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: 85GKY

Calculation Name: 5SV7-D-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: D

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2318803.981918
FMO2-HF: Nuclear repulsion 2235185.07823
FMO2-HF: Total energy -83618.903689
FMO2-MP2: Total energy -83862.848856


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(D:104:SER)


Summations of interaction energy for fragment #1(D: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.
-18.356-15.80411.132-6.985-6.697-0.036
Interaction energy analysis for fragmet #1(D:104:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.046
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].
3D106VAL0-0.033-0.0183.831-0.8570.162-0.013-0.595-0.4100.002
4D107ILE0-0.043-0.0086.8860.7480.7480.0000.0000.0000.000
5D108ILE00.018-0.0089.742-0.093-0.0930.0000.0000.0000.000
6D109SER0-0.0280.00613.2390.1410.1410.0000.0000.0000.000
7D110THR00.0310.01316.225-0.068-0.0680.0000.0000.0000.000
8D111LEU00.0260.01319.1140.0510.0510.0000.0000.0000.000
9D112ASP-1-0.843-0.92421.637-0.208-0.2080.0000.0000.0000.000
10D113GLY0-0.043-0.02621.8840.0230.0230.0000.0000.0000.000
11D114ARG10.7640.84016.8860.1940.1940.0000.0000.0000.000
12D115ILE0-0.025-0.02412.426-0.031-0.0310.0000.0000.0000.000
13D116ALA0-0.033-0.03012.9000.0700.0700.0000.0000.0000.000
14D117ALA00.0030.0047.453-0.130-0.1300.0000.0000.0000.000
15D118LEU0-0.015-0.0028.5500.2670.2670.0000.0000.0000.000
16D119ASP-1-0.785-0.8844.454-2.471-2.408-0.001-0.014-0.0490.000
17D120PRO0-0.030-0.0133.8671.0771.2780.001-0.045-0.1560.000
18D121GLU-1-0.936-0.9693.287-10.750-8.4740.096-1.240-1.133-0.010
19D122ASN0-0.045-0.0276.8210.8850.8850.0000.0000.0000.000
20D123HIS00.0570.0289.5320.1680.1680.0000.0000.0000.000
21D124GLY0-0.054-0.03210.580-0.027-0.0270.0000.0000.0000.000
22D125LYS10.9010.9649.6490.3360.3360.0000.0000.0000.000
23D126LYS10.8730.9339.5230.1350.1350.0000.0000.0000.000
24D127GLN0-0.026-0.0275.3890.5480.5480.0000.0000.0000.000
25D128TRP0-0.051-0.0157.231-0.105-0.1050.0000.0000.0000.000
26D129ASP-1-0.794-0.89511.382-0.278-0.2780.0000.0000.0000.000
27D130LEU0-0.0280.01213.9530.0560.0560.0000.0000.0000.000
28D131ASP-1-0.749-0.83516.000-0.113-0.1130.0000.0000.0000.000
29D132VAL0-0.034-0.01719.7570.0320.0320.0000.0000.0000.000
30D133GLY00.0690.02521.251-0.018-0.0180.0000.0000.0000.000
31D134SER0-0.098-0.05724.063-0.009-0.0090.0000.0000.0000.000
32D135GLY00.0320.02425.388-0.009-0.0090.0000.0000.0000.000
33D136SER0-0.019-0.00225.170-0.011-0.0110.0000.0000.0000.000
34D137LEU0-0.0120.00421.6690.0170.0170.0000.0000.0000.000
35D138VAL00.0010.00925.9750.0150.0150.0000.0000.0000.000
36D139SER0-0.049-0.01828.8830.0010.0010.0000.0000.0000.000
37D140SER0-0.016-0.03532.2270.0010.0010.0000.0000.0000.000
38D141SER0-0.0600.02235.423-0.005-0.0050.0000.0000.0000.000
39D142LEU00.0620.04136.3180.0070.0070.0000.0000.0000.000
40D151LYS10.7640.84244.2990.0840.0840.0000.0000.0000.000
41D152MET0-0.015-0.00937.8240.0020.0020.0000.0000.0000.000
42D153ILE00.0000.02038.358-0.004-0.0040.0000.0000.0000.000
43D154ILE00.009-0.00633.3960.0000.0000.0000.0000.0000.000
44D155PRO0-0.0090.01331.9270.0020.0020.0000.0000.0000.000
45D156SER0-0.002-0.00927.952-0.019-0.0190.0000.0000.0000.000
46D157LEU00.008-0.01523.3110.0150.0150.0000.0000.0000.000
47D158ASP-1-0.863-0.90825.047-0.111-0.1110.0000.0000.0000.000
48D159GLY0-0.022-0.04026.5700.0230.0230.0000.0000.0000.000
49D160ALA00.0240.04130.3590.0090.0090.0000.0000.0000.000
50D161LEU0-0.006-0.01432.843-0.001-0.0010.0000.0000.0000.000
51D162PHE00.010-0.00631.8960.0000.0000.0000.0000.0000.000
52D163GLN0-0.057-0.00937.0290.0040.0040.0000.0000.0000.000
53D164TRP00.0390.01039.030-0.001-0.0010.0000.0000.0000.000
54D165ASP-1-0.802-0.89840.964-0.078-0.0780.0000.0000.0000.000
55D166GLN00.0130.01644.058-0.001-0.0010.0000.0000.0000.000
56D167ASP-1-0.832-0.88845.063-0.082-0.0820.0000.0000.0000.000
57D168ARG10.7620.84946.2930.0820.0820.0000.0000.0000.000
58D169GLU-1-0.911-0.96141.842-0.134-0.1340.0000.0000.0000.000
59D170SER00.0050.03141.632-0.007-0.0070.0000.0000.0000.000
60D171MET0-0.059-0.03135.4130.0050.0050.0000.0000.0000.000
61D172GLU-1-0.831-0.90639.109-0.095-0.0950.0000.0000.0000.000
62D173THR0-0.004-0.01138.467-0.006-0.0060.0000.0000.0000.000
63D174VAL0-0.0180.00238.8310.0060.0060.0000.0000.0000.000
64D175PRO0-0.021-0.00539.690-0.002-0.0020.0000.0000.0000.000
65D176PHE00.025-0.00339.4090.0060.0060.0000.0000.0000.000
66D177THR00.012-0.00933.317-0.009-0.0090.0000.0000.0000.000
67D178VAL00.0370.01933.0760.0070.0070.0000.0000.0000.000
68D179GLU-1-0.786-0.90131.332-0.021-0.0210.0000.0000.0000.000
69D180SER0-0.0220.00535.1290.0030.0030.0000.0000.0000.000
70D181LEU00.0170.00638.0150.0030.0030.0000.0000.0000.000
71D182LEU0-0.066-0.02235.6700.0050.0050.0000.0000.0000.000
72D183GLU-1-0.957-0.96438.644-0.008-0.0080.0000.0000.0000.000
73D184SER0-0.004-0.00741.711-0.004-0.0040.0000.0000.0000.000
74D185SER0-0.067-0.04242.881-0.004-0.0040.0000.0000.0000.000
75D186TYR0-0.040-0.02442.7790.0010.0010.0000.0000.0000.000
76D187LYS10.8510.92847.5990.0300.0300.0000.0000.0000.000
77D188PHE00.025-0.00346.8260.0010.0010.0000.0000.0000.000
78D189GLY0-0.0160.00149.9520.0020.0020.0000.0000.0000.000
79D190ASP-1-0.907-0.95051.143-0.024-0.0240.0000.0000.0000.000
80D191ASP-1-0.878-0.93151.943-0.026-0.0260.0000.0000.0000.000
81D192VAL0-0.060-0.03547.5840.0020.0020.0000.0000.0000.000
82D193VAL0-0.040-0.01846.6890.0010.0010.0000.0000.0000.000
83D194LEU00.0260.00642.248-0.003-0.0030.0000.0000.0000.000
84D195VAL0-0.024-0.01639.8890.0060.0060.0000.0000.0000.000
85D196GLY00.0390.00137.095-0.008-0.0080.0000.0000.0000.000
86D197GLY00.0260.00334.8740.0070.0070.0000.0000.0000.000
87D198LYS10.8400.94028.601-0.009-0.0090.0000.0000.0000.000
88D199SER0-0.023-0.00728.5890.0180.0180.0000.0000.0000.000
89D200LEU00.036-0.00624.884-0.017-0.0170.0000.0000.0000.000
90D201THR0-0.0220.00922.6110.0270.0270.0000.0000.0000.000
91D202THR00.0350.00818.335-0.025-0.0250.0000.0000.0000.000
92D203TYR0-0.022-0.01317.1990.0000.0000.0000.0000.0000.000
93D204GLY00.0250.03015.6030.0340.0340.0000.0000.0000.000
94D205LEU0-0.002-0.01311.499-0.065-0.0650.0000.0000.0000.000
95D206SER00.020-0.01311.0630.0500.0500.0000.0000.0000.000
96D207ALA0-0.0230.0175.9940.3460.3460.0000.0000.0000.000
97D208TYR00.0130.0273.853-0.799-0.4680.006-0.075-0.2630.000
98D209SER00.0330.0157.4810.1380.1380.0000.0000.0000.000
99D210GLY00.035-0.0259.800-0.007-0.0070.0000.0000.0000.000
100D211LYS11.0200.97410.816-0.648-0.6480.0000.0000.0000.000
101D212VAL0-0.0200.01614.2550.0930.0930.0000.0000.0000.000
102D213ARG10.9010.97914.941-0.733-0.7330.0000.0000.0000.000
103D214TYR00.0540.01917.605-0.024-0.0240.0000.0000.0000.000
104D215ILE0-0.036-0.04519.3040.0020.0020.0000.0000.0000.000
105D216CYS0-0.0550.01221.760-0.026-0.0260.0000.0000.0000.000
106D217SER00.032-0.00523.7500.0020.0020.0000.0000.0000.000
107D218ALA00.0390.03126.8690.0090.0090.0000.0000.0000.000
108D219LEU00.0060.00429.853-0.001-0.0010.0000.0000.0000.000
109D220GLY00.0250.00929.9740.0000.0000.0000.0000.0000.000
110D221CYS0-0.019-0.01826.0380.0080.0080.0000.0000.0000.000
111D222ARG10.8940.96324.716-0.186-0.1860.0000.0000.0000.000
112D223GLN00.010-0.00421.1590.0470.0470.0000.0000.0000.000
113D224TRP0-0.001-0.00720.602-0.031-0.0310.0000.0000.0000.000
114D225ASP-1-0.939-0.96321.0480.4450.4450.0000.0000.0000.000
115D235ILE0-0.012-0.0088.444-0.109-0.1090.0000.0000.0000.000
116D236LEU0-0.020-0.0137.5060.2230.2230.0000.0000.0000.000
117D237LEU0-0.077-0.04210.629-0.133-0.1330.0000.0000.0000.000
118D238LEU00.0300.00912.979-0.065-0.0650.0000.0000.0000.000
119D239GLN0-0.0010.01815.401-0.005-0.0050.0000.0000.0000.000
120D240ARG10.8430.94218.9510.0010.0010.0000.0000.0000.000
121D241THR00.019-0.01421.4140.0250.0250.0000.0000.0000.000
122D242GLN00.0090.00324.672-0.024-0.0240.0000.0000.0000.000
123D243LYS10.8630.94627.6310.0810.0810.0000.0000.0000.000
124D244THR0-0.034-0.00930.912-0.008-0.0080.0000.0000.0000.000
125D245VAL00.0600.02834.0020.0030.0030.0000.0000.0000.000
126D246ARG10.8290.92235.9510.0210.0210.0000.0000.0000.000
127D247ALA00.0650.04640.1950.0030.0030.0000.0000.0000.000
128D248VAL0-0.022-0.00743.807-0.001-0.0010.0000.0000.0000.000
129D249GLY00.0770.04446.3730.0000.0000.0000.0000.0000.000
130D250PRO0-0.0290.00850.0870.0000.0000.0000.0000.0000.000
131D251ARG10.9670.97953.0010.0060.0060.0000.0000.0000.000
132D252SER0-0.025-0.02152.0620.0020.0020.0000.0000.0000.000
133D253GLY00.0430.02648.519-0.002-0.0020.0000.0000.0000.000
134D254ASN0-0.048-0.02547.3810.0020.0020.0000.0000.0000.000
135D255GLU-1-0.811-0.91740.725-0.039-0.0390.0000.0000.0000.000
136D256LYS10.9040.95444.8200.0260.0260.0000.0000.0000.000
137D257TRP00.0530.00540.112-0.004-0.0040.0000.0000.0000.000
138D258ASN0-0.054-0.05336.8400.0120.0120.0000.0000.0000.000
139D259PHE00.0750.02534.572-0.008-0.0080.0000.0000.0000.000
140D260SER0-0.080-0.04431.1440.0150.0150.0000.0000.0000.000
141D261VAL00.0600.04228.019-0.013-0.0130.0000.0000.0000.000
142D262GLY00.0100.00125.2850.0200.0200.0000.0000.0000.000
143D263HIS0-0.018-0.03321.374-0.028-0.0280.0000.0000.0000.000
144D264PHE0-0.008-0.03617.0220.0330.0330.0000.0000.0000.000
145D265GLU-1-0.884-0.90816.377-0.085-0.0850.0000.0000.0000.000
146D266LEU0-0.004-0.0189.7460.0710.0710.0000.0000.0000.000
147D267ARG10.9680.97412.220-0.472-0.4720.0000.0000.0000.000
148D268TYR0-0.009-0.0048.9290.0120.0120.0000.0000.0000.000
149D269ILE0-0.0310.00111.307-0.173-0.1730.0000.0000.0000.000
150D270PRO00.0370.0269.2770.1350.1350.0000.0000.0000.000
151D310ILE0-0.022-0.0207.9050.1020.1020.0000.0000.0000.000
152D311LYS10.9220.94111.4031.0681.0680.0000.0000.0000.000
153D312VAL0-0.039-0.01312.5740.0520.0520.0000.0000.0000.000
154D313SER0-0.0090.00115.2750.0890.0890.0000.0000.0000.000
155D314VAL00.0760.00818.615-0.025-0.0250.0000.0000.0000.000
156D315ALA00.0060.01821.0750.0360.0360.0000.0000.0000.000
157D316ASP-1-0.854-0.92322.266-0.425-0.4250.0000.0000.0000.000
158D317TRP0-0.018-0.00420.5850.0050.0050.0000.0000.0000.000
159D318LYS10.8720.93918.8090.5220.5220.0000.0000.0000.000
160D319VAL00.0200.01112.262-0.046-0.0460.0000.0000.0000.000
161D320MET00.0810.06011.1910.1130.1130.0000.0000.0000.000
162D333TYR00.009-0.00714.5160.0450.0450.0000.0000.0000.000
163D334GLN00.013-0.00216.450-0.052-0.0520.0000.0000.0000.000
164D335PHE00.0230.01415.5070.0260.0260.0000.0000.0000.000
165D336CYS0-0.045-0.02619.9610.0420.0420.0000.0000.0000.000
166D337THR0-0.011-0.01522.8440.0340.0340.0000.0000.0000.000
167D338PRO0-0.0230.00722.138-0.036-0.0360.0000.0000.0000.000
168D339ILE0-0.0010.00217.5840.0150.0150.0000.0000.0000.000
169D340ALA00.0370.01918.6910.0330.0330.0000.0000.0000.000
170D341SER0-0.043-0.04015.8330.0270.0270.0000.0000.0000.000
171D342ALA00.0220.00511.855-0.011-0.0110.0000.0000.0000.000
172D343TRP00.005-0.0069.0730.1390.1390.0000.0000.0000.000
173D344LEU00.0140.0034.084-0.535-0.445-0.001-0.021-0.0680.000
174D345LEU00.0100.0322.9160.9032.5560.510-0.838-1.3240.003
175D346LYS11.0280.9891.909-7.373-10.53810.522-4.205-3.152-0.031
176D347ASP-1-0.862-0.9213.6651.4321.5160.0120.048-0.1420.000
177D348GLY00.0270.0235.414-0.156-0.1560.0000.0000.0000.000
178D349LYS10.8170.8876.150-0.439-0.4390.0000.0000.0000.000
179D350VAL0-0.0030.0036.963-0.432-0.4320.0000.0000.0000.000
180D351ILE0-0.0270.0157.0410.1250.1250.0000.0000.0000.000
181D352PRO00.0190.0039.025-0.318-0.3180.0000.0000.0000.000
182D353ILE0-0.016-0.0039.930-0.143-0.1430.0000.0000.0000.000
183D354SER00.004-0.00312.6870.1540.1540.0000.0000.0000.000
184D355LEU00.0210.02416.393-0.045-0.0450.0000.0000.0000.000
185D371GLU-1-0.943-0.97839.630-0.141-0.1410.0000.0000.0000.000
186D372GLU-1-1.006-1.00939.659-0.136-0.1360.0000.0000.0000.000
187D373ASP-1-0.851-0.94337.476-0.183-0.1830.0000.0000.0000.000
188D374ILE00.0100.00635.046-0.013-0.0130.0000.0000.0000.000
189D375VAL0-0.046-0.02834.647-0.009-0.0090.0000.0000.0000.000
190D376GLU-1-0.941-0.96135.154-0.207-0.2070.0000.0000.0000.000
191D377ALA00.0600.03331.370-0.013-0.0130.0000.0000.0000.000
192D378ALA0-0.068-0.02730.564-0.018-0.0180.0000.0000.0000.000
193D379ARG10.8780.91331.7100.1500.1500.0000.0000.0000.000
194D380GLY00.0700.07331.3160.0010.0010.0000.0000.0000.000
195D381ALA0-0.039-0.02727.314-0.018-0.0180.0000.0000.0000.000
196D382THR0-0.035-0.01828.112-0.003-0.0030.0000.0000.0000.000
197D383GLU-1-0.879-0.94430.413-0.237-0.2370.0000.0000.0000.000
198D384ASN0-0.076-0.03825.600-0.040-0.0400.0000.0000.0000.000
199D385SER0-0.086-0.02525.185-0.024-0.0240.0000.0000.0000.000
200D386VAL0-0.018-0.02925.598-0.010-0.0100.0000.0000.0000.000
201D387TYR0-0.025-0.00725.472-0.012-0.0120.0000.0000.0000.000
202D388LEU00.0100.01327.5070.0130.0130.0000.0000.0000.000
203D389GLY00.0270.00228.347-0.013-0.0130.0000.0000.0000.000
204D390MET0-0.051-0.03529.0800.0230.0230.0000.0000.0000.000
205D391TYR00.002-0.00626.599-0.022-0.0220.0000.0000.0000.000
206D392ARG10.8700.92826.4320.1970.1970.0000.0000.0000.000
207D393GLY00.0420.02732.1990.0130.0130.0000.0000.0000.000
208D394GLN00.0170.01832.2410.0100.0100.0000.0000.0000.000
209D395LEU00.0570.02632.232-0.013-0.0130.0000.0000.0000.000
210D396TYR0-0.028-0.01824.5370.0160.0160.0000.0000.0000.000
211D397LEU00.0550.03229.212-0.015-0.0150.0000.0000.0000.000
212D398GLN0-0.034-0.02821.1140.0070.0070.0000.0000.0000.000
213D399SER00.0360.03125.1600.0000.0000.0000.0000.0000.000
214D400SER00.0230.02722.887-0.002-0.0020.0000.0000.0000.000