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: 53K9Z

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2326292.884928
FMO2-HF: Nuclear repulsion 2247794.587649
FMO2-HF: Total energy -78498.297279
FMO2-MP2: Total energy -78725.400094


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.
-1.7411.1050.098-1.127-1.816-0.003
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 : -0.023 / 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].
3A63ASP-1-0.865-0.9323.163-5.801-3.6840.081-1.010-1.189-0.003
4A64LEU00.0110.0065.1380.8650.921-0.0010.000-0.0540.000
5A65VAL0-0.0220.0047.037-0.017-0.0170.0000.0000.0000.000
6A66ASN0-0.001-0.00510.6980.1280.1280.0000.0000.0000.000
7A67LEU00.0220.00512.9480.0510.0510.0000.0000.0000.000
8A68GLY00.0180.01816.2440.0430.0430.0000.0000.0000.000
9A69VAL0-0.018-0.02818.5220.0160.0160.0000.0000.0000.000
10A70ALA00.0270.01319.7440.0250.0250.0000.0000.0000.000
11A71ALA0-0.025-0.00117.2150.0240.0240.0000.0000.0000.000
12A72ASN0-0.031-0.01518.7660.0310.0310.0000.0000.0000.000
13A73PHE0-0.032-0.00421.9850.0180.0180.0000.0000.0000.000
14A74ALA00.0120.01221.977-0.004-0.0040.0000.0000.0000.000
15A75ILE0-0.016-0.01723.6360.0080.0080.0000.0000.0000.000
16A76LEU0-0.0090.00023.295-0.004-0.0040.0000.0000.0000.000
17A77SER0-0.035-0.03525.5810.0010.0010.0000.0000.0000.000
18A78LYS10.9480.98426.6940.0990.0990.0000.0000.0000.000
19A79THR0-0.030-0.03430.2830.0010.0010.0000.0000.0000.000
20A80GLY00.0460.02732.1440.0060.0060.0000.0000.0000.000
21A81ILE0-0.050-0.00429.5610.0000.0000.0000.0000.0000.000
22A82THR00.0060.00232.8090.0000.0000.0000.0000.0000.000
23A83ASP-1-0.743-0.82634.0150.0100.0100.0000.0000.0000.000
24A84VAL0-0.0290.00436.028-0.001-0.0010.0000.0000.0000.000
25A85TYR0-0.020-0.02537.6420.0040.0040.0000.0000.0000.000
26A86LYS10.8110.90236.832-0.005-0.0050.0000.0000.0000.000
27A87SER00.004-0.03532.5830.0070.0070.0000.0000.0000.000
28A88ALA0-0.051-0.03332.120-0.004-0.0040.0000.0000.0000.000
29A89ILE00.0090.00727.4630.0050.0050.0000.0000.0000.000
30A90THR0-0.025-0.00625.892-0.001-0.0010.0000.0000.0000.000
31A91GLY00.0430.01424.965-0.001-0.0010.0000.0000.0000.000
32A92ASP-1-0.789-0.86025.771-0.079-0.0790.0000.0000.0000.000
33A93VAL0-0.014-0.02226.4810.0010.0010.0000.0000.0000.000
34A94GLY00.0350.00928.681-0.001-0.0010.0000.0000.0000.000
35A95ALA0-0.0070.00029.2380.0000.0000.0000.0000.0000.000
36A96SER00.0190.01830.2830.0010.0010.0000.0000.0000.000
37A97PRO00.0250.00630.693-0.004-0.0040.0000.0000.0000.000
38A98ILE0-0.055-0.02133.7550.0040.0040.0000.0000.0000.000
39A99THR00.024-0.00735.797-0.002-0.0020.0000.0000.0000.000
40A100GLY00.0340.01536.8250.0030.0030.0000.0000.0000.000
41A101ALA0-0.035-0.02937.9100.0030.0030.0000.0000.0000.000
42A102ALA0-0.0250.00136.4170.0040.0040.0000.0000.0000.000
43A103ILE0-0.0180.00033.2810.0010.0010.0000.0000.0000.000
44A104LEU0-0.013-0.01835.8410.0010.0010.0000.0000.0000.000
45A105LEU0-0.0120.01032.4960.0040.0040.0000.0000.0000.000
46A106LYS10.9310.95936.6460.0070.0070.0000.0000.0000.000
47A107CYS0-0.004-0.02037.156-0.001-0.0010.0000.0000.0000.000
48A108ASP-1-0.763-0.84736.667-0.003-0.0030.0000.0000.0000.000
49A109GLH0-0.065-0.06634.5380.0030.0030.0000.0000.0000.000
50A110VAL0-0.018-0.00330.5940.0020.0020.0000.0000.0000.000
51A111THR00.0050.01730.084-0.001-0.0010.0000.0000.0000.000
52A112GLY00.011-0.01229.244-0.002-0.0020.0000.0000.0000.000
53A113THR0-0.038-0.02329.7800.0050.0050.0000.0000.0000.000
54A114ILE00.0110.00830.588-0.003-0.0030.0000.0000.0000.000
55A115PHE00.004-0.00429.669-0.002-0.0020.0000.0000.0000.000
56A116SER00.0200.00632.9340.0020.0020.0000.0000.0000.000
57A117VAL00.0130.00133.821-0.005-0.0050.0000.0000.0000.000
58A118ASP-1-0.782-0.88435.954-0.051-0.0510.0000.0000.0000.000
59A119ALA00.0290.01639.5840.0000.0000.0000.0000.0000.000
60A120ALA0-0.0230.00641.4120.0030.0030.0000.0000.0000.000
61A121GLY00.0500.01638.954-0.004-0.0040.0000.0000.0000.000
62A122PRO0-0.012-0.00636.9870.0020.0020.0000.0000.0000.000
63A123ALA0-0.002-0.00640.038-0.003-0.0030.0000.0000.0000.000
64A125LYS10.8360.94936.2130.0430.0430.0000.0000.0000.000
65A126ILE00.0160.00534.3730.0000.0000.0000.0000.0000.000
66A127THR0-0.052-0.05435.508-0.001-0.0010.0000.0000.0000.000
67A128ASP-1-0.798-0.89332.268-0.108-0.1080.0000.0000.0000.000
68A129ALA00.0460.02032.796-0.004-0.0040.0000.0000.0000.000
69A130SER0-0.060-0.01632.085-0.008-0.0080.0000.0000.0000.000
70A131ARG10.8730.93625.6030.1110.1110.0000.0000.0000.000
71A132LEU0-0.0160.00027.433-0.010-0.0100.0000.0000.0000.000
72A133THR0-0.029-0.03327.954-0.003-0.0030.0000.0000.0000.000
73A134THR0-0.034-0.02024.382-0.009-0.0090.0000.0000.0000.000
74A135ALA00.0030.01123.462-0.017-0.0170.0000.0000.0000.000
75A136VAL00.002-0.01123.317-0.008-0.0080.0000.0000.0000.000
76A137GLY00.0060.01024.426-0.001-0.0010.0000.0000.0000.000
77A138ASP-1-0.812-0.91519.706-0.287-0.2870.0000.0000.0000.000
78A139MET0-0.045-0.01119.335-0.019-0.0190.0000.0000.0000.000
79A140GLN0-0.090-0.04320.2940.0140.0140.0000.0000.0000.000
80A141ILE00.0320.01117.330-0.010-0.0100.0000.0000.0000.000
81A142ALA00.0130.00715.784-0.041-0.0410.0000.0000.0000.000
82A143TYR0-0.045-0.03215.891-0.007-0.0070.0000.0000.0000.000
83A144ASP-1-0.812-0.91417.672-0.173-0.1730.0000.0000.0000.000
84A145ASN0-0.029-0.00612.315-0.067-0.0670.0000.0000.0000.000
85A146ALA00.0210.00913.092-0.049-0.0490.0000.0000.0000.000
86A147ALA0-0.012-0.00514.1650.0450.0450.0000.0000.0000.000
87A148GLY0-0.020-0.00616.6700.0460.0460.0000.0000.0000.000
88A149ARG10.7520.8807.5531.0841.0840.0000.0000.0000.000
89A150LEU00.000-0.00912.1550.1080.1080.0000.0000.0000.000
90A151ASN0-0.037-0.02510.632-0.004-0.0040.0000.0000.0000.000
91A152PRO0-0.0060.00810.4340.1310.1310.0000.0000.0000.000
92A153ASP-1-0.810-0.8927.7092.2032.2030.0000.0000.0000.000
93A154PHE0-0.040-0.01610.329-0.138-0.1380.0000.0000.0000.000
94A155LEU00.0270.00413.946-0.073-0.0730.0000.0000.0000.000
95A156ASN0-0.020-0.02117.241-0.005-0.0050.0000.0000.0000.000
96A157LEU00.0420.03515.561-0.023-0.0230.0000.0000.0000.000
97A158GLY0-0.024-0.02819.062-0.020-0.0200.0000.0000.0000.000
98A159ALA00.0100.01122.344-0.022-0.0220.0000.0000.0000.000
99A160GLY00.0640.04422.732-0.021-0.0210.0000.0000.0000.000
100A161THR0-0.039-0.02023.813-0.014-0.0140.0000.0000.0000.000
101A162ILE00.016-0.00518.5330.0230.0230.0000.0000.0000.000
102A163GLY00.0350.02521.3010.0210.0210.0000.0000.0000.000
103A164GLY0-0.0010.00023.7910.0050.0050.0000.0000.0000.000
104A165LYS10.8340.93518.671-0.303-0.3030.0000.0000.0000.000
105A166THR00.019-0.00215.228-0.025-0.0250.0000.0000.0000.000
106A167LEU0-0.045-0.01713.2300.0250.0250.0000.0000.0000.000
107A168THR00.0850.0479.648-0.092-0.0920.0000.0000.0000.000
108A169PRO0-0.0150.0045.313-0.219-0.2190.0000.0000.0000.000
109A170GLY00.0300.0285.8880.3260.3260.0000.0000.0000.000
110A171LEU0-0.068-0.0366.772-0.542-0.5420.0000.0000.0000.000
111A172TYR0-0.038-0.0489.3260.0120.0120.0000.0000.0000.000
112A173LYS10.9090.94712.829-0.147-0.1470.0000.0000.0000.000
113A174TRP00.006-0.00815.7470.0390.0390.0000.0000.0000.000
114A175THR0-0.011-0.00719.828-0.024-0.0240.0000.0000.0000.000
115A176SER0-0.029-0.02822.883-0.008-0.0080.0000.0000.0000.000
116A177THR00.0090.00023.564-0.005-0.0050.0000.0000.0000.000
117A178LEU0-0.0240.02218.8940.0110.0110.0000.0000.0000.000
118A179ASN0-0.031-0.02023.243-0.030-0.0300.0000.0000.0000.000
119A180ILE00.0380.01220.6410.0220.0220.0000.0000.0000.000
120A181PRO0-0.015-0.01424.353-0.012-0.0120.0000.0000.0000.000
121A182THR00.026-0.00526.089-0.008-0.0080.0000.0000.0000.000
122A183ASP-1-0.791-0.89924.1060.1930.1930.0000.0000.0000.000
123A184ILE0-0.049-0.00218.2220.0140.0140.0000.0000.0000.000
124A185THR0-0.014-0.00916.363-0.024-0.0240.0000.0000.0000.000
125A186ILE00.0050.01111.7230.0370.0370.0000.0000.0000.000
126A187SER0-0.040-0.02512.462-0.053-0.0530.0000.0000.0000.000
127A188GLY00.0570.0138.5490.1710.1710.0000.0000.0000.000
128A189SER0-0.015-0.0435.872-0.433-0.4330.0000.0000.0000.000
129A190SER0-0.001-0.0038.147-0.020-0.0200.0000.0000.0000.000
130A191THR0-0.021-0.0184.851-0.341-0.3410.0000.0000.0000.000
131A192ASP-1-0.805-0.8353.3252.1992.6190.016-0.088-0.3470.000
132A193VAL0-0.011-0.0113.859-0.749-0.4960.002-0.029-0.2260.000
133A194TRP0-0.041-0.0155.6600.5030.5030.0000.0000.0000.000
134A195ILE0-0.014-0.0058.617-0.201-0.2010.0000.0000.0000.000
135A196PHE0-0.0010.00410.9500.1360.1360.0000.0000.0000.000
136A197GLN00.0220.00614.0480.0110.0110.0000.0000.0000.000
137A198VAL0-0.040-0.02316.4440.0460.0460.0000.0000.0000.000
138A199ALA00.0250.00520.123-0.028-0.0280.0000.0000.0000.000
139A200GLY00.0110.01623.019-0.012-0.0120.0000.0000.0000.000
140A201ASN0-0.005-0.00424.531-0.014-0.0140.0000.0000.0000.000
141A202LEU00.0160.01220.3140.0140.0140.0000.0000.0000.000
142A203ASN0-0.032-0.02324.179-0.021-0.0210.0000.0000.0000.000
143A204MET0-0.0100.00823.4790.0230.0230.0000.0000.0000.000
144A205SER00.0200.00926.606-0.015-0.0150.0000.0000.0000.000
145A206SER00.002-0.00429.1450.0010.0010.0000.0000.0000.000
146A207ALA0-0.046-0.03330.5440.0060.0060.0000.0000.0000.000
147A208VAL0-0.0350.01424.7810.0070.0070.0000.0000.0000.000
148A209ARG10.9160.94723.556-0.160-0.1600.0000.0000.0000.000
149A210ILE0-0.0180.00317.7750.0210.0210.0000.0000.0000.000
150A211THR0-0.022-0.00719.215-0.030-0.0300.0000.0000.0000.000
151A212LEU0-0.012-0.00113.9840.0390.0390.0000.0000.0000.000
152A213ALA00.0290.00414.422-0.035-0.0350.0000.0000.0000.000
153A214GLY00.010-0.00212.7860.0670.0670.0000.0000.0000.000
154A215GLY00.006-0.00412.0540.0250.0250.0000.0000.0000.000
155A216ALA0-0.0240.00910.062-0.071-0.0710.0000.0000.0000.000
156A217GLN00.002-0.02010.622-0.140-0.1400.0000.0000.0000.000
157A218ALA00.0710.03611.677-0.028-0.0280.0000.0000.0000.000
158A219LYS10.8610.92411.4760.0140.0140.0000.0000.0000.000
159A220ASN0-0.057-0.0397.110-0.207-0.2070.0000.0000.0000.000
160A221ILE00.0270.0268.591-0.004-0.0040.0000.0000.0000.000
161A222PHE0-0.013-0.0048.705-0.066-0.0660.0000.0000.0000.000
162A223TRP00.0030.00013.0710.0610.0610.0000.0000.0000.000
163A224GLN00.0200.00216.246-0.015-0.0150.0000.0000.0000.000
164A225THR0-0.009-0.01517.8510.0290.0290.0000.0000.0000.000
165A226ALA00.0180.01121.525-0.019-0.0190.0000.0000.0000.000
166A227GLY00.0240.01724.134-0.006-0.0060.0000.0000.0000.000
167A228ALA0-0.031-0.00725.432-0.008-0.0080.0000.0000.0000.000
168A229VAL00.0220.00022.5760.0130.0130.0000.0000.0000.000
169A230THR0-0.036-0.02625.774-0.013-0.0130.0000.0000.0000.000
170A231LEU00.0030.00423.7240.0120.0120.0000.0000.0000.000
171A232GLY00.0400.01627.883-0.009-0.0090.0000.0000.0000.000
172A233SER00.0280.02030.3920.0020.0020.0000.0000.0000.000
173A234THR0-0.025-0.02331.6990.0070.0070.0000.0000.0000.000
174A235SER0-0.054-0.00926.9920.0070.0070.0000.0000.0000.000
175A236HIS0-0.003-0.01221.509-0.022-0.0220.0000.0000.0000.000
176A237PHE00.037-0.00818.6440.0230.0230.0000.0000.0000.000
177A238GLU-1-0.754-0.86016.6700.1400.1400.0000.0000.0000.000
178A239GLY00.0090.00815.1830.0280.0280.0000.0000.0000.000
179A240ASN0-0.052-0.02313.059-0.017-0.0170.0000.0000.0000.000
180A241ILE0-0.016-0.00816.2860.0180.0180.0000.0000.0000.000
181A242LEU00.0030.00215.417-0.018-0.0180.0000.0000.0000.000
182A243SER00.0230.00419.3860.0090.0090.0000.0000.0000.000
183A244GLN00.0110.01222.770-0.026-0.0260.0000.0000.0000.000
184A245THR0-0.026-0.01724.8000.0040.0040.0000.0000.0000.000
185A246GLY00.0560.03427.223-0.008-0.0080.0000.0000.0000.000
186A247ILE0-0.020-0.00423.0630.0060.0060.0000.0000.0000.000
187A248ASN0-0.0350.00126.957-0.009-0.0090.0000.0000.0000.000
188A249MET00.0270.04226.6880.0060.0060.0000.0000.0000.000
189A250LYS10.8760.93829.763-0.037-0.0370.0000.0000.0000.000
190A251THR00.0470.00532.4870.0020.0020.0000.0000.0000.000
191A252ALA00.0310.01733.4610.0070.0070.0000.0000.0000.000
192A253ALA0-0.0550.00728.5860.0050.0050.0000.0000.0000.000
193A254SER0-0.006-0.03025.915-0.010-0.0100.0000.0000.0000.000
194A255ILE0-0.034-0.02120.9230.0100.0100.0000.0000.0000.000
195A256ASN0-0.019-0.00318.184-0.039-0.0390.0000.0000.0000.000
196A257GLY00.037-0.02018.3390.0160.0160.0000.0000.0000.000
197A258ARG10.8250.91114.8430.1520.1520.0000.0000.0000.000
198A259MET0-0.030-0.00919.9620.0030.0030.0000.0000.0000.000
199A260MET00.0040.00617.073-0.014-0.0140.0000.0000.0000.000
200A261ALA00.007-0.00222.4150.0030.0030.0000.0000.0000.000
201A262GLN0-0.001-0.00822.745-0.006-0.0060.0000.0000.0000.000
202A263THR00.0080.00626.7270.0020.0020.0000.0000.0000.000
203A264ALA00.0180.01530.089-0.006-0.0060.0000.0000.0000.000
204A265VAL00.0150.00327.0780.0040.0040.0000.0000.0000.000
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