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: 1N5VZ

Calculation Name: 3ER6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ER6

Chain ID: A

ChEMBL ID:

UniProt ID: Q87I90

Base Structure: X-ray

Registration Date: 2023-09-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2111547.982148
FMO2-HF: Nuclear repulsion 2037556.668903
FMO2-HF: Total energy -73991.313245
FMO2-MP2: Total energy -74209.495023


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-85.673-82.7250.073-1.237-1.7840
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.939 / q_NPA : 0.966
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].
3A9LEU0-0.0150.0153.8186.1928.147-0.019-0.939-0.9970.001
4A10ARG10.8790.9456.51127.33627.3360.0000.0000.0000.000
5A11VAL00.0160.00810.1931.7031.7030.0000.0000.0000.000
6A12VAL00.0070.00313.232-0.342-0.3420.0000.0000.0000.000
7A13ALA0-0.002-0.00316.6310.6780.6780.0000.0000.0000.000
8A14LEU00.0320.01419.6110.1990.1990.0000.0000.0000.000
9A15ALA00.0030.00022.9840.4110.4110.0000.0000.0000.000
10A16PRO00.012-0.01425.8800.1730.1730.0000.0000.0000.000
11A17THR00.0520.03228.9950.3530.3530.0000.0000.0000.000
12A18GLY00.0280.01930.821-0.176-0.1760.0000.0000.0000.000
13A19ARG10.8440.91932.0058.9178.9170.0000.0000.0000.000
14A20TYR00.005-0.00431.4910.3250.3250.0000.0000.0000.000
15A21PHE00.0820.04226.609-0.069-0.0690.0000.0000.0000.000
16A22ALA00.0310.01726.483-0.414-0.4140.0000.0000.0000.000
17A23SER00.0390.02225.833-0.370-0.3700.0000.0000.0000.000
18A24ILE00.0190.02421.710-0.360-0.3600.0000.0000.0000.000
19A25ILE0-0.022-0.00821.497-0.626-0.6260.0000.0000.0000.000
20A26SER00.0730.02721.762-0.291-0.2910.0000.0000.0000.000
21A27SER0-0.059-0.04119.408-0.199-0.1990.0000.0000.0000.000
22A28LEU00.004-0.00316.308-0.572-0.5720.0000.0000.0000.000
23A29GLU-1-0.890-0.93217.144-13.867-13.8670.0000.0000.0000.000
24A30ILE0-0.053-0.01417.670-0.262-0.2620.0000.0000.0000.000
25A31LEU0-0.014-0.02513.548-0.487-0.4870.0000.0000.0000.000
26A32GLU-1-0.883-0.93713.339-21.844-21.8440.0000.0000.0000.000
27A33THR0-0.012-0.00914.168-0.648-0.6480.0000.0000.0000.000
28A34ALA0-0.0030.00113.802-0.013-0.0130.0000.0000.0000.000
29A35ALA0-0.006-0.0059.913-0.489-0.4890.0000.0000.0000.000
30A36GLU-1-0.930-0.95811.065-18.344-18.3440.0000.0000.0000.000
31A37PHE0-0.053-0.03513.6910.3490.3490.0000.0000.0000.000
32A38ALA0-0.086-0.0409.6670.5140.5140.0000.0000.0000.000
33A39GLU-1-0.962-0.97310.229-20.593-20.5930.0000.0000.0000.000
34A40PHE0-0.070-0.0232.777-4.993-4.1420.094-0.249-0.696-0.001
35A41GLN00.0580.0146.4170.3010.3010.0000.0000.0000.000
36A42GLY0-0.050-0.0164.411-2.859-2.734-0.001-0.040-0.0840.000
37A43PHE00.0160.0015.270-0.884-0.867-0.001-0.009-0.0070.000
38A44MET0-0.035-0.0187.350-0.884-0.8840.0000.0000.0000.000
39A45THR0-0.021-0.01810.0191.0511.0510.0000.0000.0000.000
40A46HIS00.0120.00411.1281.2181.2180.0000.0000.0000.000
41A47VAL0-0.0010.01316.2660.5370.5370.0000.0000.0000.000
42A48VAL0-0.028-0.00218.956-0.023-0.0230.0000.0000.0000.000
43A49THR00.003-0.02821.6700.3110.3110.0000.0000.0000.000
44A50PRO00.0590.03525.313-0.200-0.2000.0000.0000.0000.000
45A51ASN00.0260.02027.398-0.253-0.2530.0000.0000.0000.000
46A52ASN00.001-0.01923.553-0.298-0.2980.0000.0000.0000.000
47A53ARG10.8810.95525.89010.22110.2210.0000.0000.0000.000
48A54PRO00.0280.01727.891-0.229-0.2290.0000.0000.0000.000
49A55LEU0-0.0100.02127.4550.3790.3790.0000.0000.0000.000
50A56ILE00.0090.00130.1990.0260.0260.0000.0000.0000.000
51A57GLY00.0300.01632.5650.0610.0610.0000.0000.0000.000
52A58ARG10.8260.89533.3398.9728.9720.0000.0000.0000.000
53A59GLY00.0390.01135.302-0.165-0.1650.0000.0000.0000.000
54A60GLY0-0.0070.01137.3460.0000.0000.0000.0000.0000.000
55A61ILE00.0250.03030.644-0.070-0.0700.0000.0000.0000.000
56A62SER00.001-0.01031.7260.0530.0530.0000.0000.0000.000
57A63VAL0-0.003-0.00825.608-0.149-0.1490.0000.0000.0000.000
58A64GLN0-0.002-0.01324.6780.5440.5440.0000.0000.0000.000
59A65PRO00.0170.02921.817-0.410-0.4100.0000.0000.0000.000
60A66THR00.014-0.00918.2050.3740.3740.0000.0000.0000.000
61A67ALA00.0170.01416.722-0.786-0.7860.0000.0000.0000.000
62A68GLN0-0.025-0.01418.7311.3361.3360.0000.0000.0000.000
63A69TRP00.0320.00319.046-1.082-1.0820.0000.0000.0000.000
64A70GLN00.0650.03919.448-0.946-0.9460.0000.0000.0000.000
65A71SER0-0.058-0.01916.2660.0550.0550.0000.0000.0000.000
66A72PHE0-0.056-0.02512.890-1.665-1.6650.0000.0000.0000.000
67A73ASP-1-0.820-0.89415.200-16.720-16.7200.0000.0000.0000.000
68A74PHE0-0.051-0.0378.6230.4790.4790.0000.0000.0000.000
69A75THR00.027-0.01611.917-1.713-1.7130.0000.0000.0000.000
70A76ASN00.0150.0437.680-1.034-1.0340.0000.0000.0000.000
71A77ILE00.0390.02911.1691.3811.3810.0000.0000.0000.000
72A78LEU00.0000.02013.871-0.741-0.7410.0000.0000.0000.000
73A79ILE0-0.021-0.01016.9930.6070.6070.0000.0000.0000.000
74A80ILE00.0080.01119.7160.0010.0010.0000.0000.0000.000
75A81GLY00.016-0.02123.3560.2940.2940.0000.0000.0000.000
76A82SER0-0.047-0.02725.5370.3030.3030.0000.0000.0000.000
77A83ILE00.0250.00129.301-0.221-0.2210.0000.0000.0000.000
78A84GLY0-0.068-0.03231.8500.2640.2640.0000.0000.0000.000
79A85ASP-1-0.832-0.92334.679-7.780-7.7800.0000.0000.0000.000
80A86PRO0-0.005-0.00334.853-0.007-0.0070.0000.0000.0000.000
81A87LEU00.0130.01436.802-0.006-0.0060.0000.0000.0000.000
82A88GLU-1-1.006-0.98638.785-7.967-7.9670.0000.0000.0000.000
83A89SER00.025-0.01834.951-0.028-0.0280.0000.0000.0000.000
84A90LEU0-0.018-0.01033.114-0.229-0.2290.0000.0000.0000.000
85A91ASP-1-0.902-0.95735.105-8.241-8.2410.0000.0000.0000.000
86A92LYS10.8410.92336.7058.2658.2650.0000.0000.0000.000
87A93ILE0-0.081-0.02330.422-0.207-0.2070.0000.0000.0000.000
88A94ASP-1-0.883-0.94929.896-10.290-10.2900.0000.0000.0000.000
89A95PRO00.0500.01130.610-0.284-0.2840.0000.0000.0000.000
90A96ALA00.0570.03727.971-0.210-0.2100.0000.0000.0000.000
91A97LEU0-0.037-0.00724.657-0.506-0.5060.0000.0000.0000.000
92A98PHE00.001-0.01826.173-0.358-0.3580.0000.0000.0000.000
93A99ASP-1-0.924-0.95027.064-10.712-10.7120.0000.0000.0000.000
94A100TRP00.002-0.00618.698-0.193-0.1930.0000.0000.0000.000
95A101ILE0-0.021-0.01722.157-0.579-0.5790.0000.0000.0000.000
96A102ARG10.9830.99822.76910.24910.2490.0000.0000.0000.000
97A103GLU-1-0.961-0.98721.899-13.196-13.1960.0000.0000.0000.000
98A104LEU0-0.014-0.01416.639-0.529-0.5290.0000.0000.0000.000
99A105HIS00.0190.00818.580-0.868-0.8680.0000.0000.0000.000
100A106LEU0-0.061-0.02620.3380.0080.0080.0000.0000.0000.000
101A107LYS10.8400.92016.74516.21216.2120.0000.0000.0000.000
102A108GLY0-0.020-0.00116.334-0.770-0.7700.0000.0000.0000.000
103A109SER0-0.077-0.03214.530-0.508-0.5080.0000.0000.0000.000
104A110LYS10.8350.92712.27417.54817.5480.0000.0000.0000.000
105A111ILE00.0050.00416.042-0.442-0.4420.0000.0000.0000.000
106A112VAL00.0160.00717.2790.5310.5310.0000.0000.0000.000
107A113ALA0-0.0110.00920.256-0.115-0.1150.0000.0000.0000.000
108A114ILE0-0.003-0.01222.7700.2530.2530.0000.0000.0000.000
109A115ASP-1-0.814-0.91225.659-9.421-9.4210.0000.0000.0000.000
110A116THR00.008-0.00829.399-0.186-0.1860.0000.0000.0000.000
111A117GLY00.0420.04527.0460.1010.1010.0000.0000.0000.000
112A118ILE0-0.055-0.04727.469-0.150-0.1500.0000.0000.0000.000
113A119PHE00.0310.01028.8330.0530.0530.0000.0000.0000.000
114A120VAL0-0.0050.00927.4860.1260.1260.0000.0000.0000.000
115A121VAL0-0.005-0.01124.508-0.037-0.0370.0000.0000.0000.000
116A122ALA0-0.0260.00127.6100.0520.0520.0000.0000.0000.000
117A123LYS10.9640.98831.0948.9378.9370.0000.0000.0000.000
118A124ALA0-0.070-0.03927.9130.1040.1040.0000.0000.0000.000
119A125GLY00.0050.01129.359-0.104-0.1040.0000.0000.0000.000
120A126LEU0-0.075-0.04423.404-0.122-0.1220.0000.0000.0000.000
121A127LEU0-0.040-0.01025.878-0.257-0.2570.0000.0000.0000.000
122A128GLN00.0240.01826.7500.4560.4560.0000.0000.0000.000
123A129GLN0-0.048-0.03228.5060.5140.5140.0000.0000.0000.000
124A130ASN0-0.0110.00830.9210.0120.0120.0000.0000.0000.000
125A131LYS10.9430.97131.0358.5808.5800.0000.0000.0000.000
126A132ALA00.0340.00930.170-0.352-0.3520.0000.0000.0000.000
127A133VAL0-0.043-0.01128.8040.2080.2080.0000.0000.0000.000
128A134MET00.0270.02631.533-0.174-0.1740.0000.0000.0000.000
129A135HIS0-0.033-0.02132.3130.4050.4050.0000.0000.0000.000
130A136SER00.034-0.02535.0590.0520.0520.0000.0000.0000.000
131A137TYR0-0.076-0.00837.7890.1990.1990.0000.0000.0000.000
132A138PHE00.0600.00635.7940.0670.0670.0000.0000.0000.000
133A139ALA00.0070.01237.631-0.032-0.0320.0000.0000.0000.000
134A140HIS00.0280.01238.561-0.027-0.0270.0000.0000.0000.000
135A141LEU00.0300.02338.7020.0260.0260.0000.0000.0000.000
136A142PHE00.019-0.01132.640-0.045-0.0450.0000.0000.0000.000
137A143GLY0-0.017-0.00437.807-0.040-0.0400.0000.0000.0000.000
138A144GLU-1-0.929-0.97140.522-6.650-6.6500.0000.0000.0000.000
139A145LEU0-0.086-0.05137.9990.0240.0240.0000.0000.0000.000
140A146PHE00.0030.00034.804-0.150-0.1500.0000.0000.0000.000
141A147PRO0-0.0060.02638.186-0.045-0.0450.0000.0000.0000.000
142A148GLU-1-0.940-0.98236.860-7.860-7.8600.0000.0000.0000.000
143A149ILE0-0.065-0.02532.716-0.186-0.1860.0000.0000.0000.000
144A150MET0-0.025-0.00635.8410.1320.1320.0000.0000.0000.000
145A151LEU00.0170.00334.462-0.260-0.2600.0000.0000.0000.000
146A152MET0-0.040-0.01632.3060.2880.2880.0000.0000.0000.000
147A153THR00.005-0.01534.334-0.118-0.1180.0000.0000.0000.000
148A154GLU-1-0.961-0.96835.977-7.389-7.3890.0000.0000.0000.000
149A155GLN0-0.051-0.02129.3170.0640.0640.0000.0000.0000.000
150A156LYS10.9480.96629.6418.7398.7390.0000.0000.0000.000
151A157ALA0-0.008-0.01625.096-0.242-0.2420.0000.0000.0000.000
152A158LEU00.0140.02025.8060.3310.3310.0000.0000.0000.000
153A159ILE00.0080.00120.294-0.285-0.2850.0000.0000.0000.000
154A160ASP-1-0.826-0.90423.368-10.017-10.0170.0000.0000.0000.000
155A161GLY00.0210.00921.857-0.212-0.2120.0000.0000.0000.000
156A162ASN00.010-0.00916.504-0.591-0.5910.0000.0000.0000.000
157A163VAL00.0190.02318.959-0.595-0.5950.0000.0000.0000.000
158A164TYR0-0.052-0.06416.4430.2790.2790.0000.0000.0000.000
159A165LEU00.0170.01821.706-0.091-0.0910.0000.0000.0000.000
160A166SER00.012-0.05224.0910.2300.2300.0000.0000.0000.000
161A167SER00.0370.00725.9340.0570.0570.0000.0000.0000.000
162A168GLY0-0.0170.02428.9230.0000.0000.0000.0000.0000.000
163A169PRO00.023-0.00829.5400.2920.2920.0000.0000.0000.000
164A170TYR0-0.001-0.01628.485-0.365-0.3650.0000.0000.0000.000
165A171SER0-0.0180.00027.184-0.222-0.2220.0000.0000.0000.000
166A172HIS00.0430.04623.0790.1110.1110.0000.0000.0000.000
167A173SER00.0570.03222.229-0.503-0.5030.0000.0000.0000.000
168A174SER0-0.029-0.01221.494-0.427-0.4270.0000.0000.0000.000
169A175VAL00.0790.03819.684-0.263-0.2630.0000.0000.0000.000
170A176MET0-0.0080.00517.782-0.837-0.8370.0000.0000.0000.000
171A177LEU0-0.022-0.01416.522-0.760-0.7600.0000.0000.0000.000
172A178GLU-1-0.901-0.93716.788-13.297-13.2970.0000.0000.0000.000
173A179ILE00.0150.01112.827-0.645-0.6450.0000.0000.0000.000
174A180VAL0-0.018-0.02012.528-1.088-1.0880.0000.0000.0000.000
175A181GLU-1-0.899-0.95412.287-14.189-14.1890.0000.0000.0000.000
176A182GLU-1-0.860-0.90412.264-16.177-16.1770.0000.0000.0000.000
177A183TYR0-0.048-0.0276.994-0.907-0.9070.0000.0000.0000.000
178A184PHE0-0.018-0.0046.689-1.390-1.3900.0000.0000.0000.000
179A185GLY00.0210.0279.8640.3860.3860.0000.0000.0000.000
180A186LYS10.9810.95912.96313.30113.3010.0000.0000.0000.000
181A187HIS00.0220.02016.0500.4110.4110.0000.0000.0000.000
182A188THR00.0740.04112.0740.7290.7290.0000.0000.0000.000
183A189ARG10.8890.96815.09813.05313.0530.0000.0000.0000.000
184A190ASN0-0.049-0.03716.9690.5590.5590.0000.0000.0000.000
185A191LEU00.0190.00917.0550.5860.5860.0000.0000.0000.000
186A192GLY00.0530.02518.1490.2980.2980.0000.0000.0000.000
187A193ASN0-0.018-0.01619.1610.5210.5210.0000.0000.0000.000
188A194GLN0-0.018-0.00522.2780.4010.4010.0000.0000.0000.000
189A195PHE0-0.020-0.01121.0800.3730.3730.0000.0000.0000.000
190A196LEU0-0.043-0.02621.4040.2850.2850.0000.0000.0000.000
191A197SER0-0.065-0.01924.7150.4880.4880.0000.0000.0000.000
192A198THR0-0.090-0.04724.9710.5370.5370.0000.0000.0000.000