Manual

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: N1R4Q

Calculation Name: 2WUX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WUX

Chain ID: A

ChEMBL ID:

UniProt ID: P04871

Base Structure: X-ray

Registration Date: 2023-06-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2448977.318783
FMO2-HF: Nuclear repulsion 2361545.833627
FMO2-HF: Total energy -87431.485156
FMO2-MP2: Total energy -87688.52312


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:3:ASP)


Summations of interaction energy for fragment #1(A:3: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.
-65.169-58.3886.416-6.508-6.6880.066
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.835 / q_NPA : -0.925
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].
3A5SER0-0.076-0.0431.993-35.305-30.3245.767-5.624-5.1230.068
4A6TYR00.0240.0112.9998.53310.2260.650-0.879-1.464-0.002
5A7ARG10.9620.9694.713-49.263-49.156-0.001-0.005-0.1010.000
6A8PRO0-0.034-0.0017.524-2.791-2.7910.0000.0000.0000.000
7A9THR00.0300.0229.9280.8810.8810.0000.0000.0000.000
8A10ILE00.0130.0119.315-0.250-0.2500.0000.0000.0000.000
9A11GLY0-0.037-0.01912.515-0.803-0.8030.0000.0000.0000.000
10A12ARG10.8370.90514.182-16.653-16.6530.0000.0000.0000.000
11A13THR00.0460.01717.077-0.317-0.3170.0000.0000.0000.000
12A14TYR0-0.023-0.01018.1770.4230.4230.0000.0000.0000.000
13A15VAL00.0050.00023.032-0.201-0.2010.0000.0000.0000.000
14A16TYR0-0.015-0.00723.955-0.011-0.0110.0000.0000.0000.000
15A17ASP-1-0.855-0.92729.3098.0808.0800.0000.0000.0000.000
16A18ASN00.0290.00131.6380.0560.0560.0000.0000.0000.000
17A19LYS10.8990.97130.788-8.441-8.4410.0000.0000.0000.000
18A20TYR00.0310.00726.8070.3200.3200.0000.0000.0000.000
19A21TYR00.0050.00824.207-0.214-0.2140.0000.0000.0000.000
20A22LYS10.9770.99518.822-13.871-13.8710.0000.0000.0000.000
21A23ASN0-0.026-0.03415.567-0.857-0.8570.0000.0000.0000.000
22A24LEU00.0640.01519.5370.0210.0210.0000.0000.0000.000
23A25ASP-1-0.775-0.88815.14317.07917.0790.0000.0000.0000.000
24A26ALA0-0.059-0.03616.6080.1400.1400.0000.0000.0000.000
25A27VAL0-0.0240.00518.200-0.280-0.2800.0000.0000.0000.000
26A28ILE00.0100.00220.932-0.391-0.3910.0000.0000.0000.000
27A29LYS10.9080.96614.091-19.587-19.5870.0000.0000.0000.000
28A30ASN0-0.017-0.02019.9210.3760.3760.0000.0000.0000.000
29A31ALA0-0.043-0.00222.371-0.038-0.0380.0000.0000.0000.000
30A49PRO00.020-0.00315.877-0.313-0.3130.0000.0000.0000.000
31A50LEU00.0420.01018.148-0.334-0.3340.0000.0000.0000.000
32A51ASP-1-0.892-0.94513.78718.18618.1860.0000.0000.0000.000
33A52ASN0-0.037-0.00716.1290.5000.5000.0000.0000.0000.000
34A53TYR0-0.0190.00218.012-0.539-0.5390.0000.0000.0000.000
35A54LEU0-0.0100.00119.8590.4100.4100.0000.0000.0000.000
36A55VAL0-0.021-0.00522.799-0.408-0.4080.0000.0000.0000.000
37A56ALA0-0.001-0.00125.4320.2340.2340.0000.0000.0000.000
38A57GLU-1-0.935-0.98325.89710.75810.7580.0000.0000.0000.000
39A58ASP-1-0.855-0.93729.2048.1958.1950.0000.0000.0000.000
40A59PRO00.0440.01132.7780.0560.0560.0000.0000.0000.000
41A60PHE0-0.048-0.02834.617-0.107-0.1070.0000.0000.0000.000
42A61LEU0-0.041-0.00632.646-0.078-0.0780.0000.0000.0000.000
43A62GLY00.0270.04030.6590.2200.2200.0000.0000.0000.000
44A63PRO0-0.022-0.01828.905-0.268-0.2680.0000.0000.0000.000
45A64GLY00.0090.00531.819-0.166-0.1660.0000.0000.0000.000
46A65LYS10.8290.89535.294-7.195-7.1950.0000.0000.0000.000
47A66ASN00.005-0.01437.6920.0410.0410.0000.0000.0000.000
48A67GLN0-0.033-0.03240.6600.0680.0680.0000.0000.0000.000
49A68LYS10.8550.92744.361-6.427-6.4270.0000.0000.0000.000
50A69LEU00.0410.04246.673-0.095-0.0950.0000.0000.0000.000
51A70THR0-0.035-0.03450.0920.0120.0120.0000.0000.0000.000
52A71LEU0-0.020-0.01152.279-0.099-0.0990.0000.0000.0000.000
53A72PHE0-0.0040.00254.930-0.114-0.1140.0000.0000.0000.000
54A73LYS10.8580.90654.313-5.538-5.5380.0000.0000.0000.000
55A74GLH0-0.022-0.03957.960-0.094-0.0940.0000.0000.0000.000
56A75ILE00.0280.02558.7840.0870.0870.0000.0000.0000.000
57A76ARG10.7670.85559.104-5.137-5.1370.0000.0000.0000.000
58A77ASN00.0110.00660.7290.0300.0300.0000.0000.0000.000
59A78VAL0-0.008-0.00557.451-0.061-0.0610.0000.0000.0000.000
60A79LYS10.8370.89660.889-4.754-4.7540.0000.0000.0000.000
61A80PRO00.0780.05559.5350.0670.0670.0000.0000.0000.000
62A81ASP-1-0.810-0.88957.5335.3025.3020.0000.0000.0000.000
63A82THR0-0.087-0.04658.616-0.040-0.0400.0000.0000.0000.000
64A83MET0-0.0170.00751.4980.0860.0860.0000.0000.0000.000
65A84LYS10.8600.93357.204-5.009-5.0090.0000.0000.0000.000
66A85LEU0-0.0250.00256.6230.1150.1150.0000.0000.0000.000
67A86VAL0-0.0010.01053.855-0.073-0.0730.0000.0000.0000.000
68A87VAL00.0060.01354.130-0.074-0.0740.0000.0000.0000.000
69A88GLY00.0500.02356.9660.0470.0470.0000.0000.0000.000
70A89TRP0-0.0270.00052.695-0.120-0.1200.0000.0000.0000.000
71A90LYS11.0270.99958.401-4.767-4.7670.0000.0000.0000.000
72A91GLY00.0830.02456.5210.0470.0470.0000.0000.0000.000
73A92LYS11.0121.00356.927-4.826-4.8260.0000.0000.0000.000
74A93GLU-1-0.858-0.90858.8545.0385.0380.0000.0000.0000.000
75A94PHE00.0020.01049.9020.0110.0110.0000.0000.0000.000
76A95TYR00.0320.00650.968-0.013-0.0130.0000.0000.0000.000
77A96ARG10.7930.87655.141-5.094-5.0940.0000.0000.0000.000
78A97GLU-1-0.842-0.91255.7195.3455.3450.0000.0000.0000.000
79A98THR0-0.019-0.02250.2170.0780.0780.0000.0000.0000.000
80A99TRP0-0.0030.00052.4570.0230.0230.0000.0000.0000.000
81A100THR0-0.026-0.04153.769-0.010-0.0100.0000.0000.0000.000
82A101ARG10.8540.93053.642-5.515-5.5150.0000.0000.0000.000
83A102PHE00.0190.00646.1170.0400.0400.0000.0000.0000.000
84A103MET0-0.049-0.01150.5890.0980.0980.0000.0000.0000.000
85A104GLU-1-0.929-0.95353.1715.3675.3670.0000.0000.0000.000
86A105ASP-1-0.917-0.94749.5046.1526.1520.0000.0000.0000.000
87A106SER0-0.012-0.01948.7850.0920.0920.0000.0000.0000.000
88A107PHE0-0.085-0.01550.3810.0460.0460.0000.0000.0000.000
89A108PRO0-0.023-0.02451.650-0.061-0.0610.0000.0000.0000.000
90A109ILE00.0180.00046.3880.0920.0920.0000.0000.0000.000
91A110VAL0-0.034-0.02145.966-0.040-0.0400.0000.0000.0000.000
92A111ASN0-0.035-0.02742.383-0.006-0.0060.0000.0000.0000.000
93A112ASP-1-0.872-0.92241.2616.9306.9300.0000.0000.0000.000
94A113GLN0-0.007-0.03040.3080.2260.2260.0000.0000.0000.000
95A114GLU-1-0.814-0.87336.2688.1588.1580.0000.0000.0000.000
96A115VAL0-0.008-0.01139.6390.0860.0860.0000.0000.0000.000
97A116MET0-0.087-0.02033.6660.0300.0300.0000.0000.0000.000
98A117ASP-1-0.774-0.87138.1937.5617.5610.0000.0000.0000.000
99A118VAL0-0.032-0.01640.199-0.073-0.0730.0000.0000.0000.000
100A119PHE00.0180.00537.6320.0090.0090.0000.0000.0000.000
101A120LEU0-0.0060.00943.719-0.130-0.1300.0000.0000.0000.000
102A121VAL0-0.017-0.01844.2230.1060.1060.0000.0000.0000.000
103A122VAL0-0.005-0.00546.831-0.164-0.1640.0000.0000.0000.000
104A123ASN0-0.008-0.00947.693-0.016-0.0160.0000.0000.0000.000
105A124MET0-0.032-0.00148.524-0.158-0.1580.0000.0000.0000.000
106A125ARG10.9050.94551.273-5.810-5.8100.0000.0000.0000.000
107A126PRO00.0510.03353.619-0.091-0.0910.0000.0000.0000.000
108A127THR0-0.067-0.06756.8420.0340.0340.0000.0000.0000.000
109A128ARG10.9170.95959.903-4.973-4.9730.0000.0000.0000.000
110A129PRO00.0180.01458.3610.0910.0910.0000.0000.0000.000
111A130ASN0-0.034-0.04357.987-0.066-0.0660.0000.0000.0000.000
112A131ARG10.8080.91357.272-5.168-5.1680.0000.0000.0000.000
113A132CYS0-0.053-0.04053.6550.0980.0980.0000.0000.0000.000
114A133TYR00.0260.01953.184-0.030-0.0300.0000.0000.0000.000
115A134LYS10.8580.92045.261-6.619-6.6190.0000.0000.0000.000
116A135PHE00.0260.00249.317-0.123-0.1230.0000.0000.0000.000
117A136LEU0-0.020-0.00148.7440.1490.1490.0000.0000.0000.000
118A137ALA0-0.003-0.02547.791-0.125-0.1250.0000.0000.0000.000
119A138GLN00.0600.02947.1210.1460.1460.0000.0000.0000.000
120A139HIS00.0440.03744.476-0.167-0.1670.0000.0000.0000.000
121A140ALA0-0.0020.00449.5340.0200.0200.0000.0000.0000.000
122A141LEU0-0.030-0.00744.907-0.057-0.0570.0000.0000.0000.000
123A142ARG10.9000.95549.475-5.605-5.6050.0000.0000.0000.000
124A143CYS00.0470.01751.7540.1060.1060.0000.0000.0000.000
125A144ASP-1-0.824-0.90453.1935.3845.3840.0000.0000.0000.000
126A145PRO0-0.152-0.09656.9960.0010.0010.0000.0000.0000.000
127A146ASP-1-0.931-0.94859.2084.8464.8460.0000.0000.0000.000
128A147TYR00.0490.00557.4690.0930.0930.0000.0000.0000.000
129A148VAL0-0.052-0.01260.6080.0400.0400.0000.0000.0000.000
130A149PRO0-0.013-0.00258.239-0.014-0.0140.0000.0000.0000.000
131A150HIS00.0330.02460.200-0.102-0.1020.0000.0000.0000.000
132A151ASP-1-0.766-0.85460.4465.0415.0410.0000.0000.0000.000
133A152VAL0-0.020-0.02160.8650.0580.0580.0000.0000.0000.000
134A153ILE0-0.0100.01155.001-0.055-0.0550.0000.0000.0000.000
135A154ARG10.8580.89858.671-5.109-5.1090.0000.0000.0000.000
136A155ILE0-0.019-0.00452.8860.0730.0730.0000.0000.0000.000
137A156VAL0-0.004-0.01152.451-0.040-0.0400.0000.0000.0000.000
138A157GLU-1-0.944-0.95648.0396.3476.3470.0000.0000.0000.000
139A158PRO0-0.049-0.01048.2450.0630.0630.0000.0000.0000.000
140A159SER00.0200.00643.7090.1760.1760.0000.0000.0000.000
141A160TRP00.002-0.01344.152-0.124-0.1240.0000.0000.0000.000
142A161VAL0-0.0060.00843.8110.1750.1750.0000.0000.0000.000
143A162GLY00.0250.01642.255-0.027-0.0270.0000.0000.0000.000
144A163SER00.0490.00942.434-0.099-0.0990.0000.0000.0000.000
145A164ASN0-0.019-0.00442.076-0.121-0.1210.0000.0000.0000.000
146A165ASN0-0.025-0.01144.178-0.078-0.0780.0000.0000.0000.000
147A166GLU-1-0.789-0.88544.2386.7156.7150.0000.0000.0000.000
148A167TYR0-0.046-0.02444.2350.1740.1740.0000.0000.0000.000
149A168ARG10.8460.90939.174-7.536-7.5360.0000.0000.0000.000
150A169ILE00.0030.00142.1380.1210.1210.0000.0000.0000.000
151A170SER0-0.061-0.03939.736-0.102-0.1020.0000.0000.0000.000
152A171LEU0-0.011-0.02541.875-0.106-0.1060.0000.0000.0000.000
153A172ALA00.0250.02940.398-0.131-0.1310.0000.0000.0000.000
154A173LYS10.9320.97039.657-7.095-7.0950.0000.0000.0000.000
155A187TYR00.0630.02247.902-0.028-0.0280.0000.0000.0000.000
156A188THR0-0.013-0.01050.001-0.085-0.0850.0000.0000.0000.000
157A189ASN00.0380.01553.4300.0780.0780.0000.0000.0000.000
158A190SER00.0120.00056.719-0.039-0.0390.0000.0000.0000.000
159A191PHE00.0340.01756.2540.0380.0380.0000.0000.0000.000
160A192GLU-1-0.936-0.97258.0194.9144.9140.0000.0000.0000.000
161A193GLN00.0780.03156.3460.1280.1280.0000.0000.0000.000
162A194PHE0-0.037-0.01350.3930.0670.0670.0000.0000.0000.000
163A195ILE0-0.042-0.03654.1960.0760.0760.0000.0000.0000.000
164A196ASP-1-0.853-0.91156.5215.1385.1380.0000.0000.0000.000
165A197ARG10.7810.90151.520-5.716-5.7160.0000.0000.0000.000
166A198VAL00.031-0.00151.8320.1160.1160.0000.0000.0000.000
167A199ILE0-0.0110.00348.2960.1100.1100.0000.0000.0000.000
168A200TRP0-0.042-0.01749.2340.1260.1260.0000.0000.0000.000
169A201GLU-1-0.907-0.94849.3935.9525.9520.0000.0000.0000.000
170A202ASN0-0.101-0.04045.0800.2120.2120.0000.0000.0000.000
171A203PHE0-0.012-0.01244.9010.1450.1450.0000.0000.0000.000
172A204TYR00.0400.03544.422-0.087-0.0870.0000.0000.0000.000
173A205LYS10.9060.96148.708-5.462-5.4620.0000.0000.0000.000
174A206PRO0-0.0170.00949.050-0.035-0.0350.0000.0000.0000.000
175A207ILE0-0.049-0.01851.074-0.136-0.1360.0000.0000.0000.000
176A208VAL00.043-0.00150.0830.1140.1140.0000.0000.0000.000
177A209TYR0-0.034-0.02852.316-0.113-0.1130.0000.0000.0000.000
178A210ILE00.016-0.00950.5860.1380.1380.0000.0000.0000.000
179A211GLY00.0430.01153.182-0.152-0.1520.0000.0000.0000.000
180A212THR0-0.038-0.00953.2850.0860.0860.0000.0000.0000.000
181A213ASP-1-0.805-0.89551.0776.0106.0100.0000.0000.0000.000
182A214SER0-0.014-0.02954.008-0.032-0.0320.0000.0000.0000.000
183A215ALA0-0.008-0.00757.120-0.030-0.0300.0000.0000.0000.000
184A216GLU-1-0.859-0.92360.2404.9104.9100.0000.0000.0000.000
185A217GLU-1-0.829-0.89961.1094.7814.7810.0000.0000.0000.000
186A218GLU-1-0.765-0.84857.8205.3305.3300.0000.0000.0000.000
187A219GLU-1-0.915-0.92460.5904.9014.9010.0000.0000.0000.000
188A220ILE0-0.022-0.00955.3390.0760.0760.0000.0000.0000.000
189A221LEU0-0.001-0.00756.749-0.075-0.0750.0000.0000.0000.000
190A222LEU0-0.017-0.02153.6830.1180.1180.0000.0000.0000.000
191A223GLU-1-0.830-0.89850.7265.9245.9240.0000.0000.0000.000
192A224VAL00.0050.01051.5660.1290.1290.0000.0000.0000.000
193A225SER0-0.008-0.01348.477-0.091-0.0910.0000.0000.0000.000
194A226LEU00.0230.02847.5070.0490.0490.0000.0000.0000.000
195A227VAL0-0.030-0.01141.854-0.033-0.0330.0000.0000.0000.000
196A228PHE00.0410.01443.1320.0760.0760.0000.0000.0000.000
197A229LYS10.8140.91535.226-8.282-8.2820.0000.0000.0000.000
198A230VAL0-0.012-0.00839.488-0.031-0.0310.0000.0000.0000.000
199A231LYS10.8300.89233.113-8.474-8.4740.0000.0000.0000.000
200A232GLU-1-0.827-0.89637.2147.0717.0710.0000.0000.0000.000
201A233PHE0-0.037-0.02133.9560.2760.2760.0000.0000.0000.000
202A234ALA00.0200.01438.288-0.169-0.1690.0000.0000.0000.000
203A235PRO0-0.016-0.00838.7210.1940.1940.0000.0000.0000.000
204A236ASP-1-0.942-0.95637.4717.8977.8970.0000.0000.0000.000
205A237ALA0-0.022-0.02439.592-0.062-0.0620.0000.0000.0000.000
206A238PRO0-0.0280.00643.338-0.022-0.0220.0000.0000.0000.000
207A239LEU00.0210.01246.091-0.070-0.0700.0000.0000.0000.000
208A240PHE0-0.027-0.02348.651-0.030-0.0300.0000.0000.0000.000
209A241THR0-0.002-0.00652.306-0.015-0.0150.0000.0000.0000.000
210A242GLY0-0.0230.02155.9970.0250.0250.0000.0000.0000.000
211A243PRO00.000-0.01957.796-0.073-0.0730.0000.0000.0000.000
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