Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5J82Z

Calculation Name: 3A3T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A3T

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K189

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:


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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2150006.268059
FMO2-HF: Nuclear repulsion 2073608.302539
FMO2-HF: Total energy -76397.965519
FMO2-MP2: Total energy -76619.131147


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:-4:ASP)


Summations of interaction energy for fragment #1(A:-4:ASP)
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.
26.16523.96913.684-6.253-5.2330.081
Interaction energy analysis for fragmet #1(A:-4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.969
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].
3A-2ASP-1-0.881-0.9403.85335.44636.6210.001-0.446-0.7290.003
4A-1LYS10.8880.9386.016-28.711-28.7110.0000.0000.0000.000
5A24ALA0-0.007-0.0148.806-0.590-0.5900.0000.0000.0000.000
6A25GLY0-0.019-0.01411.8350.2270.2270.0000.0000.0000.000
7A26LEU0-0.060-0.0356.8960.3580.3580.0000.0000.0000.000
8A27VAL00.0520.0337.8581.8701.8700.0000.0000.0000.000
9A28GLU-1-0.803-0.9018.57329.58029.5800.0000.0000.0000.000
10A29GLY0-0.020-0.01110.336-1.536-1.5360.0000.0000.0000.000
11A30GLN0-0.115-0.05813.344-2.288-2.2880.0000.0000.0000.000
12A31ASN0-0.044-0.02011.872-0.162-0.1620.0000.0000.0000.000
13A32TYR0-0.0010.0006.0740.9740.9740.0000.0000.0000.000
14A33THR00.005-0.01511.998-0.028-0.0280.0000.0000.0000.000
15A34VAL0-0.038-0.0187.6780.1580.1580.0000.0000.0000.000
16A35LEU0-0.030-0.00910.616-2.402-2.4020.0000.0000.0000.000
17A36ALA0-0.019-0.01412.5151.4261.4260.0000.0000.0000.000
18A37ASN0-0.024-0.01814.4900.3460.3460.0000.0000.0000.000
19A38PRO0-0.001-0.00112.228-0.494-0.4940.0000.0000.0000.000
20A39ILE00.0070.01414.733-1.358-1.3580.0000.0000.0000.000
21A40PRO0-0.043-0.02717.0580.5970.5970.0000.0000.0000.000
22A41GLN00.001-0.00315.5810.2810.2810.0000.0000.0000.000
23A42GLN0-0.004-0.01419.460-0.395-0.3950.0000.0000.0000.000
24A43GLN0-0.0080.00421.201-0.778-0.7780.0000.0000.0000.000
25A44ALA00.0200.00719.2290.7510.7510.0000.0000.0000.000
26A45GLY0-0.028-0.00617.8590.9750.9750.0000.0000.0000.000
27A46LYS10.8680.94117.909-14.357-14.3570.0000.0000.0000.000
28A47VAL00.0100.03413.4000.9910.9910.0000.0000.0000.000
29A48GLU-1-0.736-0.82815.77414.99114.9910.0000.0000.0000.000
30A49VAL00.0010.00316.1451.3471.3470.0000.0000.0000.000
31A50LEU00.017-0.00418.296-1.087-1.0870.0000.0000.0000.000
32A51GLU-1-0.866-0.94419.96912.92112.9210.0000.0000.0000.000
33A52PHE00.0260.01420.309-0.646-0.6460.0000.0000.0000.000
34A53PHE00.030-0.00924.132-0.065-0.0650.0000.0000.0000.000
35A54GLY00.0830.02027.448-0.071-0.0710.0000.0000.0000.000
36A55TYR0-0.028-0.04831.148-0.058-0.0580.0000.0000.0000.000
37A56PHE00.014-0.00131.272-0.276-0.2760.0000.0000.0000.000
38A57CYS0-0.0020.03527.9650.2200.2200.0000.0000.0000.000
39A58PRO00.013-0.01132.2790.0730.0730.0000.0000.0000.000
40A59HIS00.0220.00727.657-0.147-0.1470.0000.0000.0000.000
41A61ALA0-0.0110.01128.9840.0740.0740.0000.0000.0000.000
42A62HIS0-0.033-0.01530.576-0.131-0.1310.0000.0000.0000.000
43A63LEU00.0080.02323.2630.0870.0870.0000.0000.0000.000
44A64GLU-1-0.772-0.87927.20010.76110.7610.0000.0000.0000.000
45A65PRO0-0.029-0.02028.5390.0820.0820.0000.0000.0000.000
46A66VAL0-0.0180.00425.352-0.187-0.1870.0000.0000.0000.000
47A67LEU00.0410.01121.5440.2510.2510.0000.0000.0000.000
48A68SER0-0.012-0.04224.9740.2790.2790.0000.0000.0000.000
49A69LYS10.8310.90027.644-10.112-10.1120.0000.0000.0000.000
50A70HIS10.8330.91319.332-14.977-14.9770.0000.0000.0000.000
51A71ALA00.0680.04223.4670.2700.2700.0000.0000.0000.000
52A72LYS10.7860.88624.497-10.385-10.3850.0000.0000.0000.000
53A73SER0-0.095-0.05624.284-0.272-0.2720.0000.0000.0000.000
54A74PHE00.0120.01120.4100.5390.5390.0000.0000.0000.000
55A75LYS10.8600.92315.617-19.499-19.4990.0000.0000.0000.000
56A76ASP-1-0.856-0.93121.24913.14413.1440.0000.0000.0000.000
57A77ASP-1-0.894-0.93516.71818.36418.3640.0000.0000.0000.000
58A78MET0-0.0280.01416.5721.2801.2800.0000.0000.0000.000
59A79TYR0-0.042-0.06119.414-0.938-0.9380.0000.0000.0000.000
60A80LEU00.0180.00920.5230.6220.6220.0000.0000.0000.000
61A81ARG10.6980.83420.845-15.073-15.0730.0000.0000.0000.000
62A82THR00.0090.00223.2970.2320.2320.0000.0000.0000.000
63A83GLU-1-0.797-0.88324.13612.04612.0460.0000.0000.0000.000
64A84HIS0-0.031-0.02426.719-0.099-0.0990.0000.0000.0000.000
65A85VAL00.0220.00626.304-0.112-0.1120.0000.0000.0000.000
66A86VAL0-0.031-0.03428.892-0.503-0.5030.0000.0000.0000.000
67A87TRP00.017-0.01327.224-0.255-0.2550.0000.0000.0000.000
68A88GLN0-0.064-0.04532.290-0.105-0.1050.0000.0000.0000.000
69A89LYS10.9400.95435.979-7.638-7.6380.0000.0000.0000.000
70A90GLU-1-0.836-0.90838.6347.9407.9400.0000.0000.0000.000
71A91MET0-0.0470.01233.210-0.010-0.0100.0000.0000.0000.000
72A92LEU00.0640.04334.7610.1070.1070.0000.0000.0000.000
73A93THR0-0.068-0.01936.6890.0380.0380.0000.0000.0000.000
74A94LEU0-0.002-0.00335.716-0.081-0.0810.0000.0000.0000.000
75A95ALA00.0620.03932.6840.0980.0980.0000.0000.0000.000
76A96ARG10.8230.91634.040-7.803-7.8030.0000.0000.0000.000
77A97LEU0-0.039-0.02536.922-0.110-0.1100.0000.0000.0000.000
78A98ALA00.0310.01832.022-0.037-0.0370.0000.0000.0000.000
79A99ALA00.0040.00933.3630.0320.0320.0000.0000.0000.000
80A100ALA0-0.004-0.00434.286-0.044-0.0440.0000.0000.0000.000
81A101VAL00.0050.00434.519-0.186-0.1860.0000.0000.0000.000
82A102ASP-1-0.837-0.90530.90810.49210.4920.0000.0000.0000.000
83A103MET0-0.085-0.02333.6460.0970.0970.0000.0000.0000.000
84A104ALA0-0.042-0.01536.706-0.147-0.1470.0000.0000.0000.000
85A105ALA0-0.015-0.01937.444-0.212-0.2120.0000.0000.0000.000
86A106ALA00.0790.05532.8780.0700.0700.0000.0000.0000.000
87A107ASP-1-0.917-0.95733.5459.0899.0890.0000.0000.0000.000
88A108SER0-0.105-0.06035.588-0.154-0.1540.0000.0000.0000.000
89A109LYS10.8330.90829.144-10.973-10.9730.0000.0000.0000.000
90A110ASP-1-0.772-0.84531.67310.07910.0790.0000.0000.0000.000
91A111VAL0-0.011-0.00733.971-0.083-0.0830.0000.0000.0000.000
92A112ALA00.0090.01436.665-0.157-0.1570.0000.0000.0000.000
93A113ASN00.0300.00231.207-0.427-0.4270.0000.0000.0000.000
94A114SER00.0110.01835.221-0.040-0.0400.0000.0000.0000.000
95A115HIS0-0.066-0.04436.508-0.291-0.2910.0000.0000.0000.000
96A116ILE0-0.021-0.00836.964-0.190-0.1900.0000.0000.0000.000
97A117PHE00.0290.00630.473-0.111-0.1110.0000.0000.0000.000
98A118ASP-1-0.889-0.91236.6877.6157.6150.0000.0000.0000.000
99A119ALA00.0120.00139.803-0.165-0.1650.0000.0000.0000.000
100A120MET0-0.062-0.01338.161-0.097-0.0970.0000.0000.0000.000
101A121VAL0-0.0050.00535.363-0.122-0.1220.0000.0000.0000.000
102A122ASN0-0.048-0.02938.662-0.041-0.0410.0000.0000.0000.000
103A123GLN0-0.045-0.02841.825-0.219-0.2190.0000.0000.0000.000
104A124LYS10.8230.90941.281-7.913-7.9130.0000.0000.0000.000
105A125ILE00.0120.01443.894-0.119-0.1190.0000.0000.0000.000
106A126LYS10.9720.99042.907-6.877-6.8770.0000.0000.0000.000
107A127LEU00.029-0.00240.542-0.103-0.1030.0000.0000.0000.000
108A128GLN00.0670.02939.748-0.043-0.0430.0000.0000.0000.000
109A129ASN0-0.051-0.02741.432-0.006-0.0060.0000.0000.0000.000
110A130PRO00.0630.01843.940-0.049-0.0490.0000.0000.0000.000
111A131GLU-1-0.953-0.95945.6736.1956.1950.0000.0000.0000.000
112A132VAL0-0.017-0.01846.474-0.065-0.0650.0000.0000.0000.000
113A133LEU00.0210.02041.345-0.032-0.0320.0000.0000.0000.000
114A134LYS10.8800.91845.325-6.760-6.7600.0000.0000.0000.000
115A135LYS10.7930.88447.585-6.284-6.2840.0000.0000.0000.000
116A136TRP00.0630.02441.299-0.015-0.0150.0000.0000.0000.000
117A137LEU00.0010.00042.0540.0130.0130.0000.0000.0000.000
118A138GLY0-0.0050.00246.164-0.027-0.0270.0000.0000.0000.000
119A139GLU-1-0.856-0.91849.3986.1826.1820.0000.0000.0000.000
120A140GLN0-0.080-0.02344.1140.0430.0430.0000.0000.0000.000
121A141THR0-0.020-0.03347.282-0.129-0.1290.0000.0000.0000.000
122A142ALA0-0.0190.01043.858-0.023-0.0230.0000.0000.0000.000
123A143PHE00.0330.01441.1560.1680.1680.0000.0000.0000.000
124A144ASP-1-0.814-0.90642.8846.9856.9850.0000.0000.0000.000
125A145GLY00.0200.00043.5510.1260.1260.0000.0000.0000.000
126A146LYS10.9060.95744.709-6.505-6.5050.0000.0000.0000.000
127A147LYS10.9200.96441.033-7.851-7.8510.0000.0000.0000.000
128A148VAL00.0120.00039.7330.0950.0950.0000.0000.0000.000
129A149LEU0-0.015-0.00142.1030.0980.0980.0000.0000.0000.000
130A150ALA00.0190.00844.8500.0080.0080.0000.0000.0000.000
131A151ALA00.0160.01639.7390.0160.0160.0000.0000.0000.000
132A152TYR00.0150.01440.2720.0010.0010.0000.0000.0000.000
133A153GLU-1-0.879-0.93541.7696.7206.7200.0000.0000.0000.000
134A154SER0-0.077-0.04141.305-0.012-0.0120.0000.0000.0000.000
135A155PRO00.031-0.01341.8230.1120.1120.0000.0000.0000.000
136A156GLU-1-0.817-0.88835.8679.1459.1450.0000.0000.0000.000
137A157SER00.0260.00336.5420.2860.2860.0000.0000.0000.000
138A158GLN0-0.062-0.03736.387-0.035-0.0350.0000.0000.0000.000
139A159ALA00.0400.02435.6940.2020.2020.0000.0000.0000.000
140A160ARG10.7950.87932.294-9.303-9.3030.0000.0000.0000.000
141A161ALA00.0370.01931.6560.3510.3510.0000.0000.0000.000
142A162ASP-1-0.827-0.91532.4679.1629.1620.0000.0000.0000.000
143A163LYS10.7760.87525.220-12.316-12.3160.0000.0000.0000.000
144A164MET0-0.0050.01528.0170.3290.3290.0000.0000.0000.000
145A165GLN0-0.039-0.01828.1030.1240.1240.0000.0000.0000.000
146A166GLU-1-0.794-0.87026.14212.74612.7460.0000.0000.0000.000
147A167LEU0-0.0020.00122.8050.5220.5220.0000.0000.0000.000
148A168THR0-0.027-0.03323.8680.5270.5270.0000.0000.0000.000
149A169GLU-1-0.904-0.94125.20310.81010.8100.0000.0000.0000.000
150A170THR0-0.078-0.04722.3430.2030.2030.0000.0000.0000.000
151A171PHE0-0.050-0.03618.5480.4720.4720.0000.0000.0000.000
152A172GLN0-0.060-0.02320.7611.0451.0450.0000.0000.0000.000
153A173ILE00.0120.02020.3880.1220.1220.0000.0000.0000.000
154A174ASP-1-0.880-0.93323.41712.91212.9120.0000.0000.0000.000
155A175GLY00.0040.00224.559-0.605-0.6050.0000.0000.0000.000
156A176THR0-0.064-0.00924.6160.3270.3270.0000.0000.0000.000
157A177PRO0-0.005-0.02923.988-0.509-0.5090.0000.0000.0000.000
158A178THR0-0.035-0.03319.5050.4480.4480.0000.0000.0000.000
159A179VAL00.0000.00317.582-0.120-0.1200.0000.0000.0000.000
160A180ILE0-0.0050.00814.7370.8280.8280.0000.0000.0000.000
161A181VAL00.010-0.00212.557-1.083-1.0830.0000.0000.0000.000
162A182GLY00.0380.01212.0171.9951.9950.0000.0000.0000.000
163A183GLY0-0.0240.00412.6710.9250.9250.0000.0000.0000.000
164A184LYS10.8570.9176.278-46.768-46.7680.0000.0000.0000.000
165A185TYR0-0.032-0.0565.1590.6760.717-0.001-0.001-0.0390.000
166A186LYS10.8940.94011.386-18.876-18.8760.0000.0000.0000.000
167A187VAL00.013-0.00313.6881.3551.3550.0000.0000.0000.000
168A188GLU-1-0.846-0.87715.10517.39517.3950.0000.0000.0000.000
169A189PHE0-0.034-0.03017.377-0.065-0.0650.0000.0000.0000.000
170A190ALA00.0110.02719.926-0.522-0.5220.0000.0000.0000.000
171A191ASP-1-0.821-0.87921.77712.53512.5350.0000.0000.0000.000
172A192TRP00.0380.00422.1200.7640.7640.0000.0000.0000.000
173A193GLU-1-0.875-0.94522.41712.33112.3310.0000.0000.0000.000
174A194SER0-0.068-0.07919.4480.8020.8020.0000.0000.0000.000
175A195GLY00.0540.02718.1461.1131.1130.0000.0000.0000.000
176A196MET0-0.046-0.01717.9350.9810.9810.0000.0000.0000.000
177A197ASN0-0.014-0.00817.1780.4520.4520.0000.0000.0000.000
178A198THR0-0.026-0.01713.1471.2921.2920.0000.0000.0000.000
179A199ILE0-0.004-0.00513.2971.7891.7890.0000.0000.0000.000
180A200ASP-1-0.825-0.90014.23218.11018.1100.0000.0000.0000.000
181A201LEU0-0.045-0.01810.6501.1721.1720.0000.0000.0000.000
182A202LEU00.0390.0188.8553.0773.0770.0000.0000.0000.000
183A203ALA0-0.004-0.0089.7352.4202.4200.0000.0000.0000.000
184A204ASP-1-0.797-0.87511.26021.53721.5370.0000.0000.0000.000
185A205LYS10.8420.9191.763-114.398-118.00313.685-5.800-4.2800.078
186A206VAL0-0.008-0.0057.0533.5893.5890.0000.0000.0000.000
187A207ARG10.8010.8429.062-21.365-21.3650.0000.0000.0000.000
188A208GLU-1-0.865-0.9127.04026.39526.3950.0000.0000.0000.000
189A209GLU-1-0.755-0.8194.65559.45759.650-0.001-0.006-0.1850.000
190A210GLN0-0.065-0.0477.593-2.377-2.3770.0000.0000.0000.000
191A211LYS10.7350.86410.646-28.481-28.4810.0000.0000.0000.000
192A212ALA0-0.041-0.0068.501-1.469-1.4690.0000.0000.0000.000