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: 7G1KK

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062087.150508
FMO2-HF: Nuclear repulsion 1987359.458542
FMO2-HF: Total energy -74727.691966
FMO2-MP2: Total energy -74944.700073


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.
-10.179-4.433.098-3.934-4.914-0.023
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 : -0.024 / q_NPA : -0.027
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].
3A0ALA00.0910.0563.866-0.8970.172-0.008-0.419-0.6420.001
4A1MET0-0.027-0.0072.2560.4630.7192.201-1.008-1.4490.002
5A2SER0-0.073-0.0403.4121.8152.2520.003-0.170-0.2710.000
6A3GLU-1-0.878-0.9145.461-0.545-0.5450.0000.0000.0000.000
7A4TYR0-0.044-0.0407.7880.5680.5680.0000.0000.0000.000
8A5ARG10.8580.9296.8081.6931.6930.0000.0000.0000.000
9A6THR00.011-0.00110.4960.0580.0580.0000.0000.0000.000
10A7VAL00.0390.00511.623-0.080-0.0800.0000.0000.0000.000
11A8SER0-0.072-0.05012.693-0.002-0.0020.0000.0000.0000.000
12A9ALA0-0.012-0.00912.4940.0220.0220.0000.0000.0000.000
13A10ALA00.0600.0299.8590.0040.0040.0000.0000.0000.000
14A11ALA0-0.023-0.01411.8500.0840.0840.0000.0000.0000.000
15A12MET0-0.037-0.00815.0170.0780.0780.0000.0000.0000.000
16A13LEU0-0.049-0.02313.9770.0410.0410.0000.0000.0000.000
17A14GLY00.0330.04111.9660.0070.0070.0000.0000.0000.000
18A15THR0-0.020-0.05110.6910.1440.1440.0000.0000.0000.000
19A16TYR00.004-0.01512.498-0.079-0.0790.0000.0000.0000.000
20A17GLU-1-0.771-0.8899.5780.0140.0140.0000.0000.0000.000
21A18ASP-1-0.768-0.8547.652-0.843-0.8430.0000.0000.0000.000
22A19PHE00.008-0.0098.205-0.219-0.2190.0000.0000.0000.000
23A20LEU0-0.020-0.00910.1080.0020.0020.0000.0000.0000.000
24A21GLU-1-0.833-0.9042.642-7.751-4.1420.899-2.219-2.289-0.027
25A22LEU0-0.008-0.0036.2010.1900.1900.0000.0000.0000.000
26A23PHE0-0.060-0.0318.1070.1650.1650.0000.0000.0000.000
27A24GLU-1-0.856-0.9369.3140.2940.2940.0000.0000.0000.000
28A25LYS10.8420.9103.630-5.094-4.7160.003-0.118-0.2630.001
29A26GLY00.0340.0247.685-0.109-0.1090.0000.0000.0000.000
30A27TYR0-0.122-0.0789.1770.1330.1330.0000.0000.0000.000
31A28GLU-1-0.832-0.89312.134-0.436-0.4360.0000.0000.0000.000
32A29ASP-1-0.768-0.86514.401-0.031-0.0310.0000.0000.0000.000
33A30LYS10.8680.92113.081-0.182-0.1820.0000.0000.0000.000
34A31GLU-1-0.855-0.91516.961-0.028-0.0280.0000.0000.0000.000
35A32SER0-0.056-0.06519.735-0.005-0.0050.0000.0000.0000.000
36A33VAL0-0.022-0.00515.448-0.010-0.0100.0000.0000.0000.000
37A34LEU0-0.0130.00718.850-0.007-0.0070.0000.0000.0000.000
38A35LYS10.8290.90821.1570.0470.0470.0000.0000.0000.000
39A36SER0-0.013-0.00520.759-0.013-0.0130.0000.0000.0000.000
40A37ASN00.0180.00423.3590.0170.0170.0000.0000.0000.000
41A38ILE00.0330.02316.563-0.006-0.0060.0000.0000.0000.000
42A39LEU00.0570.02020.319-0.016-0.0160.0000.0000.0000.000
43A40TYR0-0.028-0.02522.4510.0030.0030.0000.0000.0000.000
44A41ASP-1-0.823-0.87718.724-0.300-0.3000.0000.0000.0000.000
45A42VAL00.0070.00917.869-0.009-0.0090.0000.0000.0000.000
46A43LEU0-0.056-0.03419.9160.0080.0080.0000.0000.0000.000
47A44ARG10.8000.87722.1290.2450.2450.0000.0000.0000.000
48A45ASN0-0.031-0.00716.0670.0090.0090.0000.0000.0000.000
49A46ASN0-0.035-0.02420.1020.0470.0470.0000.0000.0000.000
50A47ASN00.0390.03416.2180.0510.0510.0000.0000.0000.000
51A48ASP-1-0.757-0.89219.982-0.090-0.0900.0000.0000.0000.000
52A49GLU-1-0.877-0.92017.5030.0210.0210.0000.0000.0000.000
53A50ALA00.0100.00716.2750.0140.0140.0000.0000.0000.000
54A51ARG10.8050.90717.8960.0850.0850.0000.0000.0000.000
55A52TYR00.0120.01720.8890.0080.0080.0000.0000.0000.000
56A53LYS10.7980.87115.611-0.042-0.0420.0000.0000.0000.000
57A54ILE0-0.0010.00414.8490.0190.0190.0000.0000.0000.000
58A55SER0-0.017-0.01417.7880.0020.0020.0000.0000.0000.000
59A56MET0-0.031-0.00921.3550.0120.0120.0000.0000.0000.000
60A57PHE0-0.013-0.00314.9970.0140.0140.0000.0000.0000.000
61A58LEU00.0330.00817.0470.0120.0120.0000.0000.0000.000
62A59ILE0-0.002-0.00420.2410.0080.0080.0000.0000.0000.000
63A60ASN0-0.048-0.02922.8560.0020.0020.0000.0000.0000.000
64A61LYS10.8990.96617.181-0.082-0.0820.0000.0000.0000.000
65A62GLY0-0.0130.00421.8520.0040.0040.0000.0000.0000.000
66A63ALA0-0.028-0.01221.430-0.007-0.0070.0000.0000.0000.000
67A64ASP-1-0.822-0.91323.455-0.065-0.0650.0000.0000.0000.000
68A65ILE0-0.032-0.02425.994-0.008-0.0080.0000.0000.0000.000
69A66LYS10.7640.86728.6360.0380.0380.0000.0000.0000.000
70A67SER00.0030.01527.1090.0030.0030.0000.0000.0000.000
71A68ARG10.7870.86529.6930.0710.0710.0000.0000.0000.000
72A69THR0-0.012-0.02128.477-0.004-0.0040.0000.0000.0000.000
73A70LYS10.9780.99530.5290.1500.1500.0000.0000.0000.000
74A71GLU-1-0.833-0.90032.417-0.121-0.1210.0000.0000.0000.000
75A72GLY0-0.049-0.02734.1610.0090.0090.0000.0000.0000.000
76A73THR0-0.051-0.02031.7420.0090.0090.0000.0000.0000.000
77A74THR00.0460.01431.370-0.009-0.0090.0000.0000.0000.000
78A75LEU00.0730.03226.011-0.005-0.0050.0000.0000.0000.000
79A76PHE00.031-0.00229.043-0.003-0.0030.0000.0000.0000.000
80A77PHE0-0.0210.00331.0450.0010.0010.0000.0000.0000.000
81A78PRO0-0.025-0.00726.1080.0020.0020.0000.0000.0000.000
82A79LEU00.0180.02827.827-0.001-0.0010.0000.0000.0000.000
83A80PHE00.032-0.00328.7400.0050.0050.0000.0000.0000.000
84A81GLN0-0.060-0.02329.9280.0110.0110.0000.0000.0000.000
85A82GLY00.0410.02327.2710.0010.0010.0000.0000.0000.000
86A83GLY00.0070.01227.9860.0010.0010.0000.0000.0000.000
87A84GLY0-0.007-0.00928.9520.0100.0100.0000.0000.0000.000
88A85ASN0-0.056-0.03426.4560.0110.0110.0000.0000.0000.000
89A86ASP-1-0.796-0.88426.670-0.028-0.0280.0000.0000.0000.000
90A87ILE00.0590.03129.139-0.003-0.0030.0000.0000.0000.000
91A88THR00.0030.01130.0810.0000.0000.0000.0000.0000.000
92A89GLY00.0570.02227.3990.0020.0020.0000.0000.0000.000
93A90THR0-0.030-0.03328.392-0.007-0.0070.0000.0000.0000.000
94A91THR0-0.042-0.03030.125-0.002-0.0020.0000.0000.0000.000
95A92GLU-1-0.877-0.95429.3350.0000.0000.0000.0000.0000.000
96A93LEU0-0.008-0.00324.9610.0000.0000.0000.0000.0000.000
97A94CYS0-0.033-0.00629.078-0.002-0.0020.0000.0000.0000.000
98A95LYS10.7940.90132.5560.0020.0020.0000.0000.0000.000
99A96ILE00.0440.01928.2940.0000.0000.0000.0000.0000.000
100A97PHE00.000-0.01826.218-0.001-0.0010.0000.0000.0000.000
101A98LEU0-0.029-0.01231.599-0.001-0.0010.0000.0000.0000.000
102A99GLU-1-0.839-0.90833.494-0.003-0.0030.0000.0000.0000.000
103A100LYS10.8840.95827.3510.0130.0130.0000.0000.0000.000
104A101GLY0-0.0020.00533.181-0.003-0.0030.0000.0000.0000.000
105A102ALA0-0.0030.00932.176-0.003-0.0030.0000.0000.0000.000
106A103ASP-1-0.782-0.86734.253-0.050-0.0500.0000.0000.0000.000
107A104ILE00.0250.01435.957-0.006-0.0060.0000.0000.0000.000
108A105THR0-0.057-0.03637.7250.0010.0010.0000.0000.0000.000
109A106ALA0-0.0100.00537.8940.0000.0000.0000.0000.0000.000
110A107LEU0-0.011-0.00839.284-0.001-0.0010.0000.0000.0000.000
111A108TYR00.0350.01433.099-0.002-0.0020.0000.0000.0000.000
112A109LYS10.9230.93337.4430.0770.0770.0000.0000.0000.000
113A110PRO0-0.0060.01235.3150.0030.0030.0000.0000.0000.000
114A111TYR00.010-0.00936.2170.0020.0020.0000.0000.0000.000
115A112LYS10.8330.91840.5760.0580.0580.0000.0000.0000.000
116A113ILE00.0270.02837.5730.0040.0040.0000.0000.0000.000
117A114VAL00.0350.01040.160-0.003-0.0030.0000.0000.0000.000
118A115VAL0-0.0070.00334.412-0.002-0.0020.0000.0000.0000.000
119A116PHE00.0930.03735.466-0.004-0.0040.0000.0000.0000.000
120A117LYS10.8310.92637.2510.0600.0600.0000.0000.0000.000
121A118ASN00.0120.00433.4030.0050.0050.0000.0000.0000.000
122A119ILE00.0210.01835.0720.0010.0010.0000.0000.0000.000
123A120PHE0-0.052-0.03037.1270.0030.0030.0000.0000.0000.000
124A121ASN0-0.002-0.01837.3060.0060.0060.0000.0000.0000.000
125A122TYR0-0.011-0.00232.4540.0000.0000.0000.0000.0000.000
126A123PHE0-0.0200.00136.0230.0050.0050.0000.0000.0000.000
127A124VAL00.0320.02134.7650.0010.0010.0000.0000.0000.000
128A125ASP-1-0.833-0.92837.944-0.015-0.0150.0000.0000.0000.000
129A126GLU-1-0.731-0.86540.465-0.025-0.0250.0000.0000.0000.000
130A127ASN0-0.044-0.02942.1930.0000.0000.0000.0000.0000.000
131A128GLU-1-0.863-0.93736.481-0.013-0.0130.0000.0000.0000.000
132A129MET0-0.0320.00237.191-0.002-0.0020.0000.0000.0000.000
133A130ILE0-0.021-0.00239.523-0.001-0.0010.0000.0000.0000.000
134A131PRO0-0.015-0.01137.6820.0000.0000.0000.0000.0000.000
135A132LEU00.0610.03834.967-0.001-0.0010.0000.0000.0000.000
136A133TYR0-0.039-0.06938.096-0.003-0.0030.0000.0000.0000.000
137A134LYS10.9450.97541.6230.0060.0060.0000.0000.0000.000
138A135LEU0-0.0100.02935.6920.0000.0000.0000.0000.0000.000
139A136ILE00.0270.01937.629-0.001-0.0010.0000.0000.0000.000
140A137PHE0-0.024-0.03540.7650.0000.0000.0000.0000.0000.000
141A138SER0-0.032-0.02842.8990.0020.0020.0000.0000.0000.000
142A139GLN0-0.0230.00040.4390.0010.0010.0000.0000.0000.000
143A140SER0-0.0090.01743.8470.0010.0010.0000.0000.0000.000
144A141GLY00.0520.01944.815-0.002-0.0020.0000.0000.0000.000
145A142LEU0-0.0060.00141.857-0.003-0.0030.0000.0000.0000.000
146A143GLN00.001-0.00943.3120.0020.0020.0000.0000.0000.000
147A144LEU0-0.021-0.02645.004-0.002-0.0020.0000.0000.0000.000
148A145LEU00.007-0.00847.3940.0000.0000.0000.0000.0000.000
149A146ILE0-0.0020.01246.9680.0000.0000.0000.0000.0000.000
150A147LYS10.8130.89347.6360.0350.0350.0000.0000.0000.000
151A148ASP-1-0.723-0.86944.222-0.057-0.0570.0000.0000.0000.000
152A149LYS10.8110.90541.2090.0820.0820.0000.0000.0000.000
153A150TRP0-0.011-0.00840.883-0.001-0.0010.0000.0000.0000.000
154A151GLY00.0010.02148.0530.0020.0020.0000.0000.0000.000
155A152LEU0-0.046-0.01946.3720.0030.0030.0000.0000.0000.000
156A153THR0-0.035-0.03747.322-0.002-0.0020.0000.0000.0000.000
157A154ALA00.0110.00144.774-0.001-0.0010.0000.0000.0000.000
158A155LEU00.0700.03346.1800.0000.0000.0000.0000.0000.000
159A156GLU-1-0.839-0.90149.355-0.035-0.0350.0000.0000.0000.000
160A157PHE0-0.011-0.00841.7310.0000.0000.0000.0000.0000.000
161A158VAL00.0490.02344.5720.0000.0000.0000.0000.0000.000
162A159LYS10.9130.96947.0810.0310.0310.0000.0000.0000.000
163A160ARG10.8670.94549.0030.0420.0420.0000.0000.0000.000
164A161CYS0-0.0050.01544.970-0.003-0.0030.0000.0000.0000.000
165A162GLN00.0200.01046.0320.0010.0010.0000.0000.0000.000
166A163LYS10.8390.93040.1240.0330.0330.0000.0000.0000.000
167A164PRO00.0580.02446.1770.0000.0000.0000.0000.0000.000
168A165ILE0-0.015-0.01346.1690.0010.0010.0000.0000.0000.000
169A166ALA00.0120.00844.1650.0000.0000.0000.0000.0000.000
170A167LEU0-0.005-0.00246.0710.0000.0000.0000.0000.0000.000
171A168LYS10.8920.93949.3450.0150.0150.0000.0000.0000.000
172A169MET0-0.010-0.00945.4370.0010.0010.0000.0000.0000.000
173A170MET0-0.039-0.00846.162-0.001-0.0010.0000.0000.0000.000
174A171GLU-1-0.921-0.96449.027-0.021-0.0210.0000.0000.0000.000
175A172ASP-1-0.858-0.91851.906-0.014-0.0140.0000.0000.0000.000
176A173TYR0-0.053-0.03046.1500.0000.0000.0000.0000.0000.000
177A174ILE0-0.005-0.01650.7140.0000.0000.0000.0000.0000.000
178A175LYS10.9380.97152.9880.0140.0140.0000.0000.0000.000
179A176LYS10.8800.94949.1810.0160.0160.0000.0000.0000.000
180A177TYR0-0.033-0.03547.5830.0020.0020.0000.0000.0000.000
181A178ASN00.0130.01453.680-0.001-0.0010.0000.0000.0000.000
182A179LEU00.0100.03150.166-0.001-0.0010.0000.0000.0000.000
183A180LYS10.8070.87754.7140.0230.0230.0000.0000.0000.000
184A181GLU-1-0.833-0.89754.468-0.035-0.0350.0000.0000.0000.000