FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 82LQY

Calculation Name: 1B78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B78

Chain ID: A

ChEMBL ID:

UniProt ID: Q57679

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2039809.414281
FMO2-HF: Nuclear repulsion 1967043.519586
FMO2-HF: Total energy -72765.894695
FMO2-MP2: Total energy -72983.212391


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:10:LYS)


Summations of interaction energy for fragment #1(A:10: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.
-126.156-113.5467.771-8.414-11.967-0.092
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.886 / q_NPA : 0.949
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].
3A12TYR00.0280.0042.616-10.777-6.6741.620-1.697-4.025-0.011
4A13PHE00.0450.0065.3344.4944.528-0.001-0.002-0.0310.000
5A14ALA00.0230.0198.823-0.682-0.6820.0000.0000.0000.000
6A15THR00.0230.00611.3952.5372.5370.0000.0000.0000.000
7A16GLY00.0410.02713.318-1.264-1.2640.0000.0000.0000.000
8A17ASN0-0.029-0.02315.586-0.028-0.0280.0000.0000.0000.000
9A18PRO00.0610.01412.961-0.795-0.7950.0000.0000.0000.000
10A19ASN00.026-0.00313.208-1.722-1.7220.0000.0000.0000.000
11A20LYS10.8380.93713.83316.97416.9740.0000.0000.0000.000
12A21ILE00.0140.0228.2500.1260.1260.0000.0000.0000.000
13A22LYS10.9200.96210.39720.59720.5970.0000.0000.0000.000
14A23GLU-1-0.839-0.89712.603-16.040-16.0400.0000.0000.0000.000
15A24ALA00.0080.00210.2210.3730.3730.0000.0000.0000.000
16A25ASN00.0710.0166.9080.0540.0540.0000.0000.0000.000
17A26ILE0-0.031-0.01710.1620.6830.6830.0000.0000.0000.000
18A27ILE0-0.060-0.03213.5020.9510.9510.0000.0000.0000.000
19A28LEU00.0420.0128.1640.7490.7490.0000.0000.0000.000
20A29LYS10.9081.00210.19116.59416.5940.0000.0000.0000.000
21A30ASP-1-0.888-0.94711.510-17.386-17.3860.0000.0000.0000.000
22A31LEU0-0.037-0.0168.9310.8740.8740.0000.0000.0000.000
23A32LYS10.9550.9618.62117.15617.1560.0000.0000.0000.000
24A33ASP-1-0.948-0.9556.608-23.729-23.7290.0000.0000.0000.000
25A34VAL0-0.037-0.0194.275-1.094-0.8130.000-0.051-0.2310.000
26A35GLU-1-0.922-0.9482.810-41.182-40.1320.151-0.413-0.788-0.001
27A36ILE0-0.028-0.0172.523-10.749-7.5091.728-2.482-2.486-0.028
28A37GLU-1-0.912-0.9792.254-103.168-99.3004.274-3.767-4.375-0.052
29A38GLN0-0.035-0.0214.9323.1783.212-0.001-0.002-0.0310.000
30A39ILE00.0320.0236.762-3.282-3.2820.0000.0000.0000.000
31A40LYS10.8980.9408.53627.41527.4150.0000.0000.0000.000
32A41ILE00.0170.01310.8670.7440.7440.0000.0000.0000.000
33A42SER0-0.042-0.01713.6280.1060.1060.0000.0000.0000.000
34A43TYR00.025-0.00115.460-0.719-0.7190.0000.0000.0000.000
35A44PRO00.0070.00718.5200.2820.2820.0000.0000.0000.000
36A45GLU-1-0.937-0.95220.883-14.177-14.1770.0000.0000.0000.000
37A46ILE0-0.043-0.02722.8010.4460.4460.0000.0000.0000.000
38A47GLN0-0.011-0.01425.7920.1610.1610.0000.0000.0000.000
39A48GLY00.0390.02328.5910.1150.1150.0000.0000.0000.000
40A49THR0-0.036-0.03427.250-0.152-0.1520.0000.0000.0000.000
41A50LEU00.017-0.00723.242-0.195-0.1950.0000.0000.0000.000
42A51GLU-1-0.795-0.87222.302-11.779-11.7790.0000.0000.0000.000
43A52GLU-1-0.825-0.88822.091-10.849-10.8490.0000.0000.0000.000
44A53VAL00.0150.02221.108-0.395-0.3950.0000.0000.0000.000
45A54ALA0-0.003-0.00318.113-0.660-0.6600.0000.0000.0000.000
46A55GLU-1-0.859-0.93917.948-13.487-13.4870.0000.0000.0000.000
47A56PHE0-0.036-0.01419.008-0.466-0.4660.0000.0000.0000.000
48A57GLY00.023-0.00217.948-0.351-0.3510.0000.0000.0000.000
49A58ALA0-0.015-0.01314.370-0.927-0.9270.0000.0000.0000.000
50A59LYS10.9210.95014.40112.44012.4400.0000.0000.0000.000
51A60TRP0-0.0130.01016.488-0.181-0.1810.0000.0000.0000.000
52A61VAL00.024-0.00111.157-0.445-0.4450.0000.0000.0000.000
53A62TYR0-0.0170.02010.066-0.639-0.6390.0000.0000.0000.000
54A63ASN00.009-0.00112.887-0.211-0.2110.0000.0000.0000.000
55A64ILE0-0.065-0.02513.5100.2530.2530.0000.0000.0000.000
56A65LEU0-0.086-0.0576.650-0.892-0.8920.0000.0000.0000.000
57A66LYS10.8950.95510.53717.85117.8510.0000.0000.0000.000
58A67LYS10.9210.9644.85943.44943.4490.0000.0000.0000.000
59A68PRO00.0260.0154.8300.9540.9540.0000.0000.0000.000
60A69VAL0-0.040-0.0116.243-4.510-4.5100.0000.0000.0000.000
61A70ILE0-0.017-0.0058.5722.3822.3820.0000.0000.0000.000
62A71VAL00.0200.00810.957-1.110-1.1100.0000.0000.0000.000
63A72GLU-1-0.800-0.87113.885-15.415-15.4150.0000.0000.0000.000
64A73ASP-1-0.848-0.91316.721-13.164-13.1640.0000.0000.0000.000
65A74SER0-0.052-0.06120.4480.1550.1550.0000.0000.0000.000
66A75GLY0-0.0110.00422.9730.0930.0930.0000.0000.0000.000
67A76PHE0-0.017-0.00726.729-0.051-0.0510.0000.0000.0000.000
68A77PHE0-0.037-0.01327.4880.0700.0700.0000.0000.0000.000
69A78VAL00.0740.03432.5230.0680.0680.0000.0000.0000.000
70A79GLU-1-0.862-0.90736.166-7.674-7.6740.0000.0000.0000.000
71A80ALA0-0.0080.00738.3000.1020.1020.0000.0000.0000.000
72A81LEU0-0.039-0.02738.2610.1550.1550.0000.0000.0000.000
73A82ASN0-0.032-0.01538.856-0.075-0.0750.0000.0000.0000.000
74A83GLY0-0.025-0.01034.707-0.111-0.1110.0000.0000.0000.000
75A84PHE00.0140.02133.614-0.350-0.3500.0000.0000.0000.000
76A85PRO0-0.004-0.01431.9460.1100.1100.0000.0000.0000.000
77A86GLY00.0640.01830.338-0.079-0.0790.0000.0000.0000.000
78A87THR00.0060.02326.521-0.129-0.1290.0000.0000.0000.000
79A88TYR00.0300.02027.373-0.373-0.3730.0000.0000.0000.000
80A89SER00.019-0.01527.7030.2630.2630.0000.0000.0000.000
81A90LYS10.9981.00021.49213.65313.6530.0000.0000.0000.000
82A91PHE00.0630.03628.5330.1730.1730.0000.0000.0000.000
83A92VAL00.0250.01431.2150.2330.2330.0000.0000.0000.000
84A93GLN0-0.058-0.03330.6230.2850.2850.0000.0000.0000.000
85A94GLU-1-0.953-0.98629.295-10.435-10.4350.0000.0000.0000.000
86A95THR0-0.085-0.02133.5860.2850.2850.0000.0000.0000.000
87A96ILE0-0.010-0.01636.7240.2570.2570.0000.0000.0000.000
88A97GLY00.0310.03235.3300.1580.1580.0000.0000.0000.000
89A98ASN0-0.007-0.03434.101-0.077-0.0770.0000.0000.0000.000
90A99GLU-1-0.873-0.93837.177-7.398-7.3980.0000.0000.0000.000
91A100GLY00.0180.01639.8110.2020.2020.0000.0000.0000.000
92A101ILE0-0.055-0.02636.0210.1000.1000.0000.0000.0000.000
93A102LEU0-0.001-0.00339.4420.1200.1200.0000.0000.0000.000
94A103LYS10.9170.98242.0976.5936.5930.0000.0000.0000.000
95A104LEU0-0.045-0.03340.0940.1480.1480.0000.0000.0000.000
96A105LEU0-0.049-0.03639.6350.0920.0920.0000.0000.0000.000
97A106GLU-1-0.862-0.93743.880-6.406-6.4060.0000.0000.0000.000
98A107GLY0-0.030-0.00947.2110.0730.0730.0000.0000.0000.000
99A108LYS10.8620.93544.5126.8586.8580.0000.0000.0000.000
100A109ASP-1-0.878-0.94046.431-6.261-6.2610.0000.0000.0000.000
101A110ASN0-0.090-0.05841.050-0.142-0.1420.0000.0000.0000.000
102A111ARG10.9100.94341.1817.0957.0950.0000.0000.0000.000
103A112ASN00.0350.03037.571-0.211-0.2110.0000.0000.0000.000
104A113ALA00.000-0.00934.1500.0040.0040.0000.0000.0000.000
105A114TYR0-0.068-0.03128.8030.0820.0820.0000.0000.0000.000
106A115PHE00.0450.04726.237-0.060-0.0600.0000.0000.0000.000
107A116LYS10.8360.89224.21211.00911.0090.0000.0000.0000.000
108A117THR0-0.003-0.01718.513-0.027-0.0270.0000.0000.0000.000
109A118VAL0-0.038-0.02719.4230.2530.2530.0000.0000.0000.000
110A119ILE00.0130.01213.038-0.297-0.2970.0000.0000.0000.000
111A120GLY00.004-0.01515.3170.7110.7110.0000.0000.0000.000
112A121TYR0-0.064-0.0597.719-1.763-1.7630.0000.0000.0000.000
113A122CYS0-0.019-0.01411.2131.9721.9720.0000.0000.0000.000
114A123ASP-1-0.733-0.8318.994-21.976-21.9760.0000.0000.0000.000
115A124GLU-1-0.845-0.9358.479-22.608-22.6080.0000.0000.0000.000
116A125ASN0-0.078-0.03612.3761.6951.6950.0000.0000.0000.000
117A126GLY0-0.0060.01114.1781.0041.0040.0000.0000.0000.000
118A127VAL0-0.016-0.02614.209-0.801-0.8010.0000.0000.0000.000
119A128ARG10.8880.96013.92615.40515.4050.0000.0000.0000.000
120A129LEU00.0030.00715.794-0.626-0.6260.0000.0000.0000.000
121A130PHE00.0020.00713.6840.3420.3420.0000.0000.0000.000
122A131LYS10.8810.90617.85511.48811.4880.0000.0000.0000.000
123A132GLY00.0530.03220.6970.0290.0290.0000.0000.0000.000
124A133ILE0-0.100-0.06122.0980.0060.0060.0000.0000.0000.000
125A134VAL00.0390.04025.679-0.023-0.0230.0000.0000.0000.000
126A135LYS10.9580.95628.1628.8248.8240.0000.0000.0000.000
127A136GLY00.0660.02531.815-0.085-0.0850.0000.0000.0000.000
128A137ARG10.9500.99234.5027.7717.7710.0000.0000.0000.000
129A138VAL0-0.020-0.01836.730-0.183-0.1830.0000.0000.0000.000
130A139SER0-0.042-0.03638.3700.1460.1460.0000.0000.0000.000
131A140GLU-1-0.899-0.96940.425-6.776-6.7760.0000.0000.0000.000
132A141GLU-1-0.910-0.95342.275-6.934-6.9340.0000.0000.0000.000
133A142ILE0-0.0370.02437.996-0.225-0.2250.0000.0000.0000.000
134A143ARG10.8310.94538.1427.9727.9720.0000.0000.0000.000
135A144SER0-0.005-0.02735.229-0.338-0.3380.0000.0000.0000.000
136A145LYS10.9410.97034.9118.5198.5190.0000.0000.0000.000
137A146GLY0-0.022-0.00133.486-0.060-0.0600.0000.0000.0000.000
138A147TYR0-0.022-0.01529.581-0.225-0.2250.0000.0000.0000.000
139A148GLY0-0.011-0.00728.320-0.312-0.3120.0000.0000.0000.000
140A149PHE0-0.099-0.03922.573-0.217-0.2170.0000.0000.0000.000
141A150ALA00.0440.01028.2940.0760.0760.0000.0000.0000.000
142A151TYR00.032-0.00929.7230.2480.2480.0000.0000.0000.000
143A152ASP-1-0.816-0.90227.800-10.684-10.6840.0000.0000.0000.000
144A153SER0-0.033-0.02731.2100.1950.1950.0000.0000.0000.000
145A154ILE00.0180.01934.4960.2360.2360.0000.0000.0000.000
146A155PHE0-0.0280.00530.2800.1230.1230.0000.0000.0000.000
147A156ILE00.0050.00433.747-0.161-0.1610.0000.0000.0000.000
148A157PRO0-0.058-0.01430.7860.0340.0340.0000.0000.0000.000
149A158GLU-1-0.934-1.00330.260-9.412-9.4120.0000.0000.0000.000
150A159GLU-1-0.944-0.96334.131-7.437-7.4370.0000.0000.0000.000
151A160GLU-1-0.828-0.88333.464-8.457-8.4570.0000.0000.0000.000
152A161GLU-1-0.888-0.94336.511-6.967-6.9670.0000.0000.0000.000
153A162ARG10.7330.84933.9058.8118.8110.0000.0000.0000.000
154A163THR00.023-0.02534.879-0.161-0.1610.0000.0000.0000.000
155A164PHE00.0470.00927.463-0.152-0.1520.0000.0000.0000.000
156A165ALA0-0.045-0.01530.729-0.241-0.2410.0000.0000.0000.000
157A166GLU-1-0.869-0.93532.401-7.995-7.9950.0000.0000.0000.000
158A167MET0-0.065-0.01630.4400.1090.1090.0000.0000.0000.000
159A168THR00.020-0.00328.994-0.381-0.3810.0000.0000.0000.000
160A169THR0-0.002-0.01522.549-0.001-0.0010.0000.0000.0000.000
161A170GLU-1-0.858-0.94824.842-11.979-11.9790.0000.0000.0000.000
162A171GLU-1-0.835-0.88026.069-9.416-9.4160.0000.0000.0000.000
163A172LYS10.8740.95226.07311.05911.0590.0000.0000.0000.000
164A173SER0-0.109-0.07622.259-0.279-0.2790.0000.0000.0000.000
165A174GLN0-0.015-0.02721.931-0.613-0.6130.0000.0000.0000.000
166A175ILE00.0670.04023.999-0.127-0.1270.0000.0000.0000.000
167A176SER00.0130.02922.0720.0100.0100.0000.0000.0000.000
168A177HIS00.0530.02422.773-0.143-0.1430.0000.0000.0000.000
169A178ARG10.8270.88516.44315.39215.3920.0000.0000.0000.000
170A179LYS10.8550.93318.06112.83112.8310.0000.0000.0000.000
171A180LYS10.9640.97018.39611.25511.2550.0000.0000.0000.000
172A181ALA00.0060.00917.9360.0140.0140.0000.0000.0000.000
173A182PHE00.023-0.00911.366-0.599-0.5990.0000.0000.0000.000
174A183GLU-1-0.819-0.89614.308-15.018-15.0180.0000.0000.0000.000
175A184GLU-1-0.946-0.95516.712-12.458-12.4580.0000.0000.0000.000
176A185PHE0-0.038-0.0258.587-0.183-0.1830.0000.0000.0000.000
177A186LYS10.9220.95312.01715.45515.4550.0000.0000.0000.000
178A187LYS10.8840.95413.07612.31412.3140.0000.0000.0000.000
179A188PHE00.002-0.00310.2200.1760.1760.0000.0000.0000.000
180A189LEU0-0.065-0.0457.806-0.204-0.2040.0000.0000.0000.000
181A190LEU00.003-0.01411.102-0.186-0.1860.0000.0000.0000.000
182A191ASP-1-0.941-0.95413.421-13.146-13.1460.0000.0000.0000.000
183A192ARG10.7790.9026.67321.18621.1860.0000.0000.0000.000
184A193ILE0-0.032-0.00412.4010.1390.1390.0000.0000.0000.000