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: 434NN

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2323760.401705
FMO2-HF: Nuclear repulsion 2245262.630243
FMO2-HF: Total energy -78497.771462
FMO2-MP2: Total energy -78724.795684


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.
-2.6490.6310.572-1.351-2.502-0.009
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 : -0.031 / q_NPA : -0.031
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-1-0.870-0.9402.692-6.558-4.1030.554-1.191-1.819-0.009
4A64LEU00.0300.0095.0920.8150.872-0.001-0.001-0.0550.000
5A65VAL0-0.0140.0067.096-0.002-0.0020.0000.0000.0000.000
6A66ASN0-0.020-0.01110.5420.1160.1160.0000.0000.0000.000
7A67LEU00.0300.00912.9310.0560.0560.0000.0000.0000.000
8A68GLY00.0240.02216.1860.0520.0520.0000.0000.0000.000
9A69VAL0-0.019-0.03418.3410.0150.0150.0000.0000.0000.000
10A70ALA00.0430.02619.6090.0270.0270.0000.0000.0000.000
11A71ALA0-0.029-0.00817.0340.0240.0240.0000.0000.0000.000
12A72ASN0-0.093-0.05518.7320.0210.0210.0000.0000.0000.000
13A73PHE0-0.0190.00621.7520.0200.0200.0000.0000.0000.000
14A74ALA0-0.010-0.00821.742-0.009-0.0090.0000.0000.0000.000
15A75ILE0-0.004-0.00623.3720.0080.0080.0000.0000.0000.000
16A76LEU00.0060.00723.284-0.004-0.0040.0000.0000.0000.000
17A77SER0-0.052-0.04825.4460.0000.0000.0000.0000.0000.000
18A78LYS10.9730.99926.8990.1030.1030.0000.0000.0000.000
19A79THR0-0.039-0.03730.1860.0020.0020.0000.0000.0000.000
20A80GLY00.0220.01931.9410.0060.0060.0000.0000.0000.000
21A81ILE0-0.035-0.00229.8360.0000.0000.0000.0000.0000.000
22A82THR00.0000.01332.9380.0020.0020.0000.0000.0000.000
23A83ASP-1-0.727-0.82133.921-0.012-0.0120.0000.0000.0000.000
24A84VAL0-0.0480.00835.9760.0000.0000.0000.0000.0000.000
25A85TYR0-0.032-0.02837.1430.0020.0020.0000.0000.0000.000
26A86LYS10.8140.90037.0090.0170.0170.0000.0000.0000.000
27A87SER00.015-0.02832.2290.0070.0070.0000.0000.0000.000
28A88ALA0-0.046-0.02931.749-0.003-0.0030.0000.0000.0000.000
29A89ILE00.0070.00127.4250.0040.0040.0000.0000.0000.000
30A90THR0-0.026-0.00526.042-0.002-0.0020.0000.0000.0000.000
31A91GLY00.0380.00525.176-0.005-0.0050.0000.0000.0000.000
32A92ASP-1-0.788-0.88425.870-0.111-0.1110.0000.0000.0000.000
33A93VAL0-0.017-0.01726.403-0.002-0.0020.0000.0000.0000.000
34A94GLY00.0280.00728.434-0.001-0.0010.0000.0000.0000.000
35A95ALA0-0.022-0.00329.0090.0010.0010.0000.0000.0000.000
36A96SER00.0450.02930.3010.0020.0020.0000.0000.0000.000
37A97PRO00.004-0.00630.478-0.005-0.0050.0000.0000.0000.000
38A98ILE0-0.034-0.00933.7980.0040.0040.0000.0000.0000.000
39A99THR0-0.012-0.02135.783-0.002-0.0020.0000.0000.0000.000
40A100GLY00.0650.03636.5490.0020.0020.0000.0000.0000.000
41A101ALA0-0.026-0.02037.6160.0020.0020.0000.0000.0000.000
42A102ALA0-0.025-0.01136.2650.0040.0040.0000.0000.0000.000
43A103ILE0-0.046-0.02133.0280.0020.0020.0000.0000.0000.000
44A104LEU0-0.031-0.01835.9580.0010.0010.0000.0000.0000.000
45A105LEU00.0170.02532.2940.0040.0040.0000.0000.0000.000
46A106LYS10.9300.94736.6470.0210.0210.0000.0000.0000.000
47A107CYS0-0.019-0.02936.945-0.002-0.0020.0000.0000.0000.000
48A108ASP-1-0.781-0.86336.846-0.022-0.0220.0000.0000.0000.000
49A109GLH0-0.058-0.06934.6270.0030.0030.0000.0000.0000.000
50A110VAL0-0.0100.00930.6410.0010.0010.0000.0000.0000.000
51A111THR0-0.039-0.00330.5030.0010.0010.0000.0000.0000.000
52A112GLY00.0330.00329.563-0.004-0.0040.0000.0000.0000.000
53A113THR0-0.039-0.01929.9840.0080.0080.0000.0000.0000.000
54A114ILE0-0.009-0.00330.598-0.004-0.0040.0000.0000.0000.000
55A115PHE00.030-0.00229.5470.0000.0000.0000.0000.0000.000
56A116SER00.001-0.00232.8730.0020.0020.0000.0000.0000.000
57A117VAL00.0160.00133.773-0.006-0.0060.0000.0000.0000.000
58A118ASP-1-0.777-0.89236.015-0.063-0.0630.0000.0000.0000.000
59A119ALA00.0150.01539.6680.0000.0000.0000.0000.0000.000
60A120ALA0-0.031-0.01241.2560.0030.0030.0000.0000.0000.000
61A121GLY00.0320.01239.273-0.005-0.0050.0000.0000.0000.000
62A122PRO00.0010.00637.1210.0020.0020.0000.0000.0000.000
63A123ALA00.009-0.00640.229-0.003-0.0030.0000.0000.0000.000
64A125LYS10.8640.96636.5940.0560.0560.0000.0000.0000.000
65A126ILE00.0190.01334.6320.0010.0010.0000.0000.0000.000
66A127THR0-0.068-0.05235.556-0.001-0.0010.0000.0000.0000.000
67A128ASP-1-0.821-0.93232.330-0.132-0.1320.0000.0000.0000.000
68A129ALA00.0510.03132.724-0.006-0.0060.0000.0000.0000.000
69A130SER0-0.0270.00232.305-0.007-0.0070.0000.0000.0000.000
70A131ARG10.9490.99626.1930.1440.1440.0000.0000.0000.000
71A132LEU0-0.011-0.00527.631-0.013-0.0130.0000.0000.0000.000
72A133THR0-0.040-0.02728.087-0.002-0.0020.0000.0000.0000.000
73A134THR0-0.007-0.00724.372-0.007-0.0070.0000.0000.0000.000
74A135ALA0-0.0170.00323.704-0.018-0.0180.0000.0000.0000.000
75A136VAL0-0.007-0.01723.247-0.012-0.0120.0000.0000.0000.000
76A137GLY0-0.004-0.00424.205-0.001-0.0010.0000.0000.0000.000
77A138ASP-1-0.802-0.90419.930-0.320-0.3200.0000.0000.0000.000
78A139MET0-0.030-0.00519.362-0.025-0.0250.0000.0000.0000.000
79A140GLN0-0.118-0.05619.9360.0090.0090.0000.0000.0000.000
80A141ILE00.0570.02617.523-0.005-0.0050.0000.0000.0000.000
81A142ALA00.0030.00815.805-0.038-0.0380.0000.0000.0000.000
82A143TYR0-0.073-0.04615.823-0.009-0.0090.0000.0000.0000.000
83A144ASP-1-0.809-0.90417.603-0.175-0.1750.0000.0000.0000.000
84A145ASN0-0.033-0.01012.140-0.068-0.0680.0000.0000.0000.000
85A146ALA00.011-0.00412.881-0.028-0.0280.0000.0000.0000.000
86A147ALA0-0.006-0.00213.9480.0530.0530.0000.0000.0000.000
87A148GLY0-0.0250.00316.0640.0490.0490.0000.0000.0000.000
88A149ARG10.7520.8777.2711.1721.1720.0000.0000.0000.000
89A150LEU00.009-0.00812.0690.1030.1030.0000.0000.0000.000
90A151ASN0-0.072-0.03110.7700.0010.0010.0000.0000.0000.000
91A152PRO0-0.013-0.01010.5460.1290.1290.0000.0000.0000.000
92A153ASP-1-0.776-0.8737.5282.0142.0140.0000.0000.0000.000
93A154PHE0-0.035-0.02110.591-0.105-0.1050.0000.0000.0000.000
94A155LEU00.004-0.00613.967-0.076-0.0760.0000.0000.0000.000
95A156ASN0-0.022-0.02117.280-0.009-0.0090.0000.0000.0000.000
96A157LEU00.0800.05215.878-0.021-0.0210.0000.0000.0000.000
97A158GLY0-0.045-0.04219.037-0.027-0.0270.0000.0000.0000.000
98A159ALA00.0150.02922.241-0.023-0.0230.0000.0000.0000.000
99A160GLY00.0300.02222.473-0.022-0.0220.0000.0000.0000.000
100A161THR0-0.027-0.01523.760-0.019-0.0190.0000.0000.0000.000
101A162ILE0-0.012-0.01718.6000.0210.0210.0000.0000.0000.000
102A163GLY00.0130.01421.5640.0170.0170.0000.0000.0000.000
103A164GLY00.0060.00323.3610.0100.0100.0000.0000.0000.000
104A165LYS10.8830.95118.505-0.348-0.3480.0000.0000.0000.000
105A166THR00.0180.00115.066-0.031-0.0310.0000.0000.0000.000
106A167LEU0-0.043-0.00913.1920.0400.0400.0000.0000.0000.000
107A168THR00.0630.03410.088-0.083-0.0830.0000.0000.0000.000
108A169PRO0-0.0100.0095.357-0.223-0.2230.0000.0000.0000.000
109A170GLY00.0520.0355.8380.3860.3860.0000.0000.0000.000
110A171LEU0-0.055-0.0326.828-0.493-0.4930.0000.0000.0000.000
111A172TYR0-0.038-0.0449.2760.0580.0580.0000.0000.0000.000
112A173LYS10.9130.95112.782-0.195-0.1950.0000.0000.0000.000
113A174TRP00.010-0.00915.7430.0440.0440.0000.0000.0000.000
114A175THR0-0.005-0.01119.679-0.024-0.0240.0000.0000.0000.000
115A176SER00.0020.00422.577-0.012-0.0120.0000.0000.0000.000
116A177THR0-0.034-0.01823.507-0.003-0.0030.0000.0000.0000.000
117A178LEU0-0.0170.01619.1190.0120.0120.0000.0000.0000.000
118A179ASN0-0.016-0.01123.346-0.033-0.0330.0000.0000.0000.000
119A180ILE00.0440.01120.2060.0220.0220.0000.0000.0000.000
120A181PRO0-0.016-0.01424.138-0.014-0.0140.0000.0000.0000.000
121A182THR00.0290.00125.558-0.005-0.0050.0000.0000.0000.000
122A183ASP-1-0.796-0.89823.6320.1780.1780.0000.0000.0000.000
123A184ILE0-0.0240.00617.6920.0150.0150.0000.0000.0000.000
124A185THR0-0.035-0.02016.113-0.028-0.0280.0000.0000.0000.000
125A186ILE0-0.0020.01011.5960.0370.0370.0000.0000.0000.000
126A187SER0-0.028-0.02212.290-0.054-0.0540.0000.0000.0000.000
127A188GLY00.0410.0078.5980.1660.1660.0000.0000.0000.000
128A189SER0-0.027-0.0456.070-0.468-0.4680.0000.0000.0000.000
129A190SER00.0020.0028.205-0.033-0.0330.0000.0000.0000.000
130A191THR0-0.009-0.0134.673-0.427-0.390-0.001-0.003-0.0330.000
131A192ASP-1-0.813-0.8463.3962.1692.6180.016-0.112-0.3530.000
132A193VAL0-0.007-0.0113.737-0.831-0.5490.004-0.044-0.2420.000
133A194TRP0-0.034-0.0065.4640.4540.4540.0000.0000.0000.000
134A195ILE0-0.017-0.0098.121-0.198-0.1980.0000.0000.0000.000
135A196PHE0-0.007-0.00710.5870.1450.1450.0000.0000.0000.000
136A197GLN00.0330.01613.9510.0060.0060.0000.0000.0000.000
137A198VAL0-0.018-0.01816.3450.0520.0520.0000.0000.0000.000
138A199ALA00.0150.00219.909-0.030-0.0300.0000.0000.0000.000
139A200GLY0-0.0030.01322.679-0.013-0.0130.0000.0000.0000.000
140A201ASN0-0.027-0.01924.599-0.016-0.0160.0000.0000.0000.000
141A202LEU00.0340.02220.2170.0160.0160.0000.0000.0000.000
142A203ASN0-0.050-0.03724.142-0.024-0.0240.0000.0000.0000.000
143A204MET00.0040.01422.8130.0230.0230.0000.0000.0000.000
144A205SER00.0130.00626.001-0.015-0.0150.0000.0000.0000.000
145A206SER00.002-0.01228.4880.0010.0010.0000.0000.0000.000
146A207ALA0-0.050-0.02829.8780.0070.0070.0000.0000.0000.000
147A208VAL0-0.0250.02124.0000.0070.0070.0000.0000.0000.000
148A209ARG10.9320.96223.831-0.129-0.1290.0000.0000.0000.000
149A210ILE0-0.019-0.00517.3670.0210.0210.0000.0000.0000.000
150A211THR0-0.026-0.00818.967-0.029-0.0290.0000.0000.0000.000
151A212LEU0-0.0050.00913.9680.0390.0390.0000.0000.0000.000
152A213ALA00.006-0.00914.459-0.031-0.0310.0000.0000.0000.000
153A214GLY00.0340.00113.1980.0610.0610.0000.0000.0000.000
154A215GLY00.0120.00612.4430.0520.0520.0000.0000.0000.000
155A216ALA0-0.0100.01410.136-0.056-0.0560.0000.0000.0000.000
156A217GLN00.006-0.02210.107-0.130-0.1300.0000.0000.0000.000
157A218ALA00.0760.03911.567-0.032-0.0320.0000.0000.0000.000
158A219LYS10.8460.92811.4050.1730.1730.0000.0000.0000.000
159A220ASN0-0.068-0.0367.354-0.250-0.2500.0000.0000.0000.000
160A221ILE00.0280.0248.5720.0260.0260.0000.0000.0000.000
161A222PHE0-0.016-0.0048.657-0.063-0.0630.0000.0000.0000.000
162A223TRP0-0.002-0.00312.7930.0690.0690.0000.0000.0000.000
163A224GLN00.0170.01415.911-0.013-0.0130.0000.0000.0000.000
164A225THR0-0.003-0.01517.4120.0340.0340.0000.0000.0000.000
165A226ALA00.0270.01220.995-0.020-0.0200.0000.0000.0000.000
166A227GLY00.0150.01723.719-0.007-0.0070.0000.0000.0000.000
167A228ALA0-0.060-0.02025.119-0.006-0.0060.0000.0000.0000.000
168A229VAL00.0450.01522.4710.0130.0130.0000.0000.0000.000
169A230THR0-0.042-0.03125.719-0.014-0.0140.0000.0000.0000.000
170A231LEU00.0200.01623.3870.0140.0140.0000.0000.0000.000
171A232GLY00.0290.01027.417-0.010-0.0100.0000.0000.0000.000
172A233SER00.0350.02529.7120.0000.0000.0000.0000.0000.000
173A234THR0-0.024-0.02831.1730.0080.0080.0000.0000.0000.000
174A235SER0-0.060-0.01126.2810.0060.0060.0000.0000.0000.000
175A236HIS0-0.028-0.03621.216-0.020-0.0200.0000.0000.0000.000
176A237PHE00.0450.00018.5380.0260.0260.0000.0000.0000.000
177A238GLU-1-0.749-0.86216.4620.0790.0790.0000.0000.0000.000
178A239GLY00.0240.01615.1830.0230.0230.0000.0000.0000.000
179A240ASN0-0.055-0.03113.202-0.011-0.0110.0000.0000.0000.000
180A241ILE00.0030.01216.2050.0120.0120.0000.0000.0000.000
181A242LEU00.000-0.00815.377-0.016-0.0160.0000.0000.0000.000
182A243SER00.0280.01119.2250.0140.0140.0000.0000.0000.000
183A244GLN0-0.0040.00522.475-0.025-0.0250.0000.0000.0000.000
184A245THR0-0.003-0.01124.6370.0040.0040.0000.0000.0000.000
185A246GLY00.0280.02126.795-0.009-0.0090.0000.0000.0000.000
186A247ILE0-0.019-0.01122.9180.0070.0070.0000.0000.0000.000
187A248ASN0-0.038-0.00426.942-0.010-0.0100.0000.0000.0000.000
188A249MET00.0040.02426.5640.0060.0060.0000.0000.0000.000
189A250LYS10.9040.95629.856-0.028-0.0280.0000.0000.0000.000
190A251THR00.0400.00532.0800.0000.0000.0000.0000.0000.000
191A252ALA00.0140.00732.8770.0070.0070.0000.0000.0000.000
192A253ALA0-0.0500.01328.0100.0040.0040.0000.0000.0000.000
193A254SER0-0.005-0.02725.632-0.010-0.0100.0000.0000.0000.000
194A255ILE0-0.034-0.02120.6150.0120.0120.0000.0000.0000.000
195A256ASN0-0.042-0.01318.529-0.037-0.0370.0000.0000.0000.000
196A257GLY00.037-0.01518.0250.0130.0130.0000.0000.0000.000
197A258ARG10.8480.92915.0370.2200.2200.0000.0000.0000.000
198A259MET0-0.032-0.00820.0390.0110.0110.0000.0000.0000.000
199A260MET0-0.006-0.00717.031-0.016-0.0160.0000.0000.0000.000
200A261ALA00.0140.01122.3620.0040.0040.0000.0000.0000.000
201A262GLN00.011-0.00822.410-0.001-0.0010.0000.0000.0000.000
202A263THR00.0070.00526.6800.0030.0030.0000.0000.0000.000
203A264ALA00.0110.00729.741-0.007-0.0070.0000.0000.0000.000
204A265VAL00.0220.01226.7230.0050.0050.0000.0000.0000.000
205A266THR0-0.067-0.05129.5780.0010.0010.0000.0000.0000.000
206A267LEU00.0470.00928.6930.0040.0040.0000.0000.0000.000
207A268GLN00.001-0.01732.4460.0030.0030.0000.0000.0000.000
208A269MET0-0.015-0.00134.0860.0060.0060.0000.0000.0000.000
209A270ASN00.0070.00129.2890.0010.0010.0000.0000.0000.000
210A271THR00.0200.01527.405-0.006-0.0060.0000.0000.0000.000
211A272VAL0-0.012-0.01624.6150.0070.0070.0000.0000.0000.000
212A273THR00.0090.00122.409-0.003-0.0030.0000.0000.0000.000
213A274ILE0-0.0010.01119.8960.0040.0040.0000.0000.0000.000
214A275PRO0-0.0270.00316.2740.0070.0070.0000.0000.0000.000
215A276GLN00.0070.01515.906-0.041-0.0410.0000.0000.0000.000