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: K36R3

Calculation Name: 4NU2-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: 4NU2

Chain ID: A

ChEMBL ID:
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UniProt ID: H7FWB6

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2323892.775296
FMO2-HF: Nuclear repulsion 2245395.847895
FMO2-HF: Total energy -78496.927401
FMO2-MP2: Total energy -78724.037227


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:61:THR)


Summations of interaction energy for fragment #1(A:61:THR)
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.
-4.605-0.8021.089-1.847-3.043-0.003
Interaction energy analysis for fragmet #1(A:61:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.003
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].
3A63ASP-1-0.863-0.9312.602-7.230-4.3651.073-1.680-2.257-0.003
4A64LEU00.019-0.0104.7080.7810.841-0.001-0.002-0.0570.000
5A65VAL0-0.0230.0006.9330.0450.0450.0000.0000.0000.000
6A66ASN0-0.026-0.01210.3990.1680.1680.0000.0000.0000.000
7A67LEU00.0430.01412.6730.0660.0660.0000.0000.0000.000
8A68GLY00.0210.01715.9850.0750.0750.0000.0000.0000.000
9A69VAL0-0.039-0.04418.0710.0140.0140.0000.0000.0000.000
10A70ALA00.0330.01619.5040.0340.0340.0000.0000.0000.000
11A71ALA0-0.030-0.01016.8720.0190.0190.0000.0000.0000.000
12A72ASN0-0.070-0.03518.6680.0180.0180.0000.0000.0000.000
13A73PHE0-0.0210.01121.7430.0340.0340.0000.0000.0000.000
14A74ALA00.003-0.00621.815-0.027-0.0270.0000.0000.0000.000
15A75ILE0-0.003-0.00623.463-0.002-0.0020.0000.0000.0000.000
16A76LEU00.0030.00723.3460.0060.0060.0000.0000.0000.000
17A77SER0-0.043-0.03425.503-0.008-0.0080.0000.0000.0000.000
18A78LYS10.9700.99327.1960.2410.2410.0000.0000.0000.000
19A79THR0-0.047-0.03730.1720.0060.0060.0000.0000.0000.000
20A80GLY00.0160.01432.0010.0110.0110.0000.0000.0000.000
21A81ILE0-0.029-0.00829.947-0.008-0.0080.0000.0000.0000.000
22A82THR00.0090.01933.0350.0090.0090.0000.0000.0000.000
23A83ASP-1-0.748-0.84233.877-0.102-0.1020.0000.0000.0000.000
24A84VAL0-0.0520.01535.9020.0050.0050.0000.0000.0000.000
25A85TYR0-0.041-0.03136.9710.0000.0000.0000.0000.0000.000
26A86LYS10.8830.94536.7350.0850.0850.0000.0000.0000.000
27A87SER00.024-0.02532.1280.0050.0050.0000.0000.0000.000
28A88ALA0-0.043-0.03031.4830.0020.0020.0000.0000.0000.000
29A89ILE00.0080.00427.506-0.004-0.0040.0000.0000.0000.000
30A90THR0-0.027-0.00926.1540.0070.0070.0000.0000.0000.000
31A91GLY00.0310.00425.305-0.018-0.0180.0000.0000.0000.000
32A92ASP-1-0.843-0.91225.964-0.212-0.2120.0000.0000.0000.000
33A93VAL0-0.008-0.01026.474-0.013-0.0130.0000.0000.0000.000
34A94GLY00.0230.00228.4620.0080.0080.0000.0000.0000.000
35A95ALA0-0.016-0.00129.028-0.007-0.0070.0000.0000.0000.000
36A96SER00.0310.02130.3120.0080.0080.0000.0000.0000.000
37A97PRO0-0.002-0.00730.393-0.012-0.0120.0000.0000.0000.000
38A98ILE0-0.029-0.00433.7150.0100.0100.0000.0000.0000.000
39A99THR00.002-0.00135.726-0.003-0.0030.0000.0000.0000.000
40A100GLY00.0630.02736.539-0.001-0.0010.0000.0000.0000.000
41A101ALA0-0.049-0.02837.6030.0020.0020.0000.0000.0000.000
42A102ALA0-0.028-0.01536.3880.0050.0050.0000.0000.0000.000
43A103ILE0-0.044-0.01632.949-0.003-0.0030.0000.0000.0000.000
44A104LEU0-0.038-0.02436.0450.0050.0050.0000.0000.0000.000
45A105LEU00.0230.02532.0480.0040.0040.0000.0000.0000.000
46A106LYS10.9340.95236.7230.0840.0840.0000.0000.0000.000
47A107CYS0-0.028-0.02837.027-0.004-0.0040.0000.0000.0000.000
48A108ASP-1-0.822-0.89836.946-0.086-0.0860.0000.0000.0000.000
49A109GLH0-0.080-0.07134.4810.0030.0030.0000.0000.0000.000
50A110VAL0-0.0100.00530.830-0.004-0.0040.0000.0000.0000.000
51A111THR0-0.046-0.00630.3510.0080.0080.0000.0000.0000.000
52A112GLY00.0430.00829.645-0.011-0.0110.0000.0000.0000.000
53A113THR0-0.028-0.00330.0100.0170.0170.0000.0000.0000.000
54A114ILE00.0080.00130.626-0.011-0.0110.0000.0000.0000.000
55A115PHE00.017-0.00529.0590.0050.0050.0000.0000.0000.000
56A116SER0-0.0040.00432.826-0.003-0.0030.0000.0000.0000.000
57A117VAL00.0230.00133.714-0.005-0.0050.0000.0000.0000.000
58A118ASP-1-0.777-0.89735.891-0.128-0.1280.0000.0000.0000.000
59A119ALA00.0140.00739.578-0.001-0.0010.0000.0000.0000.000
60A120ALA0-0.015-0.00541.1610.0050.0050.0000.0000.0000.000
61A121GLY00.0220.00939.287-0.008-0.0080.0000.0000.0000.000
62A122PRO00.0040.00937.1810.0070.0070.0000.0000.0000.000
63A123ALA00.010-0.00640.292-0.003-0.0030.0000.0000.0000.000
64A125LYS10.8720.96236.6970.1150.1150.0000.0000.0000.000
65A126ILE00.0190.01634.5060.0040.0040.0000.0000.0000.000
66A127THR0-0.077-0.05335.473-0.004-0.0040.0000.0000.0000.000
67A128ASP-1-0.864-0.95732.591-0.204-0.2040.0000.0000.0000.000
68A129ALA00.0480.03032.549-0.012-0.0120.0000.0000.0000.000
69A130SER0-0.0090.00231.856-0.012-0.0120.0000.0000.0000.000
70A131ARG10.9971.00825.5370.2530.2530.0000.0000.0000.000
71A132LEU00.0040.00227.425-0.022-0.0220.0000.0000.0000.000
72A133THR0-0.036-0.01327.918-0.009-0.0090.0000.0000.0000.000
73A134THR0-0.005-0.00224.043-0.012-0.0120.0000.0000.0000.000
74A135ALA0-0.0150.00023.513-0.029-0.0290.0000.0000.0000.000
75A136VAL0-0.001-0.01023.084-0.027-0.0270.0000.0000.0000.000
76A137GLY0-0.019-0.01324.039-0.011-0.0110.0000.0000.0000.000
77A138ASP-1-0.795-0.89819.632-0.489-0.4890.0000.0000.0000.000
78A139MET0-0.022-0.00319.156-0.049-0.0490.0000.0000.0000.000
79A140GLN0-0.096-0.03919.822-0.003-0.0030.0000.0000.0000.000
80A141ILE00.0560.02517.172-0.021-0.0210.0000.0000.0000.000
81A142ALA00.0040.00615.620-0.067-0.0670.0000.0000.0000.000
82A143TYR0-0.062-0.02815.707-0.054-0.0540.0000.0000.0000.000
83A144ASP-1-0.821-0.91617.535-0.437-0.4370.0000.0000.0000.000
84A145ASN0-0.031-0.01611.871-0.140-0.1400.0000.0000.0000.000
85A146ALA00.008-0.00312.825-0.093-0.0930.0000.0000.0000.000
86A147ALA0-0.0110.00013.898-0.002-0.0020.0000.0000.0000.000
87A148GLY0-0.0260.00215.9680.0520.0520.0000.0000.0000.000
88A149ARG10.7740.9017.1711.9151.9150.0000.0000.0000.000
89A150LEU00.004-0.01211.6590.1600.1600.0000.0000.0000.000
90A151ASN0-0.075-0.0329.738-0.010-0.0100.0000.0000.0000.000
91A152PRO00.007-0.0099.900-0.048-0.0480.0000.0000.0000.000
92A153ASP-1-0.787-0.8827.3130.3200.3200.0000.0000.0000.000
93A154PHE0-0.035-0.02610.4090.0770.0770.0000.0000.0000.000
94A155LEU00.002-0.00713.939-0.103-0.1030.0000.0000.0000.000
95A156ASN0-0.039-0.02017.2480.0210.0210.0000.0000.0000.000
96A157LEU00.0690.04415.7750.0170.0170.0000.0000.0000.000
97A158GLY0-0.033-0.03219.013-0.023-0.0230.0000.0000.0000.000
98A159ALA00.0160.02622.220-0.011-0.0110.0000.0000.0000.000
99A160GLY00.0230.01622.447-0.014-0.0140.0000.0000.0000.000
100A161THR0-0.049-0.02223.732-0.018-0.0180.0000.0000.0000.000
101A162ILE00.001-0.01218.4400.0220.0220.0000.0000.0000.000
102A163GLY00.0140.01021.6610.0140.0140.0000.0000.0000.000
103A164GLY00.0020.00123.5720.0140.0140.0000.0000.0000.000
104A165LYS10.8920.95518.487-0.200-0.2000.0000.0000.0000.000
105A166THR00.0180.00215.484-0.034-0.0340.0000.0000.0000.000
106A167LEU0-0.039-0.00713.2240.0500.0500.0000.0000.0000.000
107A168THR00.0640.03310.100-0.093-0.0930.0000.0000.0000.000
108A169PRO0-0.0290.0055.513-0.307-0.3070.0000.0000.0000.000
109A170GLY00.0700.0415.8090.3990.3990.0000.0000.0000.000
110A171LEU0-0.062-0.0266.803-0.296-0.2960.0000.0000.0000.000
111A172TYR0-0.028-0.0469.2400.1460.1460.0000.0000.0000.000
112A173LYS10.9851.00112.7490.2020.2020.0000.0000.0000.000
113A174TRP00.009-0.00815.8670.0630.0630.0000.0000.0000.000
114A175THR0-0.032-0.02719.644-0.031-0.0310.0000.0000.0000.000
115A176SER00.0060.00522.5400.0030.0030.0000.0000.0000.000
116A177THR0-0.042-0.02023.472-0.020-0.0200.0000.0000.0000.000
117A178LEU00.0000.02818.9940.0160.0160.0000.0000.0000.000
118A179ASN00.005-0.00923.246-0.024-0.0240.0000.0000.0000.000
119A180ILE00.0320.00520.2190.0180.0180.0000.0000.0000.000
120A181PRO0-0.025-0.02524.055-0.008-0.0080.0000.0000.0000.000
121A182THR00.0330.02525.5780.0010.0010.0000.0000.0000.000
122A183ASP-1-0.814-0.91523.7140.0600.0600.0000.0000.0000.000
123A184ILE0-0.0180.00717.7150.0170.0170.0000.0000.0000.000
124A185THR0-0.037-0.02016.353-0.023-0.0230.0000.0000.0000.000
125A186ILE0-0.0050.01011.7090.0320.0320.0000.0000.0000.000
126A187SER0-0.018-0.01612.567-0.054-0.0540.0000.0000.0000.000
127A188GLY00.0440.0039.0080.2030.2030.0000.0000.0000.000
128A189SER00.0180.0085.990-0.505-0.5050.0000.0000.0000.000
129A190SER0-0.013-0.0098.426-0.184-0.1840.0000.0000.0000.000
130A191THR0-0.062-0.0504.981-0.406-0.4060.0000.0000.0000.000
131A192ASP-1-0.816-0.8693.5830.9121.4020.010-0.107-0.3920.000
132A193VAL0-0.022-0.0213.619-0.592-0.2540.008-0.058-0.2880.000
133A194TRP0-0.056-0.0165.1120.4250.475-0.0010.000-0.0490.000
134A195ILE0-0.018-0.0078.166-0.133-0.1330.0000.0000.0000.000
135A196PHE0-0.004-0.00610.3340.1110.1110.0000.0000.0000.000
136A197GLN0-0.008-0.01613.8370.0490.0490.0000.0000.0000.000
137A198VAL0-0.018-0.01916.3010.0660.0660.0000.0000.0000.000
138A199ALA00.002-0.00719.843-0.019-0.0190.0000.0000.0000.000
139A200GLY0-0.0070.01322.6400.0030.0030.0000.0000.0000.000
140A201ASN0-0.025-0.02024.388-0.027-0.0270.0000.0000.0000.000
141A202LEU00.0360.02019.9060.0080.0080.0000.0000.0000.000
142A203ASN0-0.044-0.02823.810-0.013-0.0130.0000.0000.0000.000
143A204MET00.0140.02022.9440.0120.0120.0000.0000.0000.000
144A205SER00.0030.00125.809-0.007-0.0070.0000.0000.0000.000
145A206SER00.007-0.01828.361-0.001-0.0010.0000.0000.0000.000
146A207ALA0-0.044-0.02229.7950.0080.0080.0000.0000.0000.000
147A208VAL0-0.0390.01823.9340.0080.0080.0000.0000.0000.000
148A209ARG10.9620.97723.892-0.018-0.0180.0000.0000.0000.000
149A210ILE0-0.011-0.00417.2270.0220.0220.0000.0000.0000.000
150A211THR0-0.022-0.00518.907-0.029-0.0290.0000.0000.0000.000
151A212LEU0-0.0030.00913.8810.0240.0240.0000.0000.0000.000
152A213ALA00.004-0.00914.689-0.003-0.0030.0000.0000.0000.000
153A214GLY00.026-0.00213.5060.0290.0290.0000.0000.0000.000
154A215GLY00.0120.00612.5320.0430.0430.0000.0000.0000.000
155A216ALA0-0.0020.01810.259-0.127-0.1270.0000.0000.0000.000
156A217GLN0-0.017-0.02510.287-0.003-0.0030.0000.0000.0000.000
157A218ALA00.0870.04511.334-0.085-0.0850.0000.0000.0000.000
158A219LYS10.8760.93611.1070.5610.5610.0000.0000.0000.000
159A220ASN0-0.026-0.0067.282-0.282-0.2820.0000.0000.0000.000
160A221ILE00.0320.0238.314-0.045-0.0450.0000.0000.0000.000
161A222PHE0-0.024-0.0158.7620.0090.0090.0000.0000.0000.000
162A223TRP0-0.003-0.00312.6840.0320.0320.0000.0000.0000.000
163A224GLN00.0270.02015.722-0.021-0.0210.0000.0000.0000.000
164A225THR0-0.017-0.02917.3830.0270.0270.0000.0000.0000.000
165A226ALA00.0180.01220.901-0.010-0.0100.0000.0000.0000.000
166A227GLY00.0250.01823.7060.0100.0100.0000.0000.0000.000
167A228ALA0-0.052-0.01125.019-0.015-0.0150.0000.0000.0000.000
168A229VAL00.0450.01722.3870.0100.0100.0000.0000.0000.000
169A230THR0-0.046-0.02925.4750.0000.0000.0000.0000.0000.000
170A231LEU00.0150.01123.2120.0120.0120.0000.0000.0000.000
171A232GLY00.0290.00827.116-0.001-0.0010.0000.0000.0000.000
172A233SER00.0040.00429.486-0.001-0.0010.0000.0000.0000.000
173A234THR00.017-0.00931.0130.0100.0100.0000.0000.0000.000
174A235SER0-0.070-0.01026.2860.0020.0020.0000.0000.0000.000
175A236HIS0-0.033-0.02121.031-0.009-0.0090.0000.0000.0000.000
176A237PHE00.0400.00018.3350.0220.0220.0000.0000.0000.000
177A238GLU-1-0.751-0.87616.259-0.131-0.1310.0000.0000.0000.000
178A239GLY00.0180.01014.9240.0020.0020.0000.0000.0000.000
179A240ASN0-0.031-0.01113.2920.0740.0740.0000.0000.0000.000
180A241ILE00.0010.00716.109-0.009-0.0090.0000.0000.0000.000
181A242LEU00.002-0.00415.4430.0010.0010.0000.0000.0000.000
182A243SER00.0300.01019.3330.0010.0010.0000.0000.0000.000
183A244GLN0-0.0230.00122.525-0.020-0.0200.0000.0000.0000.000
184A245THR0-0.016-0.01624.7070.0220.0220.0000.0000.0000.000
185A246GLY00.0270.01526.863-0.010-0.0100.0000.0000.0000.000
186A247ILE0-0.011-0.00822.997-0.003-0.0030.0000.0000.0000.000
187A248ASN0-0.0150.02126.8340.0010.0010.0000.0000.0000.000
188A249MET0-0.0010.02226.0610.0010.0010.0000.0000.0000.000
189A250LYS10.8910.94929.5750.0800.0800.0000.0000.0000.000
190A251THR00.036-0.00231.778-0.003-0.0030.0000.0000.0000.000
191A252ALA00.0220.00832.6380.0070.0070.0000.0000.0000.000
192A253ALA0-0.0520.01627.6910.0040.0040.0000.0000.0000.000
193A254SER0-0.014-0.04525.316-0.003-0.0030.0000.0000.0000.000
194A255ILE0-0.033-0.02020.4020.0060.0060.0000.0000.0000.000
195A256ASN0-0.0160.00618.250-0.024-0.0240.0000.0000.0000.000
196A257GLY00.023-0.01717.908-0.014-0.0140.0000.0000.0000.000
197A258ARG10.8360.91915.5100.4750.4750.0000.0000.0000.000
198A259MET0-0.036-0.01120.0240.0010.0010.0000.0000.0000.000
199A260MET0-0.013-0.01217.149-0.003-0.0030.0000.0000.0000.000
200A261ALA00.0250.01222.464-0.007-0.0070.0000.0000.0000.000
201A262GLN00.0340.00522.5490.0220.0220.0000.0000.0000.000
202A263THR0-0.0160.00826.7020.0090.0090.0000.0000.0000.000
203A264ALA00.0230.00829.810-0.005-0.0050.0000.0000.0000.000
204A265VAL00.0250.01126.928-0.002-0.0020.0000.0000.0000.000
205A266THR0-0.078-0.06529.5860.0110.0110.0000.0000.0000.000
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