FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: KGK33

Calculation Name: 4J80-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J80

Chain ID: A

ChEMBL ID:

UniProt ID: Q56237

Base Structure: X-ray

Registration Date: 2023-09-22

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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2781162.65087
FMO2-HF: Nuclear repulsion 2677085.189214
FMO2-HF: Total energy -104077.461656
FMO2-MP2: Total energy -104384.18865


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-10.447-4.092.249-3.667-4.938-0.026
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.011
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].
3A4LYS10.8120.8913.8510.5091.722-0.010-0.613-0.5900.002
4A5LYS10.7900.8935.867-0.623-0.6230.0000.0000.0000.000
5A6ASP-1-0.816-0.8927.823-0.211-0.2110.0000.0000.0000.000
6A7TYR00.001-0.0508.125-0.013-0.0130.0000.0000.0000.000
7A8TYR0-0.073-0.05912.9850.0090.0090.0000.0000.0000.000
8A9ALA0-0.008-0.00414.6320.0120.0120.0000.0000.0000.000
9A10ILE0-0.036-0.00910.7140.0010.0010.0000.0000.0000.000
10A11LEU0-0.046-0.02415.274-0.008-0.0080.0000.0000.0000.000
11A12GLY0-0.018-0.00318.387-0.020-0.0200.0000.0000.0000.000
12A13VAL0-0.064-0.02619.281-0.019-0.0190.0000.0000.0000.000
13A14PRO00.0180.00620.0530.0030.0030.0000.0000.0000.000
14A15ARG10.9010.93416.0530.1660.1660.0000.0000.0000.000
15A16ASN0-0.017-0.01920.001-0.017-0.0170.0000.0000.0000.000
16A17ALA00.0050.02321.893-0.001-0.0010.0000.0000.0000.000
17A18THR00.015-0.03323.111-0.016-0.0160.0000.0000.0000.000
18A19GLN00.034-0.00320.8220.0040.0040.0000.0000.0000.000
19A20GLU-1-0.764-0.84924.3030.0030.0030.0000.0000.0000.000
20A21GLU-1-0.855-0.88724.903-0.002-0.0020.0000.0000.0000.000
21A22ILE00.0570.03619.6730.0170.0170.0000.0000.0000.000
22A23LYS10.8460.92222.3410.0160.0160.0000.0000.0000.000
23A24ARG10.8010.87424.5370.0000.0000.0000.0000.0000.000
24A25ALA0-0.0080.00822.1600.0080.0080.0000.0000.0000.000
25A26TYR00.0350.01019.6740.0060.0060.0000.0000.0000.000
26A27LYS10.9260.95722.103-0.023-0.0230.0000.0000.0000.000
27A28ARG10.8990.95525.388-0.070-0.0700.0000.0000.0000.000
28A29LEU00.0180.01019.9200.0030.0030.0000.0000.0000.000
29A30ALA00.0420.01722.0990.0140.0140.0000.0000.0000.000
30A31ARG10.9280.95222.970-0.066-0.0660.0000.0000.0000.000
31A32GLN0-0.0420.00124.095-0.011-0.0110.0000.0000.0000.000
32A33TYR0-0.020-0.02221.5020.0140.0140.0000.0000.0000.000
33A34HIS0-0.011-0.00322.9960.0070.0070.0000.0000.0000.000
34A35PRO00.0820.03922.709-0.006-0.0060.0000.0000.0000.000
35A36ASP-1-0.864-0.90925.3970.0880.0880.0000.0000.0000.000
36A37VAL0-0.052-0.01827.879-0.005-0.0050.0000.0000.0000.000
37A38ASN0-0.050-0.02125.2440.0040.0040.0000.0000.0000.000
38A39LYS10.8510.91626.461-0.108-0.1080.0000.0000.0000.000
39A40SER0-0.009-0.00624.349-0.004-0.0040.0000.0000.0000.000
40A41PRO00.001-0.00222.7010.0030.0030.0000.0000.0000.000
41A42GLU-1-0.827-0.91619.5100.2820.2820.0000.0000.0000.000
42A43ALA0-0.083-0.04919.1450.0230.0230.0000.0000.0000.000
43A44GLU-1-0.872-0.91918.4890.2040.2040.0000.0000.0000.000
44A45GLU-1-0.873-0.95014.6530.4480.4480.0000.0000.0000.000
45A46LYS10.8890.94815.037-0.463-0.4630.0000.0000.0000.000
46A47PHE00.0410.01516.851-0.023-0.0230.0000.0000.0000.000
47A48LYS10.8350.92412.273-0.451-0.4510.0000.0000.0000.000
48A49GLU-1-0.836-0.90510.4320.8440.8440.0000.0000.0000.000
49A50ILE0-0.045-0.02413.364-0.066-0.0660.0000.0000.0000.000
50A51ASN0-0.015-0.02316.324-0.075-0.0750.0000.0000.0000.000
51A52GLU-1-0.700-0.7848.0830.4750.4750.0000.0000.0000.000
52A53ALA00.0210.00512.868-0.073-0.0730.0000.0000.0000.000
53A54TYR0-0.021-0.02113.670-0.063-0.0630.0000.0000.0000.000
54A55ALA00.0100.02414.417-0.029-0.0290.0000.0000.0000.000
55A56VAL0-0.0200.00011.140-0.044-0.0440.0000.0000.0000.000
56A57MET0-0.041-0.02614.605-0.028-0.0280.0000.0000.0000.000
57A58SER0-0.052-0.03516.978-0.006-0.0060.0000.0000.0000.000
58A59ASP-1-0.808-0.89418.720-0.154-0.1540.0000.0000.0000.000
59A60PRO0-0.005-0.02118.916-0.019-0.0190.0000.0000.0000.000
60A61GLU-1-0.787-0.84419.769-0.245-0.2450.0000.0000.0000.000
61A62LYS10.8430.93015.1050.1270.1270.0000.0000.0000.000
62A63ARG10.8420.91314.6930.0490.0490.0000.0000.0000.000
63A64ARG10.8140.87615.7270.2490.2490.0000.0000.0000.000
64A65ILE0-0.0010.00912.659-0.026-0.0260.0000.0000.0000.000
65A66TYR00.007-0.0199.154-0.065-0.0650.0000.0000.0000.000
66A67ASP-1-0.821-0.88711.951-0.258-0.2580.0000.0000.0000.000
67A68THR0-0.110-0.07814.516-0.007-0.0070.0000.0000.0000.000
68A69TYR0-0.028-0.0244.8610.4610.4610.0000.0000.0000.000
69A70GLY00.0190.0169.5560.0030.0030.0000.0000.0000.000
70A71THR0-0.043-0.02710.3390.0600.0600.0000.0000.0000.000
71A72THR0-0.042-0.01513.0090.0820.0820.0000.0000.0000.000
72A73GLU-1-0.932-0.9689.472-0.818-0.8180.0000.0000.0000.000
73A74ALA00.0190.0198.656-0.241-0.2410.0000.0000.0000.000
74A75PRO00.0100.0137.9530.1040.1040.0000.0000.0000.000
75A76PRO0-0.028-0.01010.1260.1150.1150.0000.0000.0000.000
76A77PRO0-0.008-0.02213.876-0.006-0.0060.0000.0000.0000.000
77A78PRO0-0.0050.02316.5820.0030.0030.0000.0000.0000.000
78A79PRO00.0070.01017.7900.0250.0250.0000.0000.0000.000
79A80PRO0-0.027-0.04421.1180.0010.0010.0000.0000.0000.000
80A81GLY0-0.0050.00323.3570.0150.0150.0000.0000.0000.000
81A82GLY0-0.017-0.00119.1760.0060.0060.0000.0000.0000.000
82A83TYR0-0.025-0.01914.2980.0340.0340.0000.0000.0000.000
83A84ASP-1-0.836-0.88818.114-0.095-0.0950.0000.0000.0000.000
84A85PHE00.009-0.01613.549-0.005-0.0050.0000.0000.0000.000
85A86SER0-0.046-0.05218.7310.0250.0250.0000.0000.0000.000
86A87GLY0-0.055-0.02422.1230.0020.0020.0000.0000.0000.000
87A88PHE0-0.017-0.01016.8190.0170.0170.0000.0000.0000.000
88A89ASP-1-0.877-0.92217.3230.0380.0380.0000.0000.0000.000
89A90VAL0-0.046-0.04013.6220.0240.0240.0000.0000.0000.000
90A91GLU-1-0.937-0.96312.687-0.080-0.0800.0000.0000.0000.000
91A92ASP-1-0.828-0.90012.6580.3050.3050.0000.0000.0000.000
92A93PHE0-0.038-0.0159.8710.1200.1200.0000.0000.0000.000
93A94SER0-0.005-0.0375.7880.0250.0250.0000.0000.0000.000
94A95GLU-1-0.893-0.9543.1350.4000.8780.069-0.152-0.3950.000
95A96PHE00.0110.0152.196-3.570-1.5291.285-1.480-1.846-0.004
96A97PHE00.0170.0122.9200.6780.1230.1540.630-0.2280.000
97A98GLN0-0.021-0.0416.422-0.152-0.1520.0000.0000.0000.000
98A99GLU-1-0.917-0.9292.653-9.374-6.1940.751-2.052-1.879-0.024
99A100LEU0-0.047-0.0146.3240.3180.3180.0000.0000.0000.000
100A101PHE0-0.001-0.0228.1920.2000.2000.0000.0000.0000.000
101A102GLY00.0730.0449.8350.1240.1240.0000.0000.0000.000
102A103PRO0-0.046-0.03510.8350.1160.1160.0000.0000.0000.000
103A104GLY0-0.039-0.02114.0660.0640.0640.0000.0000.0000.000
104A105LEU0-0.0260.00511.5280.0510.0510.0000.0000.0000.000
105A106PHE0-0.0150.00015.5650.0090.0090.0000.0000.0000.000
106A107GLY00.0840.03918.8890.0150.0150.0000.0000.0000.000
107A108LYS10.8360.92320.5170.0610.0610.0000.0000.0000.000
108A109GLY00.0330.03424.123-0.003-0.0030.0000.0000.0000.000
109A110ARG10.9080.94626.1430.0990.0990.0000.0000.0000.000
110A111ASP-1-0.769-0.88429.293-0.057-0.0570.0000.0000.0000.000
111A112LEU0-0.060-0.02932.078-0.003-0.0030.0000.0000.0000.000
112A113ARG10.9360.97135.2490.0430.0430.0000.0000.0000.000
113A114ALA00.0020.01038.992-0.003-0.0030.0000.0000.0000.000
114A115GLU-1-0.814-0.88141.681-0.034-0.0340.0000.0000.0000.000
115A116LEU0-0.022-0.01445.463-0.002-0.0020.0000.0000.0000.000
116A117PRO0-0.001-0.00947.4550.0020.0020.0000.0000.0000.000
117A118LEU0-0.0190.00950.984-0.001-0.0010.0000.0000.0000.000
118A119THR0-0.013-0.04153.7610.0000.0000.0000.0000.0000.000
119A120LEU00.021-0.00257.2370.0000.0000.0000.0000.0000.000
120A121GLU-1-0.746-0.84659.512-0.022-0.0220.0000.0000.0000.000
121A122GLU-1-0.795-0.87354.663-0.030-0.0300.0000.0000.0000.000
122A123ALA00.0010.00054.7860.0000.0000.0000.0000.0000.000
123A124PHE0-0.074-0.03155.8140.0010.0010.0000.0000.0000.000
124A125HIS00.004-0.01358.2330.0010.0010.0000.0000.0000.000
125A126GLY0-0.043-0.00153.7440.0010.0010.0000.0000.0000.000
126A127GLY00.0090.00352.816-0.001-0.0010.0000.0000.0000.000
127A128GLU-1-0.839-0.92047.194-0.030-0.0300.0000.0000.0000.000
128A129ARG10.8310.89147.8750.0320.0320.0000.0000.0000.000
129A130VAL0-0.009-0.00344.494-0.001-0.0010.0000.0000.0000.000
130A131VAL0-0.021-0.01843.1610.0010.0010.0000.0000.0000.000
131A132GLU-1-0.854-0.93141.689-0.057-0.0570.0000.0000.0000.000
132A133VAL00.0100.00939.4380.0010.0010.0000.0000.0000.000
133A134ALA00.012-0.01038.288-0.003-0.0030.0000.0000.0000.000
134A135GLY00.0250.02335.189-0.003-0.0030.0000.0000.0000.000
135A136ARG10.7810.88633.2270.0720.0720.0000.0000.0000.000
136A137ARG10.9450.97536.8880.0540.0540.0000.0000.0000.000
137A138VAL0-0.007-0.00638.063-0.002-0.0020.0000.0000.0000.000
138A139SER0-0.001-0.00840.4460.0010.0010.0000.0000.0000.000
139A140VAL0-0.030-0.00442.3590.0000.0000.0000.0000.0000.000
140A141ARG10.8750.93244.4390.0260.0260.0000.0000.0000.000
141A142MET0-0.0140.01747.132-0.001-0.0010.0000.0000.0000.000
142A143PRO0-0.011-0.00449.4920.0010.0010.0000.0000.0000.000
143A144PRO00.0300.01752.417-0.001-0.0010.0000.0000.0000.000
144A145GLY0-0.008-0.00756.0930.0010.0010.0000.0000.0000.000
145A146VAL0-0.052-0.01050.4480.0000.0000.0000.0000.0000.000
146A147ARG10.9070.92852.7730.0170.0170.0000.0000.0000.000
147A148GLU-1-0.762-0.87052.026-0.028-0.0280.0000.0000.0000.000
148A149GLY0-0.0020.01248.8710.0010.0010.0000.0000.0000.000
149A150SER0-0.065-0.04848.0530.0010.0010.0000.0000.0000.000
150A151VAL0-0.013-0.01042.177-0.002-0.0020.0000.0000.0000.000
151A152ILE0-0.016-0.00243.6840.0020.0020.0000.0000.0000.000
152A153ARG10.8750.91535.5480.0280.0280.0000.0000.0000.000
153A154VAL00.0140.00737.5880.0020.0020.0000.0000.0000.000
154A155PRO0-0.019-0.01234.557-0.003-0.0030.0000.0000.0000.000
155A156GLY00.0360.01131.152-0.001-0.0010.0000.0000.0000.000
156A157MET0-0.022-0.00631.289-0.007-0.0070.0000.0000.0000.000
157A158GLY0-0.0100.00932.517-0.001-0.0010.0000.0000.0000.000
158A159GLY0-0.0090.00029.457-0.004-0.0040.0000.0000.0000.000
159A160GLN00.018-0.00624.9370.0000.0000.0000.0000.0000.000
160A161GLY00.0300.00822.438-0.002-0.0020.0000.0000.0000.000
161A162ASN0-0.0310.02218.2280.0210.0210.0000.0000.0000.000
162A163PRO00.0530.01721.8580.0050.0050.0000.0000.0000.000
163A164PRO00.0360.00824.621-0.005-0.0050.0000.0000.0000.000
164A165GLY0-0.021-0.00427.0330.0090.0090.0000.0000.0000.000
165A166ASP-1-0.823-0.90030.068-0.043-0.0430.0000.0000.0000.000
166A167LEU0-0.015-0.02033.778-0.004-0.0040.0000.0000.0000.000
167A168LEU0-0.038-0.02136.7150.0050.0050.0000.0000.0000.000
168A169LEU00.0380.01839.529-0.001-0.0010.0000.0000.0000.000
169A170VAL0-0.037-0.02342.5710.0030.0030.0000.0000.0000.000
170A171VAL00.0230.01045.511-0.001-0.0010.0000.0000.0000.000
171A172ARG10.7520.84347.8160.0320.0320.0000.0000.0000.000
172A173MET0-0.036-0.01051.5740.0000.0000.0000.0000.0000.000
173A174LEU0-0.005-0.00454.1290.0000.0000.0000.0000.0000.000
174A175PRO0-0.026-0.00657.2000.0010.0010.0000.0000.0000.000
175A176HIS00.002-0.03160.7910.0000.0000.0000.0000.0000.000
176A177PRO0-0.019-0.00963.4650.0010.0010.0000.0000.0000.000
177A178VAL0-0.032-0.01066.8870.0010.0010.0000.0000.0000.000
178A179PHE0-0.028-0.00665.2660.0010.0010.0000.0000.0000.000
179A180ARG10.8370.89264.6580.0150.0150.0000.0000.0000.000
180A181LEU0-0.023-0.01059.0290.0010.0010.0000.0000.0000.000
181A182GLU-1-0.809-0.87762.710-0.014-0.0140.0000.0000.0000.000
182A183GLY00.0240.01260.5660.0010.0010.0000.0000.0000.000
183A184GLN0-0.052-0.04159.809-0.001-0.0010.0000.0000.0000.000
184A185ASP-1-0.767-0.84661.948-0.012-0.0120.0000.0000.0000.000
185A186LEU0-0.022-0.01463.279-0.001-0.0010.0000.0000.0000.000
186A187TYR0-0.033-0.01966.6390.0010.0010.0000.0000.0000.000
187A188ALA00.0630.03168.805-0.001-0.0010.0000.0000.0000.000
188A189THR00.0030.00871.4840.0010.0010.0000.0000.0000.000
189A190LEU0-0.007-0.00874.8350.0000.0000.0000.0000.0000.000
190A191ASP-1-0.779-0.85677.616-0.014-0.0140.0000.0000.0000.000
191A192VAL0-0.0030.00080.3360.0000.0000.0000.0000.0000.000
192A193PRO00.0160.00383.5940.0000.0000.0000.0000.0000.000
193A194ALA00.0470.02586.7530.0000.0000.0000.0000.0000.000
194A195PRO00.0180.00389.3670.0000.0000.0000.0000.0000.000
195A196ILE00.0160.00486.8250.0000.0000.0000.0000.0000.000
196A197ALA00.0260.02887.0250.0000.0000.0000.0000.0000.000
197A198VAL0-0.042-0.01988.6080.0000.0000.0000.0000.0000.000
198A199VAL0-0.031-0.02692.3510.0000.0000.0000.0000.0000.000
199A200GLY00.0060.01489.4420.0000.0000.0000.0000.0000.000
200A201GLY0-0.001-0.01088.2270.0000.0000.0000.0000.0000.000
201A202LYS10.7950.89083.5390.0100.0100.0000.0000.0000.000
202A203VAL00.0150.01480.8510.0000.0000.0000.0000.0000.000
203A204ARG10.8400.91176.5180.0130.0130.0000.0000.0000.000
204A205ALA00.0430.02675.5870.0000.0000.0000.0000.0000.000
205A206MET0-0.024-0.02069.8390.0000.0000.0000.0000.0000.000
206A207THR0-0.004-0.00268.7050.0000.0000.0000.0000.0000.000
207A208LEU00.0240.00462.2110.0000.0000.0000.0000.0000.000
208A209GLU-1-0.745-0.85464.802-0.016-0.0160.0000.0000.0000.000
209A210GLY00.0150.01166.8750.0000.0000.0000.0000.0000.000
210A211PRO0-0.018-0.00169.7840.0000.0000.0000.0000.0000.000
211A212VAL00.0530.02872.8410.0000.0000.0000.0000.0000.000
212A213GLU-1-0.852-0.92175.589-0.011-0.0110.0000.0000.0000.000
213A214VAL00.0070.00577.6810.0000.0000.0000.0000.0000.000
214A215ALA00.0160.00980.3130.0000.0000.0000.0000.0000.000
215A216VAL0-0.004-0.00582.8330.0000.0000.0000.0000.0000.000
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