Manual

About

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: 6N13Z

Calculation Name: 1XT9-A-Xray372

Preferred Name: NEDD8

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1XT9

Chain ID: A

ChEMBL ID: CHEMBL4295831

UniProt ID: Q15843

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2563104.485633
FMO2-HF: Nuclear repulsion 2479085.003248
FMO2-HF: Total energy -84019.482385
FMO2-MP2: Total energy -84264.093343


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-23.671-48.46664.212-20.551-18.8660.172
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.750 / q_NPA : -0.864
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].
3A4VAL00.0120.0123.44011.11613.5720.102-1.290-1.2690.003
4A5VAL0-0.039-0.0255.118-2.932-2.814-0.001-0.006-0.1100.000
5A6LEU0-0.014-0.0177.394-4.377-4.3770.0000.0000.0000.000
6A7SER0-0.032-0.00110.1131.5971.5970.0000.0000.0000.000
7A8TYR0-0.020-0.02412.541-1.590-1.5900.0000.0000.0000.000
8A9MET0-0.041-0.01415.308-0.076-0.0760.0000.0000.0000.000
9A10ASP-1-0.875-0.92716.96016.88616.8860.0000.0000.0000.000
10A11SER0-0.105-0.02713.1921.2881.2880.0000.0000.0000.000
11A12LEU0-0.030-0.0297.1780.1400.1400.0000.0000.0000.000
12A13LEU00.0080.0047.4611.5681.5680.0000.0000.0000.000
13A14ARG10.9090.9412.621-62.706-59.0571.059-1.957-2.7510.013
14A15GLN00.0130.0032.324-12.917-14.7988.575-2.353-4.3410.034
15A16SER0-0.089-0.0651.564-36.838-66.58454.377-14.835-9.7960.112
16A17ASP-1-0.707-0.8563.47535.78036.3890.100-0.110-0.5990.010
17A18VAL00.004-0.0055.589-7.943-7.9430.0000.0000.0000.000
18A19SER0-0.030-0.0236.057-6.968-6.9680.0000.0000.0000.000
19A20LEU0-0.0390.0027.947-4.183-4.1830.0000.0000.0000.000
20A21LEU0-0.013-0.01110.009-3.352-3.3520.0000.0000.0000.000
21A22ASP-1-0.876-0.89911.35523.21123.2110.0000.0000.0000.000
22A23PRO0-0.043-0.00913.5810.3480.3480.0000.0000.0000.000
23A24PRO0-0.042-0.03216.476-0.014-0.0140.0000.0000.0000.000
24A25SER00.007-0.00112.214-0.174-0.1740.0000.0000.0000.000
25A26TRP0-0.0050.00613.924-0.837-0.8370.0000.0000.0000.000
26A27LEU00.0050.00612.4661.8781.8780.0000.0000.0000.000
27A28ASN00.0330.0107.830-3.453-3.4530.0000.0000.0000.000
28A29ASP-1-0.835-0.93411.36225.49225.4920.0000.0000.0000.000
29A30HIS0-0.014-0.0037.073-4.162-4.1620.0000.0000.0000.000
30A31ILE0-0.022-0.0019.389-1.544-1.5440.0000.0000.0000.000
31A32ILE0-0.012-0.01912.208-1.563-1.5630.0000.0000.0000.000
32A33GLY00.0370.01214.782-1.267-1.2670.0000.0000.0000.000
33A34PHE00.0130.01012.688-1.093-1.0930.0000.0000.0000.000
34A35ALA0-0.015-0.00814.719-1.307-1.3070.0000.0000.0000.000
35A36PHE0-0.020-0.03417.467-1.131-1.1310.0000.0000.0000.000
36A37GLU-1-0.739-0.86816.95015.61815.6180.0000.0000.0000.000
37A38TYR0-0.043-0.02318.055-0.983-0.9830.0000.0000.0000.000
38A39PHE0-0.038-0.03119.842-0.765-0.7650.0000.0000.0000.000
39A40ALA00.0080.00022.560-0.671-0.6710.0000.0000.0000.000
40A41ASN00.001-0.00421.035-1.132-1.1320.0000.0000.0000.000
41A42SER0-0.052-0.01422.187-0.482-0.4820.0000.0000.0000.000
42A43GLN0-0.061-0.03623.4400.0390.0390.0000.0000.0000.000
43A44PHE0-0.048-0.05325.315-0.593-0.5930.0000.0000.0000.000
44A45HIS00.0320.03426.744-0.515-0.5150.0000.0000.0000.000
45A46ASP-1-0.828-0.89827.9969.9569.9560.0000.0000.0000.000
46A47CYS0-0.115-0.05530.545-0.418-0.4180.0000.0000.0000.000
47A48SER00.0580.01929.8250.0630.0630.0000.0000.0000.000
48A49ASP-1-0.903-0.94430.7989.1859.1850.0000.0000.0000.000
49A50HIS0-0.082-0.05133.702-0.125-0.1250.0000.0000.0000.000
50A51VAL0-0.041-0.02928.209-0.041-0.0410.0000.0000.0000.000
51A52SER00.0070.02227.6570.2580.2580.0000.0000.0000.000
52A53PHE00.030-0.00323.146-0.181-0.1810.0000.0000.0000.000
53A54ILE00.001-0.00823.2480.3430.3430.0000.0000.0000.000
54A55SER00.0740.03217.834-0.244-0.2440.0000.0000.0000.000
55A56PRO00.0220.02316.357-0.848-0.8480.0000.0000.0000.000
56A57GLU-1-0.828-0.91914.58519.78519.7850.0000.0000.0000.000
57A58VAL00.0250.01718.179-0.763-0.7630.0000.0000.0000.000
58A59THR0-0.036-0.03921.454-1.014-1.0140.0000.0000.0000.000
59A60GLN00.003-0.01520.066-0.957-0.9570.0000.0000.0000.000
60A61PHE00.0000.00522.082-0.573-0.5730.0000.0000.0000.000
61A62ILE00.0020.00323.629-0.599-0.5990.0000.0000.0000.000
62A63LYS10.7730.88723.813-13.656-13.6560.0000.0000.0000.000
63A64CYS0-0.045-0.02523.999-0.295-0.2950.0000.0000.0000.000
64A65THR00.0390.04626.644-0.210-0.2100.0000.0000.0000.000
65A66SER0-0.118-0.04928.281-0.231-0.2310.0000.0000.0000.000
66A67ASN0-0.076-0.04429.0640.0950.0950.0000.0000.0000.000
67A68PRO00.0400.01232.357-0.071-0.0710.0000.0000.0000.000
68A69ALA00.0010.01133.886-0.282-0.2820.0000.0000.0000.000
69A70GLU-1-0.846-0.92528.91210.25910.2590.0000.0000.0000.000
70A71ILE00.006-0.01129.5750.2260.2260.0000.0000.0000.000
71A72ALA0-0.014-0.03830.4880.1550.1550.0000.0000.0000.000
72A73MET0-0.024-0.02430.0070.0890.0890.0000.0000.0000.000
73A74PHE0-0.008-0.00122.6140.1650.1650.0000.0000.0000.000
74A75LEU00.018-0.00527.3230.2820.2820.0000.0000.0000.000
75A76GLU-1-0.966-0.95929.4319.1219.1210.0000.0000.0000.000
76A77PRO0-0.038-0.03228.093-0.173-0.1730.0000.0000.0000.000
77A78LEU0-0.008-0.00625.8100.0540.0540.0000.0000.0000.000
78A79ASP-1-0.859-0.90929.7728.9668.9660.0000.0000.0000.000
79A80LEU00.002-0.01728.939-0.050-0.0500.0000.0000.0000.000
80A81PRO0-0.037-0.01032.935-0.125-0.1250.0000.0000.0000.000
81A82ASN0-0.090-0.06036.058-0.479-0.4790.0000.0000.0000.000
82A83LYS10.8720.98230.688-10.286-10.2860.0000.0000.0000.000
83A84ARG10.9370.96134.702-8.777-8.7770.0000.0000.0000.000
84A85VAL0-0.033-0.03030.745-0.142-0.1420.0000.0000.0000.000
85A86VAL00.0220.02128.4850.2200.2200.0000.0000.0000.000
86A87PHE00.0060.01025.586-0.193-0.1930.0000.0000.0000.000
87A88LEU00.0240.01524.4210.2970.2970.0000.0000.0000.000
88A89ALA00.0260.02520.185-0.262-0.2620.0000.0000.0000.000
89A90ILE0-0.028-0.01721.5790.3130.3130.0000.0000.0000.000
90A91ASN00.0590.02417.799-0.068-0.0680.0000.0000.0000.000
91A92ASP-1-0.763-0.88321.45313.97313.9730.0000.0000.0000.000
92A93ASN00.0190.00118.382-1.237-1.2370.0000.0000.0000.000
93A94SER0-0.028-0.00821.793-0.323-0.3230.0000.0000.0000.000
94A95ASN0-0.040-0.02121.429-0.390-0.3900.0000.0000.0000.000
95A96GLN00.0150.00720.0340.4720.4720.0000.0000.0000.000
96A97ALA0-0.027-0.00318.5050.7200.7200.0000.0000.0000.000
97A98ALA00.0360.01713.385-0.061-0.0610.0000.0000.0000.000
98A99GLY0-0.007-0.01615.352-0.525-0.5250.0000.0000.0000.000
99A100GLY0-0.0210.00116.1650.4870.4870.0000.0000.0000.000
100A101THR0-0.116-0.06417.9740.4990.4990.0000.0000.0000.000
101A102HIS0-0.049-0.03920.2980.4970.4970.0000.0000.0000.000
102A103TRP0-0.019-0.02015.064-0.486-0.4860.0000.0000.0000.000
103A104SER0-0.044-0.09521.199-0.588-0.5880.0000.0000.0000.000
104A105LEU00.0160.01723.7620.4110.4110.0000.0000.0000.000
105A106LEU0-0.019-0.01425.812-0.562-0.5620.0000.0000.0000.000
106A107VAL0-0.011-0.01128.1780.2230.2230.0000.0000.0000.000
107A108TYR00.0240.02130.695-0.432-0.4320.0000.0000.0000.000
108A109LEU00.006-0.00433.2800.0740.0740.0000.0000.0000.000
109A110GLN00.0360.02436.198-0.312-0.3120.0000.0000.0000.000
110A111ASP-1-1.021-0.99438.6337.7177.7170.0000.0000.0000.000
111A112LYS10.9450.95539.012-8.195-8.1950.0000.0000.0000.000
112A113ASN0-0.0060.01140.0700.0260.0260.0000.0000.0000.000
113A114SER0-0.002-0.02138.180-0.183-0.1830.0000.0000.0000.000
114A115PHE00.0190.00931.9340.2150.2150.0000.0000.0000.000
115A116PHE0-0.044-0.02433.428-0.294-0.2940.0000.0000.0000.000
116A117HIS0-0.0040.04828.5520.7880.7880.0000.0000.0000.000
117A118TYR00.0330.00028.665-0.317-0.3170.0000.0000.0000.000
118A119ASP-1-0.725-0.87027.39412.34612.3460.0000.0000.0000.000
119A120SER0-0.026-0.02425.150-0.182-0.1820.0000.0000.0000.000
120A121HIS0-0.027-0.01226.829-0.186-0.1860.0000.0000.0000.000
121A122SER0-0.009-0.03028.665-0.044-0.0440.0000.0000.0000.000
122A123ARG10.9400.97731.707-8.910-8.9100.0000.0000.0000.000
123A124SER00.0150.03227.348-0.202-0.2020.0000.0000.0000.000
124A125ASN00.046-0.00123.568-0.069-0.0690.0000.0000.0000.000
125A126SER0-0.088-0.02728.010-0.180-0.1800.0000.0000.0000.000
126A127VAL00.016-0.00230.783-0.134-0.1340.0000.0000.0000.000
127A128HIS00.0360.03226.439-0.096-0.0960.0000.0000.0000.000
128A129ALA00.0460.02828.5820.0520.0520.0000.0000.0000.000
129A130LYS10.9170.96329.527-9.101-9.1010.0000.0000.0000.000
130A131GLN00.0210.01329.2350.0900.0900.0000.0000.0000.000
131A132VAL00.001-0.01526.649-0.093-0.0930.0000.0000.0000.000
132A133ALA0-0.0060.00329.868-0.083-0.0830.0000.0000.0000.000
133A134GLU-1-0.892-0.95432.9218.8048.8040.0000.0000.0000.000
134A135LYS10.8070.91430.332-10.609-10.6090.0000.0000.0000.000
135A136LEU00.0060.00329.7620.1500.1500.0000.0000.0000.000
136A137GLU-1-1.015-0.99633.3688.0228.0220.0000.0000.0000.000
137A138ALA0-0.023-0.01935.917-0.238-0.2380.0000.0000.0000.000
138A139PHE0-0.0030.01733.493-0.101-0.1010.0000.0000.0000.000
139A140LEU00.0050.01732.8580.0040.0040.0000.0000.0000.000
140A141GLY00.0340.01736.706-0.057-0.0570.0000.0000.0000.000
141A142ARG10.8850.95039.088-7.286-7.2860.0000.0000.0000.000
142A143LYS10.9530.98142.684-7.331-7.3310.0000.0000.0000.000
143A144GLY0-0.011-0.00245.219-0.132-0.1320.0000.0000.0000.000
144A145ASP-1-0.864-0.93144.8606.8676.8670.0000.0000.0000.000
145A146LYS10.9200.94644.076-7.257-7.2570.0000.0000.0000.000
146A147LEU00.0430.04037.6110.0330.0330.0000.0000.0000.000
147A148ALA0-0.081-0.02540.5210.0050.0050.0000.0000.0000.000
148A149PHE00.0470.02632.5710.1560.1560.0000.0000.0000.000
149A150VAL0-0.038-0.01636.719-0.201-0.2010.0000.0000.0000.000
150A151GLU-1-0.891-0.94433.18010.20910.2090.0000.0000.0000.000
151A152GLU-1-0.858-0.93333.7808.4648.4640.0000.0000.0000.000
152A153LYS10.8950.95734.240-8.458-8.4580.0000.0000.0000.000
153A154ALA00.0210.00630.447-0.005-0.0050.0000.0000.0000.000
154A155PRO0-0.046-0.02228.594-0.111-0.1110.0000.0000.0000.000
155A156ALA00.0050.01029.1520.2700.2700.0000.0000.0000.000
156A157GLN0-0.010-0.01323.404-0.044-0.0440.0000.0000.0000.000
157A158GLN0-0.018-0.02326.845-0.148-0.1480.0000.0000.0000.000
158A159ASN0-0.028-0.00422.6700.1580.1580.0000.0000.0000.000
159A160SER00.013-0.00522.479-0.045-0.0450.0000.0000.0000.000
160A161TYR00.0260.01718.0340.0330.0330.0000.0000.0000.000
161A162ASP-1-0.734-0.85318.57916.94416.9440.0000.0000.0000.000
162A163CYS0-0.0510.01420.3750.1980.1980.0000.0000.0000.000
163A164GLY00.0840.02017.820-0.300-0.3000.0000.0000.0000.000
164A165MET00.0380.02317.5960.4120.4120.0000.0000.0000.000
165A166TYR00.0090.00719.714-0.594-0.5940.0000.0000.0000.000
166A167VAL0-0.0140.02020.895-0.620-0.6200.0000.0000.0000.000
167A168ILE00.0100.03717.741-0.483-0.4830.0000.0000.0000.000
168A169CYS0-0.037-0.02421.198-0.512-0.5120.0000.0000.0000.000
169A170ASN00.019-0.00323.908-0.959-0.9590.0000.0000.0000.000
170A171THR0-0.006-0.01423.808-0.520-0.5200.0000.0000.0000.000
171A172GLU-1-0.816-0.89124.00112.72012.7200.0000.0000.0000.000
172A173ALA0-0.016-0.02025.871-0.492-0.4920.0000.0000.0000.000
173A174LEU0-0.019-0.01528.989-0.447-0.4470.0000.0000.0000.000
174A175CYS0-0.0260.00627.748-0.376-0.3760.0000.0000.0000.000
175A176GLN00.0120.01128.353-0.461-0.4610.0000.0000.0000.000
176A177ASN0-0.024-0.03131.593-0.281-0.2810.0000.0000.0000.000
177A178PHE0-0.085-0.03732.403-0.310-0.3100.0000.0000.0000.000
178A179PHE00.006-0.01430.385-0.313-0.3130.0000.0000.0000.000
179A180ARG10.7710.89029.986-10.282-10.2820.0000.0000.0000.000
180A181GLN0-0.026-0.00834.798-0.127-0.1270.0000.0000.0000.000
181A182GLN0-0.0250.00833.700-0.201-0.2010.0000.0000.0000.000
182A183THR0-0.016-0.02336.621-0.104-0.1040.0000.0000.0000.000
183A184GLU-1-0.891-0.93633.4319.0579.0570.0000.0000.0000.000
184A185SER0-0.0110.01535.8070.0830.0830.0000.0000.0000.000
185A186LEU00.0600.01930.3340.0860.0860.0000.0000.0000.000
186A187LEU0-0.031-0.01931.9490.2020.2020.0000.0000.0000.000
187A188GLN0-0.044-0.01334.024-0.109-0.1090.0000.0000.0000.000
188A189LEU0-0.013-0.00329.9210.0590.0590.0000.0000.0000.000
189A190LEU0-0.023-0.01626.6210.2990.2990.0000.0000.0000.000
190A191THR00.0150.01529.2220.1040.1040.0000.0000.0000.000
191A192PRO00.0440.00026.3940.3600.3600.0000.0000.0000.000
192A193ALA00.0090.00225.1460.5310.5310.0000.0000.0000.000
193A194TYR00.0060.00125.2780.5100.5100.0000.0000.0000.000
194A195ILE00.0550.02021.5740.3610.3610.0000.0000.0000.000
195A196THR0-0.040-0.01920.6010.7550.7550.0000.0000.0000.000
196A197LYS10.9300.96920.473-11.804-11.8040.0000.0000.0000.000
197A198LYS10.8670.93420.880-12.785-12.7850.0000.0000.0000.000
198A199ARG10.7720.86014.466-19.237-19.2370.0000.0000.0000.000
199A200GLY00.0010.00816.0641.2351.2350.0000.0000.0000.000
200A201GLU-1-0.829-0.92017.45113.74813.7480.0000.0000.0000.000
201A202TRP00.0150.00015.4600.5570.5570.0000.0000.0000.000
202A203LYS10.8630.92911.132-23.738-23.7380.0000.0000.0000.000
203A204ASP-1-0.853-0.94513.74718.26618.2660.0000.0000.0000.000
204A205LEU0-0.0340.02416.3960.0920.0920.0000.0000.0000.000
205A206ILE00.0180.01010.0620.1490.1490.0000.0000.0000.000
206A207THR0-0.045-0.03411.9190.0600.0600.0000.0000.0000.000
207A208THR0-0.018-0.02013.447-0.611-0.6110.0000.0000.0000.000
208A209LEU0-0.053-0.03015.101-0.556-0.5560.0000.0000.0000.000
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