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: 6Y8YZ

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 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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1627263.081817
FMO2-HF: Nuclear repulsion 1559913.905275
FMO2-HF: Total energy -67349.176542
FMO2-MP2: Total energy -67549.85603


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.
-141.739-153.02956.148-22.532-22.327-0.102
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 : 0.849 / q_NPA : 0.935
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].
3B57THR00.012-0.0043.3750.3342.265-0.006-0.798-1.127-0.001
4B58SER0-0.059-0.0225.7725.0615.0610.0000.0000.0000.000
5B59THR00.022-0.0239.324-1.621-1.6210.0000.0000.0000.000
6B60ALA0-0.0150.00411.5191.7061.7060.0000.0000.0000.000
7B61ILE00.001-0.00514.921-0.555-0.5550.0000.0000.0000.000
8B62ILE00.0270.00317.6180.7060.7060.0000.0000.0000.000
9B63THR0-0.009-0.02120.3250.1270.1270.0000.0000.0000.000
10B64GLN00.0690.02923.6100.0970.0970.0000.0000.0000.000
11B65PRO0-0.0180.02426.7240.0240.0240.0000.0000.0000.000
12B66ASP-1-0.877-0.95628.833-9.959-9.9590.0000.0000.0000.000
13B67ALA00.0420.00131.5980.0880.0880.0000.0000.0000.000
14B68ALA0-0.0210.00134.4990.1700.1700.0000.0000.0000.000
15B69GLN00.0420.00427.8650.1750.1750.0000.0000.0000.000
16B70VAL0-0.0210.01032.408-0.013-0.0130.0000.0000.0000.000
17B71ALA0-0.009-0.02034.9080.1730.1730.0000.0000.0000.000
18B72THR00.0340.02236.9100.2830.2830.0000.0000.0000.000
19B73TYR00.0720.03636.3290.2570.2570.0000.0000.0000.000
20B74THR00.007-0.01937.6550.0880.0880.0000.0000.0000.000
21B75ASN0-0.019-0.00739.6040.2990.2990.0000.0000.0000.000
22B76ALA00.0220.02841.3050.2050.2050.0000.0000.0000.000
23B77LEU00.0210.01138.4290.1610.1610.0000.0000.0000.000
24B78ASN00.0020.00442.7460.1530.1530.0000.0000.0000.000
25B79VAL0-0.050-0.02045.5660.1660.1660.0000.0000.0000.000
26B80LEU0-0.031-0.01943.6980.1520.1520.0000.0000.0000.000
27B81TYR0-0.025-0.00943.6710.0450.0450.0000.0000.0000.000
28B82GLY00.011-0.00247.2940.0600.0600.0000.0000.0000.000
29B83GLY0-0.033-0.01647.441-0.106-0.1060.0000.0000.0000.000
30B84ASN0-0.047-0.02646.5500.0240.0240.0000.0000.0000.000
31B85ALA0-0.0140.01743.346-0.155-0.1550.0000.0000.0000.000
32B86PRO00.0030.01538.5620.0470.0470.0000.0000.0000.000
33B87LYS10.9660.97339.1567.8167.8160.0000.0000.0000.000
34B88ILE00.0360.00836.832-0.176-0.1760.0000.0000.0000.000
35B89SER00.0420.00534.973-0.129-0.1290.0000.0000.0000.000
36B90GLU-1-0.944-0.96933.696-8.730-8.7300.0000.0000.0000.000
37B91VAL00.0150.01833.672-0.268-0.2680.0000.0000.0000.000
38B92GLN0-0.045-0.03830.8610.0640.0640.0000.0000.0000.000
39B93ALA00.0240.01029.372-0.456-0.4560.0000.0000.0000.000
40B94ASN0-0.015-0.00528.808-0.464-0.4640.0000.0000.0000.000
41B95PHE00.0340.02228.709-0.289-0.2890.0000.0000.0000.000
42B96ILE00.0340.02222.574-0.377-0.3770.0000.0000.0000.000
43B97SER0-0.057-0.02124.096-0.781-0.7810.0000.0000.0000.000
44B98ARG10.9480.95224.5169.8159.8150.0000.0000.0000.000
45B99PHE00.0180.03818.815-0.448-0.4480.0000.0000.0000.000
46B100SER0-0.033-0.03219.900-0.565-0.5650.0000.0000.0000.000
47B101SER0-0.019-0.00519.843-0.890-0.8900.0000.0000.0000.000
48B102ALA00.1000.05221.289-0.390-0.3900.0000.0000.0000.000
49B103PHE0-0.006-0.02613.809-0.910-0.9100.0000.0000.0000.000
50B104SER0-0.067-0.04616.175-1.209-1.2090.0000.0000.0000.000
51B105ALA00.0350.03116.843-0.494-0.4940.0000.0000.0000.000
52B106LEU0-0.027-0.01714.918-0.513-0.5130.0000.0000.0000.000
53B107SER0-0.049-0.05511.621-0.663-0.6630.0000.0000.0000.000
54B108GLU-1-0.890-0.92212.693-21.278-21.2780.0000.0000.0000.000
55B109VAL0-0.030-0.01914.633-0.263-0.2630.0000.0000.0000.000
56B110LEU0-0.021-0.01111.069-0.341-0.3410.0000.0000.0000.000
57B111ASP-1-0.886-0.9349.687-30.423-30.4230.0000.0000.0000.000
58B112ASN0-0.071-0.02211.462-0.283-0.2830.0000.0000.0000.000
59B113GLN0-0.058-0.03712.3842.9522.9520.0000.0000.0000.000
60B114LYS10.8960.94413.42214.05014.0500.0000.0000.0000.000
61B115GLU-1-0.945-0.9629.079-28.010-28.0100.0000.0000.0000.000
62B116ARG10.9570.9957.63028.30628.3060.0000.0000.0000.000
63B117GLU-1-0.785-0.8177.372-29.433-29.4330.0000.0000.0000.000
64B118LYS10.8690.9203.43743.96644.2880.005-0.043-0.2850.000
65B119LEU00.0650.0366.688-3.033-3.0330.0000.0000.0000.000
66B120THR0-0.046-0.0048.417-0.869-0.8690.0000.0000.0000.000
67B121ILE00.0300.01210.6260.7660.7660.0000.0000.0000.000
68B122GLU-1-0.844-0.88411.335-24.458-24.4580.0000.0000.0000.000
69B123GLN00.0180.00114.9410.2310.2310.0000.0000.0000.000
70B124SER00.0340.00316.440-0.358-0.3580.0000.0000.0000.000
71B125VAL00.0190.01517.508-0.343-0.3430.0000.0000.0000.000
72B126LYS10.7770.84614.53720.55420.5540.0000.0000.0000.000
73B127GLY00.0410.02419.6590.5410.5410.0000.0000.0000.000
74B128GLN0-0.071-0.02822.2950.9810.9810.0000.0000.0000.000
75B129ALA0-0.022-0.01822.516-0.514-0.5140.0000.0000.0000.000
76B130LEU00.0150.02422.735-0.391-0.3910.0000.0000.0000.000
77B131PRO0-0.033-0.00820.2020.4820.4820.0000.0000.0000.000
78B132LEU00.0590.04218.245-0.302-0.3020.0000.0000.0000.000
79B133SER0-0.066-0.02214.0310.6180.6180.0000.0000.0000.000
80B134VAL00.0280.02012.884-0.861-0.8610.0000.0000.0000.000
81B135SER0-0.011-0.0077.552-0.588-0.5880.0000.0000.0000.000
82B136TYR0-0.012-0.0958.175-0.284-0.2840.0000.0000.0000.000
83B137VAL0-0.032-0.0021.967-4.583-9.48010.592-2.101-3.593-0.006
84B138SER00.0340.0214.0815.9626.186-0.001-0.037-0.1860.000
85B139THR0-0.001-0.0102.732-9.758-7.4660.789-1.692-1.389-0.016
86B140THR00.0400.0163.049-3.567-1.9840.083-0.980-0.686-0.009
87B141ALA00.0230.0135.487-0.331-0.3310.0000.0000.0000.000
88B142GLU-1-0.773-0.8797.379-19.156-19.1560.0000.0000.0000.000
89B143GLY0-0.0020.0028.4701.1111.1110.0000.0000.0000.000
90B144ALA00.0240.0066.3780.4010.4010.0000.0000.0000.000
91B145GLN0-0.056-0.0368.3011.5511.5510.0000.0000.0000.000
92B146ARG10.8340.89311.59119.11919.1190.0000.0000.0000.000
93B147ARG10.9480.96410.28821.27721.2770.0000.0000.0000.000
94B148LEU0-0.033-0.00211.4990.8900.8900.0000.0000.0000.000
95B149ALA0-0.001-0.01913.0031.0581.0580.0000.0000.0000.000
96B150GLU-1-0.840-0.88315.457-16.468-16.4680.0000.0000.0000.000
97B151TYR00.009-0.03111.8491.3631.3630.0000.0000.0000.000
98B152ILE0-0.070-0.03915.9680.5820.5820.0000.0000.0000.000
99B153GLN0-0.081-0.04118.4960.2640.2640.0000.0000.0000.000
100B154GLN0-0.015-0.01118.9290.8950.8950.0000.0000.0000.000
101B155VAL00.0050.00518.6080.4800.4800.0000.0000.0000.000
102B156ASP-1-0.835-0.94821.478-11.954-11.9540.0000.0000.0000.000
103B157GLU-1-0.855-0.91724.175-11.955-11.9550.0000.0000.0000.000
104B158GLU-1-1.010-0.99122.920-12.562-12.5620.0000.0000.0000.000
105B159VAL00.0240.01824.4540.4450.4450.0000.0000.0000.000
106B160ALA00.020-0.00327.0490.5190.5190.0000.0000.0000.000
107B161LYS10.9530.98129.33210.43110.4310.0000.0000.0000.000
108B162GLU-1-0.965-0.99029.310-10.502-10.5020.0000.0000.0000.000
109B163LEU00.0180.01330.4650.3360.3360.0000.0000.0000.000
110B164GLU-1-0.924-0.98533.185-9.216-9.2160.0000.0000.0000.000
111B165VAL0-0.073-0.03834.8380.3690.3690.0000.0000.0000.000
112B166ASP-1-0.821-0.91134.697-8.944-8.9440.0000.0000.0000.000
113B167LEU0-0.015-0.00237.6400.3060.3060.0000.0000.0000.000
114B168LYS10.8490.92737.1458.8818.8810.0000.0000.0000.000
115B169ASP-1-0.920-0.93240.257-7.532-7.5320.0000.0000.0000.000
116B170ASN00.034-0.01241.1560.2830.2830.0000.0000.0000.000
117B171ILE0-0.051-0.00842.9240.1940.1940.0000.0000.0000.000
118B172THR0-0.0030.01545.5020.2700.2700.0000.0000.0000.000
119B173LEU0-0.044-0.03544.2080.2410.2410.0000.0000.0000.000
120B174GLN0-0.0150.00247.2970.0740.0740.0000.0000.0000.000
121B175THR0-0.005-0.04149.0000.0760.0760.0000.0000.0000.000
122B176LYS10.8940.95248.5576.7366.7360.0000.0000.0000.000
123B177THR00.0120.00752.624-0.003-0.0030.0000.0000.0000.000
124B178LEU0-0.069-0.03651.9050.1130.1130.0000.0000.0000.000
125B179GLN0-0.041-0.03955.0360.0700.0700.0000.0000.0000.000
126B180GLU-1-0.797-0.89155.615-5.814-5.8140.0000.0000.0000.000
127B181SER0-0.071-0.03058.5610.0820.0820.0000.0000.0000.000
128B182LEU0-0.037-0.03859.5510.0950.0950.0000.0000.0000.000
129B183GLU-1-0.872-0.92861.328-5.083-5.0830.0000.0000.0000.000
130B184THR0-0.102-0.03961.9380.0300.0300.0000.0000.0000.000
131B185GLN0-0.142-0.08464.531-0.010-0.0100.0000.0000.0000.000
132B186GLU-1-0.918-0.93066.607-4.623-4.6230.0000.0000.0000.000
133B251SER00.0310.00867.1950.0300.0300.0000.0000.0000.000
134B252PRO0-0.002-0.01067.075-0.051-0.0510.0000.0000.0000.000
135B253ALA00.0520.02562.287-0.039-0.0390.0000.0000.0000.000
136B254TYR00.022-0.00661.930-0.092-0.0920.0000.0000.0000.000
137B255TYR00.0180.01762.009-0.074-0.0740.0000.0000.0000.000
138B256GLN00.015-0.01158.2860.0520.0520.0000.0000.0000.000
139B257THR00.0310.01856.731-0.104-0.1040.0000.0000.0000.000
140B258LYS10.9310.97557.0705.1605.1600.0000.0000.0000.000
141B259GLN0-0.0080.00057.400-0.055-0.0550.0000.0000.0000.000
142B260THR00.0610.03452.901-0.056-0.0560.0000.0000.0000.000
143B261LEU00.0270.01752.587-0.137-0.1370.0000.0000.0000.000
144B262LEU0-0.018-0.00253.458-0.069-0.0690.0000.0000.0000.000
145B263ASP-1-0.831-0.93050.767-6.268-6.2680.0000.0000.0000.000
146B264ILE0-0.083-0.03548.732-0.125-0.1250.0000.0000.0000.000
147B265LYS10.8570.93849.0236.1996.1990.0000.0000.0000.000
148B266ASN0-0.065-0.02549.949-0.155-0.1550.0000.0000.0000.000
149B267LEU00.0240.03644.611-0.086-0.0860.0000.0000.0000.000
150B268LYS10.8730.91743.8676.7766.7760.0000.0000.0000.000
151B269VAL00.0180.02038.026-0.073-0.0730.0000.0000.0000.000
152B270THR0-0.039-0.03337.662-0.147-0.1470.0000.0000.0000.000
153B271ALA00.0040.00034.212-0.069-0.0690.0000.0000.0000.000
154B272ASP-1-0.892-0.93731.460-10.194-10.1940.0000.0000.0000.000
155B273THR0-0.118-0.05233.4840.0490.0490.0000.0000.0000.000
156B274VAL0-0.061-0.02331.545-0.084-0.0840.0000.0000.0000.000
157B275HIS00.0570.03927.792-0.028-0.0280.0000.0000.0000.000
158B276VAL00.003-0.00725.1800.2200.2200.0000.0000.0000.000
159B277TYR0-0.021-0.02221.845-0.339-0.3390.0000.0000.0000.000
160B278ARG10.9340.98624.31911.87211.8720.0000.0000.0000.000
161B279TYR0-0.009-0.01018.283-0.130-0.1300.0000.0000.0000.000
162B280VAL0-0.057-0.01320.9870.7030.7030.0000.0000.0000.000
163B281MET0-0.076-0.04316.9730.0490.0490.0000.0000.0000.000
164B282LYS11.0011.00318.29813.27813.2780.0000.0000.0000.000
165B283PRO00.0090.00213.962-0.182-0.1820.0000.0000.0000.000
166B284THR00.0430.03611.8520.2110.2110.0000.0000.0000.000
167B285LEU00.0550.04111.363-1.982-1.9820.0000.0000.0000.000
168B286PRO0-0.092-0.0077.6621.1581.1580.0000.0000.0000.000
169B287VAL00.0530.0129.6860.4480.4480.0000.0000.0000.000
170B288ARG10.9380.9699.28924.35224.3520.0000.0000.0000.000
171B289ARG10.8620.9181.85519.08211.58718.955-5.849-5.6110.049
172B290ASP-1-0.774-0.8961.663-123.076-128.90925.733-10.961-8.939-0.119
173B291SER0-0.009-0.0074.0788.0508.400-0.001-0.045-0.3040.000
174B292PRO0-0.0030.0084.350-7.806-7.573-0.001-0.026-0.2070.000