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: R8V88

Calculation Name: 3B8P-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: B

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 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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1628514.15312
FMO2-HF: Nuclear repulsion 1561162.620896
FMO2-HF: Total energy -67351.532224
FMO2-MP2: Total energy -67551.975447


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(B:55:LYS)


Summations of interaction energy for fragment #1(B:55:LYS)
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.
-149.064-156.16448.014-20.108-20.804-0.092
Interaction energy analysis for fragmet #1(B:55:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.939
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].
3B57THR00.0080.0043.016-0.7351.3030.035-0.872-1.201-0.003
4B58SER0-0.047-0.0145.2745.6865.734-0.001-0.001-0.0450.000
5B59THR00.007-0.0258.913-2.242-2.2420.0000.0000.0000.000
6B60ALA00.0000.01011.1101.5631.5630.0000.0000.0000.000
7B61ILE0-0.011-0.00414.564-0.520-0.5200.0000.0000.0000.000
8B62ILE00.0320.02517.3080.8990.8990.0000.0000.0000.000
9B63THR0-0.016-0.02120.0640.1020.1020.0000.0000.0000.000
10B64GLN00.0610.03523.318-0.004-0.0040.0000.0000.0000.000
11B65PRO00.0370.04126.3610.0350.0350.0000.0000.0000.000
12B66ASP-1-0.875-0.94728.498-10.069-10.0690.0000.0000.0000.000
13B67ALA00.0590.00231.4450.0800.0800.0000.0000.0000.000
14B68ALA0-0.008-0.00634.6170.2200.2200.0000.0000.0000.000
15B69GLN00.012-0.00527.3730.0780.0780.0000.0000.0000.000
16B70VAL00.0160.01932.132-0.081-0.0810.0000.0000.0000.000
17B71ALA0-0.0010.00634.5750.2190.2190.0000.0000.0000.000
18B72THR0-0.028-0.01936.1860.2900.2900.0000.0000.0000.000
19B73TYR00.039-0.00135.8140.2920.2920.0000.0000.0000.000
20B74THR00.008-0.01137.3730.1040.1040.0000.0000.0000.000
21B75ASN0-0.023-0.01839.3630.3290.3290.0000.0000.0000.000
22B76ALA00.0270.02340.9580.2120.2120.0000.0000.0000.000
23B77LEU00.0030.00438.0230.1470.1470.0000.0000.0000.000
24B78ASN0-0.016-0.02642.4890.1170.1170.0000.0000.0000.000
25B79VAL0-0.039-0.01845.1540.1780.1780.0000.0000.0000.000
26B80LEU0-0.0270.00143.2260.1500.1500.0000.0000.0000.000
27B81TYR0-0.021-0.00343.0410.0690.0690.0000.0000.0000.000
28B82GLY00.0220.01747.1450.0950.0950.0000.0000.0000.000
29B83GLY0-0.045-0.03546.938-0.137-0.1370.0000.0000.0000.000
30B84ASN0-0.045-0.02046.3990.0330.0330.0000.0000.0000.000
31B85ALA00.0020.02242.722-0.149-0.1490.0000.0000.0000.000
32B86PRO0-0.027-0.00338.0060.0190.0190.0000.0000.0000.000
33B87LYS10.8780.90738.8527.9617.9610.0000.0000.0000.000
34B88ILE00.0130.00636.311-0.203-0.2030.0000.0000.0000.000
35B89SER00.0500.01934.254-0.160-0.1600.0000.0000.0000.000
36B90GLU-1-0.834-0.89833.279-8.604-8.6040.0000.0000.0000.000
37B91VAL0-0.0100.00633.646-0.212-0.2120.0000.0000.0000.000
38B92GLN0-0.049-0.03730.6620.0020.0020.0000.0000.0000.000
39B93ALA00.0380.01429.183-0.465-0.4650.0000.0000.0000.000
40B94ASN0-0.021-0.01328.690-0.436-0.4360.0000.0000.0000.000
41B95PHE00.0280.01828.614-0.294-0.2940.0000.0000.0000.000
42B96ILE00.0390.01922.343-0.382-0.3820.0000.0000.0000.000
43B97SER0-0.0620.00123.904-0.584-0.5840.0000.0000.0000.000
44B98ARG10.8140.87924.5789.8279.8270.0000.0000.0000.000
45B99PHE00.0270.01518.852-0.501-0.5010.0000.0000.0000.000
46B100SER0-0.035-0.04719.802-0.652-0.6520.0000.0000.0000.000
47B101SER0-0.0130.00619.620-0.933-0.9330.0000.0000.0000.000
48B102ALA00.0750.04620.831-0.540-0.5400.0000.0000.0000.000
49B103PHE00.017-0.00413.381-0.786-0.7860.0000.0000.0000.000
50B104SER0-0.066-0.04716.174-1.189-1.1890.0000.0000.0000.000
51B105ALA00.0350.01916.716-0.777-0.7770.0000.0000.0000.000
52B106LEU00.0180.00815.448-0.491-0.4910.0000.0000.0000.000
53B107SER0-0.001-0.02112.196-1.571-1.5710.0000.0000.0000.000
54B108GLU-1-0.976-0.98213.074-21.331-21.3310.0000.0000.0000.000
55B109VAL0-0.048-0.03015.092-0.135-0.1350.0000.0000.0000.000
56B110LEU0-0.0040.01011.905-0.265-0.2650.0000.0000.0000.000
57B111ASP-1-0.786-0.8509.021-32.121-32.1210.0000.0000.0000.000
58B112ASN0-0.059-0.01711.4640.1940.1940.0000.0000.0000.000
59B113GLN0-0.048-0.03412.1612.7842.7840.0000.0000.0000.000
60B114LYS10.9000.92913.63113.93413.9340.0000.0000.0000.000
61B115GLU-1-0.960-0.9628.769-28.977-28.9770.0000.0000.0000.000
62B116ARG10.8260.8968.08727.44027.4400.0000.0000.0000.000
63B117GLU-1-0.731-0.8138.212-29.211-29.2110.0000.0000.0000.000
64B118LYS10.8490.9103.89742.60342.8000.000-0.020-0.1770.000
65B119LEU00.0700.0346.994-4.088-4.0880.0000.0000.0000.000
66B120THR0-0.056-0.0278.290-2.116-2.1160.0000.0000.0000.000
67B121ILE00.0050.00810.2520.7430.7430.0000.0000.0000.000
68B122GLU-1-0.806-0.87212.108-23.083-23.0830.0000.0000.0000.000
69B123GLN00.0540.02815.1040.2200.2200.0000.0000.0000.000
70B124SER0-0.001-0.01916.254-0.387-0.3870.0000.0000.0000.000
71B125VAL0-0.028-0.00417.323-0.326-0.3260.0000.0000.0000.000
72B126LYS10.8130.88414.15421.10521.1050.0000.0000.0000.000
73B127GLY00.0470.03019.7580.5520.5520.0000.0000.0000.000
74B128GLN0-0.097-0.05022.3230.8850.8850.0000.0000.0000.000
75B129ALA0-0.011-0.01522.465-0.522-0.5220.0000.0000.0000.000
76B130LEU00.0090.02222.552-0.293-0.2930.0000.0000.0000.000
77B131PRO0-0.013-0.00420.3720.4920.4920.0000.0000.0000.000
78B132LEU00.0270.00917.743-0.136-0.1360.0000.0000.0000.000
79B133SER0-0.027-0.01313.0810.7690.7690.0000.0000.0000.000
80B134VAL00.0060.00812.618-0.072-0.0720.0000.0000.0000.000
81B135SER0-0.016-0.0147.8100.0500.0500.0000.0000.0000.000
82B136TYR00.004-0.0358.087-0.455-0.4550.0000.0000.0000.000
83B137VAL0-0.043-0.0142.176-7.980-8.5674.660-1.162-2.910-0.008
84B138SER00.0390.0324.3095.6635.913-0.001-0.035-0.2140.000
85B139THR00.018-0.0052.540-11.064-9.1221.479-1.812-1.609-0.018
86B140THR0-0.004-0.0143.468-0.3730.3820.013-0.445-0.323-0.003
87B141ALA00.0580.0265.590-1.307-1.3070.0000.0000.0000.000
88B142GLU-1-0.768-0.8677.850-19.219-19.2190.0000.0000.0000.000
89B143GLY00.0100.0128.6800.7930.7930.0000.0000.0000.000
90B144ALA00.015-0.0096.4590.2390.2390.0000.0000.0000.000
91B145GLN0-0.082-0.0578.4871.4761.4760.0000.0000.0000.000
92B146ARG10.8320.88811.92219.45719.4570.0000.0000.0000.000
93B147ARG10.8560.9129.93321.39721.3970.0000.0000.0000.000
94B148LEU0-0.0150.00211.0000.8000.8000.0000.0000.0000.000
95B149ALA0-0.021-0.01413.1821.1731.1730.0000.0000.0000.000
96B150GLU-1-0.838-0.88215.885-16.523-16.5230.0000.0000.0000.000
97B151TYR00.007-0.03512.0601.2271.2270.0000.0000.0000.000
98B152ILE0-0.050-0.02015.3550.6350.6350.0000.0000.0000.000
99B153GLN0-0.081-0.04618.3690.5370.5370.0000.0000.0000.000
100B154GLN0-0.006-0.00619.660-0.096-0.0960.0000.0000.0000.000
101B155VAL00.0180.00518.5480.5950.5950.0000.0000.0000.000
102B156ASP-1-0.805-0.91221.586-11.979-11.9790.0000.0000.0000.000
103B157GLU-1-0.864-0.92324.096-12.071-12.0710.0000.0000.0000.000
104B158GLU-1-0.949-0.96823.125-13.317-13.3170.0000.0000.0000.000
105B159VAL00.0180.00724.5060.5240.5240.0000.0000.0000.000
106B160ALA00.0180.01327.2180.5200.5200.0000.0000.0000.000
107B161LYS10.9650.98229.48810.45810.4580.0000.0000.0000.000
108B162GLU-1-0.902-0.94329.685-10.550-10.5500.0000.0000.0000.000
109B163LEU00.0390.02130.7140.4250.4250.0000.0000.0000.000
110B164GLU-1-0.804-0.88933.019-8.946-8.9460.0000.0000.0000.000
111B165VAL0-0.073-0.02834.9770.3640.3640.0000.0000.0000.000
112B166ASP-1-0.781-0.87034.639-9.048-9.0480.0000.0000.0000.000
113B167LEU0-0.030-0.00837.4200.3190.3190.0000.0000.0000.000
114B168LYS10.7880.87137.5128.8658.8650.0000.0000.0000.000
115B169ASP-1-0.902-0.93540.591-7.352-7.3520.0000.0000.0000.000
116B170ASN00.017-0.01940.3250.3840.3840.0000.0000.0000.000
117B171ILE0-0.0130.00443.0760.2080.2080.0000.0000.0000.000
118B172THR0-0.026-0.00145.1470.2740.2740.0000.0000.0000.000
119B173LEU0-0.057-0.02244.5340.2310.2310.0000.0000.0000.000
120B174GLN00.026-0.00347.0080.0810.0810.0000.0000.0000.000
121B175THR0-0.031-0.03848.8140.1730.1730.0000.0000.0000.000
122B176LYS10.8650.93148.4786.8076.8070.0000.0000.0000.000
123B177THR0-0.045-0.02552.361-0.011-0.0110.0000.0000.0000.000
124B178LEU0-0.034-0.00251.8880.0870.0870.0000.0000.0000.000
125B179GLN00.0220.01855.1900.0650.0650.0000.0000.0000.000
126B180GLU-1-0.779-0.89355.735-5.798-5.7980.0000.0000.0000.000
127B181SER0-0.084-0.04758.6570.1180.1180.0000.0000.0000.000
128B182LEU0-0.048-0.03560.2790.0950.0950.0000.0000.0000.000
129B183GLU-1-0.886-0.94761.362-5.096-5.0960.0000.0000.0000.000
130B184THR0-0.099-0.05361.8130.0510.0510.0000.0000.0000.000
131B185GLN0-0.156-0.07364.400-0.014-0.0140.0000.0000.0000.000
132B186GLU-1-0.890-0.92666.689-4.647-4.6470.0000.0000.0000.000
133B251SER00.0370.01166.8790.0350.0350.0000.0000.0000.000
134B252PRO00.008-0.00366.471-0.065-0.0650.0000.0000.0000.000
135B253ALA00.0510.01761.910-0.048-0.0480.0000.0000.0000.000
136B254TYR00.0110.00361.511-0.067-0.0670.0000.0000.0000.000
137B255TYR00.0340.02161.933-0.051-0.0510.0000.0000.0000.000
138B256GLN00.013-0.00358.460-0.001-0.0010.0000.0000.0000.000
139B257THR00.0320.01356.629-0.089-0.0890.0000.0000.0000.000
140B258LYS10.8660.93557.0305.1665.1660.0000.0000.0000.000
141B259GLN0-0.035-0.00556.969-0.022-0.0220.0000.0000.0000.000
142B260THR00.0800.03452.585-0.054-0.0540.0000.0000.0000.000
143B261LEU00.0040.01752.367-0.139-0.1390.0000.0000.0000.000
144B262LEU00.0030.00753.531-0.060-0.0600.0000.0000.0000.000
145B263ASP-1-0.820-0.91650.463-6.321-6.3210.0000.0000.0000.000
146B264ILE0-0.038-0.01847.909-0.152-0.1520.0000.0000.0000.000
147B265LYS10.8010.89249.3106.3666.3660.0000.0000.0000.000
148B266ASN0-0.059-0.00849.638-0.151-0.1510.0000.0000.0000.000
149B267LEU00.0490.02544.408-0.089-0.0890.0000.0000.0000.000
150B268LYS10.8490.91544.0416.8046.8040.0000.0000.0000.000
151B269VAL00.0230.02238.168-0.098-0.0980.0000.0000.0000.000
152B270THR00.004-0.00938.368-0.082-0.0820.0000.0000.0000.000
153B271ALA00.0410.02134.643-0.095-0.0950.0000.0000.0000.000
154B272ASP-1-0.935-0.95832.650-10.000-10.0000.0000.0000.0000.000
155B273THR0-0.097-0.05034.2590.0030.0030.0000.0000.0000.000
156B274VAL0-0.0190.00331.8060.1080.1080.0000.0000.0000.000
157B275HIS0-0.008-0.00127.2700.0310.0310.0000.0000.0000.000
158B276VAL0-0.022-0.02324.9450.2410.2410.0000.0000.0000.000
159B277TYR0-0.038-0.01921.229-0.604-0.6040.0000.0000.0000.000
160B278ARG10.8840.95023.67612.01212.0120.0000.0000.0000.000
161B279TYR00.0430.01717.928-0.776-0.7760.0000.0000.0000.000
162B280VAL0-0.027-0.00320.9370.7440.7440.0000.0000.0000.000
163B281MET0-0.067-0.03216.4630.1200.1200.0000.0000.0000.000
164B282LYS10.9640.96918.04413.54713.5470.0000.0000.0000.000
165B283PRO00.0120.01414.385-0.346-0.3460.0000.0000.0000.000
166B284THR00.0330.03111.8670.3520.3520.0000.0000.0000.000
167B285LEU00.0430.04011.491-1.962-1.9620.0000.0000.0000.000
168B286PRO0-0.054-0.0077.5831.3601.3600.0000.0000.0000.000
169B287VAL00.011-0.0049.5540.1470.1470.0000.0000.0000.000
170B288ARG10.9240.9619.68826.13326.1330.0000.0000.0000.000
171B289ARG10.8720.9221.80316.5239.59818.256-5.926-5.4060.047
172B290ASP-1-0.745-0.8701.667-119.409-125.02223.571-9.673-8.285-0.107
173B291SER00.007-0.0024.1688.8759.2690.000-0.075-0.3190.000
174B292PRO0-0.0220.0024.071-9.843-9.4420.002-0.087-0.3150.000