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: R9718

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2568282.76755
FMO2-HF: Nuclear repulsion 2484261.399411
FMO2-HF: Total energy -84021.368139
FMO2-MP2: Total energy -84265.732554


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.
-67.437-79.97552.122-20.173-19.4110.18
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 : -0.828 / q_NPA : -0.874
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].
3A4VAL00.017-0.0013.7169.23110.8460.022-0.669-0.9680.002
4A5VAL0-0.040-0.0095.355-4.223-4.2230.0000.0000.0000.000
5A6LEU0-0.024-0.0217.632-4.677-4.6770.0000.0000.0000.000
6A7SER00.0080.0049.8922.8462.8460.0000.0000.0000.000
7A8TYR0-0.061-0.03712.574-1.566-1.5660.0000.0000.0000.000
8A9MET00.0020.02315.6990.2380.2380.0000.0000.0000.000
9A10ASP-1-0.880-0.92116.78117.43217.4320.0000.0000.0000.000
10A11SER0-0.095-0.04913.5381.4061.4060.0000.0000.0000.000
11A12LEU0-0.031-0.0307.2830.5110.5110.0000.0000.0000.000
12A13LEU00.0100.0067.7001.4031.4030.0000.0000.0000.000
13A14ARG10.8920.9211.959-105.677-109.79620.311-7.969-8.2230.069
14A15GLN00.0260.0062.473-12.838-11.5442.911-1.484-2.7210.020
15A16SER0-0.042-0.0411.735-40.735-52.57628.814-9.806-7.1670.085
16A17ASP-1-0.715-0.8373.67538.18938.7020.064-0.245-0.3320.004
17A18VAL00.004-0.0125.914-7.526-7.5260.0000.0000.0000.000
18A19SER0-0.043-0.0316.013-6.119-6.1190.0000.0000.0000.000
19A20LEU0-0.043-0.0088.292-3.899-3.8990.0000.0000.0000.000
20A21LEU00.0160.00910.475-3.045-3.0450.0000.0000.0000.000
21A22ASP-1-0.817-0.87111.40122.73522.7350.0000.0000.0000.000
22A23PRO0-0.0350.00113.8110.4900.4900.0000.0000.0000.000
23A24PRO0-0.042-0.02916.6190.0140.0140.0000.0000.0000.000
24A25SER0-0.005-0.00812.427-0.151-0.1510.0000.0000.0000.000
25A26TRP0-0.037-0.01114.533-0.543-0.5430.0000.0000.0000.000
26A27LEU00.0090.00912.9341.7551.7550.0000.0000.0000.000
27A28ASN00.010-0.0108.316-2.595-2.5950.0000.0000.0000.000
28A29ASP-1-0.825-0.92611.03726.61326.6130.0000.0000.0000.000
29A30HIS0-0.040-0.0276.918-4.427-4.4270.0000.0000.0000.000
30A31ILE0-0.0030.0039.338-1.612-1.6120.0000.0000.0000.000
31A32ILE0-0.029-0.00812.369-1.794-1.7940.0000.0000.0000.000
32A33GLY00.0430.01114.786-1.425-1.4250.0000.0000.0000.000
33A34PHE00.0130.00213.057-1.038-1.0380.0000.0000.0000.000
34A35ALA0-0.009-0.00515.074-1.187-1.1870.0000.0000.0000.000
35A36PHE0-0.033-0.03317.655-1.161-1.1610.0000.0000.0000.000
36A37GLU-1-0.769-0.89117.40515.72715.7270.0000.0000.0000.000
37A38TYR0-0.006-0.00118.251-1.017-1.0170.0000.0000.0000.000
38A39PHE0-0.049-0.03420.139-0.774-0.7740.0000.0000.0000.000
39A40ALA0-0.008-0.00622.771-0.659-0.6590.0000.0000.0000.000
40A41ASN0-0.036-0.02421.298-1.063-1.0630.0000.0000.0000.000
41A42SER0-0.050-0.01722.488-0.298-0.2980.0000.0000.0000.000
42A43GLN0-0.043-0.01423.803-0.172-0.1720.0000.0000.0000.000
43A44PHE00.011-0.01725.693-0.575-0.5750.0000.0000.0000.000
44A45HIS00.0100.02126.707-0.520-0.5200.0000.0000.0000.000
45A46ASP-1-0.783-0.86128.29310.13610.1360.0000.0000.0000.000
46A47CYS0-0.079-0.04130.740-0.405-0.4050.0000.0000.0000.000
47A48SER00.0260.01430.0650.0160.0160.0000.0000.0000.000
48A49ASP-1-0.918-0.94731.1289.3389.3380.0000.0000.0000.000
49A50HIS0-0.037-0.02733.891-0.220-0.2200.0000.0000.0000.000
50A51VAL0-0.032-0.01728.742-0.088-0.0880.0000.0000.0000.000
51A52SER00.0220.01727.3520.2720.2720.0000.0000.0000.000
52A53PHE00.0460.00523.038-0.222-0.2220.0000.0000.0000.000
53A54ILE00.0240.01622.6690.6060.6060.0000.0000.0000.000
54A55SER00.031-0.02117.689-0.363-0.3630.0000.0000.0000.000
55A56PRO00.0090.01116.115-0.759-0.7590.0000.0000.0000.000
56A57GLU-1-0.809-0.87614.55019.99919.9990.0000.0000.0000.000
57A58VAL00.0110.01317.859-0.820-0.8200.0000.0000.0000.000
58A59THR0-0.027-0.02121.244-1.048-1.0480.0000.0000.0000.000
59A60GLN00.022-0.00619.476-0.966-0.9660.0000.0000.0000.000
60A61PHE0-0.004-0.00121.647-0.558-0.5580.0000.0000.0000.000
61A62ILE00.0240.00623.216-0.591-0.5910.0000.0000.0000.000
62A63LYS10.7700.88524.059-13.734-13.7340.0000.0000.0000.000
63A64CYS0-0.063-0.03523.707-0.424-0.4240.0000.0000.0000.000
64A65THR00.0030.01126.261-0.234-0.2340.0000.0000.0000.000
65A66SER0-0.043-0.01127.822-0.221-0.2210.0000.0000.0000.000
66A67ASN0-0.032-0.01329.260-0.084-0.0840.0000.0000.0000.000
67A68PRO00.009-0.00232.294-0.055-0.0550.0000.0000.0000.000
68A69ALA00.0300.01833.617-0.266-0.2660.0000.0000.0000.000
69A70GLU-1-0.889-0.93728.77110.56610.5660.0000.0000.0000.000
70A71ILE00.009-0.01128.9250.1950.1950.0000.0000.0000.000
71A72ALA00.007-0.00429.9990.1050.1050.0000.0000.0000.000
72A73MET0-0.033-0.01929.7450.0570.0570.0000.0000.0000.000
73A74PHE0-0.002-0.00121.6290.1660.1660.0000.0000.0000.000
74A75LEU00.004-0.00127.1210.3170.3170.0000.0000.0000.000
75A76GLU-1-0.931-0.95029.2829.2169.2160.0000.0000.0000.000
76A77PRO0-0.065-0.04427.675-0.176-0.1760.0000.0000.0000.000
77A78LEU00.0030.00625.3130.1600.1600.0000.0000.0000.000
78A79ASP-1-0.818-0.89029.3829.1509.1500.0000.0000.0000.000
79A80LEU00.0270.01728.599-0.115-0.1150.0000.0000.0000.000
80A81PRO0-0.020-0.00832.691-0.129-0.1290.0000.0000.0000.000
81A82ASN0-0.083-0.06036.026-0.441-0.4410.0000.0000.0000.000
82A83LYS10.8010.92631.060-10.003-10.0030.0000.0000.0000.000
83A84ARG10.8900.93434.288-8.786-8.7860.0000.0000.0000.000
84A85VAL0-0.028-0.02131.100-0.164-0.1640.0000.0000.0000.000
85A86VAL00.0170.00628.4440.2060.2060.0000.0000.0000.000
86A87PHE00.0100.00825.800-0.205-0.2050.0000.0000.0000.000
87A88LEU00.003-0.00324.4020.2440.2440.0000.0000.0000.000
88A89ALA00.0240.02320.128-0.283-0.2830.0000.0000.0000.000
89A90ILE0-0.026-0.00821.3840.4350.4350.0000.0000.0000.000
90A91ASN00.0380.00917.836-0.035-0.0350.0000.0000.0000.000
91A92ASP-1-0.709-0.86521.57814.14614.1460.0000.0000.0000.000
92A93ASN0-0.0010.00118.063-1.336-1.3360.0000.0000.0000.000
93A94SER0-0.030-0.00721.645-0.444-0.4440.0000.0000.0000.000
94A95ASN0-0.041-0.01521.495-0.530-0.5300.0000.0000.0000.000
95A96GLN00.0270.01619.1630.2600.2600.0000.0000.0000.000
96A97ALA0-0.017-0.00218.3660.7750.7750.0000.0000.0000.000
97A98ALA00.0300.01613.408-0.190-0.1900.0000.0000.0000.000
98A99GLY00.006-0.00615.552-0.257-0.2570.0000.0000.0000.000
99A100GLY0-0.008-0.00316.5600.1720.1720.0000.0000.0000.000
100A101THR0-0.134-0.07418.6160.1420.1420.0000.0000.0000.000
101A102HIS0-0.038-0.03020.5300.3620.3620.0000.0000.0000.000
102A103TRP0-0.0110.00015.236-0.214-0.2140.0000.0000.0000.000
103A104SER0-0.041-0.05121.646-0.534-0.5340.0000.0000.0000.000
104A105LEU00.0090.00823.9760.4290.4290.0000.0000.0000.000
105A106LEU0-0.0120.00226.108-0.595-0.5950.0000.0000.0000.000
106A107VAL0-0.005-0.00927.9140.3270.3270.0000.0000.0000.000
107A108TYR00.0080.00630.628-0.415-0.4150.0000.0000.0000.000
108A109LEU0-0.001-0.00233.3260.1160.1160.0000.0000.0000.000
109A110GLN00.0150.01336.149-0.348-0.3480.0000.0000.0000.000
110A111ASP-1-0.913-0.94838.5157.8717.8710.0000.0000.0000.000
111A112LYS10.8340.90239.658-8.256-8.2560.0000.0000.0000.000
112A113ASN00.0130.01339.9120.0900.0900.0000.0000.0000.000
113A114SER0-0.005-0.00338.043-0.180-0.1800.0000.0000.0000.000
114A115PHE00.0460.02232.5050.2190.2190.0000.0000.0000.000
115A116PHE0-0.020-0.01433.435-0.372-0.3720.0000.0000.0000.000
116A117HIS0-0.0100.00029.0680.7270.7270.0000.0000.0000.000
117A118TYR0-0.015-0.04529.004-0.213-0.2130.0000.0000.0000.000
118A119ASP-1-0.740-0.86227.77612.05212.0520.0000.0000.0000.000
119A120SER00.000-0.02125.476-0.223-0.2230.0000.0000.0000.000
120A121HIS0-0.033-0.01826.838-0.224-0.2240.0000.0000.0000.000
121A122SER0-0.0090.00228.802-0.120-0.1200.0000.0000.0000.000
122A123ARG10.9160.96331.417-9.028-9.0280.0000.0000.0000.000
123A124SER00.0220.01427.772-0.136-0.1360.0000.0000.0000.000
124A125ASN00.017-0.00923.421-0.070-0.0700.0000.0000.0000.000
125A126SER0-0.096-0.07127.920-0.094-0.0940.0000.0000.0000.000
126A127VAL00.003-0.00630.756-0.114-0.1140.0000.0000.0000.000
127A128HIS00.0570.04926.224-0.065-0.0650.0000.0000.0000.000
128A129ALA00.0410.01528.3770.0820.0820.0000.0000.0000.000
129A130LYS10.8250.92429.424-9.292-9.2920.0000.0000.0000.000
130A131GLN00.0360.02428.9070.2220.2220.0000.0000.0000.000
131A132VAL0-0.013-0.01226.333-0.017-0.0170.0000.0000.0000.000
132A133ALA0-0.016-0.01129.613-0.123-0.1230.0000.0000.0000.000
133A134GLU-1-0.891-0.96232.7558.9988.9980.0000.0000.0000.000
134A135LYS10.7380.86329.402-11.005-11.0050.0000.0000.0000.000
135A136LEU0-0.014-0.00229.6160.1800.1800.0000.0000.0000.000
136A137GLU-1-0.936-0.96733.0558.2118.2110.0000.0000.0000.000
137A138ALA0-0.077-0.04536.034-0.260-0.2600.0000.0000.0000.000
138A139PHE00.015-0.00233.107-0.107-0.1070.0000.0000.0000.000
139A140LEU0-0.030-0.00432.2110.0690.0690.0000.0000.0000.000
140A141GLY00.0660.03436.180-0.041-0.0410.0000.0000.0000.000
141A142ARG10.8020.88639.100-7.320-7.3200.0000.0000.0000.000
142A143LYS10.9520.97342.485-7.592-7.5920.0000.0000.0000.000
143A144GLY00.0210.00545.092-0.174-0.1740.0000.0000.0000.000
144A145ASP-1-0.874-0.91245.1136.8876.8870.0000.0000.0000.000
145A146LYS10.8820.93243.087-7.435-7.4350.0000.0000.0000.000
146A147LEU00.0520.06337.408-0.006-0.0060.0000.0000.0000.000
147A148ALA0-0.061-0.02940.284-0.153-0.1530.0000.0000.0000.000
148A149PHE00.0680.02732.4180.1940.1940.0000.0000.0000.000
149A150VAL0-0.031-0.00236.607-0.226-0.2260.0000.0000.0000.000
150A151GLU-1-0.782-0.86933.7709.9279.9270.0000.0000.0000.000
151A152GLU-1-0.801-0.87933.8228.6938.6930.0000.0000.0000.000
152A153LYS10.8780.95434.749-8.565-8.5650.0000.0000.0000.000
153A154ALA00.0230.00330.378-0.007-0.0070.0000.0000.0000.000
154A155PRO0-0.056-0.02629.213-0.194-0.1940.0000.0000.0000.000
155A156ALA00.0000.01329.2690.3470.3470.0000.0000.0000.000
156A157GLN00.0190.01423.8990.0240.0240.0000.0000.0000.000
157A158GLN0-0.030-0.02727.075-0.277-0.2770.0000.0000.0000.000
158A159ASN0-0.028-0.01622.8370.2120.2120.0000.0000.0000.000
159A160SER00.0300.00822.794-0.086-0.0860.0000.0000.0000.000
160A161TYR00.0090.00318.2920.1620.1620.0000.0000.0000.000
161A162ASP-1-0.715-0.84718.92416.58516.5850.0000.0000.0000.000
162A163CYS0-0.0640.00320.7190.2390.2390.0000.0000.0000.000
163A164GLY00.0820.02918.122-0.275-0.2750.0000.0000.0000.000
164A165MET00.0240.01917.7590.3770.3770.0000.0000.0000.000
165A166TYR00.004-0.00319.999-0.483-0.4830.0000.0000.0000.000
166A167VAL0-0.0020.02721.212-0.617-0.6170.0000.0000.0000.000
167A168ILE00.0320.03618.198-0.563-0.5630.0000.0000.0000.000
168A169CYS0-0.023-0.01421.657-0.507-0.5070.0000.0000.0000.000
169A170ASN0-0.023-0.04424.331-1.005-1.0050.0000.0000.0000.000
170A171THR00.0110.00323.988-0.476-0.4760.0000.0000.0000.000
171A172GLU-1-0.787-0.88224.29312.72412.7240.0000.0000.0000.000
172A173ALA0-0.012-0.01426.214-0.464-0.4640.0000.0000.0000.000
173A174LEU0-0.017-0.00529.374-0.453-0.4530.0000.0000.0000.000
174A175CYS0-0.0280.00127.928-0.348-0.3480.0000.0000.0000.000
175A176GLN0-0.002-0.00729.462-0.297-0.2970.0000.0000.0000.000
176A177ASN0-0.032-0.03031.898-0.340-0.3400.0000.0000.0000.000
177A178PHE0-0.057-0.02832.350-0.304-0.3040.0000.0000.0000.000
178A179PHE0-0.004-0.01030.748-0.254-0.2540.0000.0000.0000.000
179A180ARG10.7500.84729.925-10.370-10.3700.0000.0000.0000.000
180A181GLN0-0.036-0.01235.150-0.102-0.1020.0000.0000.0000.000
181A182GLN0-0.0370.00134.218-0.201-0.2010.0000.0000.0000.000
182A183THR00.000-0.01737.176-0.088-0.0880.0000.0000.0000.000
183A184GLU-1-0.902-0.93933.4538.9118.9110.0000.0000.0000.000
184A185SER00.0000.00835.5940.1560.1560.0000.0000.0000.000
185A186LEU00.0700.02430.6350.1200.1200.0000.0000.0000.000
186A187LEU0-0.052-0.03832.1110.2220.2220.0000.0000.0000.000
187A188GLN0-0.062-0.01234.430-0.237-0.2370.0000.0000.0000.000
188A189LEU00.0290.01629.7350.0590.0590.0000.0000.0000.000
189A190LEU0-0.044-0.00426.9360.2710.2710.0000.0000.0000.000
190A191THR00.013-0.00229.1220.1590.1590.0000.0000.0000.000
191A192PRO00.0530.00626.2520.3740.3740.0000.0000.0000.000
192A193ALA00.0020.02125.3060.5210.5210.0000.0000.0000.000
193A194TYR00.0050.00725.6250.2270.2270.0000.0000.0000.000
194A195ILE00.013-0.00122.1920.4910.4910.0000.0000.0000.000
195A196THR0-0.021-0.03620.9850.6610.6610.0000.0000.0000.000
196A197LYS10.8490.91420.775-11.723-11.7230.0000.0000.0000.000
197A198LYS10.8310.90421.017-12.900-12.9000.0000.0000.0000.000
198A199ARG10.7610.85514.722-18.808-18.8080.0000.0000.0000.000
199A200GLY00.0080.02016.2881.1371.1370.0000.0000.0000.000
200A201GLU-1-0.780-0.87717.48813.91213.9120.0000.0000.0000.000
201A202TRP00.0270.01115.7100.5220.5220.0000.0000.0000.000
202A203LYS10.8600.91811.239-23.824-23.8240.0000.0000.0000.000
203A204ASP-1-0.897-0.94514.03317.97217.9720.0000.0000.0000.000
204A205LEU0-0.0360.00616.839-0.060-0.0600.0000.0000.0000.000
205A206ILE00.005-0.00410.3840.2430.2430.0000.0000.0000.000
206A207THR0-0.030-0.03611.7160.2530.2530.0000.0000.0000.000
207A208THR0-0.034-0.02313.658-0.673-0.6730.0000.0000.0000.000
208A209LEU0-0.033-0.01215.117-0.525-0.5250.0000.0000.0000.000
209A210ALA00.0000.02111.711-0.183-0.1830.0000.0000.0000.000
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