-0.04054.298-0.001-0.0010.0000.0000.0000.000
110B813ALA0-0.006-0.00756.574-0.001-0.0010.0000.0000.0000.000
111B814GLY0-0.018-0.00158.9530.0000.0000.0000.0000.0000.000
112B815GLU-1-0.881-0.92760.599-0.018-0.0180.0000.0000.0000.000
113B816ILE0-0.030-0.03163.3830.0000.0000.0000.0000.0000.000
114B817SER0-0.030-0.02264.0980.0010.0010.0000.0000.0000.000
115B818LEU0-0.026-0.02364.3410.0010.0010.0000.0000.0000.000
116B819LEU0-0.025-0.00765.619-0.001-0.0010.0000.0000.0000.000
117B820ILE00.0050.00065.0430.0010.0010.0000.0000.0000.000
118B821LEU0-0.045-0.02967.153-0.001-0.0010.0000.0000.0000.000
119B822ASP-1-0.916-0.96667.690-0.009-0.0090.0000.0000.0000.000
120B823GLU-1-0.826-0.89869.685-0.008-0.0080.0000.0000.0000.000
121B824PRO0-0.021-0.00472.3180.0000.0000.0000.0000.0000.000
122B825THR0-0.026-0.05073.2860.0000.0000.0000.0000.0000.000
123B826PRO0-0.0110.02772.8790.0010.0010.0000.0000.0000.000
124B827TYR0-0.040-0.04773.8860.0000.0000.0000.0000.0000.000
125B828LEU00.0360.00879.1470.0000.0000.0000.0000.0000.000
126B829ASP-1-0.833-0.87981.783-0.009-0.0090.0000.0000.0000.000
127B830GLU-1-0.769-0.89383.659-0.008-0.0080.0000.0000.0000.000
128B831GLU-1-0.850-0.90482.969-0.011-0.0110.0000.0000.0000.000
129B832ARG10.8090.87477.2960.0100.0100.0000.0000.0000.000
130B833ARG10.7630.85880.6910.0080.0080.0000.0000.0000.000
131B834ARG10.9660.97581.8570.0080.0080.0000.0000.0000.000
132B835LYS10.9090.96681.0150.0120.0120.0000.0000.0000.000
133B836LEU0-0.019-0.00275.3220.0000.0000.0000.0000.0000.000
134B837ILE00.062-0.00178.8480.0000.0000.0000.0000.0000.000
135B838THR0-0.0250.00080.5740.0000.0000.0000.0000.0000.000
136B839ILE0-0.044-0.01776.2760.0000.0000.0000.0000.0000.000
137B840MET0-0.081-0.02974.7270.0000.0000.0000.0000.0000.000
138B841GLU-1-0.967-0.98377.824-0.010-0.0100.0000.0000.0000.000
139B842ARG10.8400.90480.0290.0120.0120.0000.0000.0000.000
140B843TYR0-0.001-0.00970.4830.0000.0000.0000.0000.0000.000
141B844LEU00.001-0.01172.5920.0000.0000.0000.0000.0000.000
142B845LYS10.8350.92674.8010.0100.0100.0000.0000.0000.000
143B846LYS10.7610.87073.6470.0150.0150.0000.0000.0000.000
144B847ILE0-0.058-0.02069.430-0.001-0.0010.0000.0000.0000.000
145B848PRO0-0.0250.00069.3190.0010.0010.0000.0000.0000.000
146B849GLN0-0.001-0.00369.4710.0000.0000.0000.0000.0000.000
147B850VAL00.0190.00470.179-0.001-0.0010.0000.0000.0000.000
148B851ILE0-0.048-0.02268.6750.0010.0010.0000.0000.0000.000
149B852LEU00.0210.01271.0950.0000.0000.0000.0000.0000.000
150B853VAL0-0.020-0.00470.3540.0010.0010.0000.0000.0000.000
151B854SER00.006-0.02973.3220.0000.0000.0000.0000.0000.000
152B855HIS0-0.035-0.00276.1030.0010.0010.0000.0000.0000.000
153B856ASP-1-0.767-0.84879.039-0.008-0.0080.0000.0000.0000.000
154B857GLU-1-0.734-0.84880.997-0.006-0.0060.0000.0000.0000.000
155B858GLU-1-0.884-0.92083.405-0.008-0.0080.0000.0000.0000.000
156B859LEU00.0070.00577.7740.0000.0000.0000.0000.0000.000
157B860LYS10.7710.85981.8610.0060.0060.0000.0000.0000.000
158B861ASP-1-0.926-0.95883.733-0.008-0.0080.0000.0000.0000.000
159B862ALA00.0030.01481.0470.0000.0000.0000.0000.0000.000
160B863ALA0-0.028-0.00779.8930.0000.0000.0000.0000.0000.000
161B864ASP-1-0.821-0.89979.281-0.010-0.0100.0000.0000.0000.000
162B865HIS10.7810.87177.4800.0090.0090.0000.0000.0000.000
163B866VAL00.0740.05679.4630.0000.0000.0000.0000.0000.000
164B867ILE0-0.010-0.01676.3600.0000.0000.0000.0000.0000.000
165B868ARG10.8700.92778.9740.0050.0050.0000.0000.0000.000
166B869ILE0-0.005-0.00774.6870.0000.0000.0000.0000.0000.000
167B870SER00.0210.01978.9450.0000.0000.0000.0000.0000.000
168B871LEU00.012-0.00476.3380.0000.0000.0000.0000.0000.000
169B872GLU-1-0.910-0.95780.183-0.003-0.0030.0000.0000.0000.000
170B873ASN0-0.054-0.03781.4250.0000.0000.0000.0000.0000.000
171B874GLY00.0040.00978.8830.0000.0000.0000.0000.0000.000
172B875SER0-0.0180.00176.3620.0000.0000.0000.0000.0000.000
173B876SER0-0.005-0.01874.2400.0000.0000.0000.0000.0000.000
174B877LYS10.9380.99477.0590.0030.0030.0000.0000.0000.000
175B878VAL00.002-0.01376.2510.0000.0000.0000.0000.0000.000
176B879GLU-1-0.918-0.96379.568-0.004-0.0040.0000.0000.0000.000
177B880VAL0-0.032-0.02579.9910.0000.0000.0000.0000.0000.000
178B881VAL00.0030.01082.5250.0000.0000.0000.0000.0000.000
179B882SER00.0120.01081.8610.0000.0000.0000.0000.0000.000