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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: N1L1Q

Calculation Name: 3BT3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BT3

Chain ID: A

ChEMBL ID:

UniProt ID: A9KJQ6

Base Structure: X-ray

Registration Date: 2023-03-14

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 131
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1127012.688401
FMO2-HF: Nuclear repulsion 1074179.591338
FMO2-HF: Total energy -52833.097063
FMO2-MP2: Total energy -52985.786577


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:134:GLU)


Summations of interaction energy for fragment #1(A:134: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.
59.5871.6267.164-7.477-11.7320.023
Interaction energy analysis for fragmet #1(A:134:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.854 / q_NPA : -0.920
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].
3A136GLY0-0.0170.0023.843-2.916-0.778-0.012-1.094-1.0320.003
4A137TYR00.0080.0082.612-7.295-4.9254.469-1.685-5.154-0.015
5A138VAL0-0.008-0.0072.7040.0554.2422.106-2.988-3.3040.011
6A139VAL00.0260.0232.667-17.614-14.3500.602-1.696-2.1700.024
7A140ARG10.8730.9294.697-36.029-35.942-0.001-0.014-0.0720.000
8A141GLU-1-0.741-0.8658.30619.95219.9520.0000.0000.0000.000
9A142ASN0-0.058-0.0508.8452.0442.0440.0000.0000.0000.000
10A143GLY00.0410.04510.933-0.584-0.5840.0000.0000.0000.000
11A144PRO0-0.0100.00014.7240.3740.3740.0000.0000.0000.000
12A145VAL00.0040.00716.517-0.493-0.4930.0000.0000.0000.000
13A146TYR0-0.032-0.04119.093-0.256-0.2560.0000.0000.0000.000
14A147PHE0-0.019-0.00420.603-0.005-0.0050.0000.0000.0000.000
15A148THR00.001-0.01025.592-0.357-0.3570.0000.0000.0000.000
16A149LYS10.8790.92229.284-9.447-9.4470.0000.0000.0000.000
17A150ASP-1-0.838-0.92232.4378.7808.7800.0000.0000.0000.000
18A151MET00.0060.01627.4470.1150.1150.0000.0000.0000.000
19A152ASP-1-0.745-0.85030.8879.3349.3340.0000.0000.0000.000
20A153LYS10.8460.92533.572-9.386-9.3860.0000.0000.0000.000
21A154THR0-0.059-0.04628.158-0.042-0.0420.0000.0000.0000.000
22A155VAL0-0.012-0.00828.4640.1850.1850.0000.0000.0000.000
23A156LYS10.9380.97030.553-8.935-8.9350.0000.0000.0000.000
24A157TRP00.0340.01329.0720.0490.0490.0000.0000.0000.000
25A158PHE0-0.004-0.01725.6480.0840.0840.0000.0000.0000.000
26A159GLU-1-0.902-0.95430.3879.7719.7710.0000.0000.0000.000
27A160GLU-1-0.976-0.99132.4428.3608.3600.0000.0000.0000.000
28A161ILE0-0.052-0.02933.841-0.140-0.1400.0000.0000.0000.000
29A162LEU0-0.051-0.03728.0420.0520.0520.0000.0000.0000.000
30A163GLY0-0.0170.01030.6830.1820.1820.0000.0000.0000.000
31A164TRP0-0.080-0.03822.6130.4740.4740.0000.0000.0000.000
32A165SER00.0310.00127.155-0.608-0.6080.0000.0000.0000.000
33A166GLY0-0.005-0.02426.6700.4850.4850.0000.0000.0000.000
34A167ASP-1-0.900-0.93626.47610.81810.8180.0000.0000.0000.000
35A168ILE0-0.107-0.05627.0990.3770.3770.0000.0000.0000.000
36A169VAL00.0350.02224.289-0.299-0.2990.0000.0000.0000.000
37A170ALA0-0.031-0.01526.813-0.178-0.1780.0000.0000.0000.000
38A171ARG10.7940.87028.568-9.320-9.3200.0000.0000.0000.000
39A172ASP-1-0.727-0.83731.5269.2579.2570.0000.0000.0000.000
40A173ASP-1-0.976-0.99933.4468.4478.4470.0000.0000.0000.000
41A174GLU-1-0.988-0.98736.7217.8597.8590.0000.0000.0000.000
42A175GLY0-0.0180.00036.363-0.197-0.1970.0000.0000.0000.000
43A176PHE0-0.046-0.02033.6450.1470.1470.0000.0000.0000.000
44A177GLY00.002-0.00130.1800.1310.1310.0000.0000.0000.000
45A178ASP-1-0.862-0.93327.00310.59610.5960.0000.0000.0000.000
46A179TYR0-0.028-0.04619.5640.3580.3580.0000.0000.0000.000
47A180GLY00.0200.01123.971-0.574-0.5740.0000.0000.0000.000
48A181CYS0-0.075-0.01321.6930.6920.6920.0000.0000.0000.000
49A182VAL00.0650.03023.204-0.626-0.6260.0000.0000.0000.000
50A183PHE0-0.020-0.03021.9020.8660.8660.0000.0000.0000.000
51A184ASP-1-0.809-0.88421.94313.88413.8840.0000.0000.0000.000
52A185TYR0-0.0080.00020.0060.0070.0070.0000.0000.0000.000
53A186PRO00.0470.02825.947-0.034-0.0340.0000.0000.0000.000
54A187SER00.0550.01226.7610.4110.4110.0000.0000.0000.000
55A188GLU-1-0.920-0.96027.12610.74710.7470.0000.0000.0000.000
56A189VAL0-0.074-0.03222.2340.3240.3240.0000.0000.0000.000
57A190ALA00.0290.01221.0750.0410.0410.0000.0000.0000.000
58A191VAL0-0.037-0.00921.9290.2150.2150.0000.0000.0000.000
59A192ALA0-0.056-0.01724.042-0.094-0.0940.0000.0000.0000.000
60A193HIS-1-0.851-0.91616.74317.17417.1740.0000.0000.0000.000
61A194LEU0-0.049-0.02117.7540.2240.2240.0000.0000.0000.000
62A195THR0-0.028-0.04014.767-0.168-0.1680.0000.0000.0000.000
63A196PRO0-0.156-0.09612.7061.6881.6880.0000.0000.0000.000
64A197PHE00.0310.04714.966-0.826-0.8260.0000.0000.0000.000
65A198ARG10.7820.87014.835-14.321-14.3210.0000.0000.0000.000
66A199GLY00.0420.03617.018-0.393-0.3930.0000.0000.0000.000
67A200PHE0-0.060-0.03218.4960.9240.9240.0000.0000.0000.000
68A201HIS00.0400.03015.499-1.466-1.4660.0000.0000.0000.000
69A202LEU0-0.049-0.02520.224-0.051-0.0510.0000.0000.0000.000
70A203PHE00.026-0.00518.6480.1590.1590.0000.0000.0000.000
71A204LYS10.8010.87424.549-10.433-10.4330.0000.0000.0000.000
72A205GLY0-0.047-0.03326.6060.3340.3340.0000.0000.0000.000
73A206GLU-1-0.879-0.93027.9769.4919.4910.0000.0000.0000.000
74A207PRO00.0310.02427.5660.4350.4350.0000.0000.0000.000
75A208ILE00.013-0.00222.538-0.124-0.1240.0000.0000.0000.000
76A209LYS10.8770.94026.630-10.392-10.3920.0000.0000.0000.000
77A210GLY00.0220.00027.050-0.062-0.0620.0000.0000.0000.000
78A211VAL0-0.046-0.01923.021-0.119-0.1190.0000.0000.0000.000
79A212ALA00.0070.01622.9080.5290.5290.0000.0000.0000.000
80A213GLY00.0360.01220.8060.7040.7040.0000.0000.0000.000
81A214PHE0-0.062-0.03219.414-0.787-0.7870.0000.0000.0000.000
82A215MET0-0.0110.01319.8500.9080.9080.0000.0000.0000.000
83A216MET0-0.0140.00120.291-0.610-0.6100.0000.0000.0000.000
84A217ILE0-0.028-0.02122.2350.2700.2700.0000.0000.0000.000
85A218GLU-1-0.937-0.97225.00411.56611.5660.0000.0000.0000.000
86A219GLY00.0090.01327.962-0.160-0.1600.0000.0000.0000.000
87A220ILE0-0.015-0.02628.978-0.187-0.1870.0000.0000.0000.000
88A221ASP-1-0.804-0.88931.5339.0409.0400.0000.0000.0000.000
89A222ALA0-0.031-0.01233.696-0.249-0.2490.0000.0000.0000.000
90A223LEU00.0430.03828.971-0.126-0.1260.0000.0000.0000.000
91A224HIS00.0290.02132.979-0.374-0.3740.0000.0000.0000.000
92A225LYS10.7750.86535.453-7.983-7.9830.0000.0000.0000.000
93A226TYR00.0080.01534.603-0.249-0.2490.0000.0000.0000.000
94A227VAL00.0080.01333.110-0.128-0.1280.0000.0000.0000.000
95A228LYS10.8390.92536.253-8.417-8.4170.0000.0000.0000.000
96A229GLU-1-0.851-0.91039.7817.5347.5340.0000.0000.0000.000
97A230ASN0-0.094-0.04137.825-0.284-0.2840.0000.0000.0000.000
98A231GLY0-0.0080.00540.0560.0020.0020.0000.0000.0000.000
99A232TRP0-0.050-0.02134.614-0.160-0.1600.0000.0000.0000.000
100A233ASP-1-0.804-0.93938.5187.7607.7600.0000.0000.0000.000
101A234GLN0-0.116-0.03536.3330.0770.0770.0000.0000.0000.000
102A235ILE0-0.011-0.01433.1750.3740.3740.0000.0000.0000.000
103A236SER0-0.022-0.01133.892-0.151-0.1510.0000.0000.0000.000
104A237ASP-1-0.879-0.95435.6058.3168.3160.0000.0000.0000.000
105A238ILE0-0.040-0.00933.2010.2570.2570.0000.0000.0000.000
106A239TYR0-0.061-0.04129.806-0.317-0.3170.0000.0000.0000.000
107A240THR0-0.008-0.01832.4770.3030.3030.0000.0000.0000.000
108A241GLN0-0.007-0.01027.778-0.281-0.2810.0000.0000.0000.000
109A242PRO0-0.016-0.02629.9260.0630.0630.0000.0000.0000.000
110A243TRP0-0.068-0.02323.7510.0600.0600.0000.0000.0000.000
111A244GLY00.0080.01425.9100.4220.4220.0000.0000.0000.000
112A245ALA0-0.0010.00226.1670.1730.1730.0000.0000.0000.000
113A246ARG10.7590.84228.329-10.050-10.0500.0000.0000.0000.000
114A247GLU-1-0.730-0.82427.15912.44212.4420.0000.0000.0000.000
115A248CYS0-0.0180.00929.696-0.467-0.4670.0000.0000.0000.000
116A249SER0-0.026-0.01529.3640.4660.4660.0000.0000.0000.000
117A250ILE00.0400.01829.983-0.405-0.4050.0000.0000.0000.000
118A251THR0-0.0080.00630.3080.4530.4530.0000.0000.0000.000
119A252THR00.0350.00528.344-0.306-0.3060.0000.0000.0000.000
120A253THR0-0.0050.00531.756-0.272-0.2720.0000.0000.0000.000
121A254ASP-1-0.791-0.85130.37810.13410.1340.0000.0000.0000.000
122A255GLY0-0.029-0.01132.3790.0020.0020.0000.0000.0000.000
123A256CYS0-0.087-0.02227.1310.1060.1060.0000.0000.0000.000
124A257ILE00.0000.00528.048-0.270-0.2700.0000.0000.0000.000
125A258LEU00.0060.01224.3530.6460.6460.0000.0000.0000.000
126A259ARG10.8000.86423.408-13.403-13.4030.0000.0000.0000.000
127A260PHE00.0590.01824.6390.6480.6480.0000.0000.0000.000
128A261PHE00.010-0.01820.536-0.519-0.5190.0000.0000.0000.000
129A262GLU-1-0.718-0.83325.56610.81410.8140.0000.0000.0000.000
130A263SER0-0.032-0.00924.744-0.110-0.1100.0000.0000.0000.000
131A264ILE0-0.023-0.01226.789-0.342-0.3420.0000.0000.0000.000