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: Z642N

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2562584.51949
FMO2-HF: Nuclear repulsion 2478563.860954
FMO2-HF: Total energy -84020.658536
FMO2-MP2: Total energy -84265.143985


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.
-44.064-60.52353.318-18.874-17.9840.156
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 : -0.822 / q_NPA : -0.876
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].
3A4VAL00.0120.0143.18312.67115.1580.336-1.243-1.5800.002
4A5VAL0-0.048-0.0284.893-3.656-3.521-0.001-0.007-0.1270.000
5A6LEU0-0.019-0.0157.257-4.684-4.6840.0000.0000.0000.000
6A7SER00.0140.01010.0472.0942.0940.0000.0000.0000.000
7A8TYR0-0.057-0.03812.435-1.692-1.6920.0000.0000.0000.000
8A9MET0-0.031-0.00415.262-0.012-0.0120.0000.0000.0000.000
9A10ASP-1-0.859-0.91916.90217.30717.3070.0000.0000.0000.000
10A11SER0-0.100-0.02713.2881.2481.2480.0000.0000.0000.000
11A12LEU0-0.034-0.0317.6290.3900.3900.0000.0000.0000.000
12A13LEU00.0130.0067.5471.4951.4950.0000.0000.0000.000
13A14ARG10.8990.9402.425-77.608-73.2952.054-2.525-3.8420.023
14A15GLN00.0300.0092.243-13.462-14.8677.542-2.166-3.9700.030
15A16SER0-0.074-0.0671.557-43.095-65.62443.341-12.670-8.1420.097
16A17ASP-1-0.710-0.8353.80537.06537.6050.046-0.263-0.3230.004
17A18VAL00.013-0.0025.790-7.849-7.8490.0000.0000.0000.000
18A19SER0-0.048-0.0405.851-6.457-6.4570.0000.0000.0000.000
19A20LEU0-0.038-0.0018.148-4.071-4.0710.0000.0000.0000.000
20A21LEU0-0.001-0.00810.319-3.244-3.2440.0000.0000.0000.000
21A22ASP-1-0.841-0.87611.48222.77022.7700.0000.0000.0000.000
22A23PRO0-0.0230.00913.8480.3760.3760.0000.0000.0000.000
23A24PRO0-0.051-0.03416.7600.0050.0050.0000.0000.0000.000
24A25SER0-0.004-0.01012.359-0.127-0.1270.0000.0000.0000.000
25A26TRP0-0.0090.00514.034-0.738-0.7380.0000.0000.0000.000
26A27LEU00.0060.00612.5061.8411.8410.0000.0000.0000.000
27A28ASN00.0350.0047.881-3.144-3.1440.0000.0000.0000.000
28A29ASP-1-0.844-0.94311.35425.26625.2660.0000.0000.0000.000
29A30HIS0-0.037-0.0236.782-4.575-4.5750.0000.0000.0000.000
30A31ILE0-0.014-0.0019.491-1.593-1.5930.0000.0000.0000.000
31A32ILE0-0.036-0.01712.397-1.572-1.5720.0000.0000.0000.000
32A33GLY00.0560.02014.623-1.272-1.2720.0000.0000.0000.000
33A34PHE00.0110.00712.802-1.066-1.0660.0000.0000.0000.000
34A35ALA0-0.015-0.00814.836-1.311-1.3110.0000.0000.0000.000
35A36PHE0-0.015-0.03417.618-1.128-1.1280.0000.0000.0000.000
36A37GLU-1-0.751-0.87517.19115.75515.7550.0000.0000.0000.000
37A38TYR0-0.024-0.01418.093-1.073-1.0730.0000.0000.0000.000
38A39PHE0-0.045-0.03319.917-0.770-0.7700.0000.0000.0000.000
39A40ALA00.0070.00422.647-0.695-0.6950.0000.0000.0000.000
40A41ASN0-0.007-0.00821.112-1.034-1.0340.0000.0000.0000.000
41A42SER0-0.052-0.01722.178-0.489-0.4890.0000.0000.0000.000
42A43GLN0-0.049-0.02023.502-0.150-0.1500.0000.0000.0000.000
43A44PHE0-0.025-0.03925.393-0.616-0.6160.0000.0000.0000.000
44A45HIS00.0170.02326.646-0.547-0.5470.0000.0000.0000.000
45A46ASP-1-0.780-0.84828.04110.06810.0680.0000.0000.0000.000
46A47CYS0-0.127-0.06530.613-0.442-0.4420.0000.0000.0000.000
47A48SER00.0630.02029.8970.0670.0670.0000.0000.0000.000
48A49ASP-1-0.929-0.94930.8619.3279.3270.0000.0000.0000.000
49A50HIS0-0.036-0.02433.768-0.225-0.2250.0000.0000.0000.000
50A51VAL0-0.051-0.03728.449-0.046-0.0460.0000.0000.0000.000
51A52SER00.0590.04827.2440.1860.1860.0000.0000.0000.000
52A53PHE00.000-0.01323.130-0.170-0.1700.0000.0000.0000.000
53A54ILE0-0.005-0.01322.9920.3690.3690.0000.0000.0000.000
54A55SER00.023-0.02117.703-0.293-0.2930.0000.0000.0000.000
55A56PRO00.0310.01716.058-0.840-0.8400.0000.0000.0000.000
56A57GLU-1-0.806-0.87914.71619.64719.6470.0000.0000.0000.000
57A58VAL00.0240.01918.052-0.810-0.8100.0000.0000.0000.000
58A59THR0-0.030-0.02321.316-1.052-1.0520.0000.0000.0000.000
59A60GLN00.008-0.01119.787-0.978-0.9780.0000.0000.0000.000
60A61PHE00.0090.00621.979-0.584-0.5840.0000.0000.0000.000
61A62ILE00.0160.00923.523-0.622-0.6220.0000.0000.0000.000
62A63LYS10.7810.89723.932-13.658-13.6580.0000.0000.0000.000
63A64CYS0-0.052-0.03523.932-0.323-0.3230.0000.0000.0000.000
64A65THR00.0300.02826.584-0.237-0.2370.0000.0000.0000.000
65A66SER0-0.082-0.02628.198-0.216-0.2160.0000.0000.0000.000
66A67ASN0-0.054-0.02929.2660.0100.0100.0000.0000.0000.000
67A68PRO00.0220.00832.268-0.073-0.0730.0000.0000.0000.000
68A69ALA00.0160.01433.945-0.275-0.2750.0000.0000.0000.000
69A70GLU-1-0.863-0.92228.97510.40610.4060.0000.0000.0000.000
70A71ILE0-0.005-0.03029.4230.2080.2080.0000.0000.0000.000
71A72ALA0-0.003-0.00430.3340.1690.1690.0000.0000.0000.000
72A73MET0-0.021-0.02030.3260.1120.1120.0000.0000.0000.000
73A74PHE00.0010.00622.1970.1650.1650.0000.0000.0000.000
74A75LEU00.023-0.00227.1970.3030.3030.0000.0000.0000.000
75A76GLU-1-0.958-0.95829.2439.2149.2140.0000.0000.0000.000
76A77PRO0-0.045-0.03328.016-0.189-0.1890.0000.0000.0000.000
77A78LEU0-0.004-0.00525.5000.0510.0510.0000.0000.0000.000
78A79ASP-1-0.805-0.88229.5569.1219.1210.0000.0000.0000.000
79A80LEU00.0340.01328.644-0.113-0.1130.0000.0000.0000.000
80A81PRO0-0.027-0.00432.739-0.132-0.1320.0000.0000.0000.000
81A82ASN0-0.112-0.07035.850-0.467-0.4670.0000.0000.0000.000
82A83LYS10.8150.93431.305-9.973-9.9730.0000.0000.0000.000
83A84ARG10.8780.92234.530-8.871-8.8710.0000.0000.0000.000
84A85VAL0-0.029-0.02530.909-0.147-0.1470.0000.0000.0000.000
85A86VAL00.0130.01528.2560.2420.2420.0000.0000.0000.000
86A87PHE00.0180.01325.567-0.205-0.2050.0000.0000.0000.000
87A88LEU00.0290.01824.2760.3240.3240.0000.0000.0000.000
88A89ALA00.0210.02420.075-0.267-0.2670.0000.0000.0000.000
89A90ILE0-0.030-0.02021.4830.3300.3300.0000.0000.0000.000
90A91ASN00.0600.02617.768-0.102-0.1020.0000.0000.0000.000
91A92ASP-1-0.752-0.87721.41913.88113.8810.0000.0000.0000.000
92A93ASN00.0260.00818.415-1.231-1.2310.0000.0000.0000.000
93A94SER0-0.033-0.00621.810-0.308-0.3080.0000.0000.0000.000
94A95ASN0-0.042-0.01721.514-0.360-0.3600.0000.0000.0000.000
95A96GLN00.0180.00719.4300.3340.3340.0000.0000.0000.000
96A97ALA0-0.026-0.00518.5510.7450.7450.0000.0000.0000.000
97A98ALA00.0320.01613.402-0.037-0.0370.0000.0000.0000.000
98A99GLY0-0.002-0.01415.388-0.562-0.5620.0000.0000.0000.000
99A100GLY0-0.0150.00516.1940.5200.5200.0000.0000.0000.000
100A101THR0-0.136-0.07818.0420.3720.3720.0000.0000.0000.000
101A102HIS0-0.034-0.03920.3590.5500.5500.0000.0000.0000.000
102A103TRP0-0.013-0.01114.940-0.401-0.4010.0000.0000.0000.000
103A104SER0-0.034-0.05421.173-0.522-0.5220.0000.0000.0000.000
104A105LEU00.0080.02123.6850.4280.4280.0000.0000.0000.000
105A106LEU0-0.025-0.01325.722-0.568-0.5680.0000.0000.0000.000
106A107VAL0-0.019-0.01828.0540.2330.2330.0000.0000.0000.000
107A108TYR00.0220.01530.568-0.417-0.4170.0000.0000.0000.000
108A109LEU00.0140.00433.1380.0840.0840.0000.0000.0000.000
109A110GLN00.0280.02136.046-0.355-0.3550.0000.0000.0000.000
110A111ASP-1-0.935-0.94838.4687.7817.7810.0000.0000.0000.000
111A112LYS10.8680.91339.411-8.259-8.2590.0000.0000.0000.000
112A113ASN0-0.0040.00839.8300.0450.0450.0000.0000.0000.000
113A114SER00.003-0.00838.191-0.213-0.2130.0000.0000.0000.000
114A115PHE00.0170.00132.2750.2150.2150.0000.0000.0000.000
115A116PHE0-0.026-0.01933.314-0.304-0.3040.0000.0000.0000.000
116A117HIS0-0.0130.00428.7490.7600.7600.0000.0000.0000.000
117A118TYR00.032-0.00128.614-0.274-0.2740.0000.0000.0000.000
118A119ASP-1-0.730-0.85927.37512.15612.1560.0000.0000.0000.000
119A120SER0-0.023-0.02825.089-0.183-0.1830.0000.0000.0000.000
120A121HIS0-0.036-0.02226.835-0.269-0.2690.0000.0000.0000.000
121A122SER0-0.005-0.01028.681-0.037-0.0370.0000.0000.0000.000
122A123ARG10.9290.96831.680-8.908-8.9080.0000.0000.0000.000
123A124SER00.0270.03327.362-0.180-0.1800.0000.0000.0000.000
124A125ASN00.034-0.00723.492-0.141-0.1410.0000.0000.0000.000
125A126SER0-0.082-0.05828.001-0.161-0.1610.0000.0000.0000.000
126A127VAL00.011-0.00230.876-0.122-0.1220.0000.0000.0000.000
127A128HIS00.0600.04526.400-0.059-0.0590.0000.0000.0000.000
128A129ALA00.0310.01628.5490.0670.0670.0000.0000.0000.000
129A130LYS10.8640.94529.467-9.241-9.2410.0000.0000.0000.000
130A131GLN00.0220.01429.0550.1680.1680.0000.0000.0000.000
131A132VAL0-0.009-0.01926.456-0.084-0.0840.0000.0000.0000.000
132A133ALA0-0.006-0.00129.780-0.077-0.0770.0000.0000.0000.000
133A134GLU-1-0.867-0.94432.8218.8998.8990.0000.0000.0000.000
134A135LYS10.7390.86629.920-10.799-10.7990.0000.0000.0000.000
135A136LEU0-0.013-0.00629.7260.1690.1690.0000.0000.0000.000
136A137GLU-1-1.012-0.99133.2408.1138.1130.0000.0000.0000.000
137A138ALA0-0.030-0.02435.782-0.242-0.2420.0000.0000.0000.000
138A139PHE0-0.010-0.01333.366-0.116-0.1160.0000.0000.0000.000
139A140LEU0-0.0190.00332.4490.0190.0190.0000.0000.0000.000
140A141GLY00.0540.02836.543-0.061-0.0610.0000.0000.0000.000
141A142ARG10.8250.89638.936-7.350-7.3500.0000.0000.0000.000
142A143LYS10.9670.98742.526-7.468-7.4680.0000.0000.0000.000
143A144GLY0-0.0070.00045.061-0.132-0.1320.0000.0000.0000.000
144A145ASP-1-0.850-0.91144.9086.8796.8790.0000.0000.0000.000
145A146LYS10.9370.95944.070-7.303-7.3030.0000.0000.0000.000
146A147LEU00.0320.04237.3040.0200.0200.0000.0000.0000.000
147A148ALA0-0.072-0.01840.4180.0040.0040.0000.0000.0000.000
148A149PHE00.0570.02832.2820.1670.1670.0000.0000.0000.000
149A150VAL0-0.014-0.01136.604-0.203-0.2030.0000.0000.0000.000
150A151GLU-1-0.848-0.89233.33310.02710.0270.0000.0000.0000.000
151A152GLU-1-0.876-0.93533.7838.4678.4670.0000.0000.0000.000
152A153LYS10.8990.96134.190-8.497-8.4970.0000.0000.0000.000
153A154ALA00.0240.00630.485-0.004-0.0040.0000.0000.0000.000
154A155PRO0-0.050-0.02228.893-0.104-0.1040.0000.0000.0000.000
155A156ALA00.0020.01129.2760.2670.2670.0000.0000.0000.000
156A157GLN00.0000.00423.320-0.016-0.0160.0000.0000.0000.000
157A158GLN0-0.026-0.02627.149-0.246-0.2460.0000.0000.0000.000
158A159ASN0-0.045-0.02222.7820.1820.1820.0000.0000.0000.000
159A160SER00.024-0.00822.889-0.055-0.0550.0000.0000.0000.000
160A161TYR00.0060.00118.1490.0730.0730.0000.0000.0000.000
161A162ASP-1-0.715-0.83818.63616.80816.8080.0000.0000.0000.000
162A163CYS0-0.0520.00920.3400.2060.2060.0000.0000.0000.000
163A164GLY00.0830.02117.797-0.275-0.2750.0000.0000.0000.000
164A165MET00.0310.02517.8410.4570.4570.0000.0000.0000.000
165A166TYR00.0070.01419.987-0.547-0.5470.0000.0000.0000.000
166A167VAL0-0.0030.02920.911-0.604-0.6040.0000.0000.0000.000
167A168ILE00.0270.03217.985-0.491-0.4910.0000.0000.0000.000
168A169CYS0-0.035-0.02821.428-0.490-0.4900.0000.0000.0000.000
169A170ASN0-0.016-0.03324.140-0.959-0.9590.0000.0000.0000.000
170A171THR00.0110.00323.981-0.531-0.5310.0000.0000.0000.000
171A172GLU-1-0.806-0.87524.08712.87912.8790.0000.0000.0000.000
172A173ALA0-0.019-0.02126.055-0.482-0.4820.0000.0000.0000.000
173A174LEU0-0.014-0.00929.190-0.437-0.4370.0000.0000.0000.000
174A175CYS0-0.0240.00327.924-0.370-0.3700.0000.0000.0000.000
175A176GLN00.0030.00229.292-0.331-0.3310.0000.0000.0000.000
176A177ASN0-0.035-0.03531.755-0.284-0.2840.0000.0000.0000.000
177A178PHE0-0.079-0.03432.281-0.309-0.3090.0000.0000.0000.000
178A179PHE00.002-0.01630.623-0.299-0.2990.0000.0000.0000.000
179A180ARG10.7330.84429.710-10.492-10.4920.0000.0000.0000.000
180A181GLN0-0.031-0.01334.929-0.113-0.1130.0000.0000.0000.000
181A182GLN0-0.0290.00533.858-0.184-0.1840.0000.0000.0000.000
182A183THR00.007-0.01436.790-0.093-0.0930.0000.0000.0000.000
183A184GLU-1-0.913-0.94133.5548.9698.9690.0000.0000.0000.000
184A185SER00.0010.01636.0270.0910.0910.0000.0000.0000.000
185A186LEU00.0650.02230.5910.0910.0910.0000.0000.0000.000
186A187LEU0-0.047-0.02732.2040.2040.2040.0000.0000.0000.000
187A188GLN0-0.037-0.00834.294-0.121-0.1210.0000.0000.0000.000
188A189LEU0-0.014-0.00429.9040.0560.0560.0000.0000.0000.000
189A190LEU0-0.026-0.01626.9820.2900.2900.0000.0000.0000.000
190A191THR00.0180.01229.4790.0890.0890.0000.0000.0000.000
191A192PRO00.0490.00326.6770.3620.3620.0000.0000.0000.000
192A193ALA00.0000.00125.4190.5040.5040.0000.0000.0000.000
193A194TYR00.0250.01025.5230.3340.3340.0000.0000.0000.000
194A195ILE00.0380.01121.9850.4040.4040.0000.0000.0000.000
195A196THR0-0.007-0.01120.8570.6230.6230.0000.0000.0000.000
196A197LYS10.8790.93320.709-11.760-11.7600.0000.0000.0000.000
197A198LYS10.8720.92821.055-13.010-13.0100.0000.0000.0000.000
198A199ARG10.7660.85314.782-19.046-19.0460.0000.0000.0000.000
199A200GLY0-0.0030.00616.2721.2401.2400.0000.0000.0000.000
200A201GLU-1-0.811-0.89417.60313.79713.7970.0000.0000.0000.000
201A202TRP00.004-0.00715.7030.5750.5750.0000.0000.0000.000
202A203LYS10.8240.90211.241-23.964-23.9640.0000.0000.0000.000
203A204ASP-1-0.872-0.94913.84318.39818.3980.0000.0000.0000.000
204A205LEU0-0.0430.00816.4400.0580.0580.0000.0000.0000.000
205A206ILE00.0150.00710.1490.2230.2230.0000.0000.0000.000
206A207THR0-0.004-0.01011.5480.0640.0640.0000.0000.0000.000
207A208THR0-0.028-0.02313.446-0.586-0.5860.0000.0000.0000.000
208A209LEU0-0.041-0.01915.052-0.535-0.5350.0000.0000.0000.000
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