FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 76JGK

Calculation Name: 3DCF-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3DCF

Chain ID: A

ChEMBL ID:
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UniProt ID: Q47L40

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1990352.862538
FMO2-HF: Nuclear repulsion 1915299.159025
FMO2-HF: Total energy -75053.703513
FMO2-MP2: Total energy -75277.113602


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:29:ASN)


Summations of interaction energy for fragment #1(A:29:ASN)
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.
-9.654-5.5313.168-3.226-4.0650.011
Interaction energy analysis for fragmet #1(A:29:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : -0.017
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].
3A31ARG10.9250.9643.8780.7331.658-0.008-0.347-0.5700.001
4A32ARG10.9831.0042.036-11.373-9.6353.013-2.431-2.3200.011
5A33THR00.0720.0362.7022.9474.2440.165-0.432-1.031-0.001
6A34GLN00.0080.0114.633-0.399-0.313-0.001-0.010-0.0740.000
7A35ILE0-0.039-0.0266.7830.0160.0160.0000.0000.0000.000
8A36ILE00.0050.0005.212-0.015-0.0150.0000.0000.0000.000
9A37LYS10.8850.9698.590-0.760-0.7600.0000.0000.0000.000
10A38VAL0-0.016-0.01310.645-0.170-0.1700.0000.0000.0000.000
11A39ALA0-0.001-0.00411.726-0.119-0.1190.0000.0000.0000.000
12A40THR0-0.002-0.01012.065-0.089-0.0890.0000.0000.0000.000
13A41GLU-1-0.880-0.94614.5590.2910.2910.0000.0000.0000.000
14A42LEU0-0.020-0.00916.232-0.073-0.0730.0000.0000.0000.000
15A43PHE0-0.017-0.03314.824-0.048-0.0480.0000.0000.0000.000
16A44ARG10.9260.95618.859-0.398-0.3980.0000.0000.0000.000
17A45GLU-1-0.989-0.97020.7880.2350.2350.0000.0000.0000.000
18A46LYS10.8890.96821.914-0.376-0.3760.0000.0000.0000.000
19A47GLY00.1030.06222.276-0.028-0.0280.0000.0000.0000.000
20A48TYR0-0.018-0.00817.7260.0280.0280.0000.0000.0000.000
21A49TYR00.0300.00021.5660.0250.0250.0000.0000.0000.000
22A50ALA00.0130.02524.383-0.015-0.0150.0000.0000.0000.000
23A51THR0-0.026-0.01118.269-0.024-0.0240.0000.0000.0000.000
24A52SER0-0.005-0.00920.2200.0350.0350.0000.0000.0000.000
25A53LEU0-0.004-0.02913.9190.0170.0170.0000.0000.0000.000
26A54ASP-1-0.894-0.95316.7600.3990.3990.0000.0000.0000.000
27A55ASP-1-0.806-0.89719.2490.3500.3500.0000.0000.0000.000
28A56ILE00.006-0.00412.590-0.018-0.0180.0000.0000.0000.000
29A57ALA0-0.017-0.02114.623-0.008-0.0080.0000.0000.0000.000
30A58ASP-1-0.847-0.87915.6350.1980.1980.0000.0000.0000.000
31A59ARG10.8060.88716.090-0.368-0.3680.0000.0000.0000.000
32A60ILE0-0.063-0.02810.676-0.043-0.0430.0000.0000.0000.000
33A61GLY00.0100.02514.262-0.074-0.0740.0000.0000.0000.000
34A62PHE0-0.043-0.0439.637-0.039-0.0390.0000.0000.0000.000
35A63THR00.0600.02914.8050.0260.0260.0000.0000.0000.000
36A64LYS10.9810.97015.431-0.416-0.4160.0000.0000.0000.000
37A65PRO0-0.020-0.03616.0090.0570.0570.0000.0000.0000.000
38A66ALA00.0030.01912.2390.0350.0350.0000.0000.0000.000
39A67ILE00.0310.02211.1050.0620.0620.0000.0000.0000.000
40A68TYR00.0460.04211.5500.1790.1790.0000.0000.0000.000
41A69TYR0-0.0480.0026.6100.0690.0690.0000.0000.0000.000
42A70TYR0-0.019-0.0044.3540.0250.102-0.001-0.006-0.0700.000
43A71PHE0-0.010-0.0256.9370.3370.3370.0000.0000.0000.000
44A72LYS10.9120.93111.713-0.913-0.9130.0000.0000.0000.000
45A73SER00.0130.00415.031-0.114-0.1140.0000.0000.0000.000
46A74LYS10.8710.92214.943-0.390-0.3900.0000.0000.0000.000
47A75GLU-1-0.813-0.90715.8920.7230.7230.0000.0000.0000.000
48A76ASP-1-0.896-0.95012.6871.1001.1000.0000.0000.0000.000
49A77VAL0-0.044-0.01810.9770.3140.3140.0000.0000.0000.000
50A78LEU00.0410.01811.5900.2470.2470.0000.0000.0000.000
51A79PHE0-0.001-0.00410.6900.0500.0500.0000.0000.0000.000
52A80ALA0-0.032-0.0167.5210.1090.1090.0000.0000.0000.000
53A81ILE00.0010.0018.6550.3880.3880.0000.0000.0000.000
54A82VAL00.0300.01610.833-0.092-0.0920.0000.0000.0000.000
55A83ASN0-0.029-0.0309.076-0.343-0.3430.0000.0000.0000.000
56A84SER0-0.0090.0117.402-0.165-0.1650.0000.0000.0000.000
57A85ILE00.0330.0218.905-0.327-0.3270.0000.0000.0000.000
58A86VAL0-0.050-0.02912.566-0.200-0.2000.0000.0000.0000.000
59A87ASP-1-0.915-0.9657.7370.0420.0420.0000.0000.0000.000
60A88GLU-1-0.884-0.95110.2850.1850.1850.0000.0000.0000.000
61A89ALA0-0.073-0.04112.355-0.144-0.1440.0000.0000.0000.000
62A90LEU0-0.0060.00013.668-0.077-0.0770.0000.0000.0000.000
63A91GLU-1-0.929-0.9669.958-0.515-0.5150.0000.0000.0000.000
64A92ARG10.8640.93814.654-0.278-0.2780.0000.0000.0000.000
65A93PHE0-0.0170.00217.713-0.015-0.0150.0000.0000.0000.000
66A94HIS00.006-0.01216.085-0.034-0.0340.0000.0000.0000.000
67A95ALA0-0.0200.00418.336-0.015-0.0150.0000.0000.0000.000
68A96ILE0-0.026-0.00619.996-0.006-0.0060.0000.0000.0000.000
69A97ALA00.007-0.00122.593-0.001-0.0010.0000.0000.0000.000
70A98ALA0-0.050-0.02321.5800.0000.0000.0000.0000.0000.000
71A99GLY00.0080.01823.579-0.021-0.0210.0000.0000.0000.000
72A100PRO0-0.048-0.03925.4230.0070.0070.0000.0000.0000.000
73A101GLY00.0320.02529.0610.0070.0070.0000.0000.0000.000
74A102SER0-0.017-0.02431.703-0.008-0.0080.0000.0000.0000.000
75A103PRO00.020-0.00831.2000.0020.0020.0000.0000.0000.000
76A104GLY00.0490.02631.6080.0070.0070.0000.0000.0000.000
77A105GLU-1-0.925-0.94632.701-0.029-0.0290.0000.0000.0000.000
78A106ARG10.8490.93227.3310.0770.0770.0000.0000.0000.000
79A107ILE0-0.0030.00428.0910.0110.0110.0000.0000.0000.000
80A108HIS00.0280.01029.3540.0150.0150.0000.0000.0000.000
81A109ALA0-0.013-0.01327.1750.0120.0120.0000.0000.0000.000
82A110LEU0-0.012-0.00923.2920.0130.0130.0000.0000.0000.000
83A111LEU00.0330.02025.3110.0250.0250.0000.0000.0000.000
84A112VAL00.0040.02227.7320.0210.0210.0000.0000.0000.000
85A113GLU-1-0.903-0.95120.9000.1300.1300.0000.0000.0000.000
86A114HIS00.0410.02922.3500.0260.0260.0000.0000.0000.000
87A115THR00.000-0.02523.8050.0320.0320.0000.0000.0000.000
88A116ARG10.8910.94224.087-0.056-0.0560.0000.0000.0000.000
89A117THR0-0.019-0.01818.7570.0260.0260.0000.0000.0000.000
90A118ILE0-0.0230.00221.1900.0540.0540.0000.0000.0000.000
91A119LEU0-0.008-0.01423.4840.0230.0230.0000.0000.0000.000
92A120ARG10.9060.96720.964-0.176-0.1760.0000.0000.0000.000
93A121ASN0-0.071-0.04117.4480.1010.1010.0000.0000.0000.000
94A122LEU00.0620.03920.5360.0210.0210.0000.0000.0000.000
95A123ASP-1-0.863-0.93321.2940.3900.3900.0000.0000.0000.000
96A124ALA0-0.040-0.02617.5140.0240.0240.0000.0000.0000.000
97A125ASN00.011-0.00419.3800.0040.0040.0000.0000.0000.000
98A126THR00.0160.01322.041-0.024-0.0240.0000.0000.0000.000
99A127LEU0-0.040-0.01517.940-0.004-0.0040.0000.0000.0000.000
100A128PHE0-0.060-0.03017.0350.0250.0250.0000.0000.0000.000
101A129TYR0-0.008-0.00620.818-0.011-0.0110.0000.0000.0000.000
102A130ASN00.0080.02724.558-0.031-0.0310.0000.0000.0000.000
103A131GLU-1-0.871-0.95125.1010.3160.3160.0000.0000.0000.000
104A132ARG10.7080.84519.792-0.488-0.4880.0000.0000.0000.000
105A133GLY00.0130.02223.990-0.008-0.0080.0000.0000.0000.000
106A134LEU0-0.067-0.05423.469-0.021-0.0210.0000.0000.0000.000
107A135LEU00.0020.02420.7270.0220.0220.0000.0000.0000.000
108A136SER0-0.019-0.01518.138-0.024-0.0240.0000.0000.0000.000
109A137PRO00.0710.01619.6250.0260.0260.0000.0000.0000.000
110A138GLU-1-0.862-0.94416.5350.2910.2910.0000.0000.0000.000
111A139ARG10.8560.94213.363-1.049-1.0490.0000.0000.0000.000
112A140GLU-1-0.753-0.87816.3280.4660.4660.0000.0000.0000.000
113A141ARG10.8750.93418.448-0.240-0.2400.0000.0000.0000.000
114A142GLU-1-0.879-0.93612.1670.3140.3140.0000.0000.0000.000
115A143MET0-0.0010.00613.357-0.020-0.0200.0000.0000.0000.000
116A144ARG10.8340.91917.269-0.387-0.3870.0000.0000.0000.000
117A145LYS10.8520.93513.855-0.189-0.1890.0000.0000.0000.000
118A146ARG10.9080.96410.619-0.315-0.3150.0000.0000.0000.000
119A147GLU-1-0.799-0.90216.9100.2320.2320.0000.0000.0000.000
120A148ARG10.9310.96120.542-0.164-0.1640.0000.0000.0000.000
121A149GLU-1-0.855-0.92715.700-0.011-0.0110.0000.0000.0000.000
122A150TYR00.0120.00717.538-0.037-0.0370.0000.0000.0000.000
123A151THR0-0.025-0.01421.338-0.018-0.0180.0000.0000.0000.000
124A152GLU-1-0.945-0.98523.1290.0090.0090.0000.0000.0000.000
125A153ILE0-0.055-0.01719.389-0.017-0.0170.0000.0000.0000.000
126A154MET00.0110.01324.007-0.007-0.0070.0000.0000.0000.000
127A155GLN00.004-0.00626.8740.0060.0060.0000.0000.0000.000
128A156ARG10.9200.95622.6220.0480.0480.0000.0000.0000.000
129A157LEU00.0490.02926.755-0.004-0.0040.0000.0000.0000.000
130A158TYR0-0.003-0.02429.8610.0010.0010.0000.0000.0000.000
131A159ALA0-0.005-0.01132.5350.0000.0000.0000.0000.0000.000
132A160GLU-1-0.952-0.97430.335-0.058-0.0580.0000.0000.0000.000
133A161GLY00.0470.00734.306-0.002-0.0020.0000.0000.0000.000
134A162VAL0-0.0260.00936.0910.0010.0010.0000.0000.0000.000
135A163ALA0-0.035-0.01637.9320.0000.0000.0000.0000.0000.000
136A164THR0-0.078-0.04137.927-0.001-0.0010.0000.0000.0000.000
137A165GLY0-0.024-0.00440.636-0.001-0.0010.0000.0000.0000.000
138A166GLU-1-0.855-0.91136.645-0.019-0.0190.0000.0000.0000.000
139A167LEU0-0.063-0.02534.3830.0040.0040.0000.0000.0000.000
140A168LEU0-0.007-0.00439.009-0.001-0.0010.0000.0000.0000.000
141A169ASP-1-0.896-0.94639.5800.0090.0090.0000.0000.0000.000
142A170VAL0-0.050-0.01937.6230.0030.0030.0000.0000.0000.000
143A171ASP-1-0.827-0.93035.8140.0330.0330.0000.0000.0000.000
144A172PRO00.0410.00732.8470.0060.0060.0000.0000.0000.000
145A173THR0-0.0030.02330.9150.0050.0050.0000.0000.0000.000
146A174VAL0-0.022-0.00832.3250.0110.0110.0000.0000.0000.000
147A175ALA00.0070.02634.2940.0080.0080.0000.0000.0000.000
148A176THR0-0.004-0.02427.8450.0050.0050.0000.0000.0000.000
149A177ALA00.0240.00629.6420.0110.0110.0000.0000.0000.000
150A178THR0-0.046-0.02430.6880.0130.0130.0000.0000.0000.000
151A179LEU0-0.028-0.01831.1970.0060.0060.0000.0000.0000.000
152A180LEU00.0220.00725.2300.0070.0070.0000.0000.0000.000
153A181GLY00.0200.01528.5260.0170.0170.0000.0000.0000.000
154A182ALA0-0.037-0.02330.4580.0100.0100.0000.0000.0000.000
155A183ALA0-0.0010.01127.8530.0030.0030.0000.0000.0000.000
156A184ILE0-0.0060.00625.2060.0130.0130.0000.0000.0000.000
157A185TRP00.020-0.00227.6400.0180.0180.0000.0000.0000.000
158A186THR0-0.008-0.02428.5950.0070.0070.0000.0000.0000.000
159A187TYR0-0.017-0.00926.320-0.004-0.0040.0000.0000.0000.000
160A188ARG10.9000.96028.215-0.172-0.1720.0000.0000.0000.000
161A189TRP0-0.066-0.02331.389-0.007-0.0070.0000.0000.0000.000
162A190TYR0-0.023-0.01528.874-0.006-0.0060.0000.0000.0000.000
163A191ASP-1-0.873-0.93031.3100.1670.1670.0000.0000.0000.000
164A192PRO0-0.037-0.03728.908-0.010-0.0100.0000.0000.0000.000
165A193GLU-1-0.974-0.96831.3580.1560.1560.0000.0000.0000.000
166A194GLY0-0.0110.00634.436-0.011-0.0110.0000.0000.0000.000
167A195ARG10.8860.92536.514-0.091-0.0910.0000.0000.0000.000
168A196LEU0-0.042-0.00636.536-0.004-0.0040.0000.0000.0000.000
169A197SER00.029-0.00332.8750.0090.0090.0000.0000.0000.000
170A198ALA00.019-0.01328.390-0.001-0.0010.0000.0000.0000.000
171A199ASP-1-0.910-0.96130.0020.0860.0860.0000.0000.0000.000
172A200GLU-1-0.857-0.91531.7660.0700.0700.0000.0000.0000.000
173A201VAL0-0.008-0.00132.134-0.005-0.0050.0000.0000.0000.000
174A202VAL00.0100.00528.573-0.001-0.0010.0000.0000.0000.000
175A203GLU-1-0.860-0.91631.5180.0400.0400.0000.0000.0000.000
176A204GLN00.004-0.00534.466-0.003-0.0030.0000.0000.0000.000
177A205ILE0-0.0060.00932.000-0.004-0.0040.0000.0000.0000.000
178A206THR0-0.021-0.03030.999-0.007-0.0070.0000.0000.0000.000
179A207ARG10.8890.95134.104-0.050-0.0500.0000.0000.0000.000
180A208LEU0-0.057-0.03337.739-0.005-0.0050.0000.0000.0000.000
181A209LEU0-0.040-0.03533.055-0.004-0.0040.0000.0000.0000.000
182A210LEU0-0.0250.01836.339-0.003-0.0030.0000.0000.0000.000
183A211ASN0-0.044-0.01937.824-0.009-0.0090.0000.0000.0000.000
184A212GLY00.0200.02940.715-0.002-0.0020.0000.0000.0000.000
185A213TYR00.002-0.01942.3180.0000.0000.0000.0000.0000.000
186A214ARG10.9000.96344.486-0.028-0.0280.0000.0000.0000.000
187A215ARG10.9890.98247.275-0.027-0.0270.0000.0000.0000.000
188A216PRO00.0300.01947.4100.0000.0000.0000.0000.0000.000
189A217ALA0-0.0010.00950.020-0.001-0.0010.0000.0000.0000.000