Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 721VK

Calculation Name: 3H13-A-Xray372

Preferred Name: CASP8 and FADD-like apoptosis regulator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3H13

Chain ID: A

ChEMBL ID: CHEMBL1955713

UniProt ID: O15519

Base Structure: X-ray

Registration Date: 2023-09-20

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2674616.264472
FMO2-HF: Nuclear repulsion 2587435.028959
FMO2-HF: Total energy -87181.235513
FMO2-MP2: Total energy -87428.591408


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(A:240:PRO)


Summations of interaction energy for fragment #1(A:240:PRO)
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.
0.3532.251-0.01-0.895-0.9930.002
Interaction energy analysis for fragmet #1(A:240:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3A242GLU-1-0.775-0.8583.843-1.5370.361-0.010-0.895-0.9930.002
4A243ARG10.9280.9596.2220.5850.5850.0000.0000.0000.000
5A244TYR0-0.017-0.0408.8190.1050.1050.0000.0000.0000.000
6A245LYS10.7960.88112.2820.0160.0160.0000.0000.0000.000
7A246MET0-0.014-0.00613.3900.0060.0060.0000.0000.0000.000
8A247LYS10.8690.91312.274-0.052-0.0520.0000.0000.0000.000
9A248SER0-0.029-0.00917.6810.0080.0080.0000.0000.0000.000
10A249LYS10.8960.98321.046-0.009-0.0090.0000.0000.0000.000
11A250PRO00.0930.03424.2390.0070.0070.0000.0000.0000.000
12A251LEU00.0030.00619.0890.0000.0000.0000.0000.0000.000
13A252GLY00.0250.01122.079-0.007-0.0070.0000.0000.0000.000
14A253ILE00.0220.03224.7520.0020.0020.0000.0000.0000.000
15A254CYS0-0.079-0.04027.259-0.009-0.0090.0000.0000.0000.000
16A255LEU00.0020.00929.0050.0050.0050.0000.0000.0000.000
17A256ILE00.005-0.00731.899-0.005-0.0050.0000.0000.0000.000
18A257ILE00.0200.00834.2380.0050.0050.0000.0000.0000.000
19A258ASP-1-0.763-0.87937.255-0.046-0.0460.0000.0000.0000.000
20A259CYS0-0.084-0.03639.3670.0030.0030.0000.0000.0000.000
21A260ILE0-0.052-0.02741.1080.0020.0020.0000.0000.0000.000
22A261GLY0-0.005-0.00642.1420.0020.0020.0000.0000.0000.000
23A262ASN00.013-0.00340.6680.0000.0000.0000.0000.0000.000
24A263GLU-1-0.811-0.89234.775-0.053-0.0530.0000.0000.0000.000
25A264THR0-0.027-0.04236.977-0.001-0.0010.0000.0000.0000.000
26A265GLU-1-0.771-0.86036.521-0.038-0.0380.0000.0000.0000.000
27A266LEU00.0350.03733.652-0.002-0.0020.0000.0000.0000.000
28A267LEU00.0270.00729.073-0.004-0.0040.0000.0000.0000.000
29A268ARG10.9220.96230.6480.0330.0330.0000.0000.0000.000
30A269ASP-1-0.812-0.88331.771-0.044-0.0440.0000.0000.0000.000
31A270THR0-0.121-0.07126.798-0.001-0.0010.0000.0000.0000.000
32A271PHE00.040-0.00824.238-0.004-0.0040.0000.0000.0000.000
33A272THR00.0210.00927.0480.0020.0020.0000.0000.0000.000
34A273SER0-0.031-0.00727.8640.0000.0000.0000.0000.0000.000
35A274LEU0-0.093-0.04622.0090.0000.0000.0000.0000.0000.000
36A275GLY0-0.0100.00222.973-0.003-0.0030.0000.0000.0000.000
37A276TYR0-0.053-0.04421.239-0.002-0.0020.0000.0000.0000.000
38A277GLU-1-0.826-0.90226.631-0.026-0.0260.0000.0000.0000.000
39A278VAL0-0.040-0.03229.971-0.003-0.0030.0000.0000.0000.000
40A279GLN0-0.042-0.01532.1070.0050.0050.0000.0000.0000.000
41A280LYS10.7960.86634.8360.0380.0380.0000.0000.0000.000
42A281PHE0-0.017-0.00536.4310.0030.0030.0000.0000.0000.000
43A282LEU00.0240.00540.008-0.003-0.0030.0000.0000.0000.000
44A283HIS0-0.025-0.01742.8420.0020.0020.0000.0000.0000.000
45A284LEU00.0060.02240.3700.0020.0020.0000.0000.0000.000
46A285SER00.0820.04344.395-0.002-0.0020.0000.0000.0000.000
47A286MET0-0.019-0.00543.130-0.001-0.0010.0000.0000.0000.000
48A287HIS00.0180.00942.818-0.002-0.0020.0000.0000.0000.000
49A288GLY00.0290.01443.7170.0000.0000.0000.0000.0000.000
50A289ILE0-0.006-0.00838.168-0.001-0.0010.0000.0000.0000.000
51A290SER0-0.010-0.01138.860-0.002-0.0020.0000.0000.0000.000
52A291GLN0-0.037-0.00539.3570.0000.0000.0000.0000.0000.000
53A292ILE00.0140.00236.9980.0000.0000.0000.0000.0000.000
54A293LEU0-0.028-0.02233.629-0.001-0.0010.0000.0000.0000.000
55A294GLY00.024-0.00534.766-0.001-0.0010.0000.0000.0000.000
56A295GLN00.0250.01336.1030.0020.0020.0000.0000.0000.000
57A296PHE00.038-0.00531.9850.0010.0010.0000.0000.0000.000
58A297ALA0-0.0260.00231.050-0.001-0.0010.0000.0000.0000.000
59A298CYS0-0.044-0.02231.2980.0010.0010.0000.0000.0000.000
60A299MET0-0.0300.02231.5730.0020.0020.0000.0000.0000.000
61A300PRO00.0340.00530.652-0.002-0.0020.0000.0000.0000.000
62A301GLU-1-0.784-0.92129.435-0.014-0.0140.0000.0000.0000.000
63A302HIS00.009-0.00226.026-0.003-0.0030.0000.0000.0000.000
64A303ARG10.8410.94024.703-0.014-0.0140.0000.0000.0000.000
65A304ASP-1-0.933-0.97423.9660.0090.0090.0000.0000.0000.000
66A305TYR0-0.046-0.03122.9180.0010.0010.0000.0000.0000.000
67A306ASP-1-0.713-0.85117.857-0.037-0.0370.0000.0000.0000.000
68A307SER0-0.046-0.01418.917-0.024-0.0240.0000.0000.0000.000
69A308PHE00.0390.02121.1950.0130.0130.0000.0000.0000.000
70A309VAL00.0000.01123.968-0.013-0.0130.0000.0000.0000.000
71A310CYS0-0.043-0.00526.1780.0110.0110.0000.0000.0000.000
72A311VAL00.0310.01229.407-0.007-0.0070.0000.0000.0000.000
73A312LEU0-0.014-0.00631.6140.0050.0050.0000.0000.0000.000
74A313VAL00.0220.01434.814-0.004-0.0040.0000.0000.0000.000
75A314SER0-0.021-0.03537.5340.0050.0050.0000.0000.0000.000
76A315ARG11.0291.03140.4850.0340.0340.0000.0000.0000.000
77A316GLY00.0410.01041.4770.0000.0000.0000.0000.0000.000
78A317GLY00.0720.06141.6990.0010.0010.0000.0000.0000.000
79A318SER0-0.009-0.00938.843-0.002-0.0020.0000.0000.0000.000
80A319GLN0-0.025-0.02835.380-0.002-0.0020.0000.0000.0000.000
81A320SER0-0.026-0.00237.1990.0010.0010.0000.0000.0000.000
82A321VAL00.0220.01837.792-0.001-0.0010.0000.0000.0000.000
83A322TYR00.0530.00540.6090.0010.0010.0000.0000.0000.000
84A323GLY00.0380.03342.5310.0020.0020.0000.0000.0000.000
85A324VAL0-0.088-0.06443.5700.0000.0000.0000.0000.0000.000
86A325ASP-1-0.828-0.90346.920-0.029-0.0290.0000.0000.0000.000
87A326GLN0-0.049-0.01548.612-0.001-0.0010.0000.0000.0000.000
88A327THR00.007-0.01347.2330.0010.0010.0000.0000.0000.000
89A328HIS00.0550.02248.317-0.002-0.0020.0000.0000.0000.000
90A329SER0-0.058-0.01546.117-0.001-0.0010.0000.0000.0000.000
91A330GLY00.042-0.00243.3190.0010.0010.0000.0000.0000.000
92A331LEU0-0.030-0.00538.6920.0000.0000.0000.0000.0000.000
93A332PRO00.010-0.00638.100-0.003-0.0030.0000.0000.0000.000
94A333LEU00.0530.01433.612-0.001-0.0010.0000.0000.0000.000
95A334HIS0-0.004-0.00532.678-0.005-0.0050.0000.0000.0000.000
96A335HIS00.016-0.01233.305-0.002-0.0020.0000.0000.0000.000
97A336ILE00.0350.02932.2080.0010.0010.0000.0000.0000.000
98A337ARG10.9540.98828.5020.0840.0840.0000.0000.0000.000
99A338ARG10.9180.96629.5130.0420.0420.0000.0000.0000.000
100A339MET0-0.062-0.02131.2920.0020.0020.0000.0000.0000.000
101A340PHE00.0350.01427.6190.0020.0020.0000.0000.0000.000
102A341MET0-0.051-0.00626.272-0.005-0.0050.0000.0000.0000.000
103A342GLY00.0160.01124.9030.0050.0050.0000.0000.0000.000
104A343ASP-1-0.833-0.91425.648-0.046-0.0460.0000.0000.0000.000
105A344SER0-0.047-0.02428.9180.0040.0040.0000.0000.0000.000
106A345CYS0-0.046-0.02127.8700.0030.0030.0000.0000.0000.000
107A346PRO00.0400.01326.233-0.005-0.0050.0000.0000.0000.000
108A347TYR0-0.044-0.00224.9320.0010.0010.0000.0000.0000.000
109A348LEU00.0270.01423.413-0.001-0.0010.0000.0000.0000.000
110A349ALA00.0000.00622.078-0.016-0.0160.0000.0000.0000.000
111A350GLY0-0.056-0.02618.0090.0070.0070.0000.0000.0000.000
112A351LYS10.7950.91517.0830.0200.0200.0000.0000.0000.000
113A352PRO0-0.055-0.01816.8900.0010.0010.0000.0000.0000.000
114A353LYS10.8760.95719.3940.1290.1290.0000.0000.0000.000
115A354MET0-0.065-0.03120.618-0.015-0.0150.0000.0000.0000.000
116A355PHE00.0180.00724.0450.0120.0120.0000.0000.0000.000
117A356PHE00.009-0.00123.510-0.009-0.0090.0000.0000.0000.000
118A357ILE00.0160.00229.1670.0080.0080.0000.0000.0000.000
119A358GLN00.0560.05332.669-0.005-0.0050.0000.0000.0000.000
120A359ASN0-0.014-0.03135.5260.0060.0060.0000.0000.0000.000
121A360TYR00.0300.01838.277-0.002-0.0020.0000.0000.0000.000
122A361VAL00.002-0.00840.3200.0020.0020.0000.0000.0000.000
123A362VAL00.0200.01743.2200.0000.0000.0000.0000.0000.000
124A363SER0-0.044-0.04345.2260.0000.0000.0000.0000.0000.000
125A396HIS00.0550.01219.610-0.006-0.0060.0000.0000.0000.000
126A397ARG10.8760.92821.8390.0510.0510.0000.0000.0000.000
127A398GLU-1-0.936-0.97523.684-0.096-0.0960.0000.0000.0000.000
128A399ALA00.0390.04918.172-0.013-0.0130.0000.0000.0000.000
129A400ASP-1-0.780-0.84316.552-0.189-0.1890.0000.0000.0000.000
130A401PHE00.0020.01419.0780.0130.0130.0000.0000.0000.000
131A402PHE00.023-0.00620.054-0.019-0.0190.0000.0000.0000.000
132A403TRP00.017-0.00722.6180.0150.0150.0000.0000.0000.000
133A404SER0-0.011-0.00525.9900.0000.0000.0000.0000.0000.000
134A405LEU0-0.018-0.01327.5560.0070.0070.0000.0000.0000.000
135A406CYS0-0.0330.00331.204-0.001-0.0010.0000.0000.0000.000
136A407THR0-0.014-0.01033.5630.0050.0050.0000.0000.0000.000
137A408ALA00.0340.01136.972-0.002-0.0020.0000.0000.0000.000
138A409ASP-1-0.726-0.81539.903-0.041-0.0410.0000.0000.0000.000
139A410MET00.0470.00643.6170.0000.0000.0000.0000.0000.000
140A411SER00.009-0.01645.9240.0010.0010.0000.0000.0000.000
141A412LEU0-0.019-0.00442.0690.0010.0010.0000.0000.0000.000
142A413LEU0-0.059-0.03643.2670.0010.0010.0000.0000.0000.000
143A414GLU-1-0.969-0.98346.991-0.033-0.0330.0000.0000.0000.000
144A415GLN0-0.036-0.00547.5910.0000.0000.0000.0000.0000.000
145A416SER00.0090.00046.9800.0010.0010.0000.0000.0000.000
146A417HIS00.0050.00945.951-0.001-0.0010.0000.0000.0000.000
147A418SER00.0040.00744.916-0.001-0.0010.0000.0000.0000.000
148A419SER0-0.012-0.00943.4470.0000.0000.0000.0000.0000.000
149A420PRO0-0.0100.01337.817-0.001-0.0010.0000.0000.0000.000
150A421SER0-0.008-0.00836.230-0.001-0.0010.0000.0000.0000.000
151A422LEU00.0920.02635.442-0.002-0.0020.0000.0000.0000.000
152A423TYR0-0.002-0.01529.086-0.002-0.0020.0000.0000.0000.000
153A424LEU00.007-0.00131.717-0.005-0.0050.0000.0000.0000.000
154A425GLN0-0.039-0.02032.299-0.002-0.0020.0000.0000.0000.000
155A426CYS0-0.027-0.00330.065-0.004-0.0040.0000.0000.0000.000
156A427LEU00.0290.01325.870-0.006-0.0060.0000.0000.0000.000
157A428SER0-0.038-0.02727.361-0.003-0.0030.0000.0000.0000.000
158A429GLN0-0.025-0.01628.5250.0000.0000.0000.0000.0000.000
159A430LYS10.8450.89124.5840.1180.1180.0000.0000.0000.000
160A431LEU0-0.012-0.00122.471-0.007-0.0070.0000.0000.0000.000
161A432ARG10.8310.91223.8290.0580.0580.0000.0000.0000.000
162A433GLN00.015-0.00325.8860.0010.0010.0000.0000.0000.000
163A434GLU-1-0.797-0.87421.506-0.130-0.1300.0000.0000.0000.000
164A435ARG10.8590.93820.3210.0610.0610.0000.0000.0000.000
165A436LYS10.9270.96516.4610.0880.0880.0000.0000.0000.000
166A437ARG10.7980.87615.4070.1440.1440.0000.0000.0000.000
167A438PRO0-0.014-0.01813.1380.0070.0070.0000.0000.0000.000
168A439LEU00.0170.00815.7420.0250.0250.0000.0000.0000.000
169A440LEU00.002-0.01015.7600.0220.0220.0000.0000.0000.000
170A441ASP-1-0.851-0.93115.844-0.308-0.3080.0000.0000.0000.000
171A442LEU0-0.022-0.00718.7570.0240.0240.0000.0000.0000.000
172A443HIS00.0300.03021.5750.0220.0220.0000.0000.0000.000
173A444ILE0-0.0060.01119.9830.0150.0150.0000.0000.0000.000
174A445GLU-1-0.780-0.85322.503-0.134-0.1340.0000.0000.0000.000
175A446LEU00.0000.00625.0210.0120.0120.0000.0000.0000.000
176A447ASN0-0.014-0.01624.9120.0130.0130.0000.0000.0000.000
177A448GLY00.0170.01127.0900.0080.0080.0000.0000.0000.000
178A449TYR00.0190.00328.8140.0070.0070.0000.0000.0000.000
179A450MET0-0.027-0.02030.8410.0080.0080.0000.0000.0000.000
180A451TYR0-0.031-0.01229.3380.0040.0040.0000.0000.0000.000
181A452ASP-1-0.822-0.86333.095-0.063-0.0630.0000.0000.0000.000
182A453TRP00.0330.01234.9550.0040.0040.0000.0000.0000.000
183A454ASN00.030-0.01335.3740.0060.0060.0000.0000.0000.000
184A455SER0-0.127-0.06037.4180.0040.0040.0000.0000.0000.000
185A456ARG10.8190.87736.8220.0620.0620.0000.0000.0000.000
186A457VAL0-0.0080.02641.0010.0030.0030.0000.0000.0000.000
187A458SER0-0.040-0.05543.560-0.001-0.0010.0000.0000.0000.000
188A459ALA0-0.004-0.03543.576-0.002-0.0020.0000.0000.0000.000
189A460LYS10.8710.93043.2850.0370.0370.0000.0000.0000.000
190A461GLU-1-0.784-0.85943.235-0.043-0.0430.0000.0000.0000.000
191A462LYS10.7860.92539.0360.0520.0520.0000.0000.0000.000
192A463TYR00.013-0.00335.5200.0010.0010.0000.0000.0000.000
193A464TYR00.0010.01234.505-0.004-0.0040.0000.0000.0000.000
194A465VAL00.008-0.00728.8040.0010.0010.0000.0000.0000.000
195A466TRP0-0.0110.00728.953-0.003-0.0030.0000.0000.0000.000
196A467LEU0-0.023-0.01321.843-0.001-0.0010.0000.0000.0000.000
197A468GLN00.0020.01123.8790.0030.0030.0000.0000.0000.000
198A469HIS0-0.011-0.02116.7590.0030.0030.0000.0000.0000.000
199A470THR0-0.003-0.02319.525-0.004-0.0040.0000.0000.0000.000
200A471LEU0-0.032-0.00315.404-0.002-0.0020.0000.0000.0000.000
201A472ARG10.8340.88213.0070.2000.2000.0000.0000.0000.000
202A473LYS10.8080.8989.3540.2640.2640.0000.0000.0000.000
203A474LYS10.8670.9288.8620.9510.9510.0000.0000.0000.000
204A475LEU00.0200.00311.2230.0230.0230.0000.0000.0000.000
205A476ILE0-0.008-0.00211.3440.0080.0080.0000.0000.0000.000
206A477LEU00.0020.00815.0830.0130.0130.0000.0000.0000.000
207A478SER00.0420.00916.7010.0200.0200.0000.0000.0000.000
208A479TYR0-0.015-0.00512.785-0.024-0.0240.0000.0000.0000.000