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

tag_button

FMODB ID: N9Z6Q

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2317961.90533
FMO2-HF: Nuclear repulsion 2234341.073922
FMO2-HF: Total energy -83620.831408
FMO2-MP2: Total energy -83864.548196


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.
-26.021-21.97517.21-11.429-9.826-0.089
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 : -0.048 / q_NPA : -0.036
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].
3D106VAL0-0.0010.0043.863-1.687-0.410-0.004-0.693-0.5800.002
4D107ILE0-0.034-0.0256.8420.9350.9350.0000.0000.0000.000
5D108ILE00.009-0.0049.793-0.255-0.2550.0000.0000.0000.000
6D109SER00.0080.01013.4100.1660.1660.0000.0000.0000.000
7D110THR00.011-0.02616.537-0.098-0.0980.0000.0000.0000.000
8D111LEU00.0740.03819.6520.0440.0440.0000.0000.0000.000
9D112ASP-1-0.798-0.86021.9790.0440.0440.0000.0000.0000.000
10D113GLY0-0.041-0.01622.8110.0210.0210.0000.0000.0000.000
11D114ARG10.7250.82017.767-0.203-0.2030.0000.0000.0000.000
12D115ILE0-0.0010.00413.707-0.029-0.0290.0000.0000.0000.000
13D116ALA0-0.019-0.02713.6130.0690.0690.0000.0000.0000.000
14D117ALA0-0.0010.0128.171-0.081-0.0810.0000.0000.0000.000
15D118LEU00.000-0.0067.857-0.018-0.0180.0000.0000.0000.000
16D119ASP-1-0.769-0.8793.5900.3290.5260.006-0.061-0.1420.000
17D120PRO0-0.024-0.0073.3580.4550.8290.008-0.065-0.3170.000
18D121GLU-1-0.883-0.9562.362-18.214-13.3864.590-4.899-4.519-0.052
19D122ASN0-0.086-0.0486.0670.6590.6590.0000.0000.0000.000
20D123HIS00.022-0.0017.9890.2340.2340.0000.0000.0000.000
21D124GLY00.0140.0208.932-0.021-0.0210.0000.0000.0000.000
22D125LYS10.8930.9618.289-0.359-0.3590.0000.0000.0000.000
23D126LYS10.8910.9448.395-0.291-0.2910.0000.0000.0000.000
24D127GLN0-0.075-0.0485.4360.4280.4280.0000.0000.0000.000
25D128TRP0-0.032-0.0278.389-0.428-0.4280.0000.0000.0000.000
26D129ASP-1-0.757-0.86312.1840.3340.3340.0000.0000.0000.000
27D130LEU0-0.039-0.01814.8970.0530.0530.0000.0000.0000.000
28D131ASP-1-0.774-0.84917.5380.2300.2300.0000.0000.0000.000
29D132VAL0-0.021-0.00420.8380.0090.0090.0000.0000.0000.000
30D133GLY00.022-0.00122.364-0.032-0.0320.0000.0000.0000.000
31D134SER0-0.081-0.04224.955-0.019-0.0190.0000.0000.0000.000
32D135GLY00.0530.04326.772-0.021-0.0210.0000.0000.0000.000
33D136SER00.0160.01525.7100.0120.0120.0000.0000.0000.000
34D137LEU0-0.046-0.00921.3910.0070.0070.0000.0000.0000.000
35D138VAL00.0200.02225.8020.0030.0030.0000.0000.0000.000
36D139SER0-0.083-0.05228.9760.0100.0100.0000.0000.0000.000
37D140SER0-0.006-0.01432.4570.0010.0010.0000.0000.0000.000
38D141SER0-0.0660.00535.723-0.004-0.0040.0000.0000.0000.000
39D142LEU00.0280.02236.2170.0010.0010.0000.0000.0000.000
40D151LYS10.7480.83444.2080.0510.0510.0000.0000.0000.000
41D152MET0-0.059-0.02438.0620.0060.0060.0000.0000.0000.000
42D153ILE00.0040.01738.416-0.005-0.0050.0000.0000.0000.000
43D154ILE00.000-0.00733.6770.0030.0030.0000.0000.0000.000
44D155PRO0-0.021-0.00131.970-0.001-0.0010.0000.0000.0000.000
45D156SER00.007-0.01328.200-0.016-0.0160.0000.0000.0000.000
46D157LEU0-0.009-0.02223.2810.0180.0180.0000.0000.0000.000
47D158ASP-1-0.848-0.89825.465-0.054-0.0540.0000.0000.0000.000
48D159GLY00.010-0.02526.6440.0210.0210.0000.0000.0000.000
49D160ALA00.0230.03630.4680.0070.0070.0000.0000.0000.000
50D161LEU0-0.028-0.02132.6660.0010.0010.0000.0000.0000.000
51D162PHE00.0150.01332.244-0.003-0.0030.0000.0000.0000.000
52D163GLN0-0.034-0.02737.3600.0100.0100.0000.0000.0000.000
53D164TRP0-0.001-0.00338.8650.0000.0000.0000.0000.0000.000
54D165ASP-1-0.771-0.89340.702-0.048-0.0480.0000.0000.0000.000
55D166GLN00.0380.02644.1610.0010.0010.0000.0000.0000.000
56D167ASP-1-0.811-0.87244.996-0.054-0.0540.0000.0000.0000.000
57D168ARG10.7320.83446.1290.0580.0580.0000.0000.0000.000
58D169GLU-1-0.904-0.93741.617-0.100-0.1000.0000.0000.0000.000
59D170SER00.0170.01941.584-0.007-0.0070.0000.0000.0000.000
60D171MET0-0.059-0.03235.4630.0090.0090.0000.0000.0000.000
61D172GLU-1-0.816-0.88638.718-0.074-0.0740.0000.0000.0000.000
62D173THR00.007-0.00438.444-0.001-0.0010.0000.0000.0000.000
63D174VAL00.0070.00238.8800.0050.0050.0000.0000.0000.000
64D175PRO0-0.0250.00639.612-0.002-0.0020.0000.0000.0000.000
65D176PHE00.0240.00739.3830.0060.0060.0000.0000.0000.000
66D177THR00.023-0.00533.136-0.009-0.0090.0000.0000.0000.000
67D178VAL0-0.018-0.00632.8000.0070.0070.0000.0000.0000.000
68D179GLU-1-0.792-0.89831.0560.0240.0240.0000.0000.0000.000
69D180SER0-0.018-0.02035.0610.0030.0030.0000.0000.0000.000
70D181LEU0-0.005-0.00538.1040.0000.0000.0000.0000.0000.000
71D182LEU0-0.079-0.02835.6020.0040.0040.0000.0000.0000.000
72D183GLU-1-0.905-0.92039.1860.0110.0110.0000.0000.0000.000
73D184SER0-0.038-0.05141.638-0.002-0.0020.0000.0000.0000.000
74D185SER0-0.033-0.00742.369-0.005-0.0050.0000.0000.0000.000
75D186TYR0-0.045-0.04042.654-0.002-0.0020.0000.0000.0000.000
76D187LYS10.8600.93547.4090.0040.0040.0000.0000.0000.000
77D188PHE00.0190.00246.6150.0030.0030.0000.0000.0000.000
78D189GLY0-0.0080.00249.8250.0000.0000.0000.0000.0000.000
79D190ASP-1-0.907-0.93151.4350.0020.0020.0000.0000.0000.000
80D191ASP-1-0.848-0.93251.8030.0050.0050.0000.0000.0000.000
81D192VAL0-0.081-0.04547.5080.0040.0040.0000.0000.0000.000
82D193VAL0-0.038-0.01647.090-0.001-0.0010.0000.0000.0000.000
83D194LEU00.0120.01042.2340.0010.0010.0000.0000.0000.000
84D195VAL0-0.005-0.00540.8910.0050.0050.0000.0000.0000.000
85D196GLY00.006-0.01337.584-0.004-0.0040.0000.0000.0000.000
86D197GLY0-0.007-0.00335.1860.0060.0060.0000.0000.0000.000
87D198LYS10.8920.94228.533-0.056-0.0560.0000.0000.0000.000
88D199SER0-0.0170.00129.0430.0130.0130.0000.0000.0000.000
89D200LEU00.0400.00925.199-0.013-0.0130.0000.0000.0000.000
90D201THR0-0.023-0.00623.9430.0150.0150.0000.0000.0000.000
91D202THR0-0.017-0.01419.309-0.001-0.0010.0000.0000.0000.000
92D203TYR0-0.020-0.00918.2050.0010.0010.0000.0000.0000.000
93D204GLY00.0240.02416.3710.0510.0510.0000.0000.0000.000
94D205LEU00.019-0.00512.697-0.042-0.0420.0000.0000.0000.000
95D206SER0-0.014-0.02812.375-0.007-0.0070.0000.0000.0000.000
96D207ALA0-0.0130.0197.0690.2820.2820.0000.0000.0000.000
97D208TYR00.0440.0234.6300.3370.449-0.001-0.005-0.1060.000
98D209SER00.0080.0158.547-0.225-0.2250.0000.0000.0000.000
99D210GLY00.020-0.01210.818-0.257-0.2570.0000.0000.0000.000
100D211LYS10.9670.97011.400-0.993-0.9930.0000.0000.0000.000
101D212VAL00.0020.01714.9810.0890.0890.0000.0000.0000.000
102D213ARG10.8490.93315.885-0.819-0.8190.0000.0000.0000.000
103D214TYR00.029-0.00218.449-0.050-0.0500.0000.0000.0000.000
104D215ILE00.006-0.00820.2630.0280.0280.0000.0000.0000.000
105D216CYS0-0.0610.00622.897-0.046-0.0460.0000.0000.0000.000
106D217SER00.0730.02124.843-0.012-0.0120.0000.0000.0000.000
107D218ALA00.0560.03327.8390.0040.0040.0000.0000.0000.000
108D219LEU0-0.0050.00831.236-0.005-0.0050.0000.0000.0000.000
109D220GLY00.0490.03531.0970.0090.0090.0000.0000.0000.000
110D221CYS00.000-0.01326.2370.0120.0120.0000.0000.0000.000
111D222ARG10.8590.92425.880-0.283-0.2830.0000.0000.0000.000
112D223GLN0-0.008-0.02322.0150.0650.0650.0000.0000.0000.000
113D224TRP00.0240.02621.710-0.032-0.0320.0000.0000.0000.000
114D225ASP-1-0.900-0.93921.7650.5820.5820.0000.0000.0000.000
115D235ILE0-0.025-0.0149.159-0.086-0.0860.0000.0000.0000.000
116D236LEU0-0.010-0.0018.4610.0770.0770.0000.0000.0000.000
117D237LEU0-0.033-0.02211.345-0.085-0.0850.0000.0000.0000.000
118D238LEU00.0200.01513.751-0.058-0.0580.0000.0000.0000.000
119D239GLN0-0.021-0.00416.0730.0010.0010.0000.0000.0000.000
120D240ARG10.8140.90919.166-0.161-0.1610.0000.0000.0000.000
121D241THR00.014-0.01621.7160.0070.0070.0000.0000.0000.000
122D242GLN0-0.021-0.01924.7660.0010.0010.0000.0000.0000.000
123D243LYS10.8040.92127.6830.0170.0170.0000.0000.0000.000
124D244THR00.0000.00030.709-0.007-0.0070.0000.0000.0000.000
125D245VAL00.0340.02333.8480.0040.0040.0000.0000.0000.000
126D246ARG10.8690.92737.125-0.049-0.0490.0000.0000.0000.000
127D247ALA00.0610.05340.3900.0010.0010.0000.0000.0000.000
128D248VAL00.003-0.00644.0190.0000.0000.0000.0000.0000.000
129D249GLY00.0570.02646.698-0.002-0.0020.0000.0000.0000.000
130D250PRO0-0.0090.01850.4650.0000.0000.0000.0000.0000.000
131D251ARG10.9610.97353.405-0.029-0.0290.0000.0000.0000.000
132D252SER00.0110.00152.7140.0020.0020.0000.0000.0000.000
133D253GLY00.0420.03549.311-0.002-0.0020.0000.0000.0000.000
134D254ASN0-0.035-0.03247.8170.0040.0040.0000.0000.0000.000
135D255GLU-1-0.764-0.87541.4100.0240.0240.0000.0000.0000.000
136D256LYS10.7920.90345.268-0.018-0.0180.0000.0000.0000.000
137D257TRP00.0570.01640.209-0.003-0.0030.0000.0000.0000.000
138D258ASN0-0.049-0.04236.9250.0100.0100.0000.0000.0000.000
139D259PHE00.0550.01034.933-0.007-0.0070.0000.0000.0000.000
140D260SER0-0.026-0.01831.4830.0090.0090.0000.0000.0000.000
141D261VAL00.0320.01528.386-0.010-0.0100.0000.0000.0000.000
142D262GLY00.0180.01325.2870.0170.0170.0000.0000.0000.000
143D263HIS0-0.020-0.02921.779-0.020-0.0200.0000.0000.0000.000
144D264PHE0-0.016-0.02817.1140.0570.0570.0000.0000.0000.000
145D265GLU-1-0.867-0.90616.341-0.033-0.0330.0000.0000.0000.000
146D266LEU0-0.003-0.0139.9410.1120.1120.0000.0000.0000.000
147D267ARG10.9330.96912.555-0.502-0.5020.0000.0000.0000.000
148D268TYR00.005-0.0019.7760.1660.1660.0000.0000.0000.000
149D269ILE0-0.002-0.00511.771-0.248-0.2480.0000.0000.0000.000
150D270PRO0-0.0140.00610.3480.0980.0980.0000.0000.0000.000
151D310ILE0-0.038-0.0257.3880.0740.0740.0000.0000.0000.000
152D311LYS10.9480.96210.3541.0961.0960.0000.0000.0000.000
153D312VAL0-0.0060.00112.667-0.028-0.0280.0000.0000.0000.000
154D313SER0-0.018-0.00515.3580.0620.0620.0000.0000.0000.000
155D314VAL00.0580.00918.955-0.006-0.0060.0000.0000.0000.000
156D315ALA00.0340.01921.6450.0300.0300.0000.0000.0000.000
157D316ASP-1-0.837-0.90621.982-0.301-0.3010.0000.0000.0000.000
158D317TRP0-0.034-0.00820.7440.0090.0090.0000.0000.0000.000
159D318LYS10.8330.90618.1560.3750.3750.0000.0000.0000.000
160D319VAL00.0140.01111.575-0.047-0.0470.0000.0000.0000.000
161D320MET00.0520.04310.1990.0630.0630.0000.0000.0000.000
162D333TYR00.005-0.01013.3010.0540.0540.0000.0000.0000.000
163D334GLN00.0240.00415.358-0.057-0.0570.0000.0000.0000.000
164D335PHE00.0020.00715.5450.0510.0510.0000.0000.0000.000
165D336CYS0-0.043-0.02719.5260.0020.0020.0000.0000.0000.000
166D337THR0-0.014-0.04522.3460.0310.0310.0000.0000.0000.000
167D338PRO0-0.0090.02822.002-0.022-0.0220.0000.0000.0000.000
168D339ILE00.002-0.00517.2400.0370.0370.0000.0000.0000.000
169D340ALA00.0300.01418.7810.0090.0090.0000.0000.0000.000
170D341SER0-0.019-0.02115.941-0.002-0.0020.0000.0000.0000.000
171D342ALA00.0030.00512.0900.0590.0590.0000.0000.0000.000
172D343TRP00.0280.0149.358-0.003-0.0030.0000.0000.0000.000
173D344LEU00.0120.0094.352-0.111-0.033-0.001-0.013-0.0630.000
174D345LEU00.0120.0243.0030.0781.7100.223-0.818-1.0360.001
175D346LYS10.9380.9561.820-7.288-11.83012.385-4.880-2.964-0.040
176D347ASP-1-0.786-0.8903.6200.2840.3740.0040.005-0.0990.000
177D348GLY00.0370.0395.7620.1620.1620.0000.0000.0000.000
178D349LYS10.7960.8846.4960.6290.6290.0000.0000.0000.000
179D350VAL00.0020.0156.355-0.395-0.3950.0000.0000.0000.000
180D351ILE0-0.018-0.0047.0970.0870.0870.0000.0000.0000.000
181D352PRO00.0310.0179.229-0.182-0.1820.0000.0000.0000.000
182D353ILE0-0.039-0.02210.069-0.181-0.1810.0000.0000.0000.000
183D354SER00.0130.00312.6560.1550.1550.0000.0000.0000.000
184D355LEU00.0130.01516.357-0.036-0.0360.0000.0000.0000.000
185D371GLU-1-0.934-0.97139.793-0.160-0.1600.0000.0000.0000.000
186D372GLU-1-0.979-1.00739.456-0.144-0.1440.0000.0000.0000.000
187D373ASP-1-0.842-0.92737.314-0.200-0.2000.0000.0000.0000.000
188D374ILE00.0110.00234.857-0.013-0.0130.0000.0000.0000.000
189D375VAL0-0.051-0.01934.665-0.006-0.0060.0000.0000.0000.000
190D376GLU-1-0.968-0.97835.612-0.202-0.2020.0000.0000.0000.000
191D377ALA00.0020.00431.478-0.010-0.0100.0000.0000.0000.000
192D378ALA0-0.031-0.01230.944-0.015-0.0150.0000.0000.0000.000
193D379ARG10.9290.95531.7270.1550.1550.0000.0000.0000.000
194D380GLY00.0660.06031.3950.0030.0030.0000.0000.0000.000
195D381ALA0-0.033-0.01827.420-0.024-0.0240.0000.0000.0000.000
196D382THR0-0.110-0.07128.1740.0050.0050.0000.0000.0000.000
197D383GLU-1-0.795-0.88130.386-0.231-0.2310.0000.0000.0000.000
198D384ASN0-0.082-0.06025.853-0.024-0.0240.0000.0000.0000.000
199D385SER0-0.091-0.02925.379-0.019-0.0190.0000.0000.0000.000
200D386VAL0-0.016-0.02226.3590.0110.0110.0000.0000.0000.000
201D387TYR0-0.023-0.01325.476-0.014-0.0140.0000.0000.0000.000
202D388LEU00.0260.01227.4820.0190.0190.0000.0000.0000.000
203D389GLY00.0230.01628.326-0.013-0.0130.0000.0000.0000.000
204D390MET0-0.026-0.01129.2560.0170.0170.0000.0000.0000.000
205D391TYR00.031-0.00226.506-0.006-0.0060.0000.0000.0000.000
206D392ARG10.8380.91426.0490.0320.0320.0000.0000.0000.000
207D393GLY00.0470.02832.1100.0100.0100.0000.0000.0000.000
208D394GLN00.0190.01431.9950.0050.0050.0000.0000.0000.000
209D395LEU00.0570.02732.169-0.008-0.0080.0000.0000.0000.000
210D396TYR0-0.061-0.03024.8090.0130.0130.0000.0000.0000.000
211D397LEU00.0690.02729.565-0.013-0.0130.0000.0000.0000.000
212D398GLN0-0.050-0.03821.3540.0120.0120.0000.0000.0000.000
213D399SER00.0170.02225.334-0.002-0.0020.0000.0000.0000.000
214D400SER00.0020.01422.4930.0080.0080.0000.0000.0000.000