FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 4J5QN

Calculation Name: 5DBU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DBU

Chain ID: A

ChEMBL ID:

UniProt ID: D5AHU8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2281063.221171
FMO2-HF: Nuclear repulsion 2202625.229363
FMO2-HF: Total energy -78437.991808
FMO2-MP2: Total energy -78663.812193


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.
-2.830.8330.001-1.954-1.7090.008
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 : 0 / q_Mulliken : 0.016 / q_NPA : 0.008
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].
3A3LEU00.004-0.0123.519-2.6491.0140.001-1.954-1.7090.008
4A4ASN00.0580.0516.2280.1370.1370.0000.0000.0000.000
5A5LYS10.8830.9608.2680.8420.8420.0000.0000.0000.000
6A6TYR0-0.028-0.0375.4950.1120.1120.0000.0000.0000.000
7A7ILE00.0180.01510.7510.0970.0970.0000.0000.0000.000
8A8ASP-1-0.746-0.82514.084-0.221-0.2210.0000.0000.0000.000
9A9HIS0-0.023-0.03617.5080.0200.0200.0000.0000.0000.000
10A10THR0-0.062-0.03919.9240.0160.0160.0000.0000.0000.000
11A11ILE0-0.0050.00523.0380.0050.0050.0000.0000.0000.000
12A12LEU00.005-0.01225.9260.0030.0030.0000.0000.0000.000
13A13LYS10.9170.98029.2140.0740.0740.0000.0000.0000.000
14A14PRO00.0460.03532.280-0.004-0.0040.0000.0000.0000.000
15A15GLU-1-0.904-0.95435.436-0.057-0.0570.0000.0000.0000.000
16A16THR0-0.097-0.06330.713-0.004-0.0040.0000.0000.0000.000
17A17THR00.0330.01033.9570.0000.0000.0000.0000.0000.000
18A18GLN00.0540.01933.315-0.001-0.0010.0000.0000.0000.000
19A19GLU-1-0.873-0.93332.629-0.088-0.0880.0000.0000.0000.000
20A20GLN0-0.058-0.03130.870-0.004-0.0040.0000.0000.0000.000
21A21VAL00.0170.01128.495-0.011-0.0110.0000.0000.0000.000
22A22GLU-1-0.860-0.94627.749-0.122-0.1220.0000.0000.0000.000
23A23LYS10.9120.96927.1530.1250.1250.0000.0000.0000.000
24A24ILE0-0.019-0.00723.470-0.013-0.0130.0000.0000.0000.000
25A25LEU0-0.009-0.01223.357-0.022-0.0220.0000.0000.0000.000
26A26ALA0-0.048-0.01723.372-0.022-0.0220.0000.0000.0000.000
27A27GLU-1-0.827-0.91421.684-0.198-0.1980.0000.0000.0000.000
28A28ALA0-0.007-0.00819.192-0.032-0.0320.0000.0000.0000.000
29A29LYS10.8860.94318.4800.1600.1600.0000.0000.0000.000
30A30GLU-1-0.992-0.97119.022-0.285-0.2850.0000.0000.0000.000
31A31TYR0-0.073-0.04815.497-0.023-0.0230.0000.0000.0000.000
32A32ASP-1-0.861-0.93713.153-0.757-0.7570.0000.0000.0000.000
33A33PHE0-0.0100.01313.560-0.078-0.0780.0000.0000.0000.000
34A34ALA0-0.040-0.02512.815-0.027-0.0270.0000.0000.0000.000
35A35SER0-0.026-0.03514.2440.0350.0350.0000.0000.0000.000
36A36VAL00.0310.03018.026-0.003-0.0030.0000.0000.0000.000
37A37CYS0-0.088-0.03521.4090.0160.0160.0000.0000.0000.000
38A38VAL00.0340.01823.3780.0030.0030.0000.0000.0000.000
39A39ASN00.0300.00427.1010.0080.0080.0000.0000.0000.000
40A40PRO00.0850.04030.155-0.007-0.0070.0000.0000.0000.000
41A41THR0-0.024-0.01231.473-0.001-0.0010.0000.0000.0000.000
42A42TRP0-0.011-0.00430.091-0.002-0.0020.0000.0000.0000.000
43A43VAL0-0.0050.01927.287-0.009-0.0090.0000.0000.0000.000
44A44ALA00.0790.03628.740-0.009-0.0090.0000.0000.0000.000
45A45LEU0-0.020-0.00530.408-0.006-0.0060.0000.0000.0000.000
46A46ALA0-0.001-0.01925.723-0.008-0.0080.0000.0000.0000.000
47A47ALA00.0280.01126.023-0.015-0.0150.0000.0000.0000.000
48A48GLU-1-0.920-0.96126.552-0.125-0.1250.0000.0000.0000.000
49A49SER0-0.067-0.03527.117-0.004-0.0040.0000.0000.0000.000
50A50LEU0-0.009-0.01121.526-0.012-0.0120.0000.0000.0000.000
51A51LYS10.9171.02722.3400.1090.1090.0000.0000.0000.000
52A52ASP-1-0.972-0.98422.567-0.184-0.1840.0000.0000.0000.000
53A53SER0-0.069-0.07619.144-0.020-0.0200.0000.0000.0000.000
54A54ASP-1-0.951-0.97513.427-0.534-0.5340.0000.0000.0000.000
55A55VAL0-0.085-0.02315.950-0.024-0.0240.0000.0000.0000.000
56A56LYS10.9920.99715.8040.3170.3170.0000.0000.0000.000
57A57VAL00.0360.01719.3250.0000.0000.0000.0000.0000.000
58A58CYS0-0.0140.00120.4490.0200.0200.0000.0000.0000.000
59A59THR00.008-0.00922.5530.0040.0040.0000.0000.0000.000
60A60VAL0-0.070-0.03025.2130.0050.0050.0000.0000.0000.000
61A61ILE00.012-0.00227.4040.0010.0010.0000.0000.0000.000
62A62GLY00.0030.00129.9940.0050.0050.0000.0000.0000.000
63A63PHE0-0.0040.02427.2130.0050.0050.0000.0000.0000.000
64A64PRO0-0.009-0.02131.024-0.001-0.0010.0000.0000.0000.000
65A65LEU00.045-0.01032.0610.0040.0040.0000.0000.0000.000
66A66GLY00.0350.03133.1390.0040.0040.0000.0000.0000.000
67A67ALA0-0.031-0.01333.8130.0040.0040.0000.0000.0000.000
68A68ASN0-0.013-0.00736.0590.0000.0000.0000.0000.0000.000
69A69THR00.0260.00337.4780.0020.0020.0000.0000.0000.000
70A70PRO00.1180.04835.887-0.003-0.0030.0000.0000.0000.000
71A71ALA00.0010.00536.096-0.002-0.0020.0000.0000.0000.000
72A72VAL0-0.020-0.00537.259-0.002-0.0020.0000.0000.0000.000
73A73LYS10.7870.88832.346-0.001-0.0010.0000.0000.0000.000
74A74ALA00.0420.02332.960-0.004-0.0040.0000.0000.0000.000
75A75PHE0-0.049-0.01533.733-0.003-0.0030.0000.0000.0000.000
76A76GLU-1-0.824-0.92332.490-0.041-0.0410.0000.0000.0000.000
77A77THR0-0.031-0.04028.822-0.004-0.0040.0000.0000.0000.000
78A78LYS10.9180.95130.3070.0120.0120.0000.0000.0000.000
79A79ASP-1-0.935-0.95732.630-0.053-0.0530.0000.0000.0000.000
80A80ALA00.0110.00928.974-0.006-0.0060.0000.0000.0000.000
81A81ILE0-0.020-0.01626.883-0.009-0.0090.0000.0000.0000.000
82A82SER0-0.115-0.04728.981-0.005-0.0050.0000.0000.0000.000
83A83ASN0-0.005-0.00631.259-0.001-0.0010.0000.0000.0000.000
84A84GLY0-0.017-0.01827.974-0.005-0.0050.0000.0000.0000.000
85A85ALA0-0.057-0.01125.337-0.012-0.0120.0000.0000.0000.000
86A86ASP-1-0.880-0.94820.797-0.160-0.1600.0000.0000.0000.000
87A87GLU-1-0.815-0.91116.839-0.158-0.1580.0000.0000.0000.000
88A88ILE00.0260.01321.7690.0000.0000.0000.0000.0000.000
89A89ASP-1-0.724-0.86621.844-0.059-0.0590.0000.0000.0000.000
90A90MET00.0020.03524.373-0.002-0.0020.0000.0000.0000.000
91A91VAL0-0.0190.00426.7850.0040.0040.0000.0000.0000.000
92A92ILE00.0290.02728.6270.0000.0000.0000.0000.0000.000
93A93ASN00.0580.02230.523-0.003-0.0030.0000.0000.0000.000
94A94ILE00.0470.01431.9410.0040.0040.0000.0000.0000.000
95A95GLY00.0260.01734.5000.0020.0020.0000.0000.0000.000
96A96ALA00.0160.01036.8880.0020.0020.0000.0000.0000.000
97A97LEU00.004-0.01331.6820.0020.0020.0000.0000.0000.000
98A98LYS10.7900.88835.403-0.019-0.0190.0000.0000.0000.000
99A99THR0-0.090-0.03438.0200.0000.0000.0000.0000.0000.000
100A100GLY00.0340.01938.9370.0010.0010.0000.0000.0000.000
101A101ASN0-0.056-0.02239.2140.0030.0030.0000.0000.0000.000
102A102TYR00.057-0.00534.8410.0000.0000.0000.0000.0000.000
103A103ASP-1-0.877-0.92035.5940.0310.0310.0000.0000.0000.000
104A104LEU0-0.0120.00237.000-0.001-0.0010.0000.0000.0000.000
105A105VAL0-0.056-0.02931.986-0.002-0.0020.0000.0000.0000.000
106A106LEU00.0310.01430.877-0.002-0.0020.0000.0000.0000.000
107A107GLU-1-0.946-0.97932.7360.0120.0120.0000.0000.0000.000
108A108ASP-1-0.869-0.93932.9650.0000.0000.0000.0000.0000.000
109A109ILE00.002-0.01027.435-0.004-0.0040.0000.0000.0000.000
110A110LYS10.9680.99029.675-0.038-0.0380.0000.0000.0000.000
111A111ALA0-0.0290.00231.337-0.002-0.0020.0000.0000.0000.000
112A112VAL0-0.025-0.01327.675-0.004-0.0040.0000.0000.0000.000
113A113VAL00.0180.00325.984-0.007-0.0070.0000.0000.0000.000
114A114ALA0-0.036-0.01028.219-0.002-0.0020.0000.0000.0000.000
115A115ALA0-0.086-0.06631.150-0.002-0.0020.0000.0000.0000.000
116A116SER0-0.0020.02524.761-0.010-0.0100.0000.0000.0000.000
117A117GLY00.0150.00626.817-0.010-0.0100.0000.0000.0000.000
118A118ASP-1-0.953-0.98223.233-0.057-0.0570.0000.0000.0000.000
119A119LYS10.9050.97622.2420.0800.0800.0000.0000.0000.000
120A120LEU0-0.0110.01116.0900.0160.0160.0000.0000.0000.000
121A121VAL00.0190.00120.448-0.009-0.0090.0000.0000.0000.000
122A122LYS10.7270.84817.7300.1030.1030.0000.0000.0000.000
123A123VAL00.0300.02021.713-0.008-0.0080.0000.0000.0000.000
124A124ILE0-0.061-0.03423.6150.0070.0070.0000.0000.0000.000
125A125ILE00.003-0.01724.6480.0000.0000.0000.0000.0000.000
126A126GLU-1-0.828-0.87826.373-0.014-0.0140.0000.0000.0000.000
127A127ALA00.0250.00625.6340.0010.0010.0000.0000.0000.000
128A128CYS0-0.0400.01427.7080.0010.0010.0000.0000.0000.000
129A129LEU0-0.031-0.01030.053-0.001-0.0010.0000.0000.0000.000
130A130LEU0-0.056-0.02329.0390.0010.0010.0000.0000.0000.000
131A131THR00.019-0.00432.1780.0010.0010.0000.0000.0000.000
132A132ASP-1-0.873-0.95928.8650.0540.0540.0000.0000.0000.000
133A133ASP-1-0.885-0.95029.4750.0640.0640.0000.0000.0000.000
134A134GLU-1-0.808-0.88431.2770.0310.0310.0000.0000.0000.000
135A135LYS10.8280.92126.405-0.044-0.0440.0000.0000.0000.000
136A136VAL00.0050.00526.4420.0050.0050.0000.0000.0000.000
137A137LYS10.9430.97927.531-0.051-0.0510.0000.0000.0000.000
138A138ALA00.0360.01627.769-0.001-0.0010.0000.0000.0000.000
139A139CYS0-0.044-0.00323.3850.0000.0000.0000.0000.0000.000
140A140GLN00.011-0.00725.004-0.004-0.0040.0000.0000.0000.000
141A141LEU0-0.0010.00326.920-0.001-0.0010.0000.0000.0000.000
142A142SER0-0.018-0.03924.595-0.008-0.0080.0000.0000.0000.000
143A143GLN0-0.033-0.02520.955-0.010-0.0100.0000.0000.0000.000
144A144GLU-1-0.975-0.96724.5740.0620.0620.0000.0000.0000.000
145A145ALA0-0.091-0.06727.911-0.003-0.0030.0000.0000.0000.000
146A146GLY00.0050.01424.745-0.007-0.0070.0000.0000.0000.000
147A147ALA00.0050.01423.268-0.010-0.0100.0000.0000.0000.000
148A148ASP-1-0.817-0.91418.2480.0400.0400.0000.0000.0000.000
149A149TYR0-0.035-0.01812.6040.0300.0300.0000.0000.0000.000
150A150VAL00.0150.03818.928-0.011-0.0110.0000.0000.0000.000
151A151LYS10.8390.89919.4120.0600.0600.0000.0000.0000.000
152A152THR00.0620.00120.221-0.003-0.0030.0000.0000.0000.000
153A153SER0-0.042-0.01522.9930.0020.0020.0000.0000.0000.000
154A154THR00.009-0.04924.748-0.008-0.0080.0000.0000.0000.000
155A155GLY0-0.033-0.02026.730-0.008-0.0080.0000.0000.0000.000
156A156PHE0-0.059-0.02527.336-0.004-0.0040.0000.0000.0000.000
157A157SER00.0380.03830.3400.0030.0030.0000.0000.0000.000
158A158THR0-0.036-0.03431.481-0.003-0.0030.0000.0000.0000.000
159A159GLY00.0290.00729.039-0.001-0.0010.0000.0000.0000.000
160A160GLY0-0.038-0.02024.949-0.002-0.0020.0000.0000.0000.000
161A161ALA0-0.042-0.00920.3520.0080.0080.0000.0000.0000.000
162A162THR00.0690.03922.379-0.002-0.0020.0000.0000.0000.000
163A163VAL00.0880.02018.5680.0080.0080.0000.0000.0000.000
164A164ALA00.0030.00520.1660.0180.0180.0000.0000.0000.000
165A165ASP-1-0.790-0.88622.5010.0580.0580.0000.0000.0000.000
166A166VAL0-0.027-0.01116.3020.0070.0070.0000.0000.0000.000
167A167ALA00.0350.02018.0330.0240.0240.0000.0000.0000.000
168A168LEU0-0.041-0.01019.0730.0200.0200.0000.0000.0000.000
169A169MET00.0050.01920.3110.0010.0010.0000.0000.0000.000
170A170ARG10.8140.89312.731-0.321-0.3210.0000.0000.0000.000
171A171LYS10.9180.95618.168-0.113-0.1130.0000.0000.0000.000
172A172THR0-0.107-0.07519.746-0.002-0.0020.0000.0000.0000.000
173A173VAL0-0.021-0.00818.283-0.004-0.0040.0000.0000.0000.000
174A174GLY00.0470.03717.8220.0010.0010.0000.0000.0000.000
175A175PRO0-0.046-0.04012.673-0.008-0.0080.0000.0000.0000.000
176A176ASP-1-0.896-0.95113.1130.4800.4800.0000.0000.0000.000
177A177MET0-0.0460.02115.178-0.041-0.0410.0000.0000.0000.000
178A178GLY0-0.011-0.00314.2880.0460.0460.0000.0000.0000.000
179A179VAL00.0210.00214.562-0.025-0.0250.0000.0000.0000.000
180A180LYS10.7800.88515.0140.1070.1070.0000.0000.0000.000
181A181ALA00.0370.02316.2360.0020.0020.0000.0000.0000.000
182A182SER0-0.027-0.04617.967-0.032-0.0320.0000.0000.0000.000
183A183GLY0-0.0010.00320.666-0.001-0.0010.0000.0000.0000.000
184A184GLY0-0.032-0.01822.1060.0040.0040.0000.0000.0000.000
185A185ALA00.0590.05518.0900.0050.0050.0000.0000.0000.000
186A186ARG10.8090.90419.9460.0750.0750.0000.0000.0000.000
187A187SER0-0.033-0.07919.155-0.014-0.0140.0000.0000.0000.000
188A188TYR00.0480.02010.1700.0230.0230.0000.0000.0000.000
189A189GLU-1-0.759-0.83814.360-0.097-0.0970.0000.0000.0000.000
190A190ASP-1-0.813-0.90716.031-0.038-0.0380.0000.0000.0000.000
191A191ALA0-0.030-0.02112.8340.0250.0250.0000.0000.0000.000
192A192ILE0-0.0030.00310.0960.0360.0360.0000.0000.0000.000
193A193ALA00.0030.01512.0600.0610.0610.0000.0000.0000.000
194A194PHE0-0.005-0.03214.6530.0340.0340.0000.0000.0000.000
195A195ILE0-0.039-0.0207.7880.0340.0340.0000.0000.0000.000
196A196GLU-1-0.978-0.99410.0510.3430.3430.0000.0000.0000.000
197A197ALA0-0.053-0.00411.7810.0170.0170.0000.0000.0000.000
198A198GLY00.0040.00512.7600.0050.0050.0000.0000.0000.000
199A199ALA0-0.0260.00313.0700.0230.0230.0000.0000.0000.000
200A200SER0-0.008-0.02510.0090.0520.0520.0000.0000.0000.000
201A201ARG10.7310.84210.7200.0810.0810.0000.0000.0000.000
202A202ILE00.0380.01812.9700.0470.0470.0000.0000.0000.000
203A203GLY0-0.032-0.01515.374-0.033-0.0330.0000.0000.0000.000
204A204ALA0-0.025-0.02918.5220.0160.0160.0000.0000.0000.000
205A205SER00.0340.03520.226-0.012-0.0120.0000.0000.0000.000
206A206SER0-0.037-0.03620.0000.0070.0070.0000.0000.0000.000
207A207GLY00.0730.02717.078-0.006-0.0060.0000.0000.0000.000
208A208VAL00.0170.01716.685-0.032-0.0320.0000.0000.0000.000
209A209ALA00.0240.02215.4330.0290.0290.0000.0000.0000.000
210A210ILE0-0.039-0.00113.797-0.032-0.0320.0000.0000.0000.000
211A211MET0-0.060-0.03912.0620.0050.0050.0000.0000.0000.000