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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 8J1VY

Calculation Name: 1WJ9-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WJ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WG9

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2101782.78667
FMO2-HF: Nuclear repulsion 2028427.776315
FMO2-HF: Total energy -73355.010355
FMO2-MP2: Total energy -73574.647796


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:1:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
11.00527.89725.524-14.521-27.897-0.158
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.732 / q_NPA : 0.881
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].
3A3LEU 0-0.016-0.0073.7774.6346.208-0.001-0.630-0.943-0.002
4A4THR 00.0540.0275.5782.7962.7960.0000.0000.0000.000
5A5LYS 10.9210.9689.09721.18821.1880.0000.0000.0000.000
6A6LEU 00.0430.02912.1260.6310.6310.0000.0000.0000.000
7A7VAL 00.0050.00914.8690.1760.1760.0000.0000.0000.000
8A8LEU 00.0160.00017.2480.3410.3410.0000.0000.0000.000
9A9ASN 00.0770.04220.3110.6850.6850.0000.0000.0000.000
10A10PRO 00.012-0.00823.9140.1670.1670.0000.0000.0000.000
11A11ALA 00.0390.03026.4020.4210.4210.0000.0000.0000.000
12A12SER 00.0210.02724.8010.3730.3730.0000.0000.0000.000
13A13ARG 10.9700.97526.7379.9339.9330.0000.0000.0000.000
14A14ALA 00.0270.00124.451-0.009-0.0090.0000.0000.0000.000
15A15ALA 00.0800.03822.343-0.310-0.3100.0000.0000.0000.000
16A16ARG 10.8730.92523.0119.8949.8940.0000.0000.0000.000
17A17ARG 10.8060.90223.32212.38312.3830.0000.0000.0000.000
18A18ASP -1-0.741-0.85620.139-13.870-13.8700.0000.0000.0000.000
19A19LEU 0-0.049-0.02920.096-0.310-0.3100.0000.0000.0000.000
20A20ALA 0-0.0160.00622.2250.0430.0430.0000.0000.0000.000
21A21ASN 00.0310.01723.437-0.002-0.0020.0000.0000.0000.000
22A22PRO 00.0600.01619.159-0.471-0.4710.0000.0000.0000.000
23A23TYR 00.0140.01018.858-0.744-0.7440.0000.0000.0000.000
24A24GLU -1-0.902-0.94620.067-12.482-12.4820.0000.0000.0000.000
25A25MET 00.0210.02616.169-0.528-0.5280.0000.0000.0000.000
26A26HIS 00.0260.02912.167-0.811-0.8110.0000.0000.0000.000
27A27ARG 10.9070.97415.92511.86011.8600.0000.0000.0000.000
28A28THR 0-0.045-0.04717.687-0.155-0.1550.0000.0000.0000.000
29A29LEU 0-0.011-0.01312.380-0.649-0.6490.0000.0000.0000.000
30A30SER 0-0.029-0.03513.364-1.523-1.5230.0000.0000.0000.000
31A31LYS 10.9230.96614.30914.16614.1660.0000.0000.0000.000
32A32ALA 00.0260.03512.2010.1970.1970.0000.0000.0000.000
33A33VAL 00.0010.0038.305-1.474-1.4740.0000.0000.0000.000
34A34SER 00.0150.00811.708-0.231-0.2310.0000.0000.0000.000
35A35ARG 11.0331.02214.62816.85216.8520.0000.0000.0000.000
36A36ALA 0-0.004-0.0019.7840.1600.1600.0000.0000.0000.000
37A37LEU 0-0.067-0.04511.128-0.131-0.1310.0000.0000.0000.000
38A38GLU -1-0.976-0.96713.167-14.791-14.7910.0000.0000.0000.000
39A39GLU -1-0.919-0.96814.358-18.645-18.6450.0000.0000.0000.000
40A40GLY 0-0.0180.00213.704-0.272-0.2720.0000.0000.0000.000
41A41ARG 10.8860.94410.11423.93323.9330.0000.0000.0000.000
42A42GLU -1-0.699-0.8256.452-44.572-44.5720.0000.0000.0000.000
43A43ARG 10.8210.8975.93428.24128.2410.0000.0000.0000.000
44A44LEU 00.0280.0346.107-3.398-3.3980.0000.0000.0000.000
45A45LEU 0-0.051-0.0265.8423.1823.1820.0000.0000.0000.000
46A46TRP 00.001-0.0028.273-1.633-1.6330.0000.0000.0000.000
47A47ARG 10.7950.86810.58822.05322.0530.0000.0000.0000.000
48A48LEU 00.0470.04613.248-0.483-0.4830.0000.0000.0000.000
49A49GLU -1-0.791-0.87913.539-18.653-18.6530.0000.0000.0000.000
50A50PRO 0-0.041-0.02617.0510.6460.6460.0000.0000.0000.000
51A51ALA 00.0240.02220.579-0.178-0.1780.0000.0000.0000.000
52A52ARG 10.9660.98421.78613.11513.1150.0000.0000.0000.000
53A53GLY 00.0310.01025.2870.0760.0760.0000.0000.0000.000
54A54LEU 00.007-0.00727.905-0.097-0.0970.0000.0000.0000.000
55A55GLU -1-0.963-0.96325.123-10.818-10.8180.0000.0000.0000.000
56A56PRO 0-0.013-0.00722.633-0.213-0.2130.0000.0000.0000.000
57A57PRO 0-0.0010.00620.484-0.438-0.4380.0000.0000.0000.000
58A58VAL 00.0060.00414.985-0.467-0.4670.0000.0000.0000.000
59A59VAL 00.008-0.00412.7930.0890.0890.0000.0000.0000.000
60A60LEU 0-0.064-0.0168.505-0.649-0.6490.0000.0000.0000.000
61A61VAL 00.018-0.0098.0590.3990.3990.0000.0000.0000.000
62A62GLN 0-0.017-0.0342.599-3.945-2.1962.639-1.124-3.264-0.013
63A63THR 0-0.0090.0003.9743.5773.8590.000-0.065-0.2170.000
64A64LEU 0-0.087-0.0762.340-25.697-22.0063.063-3.259-3.496-0.034
65A65THR 0-0.069-0.0423.329-7.098-6.6460.012-0.145-0.319-0.002
66A66GLU -1-0.926-0.9645.754-32.594-32.5940.0000.0000.0000.000
67A67PRO 0-0.053-0.0206.8922.9032.9030.0000.0000.0000.000
68A68ASP -1-0.784-0.8769.776-18.231-18.2310.0000.0000.0000.000
69A69TRP 0-0.022-0.0629.8411.5441.5440.0000.0000.0000.000
70A70SER 0-0.058-0.02715.1231.2971.2970.0000.0000.0000.000
71A71VAL 0-0.020-0.00416.2460.8910.8910.0000.0000.0000.000
72A72LEU 0-0.116-0.05415.9630.4240.4240.0000.0000.0000.000
73A73ASP -1-0.885-0.93219.818-12.419-12.4190.0000.0000.0000.000
74A74GLU -1-0.895-0.95022.664-11.477-11.4770.0000.0000.0000.000
75A75GLY 0-0.025-0.02024.2620.3410.3410.0000.0000.0000.000
76A76TYR 0-0.098-0.06317.903-0.047-0.0470.0000.0000.0000.000
77A77ALA 0-0.001-0.02818.341-0.074-0.0740.0000.0000.0000.000
78A78GLN 00.0160.03719.1380.2050.2050.0000.0000.0000.000
79A79VAL 00.018-0.00814.144-0.758-0.7580.0000.0000.0000.000
80A80PHE 0-0.063-0.02513.9120.3370.3370.0000.0000.0000.000
81A81PRO 00.011-0.00613.000-1.403-1.4030.0000.0000.0000.000
82A82PRO 00.0090.0138.817-0.960-0.9600.0000.0000.0000.000
83A83LYS 10.9510.9748.13427.22727.2270.0000.0000.0000.000
84A84PRO 00.0370.0314.864-6.516-6.5160.0000.0000.0000.000
85A85PHE 0-0.003-0.0202.2995.7998.4353.921-1.903-4.654-0.008
86A86HIS 00.026-0.0061.999-58.636-53.7338.153-6.415-6.641-0.090
87A87PRO 0-0.0230.0042.7138.0688.8250.596-0.251-1.102-0.001
88A88ALA 00.0780.0405.6070.4820.4820.0000.0000.0000.000
89A89LEU 0-0.028-0.0245.3341.8411.8410.0000.0000.0000.000
90A90LYS 10.9120.9529.29121.58321.5830.0000.0000.0000.000
91A91PRO 00.0430.01312.918-0.095-0.0950.0000.0000.0000.000
92A92GLY 00.0420.03715.3100.3950.3950.0000.0000.0000.000
93A93GLN 0-0.019-0.00110.678-0.123-0.1230.0000.0000.0000.000
94A94ARG 10.9590.97513.73012.50212.5020.0000.0000.0000.000
95A95LEU 0-0.049-0.0208.950-0.653-0.6530.0000.0000.0000.000
96A96ARG 10.8940.94713.17817.63517.6350.0000.0000.0000.000
97A97PHE 0-0.011-0.01311.550-1.551-1.5510.0000.0000.0000.000
98A98ARG 10.8420.90412.02117.54917.5490.0000.0000.0000.000
99A99LEU 0-0.036-0.01211.383-1.470-1.4700.0000.0000.0000.000
100A100ARG 10.9150.97013.62315.97815.9780.0000.0000.0000.000
101A101ALA 00.003-0.01314.708-0.883-0.8830.0000.0000.0000.000
102A102ASN 00.0560.03216.6130.7010.7010.0000.0000.0000.000
103A103PRO 0-0.022-0.02419.244-0.236-0.2360.0000.0000.0000.000
104A104ALA 00.0570.03420.3240.6400.6400.0000.0000.0000.000
105A105LYS 10.9080.95320.07511.26511.2650.0000.0000.0000.000
106A106ARG 10.9510.95320.16811.86611.8660.0000.0000.0000.000
107A107LEU 00.0420.02019.9060.0810.0810.0000.0000.0000.000
108A108NME 00.0290.03922.8150.3250.3250.0000.0000.0000.000
109A116ACE 00.0770.03134.7320.0210.0210.0000.0000.0000.000
110A117LYS 10.9120.94830.7898.7658.7650.0000.0000.0000.000
111A118THR 00.1510.07828.431-0.333-0.3330.0000.0000.0000.000
112A119PRO 00.0420.01527.301-0.349-0.3490.0000.0000.0000.000
113A120ALA 00.0430.00426.198-0.323-0.3230.0000.0000.0000.000
114A121GLU -1-0.949-0.96526.374-9.628-9.6280.0000.0000.0000.000
115A122LYS 10.7920.89323.12010.17710.1770.0000.0000.0000.000
116A123VAL 00.0260.01421.773-0.573-0.5730.0000.0000.0000.000
117A124ALA 00.0610.03921.517-0.392-0.3920.0000.0000.0000.000
118A125TRP 0-0.069-0.03116.275-0.496-0.4960.0000.0000.0000.000
119A126LEU 0-0.035-0.02515.344-0.606-0.6060.0000.0000.0000.000
120A127GLU -1-0.894-0.94817.156-12.498-12.4980.0000.0000.0000.000
121A128ARG 10.9750.99018.21811.74811.7480.0000.0000.0000.000
122A129ARG 10.8230.92415.22113.44713.4470.0000.0000.0000.000
123A130LEU 00.0170.00312.257-0.987-0.9870.0000.0000.0000.000
124A131GLU -1-0.898-0.93313.776-13.392-13.3920.0000.0000.0000.000
125A132GLU -1-1.011-1.01515.865-13.893-13.8930.0000.0000.0000.000
126A133GLY 0-0.076-0.03311.853-0.533-0.5330.0000.0000.0000.000
127A134GLY 00.0080.01710.639-1.530-1.5300.0000.0000.0000.000
128A135PHE 0-0.008-0.0146.792-0.674-0.6740.0000.0000.0000.000
129A136ARG 10.9870.99312.83613.89213.8920.0000.0000.0000.000
130A137LEU 00.0300.01816.156-0.493-0.4930.0000.0000.0000.000
131A138LEU 0-0.026-0.00817.6640.3970.3970.0000.0000.0000.000
132A139GLU -1-0.906-0.95319.847-10.644-10.6440.0000.0000.0000.000
133A140GLY 0-0.027-0.02223.6020.0020.0020.0000.0000.0000.000
134A141GLU -1-0.955-0.97925.915-8.747-8.7470.0000.0000.0000.000
135A142ARG 10.9190.95028.3639.4019.4010.0000.0000.0000.000
136A143GLY 00.0370.03927.187-0.020-0.0200.0000.0000.0000.000
137A144PRO 00.0400.01522.234-0.241-0.2410.0000.0000.0000.000
138A145TRP 00.0060.01220.1020.0930.0930.0000.0000.0000.000
139A146VAL 0-0.056-0.04918.927-0.804-0.8040.0000.0000.0000.000
140A147GLN 0-0.0140.00320.8830.4050.4050.0000.0000.0000.000
141A148ILE 0-0.012-0.01121.230-0.595-0.5950.0000.0000.0000.000
142A149LEU 0-0.022-0.00320.0000.4110.4110.0000.0000.0000.000
143A150GLN 00.006-0.01122.183-0.182-0.1820.0000.0000.0000.000
144A151ASP -1-0.824-0.90222.828-11.307-11.3070.0000.0000.0000.000
145A152THR 00.0140.01223.6330.4970.4970.0000.0000.0000.000
146A153PHE 00.0170.00124.931-0.240-0.2400.0000.0000.0000.000
147A154LEU 0-0.047-0.02119.465-0.061-0.0610.0000.0000.0000.000
148A155GLU -1-0.891-0.94824.201-9.658-9.6580.0000.0000.0000.000
149A156NME 0-0.026-0.00724.167-0.081-0.0810.0000.0000.0000.000
150A169ACE 0-0.003-0.01029.0640.0350.0350.0000.0000.0000.000
151A170GLN 00.0360.01127.651-0.136-0.1360.0000.0000.0000.000
152A171VAL 0-0.0310.00621.345-0.011-0.0110.0000.0000.0000.000
153A172GLN 00.0080.00923.7630.0780.0780.0000.0000.0000.000
154A173ALA 0-0.001-0.00520.362-0.635-0.6350.0000.0000.0000.000
155A174VAL 00.005-0.00120.0320.4000.4000.0000.0000.0000.000
156A175LEU 0-0.056-0.02916.764-0.913-0.9130.0000.0000.0000.000
157A176PHE 00.018-0.00116.7500.6460.6460.0000.0000.0000.000
158A177GLU -1-0.814-0.91616.650-15.580-15.5800.0000.0000.0000.000
159A178GLY 00.0410.01816.5680.8770.8770.0000.0000.0000.000
160A179ARG 10.8880.95515.96613.19313.1930.0000.0000.0000.000
161A180LEU 00.0100.01410.9460.4470.4470.0000.0000.0000.000
162A181GLU -1-0.890-0.96614.237-13.965-13.9650.0000.0000.0000.000
163A182VAL 0-0.017-0.0079.754-0.415-0.4150.0000.0000.0000.000
164A183VAL 0-0.028-0.00512.4190.9620.9620.0000.0000.0000.000
165A184ASP -1-0.857-0.94713.021-17.789-17.7890.0000.0000.0000.000
166A185PRO 00.011-0.0079.780-1.159-1.1590.0000.0000.0000.000
167A186GLU -1-0.859-0.9248.344-28.720-28.7200.0000.0000.0000.000
168A187ARG 10.9190.9628.51614.72714.7270.0000.0000.0000.000
169A188ALA 00.0090.0248.004-0.974-0.9740.0000.0000.0000.000
170A189LEU 00.0330.0042.572-3.627-3.4731.025-0.120-1.059-0.002
171A190ALA 0-0.024-0.0184.287-3.246-3.0590.001-0.030-0.1580.000
172A191THR 0-0.053-0.0506.6820.0750.0750.0000.0000.0000.000
173A192LEU 0-0.0230.0082.823-1.186-0.0920.475-0.324-1.246-0.003
174A193ARG 10.9780.9952.28039.99740.6145.590-1.733-4.474-0.003
175A194ARG 10.8970.9653.92522.91121.7070.0501.478-0.3240.000
176A195GLY 00.1020.0487.2411.2951.2950.0000.0000.0000.000
177A196VAL 0-0.083-0.0598.6371.1001.1000.0000.0000.0000.000
178A197GLY 00.0250.00911.9240.5840.5840.0000.0000.0000.000
179A198PRO 0-0.038-0.02214.415-1.015-1.0150.0000.0000.0000.000
180A199GLY 00.0870.02616.486-0.086-0.0860.0000.0000.0000.000
181A200LYS 10.8140.91710.64520.81920.8190.0000.0000.0000.000
182A201ALA 0-0.0230.00212.774-0.940-0.9400.0000.0000.0000.000
183A202LEU 0-0.020-0.02215.2010.6270.6270.0000.0000.0000.000
184A203GLY 00.0480.03414.0280.5190.5190.0000.0000.0000.000
185A204LEU 0-0.066-0.02814.6530.2980.2980.0000.0000.0000.000
186A205GLY 00.0000.00011.937-0.902-0.9020.0000.0000.0000.000
187A206LEU 00.0050.0076.311-0.950-0.9500.0000.0000.0000.000
188A207LEU 0-0.0100.0037.8731.3381.3380.0000.0000.0000.000
189A208SER 00.0010.0027.033-1.988-1.9880.0000.0000.0000.000
190A209VAL 00.0270.0076.3431.9151.9150.0000.0000.0000.000
191A210ALA 0-0.031-0.0238.924-1.695-1.6950.0000.0000.0000.000
192A211PRO -1-0.815-0.88411.194-16.099-16.0990.0000.0000.0000.000