FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 6NN9Z

Calculation Name: 5J1H-B-Xray372

Preferred Name: Plectin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5J1H

Chain ID: B

ChEMBL ID: CHEMBL1293240

UniProt ID: Q15149

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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1756728.66786
FMO2-HF: Nuclear repulsion 1683550.774469
FMO2-HF: Total energy -73177.893391
FMO2-MP2: Total energy -73393.03839


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:750:ALA)


Summations of interaction energy for fragment #1(B:750: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.
-6.167-2.6490.073-1.504-2.0860.007
Interaction energy analysis for fragmet #1(B:750:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.006
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].
3B752ALA00.0170.0043.482-2.308-0.1010.023-1.098-1.1320.005
4B753GLN0-0.025-0.0063.370-2.721-1.6900.051-0.359-0.7230.002
5B754PHE0-0.0100.0004.689-0.910-0.736-0.001-0.030-0.1420.000
6B755PHE00.035-0.0036.524-0.037-0.0370.0000.0000.0000.000
7B756SER0-0.0130.0078.245-0.126-0.1260.0000.0000.0000.000
8B757ASP-1-0.732-0.8639.1940.2210.2210.0000.0000.0000.000
9B758VAL0-0.017-0.00610.810-0.075-0.0750.0000.0000.0000.000
10B759ARG10.9250.96612.621-0.350-0.3500.0000.0000.0000.000
11B760GLU-1-0.934-0.96513.4860.2260.2260.0000.0000.0000.000
12B761ALA00.0150.00715.112-0.039-0.0390.0000.0000.0000.000
13B762GLU-1-0.897-0.93816.9330.1450.1450.0000.0000.0000.000
14B763GLY0-0.011-0.00518.601-0.015-0.0150.0000.0000.0000.000
15B764GLN0-0.009-0.01318.128-0.006-0.0060.0000.0000.0000.000
16B765LEU00.0310.02920.910-0.015-0.0150.0000.0000.0000.000
17B766GLN00.0030.01322.986-0.010-0.0100.0000.0000.0000.000
18B767LYS10.8150.87224.238-0.118-0.1180.0000.0000.0000.000
19B768LEU00.0430.02125.507-0.006-0.0060.0000.0000.0000.000
20B769GLN00.0370.02227.190-0.003-0.0030.0000.0000.0000.000
21B770GLU-1-0.935-0.96328.5750.0880.0880.0000.0000.0000.000
22B771ALA0-0.0190.00130.191-0.004-0.0040.0000.0000.0000.000
23B772LEU00.0370.01930.778-0.004-0.0040.0000.0000.0000.000
24B773ARG10.9230.95730.682-0.063-0.0630.0000.0000.0000.000
25B774ARG10.9230.98231.176-0.066-0.0660.0000.0000.0000.000
26B775LYS10.8250.90333.646-0.043-0.0430.0000.0000.0000.000
27B776TYR0-0.054-0.07034.440-0.001-0.0010.0000.0000.0000.000
28B777SER0-0.016-0.00638.306-0.002-0.0020.0000.0000.0000.000
29B778CYS0-0.064-0.02240.7450.0010.0010.0000.0000.0000.000
30B779ASP-1-0.773-0.85944.3690.0260.0260.0000.0000.0000.000
31B780ARG10.8140.88647.728-0.019-0.0190.0000.0000.0000.000
32B781SER0-0.103-0.06749.777-0.001-0.0010.0000.0000.0000.000
33B782ALA0-0.0110.00647.6300.0000.0000.0000.0000.0000.000
34B783THR00.013-0.00249.622-0.001-0.0010.0000.0000.0000.000
35B784VAL00.0620.01449.8280.0000.0000.0000.0000.0000.000
36B785THR00.0390.00949.7140.0000.0000.0000.0000.0000.000
37B786ARG10.9881.01042.512-0.028-0.0280.0000.0000.0000.000
38B787LEU00.000-0.00245.3360.0010.0010.0000.0000.0000.000
39B788GLU-1-0.922-0.96944.8190.0130.0130.0000.0000.0000.000
40B789ASP-1-0.915-0.94943.8860.0190.0190.0000.0000.0000.000
41B790LEU0-0.048-0.03340.4030.0010.0010.0000.0000.0000.000
42B791LEU0-0.027-0.02340.0090.0010.0010.0000.0000.0000.000
43B792GLN0-0.041-0.01940.172-0.003-0.0030.0000.0000.0000.000
44B793ASP-1-0.851-0.92337.6120.0250.0250.0000.0000.0000.000
45B794ALA0-0.0440.02435.9310.0020.0020.0000.0000.0000.000
46B795GLN0-0.024-0.02234.8330.0000.0000.0000.0000.0000.000
47B796ASP-1-0.886-0.92531.7710.0280.0280.0000.0000.0000.000
48B797GLU-1-0.784-0.91030.4390.0400.0400.0000.0000.0000.000
49B798LYS10.7980.91429.558-0.012-0.0120.0000.0000.0000.000
50B799GLU-1-0.847-0.92429.8550.0030.0030.0000.0000.0000.000
51B800GLN00.0050.00326.0220.0030.0030.0000.0000.0000.000
52B801LEU0-0.068-0.03525.0600.0010.0010.0000.0000.0000.000
53B802ASN0-0.032-0.02125.531-0.003-0.0030.0000.0000.0000.000
54B803GLU-1-0.933-0.95623.3830.0070.0070.0000.0000.0000.000
55B804TYR0-0.031-0.02118.745-0.002-0.0020.0000.0000.0000.000
56B805LYS10.8270.91420.652-0.002-0.0020.0000.0000.0000.000
57B806GLY00.0370.01220.999-0.009-0.0090.0000.0000.0000.000
58B807HIS00.0330.05614.967-0.041-0.0410.0000.0000.0000.000
59B808LEU00.015-0.00316.085-0.010-0.0100.0000.0000.0000.000
60B809SER0-0.076-0.04916.995-0.019-0.0190.0000.0000.0000.000
61B810GLY00.010-0.00514.684-0.027-0.0270.0000.0000.0000.000
62B811LEU00.001-0.00811.410-0.064-0.0640.0000.0000.0000.000
63B812ALA00.0510.02212.586-0.033-0.0330.0000.0000.0000.000
64B813LYS10.8970.95712.9850.1820.1820.0000.0000.0000.000
65B814ARG10.7790.8566.6040.1210.1210.0000.0000.0000.000
66B815ALA00.0200.0338.745-0.095-0.0950.0000.0000.0000.000
67B816LYS10.8990.94310.4260.0790.0790.0000.0000.0000.000
68B817ALA0-0.038-0.00510.321-0.003-0.0030.0000.0000.0000.000
69B818VAL0-0.007-0.0183.950-0.190-0.0840.000-0.017-0.0890.000
70B819GLY00.0500.0576.2420.0250.0250.0000.0000.0000.000
71B820SER0-0.057-0.0486.0680.0270.0270.0000.0000.0000.000
72B821GLY00.0040.0108.3710.0640.0640.0000.0000.0000.000
73B822SER00.0130.00910.7800.0100.0100.0000.0000.0000.000
74B823GLY00.0550.02812.0630.0120.0120.0000.0000.0000.000
75B889ASN00.004-0.00510.076-0.045-0.0450.0000.0000.0000.000
76B890GLN00.0060.00112.031-0.010-0.0100.0000.0000.0000.000
77B891GLU-1-0.869-0.93313.7390.1060.1060.0000.0000.0000.000
78B892ALA0-0.0170.00110.2230.0210.0210.0000.0000.0000.000
79B893GLN0-0.071-0.06712.093-0.007-0.0070.0000.0000.0000.000
80B894GLU-1-0.837-0.89714.576-0.008-0.0080.0000.0000.0000.000
81B895ALA0-0.021-0.00314.0740.0130.0130.0000.0000.0000.000
82B896VAL0-0.002-0.01213.2480.0090.0090.0000.0000.0000.000
83B897THR0-0.017-0.01916.144-0.002-0.0020.0000.0000.0000.000
84B898ARG10.8810.93416.866-0.127-0.1270.0000.0000.0000.000
85B899LEU0-0.0110.00415.9640.0030.0030.0000.0000.0000.000
86B900GLU-1-0.762-0.87020.051-0.002-0.0020.0000.0000.0000.000
87B901ALA0-0.030-0.00921.956-0.002-0.0020.0000.0000.0000.000
88B902GLN00.000-0.00621.7190.0030.0030.0000.0000.0000.000
89B903HIS0-0.036-0.02122.467-0.001-0.0010.0000.0000.0000.000
90B904GLN00.0510.01724.471-0.003-0.0030.0000.0000.0000.000
91B905ALA0-0.008-0.00427.367-0.002-0.0020.0000.0000.0000.000
92B906LEU0-0.0120.00525.7810.0000.0000.0000.0000.0000.000
93B907VAL00.0040.01128.303-0.001-0.0010.0000.0000.0000.000
94B908THR0-0.035-0.02730.935-0.003-0.0030.0000.0000.0000.000
95B909LEU00.0020.00632.2560.0000.0000.0000.0000.0000.000
96B910TRP0-0.028-0.01832.402-0.002-0.0020.0000.0000.0000.000
97B911HIS00.036-0.00134.374-0.002-0.0020.0000.0000.0000.000
98B912GLN0-0.0290.00636.757-0.002-0.0020.0000.0000.0000.000
99B913LEU00.017-0.00835.3580.0000.0000.0000.0000.0000.000
100B914HIS0-0.059-0.02538.123-0.003-0.0030.0000.0000.0000.000
101B915VAL00.006-0.00339.941-0.001-0.0010.0000.0000.0000.000
102B916ASP-1-0.801-0.90942.0430.0210.0210.0000.0000.0000.000
103B917MET0-0.050-0.01539.9790.0000.0000.0000.0000.0000.000
104B918LYS10.9720.99342.697-0.011-0.0110.0000.0000.0000.000
105B919SER00.0010.01846.266-0.001-0.0010.0000.0000.0000.000
106B920LEU0-0.009-0.01746.165-0.001-0.0010.0000.0000.0000.000
107B921LEU00.0040.00347.7950.0000.0000.0000.0000.0000.000
108B922ALA00.0000.02249.979-0.001-0.0010.0000.0000.0000.000
109B923TRP0-0.022-0.01052.0630.0000.0000.0000.0000.0000.000
110B924GLN0-0.009-0.01252.414-0.001-0.0010.0000.0000.0000.000
111B925SER0-0.084-0.05653.2250.0000.0000.0000.0000.0000.000
112B926LEU00.0340.01855.909-0.001-0.0010.0000.0000.0000.000
113B927ARG10.8910.93557.782-0.012-0.0120.0000.0000.0000.000
114B928ARG10.8470.91257.279-0.010-0.0100.0000.0000.0000.000
115B929ASP-1-0.746-0.84259.3820.0080.0080.0000.0000.0000.000
116B930VAL00.009-0.01762.167-0.001-0.0010.0000.0000.0000.000
117B931GLN0-0.009-0.00663.1280.0000.0000.0000.0000.0000.000
118B932LEU0-0.022-0.01064.2490.0000.0000.0000.0000.0000.000
119B933ILE0-0.004-0.00765.9430.0000.0000.0000.0000.0000.000
120B934ARG10.8840.93467.020-0.009-0.0090.0000.0000.0000.000
121B935SER0-0.052-0.01968.5930.0000.0000.0000.0000.0000.000
122B936TRP0-0.0240.00168.6400.0000.0000.0000.0000.0000.000
123B937SER00.0880.04773.2300.0000.0000.0000.0000.0000.000
124B938LEU00.044-0.00276.9400.0000.0000.0000.0000.0000.000
125B939ALA0-0.020-0.01179.5090.0000.0000.0000.0000.0000.000
126B940THR00.0130.00373.9780.0000.0000.0000.0000.0000.000
127B941PHE0-0.0110.00972.7280.0000.0000.0000.0000.0000.000
128B942ARG10.8470.92175.909-0.005-0.0050.0000.0000.0000.000
129B943THR0-0.064-0.03276.4390.0000.0000.0000.0000.0000.000
130B944LEU0-0.0280.00870.0550.0000.0000.0000.0000.0000.000
131B945LYS10.8600.92969.268-0.005-0.0050.0000.0000.0000.000
132B946PRO00.025-0.01072.3370.0000.0000.0000.0000.0000.000
133B947GLU-1-0.829-0.92369.0200.0030.0030.0000.0000.0000.000
134B948GLU-1-0.764-0.87966.8370.0050.0050.0000.0000.0000.000
135B949GLN0-0.024-0.00767.6990.0000.0000.0000.0000.0000.000
136B950ARG10.8540.92067.478-0.003-0.0030.0000.0000.0000.000
137B951GLN00.0380.01560.8480.0000.0000.0000.0000.0000.000
138B952ALA00.0340.03263.2040.0000.0000.0000.0000.0000.000
139B953LEU00.0250.02464.0090.0000.0000.0000.0000.0000.000
140B954HIS00.0030.00558.1620.0000.0000.0000.0000.0000.000
141B955SER0-0.012-0.02759.1830.0000.0000.0000.0000.0000.000
142B956LEU00.0050.01459.0270.0000.0000.0000.0000.0000.000
143B957GLU-1-0.864-0.93159.8420.0040.0040.0000.0000.0000.000
144B958LEU0-0.021-0.00554.3560.0000.0000.0000.0000.0000.000
145B959HIS0-0.070-0.06954.3250.0000.0000.0000.0000.0000.000
146B960TYR00.0080.00855.4090.0010.0010.0000.0000.0000.000
147B961GLN0-0.044-0.04555.9230.0000.0000.0000.0000.0000.000
148B962ALA0-0.072-0.03551.4050.0000.0000.0000.0000.0000.000
149B963PHE00.0140.01051.1690.0000.0000.0000.0000.0000.000
150B964LEU0-0.0040.01052.0560.0010.0010.0000.0000.0000.000
151B965ARG10.7960.89548.557-0.007-0.0070.0000.0000.0000.000
152B966ASP-1-0.822-0.88646.8760.0090.0090.0000.0000.0000.000
153B967SER0-0.010-0.03747.4590.0010.0010.0000.0000.0000.000
154B968GLN0-0.118-0.06048.0870.0010.0010.0000.0000.0000.000
155B969ASP-1-0.888-0.94543.1140.0110.0110.0000.0000.0000.000
156B970ALA0-0.0070.01743.9800.0020.0020.0000.0000.0000.000
157B971GLY00.0460.03544.8310.0000.0000.0000.0000.0000.000
158B972GLY0-0.022-0.02745.952-0.001-0.0010.0000.0000.0000.000
159B973PHE00.0130.01948.1490.0000.0000.0000.0000.0000.000
160B974GLY00.0460.03051.0150.0000.0000.0000.0000.0000.000
161B975PRO00.007-0.02752.9540.0000.0000.0000.0000.0000.000
162B976GLU-1-0.780-0.85755.2530.0100.0100.0000.0000.0000.000
163B977ASP-1-0.887-0.95455.0290.0130.0130.0000.0000.0000.000
164B978ARG10.9490.98251.360-0.011-0.0110.0000.0000.0000.000
165B979LEU00.0120.01156.729-0.001-0.0010.0000.0000.0000.000
166B980MET0-0.060-0.02559.865-0.001-0.0010.0000.0000.0000.000
167B981ALA00.0060.00458.0500.0000.0000.0000.0000.0000.000
168B982GLU-1-0.898-0.94860.1830.0060.0060.0000.0000.0000.000
169B983ARG10.8170.87862.384-0.010-0.0100.0000.0000.0000.000
170B984GLU-1-0.844-0.90962.9270.0100.0100.0000.0000.0000.000
171B985TYR00.0350.01862.3260.0000.0000.0000.0000.0000.000
172B986GLY00.0330.02464.4010.0000.0000.0000.0000.0000.000
173B987SER0-0.052-0.03767.5540.0000.0000.0000.0000.0000.000
174B988CYS0-0.070-0.01266.5920.0000.0000.0000.0000.0000.000
175B989SER0-0.003-0.01066.7960.0000.0000.0000.0000.0000.000
176B990HIS0-0.037-0.01569.3170.0000.0000.0000.0000.0000.000
177B991HIS0-0.046-0.02271.7760.0000.0000.0000.0000.0000.000
178B992TYR00.0300.00470.7730.0000.0000.0000.0000.0000.000
179B993GLN0-0.037-0.01372.8170.0000.0000.0000.0000.0000.000
180B994GLN0-0.016-0.00375.0380.0000.0000.0000.0000.0000.000
181B995LEU0-0.058-0.00473.5050.0000.0000.0000.0000.0000.000
182B996LEU0-0.0110.00374.6290.0000.0000.0000.0000.0000.000