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: 7656K

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 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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1800830.993245
FMO2-HF: Nuclear repulsion 1727098.00465
FMO2-HF: Total energy -73732.988596
FMO2-MP2: Total energy -73952.657021


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.
-25.266-18.4423.944-4.367-6.40.012
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 : -0.875 / q_NPA : -0.950
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].
3E56TRP0-0.024-0.0213.007-2.730-0.2140.124-0.997-1.642-0.001
4E57THR0-0.002-0.0266.340-1.847-1.8470.0000.0000.0000.000
5E58SER0-0.061-0.02410.095-1.087-1.0870.0000.0000.0000.000
6E59THR00.019-0.02912.9450.0730.0730.0000.0000.0000.000
7E60ALA0-0.0030.01916.455-0.414-0.4140.0000.0000.0000.000
8E61ILE0-0.009-0.00119.9330.0510.0510.0000.0000.0000.000
9E62ILE00.0310.00323.057-0.269-0.2690.0000.0000.0000.000
10E63THR00.002-0.01725.909-0.092-0.0920.0000.0000.0000.000
11E64GLN00.0420.01529.6500.0910.0910.0000.0000.0000.000
12E65PRO0-0.0150.02732.9310.0130.0130.0000.0000.0000.000
13E66ASP-1-0.822-0.92134.1068.1608.1600.0000.0000.0000.000
14E67ALA00.035-0.01236.766-0.021-0.0210.0000.0000.0000.000
15E68ALA00.0080.01639.312-0.122-0.1220.0000.0000.0000.000
16E69GLN0-0.012-0.00432.218-0.052-0.0520.0000.0000.0000.000
17E70VAL00.0180.00737.5000.0910.0910.0000.0000.0000.000
18E71ALA00.0150.01939.815-0.151-0.1510.0000.0000.0000.000
19E72THR00.0200.01241.845-0.108-0.1080.0000.0000.0000.000
20E73TYR00.039-0.00640.656-0.204-0.2040.0000.0000.0000.000
21E74THR00.000-0.00543.199-0.042-0.0420.0000.0000.0000.000
22E75ASN0-0.013-0.00445.136-0.141-0.1410.0000.0000.0000.000
23E76ALA0-0.002-0.00446.088-0.160-0.1600.0000.0000.0000.000
24E77LEU00.0300.00543.921-0.103-0.1030.0000.0000.0000.000
25E78ASN0-0.049-0.01648.129-0.037-0.0370.0000.0000.0000.000
26E79VAL0-0.034-0.01351.234-0.131-0.1310.0000.0000.0000.000
27E80LEU00.0000.01149.137-0.130-0.1300.0000.0000.0000.000
28E81TYR0-0.021-0.01848.806-0.120-0.1200.0000.0000.0000.000
29E82GLY0-0.026-0.01753.601-0.083-0.0830.0000.0000.0000.000
30E83GLY0-0.028-0.02753.5430.0930.0930.0000.0000.0000.000
31E84ASN0-0.026-0.01853.686-0.020-0.0200.0000.0000.0000.000
32E85ALA0-0.0130.02249.4520.0890.0890.0000.0000.0000.000
33E86PRO00.0140.01045.370-0.035-0.0350.0000.0000.0000.000
34E87LYS10.8530.90745.943-6.605-6.6050.0000.0000.0000.000
35E88ILE00.0740.01742.6810.1360.1360.0000.0000.0000.000
36E89SER00.0270.00141.5660.0990.0990.0000.0000.0000.000
37E90GLU-1-0.847-0.90740.7136.9856.9850.0000.0000.0000.000
38E91VAL00.0240.03340.1660.1560.1560.0000.0000.0000.000
39E92GLN0-0.054-0.03937.4760.0280.0280.0000.0000.0000.000
40E93ALA00.0260.01536.2320.2830.2830.0000.0000.0000.000
41E94ASN0-0.014-0.01235.8390.2980.2980.0000.0000.0000.000
42E95PHE00.0530.01834.8020.1760.1760.0000.0000.0000.000
43E96ILE00.0150.01629.1030.2560.2560.0000.0000.0000.000
44E97SER0-0.069-0.02931.0870.2890.2890.0000.0000.0000.000
45E98ARG10.8730.91931.899-8.080-8.0800.0000.0000.0000.000
46E99PHE00.002-0.00624.6350.3120.3120.0000.0000.0000.000
47E100SER00.020-0.00427.1510.4280.4280.0000.0000.0000.000
48E101SER0-0.036-0.00126.9280.3340.3340.0000.0000.0000.000
49E102ALA00.0820.04527.6150.2460.2460.0000.0000.0000.000
50E103PHE00.003-0.01019.9430.5550.5550.0000.0000.0000.000
51E104SER0-0.042-0.04322.6590.5330.5330.0000.0000.0000.000
52E105ALA0-0.0030.01423.6420.2520.2520.0000.0000.0000.000
53E106LEU00.0220.00119.8770.4580.4580.0000.0000.0000.000
54E107SER0-0.065-0.05118.7200.4750.4750.0000.0000.0000.000
55E108GLU-1-0.927-0.95118.73014.56914.5690.0000.0000.0000.000
56E109VAL0-0.035-0.01820.3710.3170.3170.0000.0000.0000.000
57E110LEU00.003-0.00515.7470.4670.4670.0000.0000.0000.000
58E111ASP-1-0.886-0.92615.14821.27421.2740.0000.0000.0000.000
59E112ASN0-0.067-0.04416.5650.3670.3670.0000.0000.0000.000
60E113GLN0-0.0350.00114.501-1.655-1.6550.0000.0000.0000.000
61E114LYS10.7960.87312.087-22.642-22.6420.0000.0000.0000.000
62E115GLU-1-0.840-0.91810.98025.99225.9920.0000.0000.0000.000
63E116ARG10.8290.92711.365-19.666-19.6660.0000.0000.0000.000
64E117GLU-1-0.692-0.78010.76122.20022.2000.0000.0000.0000.000
65E118LYS10.9440.98510.465-24.936-24.9360.0000.0000.0000.000
66E119LEU00.0080.00713.0330.8360.8360.0000.0000.0000.000
67E120THR0-0.018-0.00115.875-0.386-0.3860.0000.0000.0000.000
68E121ILE00.0340.00918.380-0.067-0.0670.0000.0000.0000.000
69E122GLU-1-0.832-0.89220.48113.92113.9210.0000.0000.0000.000
70E123GLN00.0390.01423.4460.0700.0700.0000.0000.0000.000
71E124SER0-0.032-0.02824.3560.4750.4750.0000.0000.0000.000
72E125VAL0-0.0090.01825.4190.2340.2340.0000.0000.0000.000
73E126LYS10.8180.87622.865-13.189-13.1890.0000.0000.0000.000
74E127GLY00.0240.01628.114-0.261-0.2610.0000.0000.0000.000
75E128GLN0-0.082-0.03730.727-0.461-0.4610.0000.0000.0000.000
76E129ALA0-0.024-0.01330.6950.2880.2880.0000.0000.0000.000
77E130LEU00.0300.03530.2880.2270.2270.0000.0000.0000.000
78E131PRO00.0260.02227.201-0.222-0.2220.0000.0000.0000.000
79E132LEU00.0050.01125.2670.0770.0770.0000.0000.0000.000
80E133SER00.012-0.01120.7900.0060.0060.0000.0000.0000.000
81E134VAL00.0120.01519.6160.1750.1750.0000.0000.0000.000
82E135SER0-0.045-0.02714.8130.7890.7890.0000.0000.0000.000
83E136TYR0-0.008-0.03311.4080.3250.3250.0000.0000.0000.000
84E137VAL0-0.041-0.0037.1400.8150.8150.0000.0000.0000.000
85E138SER00.0540.0227.458-0.262-0.2620.0000.0000.0000.000
86E139THR00.0380.0092.9493.4954.3650.069-0.349-0.591-0.001
87E140THR0-0.052-0.0383.0531.7873.0310.141-0.619-0.766-0.006
88E141ALA00.0300.0105.735-1.438-1.4380.0000.0000.0000.000
89E142GLU-1-0.735-0.8468.14820.30120.3010.0000.0000.0000.000
90E143GLY0-0.0110.0009.188-1.374-1.3740.0000.0000.0000.000
91E144ALA00.000-0.0039.284-1.002-1.0020.0000.0000.0000.000
92E145GLN0-0.055-0.03910.911-0.832-0.8320.0000.0000.0000.000
93E146ARG10.8280.89812.021-19.682-19.6820.0000.0000.0000.000
94E147ARG10.8660.91212.593-19.206-19.2060.0000.0000.0000.000
95E148LEU0-0.049-0.01014.685-0.808-0.8080.0000.0000.0000.000
96E149ALA00.012-0.01216.422-0.760-0.7600.0000.0000.0000.000
97E150GLU-1-0.878-0.91916.97615.40315.4030.0000.0000.0000.000
98E151TYR00.009-0.03414.726-0.954-0.9540.0000.0000.0000.000
99E152ILE0-0.066-0.02620.009-0.572-0.5720.0000.0000.0000.000
100E153GLN0-0.091-0.04522.449-0.307-0.3070.0000.0000.0000.000
101E154GLN0-0.041-0.02322.340-0.025-0.0250.0000.0000.0000.000
102E155VAL00.0150.00823.097-0.404-0.4040.0000.0000.0000.000
103E156ASP-1-0.835-0.93525.6669.6859.6850.0000.0000.0000.000
104E157GLU-1-0.830-0.90427.8519.8989.8980.0000.0000.0000.000
105E158GLU-1-0.949-0.97426.43310.93610.9360.0000.0000.0000.000
106E159VAL00.0360.01029.279-0.348-0.3480.0000.0000.0000.000
107E160ALA00.0250.01731.658-0.353-0.3530.0000.0000.0000.000
108E161LYS10.8280.89630.682-9.942-9.9420.0000.0000.0000.000
109E162GLU-1-0.924-0.95632.9339.0299.0290.0000.0000.0000.000
110E163LEU0-0.0170.00335.301-0.216-0.2160.0000.0000.0000.000
111E164GLU-1-0.876-0.92037.7037.3987.3980.0000.0000.0000.000
112E165VAL0-0.020-0.02338.654-0.263-0.2630.0000.0000.0000.000
113E166ASP-1-0.732-0.85039.8017.6727.6720.0000.0000.0000.000
114E167LEU0-0.0480.00142.060-0.215-0.2150.0000.0000.0000.000
115E168LYS10.8360.88741.790-7.486-7.4860.0000.0000.0000.000
116E169ASP-1-0.877-0.93143.9306.8606.8600.0000.0000.0000.000
117E170ASN0-0.044-0.01645.252-0.233-0.2330.0000.0000.0000.000
118E171ILE00.0390.02447.755-0.166-0.1660.0000.0000.0000.000
119E172THR0-0.098-0.06048.908-0.202-0.2020.0000.0000.0000.000
120E173LEU00.0150.02750.365-0.066-0.0660.0000.0000.0000.000
121E174GLN00.0030.00552.177-0.158-0.1580.0000.0000.0000.000
122E175THR0-0.008-0.01653.722-0.157-0.1570.0000.0000.0000.000
123E176LYS10.8010.86355.548-5.407-5.4070.0000.0000.0000.000
124E177THR00.0220.02055.572-0.070-0.0700.0000.0000.0000.000
125E178LEU0-0.040-0.02556.494-0.106-0.1060.0000.0000.0000.000
126E179GLN0-0.002-0.01359.449-0.078-0.0780.0000.0000.0000.000
127E180GLU-1-0.813-0.88560.7284.9984.9980.0000.0000.0000.000
128E181SER0-0.008-0.00462.477-0.046-0.0460.0000.0000.0000.000
129E182LEU0-0.082-0.02764.014-0.063-0.0630.0000.0000.0000.000
130E183GLU-1-0.883-0.95965.6264.5674.5670.0000.0000.0000.000
131E184THR0-0.018-0.00165.876-0.069-0.0690.0000.0000.0000.000
132E185GLN0-0.058-0.02567.9810.0020.0020.0000.0000.0000.000
133E186GLU-1-0.860-0.92769.7114.2984.2980.0000.0000.0000.000
134E187VAL00.016-0.00271.241-0.078-0.0780.0000.0000.0000.000
135E188VAL00.0010.00571.317-0.028-0.0280.0000.0000.0000.000
136E189ALA0-0.047-0.02473.771-0.053-0.0530.0000.0000.0000.000
137E190GLN0-0.065-0.04575.388-0.135-0.1350.0000.0000.0000.000
138E191GLU-1-0.876-0.93176.3944.0444.0440.0000.0000.0000.000
139E192GLN0-0.034-0.02077.997-0.061-0.0610.0000.0000.0000.000
140E193LYS10.7560.88579.542-4.048-4.0480.0000.0000.0000.000
141E194ASP-1-0.801-0.91481.3433.8363.8360.0000.0000.0000.000
142E195LEU0-0.036-0.00881.355-0.031-0.0310.0000.0000.0000.000
143E196ARG10.9020.94780.833-3.934-3.9340.0000.0000.0000.000
144E197ILE00.0150.00084.812-0.048-0.0480.0000.0000.0000.000
145E198LYS10.8430.90186.833-3.671-3.6710.0000.0000.0000.000
146E199GLN0-0.043-0.00687.6440.0050.0050.0000.0000.0000.000
147E200ILE0-0.065-0.02989.583-0.034-0.0340.0000.0000.0000.000
148E201GLU-1-0.870-0.90290.8593.5253.5250.0000.0000.0000.000
149E202GLU-1-0.970-0.97392.5843.3323.3320.0000.0000.0000.000
150E253ALA00.0310.01866.616-0.025-0.0250.0000.0000.0000.000
151E254TYR00.0470.00066.0590.0490.0490.0000.0000.0000.000
152E255TYR00.0380.02466.6780.0360.0360.0000.0000.0000.000
153E256GLN00.0400.00760.802-0.036-0.0360.0000.0000.0000.000
154E257THR00.0780.05961.7400.0840.0840.0000.0000.0000.000
155E258LYS10.9190.96461.544-4.727-4.7270.0000.0000.0000.000
156E259GLN0-0.036-0.02161.981-0.001-0.0010.0000.0000.0000.000
157E260THR00.0420.00357.0890.0590.0590.0000.0000.0000.000
158E261LEU00.0270.00757.4170.0850.0850.0000.0000.0000.000
159E262LEU0-0.082-0.02157.8830.0410.0410.0000.0000.0000.000
160E263ASP-1-0.887-0.95155.6315.5015.5010.0000.0000.0000.000
161E264ILE0-0.021-0.01453.0230.1130.1130.0000.0000.0000.000
162E265LYS10.9100.96552.933-5.238-5.2380.0000.0000.0000.000
163E266ASN0-0.099-0.04754.0100.0540.0540.0000.0000.0000.000
164E267LEU00.0120.03048.9170.0470.0470.0000.0000.0000.000
165E268LYS10.9070.96143.423-6.889-6.8890.0000.0000.0000.000
166E269VAL00.009-0.01442.591-0.022-0.0220.0000.0000.0000.000
167E270THR0-0.103-0.06541.204-0.006-0.0060.0000.0000.0000.000
168E271ALA00.0420.02037.1970.0310.0310.0000.0000.0000.000
169E272ASP-1-0.852-0.92835.9657.8407.8400.0000.0000.0000.000
170E273THR0-0.056-0.01636.1540.0420.0420.0000.0000.0000.000
171E274VAL0-0.0050.00935.3690.0480.0480.0000.0000.0000.000
172E275HIS0-0.038-0.01431.2870.4070.4070.0000.0000.0000.000
173E276VAL00.011-0.00131.015-0.223-0.2230.0000.0000.0000.000
174E277TYR0-0.029-0.01425.6660.2500.2500.0000.0000.0000.000
175E278ARG10.9000.95729.788-9.206-9.2060.0000.0000.0000.000
176E279TYR00.014-0.00122.2970.3700.3700.0000.0000.0000.000
177E280VAL0-0.043-0.01425.807-0.413-0.4130.0000.0000.0000.000
178E281MET0-0.013-0.01221.0630.0590.0590.0000.0000.0000.000
179E282LYS10.9470.97921.660-11.728-11.7280.0000.0000.0000.000
180E283PRO0-0.0070.00716.7720.0610.0610.0000.0000.0000.000
181E284THR00.0510.03815.4570.1590.1590.0000.0000.0000.000
182E285LEU00.0130.03411.8210.7890.7890.0000.0000.0000.000
183E286PRO0-0.049-0.0098.936-0.523-0.5230.0000.0000.0000.000
184E287VAL00.0270.01010.3220.6340.6340.0000.0000.0000.000
185E288ARG10.8470.9058.510-25.169-25.1690.0000.0000.0000.000
186E289ARG10.9420.9802.376-70.599-68.4053.610-2.402-3.4010.020
187E290ASP-1-0.781-0.8765.93327.50427.5040.0000.0000.0000.000
188E291SER0-0.0050.0016.2184.6284.6280.0000.0000.0000.000
189E292PRO00.0130.0126.862-3.147-3.1470.0000.0000.0000.000