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: MV3QZ

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 OptAll
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 -1629518.6335
FMO2-HF: Nuclear repulsion 1558906.973336
FMO2-HF: Total energy -70611.660165
FMO2-MP2: Total energy -70821.86223


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.
-4.866-0.8021.532-2.373-3.224-0.01
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 : 0.063 / q_NPA : 0.022
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].
3B706LYS10.8600.9103.884-0.9420.412-0.003-0.626-0.7260.002
4B707GLU-1-0.879-0.9312.366-6.689-4.4461.535-1.626-2.152-0.012
5B708ASN00.0350.0133.9230.4930.9600.000-0.121-0.3460.000
6B709ARG10.8460.9015.8070.6280.6280.0000.0000.0000.000
7B710GLU-1-0.760-0.8517.736-0.309-0.3090.0000.0000.0000.000
8B711ARG10.8180.8737.7410.8990.8990.0000.0000.0000.000
9B712VAL00.0220.0139.4260.1750.1750.0000.0000.0000.000
10B713LYS10.8460.90011.8760.4840.4840.0000.0000.0000.000
11B714LYS10.8150.89712.7130.5250.5250.0000.0000.0000.000
12B715GLU-1-0.742-0.84313.960-0.385-0.3850.0000.0000.0000.000
13B716ILE00.0090.01315.8920.0460.0460.0000.0000.0000.000
14B717LYS10.9740.98717.0190.3300.3300.0000.0000.0000.000
15B718ASP-1-0.839-0.89717.778-0.314-0.3140.0000.0000.0000.000
16B719LEU0-0.009-0.00719.0420.0220.0220.0000.0000.0000.000
17B720GLU-1-0.887-0.94321.816-0.105-0.1050.0000.0000.0000.000
18B721LYS10.8640.92521.0510.2540.2540.0000.0000.0000.000
19B722ALA0-0.020-0.01324.1000.0110.0110.0000.0000.0000.000
20B723LYS10.8120.91425.8630.1120.1120.0000.0000.0000.000
21B724ASP-1-0.837-0.90827.687-0.109-0.1090.0000.0000.0000.000
22B725PHE0-0.011-0.00428.8520.0080.0080.0000.0000.0000.000
23B726THR0-0.035-0.03629.2930.0090.0090.0000.0000.0000.000
24B727GLU-1-0.878-0.93231.453-0.072-0.0720.0000.0000.0000.000
25B728GLU-1-0.941-0.96832.931-0.093-0.0930.0000.0000.0000.000
26B729LEU0-0.050-0.01934.2220.0060.0060.0000.0000.0000.000
27B730ILE00.0310.00634.7960.0060.0060.0000.0000.0000.000
28B731GLU-1-0.743-0.84237.783-0.044-0.0440.0000.0000.0000.000
29B732LYS10.9490.97338.7540.0780.0780.0000.0000.0000.000
30B733VAL00.003-0.00439.2690.0040.0040.0000.0000.0000.000
31B734LYS10.8120.89441.7230.0490.0490.0000.0000.0000.000
32B735LYS10.8430.90343.1410.0550.0550.0000.0000.0000.000
33B736TYR00.0090.00444.4440.0020.0020.0000.0000.0000.000
34B737LYS10.9470.95944.1150.0420.0420.0000.0000.0000.000
35B738ALA0-0.0170.02247.5880.0020.0020.0000.0000.0000.000
36B739LEU00.0470.01848.4040.0010.0010.0000.0000.0000.000
37B740ALA00.0130.00649.3760.0010.0010.0000.0000.0000.000
38B741ARG10.8340.91651.3580.0300.0300.0000.0000.0000.000
39B742GLU-1-0.831-0.93353.458-0.031-0.0310.0000.0000.0000.000
40B743ALA0-0.0040.01854.2460.0010.0010.0000.0000.0000.000
41B744ALA00.0010.00754.6970.0010.0010.0000.0000.0000.000
42B745LEU0-0.007-0.01956.6740.0010.0010.0000.0000.0000.000
43B746SER0-0.013-0.01659.1790.0010.0010.0000.0000.0000.000
44B747LYS10.7900.89159.1970.0280.0280.0000.0000.0000.000
45B748ILE00.007-0.00758.7990.0010.0010.0000.0000.0000.000
46B749GLY00.0370.01162.5440.0010.0010.0000.0000.0000.000
47B750GLU-1-0.813-0.87963.152-0.026-0.0260.0000.0000.0000.000
48B751LEU0-0.018-0.00762.5200.0010.0010.0000.0000.0000.000
49B752ALA00.000-0.00266.5820.0010.0010.0000.0000.0000.000
50B753SER0-0.046-0.04468.3830.0010.0010.0000.0000.0000.000
51B754GLU-1-0.915-0.95170.253-0.018-0.0180.0000.0000.0000.000
52B755ILE00.0100.01768.4520.0010.0010.0000.0000.0000.000
53B756PHE00.017-0.00872.3800.0010.0010.0000.0000.0000.000
54B757ALA00.0210.03074.2020.0010.0010.0000.0000.0000.000
55B758GLU-1-0.770-0.87375.087-0.015-0.0150.0000.0000.0000.000
56B759PHE0-0.068-0.05473.0650.0010.0010.0000.0000.0000.000
57B760THR0-0.082-0.05477.8220.0010.0010.0000.0000.0000.000
58B761GLU-1-0.840-0.88980.163-0.012-0.0120.0000.0000.0000.000
59B762GLY00.0100.01379.5980.0000.0000.0000.0000.0000.000
60B763LYS10.7470.88880.6350.0130.0130.0000.0000.0000.000
61B764TYR0-0.027-0.05576.4060.0000.0000.0000.0000.0000.000
62B765SER00.0390.01675.3750.0000.0000.0000.0000.0000.000
63B766GLU-1-0.917-0.96169.814-0.022-0.0220.0000.0000.0000.000
64B767VAL0-0.038-0.01568.0680.0010.0010.0000.0000.0000.000
65B768VAL0-0.0130.00666.238-0.001-0.0010.0000.0000.0000.000
66B769VAL00.0080.01062.0540.0010.0010.0000.0000.0000.000
67B770ARG10.7890.85162.0020.0210.0210.0000.0000.0000.000
68B771ALA00.0120.01357.1590.0010.0010.0000.0000.0000.000
69B772GLU-1-0.794-0.87258.225-0.022-0.0220.0000.0000.0000.000
70B773GLU-1-0.838-0.90852.470-0.029-0.0290.0000.0000.0000.000
71B774ASN0-0.045-0.03054.8040.0020.0020.0000.0000.0000.000
72B775LYS10.8250.92456.1000.0220.0220.0000.0000.0000.000
73B776VAL00.0310.00758.920-0.001-0.0010.0000.0000.0000.000
74B777ARG10.7650.86161.2730.0210.0210.0000.0000.0000.000
75B778LEU00.0370.01464.766-0.001-0.0010.0000.0000.0000.000
76B779PHE0-0.052-0.02366.6920.0010.0010.0000.0000.0000.000
77B780VAL00.0350.02070.5580.0000.0000.0000.0000.0000.000
78B781VAL00.0130.01372.3080.0000.0000.0000.0000.0000.000
79B782TRP0-0.021-0.02474.9230.0000.0000.0000.0000.0000.000
80B783GLU-1-0.822-0.89478.690-0.014-0.0140.0000.0000.0000.000
81B784GLY00.0250.01876.9150.0000.0000.0000.0000.0000.000
82B785LYS10.9060.95375.2910.0150.0150.0000.0000.0000.000
83B786GLU-1-0.724-0.81768.943-0.020-0.0200.0000.0000.0000.000
84B787ARG10.7730.87573.3050.0150.0150.0000.0000.0000.000
85B788PRO00.0070.01272.4660.0000.0000.0000.0000.0000.000
86B789LEU00.1010.03269.6600.0010.0010.0000.0000.0000.000
87B790THR0-0.054-0.03474.0030.0000.0000.0000.0000.0000.000
88B791PHE0-0.006-0.00376.8780.0010.0010.0000.0000.0000.000
89B792LEU00.0130.03574.8050.0000.0000.0000.0000.0000.000
90B793SER0-0.015-0.02478.9950.0000.0000.0000.0000.0000.000
91B794GLY00.019-0.00279.5000.0000.0000.0000.0000.0000.000
92B795GLY00.0550.00778.6480.0000.0000.0000.0000.0000.000
93B796GLU-1-0.763-0.87078.108-0.013-0.0130.0000.0000.0000.000
94B797ARG10.8430.92174.8990.0110.0110.0000.0000.0000.000
95B798ILE00.0150.01473.6090.0000.0000.0000.0000.0000.000
96B799ALA00.0450.03373.4370.0000.0000.0000.0000.0000.000
97B800LEU00.0150.00570.824-0.001-0.0010.0000.0000.0000.000
98B801GLY0-0.027-0.01269.409-0.001-0.0010.0000.0000.0000.000
99B802LEU00.0100.00568.682-0.001-0.0010.0000.0000.0000.000
100B803ALA00.0410.02169.281-0.001-0.0010.0000.0000.0000.000
101B804PHE00.022-0.00362.408-0.001-0.0010.0000.0000.0000.000
102B805ARG10.8710.92361.8340.0170.0170.0000.0000.0000.000
103B806LEU00.0210.01664.592-0.001-0.0010.0000.0000.0000.000
104B807ALA00.0410.02364.909-0.001-0.0010.0000.0000.0000.000
105B808MET0-0.054-0.02960.696-0.001-0.0010.0000.0000.0000.000
106B809SER0-0.016-0.00360.262-0.001-0.0010.0000.0000.0000.000
107B810LEU00.0320.02960.978-0.001-0.0010.0000.0000.0000.000
108B811TYR0-0.030-0.01854.032-0.001-0.0010.0000.0000.0000.000
109B812LEU0-0.077-0.03454.408-0.001-0.0010.0000.0000.0000.000
110B813ALA00.0040.00056.384-0.001-0.0010.0000.0000.0000.000
111B814GLY0-0.033-0.00458.8080.0000.0000.0000.0000.0000.000
112B815GLU-1-0.849-0.91160.717-0.019-0.0190.0000.0000.0000.000
113B816ILE0-0.032-0.02863.3540.0000.0000.0000.0000.0000.000
114B817SER0-0.025-0.02763.9650.0010.0010.0000.0000.0000.000
115B818LEU0-0.047-0.02864.1390.0010.0010.0000.0000.0000.000
116B819LEU0-0.022-0.00965.684-0.001-0.0010.0000.0000.0000.000
117B820ILE0-0.006-0.01264.8850.0010.0010.0000.0000.0000.000
118B821LEU0-0.039-0.02367.334-0.001-0.0010.0000.0000.0000.000
119B822ASP-1-0.878-0.95167.925-0.009-0.0090.0000.0000.0000.000
120B823GLU-1-0.840-0.89469.820-0.008-0.0080.0000.0000.0000.000
121B824PRO0-0.0080.00972.5260.0000.0000.0000.0000.0000.000
122B825THR0-0.036-0.05773.5610.0000.0000.0000.0000.0000.000
123B826PRO00.0020.02973.1300.0010.0010.0000.0000.0000.000
124B827TYR0-0.046-0.04774.1040.0000.0000.0000.0000.0000.000
125B828LEU00.0320.01279.4640.0000.0000.0000.0000.0000.000
126B829ASP-1-0.829-0.88081.879-0.009-0.0090.0000.0000.0000.000
127B830GLU-1-0.776-0.90283.634-0.008-0.0080.0000.0000.0000.000
128B831GLU-1-0.814-0.86482.807-0.011-0.0110.0000.0000.0000.000
129B832ARG10.7800.85077.3110.0090.0090.0000.0000.0000.000
130B833ARG10.7320.84580.4740.0070.0070.0000.0000.0000.000
131B834ARG10.9840.98881.7320.0080.0080.0000.0000.0000.000
132B835LYS10.8480.93281.4910.0110.0110.0000.0000.0000.000
133B836LEU0-0.0030.00375.1610.0000.0000.0000.0000.0000.000
134B837ILE00.0500.00878.8070.0000.0000.0000.0000.0000.000
135B838THR0-0.022-0.00680.6490.0000.0000.0000.0000.0000.000
136B839ILE0-0.062-0.02076.3840.0000.0000.0000.0000.0000.000
137B840MET0-0.063-0.03074.9480.0000.0000.0000.0000.0000.000
138B841GLU-1-0.950-0.97777.573-0.011-0.0110.0000.0000.0000.000
139B842ARG10.8550.90980.4160.0120.0120.0000.0000.0000.000
140B843TYR0-0.022-0.00870.8230.0000.0000.0000.0000.0000.000
141B844LEU0-0.011-0.01772.6370.0000.0000.0000.0000.0000.000
142B845LYS10.8170.90474.5530.0110.0110.0000.0000.0000.000
143B846LYS10.7660.86873.1810.0160.0160.0000.0000.0000.000
144B847ILE0-0.047-0.01069.267-0.001-0.0010.0000.0000.0000.000
145B848PRO0-0.039-0.01469.3930.0010.0010.0000.0000.0000.000
146B849GLN0-0.0060.00269.3620.0000.0000.0000.0000.0000.000
147B850VAL00.0170.00270.081-0.001-0.0010.0000.0000.0000.000
148B851ILE0-0.043-0.01368.4620.0010.0010.0000.0000.0000.000
149B852LEU00.0220.00971.3020.0000.0000.0000.0000.0000.000
150B853VAL0-0.028-0.01070.4350.0000.0000.0000.0000.0000.000
151B854SER0-0.014-0.04973.3540.0000.0000.0000.0000.0000.000
152B855HIS0-0.041-0.00976.0320.0010.0010.0000.0000.0000.000
153B856ASP-1-0.759-0.83579.138-0.008-0.0080.0000.0000.0000.000
154B857GLU-1-0.740-0.85281.093-0.006-0.0060.0000.0000.0000.000
155B858GLU-1-0.875-0.91883.177-0.008-0.0080.0000.0000.0000.000
156B859LEU0-0.002-0.00477.5190.0000.0000.0000.0000.0000.000
157B860LYS10.7730.87081.4870.0060.0060.0000.0000.0000.000
158B861ASP-1-0.903-0.95383.499-0.008-0.0080.0000.0000.0000.000
159B862ALA00.0130.02081.0040.0000.0000.0000.0000.0000.000
160B863ALA0-0.020-0.00379.451-0.001-0.0010.0000.0000.0000.000
161B864ASP-1-0.811-0.89579.304-0.010-0.0100.0000.0000.0000.000
162B865HIS10.7730.87177.4220.0100.0100.0000.0000.0000.000
163B866VAL00.0740.05879.4610.0000.0000.0000.0000.0000.000
164B867ILE0-0.023-0.02076.5890.0000.0000.0000.0000.0000.000
165B868ARG10.8570.92279.0180.0050.0050.0000.0000.0000.000
166B869ILE00.004-0.00774.5010.0000.0000.0000.0000.0000.000
167B870SER00.0010.00478.7330.0000.0000.0000.0000.0000.000
168B871LEU00.0240.00276.1870.0000.0000.0000.0000.0000.000
169B872GLU-1-0.797-0.88080.130-0.003-0.0030.0000.0000.0000.000
170B873ASN0-0.048-0.03280.9060.0000.0000.0000.0000.0000.000
171B874GLY00.0210.02078.9760.0000.0000.0000.0000.0000.000
172B875SER0-0.063-0.02576.3200.0000.0000.0000.0000.0000.000
173B876SER00.026-0.00473.7520.0000.0000.0000.0000.0000.000
174B877LYS10.8060.90876.6610.0030.0030.0000.0000.0000.000
175B878VAL00.012-0.00875.9960.0000.0000.0000.0000.0000.000
176B879GLU-1-0.900-0.95279.356-0.005-0.0050.0000.0000.0000.000
177B880VAL0-0.027-0.02079.7040.0000.0000.0000.0000.0000.000
178B881VAL00.0100.01882.2690.0000.0000.0000.0000.0000.000
179B882SER0-0.0030.00081.6350.0000.0000.0000.0000.0000.000