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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: MVQ1Z

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2673930.376555
FMO2-HF: Nuclear repulsion 2586750.014742
FMO2-HF: Total energy -87180.361813
FMO2-MP2: Total energy -87427.734366


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.
0.0591.802-0.009-0.769-0.9650.001
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 : 0.025 / q_NPA : -0.012
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-1-0.892-0.9353.843-1.1610.582-0.009-0.769-0.9650.001
4A243ARG10.9410.9646.2220.3960.3960.0000.0000.0000.000
5A244TYR0-0.044-0.0548.8960.1250.1250.0000.0000.0000.000
6A245LYS10.8980.95212.390-0.096-0.0960.0000.0000.0000.000
7A246MET0-0.0110.00013.528-0.008-0.0080.0000.0000.0000.000
8A247LYS10.8460.89112.553-0.165-0.1650.0000.0000.0000.000
9A248SER0-0.020-0.00917.8020.0050.0050.0000.0000.0000.000
10A249LYS10.8910.97921.180-0.046-0.0460.0000.0000.0000.000
11A250PRO00.0930.03624.3580.0050.0050.0000.0000.0000.000
12A251LEU00.0120.00719.1500.0030.0030.0000.0000.0000.000
13A252GLY00.0220.00622.190-0.004-0.0040.0000.0000.0000.000
14A253ILE00.0170.03124.8600.0000.0000.0000.0000.0000.000
15A254CYS0-0.078-0.03927.349-0.008-0.0080.0000.0000.0000.000
16A255LEU0-0.0030.00729.0790.0040.0040.0000.0000.0000.000
17A256ILE00.003-0.00332.006-0.005-0.0050.0000.0000.0000.000
18A257ILE00.0240.00634.2930.0040.0040.0000.0000.0000.000
19A258ASP-1-0.756-0.86437.309-0.036-0.0360.0000.0000.0000.000
20A259CYS0-0.093-0.03939.4020.0030.0030.0000.0000.0000.000
21A260ILE0-0.064-0.02841.0100.0010.0010.0000.0000.0000.000
22A261GLY0-0.020-0.02042.1710.0020.0020.0000.0000.0000.000
23A262ASN00.0290.01740.3900.0000.0000.0000.0000.0000.000
24A263GLU-1-0.798-0.88334.869-0.038-0.0380.0000.0000.0000.000
25A264THR0-0.036-0.05236.977-0.001-0.0010.0000.0000.0000.000
26A265GLU-1-0.774-0.86836.580-0.025-0.0250.0000.0000.0000.000
27A266LEU00.0050.01833.542-0.001-0.0010.0000.0000.0000.000
28A267LEU00.017-0.01629.249-0.003-0.0030.0000.0000.0000.000
29A268ARG10.9120.95830.6720.0210.0210.0000.0000.0000.000
30A269ASP-1-0.867-0.93631.805-0.027-0.0270.0000.0000.0000.000
31A270THR0-0.079-0.03026.8890.0020.0020.0000.0000.0000.000
32A271PHE00.030-0.00924.262-0.002-0.0020.0000.0000.0000.000
33A272THR00.0240.02327.0940.0030.0030.0000.0000.0000.000
34A273SER0-0.034-0.01027.5960.0020.0020.0000.0000.0000.000
35A274LEU0-0.086-0.05122.3060.0010.0010.0000.0000.0000.000
36A275GLY0-0.0070.00623.0220.0010.0010.0000.0000.0000.000
37A276TYR0-0.042-0.03021.4010.0000.0000.0000.0000.0000.000
38A277GLU-1-0.872-0.93426.706-0.004-0.0040.0000.0000.0000.000
39A278VAL0-0.035-0.02930.060-0.003-0.0030.0000.0000.0000.000
40A279GLN0-0.0220.00232.1810.0030.0030.0000.0000.0000.000
41A280LYS10.8260.88934.9110.0250.0250.0000.0000.0000.000
42A281PHE0-0.019-0.00836.6580.0030.0030.0000.0000.0000.000
43A282LEU00.0240.00540.063-0.003-0.0030.0000.0000.0000.000
44A283HIS0-0.019-0.01042.8960.0010.0010.0000.0000.0000.000
45A284LEU0-0.0010.01640.4500.0010.0010.0000.0000.0000.000
46A285SER00.0850.04444.459-0.002-0.0020.0000.0000.0000.000
47A286MET0-0.0130.01043.193-0.001-0.0010.0000.0000.0000.000
48A287HIS00.0170.00742.888-0.002-0.0020.0000.0000.0000.000
49A288GLY00.0350.01743.8090.0010.0010.0000.0000.0000.000
50A289ILE0-0.001-0.00838.2290.0000.0000.0000.0000.0000.000
51A290SER0-0.005-0.00838.947-0.001-0.0010.0000.0000.0000.000
52A291GLN0-0.0050.02139.4570.0000.0000.0000.0000.0000.000
53A292ILE00.001-0.00437.0530.0010.0010.0000.0000.0000.000
54A293LEU0-0.026-0.02433.7120.0000.0000.0000.0000.0000.000
55A294GLY00.029-0.01334.8770.0000.0000.0000.0000.0000.000
56A295GLN00.003-0.00536.1610.0030.0030.0000.0000.0000.000
57A296PHE00.012-0.00832.2070.0020.0020.0000.0000.0000.000
58A297ALA0-0.0210.01331.1520.0000.0000.0000.0000.0000.000
59A298CYS0-0.038-0.01731.3220.0010.0010.0000.0000.0000.000
60A299MET0-0.0410.00531.5950.0030.0030.0000.0000.0000.000
61A300PRO00.0400.01330.806-0.001-0.0010.0000.0000.0000.000
62A301GLU-1-0.737-0.90829.6040.0080.0080.0000.0000.0000.000
63A302HIS0-0.015-0.02026.1470.0010.0010.0000.0000.0000.000
64A303ARG10.8190.93224.860-0.035-0.0350.0000.0000.0000.000
65A304ASP-1-0.929-0.97124.1440.0400.0400.0000.0000.0000.000
66A305TYR0-0.018-0.01323.0590.0040.0040.0000.0000.0000.000
67A306ASP-1-0.772-0.87117.8690.0320.0320.0000.0000.0000.000
68A307SER0-0.053-0.03019.042-0.021-0.0210.0000.0000.0000.000
69A308PHE00.0340.02221.3050.0100.0100.0000.0000.0000.000
70A309VAL00.0010.01524.116-0.012-0.0120.0000.0000.0000.000
71A310CYS0-0.031-0.00426.2450.0090.0090.0000.0000.0000.000
72A311VAL00.0280.01129.450-0.007-0.0070.0000.0000.0000.000
73A312LEU0-0.018-0.00431.6520.0050.0050.0000.0000.0000.000
74A313VAL00.0170.01334.849-0.004-0.0040.0000.0000.0000.000
75A314SER0-0.024-0.04637.5520.0040.0040.0000.0000.0000.000
76A315ARG11.0331.03240.4960.0270.0270.0000.0000.0000.000
77A316GLY00.0450.01641.4960.0010.0010.0000.0000.0000.000
78A317GLY00.0520.05241.7560.0010.0010.0000.0000.0000.000
79A318SER0-0.012-0.01938.885-0.002-0.0020.0000.0000.0000.000
80A319GLN0-0.027-0.02935.778-0.002-0.0020.0000.0000.0000.000
81A320SER0-0.029-0.00337.2860.0010.0010.0000.0000.0000.000
82A321VAL00.0370.02437.820-0.001-0.0010.0000.0000.0000.000
83A322TYR00.0730.00740.6090.0010.0010.0000.0000.0000.000
84A323GLY00.0390.03342.5920.0020.0020.0000.0000.0000.000
85A324VAL0-0.089-0.06643.6150.0000.0000.0000.0000.0000.000
86A325ASP-1-0.849-0.91846.964-0.022-0.0220.0000.0000.0000.000
87A326GLN0-0.045-0.01548.647-0.002-0.0020.0000.0000.0000.000
88A327THR00.014-0.00747.2450.0010.0010.0000.0000.0000.000
89A328HIS00.0440.01448.345-0.002-0.0020.0000.0000.0000.000
90A329SER0-0.060-0.02546.122-0.001-0.0010.0000.0000.0000.000
91A330GLY00.0360.00543.3130.0010.0010.0000.0000.0000.000
92A331LEU0-0.031-0.00738.7180.0000.0000.0000.0000.0000.000
93A332PRO00.012-0.00338.160-0.003-0.0030.0000.0000.0000.000
94A333LEU00.0550.01833.6010.0000.0000.0000.0000.0000.000
95A334HIS0-0.011-0.01132.682-0.004-0.0040.0000.0000.0000.000
96A335HIS00.001-0.01833.307-0.002-0.0020.0000.0000.0000.000
97A336ILE00.0370.02932.1140.0010.0010.0000.0000.0000.000
98A337ARG10.9480.98428.5960.0710.0710.0000.0000.0000.000
99A338ARG10.9370.97529.5210.0330.0330.0000.0000.0000.000
100A339MET0-0.062-0.01131.3010.0020.0020.0000.0000.0000.000
101A340PHE00.0320.01427.5430.0020.0020.0000.0000.0000.000
102A341MET0-0.046-0.00826.284-0.003-0.0030.0000.0000.0000.000
103A342GLY00.0020.00624.9140.0050.0050.0000.0000.0000.000
104A343ASP-1-0.877-0.94825.660-0.031-0.0310.0000.0000.0000.000
105A344SER0-0.027-0.01828.9280.0040.0040.0000.0000.0000.000
106A345CYS0-0.057-0.01827.8230.0030.0030.0000.0000.0000.000
107A346PRO00.0360.01126.269-0.002-0.0020.0000.0000.0000.000
108A347TYR0-0.049-0.00524.9550.0040.0040.0000.0000.0000.000
109A348LEU00.0350.01523.4650.0020.0020.0000.0000.0000.000
110A349ALA00.0020.01022.099-0.015-0.0150.0000.0000.0000.000
111A350GLY0-0.056-0.02318.0350.0100.0100.0000.0000.0000.000
112A351LYS10.7780.89917.106-0.015-0.0150.0000.0000.0000.000
113A352PRO0-0.046-0.00317.042-0.004-0.0040.0000.0000.0000.000
114A353LYS10.8630.93619.4850.0870.0870.0000.0000.0000.000
115A354MET0-0.056-0.02420.572-0.016-0.0160.0000.0000.0000.000
116A355PHE00.0140.00624.0960.0110.0110.0000.0000.0000.000
117A356PHE00.0130.00323.651-0.009-0.0090.0000.0000.0000.000
118A357ILE00.0130.00129.1810.0070.0070.0000.0000.0000.000
119A358GLN00.0530.05332.681-0.006-0.0060.0000.0000.0000.000
120A359ASN0-0.005-0.02535.5220.0060.0060.0000.0000.0000.000
121A360TYR00.0180.01038.297-0.002-0.0020.0000.0000.0000.000
122A361VAL00.007-0.00440.4240.0020.0020.0000.0000.0000.000
123A362VAL00.0200.01543.2600.0000.0000.0000.0000.0000.000
124A363SER0-0.024-0.00145.2770.0000.0000.0000.0000.0000.000
125A396HIS00.0630.01719.859-0.006-0.0060.0000.0000.0000.000
126A397ARG10.9210.96521.8380.0450.0450.0000.0000.0000.000
127A398GLU-1-0.941-0.97723.410-0.086-0.0860.0000.0000.0000.000
128A399ALA00.0280.05218.122-0.013-0.0130.0000.0000.0000.000
129A400ASP-1-0.810-0.88116.632-0.138-0.1380.0000.0000.0000.000
130A401PHE00.0160.02219.0850.0140.0140.0000.0000.0000.000
131A402PHE00.014-0.00720.146-0.019-0.0190.0000.0000.0000.000
132A403TRP00.015-0.00722.6180.0150.0150.0000.0000.0000.000
133A404SER0-0.005-0.00826.028-0.001-0.0010.0000.0000.0000.000
134A405LEU0-0.004-0.00527.5860.0070.0070.0000.0000.0000.000
135A406CYS0-0.0320.00231.240-0.001-0.0010.0000.0000.0000.000
136A407THR0-0.011-0.00933.5810.0050.0050.0000.0000.0000.000
137A408ALA00.0210.00337.000-0.002-0.0020.0000.0000.0000.000
138A409ASP-1-0.782-0.87939.916-0.036-0.0360.0000.0000.0000.000
139A410MET00.0400.00043.6330.0000.0000.0000.0000.0000.000
140A411SER0-0.028-0.02445.9390.0010.0010.0000.0000.0000.000
141A412LEU00.0200.00342.1060.0010.0010.0000.0000.0000.000
142A413LEU0-0.056-0.03343.3510.0010.0010.0000.0000.0000.000
143A414GLU-1-0.996-0.99246.971-0.027-0.0270.0000.0000.0000.000
144A415GLN0-0.033-0.00447.7960.0000.0000.0000.0000.0000.000
145A416SER00.0070.01947.0080.0010.0010.0000.0000.0000.000
146A417HIS00.0090.00845.941-0.001-0.0010.0000.0000.0000.000
147A418SER0-0.025-0.00544.910-0.001-0.0010.0000.0000.0000.000
148A419SER00.011-0.02143.4170.0000.0000.0000.0000.0000.000
149A420PRO0-0.0210.00237.775-0.001-0.0010.0000.0000.0000.000
150A421SER0-0.004-0.01036.117-0.001-0.0010.0000.0000.0000.000
151A422LEU00.0820.01835.605-0.001-0.0010.0000.0000.0000.000
152A423TYR0-0.019-0.02628.911-0.001-0.0010.0000.0000.0000.000
153A424LEU00.008-0.00131.676-0.004-0.0040.0000.0000.0000.000
154A425GLN0-0.031-0.01532.270-0.001-0.0010.0000.0000.0000.000
155A426CYS0-0.0270.00229.783-0.004-0.0040.0000.0000.0000.000
156A427LEU00.0280.01026.100-0.005-0.0050.0000.0000.0000.000
157A428SER0-0.055-0.02027.327-0.003-0.0030.0000.0000.0000.000
158A429GLN00.0090.00228.4910.0020.0020.0000.0000.0000.000
159A430LYS10.9340.96924.4760.0990.0990.0000.0000.0000.000
160A431LEU00.0050.00422.314-0.005-0.0050.0000.0000.0000.000
161A432ARG10.8680.92923.8010.0440.0440.0000.0000.0000.000
162A433GLN0-0.021-0.02325.8480.0010.0010.0000.0000.0000.000
163A434GLU-1-0.854-0.91021.536-0.111-0.1110.0000.0000.0000.000
164A435ARG10.8400.93220.2220.0360.0360.0000.0000.0000.000
165A436LYS10.9260.95916.3670.0600.0600.0000.0000.0000.000
166A437ARG10.7920.85915.3450.1250.1250.0000.0000.0000.000
167A438PRO0-0.027-0.02113.4220.0100.0100.0000.0000.0000.000
168A439LEU00.0420.01915.6880.0180.0180.0000.0000.0000.000
169A440LEU00.008-0.00815.7910.0180.0180.0000.0000.0000.000
170A441ASP-1-0.855-0.92915.575-0.284-0.2840.0000.0000.0000.000
171A442LEU0-0.021-0.00118.7000.0200.0200.0000.0000.0000.000
172A443HIS00.0550.05221.5330.0220.0220.0000.0000.0000.000
173A444ILE0-0.0040.01719.9620.0130.0130.0000.0000.0000.000
174A445GLU-1-0.803-0.88722.490-0.120-0.1200.0000.0000.0000.000
175A446LEU0-0.007-0.00324.9580.0110.0110.0000.0000.0000.000
176A447ASN0-0.024-0.01425.0120.0120.0120.0000.0000.0000.000
177A448GLY00.0030.00127.0550.0070.0070.0000.0000.0000.000
178A449TYR00.002-0.00528.7760.0060.0060.0000.0000.0000.000
179A450MET0-0.014-0.01530.8020.0080.0080.0000.0000.0000.000
180A451TYR0-0.035-0.01229.1140.0030.0030.0000.0000.0000.000
181A452ASP-1-0.839-0.90033.052-0.058-0.0580.0000.0000.0000.000
182A453TRP00.0110.00234.9120.0040.0040.0000.0000.0000.000
183A454ASN00.021-0.02435.7800.0060.0060.0000.0000.0000.000
184A455SER0-0.124-0.06037.4410.0030.0030.0000.0000.0000.000
185A456ARG10.8460.91437.0350.0570.0570.0000.0000.0000.000
186A457VAL0-0.0010.02941.0750.0020.0020.0000.0000.0000.000
187A458SER0-0.034-0.02843.530-0.001-0.0010.0000.0000.0000.000
188A459ALA0-0.017-0.03943.591-0.001-0.0010.0000.0000.0000.000
189A460LYS10.9500.96543.2930.0300.0300.0000.0000.0000.000
190A461GLU-1-0.813-0.88543.070-0.038-0.0380.0000.0000.0000.000
191A462LYS10.8370.95239.0140.0480.0480.0000.0000.0000.000
192A463TYR00.0250.00135.4680.0010.0010.0000.0000.0000.000
193A464TYR0-0.0030.01034.531-0.004-0.0040.0000.0000.0000.000
194A465VAL00.010-0.00528.6800.0020.0020.0000.0000.0000.000
195A466TRP0-0.0020.00929.258-0.003-0.0030.0000.0000.0000.000
196A467LEU0-0.026-0.01821.7520.0000.0000.0000.0000.0000.000
197A468GLN00.0070.01924.411-0.002-0.0020.0000.0000.0000.000
198A469HIS0-0.010-0.01916.9090.0090.0090.0000.0000.0000.000
199A470THR00.005-0.02519.587-0.005-0.0050.0000.0000.0000.000
200A471LEU0-0.039-0.00915.3620.0000.0000.0000.0000.0000.000
201A472ARG10.8710.92212.9520.1550.1550.0000.0000.0000.000
202A473LYS10.9270.9769.9430.0920.0920.0000.0000.0000.000
203A474LYS10.9290.9809.2940.8120.8120.0000.0000.0000.000
204A475LEU00.018-0.00411.2220.0410.0410.0000.0000.0000.000
205A476ILE0-0.009-0.00611.462-0.004-0.0040.0000.0000.0000.000
206A477LEU00.0000.00915.0870.0190.0190.0000.0000.0000.000
207A478SER00.0320.01016.7350.0170.0170.0000.0000.0000.000
208A479TYR0-0.007-0.00113.167-0.010-0.0100.0000.0000.0000.000