FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R99R8

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 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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1767431.446281
FMO2-HF: Nuclear repulsion 1694252.536371
FMO2-HF: Total energy -73178.90991
FMO2-MP2: Total energy -73394.107781


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.
-4.421-1.2310.102-1.304-1.9880.005
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 : 0.012 / q_NPA : 0.001
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].
3B752ALA00.0090.0083.261-1.9160.0590.044-0.929-1.0900.004
4B753GLN0-0.034-0.0193.202-1.955-1.1150.058-0.267-0.6310.001
5B754PHE0-0.0150.0064.273-0.535-0.284-0.001-0.088-0.1630.000
6B755PHE00.032-0.0056.2860.0920.0920.0000.0000.0000.000
7B756SER0-0.0040.0107.832-0.049-0.0490.0000.0000.0000.000
8B757ASP-1-0.762-0.8558.125-0.045-0.0450.0000.0000.0000.000
9B758VAL0-0.005-0.00310.348-0.032-0.0320.0000.0000.0000.000
10B759ARG10.8760.93412.059-0.240-0.2400.0000.0000.0000.000
11B760GLU-1-0.883-0.94513.1130.1680.1680.0000.0000.0000.000
12B761ALA00.0220.01914.683-0.026-0.0260.0000.0000.0000.000
13B762GLU-1-0.808-0.88816.4080.1030.1030.0000.0000.0000.000
14B763GLY00.0000.00518.089-0.010-0.0100.0000.0000.0000.000
15B764GLN0-0.024-0.00416.846-0.034-0.0340.0000.0000.0000.000
16B765LEU00.0190.01819.844-0.011-0.0110.0000.0000.0000.000
17B766GLN0-0.004-0.01122.482-0.011-0.0110.0000.0000.0000.000
18B767LYS10.8210.88123.745-0.094-0.0940.0000.0000.0000.000
19B768LEU00.0660.03824.963-0.004-0.0040.0000.0000.0000.000
20B769GLN00.0400.02026.631-0.002-0.0020.0000.0000.0000.000
21B770GLU-1-0.904-0.92527.7800.0730.0730.0000.0000.0000.000
22B771ALA0-0.0130.00229.496-0.003-0.0030.0000.0000.0000.000
23B772LEU00.0320.01730.021-0.003-0.0030.0000.0000.0000.000
24B773ARG10.8960.94029.314-0.045-0.0450.0000.0000.0000.000
25B774ARG10.9130.97130.113-0.055-0.0550.0000.0000.0000.000
26B775LYS10.8280.90833.296-0.028-0.0280.0000.0000.0000.000
27B776TYR00.006-0.03234.123-0.002-0.0020.0000.0000.0000.000
28B777SER0-0.047-0.02937.868-0.002-0.0020.0000.0000.0000.000
29B778CYS0-0.073-0.01940.2740.0010.0010.0000.0000.0000.000
30B779ASP-1-0.791-0.87943.8020.0170.0170.0000.0000.0000.000
31B780ARG10.8510.91147.279-0.012-0.0120.0000.0000.0000.000
32B781SER0-0.088-0.05349.052-0.001-0.0010.0000.0000.0000.000
33B782ALA0-0.022-0.00247.0650.0000.0000.0000.0000.0000.000
34B783THR00.008-0.00549.014-0.001-0.0010.0000.0000.0000.000
35B784VAL00.0230.00449.3220.0000.0000.0000.0000.0000.000
36B785THR00.0780.04149.1450.0000.0000.0000.0000.0000.000
37B786ARG10.9851.00441.754-0.021-0.0210.0000.0000.0000.000
38B787LEU0-0.008-0.00844.7050.0010.0010.0000.0000.0000.000
39B788GLU-1-0.877-0.95444.4870.0080.0080.0000.0000.0000.000
40B789ASP-1-0.939-0.95443.4960.0130.0130.0000.0000.0000.000
41B790LEU0-0.034-0.02739.5840.0000.0000.0000.0000.0000.000
42B791LEU0-0.034-0.01839.6320.0000.0000.0000.0000.0000.000
43B792GLN0-0.058-0.02040.201-0.002-0.0020.0000.0000.0000.000
44B793ASP-1-0.880-0.94137.1110.0190.0190.0000.0000.0000.000
45B794ALA0-0.041-0.01935.4180.0010.0010.0000.0000.0000.000
46B795GLN0-0.057-0.04934.343-0.002-0.0020.0000.0000.0000.000
47B796ASP-1-0.852-0.89430.9350.0180.0180.0000.0000.0000.000
48B797GLU-1-0.761-0.86729.6150.0260.0260.0000.0000.0000.000
49B798LYS10.7810.90529.2420.0000.0000.0000.0000.0000.000
50B799GLU-1-0.817-0.89729.307-0.011-0.0110.0000.0000.0000.000
51B800GLN0-0.023-0.01525.8530.0010.0010.0000.0000.0000.000
52B801LEU0-0.059-0.03524.858-0.002-0.0020.0000.0000.0000.000
53B802ASN0-0.049-0.03725.294-0.006-0.0060.0000.0000.0000.000
54B803GLU-1-0.922-0.96022.930-0.008-0.0080.0000.0000.0000.000
55B804TYR0-0.050-0.06118.111-0.012-0.0120.0000.0000.0000.000
56B805LYS10.8110.90820.4490.0230.0230.0000.0000.0000.000
57B806GLY00.0300.02120.913-0.013-0.0130.0000.0000.0000.000
58B807HIS00.0140.02214.091-0.039-0.0390.0000.0000.0000.000
59B808LEU00.0150.00415.973-0.024-0.0240.0000.0000.0000.000
60B809SER0-0.054-0.03116.468-0.027-0.0270.0000.0000.0000.000
61B810GLY0-0.007-0.00714.783-0.028-0.0280.0000.0000.0000.000
62B811LEU0-0.011-0.01411.041-0.070-0.0700.0000.0000.0000.000
63B812ALA00.0400.01411.919-0.060-0.0600.0000.0000.0000.000
64B813LYS10.9280.96012.7570.1810.1810.0000.0000.0000.000
65B814ARG10.7800.8705.9950.4380.4380.0000.0000.0000.000
66B815ALA00.0130.0048.681-0.097-0.0970.0000.0000.0000.000
67B816LYS10.8990.94510.7260.1400.1400.0000.0000.0000.000
68B817ALA0-0.0170.0009.9450.0030.0030.0000.0000.0000.000
69B818VAL0-0.027-0.0093.817-0.157-0.0330.001-0.020-0.1040.000
70B819GLY00.0660.0307.1890.0230.0230.0000.0000.0000.000
71B820SER0-0.073-0.0496.473-0.093-0.0930.0000.0000.0000.000
72B821GLY00.0040.0177.9860.0780.0780.0000.0000.0000.000
73B822SER00.0060.01010.2480.0230.0230.0000.0000.0000.000
74B823GLY00.0310.01111.4920.0260.0260.0000.0000.0000.000
75B889ASN0-0.025-0.02510.310-0.047-0.0470.0000.0000.0000.000
76B890GLN00.0070.01012.192-0.007-0.0070.0000.0000.0000.000
77B891GLU-1-0.778-0.88613.8410.0200.0200.0000.0000.0000.000
78B892ALA0-0.035-0.00510.0070.0100.0100.0000.0000.0000.000
79B893GLN0-0.039-0.04611.913-0.008-0.0080.0000.0000.0000.000
80B894GLU-1-0.805-0.88114.556-0.049-0.0490.0000.0000.0000.000
81B895ALA0-0.025-0.00613.8070.0170.0170.0000.0000.0000.000
82B896VAL0-0.001-0.00813.2300.0110.0110.0000.0000.0000.000
83B897THR0-0.014-0.01216.1220.0090.0090.0000.0000.0000.000
84B898ARG10.7860.88215.946-0.051-0.0510.0000.0000.0000.000
85B899LEU0-0.0090.00315.4780.0070.0070.0000.0000.0000.000
86B900GLU-1-0.792-0.89219.666-0.034-0.0340.0000.0000.0000.000
87B901ALA0-0.024-0.00621.8110.0040.0040.0000.0000.0000.000
88B902GLN0-0.041-0.02921.0890.0020.0020.0000.0000.0000.000
89B903HIS0-0.010-0.02122.4860.0010.0010.0000.0000.0000.000
90B904GLN00.0590.02624.439-0.001-0.0010.0000.0000.0000.000
91B905ALA00.0090.01427.2690.0010.0010.0000.0000.0000.000
92B906LEU0-0.022-0.00724.8840.0020.0020.0000.0000.0000.000
93B907VAL00.0010.00427.9360.0000.0000.0000.0000.0000.000
94B908THR0-0.031-0.02630.516-0.001-0.0010.0000.0000.0000.000
95B909LEU0-0.018-0.01031.5100.0010.0010.0000.0000.0000.000
96B910TRP0-0.012-0.01232.156-0.001-0.0010.0000.0000.0000.000
97B911HIS00.0200.00434.109-0.001-0.0010.0000.0000.0000.000
98B912GLN0-0.067-0.03036.679-0.001-0.0010.0000.0000.0000.000
99B913LEU00.0360.00835.1010.0000.0000.0000.0000.0000.000
100B914HIS00.0170.02037.925-0.002-0.0020.0000.0000.0000.000
101B915VAL00.0280.00739.748-0.001-0.0010.0000.0000.0000.000
102B916ASP-1-0.783-0.87841.5130.0120.0120.0000.0000.0000.000
103B917MET0-0.033-0.00939.3310.0000.0000.0000.0000.0000.000
104B918LYS10.9100.96242.221-0.002-0.0020.0000.0000.0000.000
105B919SER0-0.046-0.02645.9490.0000.0000.0000.0000.0000.000
106B920LEU00.001-0.00545.6970.0000.0000.0000.0000.0000.000
107B921LEU00.0160.01847.4690.0000.0000.0000.0000.0000.000
108B922ALA00.0000.00649.6810.0000.0000.0000.0000.0000.000
109B923TRP0-0.053-0.03751.8020.0000.0000.0000.0000.0000.000
110B924GLN0-0.026-0.03151.766-0.001-0.0010.0000.0000.0000.000
111B925SER0-0.069-0.03752.9230.0000.0000.0000.0000.0000.000
112B926LEU00.0220.01355.5790.0000.0000.0000.0000.0000.000
113B927ARG10.8710.90857.436-0.007-0.0070.0000.0000.0000.000
114B928ARG10.8490.91256.697-0.006-0.0060.0000.0000.0000.000
115B929ASP-1-0.760-0.85559.1680.0040.0040.0000.0000.0000.000
116B930VAL0-0.006-0.03261.6710.0000.0000.0000.0000.0000.000
117B931GLN00.0050.00162.4020.0000.0000.0000.0000.0000.000
118B932LEU0-0.0180.00064.1480.0000.0000.0000.0000.0000.000
119B933ILE00.012-0.00265.3720.0000.0000.0000.0000.0000.000
120B934ARG10.8480.89966.430-0.005-0.0050.0000.0000.0000.000
121B935SER0-0.046-0.02168.0800.0000.0000.0000.0000.0000.000
122B936TRP0-0.044-0.01868.1040.0000.0000.0000.0000.0000.000
123B937SER00.0580.01672.6980.0000.0000.0000.0000.0000.000
124B938LEU00.0490.00976.4200.0000.0000.0000.0000.0000.000
125B939ALA00.0260.01578.9860.0000.0000.0000.0000.0000.000
126B940THR00.0260.02273.4230.0000.0000.0000.0000.0000.000
127B941PHE00.0130.00472.2120.0000.0000.0000.0000.0000.000
128B942ARG10.7850.89275.430-0.003-0.0030.0000.0000.0000.000
129B943THR0-0.033-0.01675.9940.0000.0000.0000.0000.0000.000
130B944LEU0-0.050-0.00169.7210.0000.0000.0000.0000.0000.000
131B945LYS10.8850.92969.502-0.002-0.0020.0000.0000.0000.000
132B946PRO00.017-0.01171.8060.0000.0000.0000.0000.0000.000
133B947GLU-1-0.836-0.91168.3660.0010.0010.0000.0000.0000.000
134B948GLU-1-0.771-0.87766.5760.0020.0020.0000.0000.0000.000
135B949GLN0-0.0070.01266.9900.0000.0000.0000.0000.0000.000
136B950ARG10.8770.92167.0740.0000.0000.0000.0000.0000.000
137B951GLN00.0130.01160.4570.0000.0000.0000.0000.0000.000
138B952ALA00.0400.03162.7670.0000.0000.0000.0000.0000.000
139B953LEU00.0060.01363.7230.0000.0000.0000.0000.0000.000
140B954HIS0-0.014-0.00758.0070.0000.0000.0000.0000.0000.000
141B955SER0-0.028-0.03458.9270.0000.0000.0000.0000.0000.000
142B956LEU00.0130.01358.7970.0000.0000.0000.0000.0000.000
143B957GLU-1-0.809-0.88059.7450.0000.0000.0000.0000.0000.000
144B958LEU0-0.035-0.00654.1470.0000.0000.0000.0000.0000.000
145B959HIS0-0.046-0.05253.6260.0000.0000.0000.0000.0000.000
146B960TYR0-0.018-0.01455.0800.0010.0010.0000.0000.0000.000
147B961GLN0-0.009-0.02655.5920.0000.0000.0000.0000.0000.000
148B962ALA0-0.061-0.02451.1710.0000.0000.0000.0000.0000.000
149B963PHE00.0270.01450.9780.0000.0000.0000.0000.0000.000
150B964LEU0-0.0030.01251.9840.0000.0000.0000.0000.0000.000
151B965ARG10.7660.86948.086-0.001-0.0010.0000.0000.0000.000
152B966ASP-1-0.760-0.86246.7440.0010.0010.0000.0000.0000.000
153B967SER0-0.050-0.05047.0360.0010.0010.0000.0000.0000.000
154B968GLN0-0.086-0.03447.9130.0010.0010.0000.0000.0000.000
155B969ASP-1-0.882-0.94943.0220.0010.0010.0000.0000.0000.000
156B970ALA0-0.0200.01343.8440.0010.0010.0000.0000.0000.000
157B971GLY00.0210.01644.2790.0000.0000.0000.0000.0000.000
158B972GLY0-0.025-0.02445.3980.0000.0000.0000.0000.0000.000
159B973PHE00.0240.01947.8580.0000.0000.0000.0000.0000.000
160B974GLY00.0450.01950.6140.0000.0000.0000.0000.0000.000
161B975PRO00.005-0.01552.8020.0000.0000.0000.0000.0000.000
162B976GLU-1-0.779-0.85355.2760.0050.0050.0000.0000.0000.000
163B977ASP-1-0.863-0.92454.8570.0080.0080.0000.0000.0000.000
164B978ARG10.9150.94950.416-0.004-0.0040.0000.0000.0000.000
165B979LEU00.0510.03456.3260.0000.0000.0000.0000.0000.000
166B980MET0-0.083-0.00258.5010.0000.0000.0000.0000.0000.000
167B981ALA00.0260.00357.7900.0000.0000.0000.0000.0000.000
168B982GLU-1-0.852-0.90959.9150.0020.0020.0000.0000.0000.000
169B983ARG10.7840.85362.093-0.005-0.0050.0000.0000.0000.000
170B984GLU-1-0.817-0.87762.5720.0060.0060.0000.0000.0000.000
171B985TYR00.020-0.01362.0170.0000.0000.0000.0000.0000.000
172B986GLY00.0310.02364.0910.0000.0000.0000.0000.0000.000
173B987SER0-0.059-0.04367.2260.0000.0000.0000.0000.0000.000
174B988CYS0-0.100-0.01865.6830.0000.0000.0000.0000.0000.000
175B989SER00.0180.01266.5640.0000.0000.0000.0000.0000.000
176B990HIS0-0.037-0.01969.1040.0000.0000.0000.0000.0000.000
177B991HIS0-0.044-0.02771.4350.0000.0000.0000.0000.0000.000
178B992TYR00.013-0.01170.4070.0000.0000.0000.0000.0000.000
179B993GLN0-0.045-0.02672.5100.0000.0000.0000.0000.0000.000
180B994GLN0-0.022-0.00174.9000.0000.0000.0000.0000.0000.000
181B995LEU0-0.062-0.00973.1150.0000.0000.0000.0000.0000.000
182B996LEU0-0.0060.01274.3880.0000.0000.0000.0000.0000.000