FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: MNJNZ

Calculation Name: 3B8P-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: E

ChEMBL ID:

UniProt ID: Q04866

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1800633.419286
FMO2-HF: Nuclear repulsion 1726901.817835
FMO2-HF: Total energy -73731.601451
FMO2-MP2: Total energy -73951.349396


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(E:54:GLU)


Summations of interaction energy for fragment #1(E:54:GLU)
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.
-2.7052.7790.669-2.286-3.868-0.006
Interaction energy analysis for fragmet #1(E:54:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.896 / q_NPA : -0.941
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].
3E56TRP0-0.034-0.0253.225-4.296-2.2670.027-0.786-1.2710.001
4E57THR00.010-0.0076.342-1.694-1.6940.0000.0000.0000.000
5E58SER0-0.057-0.01710.101-1.177-1.1770.0000.0000.0000.000
6E59THR00.006-0.03212.942-0.012-0.0120.0000.0000.0000.000
7E60ALA0-0.0010.01516.456-0.432-0.4320.0000.0000.0000.000
8E61ILE00.002-0.00319.9300.1000.1000.0000.0000.0000.000
9E62ILE00.0220.00022.923-0.249-0.2490.0000.0000.0000.000
10E63THR00.022-0.00725.907-0.080-0.0800.0000.0000.0000.000
11E64GLN00.0380.01129.6490.1030.1030.0000.0000.0000.000
12E65PRO0-0.0210.02332.9280.0090.0090.0000.0000.0000.000
13E66ASP-1-0.820-0.92334.0988.1948.1940.0000.0000.0000.000
14E67ALA00.028-0.01736.759-0.025-0.0250.0000.0000.0000.000
15E68ALA0-0.0010.01139.176-0.119-0.1190.0000.0000.0000.000
16E69GLN0-0.002-0.00132.266-0.080-0.0800.0000.0000.0000.000
17E70VAL00.0230.01437.4380.0800.0800.0000.0000.0000.000
18E71ALA00.0130.02239.803-0.151-0.1510.0000.0000.0000.000
19E72THR00.0030.00141.799-0.106-0.1060.0000.0000.0000.000
20E73TYR00.0510.01740.489-0.201-0.2010.0000.0000.0000.000
21E74THR0-0.001-0.01243.168-0.032-0.0320.0000.0000.0000.000
22E75ASN0-0.0050.00945.106-0.153-0.1530.0000.0000.0000.000
23E76ALA0-0.014-0.01245.996-0.158-0.1580.0000.0000.0000.000
24E77LEU00.0380.00843.992-0.105-0.1050.0000.0000.0000.000
25E78ASN0-0.038-0.01147.993-0.029-0.0290.0000.0000.0000.000
26E79VAL0-0.021-0.00951.107-0.130-0.1300.0000.0000.0000.000
27E80LEU00.0040.00148.702-0.128-0.1280.0000.0000.0000.000
28E81TYR0-0.010-0.00548.601-0.107-0.1070.0000.0000.0000.000
29E82GLY0-0.030-0.01953.454-0.083-0.0830.0000.0000.0000.000
30E83GLY0-0.038-0.03053.5110.0900.0900.0000.0000.0000.000
31E84ASN0-0.010-0.01253.558-0.013-0.0130.0000.0000.0000.000
32E85ALA0-0.0250.01849.2680.0870.0870.0000.0000.0000.000
33E86PRO00.0310.02245.340-0.040-0.0400.0000.0000.0000.000
34E87LYS10.9280.96645.841-6.645-6.6450.0000.0000.0000.000
35E88ILE00.0840.01942.8580.1250.1250.0000.0000.0000.000
36E89SER00.022-0.00341.5670.0950.0950.0000.0000.0000.000
37E90GLU-1-0.940-0.97540.7127.0347.0340.0000.0000.0000.000
38E91VAL00.0220.03340.2980.1630.1630.0000.0000.0000.000
39E92GLN0-0.025-0.02437.5260.0020.0020.0000.0000.0000.000
40E93ALA00.0340.01536.2320.2780.2780.0000.0000.0000.000
41E94ASN0-0.034-0.01735.8390.3020.3020.0000.0000.0000.000
42E95PHE00.0700.02134.7030.1800.1800.0000.0000.0000.000
43E96ILE00.0090.01528.9740.2550.2550.0000.0000.0000.000
44E97SER0-0.054-0.03031.0330.4270.4270.0000.0000.0000.000
45E98ARG10.9270.96831.718-8.118-8.1180.0000.0000.0000.000
46E99PHE00.0070.00124.5900.2960.2960.0000.0000.0000.000
47E100SER0-0.024-0.01726.9860.5340.5340.0000.0000.0000.000
48E101SER00.0100.00426.7420.4930.4930.0000.0000.0000.000
49E102ALA00.0830.04827.4470.2400.2400.0000.0000.0000.000
50E103PHE00.001-0.01019.7230.5380.5380.0000.0000.0000.000
51E104SER0-0.073-0.05622.4800.5870.5870.0000.0000.0000.000
52E105ALA00.0420.03723.4460.2750.2750.0000.0000.0000.000
53E106LEU00.008-0.00619.2800.4660.4660.0000.0000.0000.000
54E107SER0-0.084-0.05918.5360.4920.4920.0000.0000.0000.000
55E108GLU-1-0.897-0.93018.53514.77614.7760.0000.0000.0000.000
56E109VAL0-0.034-0.02020.1820.3350.3350.0000.0000.0000.000
57E110LEU00.008-0.00715.5120.4770.4770.0000.0000.0000.000
58E111ASP-1-0.891-0.92115.29021.01321.0130.0000.0000.0000.000
59E112ASN0-0.043-0.03516.3750.7100.7100.0000.0000.0000.000
60E113GLN0-0.053-0.00414.567-1.861-1.8610.0000.0000.0000.000
61E114LYS10.8170.89411.772-23.523-23.5230.0000.0000.0000.000
62E115GLU-1-0.866-0.94210.70827.46927.4690.0000.0000.0000.000
63E116ARG10.8230.92011.286-19.767-19.7670.0000.0000.0000.000
64E117GLU-1-0.706-0.79710.60722.22322.2230.0000.0000.0000.000
65E118LYS10.9500.99010.937-24.908-24.9080.0000.0000.0000.000
66E119LEU00.0270.00712.8400.7560.7560.0000.0000.0000.000
67E120THR00.0140.01615.687-0.084-0.0840.0000.0000.0000.000
68E121ILE00.0200.00118.451-0.101-0.1010.0000.0000.0000.000
69E122GLU-1-0.852-0.90920.86014.12414.1240.0000.0000.0000.000
70E123GLN00.0450.00823.647-0.001-0.0010.0000.0000.0000.000
71E124SER0-0.035-0.02724.3710.4520.4520.0000.0000.0000.000
72E125VAL0-0.0200.01925.4340.2250.2250.0000.0000.0000.000
73E126LYS10.8360.89922.879-13.181-13.1810.0000.0000.0000.000
74E127GLY00.0160.01228.386-0.259-0.2590.0000.0000.0000.000
75E128GLN0-0.058-0.02730.924-0.505-0.5050.0000.0000.0000.000
76E129ALA0-0.028-0.01830.7550.2760.2760.0000.0000.0000.000
77E130LEU00.0160.03130.2980.2360.2360.0000.0000.0000.000
78E131PRO00.0130.02227.177-0.222-0.2220.0000.0000.0000.000
79E132LEU00.0090.00025.4740.0650.0650.0000.0000.0000.000
80E133SER00.004-0.01220.7880.0890.0890.0000.0000.0000.000
81E134VAL00.0160.02019.6410.1630.1630.0000.0000.0000.000
82E135SER0-0.060-0.03214.9220.7400.7400.0000.0000.0000.000
83E136TYR00.019-0.02411.3920.4170.4170.0000.0000.0000.000
84E137VAL0-0.061-0.0077.2740.5980.5980.0000.0000.0000.000
85E138SER00.0420.0207.3030.3270.3270.0000.0000.0000.000
86E139THR00.0540.0083.5024.0184.8140.051-0.323-0.524-0.001
87E140THR0-0.046-0.0183.0380.6501.8710.142-0.586-0.777-0.006
88E141ALA00.0410.0075.732-1.269-1.2690.0000.0000.0000.000
89E142GLU-1-0.752-0.8468.12419.80119.8010.0000.0000.0000.000
90E143GLY0-0.001-0.0059.183-1.270-1.2700.0000.0000.0000.000
91E144ALA0-0.011-0.0069.334-0.917-0.9170.0000.0000.0000.000
92E145GLN0-0.035-0.02110.885-0.573-0.5730.0000.0000.0000.000
93E146ARG10.8340.89912.125-19.385-19.3850.0000.0000.0000.000
94E147ARG10.8680.92712.335-19.423-19.4230.0000.0000.0000.000
95E148LEU0-0.041-0.01114.653-0.786-0.7860.0000.0000.0000.000
96E149ALA0-0.003-0.02316.387-0.735-0.7350.0000.0000.0000.000
97E150GLU-1-0.853-0.90116.76815.52915.5290.0000.0000.0000.000
98E151TYR0-0.002-0.04814.746-0.892-0.8920.0000.0000.0000.000
99E152ILE0-0.076-0.03119.906-0.555-0.5550.0000.0000.0000.000
100E153GLN0-0.048-0.01822.397-0.208-0.2080.0000.0000.0000.000
101E154GLN0-0.021-0.00722.1550.0700.0700.0000.0000.0000.000
102E155VAL00.002-0.00222.941-0.388-0.3880.0000.0000.0000.000
103E156ASP-1-0.883-0.95725.5429.7039.7030.0000.0000.0000.000
104E157GLU-1-0.923-0.96227.77310.12910.1290.0000.0000.0000.000
105E158GLU-1-0.990-0.99426.56310.81610.8160.0000.0000.0000.000
106E159VAL00.0240.00329.192-0.363-0.3630.0000.0000.0000.000
107E160ALA00.0300.01831.529-0.359-0.3590.0000.0000.0000.000
108E161LYS10.9250.95531.096-9.638-9.6380.0000.0000.0000.000
109E162GLU-1-0.931-0.96032.9998.9928.9920.0000.0000.0000.000
110E163LEU0-0.037-0.00935.125-0.216-0.2160.0000.0000.0000.000
111E164GLU-1-0.967-0.99037.5897.5997.5990.0000.0000.0000.000
112E165VAL0-0.028-0.02438.508-0.265-0.2650.0000.0000.0000.000
113E166ASP-1-0.793-0.90939.9647.5987.5980.0000.0000.0000.000
114E167LEU0-0.0410.00241.928-0.215-0.2150.0000.0000.0000.000
115E168LYS10.9140.93742.395-7.340-7.3400.0000.0000.0000.000
116E169ASP-1-0.851-0.91143.8336.8686.8680.0000.0000.0000.000
117E170ASN0-0.070-0.02945.557-0.166-0.1660.0000.0000.0000.000
118E171ILE00.0140.01747.123-0.170-0.1700.0000.0000.0000.000
119E172THR0-0.096-0.07448.735-0.192-0.1920.0000.0000.0000.000
120E173LEU00.0240.02950.301-0.064-0.0640.0000.0000.0000.000
121E174GLN00.0040.00452.039-0.146-0.1460.0000.0000.0000.000
122E175THR0-0.003-0.00153.773-0.165-0.1650.0000.0000.0000.000
123E176LYS10.8050.87055.340-5.435-5.4350.0000.0000.0000.000
124E177THR00.0290.02355.485-0.066-0.0660.0000.0000.0000.000
125E178LEU0-0.045-0.02756.365-0.104-0.1040.0000.0000.0000.000
126E179GLN0-0.015-0.02559.171-0.081-0.0810.0000.0000.0000.000
127E180GLU-1-0.804-0.87160.5795.0145.0140.0000.0000.0000.000
128E181SER0-0.015-0.01462.392-0.048-0.0480.0000.0000.0000.000
129E182LEU0-0.081-0.02763.874-0.064-0.0640.0000.0000.0000.000
130E183GLU-1-0.885-0.95665.4934.5824.5820.0000.0000.0000.000
131E184THR0-0.021-0.00865.560-0.100-0.1000.0000.0000.0000.000
132E185GLN0-0.045-0.01467.7990.0040.0040.0000.0000.0000.000
133E186GLU-1-0.873-0.93069.5644.3064.3060.0000.0000.0000.000
134E187VAL00.014-0.00771.024-0.078-0.0780.0000.0000.0000.000
135E188VAL00.0210.01371.725-0.031-0.0310.0000.0000.0000.000
136E189ALA0-0.049-0.02473.622-0.054-0.0540.0000.0000.0000.000
137E190GLN0-0.072-0.05475.249-0.138-0.1380.0000.0000.0000.000
138E191GLU-1-0.862-0.91276.1944.0564.0560.0000.0000.0000.000
139E192GLN0-0.039-0.02477.912-0.064-0.0640.0000.0000.0000.000
140E193LYS10.7600.89279.527-4.051-4.0510.0000.0000.0000.000
141E194ASP-1-0.815-0.92681.1993.8513.8510.0000.0000.0000.000
142E195LEU0-0.036-0.01381.292-0.031-0.0310.0000.0000.0000.000
143E196ARG10.9070.95280.682-3.938-3.9380.0000.0000.0000.000
144E197ILE00.012-0.00784.639-0.047-0.0470.0000.0000.0000.000
145E198LYS10.8660.91786.686-3.671-3.6710.0000.0000.0000.000
146E199GLN0-0.050-0.01387.4320.0070.0070.0000.0000.0000.000
147E200ILE0-0.061-0.02789.407-0.034-0.0340.0000.0000.0000.000
148E201GLU-1-0.887-0.90190.8903.5233.5230.0000.0000.0000.000
149E202GLU-1-0.975-0.98192.4713.3353.3350.0000.0000.0000.000
150E253ALA00.0340.02066.420-0.028-0.0280.0000.0000.0000.000
151E254TYR00.047-0.00265.9210.0520.0520.0000.0000.0000.000
152E255TYR00.0450.02866.5470.0300.0300.0000.0000.0000.000
153E256GLN00.0390.00660.721-0.035-0.0350.0000.0000.0000.000
154E257THR00.0700.06061.5230.0870.0870.0000.0000.0000.000
155E258LYS10.9320.97561.418-4.734-4.7340.0000.0000.0000.000
156E259GLN0-0.050-0.03161.869-0.003-0.0030.0000.0000.0000.000
157E260THR00.0480.00356.9030.0540.0540.0000.0000.0000.000
158E261LEU00.0200.00157.4540.0860.0860.0000.0000.0000.000
159E262LEU0-0.084-0.02157.7750.0420.0420.0000.0000.0000.000
160E263ASP-1-0.875-0.94655.5775.4975.4970.0000.0000.0000.000
161E264ILE0-0.028-0.01852.9850.1140.1140.0000.0000.0000.000
162E265LYS10.9130.96852.829-5.245-5.2450.0000.0000.0000.000
163E266ASN0-0.101-0.05053.9200.0530.0530.0000.0000.0000.000
164E267LEU00.0020.03048.8050.0420.0420.0000.0000.0000.000
165E268LYS10.8850.95743.462-6.877-6.8770.0000.0000.0000.000
166E269VAL00.030-0.00742.489-0.027-0.0270.0000.0000.0000.000
167E270THR0-0.071-0.03641.074-0.007-0.0070.0000.0000.0000.000
168E271ALA00.0460.02437.1190.0190.0190.0000.0000.0000.000
169E272ASP-1-0.906-0.96735.9287.8397.8390.0000.0000.0000.000
170E273THR0-0.029-0.00436.1230.0560.0560.0000.0000.0000.000
171E274VAL0-0.043-0.01735.4060.0420.0420.0000.0000.0000.000
172E275HIS00.0020.01030.4970.4120.4120.0000.0000.0000.000
173E276VAL00.0180.00931.146-0.208-0.2080.0000.0000.0000.000
174E277TYR0-0.001-0.00525.3810.0730.0730.0000.0000.0000.000
175E278ARG10.8900.94829.795-9.137-9.1370.0000.0000.0000.000
176E279TYR0-0.022-0.01021.9870.1050.1050.0000.0000.0000.000
177E280VAL0-0.043-0.00825.810-0.400-0.4000.0000.0000.0000.000
178E281MET0-0.021-0.01821.0770.0400.0400.0000.0000.0000.000
179E282LYS10.9680.99021.590-11.562-11.5620.0000.0000.0000.000
180E283PRO0-0.0110.00316.8060.0440.0440.0000.0000.0000.000
181E284THR00.0440.02714.9510.1250.1250.0000.0000.0000.000
182E285LEU00.0110.01911.6100.7200.7200.0000.0000.0000.000
183E286PRO0-0.053-0.0058.878-0.581-0.5810.0000.0000.0000.000
184E287VAL00.0300.00510.3190.5640.5640.0000.0000.0000.000
185E288ARG10.8450.9248.256-25.089-25.0890.0000.0000.0000.000
186E289ARG10.9590.9822.462-49.480-48.0420.449-0.591-1.2960.000
187E290ASP-1-0.768-0.9005.97128.68928.6890.0000.0000.0000.000
188E291SER0-0.030-0.0075.9364.0324.0320.0000.0000.0000.000
189E292PRO00.0160.0116.940-2.966-2.9660.0000.0000.0000.000