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: JL4K9

Calculation Name: 5SV7-C-Xray372

Preferred Name: Eukaryotic translation initiation factor 2-alpha kinase 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5SV7

Chain ID: C

ChEMBL ID: CHEMBL6030

UniProt ID: Q9NZJ5

Base Structure: X-ray

Registration Date: 2023-06-22

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2217693.659969
FMO2-HF: Nuclear repulsion 2137253.822027
FMO2-HF: Total energy -80439.837942
FMO2-MP2: Total energy -80674.665063


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(C:104:SER)


Summations of interaction energy for fragment #1(C:104:SER)
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.
-29.509-23.16915.049-9.829-11.5570.026
Interaction energy analysis for fragmet #1(C:104:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.019
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].
3C106VAL00.0650.0393.7820.3362.194-0.035-0.883-0.9400.004
4C107ILE0-0.041-0.0206.697-0.029-0.0290.0000.0000.0000.000
5C108ILE00.0330.01810.0000.1420.1420.0000.0000.0000.000
6C109SER0-0.0060.00913.539-0.024-0.0240.0000.0000.0000.000
7C110THR00.0180.01116.5930.0320.0320.0000.0000.0000.000
8C111LEU00.0370.00219.6510.0130.0130.0000.0000.0000.000
9C112ASP-1-0.872-0.97121.587-0.114-0.1140.0000.0000.0000.000
10C113GLY0-0.0180.00222.412-0.005-0.0050.0000.0000.0000.000
11C114ARG10.8310.92019.7600.1830.1830.0000.0000.0000.000
12C115ILE0-0.0280.00113.1190.0200.0200.0000.0000.0000.000
13C116ALA0-0.002-0.01713.755-0.038-0.0380.0000.0000.0000.000
14C117ALA00.0240.0178.4080.0610.0610.0000.0000.0000.000
15C118LEU0-0.024-0.0218.6470.0190.0190.0000.0000.0000.000
16C119ASP-1-0.847-0.9413.991-4.885-4.777-0.001-0.067-0.0400.000
17C120PRO0-0.083-0.0184.258-2.534-2.592-0.001-0.0370.0960.000
18C121GLU-1-0.981-0.9782.278-1.962-0.7091.096-0.806-1.543-0.004
19C122ASN00.0180.0063.7751.2011.4300.005-0.074-0.1600.000
20C123HIS0-0.094-0.0487.5750.0530.0530.0000.0000.0000.000
21C124GLY00.1760.0848.1410.2530.2530.0000.0000.0000.000
22C125LYS10.8900.9369.4441.3461.3460.0000.0000.0000.000
23C126LYS10.9000.94210.2180.2070.2070.0000.0000.0000.000
24C127GLN0-0.031-0.0206.2950.5330.5330.0000.0000.0000.000
25C128TRP0-0.001-0.0098.7650.1530.1530.0000.0000.0000.000
26C129ASP-1-0.864-0.94113.116-0.358-0.3580.0000.0000.0000.000
27C130LEU0-0.0140.03315.5280.0230.0230.0000.0000.0000.000
28C131ASP-1-0.890-0.96617.946-0.096-0.0960.0000.0000.0000.000
29C132VAL0-0.021-0.00220.6080.0100.0100.0000.0000.0000.000
30C133GLY0-0.0110.00823.2790.0040.0040.0000.0000.0000.000
31C134SER0-0.052-0.05526.4040.0070.0070.0000.0000.0000.000
32C135GLY00.0390.01226.9710.0040.0040.0000.0000.0000.000
33C136SER0-0.0080.01225.610-0.002-0.0020.0000.0000.0000.000
34C137LEU00.0120.01321.0290.0070.0070.0000.0000.0000.000
35C138VAL00.0060.00025.5200.0130.0130.0000.0000.0000.000
36C139SER0-0.081-0.02328.855-0.011-0.0110.0000.0000.0000.000
37C140SER00.039-0.00832.5270.0070.0070.0000.0000.0000.000
38C141SER0-0.053-0.01435.705-0.005-0.0050.0000.0000.0000.000
39C142LEU00.0280.03738.439-0.001-0.0010.0000.0000.0000.000
40C151LYS10.9900.98144.977-0.020-0.0200.0000.0000.0000.000
41C152MET0-0.069-0.02339.6520.0000.0000.0000.0000.0000.000
42C153ILE0-0.005-0.01639.2820.0030.0030.0000.0000.0000.000
43C154ILE0-0.023-0.01834.348-0.003-0.0030.0000.0000.0000.000
44C155PRO0-0.012-0.00731.8610.0050.0050.0000.0000.0000.000
45C156SER0-0.0190.00528.950-0.002-0.0020.0000.0000.0000.000
46C157LEU0-0.007-0.01422.769-0.008-0.0080.0000.0000.0000.000
47C158ASP-1-0.852-0.91026.3280.1250.1250.0000.0000.0000.000
48C159GLY0-0.056-0.03828.2500.0030.0030.0000.0000.0000.000
49C160ALA00.0620.00830.982-0.005-0.0050.0000.0000.0000.000
50C161LEU00.0060.00733.468-0.004-0.0040.0000.0000.0000.000
51C162PHE00.0300.02332.6720.0030.0030.0000.0000.0000.000
52C163GLN0-0.015-0.01137.589-0.007-0.0070.0000.0000.0000.000
53C164TRP00.0100.00739.3920.0030.0030.0000.0000.0000.000
54C165ASP-1-0.872-0.96141.2950.0190.0190.0000.0000.0000.000
55C166GLN00.0030.01042.0830.0040.0040.0000.0000.0000.000
56C167ASP-1-0.921-0.94144.7330.0180.0180.0000.0000.0000.000
57C168ARG10.8110.90645.358-0.029-0.0290.0000.0000.0000.000
58C169GLU-1-0.887-0.93843.1070.0330.0330.0000.0000.0000.000
59C170SER0-0.121-0.06241.5070.0020.0020.0000.0000.0000.000
60C171MET00.0010.00236.093-0.004-0.0040.0000.0000.0000.000
61C172GLU-1-0.833-0.89339.4110.0550.0550.0000.0000.0000.000
62C173THR0-0.048-0.02237.115-0.001-0.0010.0000.0000.0000.000
63C174VAL0-0.032-0.02238.985-0.003-0.0030.0000.0000.0000.000
64C175PRO0-0.009-0.01839.6950.0030.0030.0000.0000.0000.000
65C176PHE0-0.012-0.00439.8900.0000.0000.0000.0000.0000.000
66C177THR00.0420.01234.392-0.001-0.0010.0000.0000.0000.000
67C178VAL0-0.045-0.03033.242-0.003-0.0030.0000.0000.0000.000
68C179GLU-1-0.857-0.92331.2830.0840.0840.0000.0000.0000.000
69C180SER00.0790.03936.005-0.002-0.0020.0000.0000.0000.000
70C181LEU0-0.015-0.00438.275-0.003-0.0030.0000.0000.0000.000
71C182LEU0-0.100-0.04135.260-0.004-0.0040.0000.0000.0000.000
72C183GLU-1-0.957-0.95739.8500.0560.0560.0000.0000.0000.000
73C184SER0-0.042-0.01842.4280.0000.0000.0000.0000.0000.000
74C192VAL0-0.044-0.03346.285-0.001-0.0010.0000.0000.0000.000
75C193VAL00.0020.01646.7210.0020.0020.0000.0000.0000.000
76C194LEU00.0250.01742.298-0.002-0.0020.0000.0000.0000.000
77C195VAL00.0050.01340.4940.0010.0010.0000.0000.0000.000
78C196GLY00.023-0.01037.5740.0000.0000.0000.0000.0000.000
79C197GLY00.0130.01135.224-0.001-0.0010.0000.0000.0000.000
80C198LYS10.9380.98727.992-0.109-0.1090.0000.0000.0000.000
81C199SER0-0.050-0.02028.558-0.003-0.0030.0000.0000.0000.000
82C200LEU00.052-0.01424.9010.0070.0070.0000.0000.0000.000
83C201THR0-0.0470.00523.620-0.008-0.0080.0000.0000.0000.000
84C202THR0-0.022-0.00519.2600.0210.0210.0000.0000.0000.000
85C203TYR00.018-0.00318.241-0.023-0.0230.0000.0000.0000.000
86C204GLY00.0130.01816.4270.0410.0410.0000.0000.0000.000
87C205LEU00.0320.03112.002-0.068-0.0680.0000.0000.0000.000
88C206SER0-0.0260.00311.4910.0960.0960.0000.0000.0000.000
89C207ALA00.022-0.0066.515-0.172-0.1720.0000.0000.0000.000
90C208TYR00.0270.0233.099-1.300-0.1400.243-0.564-0.8380.006
91C209SER0-0.073-0.0227.7300.0760.0760.0000.0000.0000.000
92C210GLY00.0550.02910.579-0.002-0.0020.0000.0000.0000.000
93C211LYS10.9590.96112.3940.2840.2840.0000.0000.0000.000
94C212VAL00.001-0.00815.6700.0390.0390.0000.0000.0000.000
95C213ARG10.9540.96615.902-0.017-0.0170.0000.0000.0000.000
96C214TYR0-0.005-0.00718.603-0.001-0.0010.0000.0000.0000.000
97C215ILE00.008-0.00120.5110.0020.0020.0000.0000.0000.000
98C216CYS0-0.043-0.00123.071-0.001-0.0010.0000.0000.0000.000
99C217SER00.0670.03125.2000.0110.0110.0000.0000.0000.000
100C218ALA00.0500.02327.4730.0020.0020.0000.0000.0000.000
101C219LEU0-0.046-0.02130.773-0.003-0.0030.0000.0000.0000.000
102C220GLY00.0080.00830.692-0.005-0.0050.0000.0000.0000.000
103C222ARG10.9310.96125.492-0.023-0.0230.0000.0000.0000.000
104C223GLN00.000-0.02123.1950.0090.0090.0000.0000.0000.000
105C224TRP00.0270.03520.304-0.004-0.0040.0000.0000.0000.000
106C236LEU0-0.002-0.0048.4850.0710.0710.0000.0000.0000.000
107C237LEU0-0.097-0.04411.703-0.119-0.1190.0000.0000.0000.000
108C238LEU00.0480.00312.6900.0440.0440.0000.0000.0000.000
109C239GLN0-0.075-0.03716.149-0.071-0.0710.0000.0000.0000.000
110C240ARG10.9160.96819.238-0.021-0.0210.0000.0000.0000.000
111C241THR0-0.0160.00321.597-0.014-0.0140.0000.0000.0000.000
112C242GLN00.0380.00624.667-0.008-0.0080.0000.0000.0000.000
113C243LYS10.8220.90827.532-0.091-0.0910.0000.0000.0000.000
114C244THR00.023-0.00630.990-0.007-0.0070.0000.0000.0000.000
115C245VAL00.0070.01033.7940.0020.0020.0000.0000.0000.000
116C246ARG10.8840.92936.155-0.012-0.0120.0000.0000.0000.000
117C247ALA00.0610.03940.3350.0030.0030.0000.0000.0000.000
118C248VAL00.0290.00243.828-0.003-0.0030.0000.0000.0000.000
119C249GLY0-0.051-0.04346.6080.0020.0020.0000.0000.0000.000
120C250PRO0-0.007-0.00950.3040.0000.0000.0000.0000.0000.000
121C251ARG10.9720.97952.113-0.007-0.0070.0000.0000.0000.000
122C252SER0-0.022-0.03251.913-0.001-0.0010.0000.0000.0000.000
123C253GLY00.0340.05049.3000.0010.0010.0000.0000.0000.000
124C254ASN00.0090.00847.536-0.001-0.0010.0000.0000.0000.000
125C255GLU-1-0.905-0.94443.5800.0030.0030.0000.0000.0000.000
126C256LYS10.8660.94645.581-0.012-0.0120.0000.0000.0000.000
127C257TRP00.0720.03339.949-0.002-0.0020.0000.0000.0000.000
128C258ASN0-0.037-0.02937.2210.0010.0010.0000.0000.0000.000
129C259PHE00.0460.01834.7900.0000.0000.0000.0000.0000.000
130C260SER0-0.0050.00430.9920.0050.0050.0000.0000.0000.000
131C261VAL00.0160.01728.667-0.006-0.0060.0000.0000.0000.000
132C262GLY00.0220.00425.7260.0030.0030.0000.0000.0000.000
133C263HIS00.0210.01721.268-0.002-0.0020.0000.0000.0000.000
134C264PHE00.0370.00516.828-0.002-0.0020.0000.0000.0000.000
135C265GLU-1-0.898-0.94116.3200.2700.2700.0000.0000.0000.000
136C266LEU00.0220.00610.030-0.020-0.0200.0000.0000.0000.000
137C267ARG10.8870.94811.977-0.397-0.3970.0000.0000.0000.000
138C268TYR00.029-0.0015.702-0.210-0.2100.0000.0000.0000.000
139C269ILE00.0230.0389.982-0.010-0.0100.0000.0000.0000.000
140C309VAL00.006-0.0048.6640.1190.1190.0000.0000.0000.000
141C310ILE00.0030.0066.794-0.200-0.2000.0000.0000.0000.000
142C311LYS10.9640.9689.585-0.320-0.3200.0000.0000.0000.000
143C312VAL00.0140.03013.045-0.096-0.0960.0000.0000.0000.000
144C313SER00.0070.00815.4310.0410.0410.0000.0000.0000.000
145C314VAL00.0450.02119.126-0.021-0.0210.0000.0000.0000.000
146C315ALA00.0130.01720.300-0.017-0.0170.0000.0000.0000.000
147C316ASP-1-0.864-0.92620.966-0.068-0.0680.0000.0000.0000.000
148C317TRP0-0.062-0.02719.747-0.012-0.0120.0000.0000.0000.000
149C318LYS10.8910.93016.4380.0690.0690.0000.0000.0000.000
150C319VAL0-0.058-0.01210.3250.0590.0590.0000.0000.0000.000
151C320MET00.010-0.01813.006-0.045-0.0450.0000.0000.0000.000
152C321ALA00.0260.0199.7680.0070.0070.0000.0000.0000.000
153C330GLU-1-0.963-0.97811.722-0.257-0.2570.0000.0000.0000.000
154C331TRP0-0.0040.0017.606-0.014-0.0140.0000.0000.0000.000
155C332GLU-1-0.874-0.95613.469-0.106-0.1060.0000.0000.0000.000
156C333TYR0-0.019-0.01112.757-0.057-0.0570.0000.0000.0000.000
157C334GLN0-0.009-0.00115.0910.0240.0240.0000.0000.0000.000
158C335PHE0-0.044-0.03713.185-0.022-0.0220.0000.0000.0000.000
159C336CYS0-0.033-0.01819.0050.0260.0260.0000.0000.0000.000
160C337THR0-0.037-0.00322.466-0.012-0.0120.0000.0000.0000.000
161C338PRO00.0280.02421.390-0.013-0.0130.0000.0000.0000.000
162C339ILE0-0.009-0.02015.5230.0040.0040.0000.0000.0000.000
163C340ALA00.0000.00518.5850.0190.0190.0000.0000.0000.000
164C341SER0-0.034-0.01615.5940.0280.0280.0000.0000.0000.000
165C342ALA00.0390.00412.033-0.068-0.0680.0000.0000.0000.000
166C343TRP0-0.002-0.0079.7290.1520.1520.0000.0000.0000.000
167C344LEU00.0270.0245.054-0.311-0.3110.0000.0000.0000.000
168C345LEU0-0.063-0.0413.019-1.4280.0580.163-0.714-0.9340.003
169C346LYS10.9970.9692.034-20.395-19.86013.534-7.196-6.8730.018
170C347ASP-1-0.895-0.9133.1120.8740.5410.0460.515-0.228-0.001
171C348GLY0-0.018-0.0174.7980.4800.582-0.001-0.003-0.0970.000
172C349LYS10.9140.9596.544-1.548-1.5480.0000.0000.0000.000
173C350VAL00.0210.0066.2650.5020.5020.0000.0000.0000.000
174C351ILE0-0.032-0.0137.358-0.244-0.2440.0000.0000.0000.000
175C352PRO00.0090.0119.5360.0290.0290.0000.0000.0000.000
176C353ILE0-0.043-0.01911.5860.0470.0470.0000.0000.0000.000
177C354SER00.0400.02614.110-0.060-0.0600.0000.0000.0000.000
178C374ILE00.0640.03834.5490.0000.0000.0000.0000.0000.000
179C375VAL00.036-0.02135.0710.0050.0050.0000.0000.0000.000
180C376GLU-1-0.846-0.92636.0090.0800.0800.0000.0000.0000.000
181C377ALA00.0060.00331.4760.0000.0000.0000.0000.0000.000
182C378ALA0-0.056-0.02531.3340.0070.0070.0000.0000.0000.000
183C379ARG10.8860.94232.373-0.073-0.0730.0000.0000.0000.000
184C380GLY00.0650.04531.322-0.002-0.0020.0000.0000.0000.000
185C381ALA0-0.056-0.02827.8800.0030.0030.0000.0000.0000.000
186C382THR0-0.046-0.01528.4110.0050.0050.0000.0000.0000.000
187C383GLU-1-0.850-0.93530.5250.0890.0890.0000.0000.0000.000
188C384ASN0-0.035-0.01325.248-0.005-0.0050.0000.0000.0000.000
189C385SER0-0.016-0.01125.4870.0160.0160.0000.0000.0000.000
190C386VAL0-0.031-0.01226.0350.0050.0050.0000.0000.0000.000
191C387TYR00.0000.00425.376-0.005-0.0050.0000.0000.0000.000
192C388LEU0-0.003-0.00327.3870.0010.0010.0000.0000.0000.000
193C389GLY00.0220.01827.665-0.005-0.0050.0000.0000.0000.000
194C390MET0-0.019-0.02828.1900.0020.0020.0000.0000.0000.000
195C391TYR00.0240.05227.227-0.014-0.0140.0000.0000.0000.000
196C392ARG10.8700.93228.3410.0670.0670.0000.0000.0000.000
197C393GLY00.029-0.00931.009-0.005-0.0050.0000.0000.0000.000
198C394GLN0-0.005-0.01332.1770.0030.0030.0000.0000.0000.000
199C395LEU00.0960.04731.907-0.003-0.0030.0000.0000.0000.000
200C396TYR0-0.061-0.03025.1980.0020.0020.0000.0000.0000.000
201C397LEU00.0470.02329.5770.0000.0000.0000.0000.0000.000
202C398GLN00.000-0.00922.334-0.005-0.0050.0000.0000.0000.000
203C399SER00.0340.01224.9230.0000.0000.0000.0000.0000.000
204C400SER0-0.011-0.01522.8290.0090.0090.0000.0000.0000.000
205C401VAL0-0.075-0.00620.5170.0310.0310.0000.0000.0000.000