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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: 2JV3R

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2678141.009783
FMO2-HF: Nuclear repulsion 2590959.469171
FMO2-HF: Total energy -87181.540612
FMO2-MP2: Total energy -87428.864659


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.
0.8572.532-0.011-0.758-0.9060.002
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 : 0.053 / q_NPA : 0.007
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-1-0.761-0.8563.875-1.0800.595-0.011-0.758-0.9060.002
4A243ARG10.9040.9526.2980.5690.5690.0000.0000.0000.000
5A244TYR0-0.012-0.0408.6400.1170.1170.0000.0000.0000.000
6A245LYS10.7960.88211.944-0.003-0.0030.0000.0000.0000.000
7A246MET0-0.007-0.00113.323-0.008-0.0080.0000.0000.0000.000
8A247LYS10.8490.90813.063-0.151-0.1510.0000.0000.0000.000
9A248SER0-0.027-0.01317.3540.0130.0130.0000.0000.0000.000
10A249LYS10.9020.96320.832-0.043-0.0430.0000.0000.0000.000
11A250PRO00.0960.05224.0160.0060.0060.0000.0000.0000.000
12A251LEU00.0040.01518.8120.0020.0020.0000.0000.0000.000
13A252GLY00.0190.01721.723-0.010-0.0100.0000.0000.0000.000
14A253ILE00.0200.03124.4900.0020.0020.0000.0000.0000.000
15A254CYS0-0.072-0.03627.008-0.011-0.0110.0000.0000.0000.000
16A255LEU00.0190.02428.9890.0050.0050.0000.0000.0000.000
17A256ILE00.0250.00631.790-0.006-0.0060.0000.0000.0000.000
18A257ILE00.016-0.00134.0390.0050.0050.0000.0000.0000.000
19A258ASP-1-0.736-0.86637.092-0.049-0.0490.0000.0000.0000.000
20A259CYS0-0.082-0.02039.4800.0040.0040.0000.0000.0000.000
21A260ILE0-0.048-0.02341.0380.0010.0010.0000.0000.0000.000
22A261GLY0-0.0040.00642.3300.0020.0020.0000.0000.0000.000
23A262ASN00.019-0.00640.6400.0010.0010.0000.0000.0000.000
24A263GLU-1-0.766-0.88234.409-0.053-0.0530.0000.0000.0000.000
25A264THR0-0.037-0.03636.601-0.001-0.0010.0000.0000.0000.000
26A265GLU-1-0.779-0.87436.295-0.036-0.0360.0000.0000.0000.000
27A266LEU00.0350.03933.573-0.001-0.0010.0000.0000.0000.000
28A267LEU00.0240.00528.811-0.004-0.0040.0000.0000.0000.000
29A268ARG10.9120.95030.2670.0310.0310.0000.0000.0000.000
30A269ASP-1-0.785-0.86331.503-0.039-0.0390.0000.0000.0000.000
31A270THR0-0.100-0.05626.4760.0010.0010.0000.0000.0000.000
32A271PHE00.051-0.00124.170-0.002-0.0020.0000.0000.0000.000
33A272THR00.0270.00826.5510.0030.0030.0000.0000.0000.000
34A273SER0-0.038-0.00527.6220.0020.0020.0000.0000.0000.000
35A274LEU0-0.083-0.03221.5550.0020.0020.0000.0000.0000.000
36A275GLY0-0.0020.01022.6470.0010.0010.0000.0000.0000.000
37A276TYR0-0.077-0.05520.828-0.001-0.0010.0000.0000.0000.000
38A277GLU-1-0.793-0.88826.303-0.020-0.0200.0000.0000.0000.000
39A278VAL0-0.045-0.02429.601-0.004-0.0040.0000.0000.0000.000
40A279GLN0-0.044-0.01931.6310.0050.0050.0000.0000.0000.000
41A280LYS10.7420.85434.5800.0380.0380.0000.0000.0000.000
42A281PHE0-0.021-0.00636.0900.0040.0040.0000.0000.0000.000
43A282LEU00.0290.00339.744-0.003-0.0030.0000.0000.0000.000
44A283HIS0-0.035-0.02342.5790.0020.0020.0000.0000.0000.000
45A284LEU00.0120.01740.2300.0020.0020.0000.0000.0000.000
46A285SER00.0830.04644.282-0.002-0.0020.0000.0000.0000.000
47A286MET0-0.025-0.01143.016-0.002-0.0020.0000.0000.0000.000
48A287HIS0-0.0070.01642.758-0.002-0.0020.0000.0000.0000.000
49A288GLY00.0330.00943.3110.0000.0000.0000.0000.0000.000
50A289ILE00.009-0.00337.961-0.001-0.0010.0000.0000.0000.000
51A290SER0-0.012-0.02238.730-0.002-0.0020.0000.0000.0000.000
52A291GLN0-0.038-0.01739.2590.0000.0000.0000.0000.0000.000
53A292ILE00.0120.01036.6880.0010.0010.0000.0000.0000.000
54A293LEU0-0.018-0.01833.531-0.001-0.0010.0000.0000.0000.000
55A294GLY00.0270.00634.707-0.001-0.0010.0000.0000.0000.000
56A295GLN00.0280.01236.1580.0020.0020.0000.0000.0000.000
57A296PHE00.053-0.00531.8910.0010.0010.0000.0000.0000.000
58A297ALA0-0.0240.00431.257-0.002-0.0020.0000.0000.0000.000
59A298CYS0-0.049-0.02331.5920.0000.0000.0000.0000.0000.000
60A299MET0-0.0330.01831.4380.0030.0030.0000.0000.0000.000
61A300PRO00.0350.01730.410-0.003-0.0030.0000.0000.0000.000
62A301GLU-1-0.819-0.92729.173-0.011-0.0110.0000.0000.0000.000
63A302HIS0-0.008-0.01826.296-0.001-0.0010.0000.0000.0000.000
64A303ARG10.8060.89224.605-0.020-0.0200.0000.0000.0000.000
65A304ASP-1-0.876-0.93023.5210.0170.0170.0000.0000.0000.000
66A305TYR0-0.042-0.02622.9630.0070.0070.0000.0000.0000.000
67A306ASP-1-0.709-0.84717.716-0.013-0.0130.0000.0000.0000.000
68A307SER0-0.056-0.03419.027-0.026-0.0260.0000.0000.0000.000
69A308PHE00.0240.01421.0670.0150.0150.0000.0000.0000.000
70A309VAL00.0050.00923.852-0.016-0.0160.0000.0000.0000.000
71A310CYS0-0.061-0.01526.0710.0110.0110.0000.0000.0000.000
72A311VAL00.0170.00329.066-0.008-0.0080.0000.0000.0000.000
73A312LEU0-0.001-0.00131.5210.0060.0060.0000.0000.0000.000
74A313VAL00.0230.01534.683-0.004-0.0040.0000.0000.0000.000
75A314SER0-0.021-0.03537.4510.0050.0050.0000.0000.0000.000
76A315ARG11.0231.02440.3980.0380.0380.0000.0000.0000.000
77A316GLY00.0270.01541.7070.0000.0000.0000.0000.0000.000
78A317GLY00.0730.05342.0090.0020.0020.0000.0000.0000.000
79A318SER00.006-0.00839.575-0.003-0.0030.0000.0000.0000.000
80A319GLN0-0.030-0.02435.160-0.002-0.0020.0000.0000.0000.000
81A320SER0-0.031-0.00237.5280.0010.0010.0000.0000.0000.000
82A321VAL00.0120.01137.8580.0000.0000.0000.0000.0000.000
83A322TYR00.021-0.01240.7940.0010.0010.0000.0000.0000.000
84A323GLY00.0380.02442.4120.0020.0020.0000.0000.0000.000
85A324VAL0-0.069-0.04443.390-0.001-0.0010.0000.0000.0000.000
86A325ASP-1-0.818-0.89446.778-0.033-0.0330.0000.0000.0000.000
87A326GLN0-0.060-0.03848.577-0.001-0.0010.0000.0000.0000.000
88A327THR0-0.019-0.01047.3350.0020.0020.0000.0000.0000.000
89A328HIS00.0370.02348.377-0.002-0.0020.0000.0000.0000.000
90A329SER0-0.0090.00346.262-0.002-0.0020.0000.0000.0000.000
91A330GLY00.0650.00543.4820.0020.0020.0000.0000.0000.000
92A331LEU0-0.021-0.00738.546-0.001-0.0010.0000.0000.0000.000
93A332PRO0-0.001-0.00938.217-0.003-0.0030.0000.0000.0000.000
94A333LEU00.0340.00733.796-0.001-0.0010.0000.0000.0000.000
95A334HIS00.007-0.00432.662-0.007-0.0070.0000.0000.0000.000
96A335HIS00.010-0.00533.129-0.003-0.0030.0000.0000.0000.000
97A336ILE00.0340.03232.1310.0010.0010.0000.0000.0000.000
98A337ARG10.9680.99628.3120.1030.1030.0000.0000.0000.000
99A338ARG10.9310.96129.5840.0520.0520.0000.0000.0000.000
100A339MET0-0.079-0.01131.8020.0030.0030.0000.0000.0000.000
101A340PHE00.0220.01027.6400.0030.0030.0000.0000.0000.000
102A341MET0-0.046-0.00526.303-0.008-0.0080.0000.0000.0000.000
103A342GLY0-0.018-0.01124.5680.0060.0060.0000.0000.0000.000
104A343ASP-1-0.812-0.90225.356-0.059-0.0590.0000.0000.0000.000
105A344SER0-0.054-0.04628.8270.0050.0050.0000.0000.0000.000
106A345CYS0-0.019-0.00927.8820.0050.0050.0000.0000.0000.000
107A346PRO00.0240.01126.023-0.005-0.0050.0000.0000.0000.000
108A347TYR0-0.029-0.00324.7200.0000.0000.0000.0000.0000.000
109A348LEU00.0180.00323.1920.0000.0000.0000.0000.0000.000
110A349ALA00.0160.01222.082-0.019-0.0190.0000.0000.0000.000
111A350GLY0-0.063-0.03017.6460.0100.0100.0000.0000.0000.000
112A351LYS10.7940.92016.7070.0150.0150.0000.0000.0000.000
113A352PRO0-0.044-0.01516.685-0.003-0.0030.0000.0000.0000.000
114A353LYS10.8410.93419.1100.1530.1530.0000.0000.0000.000
115A354MET0-0.071-0.02920.537-0.019-0.0190.0000.0000.0000.000
116A355PHE00.0240.00923.8980.0150.0150.0000.0000.0000.000
117A356PHE00.013-0.00623.261-0.012-0.0120.0000.0000.0000.000
118A357ILE0-0.0010.00329.0490.0090.0090.0000.0000.0000.000
119A358GLN00.0360.02532.536-0.006-0.0060.0000.0000.0000.000
120A359ASN00.0260.00435.4760.0080.0080.0000.0000.0000.000
121A360TYR00.0290.01338.168-0.003-0.0030.0000.0000.0000.000
122A361VAL0-0.009-0.00440.6690.0020.0020.0000.0000.0000.000
123A362VAL00.0260.01543.5530.0000.0000.0000.0000.0000.000
124A363SER0-0.042-0.03545.8250.0000.0000.0000.0000.0000.000
125A396HIS00.013-0.01219.494-0.007-0.0070.0000.0000.0000.000
126A397ARG10.8650.92522.2080.0670.0670.0000.0000.0000.000
127A398GLU-1-0.834-0.91723.740-0.117-0.1170.0000.0000.0000.000
128A399ALA00.0350.04018.626-0.016-0.0160.0000.0000.0000.000
129A400ASP-1-0.773-0.82916.454-0.226-0.2260.0000.0000.0000.000
130A401PHE00.0000.00719.0540.0220.0220.0000.0000.0000.000
131A402PHE00.009-0.01820.055-0.025-0.0250.0000.0000.0000.000
132A403TRP00.016-0.00622.5640.0170.0170.0000.0000.0000.000
133A404SER0-0.0030.00126.1130.0010.0010.0000.0000.0000.000
134A405LEU0-0.026-0.02127.6450.0090.0090.0000.0000.0000.000
135A406CYS0-0.0280.02031.416-0.001-0.0010.0000.0000.0000.000
136A407THR0-0.025-0.01533.6100.0050.0050.0000.0000.0000.000
137A408ALA00.0250.01337.212-0.002-0.0020.0000.0000.0000.000
138A409ASP-1-0.699-0.80840.054-0.047-0.0470.0000.0000.0000.000
139A410MET00.014-0.00243.8470.0010.0010.0000.0000.0000.000
140A411SER00.028-0.00146.0670.0010.0010.0000.0000.0000.000
141A412LEU0-0.009-0.00441.9400.0010.0010.0000.0000.0000.000
142A413LEU0-0.066-0.03943.1870.0010.0010.0000.0000.0000.000
143A414GLU-1-0.933-0.97946.924-0.037-0.0370.0000.0000.0000.000
144A415GLN0-0.037-0.00147.2450.0000.0000.0000.0000.0000.000
145A416SER00.000-0.01246.9980.0020.0020.0000.0000.0000.000
146A417HIS0-0.013-0.00345.754-0.001-0.0010.0000.0000.0000.000
147A418SER00.0130.01544.582-0.001-0.0010.0000.0000.0000.000
148A419SER0-0.025-0.01343.1610.0000.0000.0000.0000.0000.000
149A420PRO0-0.0190.01337.611-0.002-0.0020.0000.0000.0000.000
150A421SER00.006-0.01036.183-0.001-0.0010.0000.0000.0000.000
151A422LEU00.0590.01735.476-0.002-0.0020.0000.0000.0000.000
152A423TYR00.007-0.01729.022-0.001-0.0010.0000.0000.0000.000
153A424LEU00.0020.00531.508-0.005-0.0050.0000.0000.0000.000
154A425GLN0-0.032-0.02032.111-0.001-0.0010.0000.0000.0000.000
155A426CYS0-0.0310.00529.680-0.004-0.0040.0000.0000.0000.000
156A427LEU00.0380.01425.729-0.006-0.0060.0000.0000.0000.000
157A428SER0-0.032-0.02027.196-0.002-0.0020.0000.0000.0000.000
158A429GLN0-0.015-0.00828.2880.0000.0000.0000.0000.0000.000
159A430LYS10.8290.87624.1230.1260.1260.0000.0000.0000.000
160A431LEU0-0.014-0.00422.282-0.007-0.0070.0000.0000.0000.000
161A432ARG10.7950.89323.7950.0560.0560.0000.0000.0000.000
162A433GLN00.0160.00125.7280.0030.0030.0000.0000.0000.000
163A434GLU-1-0.781-0.86821.354-0.127-0.1270.0000.0000.0000.000
164A435ARG10.8450.90319.8910.0440.0440.0000.0000.0000.000
165A436LYS10.9280.97416.0550.0520.0520.0000.0000.0000.000
166A437ARG10.8050.88115.0100.1590.1590.0000.0000.0000.000
167A438PRO0-0.024-0.02313.0570.0090.0090.0000.0000.0000.000
168A439LEU00.0090.00415.6080.0270.0270.0000.0000.0000.000
169A440LEU00.0040.00116.2510.0220.0220.0000.0000.0000.000
170A441ASP-1-0.852-0.93415.971-0.321-0.3210.0000.0000.0000.000
171A442LEU0-0.004-0.00118.8980.0250.0250.0000.0000.0000.000
172A443HIS00.0420.03921.7230.0240.0240.0000.0000.0000.000
173A444ILE0-0.0170.00120.4240.0150.0150.0000.0000.0000.000
174A445GLU-1-0.784-0.86521.898-0.148-0.1480.0000.0000.0000.000
175A446LEU0-0.0050.00624.9480.0130.0130.0000.0000.0000.000
176A447ASN0-0.003-0.01325.5240.0160.0160.0000.0000.0000.000
177A448GLY00.0140.01427.4050.0080.0080.0000.0000.0000.000
178A449TYR00.0330.00929.0800.0080.0080.0000.0000.0000.000
179A450MET0-0.036-0.01331.0710.0090.0090.0000.0000.0000.000
180A451TYR0-0.024-0.01729.9220.0040.0040.0000.0000.0000.000
181A452ASP-1-0.833-0.86933.175-0.070-0.0700.0000.0000.0000.000
182A453TRP00.0390.01334.9560.0050.0050.0000.0000.0000.000
183A454ASN00.018-0.01435.5670.0080.0080.0000.0000.0000.000
184A455SER0-0.116-0.06137.7450.0040.0040.0000.0000.0000.000
185A456ARG10.8040.86936.5870.0700.0700.0000.0000.0000.000
186A457VAL00.0030.02841.4210.0030.0030.0000.0000.0000.000
187A458SER0-0.026-0.05644.029-0.001-0.0010.0000.0000.0000.000
188A459ALA0-0.008-0.03544.178-0.002-0.0020.0000.0000.0000.000
189A460LYS10.8260.91444.0310.0430.0430.0000.0000.0000.000
190A461GLU-1-0.786-0.86143.500-0.048-0.0480.0000.0000.0000.000
191A462LYS10.7960.93439.3770.0600.0600.0000.0000.0000.000
192A463TYR00.021-0.00435.5960.0010.0010.0000.0000.0000.000
193A464TYR00.0120.01134.979-0.005-0.0050.0000.0000.0000.000
194A465VAL0-0.003-0.01629.4230.0020.0020.0000.0000.0000.000
195A466TRP0-0.0080.01429.032-0.005-0.0050.0000.0000.0000.000
196A467LEU0-0.012-0.01722.416-0.001-0.0010.0000.0000.0000.000
197A468GLN0-0.0230.00723.6400.0040.0040.0000.0000.0000.000
198A469HIS0-0.005-0.01616.8980.0080.0080.0000.0000.0000.000
199A470THR0-0.008-0.02919.776-0.003-0.0030.0000.0000.0000.000
200A471LEU0-0.027-0.00315.5310.0010.0010.0000.0000.0000.000
201A472ARG10.8260.87613.2520.2350.2350.0000.0000.0000.000
202A473LYS10.8080.9049.1220.3060.3060.0000.0000.0000.000
203A474LYS10.8520.9128.4731.0381.0380.0000.0000.0000.000
204A475LEU00.013-0.00211.0220.0420.0420.0000.0000.0000.000
205A476ILE0-0.0140.00211.3180.0010.0010.0000.0000.0000.000
206A477LEU00.0050.01115.0740.0150.0150.0000.0000.0000.000
207A478SER00.0390.00116.5050.0280.0280.0000.0000.0000.000
208A479TYR00.0210.01112.038-0.013-0.0130.0000.0000.0000.000