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: Z663N

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 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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1757870.938455
FMO2-HF: Nuclear repulsion 1684692.392637
FMO2-HF: Total energy -73178.545818
FMO2-MP2: Total energy -73393.684941


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.
-4.86-1.4560.069-1.399-2.0720.006
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 : 0.004 / q_NPA : -0.002
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].
3B752ALA00.0080.0003.189-1.4860.5750.020-0.970-1.1110.004
4B753GLN0-0.032-0.0153.329-2.294-1.2360.050-0.382-0.7250.002
5B754PHE0-0.0060.0044.667-0.913-0.728-0.001-0.033-0.1510.000
6B755PHE00.0430.0026.5090.0030.0030.0000.0000.0000.000
7B756SER0-0.0110.0088.244-0.106-0.1060.0000.0000.0000.000
8B757ASP-1-0.740-0.8509.0010.3410.3410.0000.0000.0000.000
9B758VAL0-0.015-0.00310.845-0.075-0.0750.0000.0000.0000.000
10B759ARG10.9310.97012.594-0.278-0.2780.0000.0000.0000.000
11B760GLU-1-0.919-0.96713.5540.2660.2660.0000.0000.0000.000
12B761ALA00.0090.00815.100-0.035-0.0350.0000.0000.0000.000
13B762GLU-1-0.867-0.91416.9090.1070.1070.0000.0000.0000.000
14B763GLY0-0.001-0.00518.571-0.015-0.0150.0000.0000.0000.000
15B764GLN00.0110.02317.395-0.039-0.0390.0000.0000.0000.000
16B765LEU00.0330.02820.608-0.015-0.0150.0000.0000.0000.000
17B766GLN0-0.029-0.02022.959-0.014-0.0140.0000.0000.0000.000
18B767LYS10.8210.87124.208-0.117-0.1170.0000.0000.0000.000
19B768LEU00.0520.02925.476-0.007-0.0070.0000.0000.0000.000
20B769GLN00.0450.02327.170-0.005-0.0050.0000.0000.0000.000
21B770GLU-1-0.899-0.91728.0900.0880.0880.0000.0000.0000.000
22B771ALA0-0.016-0.00230.163-0.004-0.0040.0000.0000.0000.000
23B772LEU00.0350.02130.558-0.004-0.0040.0000.0000.0000.000
24B773ARG10.9020.94530.136-0.060-0.0600.0000.0000.0000.000
25B774ARG10.9190.98831.050-0.069-0.0690.0000.0000.0000.000
26B775LYS10.8100.88833.630-0.049-0.0490.0000.0000.0000.000
27B776TYR0-0.013-0.02934.509-0.002-0.0020.0000.0000.0000.000
28B777SER0-0.025-0.02338.299-0.002-0.0020.0000.0000.0000.000
29B778CYS0-0.054-0.01540.7200.0000.0000.0000.0000.0000.000
30B779ASP-1-0.775-0.86844.3440.0250.0250.0000.0000.0000.000
31B780ARG10.8340.89747.703-0.018-0.0180.0000.0000.0000.000
32B781SER0-0.113-0.06449.869-0.001-0.0010.0000.0000.0000.000
33B782ALA0-0.0180.00347.6190.0000.0000.0000.0000.0000.000
34B783THR00.0230.00349.596-0.001-0.0010.0000.0000.0000.000
35B784VAL00.0450.01049.8040.0010.0010.0000.0000.0000.000
36B785THR00.0450.01449.6920.0000.0000.0000.0000.0000.000
37B786ARG10.9931.00842.232-0.031-0.0310.0000.0000.0000.000
38B787LEU00.0020.00045.3110.0010.0010.0000.0000.0000.000
39B788GLU-1-0.897-0.96244.7980.0170.0170.0000.0000.0000.000
40B789ASP-1-0.928-0.95643.8690.0250.0250.0000.0000.0000.000
41B790LEU0-0.045-0.03340.2490.0010.0010.0000.0000.0000.000
42B791LEU0-0.023-0.01739.9880.0010.0010.0000.0000.0000.000
43B792GLN0-0.024-0.00740.154-0.002-0.0020.0000.0000.0000.000
44B793ASP-1-0.895-0.94137.5870.0340.0340.0000.0000.0000.000
45B794ALA0-0.047-0.01535.9090.0030.0030.0000.0000.0000.000
46B795GLN0-0.065-0.05434.816-0.001-0.0010.0000.0000.0000.000
47B796ASP-1-0.845-0.90531.7540.0430.0430.0000.0000.0000.000
48B797GLU-1-0.768-0.86930.3300.0510.0510.0000.0000.0000.000
49B798LYS10.7660.88929.541-0.018-0.0180.0000.0000.0000.000
50B799GLU-1-0.832-0.91029.7910.0170.0170.0000.0000.0000.000
51B800GLN0-0.011-0.00126.0160.0050.0050.0000.0000.0000.000
52B801LEU0-0.067-0.03525.0460.0020.0020.0000.0000.0000.000
53B802ASN0-0.048-0.04025.523-0.005-0.0050.0000.0000.0000.000
54B803GLU-1-0.931-0.95823.3010.0350.0350.0000.0000.0000.000
55B804TYR0-0.040-0.04718.400-0.002-0.0020.0000.0000.0000.000
56B805LYS10.8080.90420.646-0.008-0.0080.0000.0000.0000.000
57B806GLY00.0150.00921.002-0.010-0.0100.0000.0000.0000.000
58B807HIS00.0250.03214.676-0.033-0.0330.0000.0000.0000.000
59B808LEU00.020-0.00216.084-0.006-0.0060.0000.0000.0000.000
60B809SER0-0.057-0.02617.002-0.023-0.0230.0000.0000.0000.000
61B810GLY00.007-0.00514.691-0.026-0.0260.0000.0000.0000.000
62B811LEU00.003-0.00711.220-0.054-0.0540.0000.0000.0000.000
63B812ALA00.0510.02112.598-0.042-0.0420.0000.0000.0000.000
64B813LYS10.9020.95413.0640.1170.1170.0000.0000.0000.000
65B814ARG10.7830.8586.2900.0220.0220.0000.0000.0000.000
66B815ALA00.0140.0288.824-0.104-0.1040.0000.0000.0000.000
67B816LYS10.9210.94910.5350.0790.0790.0000.0000.0000.000
68B817ALA0-0.042-0.01110.369-0.008-0.0080.0000.0000.0000.000
69B818VAL00.001-0.0154.008-0.159-0.0590.000-0.014-0.0850.000
70B819GLY00.0510.0576.8830.0140.0140.0000.0000.0000.000
71B820SER0-0.056-0.0526.327-0.096-0.0960.0000.0000.0000.000
72B821GLY0-0.0050.0028.3770.0680.0680.0000.0000.0000.000
73B822SER00.0120.01510.7020.0170.0170.0000.0000.0000.000
74B823GLY00.0480.02211.9800.0230.0230.0000.0000.0000.000
75B889ASN0-0.029-0.01810.437-0.028-0.0280.0000.0000.0000.000
76B890GLN0-0.010-0.01112.167-0.003-0.0030.0000.0000.0000.000
77B891GLU-1-0.854-0.93113.9220.0320.0320.0000.0000.0000.000
78B892ALA0-0.035-0.00310.3160.0210.0210.0000.0000.0000.000
79B893GLN0-0.068-0.06612.2310.0150.0150.0000.0000.0000.000
80B894GLU-1-0.789-0.87314.698-0.035-0.0350.0000.0000.0000.000
81B895ALA0-0.036-0.00514.0660.0190.0190.0000.0000.0000.000
82B896VAL00.001-0.01013.1780.0160.0160.0000.0000.0000.000
83B897THR0-0.023-0.01916.1470.0070.0070.0000.0000.0000.000
84B898ARG10.8520.91316.762-0.077-0.0770.0000.0000.0000.000
85B899LEU0-0.0040.00516.0060.0060.0060.0000.0000.0000.000
86B900GLU-1-0.769-0.87820.0440.0050.0050.0000.0000.0000.000
87B901ALA0-0.029-0.00721.956-0.001-0.0010.0000.0000.0000.000
88B902GLN0-0.017-0.01421.4590.0020.0020.0000.0000.0000.000
89B903HIS0-0.027-0.02222.487-0.001-0.0010.0000.0000.0000.000
90B904GLN00.0500.01724.462-0.001-0.0010.0000.0000.0000.000
91B905ALA00.0010.00127.361-0.001-0.0010.0000.0000.0000.000
92B906LEU0-0.0130.00225.6410.0010.0010.0000.0000.0000.000
93B907VAL00.0060.01228.331-0.001-0.0010.0000.0000.0000.000
94B908THR0-0.035-0.02630.926-0.003-0.0030.0000.0000.0000.000
95B909LEU00.0100.01032.192-0.001-0.0010.0000.0000.0000.000
96B910TRP0-0.015-0.00632.396-0.003-0.0030.0000.0000.0000.000
97B911HIS00.0480.00834.360-0.001-0.0010.0000.0000.0000.000
98B912GLN0-0.038-0.00136.743-0.002-0.0020.0000.0000.0000.000
99B913LEU00.019-0.00935.3520.0000.0000.0000.0000.0000.000
100B914HIS0-0.0220.00138.118-0.003-0.0030.0000.0000.0000.000
101B915VAL00.006-0.00639.926-0.001-0.0010.0000.0000.0000.000
102B916ASP-1-0.791-0.89642.1580.0210.0210.0000.0000.0000.000
103B917MET0-0.034-0.00539.7570.0000.0000.0000.0000.0000.000
104B918LYS10.9310.97242.322-0.015-0.0150.0000.0000.0000.000
105B919SER0-0.0220.00146.251-0.001-0.0010.0000.0000.0000.000
106B920LEU00.007-0.01046.049-0.001-0.0010.0000.0000.0000.000
107B921LEU0-0.010-0.00247.7990.0000.0000.0000.0000.0000.000
108B922ALA0-0.0050.00749.961-0.001-0.0010.0000.0000.0000.000
109B923TRP0-0.055-0.03952.0470.0000.0000.0000.0000.0000.000
110B924GLN0-0.020-0.02152.253-0.001-0.0010.0000.0000.0000.000
111B925SER0-0.078-0.04053.2680.0000.0000.0000.0000.0000.000
112B926LEU00.0230.01455.892-0.001-0.0010.0000.0000.0000.000
113B927ARG10.9010.93457.754-0.013-0.0130.0000.0000.0000.000
114B928ARG10.8360.90357.226-0.012-0.0120.0000.0000.0000.000
115B929ASP-1-0.754-0.85259.4190.0100.0100.0000.0000.0000.000
116B930VAL0-0.001-0.02762.149-0.001-0.0010.0000.0000.0000.000
117B931GLN00.003-0.00562.9090.0000.0000.0000.0000.0000.000
118B932LEU0-0.020-0.00664.1850.0000.0000.0000.0000.0000.000
119B933ILE0-0.001-0.00866.0310.0000.0000.0000.0000.0000.000
120B934ARG10.8820.93766.963-0.010-0.0100.0000.0000.0000.000
121B935SER0-0.051-0.02168.5700.0000.0000.0000.0000.0000.000
122B936TRP0-0.042-0.01068.7060.0000.0000.0000.0000.0000.000
123B937SER00.0790.03873.2120.0000.0000.0000.0000.0000.000
124B938LEU00.043-0.00576.9210.0000.0000.0000.0000.0000.000
125B939ALA0-0.011-0.00779.4920.0000.0000.0000.0000.0000.000
126B940THR00.0170.01073.9980.0000.0000.0000.0000.0000.000
127B941PHE0-0.0060.00372.7370.0000.0000.0000.0000.0000.000
128B942ARG10.8500.92375.892-0.006-0.0060.0000.0000.0000.000
129B943THR0-0.041-0.01476.4120.0000.0000.0000.0000.0000.000
130B944LEU0-0.0470.00270.1270.0000.0000.0000.0000.0000.000
131B945LYS10.8780.92669.573-0.008-0.0080.0000.0000.0000.000
132B946PRO00.038-0.00372.3230.0000.0000.0000.0000.0000.000
133B947GLU-1-0.846-0.93069.0430.0060.0060.0000.0000.0000.000
134B948GLU-1-0.773-0.87566.9200.0080.0080.0000.0000.0000.000
135B949GLN0-0.0190.00267.6850.0000.0000.0000.0000.0000.000
136B950ARG10.8560.92267.429-0.005-0.0050.0000.0000.0000.000
137B951GLN00.0240.00860.8870.0000.0000.0000.0000.0000.000
138B952ALA00.0380.03263.1910.0000.0000.0000.0000.0000.000
139B953LEU00.0280.02463.9960.0000.0000.0000.0000.0000.000
140B954HIS00.0010.00558.1670.0000.0000.0000.0000.0000.000
141B955SER0-0.015-0.02759.1800.0000.0000.0000.0000.0000.000
142B956LEU00.0070.01659.0140.0000.0000.0000.0000.0000.000
143B957GLU-1-0.832-0.92059.8310.0060.0060.0000.0000.0000.000
144B958LEU0-0.025-0.00254.3420.0000.0000.0000.0000.0000.000
145B959HIS0-0.051-0.05354.0010.0010.0010.0000.0000.0000.000
146B960TYR00.0000.00455.3970.0010.0010.0000.0000.0000.000
147B961GLN0-0.043-0.04655.8710.0000.0000.0000.0000.0000.000
148B962ALA0-0.071-0.03451.4190.0000.0000.0000.0000.0000.000
149B963PHE00.0200.01151.1600.0000.0000.0000.0000.0000.000
150B964LEU00.0010.01252.0460.0000.0000.0000.0000.0000.000
151B965ARG10.7600.86148.445-0.009-0.0090.0000.0000.0000.000
152B966ASP-1-0.779-0.85246.8930.0110.0110.0000.0000.0000.000
153B967SER00.011-0.02247.4490.0010.0010.0000.0000.0000.000
154B968GLN0-0.107-0.04148.0800.0000.0000.0000.0000.0000.000
155B969ASP-1-0.887-0.94743.1490.0100.0100.0000.0000.0000.000
156B970ALA0-0.0130.01743.9700.0010.0010.0000.0000.0000.000
157B971GLY00.0360.02744.838-0.001-0.0010.0000.0000.0000.000
158B972GLY0-0.028-0.03345.9380.0000.0000.0000.0000.0000.000
159B973PHE00.0130.02348.0400.0000.0000.0000.0000.0000.000
160B974GLY00.0510.02551.0690.0000.0000.0000.0000.0000.000
161B975PRO00.006-0.01753.0820.0000.0000.0000.0000.0000.000
162B976GLU-1-0.785-0.86455.2420.0090.0090.0000.0000.0000.000
163B977ASP-1-0.855-0.93055.0620.0130.0130.0000.0000.0000.000
164B978ARG10.9090.94450.978-0.011-0.0110.0000.0000.0000.000
165B979LEU00.0290.01756.7180.0000.0000.0000.0000.0000.000
166B980MET0-0.086-0.02058.9400.0000.0000.0000.0000.0000.000
167B981ALA00.0220.01058.0240.0000.0000.0000.0000.0000.000
168B982GLU-1-0.884-0.94260.1700.0060.0060.0000.0000.0000.000
169B983ARG10.7970.86762.154-0.009-0.0090.0000.0000.0000.000
170B984GLU-1-0.834-0.90362.9370.0100.0100.0000.0000.0000.000
171B985TYR00.0140.01462.3080.0000.0000.0000.0000.0000.000
172B986GLY00.0290.02364.3880.0000.0000.0000.0000.0000.000
173B987SER0-0.054-0.03967.5430.0000.0000.0000.0000.0000.000
174B988CYS0-0.091-0.02266.5400.0000.0000.0000.0000.0000.000
175B989SER00.0170.00466.7840.0000.0000.0000.0000.0000.000
176B990HIS0-0.039-0.01569.3060.0000.0000.0000.0000.0000.000
177B991HIS0-0.048-0.02371.7560.0000.0000.0000.0000.0000.000
178B992TYR00.017-0.00470.7200.0000.0000.0000.0000.0000.000
179B993GLN0-0.041-0.01572.8050.0000.0000.0000.0000.0000.000
180B994GLN0-0.011-0.00475.0270.0000.0000.0000.0000.0000.000
181B995LEU0-0.056-0.00473.5900.0000.0000.0000.0000.0000.000
182B996LEU0-0.0080.00874.5340.0000.0000.0000.0000.0000.000