FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: M3QLZ

Calculation Name: 3T8K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T8K

Chain ID: A

ChEMBL ID:

UniProt ID: C7NDE2

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2055605.83398
FMO2-HF: Nuclear repulsion 1980878.41546
FMO2-HF: Total energy -74727.41852
FMO2-MP2: Total energy -74944.384961


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-2.6250.0293.529-2.617-3.5660.003
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.024
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].
3A0ALA00.1400.0823.806-1.465-0.034-0.014-0.593-0.8240.001
4A1MET0-0.073-0.0332.0680.214-0.1813.522-1.428-1.6990.004
5A2SER0-0.107-0.0583.1700.9251.6430.014-0.274-0.4580.000
6A3GLU-1-0.901-0.9295.079-0.359-0.278-0.001-0.003-0.0760.000
7A4TYR0-0.036-0.0317.5160.5620.5620.0000.0000.0000.000
8A5ARG10.9220.9687.1791.2101.2100.0000.0000.0000.000
9A6THR00.017-0.00810.3660.0860.0860.0000.0000.0000.000
10A7VAL00.0280.00011.888-0.058-0.0580.0000.0000.0000.000
11A8SER0-0.052-0.04812.996-0.006-0.0060.0000.0000.0000.000
12A9ALA0-0.003-0.00312.7900.0240.0240.0000.0000.0000.000
13A10ALA00.0590.02610.2270.0110.0110.0000.0000.0000.000
14A11ALA0-0.030-0.01512.1270.0630.0630.0000.0000.0000.000
15A12MET0-0.045-0.01315.3820.0600.0600.0000.0000.0000.000
16A13LEU0-0.056-0.02914.1620.0260.0260.0000.0000.0000.000
17A14GLY00.0170.03612.1550.0000.0000.0000.0000.0000.000
18A15THR0-0.013-0.04711.0050.1250.1250.0000.0000.0000.000
19A16TYR0-0.004-0.01912.778-0.048-0.0480.0000.0000.0000.000
20A17GLU-1-0.793-0.91910.0280.1120.1120.0000.0000.0000.000
21A18ASP-1-0.763-0.8508.111-0.531-0.5310.0000.0000.0000.000
22A19PHE0-0.002-0.0138.615-0.103-0.1030.0000.0000.0000.000
23A20LEU0-0.014-0.00710.9610.0150.0150.0000.0000.0000.000
24A21GLU-1-0.860-0.9113.752-0.824-0.0850.009-0.318-0.431-0.002
25A22LEU0-0.013-0.0156.4370.1480.1480.0000.0000.0000.000
26A23PHE0-0.068-0.0288.5660.0850.0850.0000.0000.0000.000
27A24GLU-1-0.871-0.9379.6990.3210.3210.0000.0000.0000.000
28A25LYS10.8470.9034.757-2.876-2.796-0.001-0.001-0.0780.000
29A26GLY00.0080.0158.220-0.055-0.0550.0000.0000.0000.000
30A27TYR0-0.047-0.0289.2890.0660.0660.0000.0000.0000.000
31A28GLU-1-0.907-0.94412.261-0.302-0.3020.0000.0000.0000.000
32A29ASP-1-0.755-0.85814.5680.0230.0230.0000.0000.0000.000
33A30LYS10.8580.91213.891-0.239-0.2390.0000.0000.0000.000
34A31GLU-1-0.862-0.92917.4370.0040.0040.0000.0000.0000.000
35A32SER0-0.056-0.05319.706-0.011-0.0110.0000.0000.0000.000
36A33VAL0-0.012-0.00415.639-0.012-0.0120.0000.0000.0000.000
37A34LEU0-0.0260.00119.077-0.009-0.0090.0000.0000.0000.000
38A35LYS10.8560.92121.4780.0150.0150.0000.0000.0000.000
39A36SER0-0.045-0.00920.886-0.012-0.0120.0000.0000.0000.000
40A37ASN00.0170.00123.3970.0170.0170.0000.0000.0000.000
41A38ILE00.0480.03116.852-0.008-0.0080.0000.0000.0000.000
42A39LEU00.0430.01420.796-0.011-0.0110.0000.0000.0000.000
43A40TYR0-0.025-0.02022.8350.0060.0060.0000.0000.0000.000
44A41ASP-1-0.831-0.88819.267-0.218-0.2180.0000.0000.0000.000
45A42VAL00.0110.01418.409-0.009-0.0090.0000.0000.0000.000
46A43LEU0-0.061-0.02820.3000.0040.0040.0000.0000.0000.000
47A44ARG10.8060.88322.3340.1850.1850.0000.0000.0000.000
48A45ASN0-0.033-0.00716.4560.0020.0020.0000.0000.0000.000
49A46ASN0-0.029-0.02120.5420.0360.0360.0000.0000.0000.000
50A47ASN00.0260.03616.9270.0400.0400.0000.0000.0000.000
51A48ASP-1-0.818-0.92320.552-0.047-0.0470.0000.0000.0000.000
52A49GLU-1-0.862-0.92818.7300.0770.0770.0000.0000.0000.000
53A50ALA0-0.005-0.00916.6820.0130.0130.0000.0000.0000.000
54A51ARG10.8620.93418.3270.0500.0500.0000.0000.0000.000
55A52TYR0-0.0020.00721.0170.0060.0060.0000.0000.0000.000
56A53LYS10.8180.90416.416-0.104-0.1040.0000.0000.0000.000
57A54ILE00.0090.00415.2960.0180.0180.0000.0000.0000.000
58A55SER0-0.026-0.01818.346-0.001-0.0010.0000.0000.0000.000
59A56MET0-0.039-0.01421.8230.0070.0070.0000.0000.0000.000
60A57PHE0-0.023-0.00315.9740.0100.0100.0000.0000.0000.000
61A58LEU00.020-0.00617.7700.0090.0090.0000.0000.0000.000
62A59ILE0-0.013-0.00620.8000.0040.0040.0000.0000.0000.000
63A60ASN0-0.057-0.03223.159-0.003-0.0030.0000.0000.0000.000
64A61LYS10.8840.96118.347-0.121-0.1210.0000.0000.0000.000
65A62GLY0-0.023-0.00622.746-0.001-0.0010.0000.0000.0000.000
66A63ALA0-0.034-0.00922.111-0.007-0.0070.0000.0000.0000.000
67A64ASP-1-0.830-0.92224.092-0.038-0.0380.0000.0000.0000.000
68A65ILE0-0.020-0.01326.708-0.006-0.0060.0000.0000.0000.000
69A66LYS10.8460.93029.1100.0140.0140.0000.0000.0000.000
70A67SER00.0240.02427.3690.0020.0020.0000.0000.0000.000
71A68ARG10.7780.86030.2090.0460.0460.0000.0000.0000.000
72A69THR0-0.015-0.01928.716-0.002-0.0020.0000.0000.0000.000
73A70LYS10.9881.00230.8090.1250.1250.0000.0000.0000.000
74A71GLU-1-0.864-0.92432.387-0.100-0.1000.0000.0000.0000.000
75A72GLY0-0.093-0.06034.3510.0060.0060.0000.0000.0000.000
76A73THR0-0.034-0.00831.9010.0080.0080.0000.0000.0000.000
77A74THR00.0570.02631.812-0.005-0.0050.0000.0000.0000.000
78A75LEU00.1000.04126.484-0.006-0.0060.0000.0000.0000.000
79A76PHE00.034-0.00429.610-0.002-0.0020.0000.0000.0000.000
80A77PHE0-0.026-0.00231.5620.0000.0000.0000.0000.0000.000
81A78PRO0-0.014-0.00126.5940.0010.0010.0000.0000.0000.000
82A79LEU00.0210.02828.203-0.001-0.0010.0000.0000.0000.000
83A80PHE00.027-0.00629.1800.0040.0040.0000.0000.0000.000
84A81GLN0-0.063-0.03330.1530.0080.0080.0000.0000.0000.000
85A82GLY00.0400.01927.517-0.001-0.0010.0000.0000.0000.000
86A83GLY00.0110.01527.9100.0010.0010.0000.0000.0000.000
87A84GLY0-0.020-0.01829.6480.0080.0080.0000.0000.0000.000
88A85ASN0-0.021-0.00527.1970.0080.0080.0000.0000.0000.000
89A86ASP-1-0.772-0.87126.8980.0010.0010.0000.0000.0000.000
90A87ILE00.0480.03129.472-0.001-0.0010.0000.0000.0000.000
91A88THR00.0190.01130.885-0.002-0.0020.0000.0000.0000.000
92A89GLY00.0660.03628.0930.0020.0020.0000.0000.0000.000
93A90THR0-0.033-0.03329.037-0.004-0.0040.0000.0000.0000.000
94A91THR0-0.056-0.04430.468-0.002-0.0020.0000.0000.0000.000
95A92GLU-1-0.877-0.94929.8710.0210.0210.0000.0000.0000.000
96A93LEU00.0130.00925.5260.0010.0010.0000.0000.0000.000
97A94CYS0-0.040-0.00929.648-0.003-0.0030.0000.0000.0000.000
98A95LYS10.7980.89832.936-0.018-0.0180.0000.0000.0000.000
99A96ILE00.0390.02128.9130.0000.0000.0000.0000.0000.000
100A97PHE00.009-0.01426.630-0.001-0.0010.0000.0000.0000.000
101A98LEU0-0.035-0.01932.090-0.001-0.0010.0000.0000.0000.000
102A99GLU-1-0.853-0.90634.3920.0150.0150.0000.0000.0000.000
103A100LYS10.9090.96229.040-0.013-0.0130.0000.0000.0000.000
104A101GLY0-0.027-0.02533.744-0.003-0.0030.0000.0000.0000.000
105A102ALA0-0.0040.01532.506-0.004-0.0040.0000.0000.0000.000
106A103ASP-1-0.766-0.87134.586-0.031-0.0310.0000.0000.0000.000
107A104ILE00.007-0.00536.811-0.004-0.0040.0000.0000.0000.000
108A105THR0-0.078-0.04338.173-0.001-0.0010.0000.0000.0000.000
109A106ALA0-0.027-0.00138.278-0.001-0.0010.0000.0000.0000.000
110A107LEU0-0.017-0.01039.200-0.001-0.0010.0000.0000.0000.000
111A108TYR00.0260.02133.489-0.002-0.0020.0000.0000.0000.000
112A109LYS10.9670.95437.9180.0600.0600.0000.0000.0000.000
113A110PRO0-0.0040.01735.7640.0030.0030.0000.0000.0000.000
114A111TYR00.006-0.01936.8680.0010.0010.0000.0000.0000.000
115A112LYS10.8480.93041.0050.0450.0450.0000.0000.0000.000
116A113ILE00.0270.02637.9010.0030.0030.0000.0000.0000.000
117A114VAL00.0310.01340.431-0.002-0.0020.0000.0000.0000.000
118A115VAL00.0180.01634.842-0.003-0.0030.0000.0000.0000.000
119A116PHE00.0800.02535.942-0.003-0.0030.0000.0000.0000.000
120A117LYS10.8720.96237.7010.0460.0460.0000.0000.0000.000
121A118ASN00.0310.01233.4440.0030.0030.0000.0000.0000.000
122A119ILE00.0220.02335.5920.0010.0010.0000.0000.0000.000
123A120PHE0-0.067-0.04037.6130.0030.0030.0000.0000.0000.000
124A121ASN0-0.026-0.03437.5570.0040.0040.0000.0000.0000.000
125A122TYR0-0.036-0.01432.8740.0010.0010.0000.0000.0000.000
126A123PHE00.0060.01136.4630.0030.0030.0000.0000.0000.000
127A124VAL00.0360.01635.2100.0010.0010.0000.0000.0000.000
128A125ASP-1-0.841-0.91038.417-0.004-0.0040.0000.0000.0000.000
129A126GLU-1-0.711-0.86640.889-0.012-0.0120.0000.0000.0000.000
130A127ASN0-0.042-0.02242.8050.0000.0000.0000.0000.0000.000
131A128GLU-1-0.891-0.96236.9720.0020.0020.0000.0000.0000.000
132A129MET0-0.042-0.00437.5450.0000.0000.0000.0000.0000.000
133A130ILE0-0.027-0.00140.034-0.001-0.0010.0000.0000.0000.000
134A131PRO0-0.007-0.00538.388-0.001-0.0010.0000.0000.0000.000
135A132LEU00.0640.03435.394-0.001-0.0010.0000.0000.0000.000
136A133TYR0-0.048-0.07238.604-0.003-0.0030.0000.0000.0000.000
137A134LYS10.9390.96742.044-0.006-0.0060.0000.0000.0000.000
138A135LEU0-0.0040.03436.4240.0000.0000.0000.0000.0000.000
139A136ILE00.0430.01938.023-0.001-0.0010.0000.0000.0000.000
140A137PHE0-0.023-0.02441.190-0.001-0.0010.0000.0000.0000.000
141A138SER0-0.055-0.03743.3620.0010.0010.0000.0000.0000.000
142A139GLN0-0.047-0.01040.6110.0010.0010.0000.0000.0000.000
143A140SER0-0.0060.01444.084-0.001-0.0010.0000.0000.0000.000
144A141GLY00.0640.02445.300-0.001-0.0010.0000.0000.0000.000
145A142LEU0-0.027-0.01242.555-0.003-0.0030.0000.0000.0000.000
146A143GLN0-0.027-0.02243.8290.0010.0010.0000.0000.0000.000
147A144LEU00.004-0.01245.570-0.002-0.0020.0000.0000.0000.000
148A145LEU00.000-0.00648.1020.0000.0000.0000.0000.0000.000
149A146ILE00.0190.02047.5470.0000.0000.0000.0000.0000.000
150A147LYS10.8210.91448.1900.0270.0270.0000.0000.0000.000
151A148ASP-1-0.737-0.88844.465-0.045-0.0450.0000.0000.0000.000
152A149LYS10.8280.91941.6440.0670.0670.0000.0000.0000.000
153A150TRP0-0.016-0.01741.228-0.001-0.0010.0000.0000.0000.000
154A151GLY0-0.0020.01448.4090.0020.0020.0000.0000.0000.000
155A152LEU0-0.041-0.01146.6340.0020.0020.0000.0000.0000.000
156A153THR0-0.037-0.03647.853-0.001-0.0010.0000.0000.0000.000
157A154ALA00.012-0.00745.2530.0000.0000.0000.0000.0000.000
158A155LEU00.0640.02546.6430.0000.0000.0000.0000.0000.000
159A156GLU-1-0.852-0.91549.683-0.027-0.0270.0000.0000.0000.000
160A157PHE0-0.013-0.00941.9940.0000.0000.0000.0000.0000.000
161A158VAL00.0560.02744.9980.0000.0000.0000.0000.0000.000
162A159LYS10.9110.97247.3870.0220.0220.0000.0000.0000.000
163A160ARG10.8890.95449.1940.0320.0320.0000.0000.0000.000
164A161CYS0-0.0220.02045.125-0.002-0.0020.0000.0000.0000.000
165A162GLN00.023-0.00146.3200.0000.0000.0000.0000.0000.000
166A163LYS10.8440.92940.6610.0210.0210.0000.0000.0000.000
167A164PRO00.0580.02646.9080.0000.0000.0000.0000.0000.000
168A165ILE0-0.007-0.00646.4870.0010.0010.0000.0000.0000.000
169A166ALA00.0260.01444.7770.0000.0000.0000.0000.0000.000
170A167LEU0-0.018-0.00646.704-0.001-0.0010.0000.0000.0000.000
171A168LYS10.8980.93949.9460.0060.0060.0000.0000.0000.000
172A169MET0-0.016-0.01045.9510.0010.0010.0000.0000.0000.000
173A170MET0-0.032-0.00646.882-0.001-0.0010.0000.0000.0000.000
174A171GLU-1-0.926-0.96749.583-0.013-0.0130.0000.0000.0000.000
175A172ASP-1-0.867-0.92052.180-0.006-0.0060.0000.0000.0000.000
176A173TYR0-0.076-0.04846.6720.0000.0000.0000.0000.0000.000
177A174ILE00.014-0.00651.3360.0000.0000.0000.0000.0000.000
178A175LYS10.9440.98153.5190.0070.0070.0000.0000.0000.000
179A176LYS10.8680.94450.3160.0060.0060.0000.0000.0000.000
180A177TYR00.010-0.00648.5880.0010.0010.0000.0000.0000.000
181A178ASN0-0.0040.01354.468-0.001-0.0010.0000.0000.0000.000
182A179LEU00.0060.01050.721-0.001-0.0010.0000.0000.0000.000
183A180LYS10.8570.92055.2110.0140.0140.0000.0000.0000.000
184A181GLU-1-0.867-0.92254.645-0.026-0.0260.0000.0000.0000.000