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: 4J89N

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 OptHSide
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 -2145048.118625
FMO2-HF: Nuclear repulsion 2068650.516472
FMO2-HF: Total energy -76397.602153
FMO2-MP2: Total energy -76618.780431


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.
41.96346.2524.308-4.41-4.1860.055
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 : -0.924 / q_NPA : -0.988
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-1-0.910-0.9453.47533.80335.5060.013-0.872-0.8450.002
4A-1LYS10.9120.9456.022-28.211-28.2110.0000.0000.0000.000
5A24ALA0-0.007-0.0158.342-0.381-0.3810.0000.0000.0000.000
6A25GLY0-0.026-0.01611.7050.1060.1060.0000.0000.0000.000
7A26LEU0-0.049-0.0287.490-0.162-0.1620.0000.0000.0000.000
8A27VAL00.0340.0197.8612.4552.4550.0000.0000.0000.000
9A28GLU-1-0.857-0.9318.36530.39630.3960.0000.0000.0000.000
10A29GLY0-0.026-0.01110.115-1.169-1.1690.0000.0000.0000.000
11A30GLN0-0.114-0.05713.001-2.231-2.2310.0000.0000.0000.000
12A31ASN0-0.005-0.01012.093-0.260-0.2600.0000.0000.0000.000
13A32TYR00.002-0.0076.1920.5100.5100.0000.0000.0000.000
14A33THR00.000-0.01712.3580.6090.6090.0000.0000.0000.000
15A34VAL00.0070.0148.3280.2650.2650.0000.0000.0000.000
16A35LEU0-0.036-0.01111.313-1.902-1.9020.0000.0000.0000.000
17A36ALA00.0000.00012.7861.4641.4640.0000.0000.0000.000
18A37ASN0-0.027-0.02414.5150.9490.9490.0000.0000.0000.000
19A38PRO00.0130.00512.588-0.550-0.5500.0000.0000.0000.000
20A39ILE0-0.0130.00115.097-1.297-1.2970.0000.0000.0000.000
21A40PRO0-0.035-0.02217.3030.5890.5890.0000.0000.0000.000
22A41GLN00.008-0.00216.0460.2210.2210.0000.0000.0000.000
23A42GLN0-0.014-0.02119.701-0.392-0.3920.0000.0000.0000.000
24A43GLN0-0.0100.00121.745-0.621-0.6210.0000.0000.0000.000
25A44ALA00.008-0.00219.8090.7000.7000.0000.0000.0000.000
26A45GLY0-0.027-0.01318.4770.7800.7800.0000.0000.0000.000
27A46LYS10.8480.94118.421-12.990-12.9900.0000.0000.0000.000
28A47VAL00.0030.00714.1470.7850.7850.0000.0000.0000.000
29A48GLU-1-0.729-0.81916.52114.66214.6620.0000.0000.0000.000
30A49VAL00.0050.00016.8391.1661.1660.0000.0000.0000.000
31A50LEU0-0.006-0.01518.700-1.010-1.0100.0000.0000.0000.000
32A51GLU-1-0.884-0.94820.45012.64312.6430.0000.0000.0000.000
33A52PHE00.0190.00320.876-0.594-0.5940.0000.0000.0000.000
34A53PHE00.020-0.01524.871-0.050-0.0500.0000.0000.0000.000
35A54GLY00.0860.01828.096-0.092-0.0920.0000.0000.0000.000
36A55TYR0-0.012-0.03331.720-0.035-0.0350.0000.0000.0000.000
37A56PHE00.000-0.00631.906-0.289-0.2890.0000.0000.0000.000
38A57CYS0-0.0250.01728.6500.2440.2440.0000.0000.0000.000
39A58PRO00.015-0.00432.7430.0830.0830.0000.0000.0000.000
40A59HIS00.0290.00728.206-0.145-0.1450.0000.0000.0000.000
41A61ALA00.0090.01129.6780.0680.0680.0000.0000.0000.000
42A62HIS0-0.041-0.02431.014-0.072-0.0720.0000.0000.0000.000
43A63LEU0-0.0030.01123.8350.0750.0750.0000.0000.0000.000
44A64GLU-1-0.787-0.88427.68010.43910.4390.0000.0000.0000.000
45A65PRO0-0.021-0.00929.2990.1140.1140.0000.0000.0000.000
46A66VAL0-0.017-0.00325.6080.0450.0450.0000.0000.0000.000
47A67LEU00.0190.00122.2580.3340.3340.0000.0000.0000.000
48A68SER0-0.019-0.03425.5480.3280.3280.0000.0000.0000.000
49A69LYS10.9070.93128.026-9.680-9.6800.0000.0000.0000.000
50A70HIS10.7920.89119.718-14.529-14.5290.0000.0000.0000.000
51A71ALA00.0710.02723.8230.3240.3240.0000.0000.0000.000
52A72LYS10.9040.96324.881-10.066-10.0660.0000.0000.0000.000
53A73SER0-0.098-0.03824.258-0.144-0.1440.0000.0000.0000.000
54A74PHE0-0.0020.00420.8680.5320.5320.0000.0000.0000.000
55A75LYS10.8770.94415.570-18.775-18.7750.0000.0000.0000.000
56A76ASP-1-0.858-0.93421.91012.70412.7040.0000.0000.0000.000
57A77ASP-1-0.904-0.94417.32117.54117.5410.0000.0000.0000.000
58A78MET0-0.0140.01017.0871.2951.2950.0000.0000.0000.000
59A79TYR0-0.023-0.04220.133-0.863-0.8630.0000.0000.0000.000
60A80LEU00.0430.02521.1200.6620.6620.0000.0000.0000.000
61A81ARG10.6960.84421.287-14.799-14.7990.0000.0000.0000.000
62A82THR00.0200.00823.7180.2490.2490.0000.0000.0000.000
63A83GLU-1-0.803-0.89224.74911.90511.9050.0000.0000.0000.000
64A84HIS0-0.027-0.02127.363-0.069-0.0690.0000.0000.0000.000
65A85VAL00.0240.01726.843-0.011-0.0110.0000.0000.0000.000
66A86VAL0-0.030-0.02829.395-0.490-0.4900.0000.0000.0000.000
67A87TRP00.014-0.01927.774-0.225-0.2250.0000.0000.0000.000
68A88GLN0-0.050-0.04232.667-0.081-0.0810.0000.0000.0000.000
69A89LYS10.9500.95836.267-7.593-7.5930.0000.0000.0000.000
70A90GLU-1-0.849-0.91138.9757.8487.8480.0000.0000.0000.000
71A91MET0-0.0390.01333.728-0.034-0.0340.0000.0000.0000.000
72A92LEU00.0710.04435.3650.0870.0870.0000.0000.0000.000
73A93THR0-0.049-0.01837.2450.0580.0580.0000.0000.0000.000
74A94LEU0-0.013-0.00936.163-0.090-0.0900.0000.0000.0000.000
75A95ALA00.0620.03733.2020.0870.0870.0000.0000.0000.000
76A96ARG10.8120.91234.568-7.692-7.6920.0000.0000.0000.000
77A97LEU0-0.042-0.02337.378-0.095-0.0950.0000.0000.0000.000
78A98ALA00.0280.01432.593-0.032-0.0320.0000.0000.0000.000
79A99ALA00.0260.02433.8510.0810.0810.0000.0000.0000.000
80A100ALA0-0.016-0.01134.796-0.039-0.0390.0000.0000.0000.000
81A101VAL0-0.014-0.00635.054-0.184-0.1840.0000.0000.0000.000
82A102ASP-1-0.847-0.90831.21210.39310.3930.0000.0000.0000.000
83A103MET0-0.112-0.04034.139-0.015-0.0150.0000.0000.0000.000
84A104ALA0-0.031-0.01436.904-0.129-0.1290.0000.0000.0000.000
85A105ALA0-0.052-0.04237.710-0.235-0.2350.0000.0000.0000.000
86A106ALA00.0580.04033.4730.1180.1180.0000.0000.0000.000
87A107ASP-1-0.927-0.96233.8838.9748.9740.0000.0000.0000.000
88A108SER0-0.072-0.03836.086-0.052-0.0520.0000.0000.0000.000
89A109LYS10.8630.92329.624-10.780-10.7800.0000.0000.0000.000
90A110ASP-1-0.830-0.88632.0939.8969.8960.0000.0000.0000.000
91A111VAL0-0.006-0.01434.543-0.088-0.0880.0000.0000.0000.000
92A112ALA0-0.0010.00937.450-0.176-0.1760.0000.0000.0000.000
93A113ASN00.0450.00532.003-0.428-0.4280.0000.0000.0000.000
94A114SER0-0.0030.01735.995-0.031-0.0310.0000.0000.0000.000
95A115HIS0-0.063-0.04737.316-0.258-0.2580.0000.0000.0000.000
96A116ILE0-0.024-0.00737.610-0.179-0.1790.0000.0000.0000.000
97A117PHE00.0290.00631.147-0.135-0.1350.0000.0000.0000.000
98A118ASP-1-0.906-0.92037.3267.5077.5070.0000.0000.0000.000
99A119ALA00.0140.00440.382-0.165-0.1650.0000.0000.0000.000
100A120MET0-0.059-0.01738.740-0.098-0.0980.0000.0000.0000.000
101A121VAL0-0.0090.00336.023-0.111-0.1110.0000.0000.0000.000
102A122ASN0-0.045-0.03839.360-0.041-0.0410.0000.0000.0000.000
103A123GLN0-0.047-0.01242.415-0.215-0.2150.0000.0000.0000.000
104A124LYS10.8210.91241.648-7.815-7.8150.0000.0000.0000.000
105A125ILE00.0200.01744.366-0.141-0.1410.0000.0000.0000.000
106A126LYS10.9480.97743.275-6.828-6.8280.0000.0000.0000.000
107A127LEU00.0560.00940.737-0.101-0.1010.0000.0000.0000.000
108A128GLN00.0530.02740.079-0.056-0.0560.0000.0000.0000.000
109A129ASN0-0.046-0.03141.723-0.027-0.0270.0000.0000.0000.000
110A130PRO00.0790.03544.475-0.062-0.0620.0000.0000.0000.000
111A131GLU-1-0.951-0.95746.1826.1006.1000.0000.0000.0000.000
112A132VAL0-0.021-0.01746.814-0.071-0.0710.0000.0000.0000.000
113A133LEU00.0110.00741.822-0.036-0.0360.0000.0000.0000.000
114A134LYS10.8700.91145.707-6.693-6.6930.0000.0000.0000.000
115A135LYS10.8120.89447.935-6.187-6.1870.0000.0000.0000.000
116A136TRP00.0540.02441.969-0.024-0.0240.0000.0000.0000.000
117A137LEU00.0310.01042.469-0.008-0.0080.0000.0000.0000.000
118A138GLY0-0.0280.00046.572-0.013-0.0130.0000.0000.0000.000
119A139GLU-1-0.869-0.93049.6776.0676.0670.0000.0000.0000.000
120A140GLN0-0.064-0.02144.7670.0430.0430.0000.0000.0000.000
121A141THR0-0.034-0.01847.750-0.053-0.0530.0000.0000.0000.000
122A142ALA0-0.0040.00344.0390.0140.0140.0000.0000.0000.000
123A143PHE00.0270.01341.7700.1410.1410.0000.0000.0000.000
124A144ASP-1-0.819-0.91543.4576.8386.8380.0000.0000.0000.000
125A145GLY00.0330.01144.5060.1040.1040.0000.0000.0000.000
126A146LYS10.8880.93445.729-6.271-6.2710.0000.0000.0000.000
127A147LYS10.9090.96741.387-7.726-7.7260.0000.0000.0000.000
128A148VAL00.0180.00640.3260.0850.0850.0000.0000.0000.000
129A149LEU0-0.013-0.00242.7020.0890.0890.0000.0000.0000.000
130A150ALA00.0190.00845.310-0.016-0.0160.0000.0000.0000.000
131A151ALA00.0110.01240.2830.0070.0070.0000.0000.0000.000
132A152TYR00.000-0.00840.811-0.003-0.0030.0000.0000.0000.000
133A153GLU-1-0.870-0.92142.3526.6606.6600.0000.0000.0000.000
134A154SER0-0.073-0.02342.077-0.031-0.0310.0000.0000.0000.000
135A155PRO00.042-0.01042.2420.1320.1320.0000.0000.0000.000
136A156GLU-1-0.805-0.88636.6498.9328.9320.0000.0000.0000.000
137A157SER00.0190.01437.1410.2880.2880.0000.0000.0000.000
138A158GLN0-0.031-0.03736.7690.0060.0060.0000.0000.0000.000
139A159ALA00.0170.01836.3340.1590.1590.0000.0000.0000.000
140A160ARG10.8440.89832.862-9.215-9.2150.0000.0000.0000.000
141A161ALA00.0180.01232.1130.3390.3390.0000.0000.0000.000
142A162ASP-1-0.844-0.91733.0239.0219.0210.0000.0000.0000.000
143A163LYS10.7770.87425.482-12.121-12.1210.0000.0000.0000.000
144A164MET0-0.0090.01628.4880.2930.2930.0000.0000.0000.000
145A165GLN0-0.032-0.02628.5470.1240.1240.0000.0000.0000.000
146A166GLU-1-0.788-0.86726.42912.47412.4740.0000.0000.0000.000
147A167LEU0-0.015-0.00323.2000.4870.4870.0000.0000.0000.000
148A168THR0-0.020-0.02624.3780.4830.4830.0000.0000.0000.000
149A169GLU-1-0.893-0.93225.65810.60510.6050.0000.0000.0000.000
150A170THR0-0.072-0.03922.6320.1870.1870.0000.0000.0000.000
151A171PHE0-0.059-0.04018.7430.3920.3920.0000.0000.0000.000
152A172GLN0-0.062-0.01721.2040.9950.9950.0000.0000.0000.000
153A173ILE00.0030.00920.8560.2560.2560.0000.0000.0000.000
154A174ASP-1-0.896-0.93923.88412.56412.5640.0000.0000.0000.000
155A175GLY00.0170.01324.835-0.500-0.5000.0000.0000.0000.000
156A176THR0-0.087-0.01725.2090.1840.1840.0000.0000.0000.000
157A177PRO00.022-0.02824.526-0.432-0.4320.0000.0000.0000.000
158A178THR0-0.030-0.02219.9250.4500.4500.0000.0000.0000.000
159A179VAL00.0030.00718.251-0.230-0.2300.0000.0000.0000.000
160A180ILE0-0.015-0.00115.1560.8910.8910.0000.0000.0000.000
161A181VAL00.0230.01113.134-0.985-0.9850.0000.0000.0000.000
162A182GLY00.0460.01512.5471.9311.9310.0000.0000.0000.000
163A183GLY0-0.038-0.00213.0810.9200.9200.0000.0000.0000.000
164A184LYS10.8660.9176.444-43.978-43.9780.0000.0000.0000.000
165A185TYR0-0.034-0.0425.5430.8490.8490.0000.0000.0000.000
166A186LYS10.8890.93111.897-18.232-18.2320.0000.0000.0000.000
167A187VAL00.0180.00514.4301.0491.0490.0000.0000.0000.000
168A188GLU-1-0.845-0.87315.46916.68216.6820.0000.0000.0000.000
169A189PHE0-0.031-0.02717.5570.0480.0480.0000.0000.0000.000
170A190ALA00.0000.02120.224-0.465-0.4650.0000.0000.0000.000
171A191ASP-1-0.822-0.88021.96612.17312.1730.0000.0000.0000.000
172A192TRP00.038-0.00722.7200.6160.6160.0000.0000.0000.000
173A193GLU-1-0.889-0.95623.20111.80911.8090.0000.0000.0000.000
174A194SER0-0.074-0.07420.2430.7390.7390.0000.0000.0000.000
175A195GLY00.0300.01018.6670.9560.9560.0000.0000.0000.000
176A196MET0-0.024-0.01018.1170.9790.9790.0000.0000.0000.000
177A197ASN0-0.008-0.00217.1390.3530.3530.0000.0000.0000.000
178A198THR0-0.0050.00513.0891.1731.1730.0000.0000.0000.000
179A199ILE00.0010.00313.5661.6381.6380.0000.0000.0000.000
180A200ASP-1-0.835-0.90414.76517.35817.3580.0000.0000.0000.000
181A201LEU0-0.044-0.02310.7581.0221.0220.0000.0000.0000.000
182A202LEU00.0380.0139.2832.5112.5110.0000.0000.0000.000
183A203ALA0-0.021-0.01010.3451.9871.9870.0000.0000.0000.000
184A204ASP-1-0.811-0.89910.69321.47721.4770.0000.0000.0000.000
185A205LYS10.8580.9442.042-101.398-98.9684.296-3.536-3.1890.053
186A206VAL00.006-0.0037.1663.6883.6880.0000.0000.0000.000
187A207ARG10.8070.8699.387-20.851-20.8510.0000.0000.0000.000
188A208GLU-1-0.882-0.9406.81226.80326.8030.0000.0000.0000.000
189A209GLU-1-0.774-0.8394.77956.66756.823-0.001-0.002-0.1520.000
190A210GLN0-0.045-0.0267.921-1.682-1.6820.0000.0000.0000.000
191A211LYS10.7260.87210.843-28.035-28.0350.0000.0000.0000.000
192A212ALA0-0.0120.0039.3240.3970.3970.0000.0000.0000.000