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

tag_button

FMODB ID: KGM93

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144148.553217
FMO2-HF: Nuclear repulsion 2067751.938689
FMO2-HF: Total energy -76396.614527
FMO2-MP2: Total energy -76617.784248


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.
82.83784.6320.026-0.782-1.0390.003
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 : -0.971 / q_NPA : -1.005
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-1-0.940-0.9593.59133.40734.8180.013-0.671-0.7530.002
4A-1LYS10.9150.9506.237-27.133-27.1330.0000.0000.0000.000
5A24ALA0-0.008-0.0168.436-0.529-0.5290.0000.0000.0000.000
6A25GLY0-0.024-0.01711.7400.0440.0440.0000.0000.0000.000
7A26LEU0-0.043-0.0277.214-0.230-0.2300.0000.0000.0000.000
8A27VAL00.0370.0178.0422.4192.4190.0000.0000.0000.000
9A28GLU-1-0.880-0.9388.44629.47729.4770.0000.0000.0000.000
10A29GLY0-0.028-0.01410.156-0.852-0.8520.0000.0000.0000.000
11A30GLN0-0.112-0.05213.078-2.028-2.0280.0000.0000.0000.000
12A31ASN00.016-0.00212.2650.1450.1450.0000.0000.0000.000
13A32TYR00.012-0.0056.3860.3700.3700.0000.0000.0000.000
14A33THR00.0330.02212.3920.7930.7930.0000.0000.0000.000
15A34VAL00.0060.0098.8400.0120.0120.0000.0000.0000.000
16A35LEU0-0.046-0.01711.941-1.550-1.5500.0000.0000.0000.000
17A36ALA00.0060.00413.3931.3921.3920.0000.0000.0000.000
18A37ASN0-0.024-0.02514.9421.0941.0940.0000.0000.0000.000
19A38PRO00.0140.00913.219-0.519-0.5190.0000.0000.0000.000
20A39ILE0-0.010-0.00115.723-1.171-1.1710.0000.0000.0000.000
21A40PRO0-0.048-0.02718.0020.4900.4900.0000.0000.0000.000
22A41GLN00.0160.00716.7950.1620.1620.0000.0000.0000.000
23A42GLN0-0.030-0.02620.378-0.355-0.3550.0000.0000.0000.000
24A43GLN00.0110.01922.394-0.548-0.5480.0000.0000.0000.000
25A44ALA00.0060.00020.2390.6280.6280.0000.0000.0000.000
26A45GLY0-0.029-0.01218.8760.7210.7210.0000.0000.0000.000
27A46LYS10.8520.92618.884-12.602-12.6020.0000.0000.0000.000
28A47VAL0-0.0050.00514.9800.7660.7660.0000.0000.0000.000
29A48GLU-1-0.744-0.85417.30414.03214.0320.0000.0000.0000.000
30A49VAL00.0130.00617.7991.0441.0440.0000.0000.0000.000
31A50LEU0-0.013-0.01919.582-0.909-0.9090.0000.0000.0000.000
32A51GLU-1-0.907-0.95221.24812.07212.0720.0000.0000.0000.000
33A52PHE00.0140.00421.742-0.524-0.5240.0000.0000.0000.000
34A53PHE00.025-0.01725.641-0.041-0.0410.0000.0000.0000.000
35A54GLY00.0840.01728.715-0.080-0.0800.0000.0000.0000.000
36A55TYR0-0.008-0.03132.319-0.030-0.0300.0000.0000.0000.000
37A56PHE00.008-0.00832.520-0.271-0.2710.0000.0000.0000.000
38A57CYS0-0.0220.01728.8910.2290.2290.0000.0000.0000.000
39A58PRO0-0.003-0.00432.9900.0850.0850.0000.0000.0000.000
40A59HIS00.0310.00928.462-0.095-0.0950.0000.0000.0000.000
41A61ALA00.0140.01329.9280.0550.0550.0000.0000.0000.000
42A62HIS0-0.024-0.01931.088-0.091-0.0910.0000.0000.0000.000
43A63LEU0-0.0070.00824.1230.0690.0690.0000.0000.0000.000
44A64GLU-1-0.870-0.93927.81510.44610.4460.0000.0000.0000.000
45A65PRO0-0.030-0.00529.5780.0920.0920.0000.0000.0000.000
46A66VAL0-0.017-0.01025.5910.0410.0410.0000.0000.0000.000
47A67LEU00.0210.00222.6570.3120.3120.0000.0000.0000.000
48A68SER00.009-0.03925.8390.3360.3360.0000.0000.0000.000
49A69LYS10.8910.92528.193-9.428-9.4280.0000.0000.0000.000
50A70HIS10.8140.91019.668-13.961-13.9610.0000.0000.0000.000
51A71ALA00.0710.01723.9770.3170.3170.0000.0000.0000.000
52A72LYS10.9110.96325.038-9.838-9.8380.0000.0000.0000.000
53A73SER0-0.124-0.04323.913-0.034-0.0340.0000.0000.0000.000
54A74PHE00.0220.02420.4150.4960.4960.0000.0000.0000.000
55A75LYS10.9520.97116.337-17.009-17.0090.0000.0000.0000.000
56A76ASP-1-0.847-0.93321.75812.19012.1900.0000.0000.0000.000
57A77ASP-1-0.930-0.97017.47916.84116.8410.0000.0000.0000.000
58A78MET0-0.0150.01417.2881.0841.0840.0000.0000.0000.000
59A79TYR0-0.019-0.02220.658-0.729-0.7290.0000.0000.0000.000
60A80LEU00.0530.02522.0620.6190.6190.0000.0000.0000.000
61A81ARG10.7270.87122.280-14.097-14.0970.0000.0000.0000.000
62A82THR00.0530.02724.6520.2030.2030.0000.0000.0000.000
63A83GLU-1-0.863-0.93025.88211.28611.2860.0000.0000.0000.000
64A84HIS0-0.036-0.02828.261-0.070-0.0700.0000.0000.0000.000
65A85VAL00.0220.01427.661-0.008-0.0080.0000.0000.0000.000
66A86VAL0-0.027-0.01930.278-0.472-0.4720.0000.0000.0000.000
67A87TRP00.017-0.03028.233-0.204-0.2040.0000.0000.0000.000
68A88GLN0-0.044-0.03733.497-0.031-0.0310.0000.0000.0000.000
69A89LYS10.9680.98437.152-7.511-7.5110.0000.0000.0000.000
70A90GLU-1-0.885-0.94939.8507.6987.6980.0000.0000.0000.000
71A91MET0-0.0390.02034.555-0.032-0.0320.0000.0000.0000.000
72A92LEU00.0690.03936.1340.0730.0730.0000.0000.0000.000
73A93THR0-0.031-0.01038.1620.0540.0540.0000.0000.0000.000
74A94LEU0-0.017-0.01136.971-0.089-0.0890.0000.0000.0000.000
75A95ALA00.0620.03734.2020.0810.0810.0000.0000.0000.000
76A96ARG10.8360.93235.531-7.552-7.5520.0000.0000.0000.000
77A97LEU0-0.051-0.02838.303-0.093-0.0930.0000.0000.0000.000
78A98ALA00.0300.01533.564-0.036-0.0360.0000.0000.0000.000
79A99ALA00.0280.02734.7650.0680.0680.0000.0000.0000.000
80A100ALA0-0.016-0.01535.714-0.040-0.0400.0000.0000.0000.000
81A101VAL0-0.025-0.00835.856-0.176-0.1760.0000.0000.0000.000
82A102ASP-1-0.866-0.92332.39610.01110.0110.0000.0000.0000.000
83A103MET0-0.128-0.05435.066-0.017-0.0170.0000.0000.0000.000
84A104ALA0-0.046-0.02437.771-0.122-0.1220.0000.0000.0000.000
85A105ALA0-0.064-0.04438.657-0.205-0.2050.0000.0000.0000.000
86A106ALA00.0370.02434.2940.1130.1130.0000.0000.0000.000
87A107ASP-1-0.907-0.95034.7968.8058.8050.0000.0000.0000.000
88A108SER0-0.082-0.04436.841-0.051-0.0510.0000.0000.0000.000
89A109LYS10.9010.94630.145-10.537-10.5370.0000.0000.0000.000
90A110ASP-1-0.816-0.86732.5749.6469.6460.0000.0000.0000.000
91A111VAL0-0.025-0.02135.101-0.083-0.0830.0000.0000.0000.000
92A112ALA0-0.0040.00138.194-0.155-0.1550.0000.0000.0000.000
93A113ASN00.1080.05332.697-0.379-0.3790.0000.0000.0000.000
94A114SER0-0.0270.00536.591-0.035-0.0350.0000.0000.0000.000
95A115HIS0-0.006-0.01237.723-0.248-0.2480.0000.0000.0000.000
96A116ILE0-0.023-0.00738.239-0.167-0.1670.0000.0000.0000.000
97A117PHE00.0320.00831.785-0.124-0.1240.0000.0000.0000.000
98A118ASP-1-0.899-0.92037.7367.3417.3410.0000.0000.0000.000
99A119ALA00.0080.00140.675-0.156-0.1560.0000.0000.0000.000
100A120MET0-0.051-0.01539.187-0.092-0.0920.0000.0000.0000.000
101A121VAL0-0.018-0.00236.297-0.096-0.0960.0000.0000.0000.000
102A122ASN0-0.038-0.03739.587-0.039-0.0390.0000.0000.0000.000
103A123GLN0-0.0180.00742.557-0.116-0.1160.0000.0000.0000.000
104A124LYS10.8090.90841.470-7.682-7.6820.0000.0000.0000.000
105A125ILE00.0120.01244.677-0.135-0.1350.0000.0000.0000.000
106A126LYS10.9170.96643.785-6.708-6.7080.0000.0000.0000.000
107A127LEU00.0550.00841.339-0.100-0.1000.0000.0000.0000.000
108A128GLN00.0700.03840.891-0.029-0.0290.0000.0000.0000.000
109A129ASN0-0.055-0.03542.508-0.049-0.0490.0000.0000.0000.000
110A130PRO00.0780.03045.514-0.061-0.0610.0000.0000.0000.000
111A131GLU-1-0.943-0.95547.1215.9785.9780.0000.0000.0000.000
112A132VAL0-0.032-0.01947.465-0.075-0.0750.0000.0000.0000.000
113A133LEU00.0160.00742.799-0.042-0.0420.0000.0000.0000.000
114A134LYS10.9320.95846.530-6.576-6.5760.0000.0000.0000.000
115A135LYS10.9130.96248.857-6.050-6.0500.0000.0000.0000.000
116A136TRP00.0530.02242.696-0.030-0.0300.0000.0000.0000.000
117A137LEU00.0330.00843.395-0.009-0.0090.0000.0000.0000.000
118A138GLY0-0.062-0.01847.391-0.013-0.0130.0000.0000.0000.000
119A139GLU-1-0.966-0.99350.4415.9985.9980.0000.0000.0000.000
120A140GLN0-0.069-0.02345.5210.0470.0470.0000.0000.0000.000
121A141THR0-0.047-0.01848.4290.0200.0200.0000.0000.0000.000
122A142ALA00.0190.01244.4890.0220.0220.0000.0000.0000.000
123A143PHE00.0190.00742.4220.1400.1400.0000.0000.0000.000
124A144ASP-1-0.825-0.92444.2756.6926.6920.0000.0000.0000.000
125A145GLY00.0310.01145.4220.1000.1000.0000.0000.0000.000
126A146LYS10.9360.95846.584-6.112-6.1120.0000.0000.0000.000
127A147LYS10.9551.00243.263-7.382-7.3820.0000.0000.0000.000
128A148VAL00.0300.01041.3860.0820.0820.0000.0000.0000.000
129A149LEU0-0.018-0.00743.6650.0900.0900.0000.0000.0000.000
130A150ALA00.0290.01246.269-0.011-0.0110.0000.0000.0000.000
131A151ALA00.0080.01241.1470.0100.0100.0000.0000.0000.000
132A152TYR0-0.012-0.01741.7350.0980.0980.0000.0000.0000.000
133A153GLU-1-0.943-0.98143.2636.5596.5590.0000.0000.0000.000
134A154SER0-0.073-0.01942.948-0.025-0.0250.0000.0000.0000.000
135A155PRO00.036-0.01143.0580.1220.1220.0000.0000.0000.000
136A156GLU-1-0.832-0.91937.3378.6968.6960.0000.0000.0000.000
137A157SER00.0120.01337.9190.2740.2740.0000.0000.0000.000
138A158GLN0-0.002-0.02037.6140.0280.0280.0000.0000.0000.000
139A159ALA00.0100.01836.9330.1530.1530.0000.0000.0000.000
140A160ARG10.8820.93532.999-9.095-9.0950.0000.0000.0000.000
141A161ALA00.0220.01232.9300.3220.3220.0000.0000.0000.000
142A162ASP-1-0.869-0.93433.8598.8598.8590.0000.0000.0000.000
143A163LYS10.8610.93826.131-11.713-11.7130.0000.0000.0000.000
144A164MET0-0.0070.01229.3380.2990.2990.0000.0000.0000.000
145A165GLN0-0.021-0.01829.4060.1390.1390.0000.0000.0000.000
146A166GLU-1-0.862-0.92726.91312.18112.1810.0000.0000.0000.000
147A167LEU0-0.043-0.02124.1420.4620.4620.0000.0000.0000.000
148A168THR0-0.014-0.01225.1880.4670.4670.0000.0000.0000.000
149A169GLU-1-0.911-0.95326.49510.39510.3950.0000.0000.0000.000
150A170THR0-0.061-0.02723.0710.1850.1850.0000.0000.0000.000
151A171PHE0-0.066-0.04019.5570.4200.4200.0000.0000.0000.000
152A172GLN0-0.050-0.01322.0340.9690.9690.0000.0000.0000.000
153A173ILE0-0.0010.01021.8760.2490.2490.0000.0000.0000.000
154A174ASP-1-0.896-0.93424.68312.18512.1850.0000.0000.0000.000
155A175GLY00.0120.01125.372-0.456-0.4560.0000.0000.0000.000
156A176THR0-0.086-0.01125.7030.1530.1530.0000.0000.0000.000
157A177PRO00.028-0.02424.642-0.401-0.4010.0000.0000.0000.000
158A178THR0-0.047-0.03220.4360.3980.3980.0000.0000.0000.000
159A179VAL00.0090.01218.802-0.218-0.2180.0000.0000.0000.000
160A180ILE0-0.0190.00016.0050.7960.7960.0000.0000.0000.000
161A181VAL00.0230.01013.786-0.888-0.8880.0000.0000.0000.000
162A182GLY00.0400.01113.4251.6601.6600.0000.0000.0000.000
163A183GLY0-0.033-0.00313.8630.8650.8650.0000.0000.0000.000
164A184LYS10.8590.9137.309-38.099-38.0990.0000.0000.0000.000
165A185TYR0-0.057-0.0716.7180.9410.9410.0000.0000.0000.000
166A186LYS10.9640.98512.639-16.802-16.8020.0000.0000.0000.000
167A187VAL00.011-0.00114.5620.9500.9500.0000.0000.0000.000
168A188GLU-1-0.914-0.94715.57115.98515.9850.0000.0000.0000.000
169A189PHE0-0.042-0.03317.6390.0110.0110.0000.0000.0000.000
170A190ALA00.0050.02520.379-0.404-0.4040.0000.0000.0000.000
171A191ASP-1-0.823-0.88022.10811.72911.7290.0000.0000.0000.000
172A192TRP00.038-0.00822.8770.5720.5720.0000.0000.0000.000
173A193GLU-1-0.899-0.95623.35611.32211.3220.0000.0000.0000.000
174A194SER0-0.078-0.07820.3980.6530.6530.0000.0000.0000.000
175A195GLY00.0390.01418.8200.8800.8800.0000.0000.0000.000
176A196MET0-0.046-0.02418.2680.7890.7890.0000.0000.0000.000
177A197ASN00.0190.01217.0130.3170.3170.0000.0000.0000.000
178A198THR0-0.0100.00113.2251.0231.0230.0000.0000.0000.000
179A199ILE0-0.006-0.00113.7181.4261.4260.0000.0000.0000.000
180A200ASP-1-0.852-0.92114.78716.51116.5110.0000.0000.0000.000
181A201LEU0-0.029-0.01610.5800.9500.9500.0000.0000.0000.000
182A202LEU00.0140.0029.5182.2652.2650.0000.0000.0000.000
183A203ALA0-0.010-0.00410.8191.6651.6650.0000.0000.0000.000
184A204ASP-1-0.886-0.93410.23120.91620.9160.0000.0000.0000.000
185A205LYS10.9290.9793.305-56.085-55.7010.013-0.111-0.2860.001
186A206VAL00.0160.0047.7263.1383.1380.0000.0000.0000.000
187A207ARG10.8200.89610.161-19.702-19.7020.0000.0000.0000.000
188A208GLU-1-1.004-1.0266.92127.80827.8080.0000.0000.0000.000
189A209GLU-1-0.777-0.8255.73845.01045.0100.0000.0000.0000.000
190A210GLN0-0.054-0.0318.132-1.425-1.4250.0000.0000.0000.000
191A211LYS10.8470.95910.910-26.398-26.3980.0000.0000.0000.000
192A212ALA0-0.0100.0039.1340.5690.5690.0000.0000.0000.000