FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2KZ7R

Calculation Name: 3DR5-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NRD3

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2365324.574836
FMO2-HF: Nuclear repulsion 2284328.203869
FMO2-HF: Total energy -80996.370967
FMO2-MP2: Total energy -81234.917732


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:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
-0.441.060.035-0.857-0.679-0.003
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.002
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].
3A4ALA 00.0440.0163.8440.6661.673-0.006-0.469-0.533-0.001
4A5PHE 00.0270.0224.3820.1530.2930.000-0.015-0.1260.000
5A6GLU -1-0.845-0.9383.468-2.935-2.5820.041-0.373-0.020-0.002
6A7TYR 00.0130.0576.9050.1310.1310.0000.0000.0000.000
7A8LEU 00.0010.0109.1890.1020.1020.0000.0000.0000.000
8A9ARG 10.9530.9736.714-0.034-0.0340.0000.0000.0000.000
9A10THR 0-0.030-0.04110.0350.0230.0230.0000.0000.0000.000
10A11TYR 0-0.038-0.00512.3850.0300.0300.0000.0000.0000.000
11A12VAL 00.0330.00014.1420.0230.0230.0000.0000.0000.000
12A13GLU -1-0.912-0.96613.4650.0210.0210.0000.0000.0000.000
13A14SER 0-0.140-0.07815.9690.0060.0060.0000.0000.0000.000
14A15THR 0-0.045-0.02517.9210.0030.0030.0000.0000.0000.000
15A16THR 0-0.053-0.01418.9010.0120.0120.0000.0000.0000.000
16A17GLU -1-0.991-0.99121.269-0.015-0.0150.0000.0000.0000.000
17A18THR 0-0.030-0.01522.8290.0050.0050.0000.0000.0000.000
18A19ASP -1-0.779-0.88824.9460.0140.0140.0000.0000.0000.000
19A20ALA 0-0.002-0.01126.5400.0020.0020.0000.0000.0000.000
20A21ALA 00.0140.00428.5270.0020.0020.0000.0000.0000.000
21A22VAL 0-0.007-0.00723.2580.0050.0050.0000.0000.0000.000
22A23ALA 0-0.016-0.01423.7520.0050.0050.0000.0000.0000.000
23A24ARG 10.9100.95524.836-0.016-0.0160.0000.0000.0000.000
24A25ALA 00.008-0.00725.8120.0030.0030.0000.0000.0000.000
25A26ARG 10.8120.89317.854-0.064-0.0640.0000.0000.0000.000
26A27GLU -1-0.927-0.96222.2830.0180.0180.0000.0000.0000.000
27A28ASP -1-0.825-0.91024.2980.0320.0320.0000.0000.0000.000
28A29ALA 0-0.056-0.04222.5200.0040.0040.0000.0000.0000.000
29A30ALA 0-0.0110.00520.8010.0090.0090.0000.0000.0000.000
30A31GLU -1-0.942-0.96622.1360.0230.0230.0000.0000.0000.000
31A32PHE 0-0.101-0.05325.465-0.001-0.0010.0000.0000.0000.000
32A33GLY 0-0.040-0.00722.1220.0050.0050.0000.0000.0000.000
33A34LEU 0-0.092-0.04822.4670.0120.0120.0000.0000.0000.000
34A35PRO 0-0.005-0.00719.1840.0030.0030.0000.0000.0000.000
35A36ALA 00.0320.00818.525-0.009-0.0090.0000.0000.0000.000
36A37PRO 0-0.0080.00716.6540.0120.0120.0000.0000.0000.000
37A38ASP -1-0.793-0.88112.4320.1800.1800.0000.0000.0000.000
38A39GLU -1-0.739-0.85315.5580.0340.0340.0000.0000.0000.000
39A40MET 00.0040.00812.641-0.007-0.0070.0000.0000.0000.000
40A41THR 0-0.019-0.02914.8510.0120.0120.0000.0000.0000.000
41A42GLY 00.0080.00217.187-0.008-0.0080.0000.0000.0000.000
42A43GLN 0-0.006-0.01219.331-0.002-0.0020.0000.0000.0000.000
43A44LEU 0-0.0080.00618.579-0.006-0.0060.0000.0000.0000.000
44A45LEU 0-0.035-0.02520.998-0.004-0.0040.0000.0000.0000.000
45A46THR 00.000-0.01423.383-0.006-0.0060.0000.0000.0000.000
46A47THR 0-0.029-0.00923.427-0.007-0.0070.0000.0000.0000.000
47A48LEU 0-0.015-0.00723.139-0.004-0.0040.0000.0000.0000.000
48A49ALA 0-0.0160.01726.697-0.003-0.0030.0000.0000.0000.000
49A50ALA 00.0050.01028.720-0.004-0.0040.0000.0000.0000.000
50A51THR 0-0.107-0.04827.610-0.002-0.0020.0000.0000.0000.000
51A52THR 0-0.044-0.03229.483-0.003-0.0030.0000.0000.0000.000
52A53ASN 00.029-0.00431.975-0.005-0.0050.0000.0000.0000.000
53A54GLY 00.0520.03435.7760.0010.0010.0000.0000.0000.000
54A55ASN 0-0.056-0.03437.603-0.003-0.0030.0000.0000.0000.000
55A56GLY 0-0.035-0.01740.5700.0010.0010.0000.0000.0000.000
56A57SER 0-0.090-0.05436.3650.0020.0020.0000.0000.0000.000
57A58THR 00.013-0.00738.658-0.003-0.0030.0000.0000.0000.000
58A59GLY 00.0300.01735.829-0.002-0.0020.0000.0000.0000.000
59A60ALA 0-0.0160.00230.5620.0030.0030.0000.0000.0000.000
60A61ILE 0-0.021-0.01131.186-0.004-0.0040.0000.0000.0000.000
61A62ALA 00.0080.01327.8260.0060.0060.0000.0000.0000.000
62A63ILE 0-0.033-0.03127.868-0.006-0.0060.0000.0000.0000.000
63A64THR 00.0420.00823.7590.0090.0090.0000.0000.0000.000
64A65PRO 00.0510.02724.692-0.009-0.0090.0000.0000.0000.000
65A66ALA 00.0360.03423.751-0.009-0.0090.0000.0000.0000.000
66A67ALA 0-0.021-0.02625.4840.0010.0010.0000.0000.0000.000
67A68GLY 00.0300.01228.059-0.003-0.0030.0000.0000.0000.000
68A69LEU 00.0420.02820.605-0.003-0.0030.0000.0000.0000.000
69A70VAL 00.004-0.00222.616-0.002-0.0020.0000.0000.0000.000
70A71GLY 00.024-0.01924.764-0.002-0.0020.0000.0000.0000.000
71A72LEU 00.0090.01026.942-0.004-0.0040.0000.0000.0000.000
72A73TYR 0-0.046-0.02820.8150.0020.0020.0000.0000.0000.000
73A74ILE 0-0.011-0.00225.874-0.002-0.0020.0000.0000.0000.000
74A75LEU 0-0.062-0.04628.101-0.003-0.0030.0000.0000.0000.000
75A76ASN 00.0160.02226.872-0.006-0.0060.0000.0000.0000.000
76A77GLY 0-0.023-0.00129.651-0.003-0.0030.0000.0000.0000.000
77A78LEU 0-0.062-0.03130.583-0.001-0.0010.0000.0000.0000.000
78A79ALA 00.0350.03133.107-0.003-0.0030.0000.0000.0000.000
79A80ASP -1-0.883-0.95036.7010.0250.0250.0000.0000.0000.000
80A81ASN 0-0.119-0.05139.0690.0010.0010.0000.0000.0000.000
81A82THR 00.0030.00536.5760.0020.0020.0000.0000.0000.000
82A83THR 0-0.047-0.02937.537-0.001-0.0010.0000.0000.0000.000
83A84LEU 00.0340.03530.3840.0030.0030.0000.0000.0000.000
84A85THR 0-0.043-0.03833.980-0.004-0.0040.0000.0000.0000.000
85A86CYS 0-0.0170.00031.8760.0050.0050.0000.0000.0000.000
86A87ILE 0-0.020-0.01231.542-0.004-0.0040.0000.0000.0000.000
87A88ASP -1-0.746-0.87329.9730.0780.0780.0000.0000.0000.000
88A89PRO 0-0.033-0.01731.780-0.005-0.0050.0000.0000.0000.000
89A90GLU -1-0.845-0.90831.8980.0540.0540.0000.0000.0000.000
90A91SER 0-0.033-0.03034.314-0.001-0.0010.0000.0000.0000.000
91A92GLU -1-0.918-0.96432.4040.0430.0430.0000.0000.0000.000
92A93HIS 10.9120.94028.983-0.067-0.0670.0000.0000.0000.000
93A94GLN 00.0270.02832.150-0.001-0.0010.0000.0000.0000.000
94A95ARG 10.8750.92035.028-0.028-0.0280.0000.0000.0000.000
95A96GLN 00.0530.02229.6580.0020.0020.0000.0000.0000.000
96A97ALA 00.0120.01531.305-0.001-0.0010.0000.0000.0000.000
97A98LYS 10.8900.93632.226-0.038-0.0380.0000.0000.0000.000
98A99ALA 0-0.062-0.01934.154-0.003-0.0030.0000.0000.0000.000
99A100LEU 00.1030.07328.454-0.002-0.0020.0000.0000.0000.000
100A101PHE 0-0.039-0.02230.382-0.002-0.0020.0000.0000.0000.000
101A102ARG 10.9070.95834.175-0.024-0.0240.0000.0000.0000.000
102A103GLU -1-0.969-0.98833.5950.0170.0170.0000.0000.0000.000
103A104ALA 00.0330.03232.184-0.003-0.0030.0000.0000.0000.000
104A105GLY 0-0.008-0.00334.1450.0000.0000.0000.0000.0000.000
105A106TYR 0-0.038-0.01931.6190.0000.0000.0000.0000.0000.000
106A107SER 0-0.009-0.03137.433-0.001-0.0010.0000.0000.0000.000
107A108PRO 00.023-0.01839.3570.0020.0020.0000.0000.0000.000
108A109SER 0-0.0250.01940.8460.0020.0020.0000.0000.0000.000
109A110ARG 10.9210.97435.659-0.031-0.0310.0000.0000.0000.000
110A111VAL 00.0220.02734.6580.0030.0030.0000.0000.0000.000
111A112ARG 10.9160.97436.618-0.045-0.0450.0000.0000.0000.000
112A113PHE 0-0.009-0.01332.4400.0020.0020.0000.0000.0000.000
113A114LEU 0-0.019-0.00936.150-0.003-0.0030.0000.0000.0000.000
114A115LEU 0-0.013-0.00936.1560.0030.0030.0000.0000.0000.000
115A116SER 0-0.023-0.01936.082-0.003-0.0030.0000.0000.0000.000
116A117ARG 10.9871.01234.069-0.062-0.0620.0000.0000.0000.000
117A118PRO 00.0650.00530.256-0.003-0.0030.0000.0000.0000.000
118A119LEU 00.008-0.01331.380-0.004-0.0040.0000.0000.0000.000
119A120ASP -1-0.897-0.92034.7500.0570.0570.0000.0000.0000.000
120A121VAL 0-0.025-0.03036.238-0.003-0.0030.0000.0000.0000.000
121A122MET 00.0280.02431.699-0.002-0.0020.0000.0000.0000.000
122A123SER 0-0.040-0.00837.192-0.003-0.0030.0000.0000.0000.000
123A124ARG 10.8730.91740.361-0.048-0.0480.0000.0000.0000.000
124A125LEU 0-0.0470.00536.721-0.003-0.0030.0000.0000.0000.000
125A126ALA 00.0060.00240.7300.0000.0000.0000.0000.0000.000
126A127ASN 00.0470.00039.8970.0040.0040.0000.0000.0000.000
127A128ASP -1-0.927-0.97138.7290.0450.0450.0000.0000.0000.000
128A129SER 0-0.0010.01238.772-0.004-0.0040.0000.0000.0000.000
129A130TYR 0-0.017-0.00534.208-0.002-0.0020.0000.0000.0000.000
130A131GLN 00.0770.06332.4260.0000.0000.0000.0000.0000.000
131A132LEU 00.004-0.00426.3320.0030.0030.0000.0000.0000.000
132A133VAL 0-0.0060.00428.722-0.004-0.0040.0000.0000.0000.000
133A134PHE 00.0420.02820.7790.0060.0060.0000.0000.0000.000
134A135GLY 00.002-0.00724.476-0.010-0.0100.0000.0000.0000.000
135A136GLN 0-0.030-0.01618.7570.0030.0030.0000.0000.0000.000
136A137VAL 0-0.021-0.02123.111-0.013-0.0130.0000.0000.0000.000
137A138SER 00.0420.02122.5480.0180.0180.0000.0000.0000.000
138A139PRO 00.0610.01520.806-0.009-0.0090.0000.0000.0000.000
139A140MET 0-0.036-0.02323.057-0.008-0.0080.0000.0000.0000.000
140A141ASP -1-0.921-0.95226.3620.0990.0990.0000.0000.0000.000
141A142LEU 0-0.036-0.00921.482-0.007-0.0070.0000.0000.0000.000
142A143LYS 10.9850.99826.160-0.100-0.1000.0000.0000.0000.000
143A144ALA 00.0220.01628.765-0.007-0.0070.0000.0000.0000.000
144A145LEU 00.009-0.00426.400-0.007-0.0070.0000.0000.0000.000
145A146VAL 00.0100.01127.090-0.005-0.0050.0000.0000.0000.000
146A147ASP -1-0.865-0.93129.8200.0840.0840.0000.0000.0000.000
147A148ALA 0-0.056-0.02633.019-0.006-0.0060.0000.0000.0000.000
148A149ALA 00.017-0.01330.699-0.005-0.0050.0000.0000.0000.000
149A150TRP 0-0.0030.01229.573-0.004-0.0040.0000.0000.0000.000
150A151PRO 0-0.014-0.00633.521-0.004-0.0040.0000.0000.0000.000
151A152LEU 00.0240.01934.713-0.004-0.0040.0000.0000.0000.000
152A153LEU 0-0.0160.01229.965-0.004-0.0040.0000.0000.0000.000
153A154ARG 10.9080.97834.664-0.046-0.0460.0000.0000.0000.000
154A155ARG 10.9090.94034.400-0.049-0.0490.0000.0000.0000.000
155A156GLY 0-0.041-0.01632.610-0.004-0.0040.0000.0000.0000.000
156A157GLY 0-0.025-0.00831.6570.0010.0010.0000.0000.0000.000
157A158ALA 00.004-0.00326.2450.0050.0050.0000.0000.0000.000
158A159LEU 00.0020.01926.050-0.004-0.0040.0000.0000.0000.000
159A160VAL 0-0.018-0.02121.3010.0090.0090.0000.0000.0000.000
160A161LEU 0-0.017-0.01521.632-0.007-0.0070.0000.0000.0000.000
161A162ALA 00.0470.00618.3410.0230.0230.0000.0000.0000.000
162A163ASP -1-0.858-0.93915.0320.2940.2940.0000.0000.0000.000
163A164ALA 0-0.0060.00316.3590.0060.0060.0000.0000.0000.000
164A165LEU 0-0.033-0.00114.357-0.012-0.0120.0000.0000.0000.000
165A166LEU 0-0.0100.00214.4990.0280.0280.0000.0000.0000.000
166A167ASP -1-0.864-0.9529.4260.8690.8690.0000.0000.0000.000
167A168GLY 0-0.076-0.0289.9820.1450.1450.0000.0000.0000.000
168A169THR 0-0.099-0.04912.325-0.070-0.0700.0000.0000.0000.000
169A170ILE 0-0.062-0.04014.054-0.056-0.0560.0000.0000.0000.000
170A171ALA 0-0.003-0.01716.1560.0120.0120.0000.0000.0000.000
171A172ASP -1-0.830-0.91814.9470.3370.3370.0000.0000.0000.000
172A173GLN 0-0.053-0.02418.173-0.012-0.0120.0000.0000.0000.000
173A174THR 0-0.024-0.01617.480-0.012-0.0120.0000.0000.0000.000
174A175ARG 10.9770.99612.471-0.422-0.4220.0000.0000.0000.000
175A176LYS 10.8860.95519.221-0.151-0.1510.0000.0000.0000.000
176A177ASP -1-0.805-0.90920.8830.1990.1990.0000.0000.0000.000
177A178ARG 10.7720.85921.517-0.170-0.1700.0000.0000.0000.000
178A179ASP -1-0.767-0.89021.3120.1690.1690.0000.0000.0000.000
179A180THR 00.0090.01318.7500.0090.0090.0000.0000.0000.000
180A181GLN 0-0.044-0.01820.759-0.006-0.0060.0000.0000.0000.000
181A182ALA 00.0130.02424.082-0.008-0.0080.0000.0000.0000.000
182A183ALA 00.0400.00719.829-0.005-0.0050.0000.0000.0000.000
183A184ARG 00.0300.03119.5720.0160.0160.0000.0000.0000.000
184A185ASP -1-0.915-0.94822.1930.1160.1160.0000.0000.0000.000
185A186ALA 00.0180.01523.404-0.009-0.0090.0000.0000.0000.000
186A187ASP -1-0.811-0.89220.1990.2190.2190.0000.0000.0000.000
187A188GLU -1-0.991-1.00222.7130.1220.1220.0000.0000.0000.000
188A189TYR 0-0.032-0.02325.265-0.013-0.0130.0000.0000.0000.000
189A190ILE 0-0.009-0.00923.582-0.009-0.0090.0000.0000.0000.000
190A191ARG 10.7860.86721.844-0.175-0.1750.0000.0000.0000.000
191A192SER 0-0.078-0.03426.128-0.009-0.0090.0000.0000.0000.000
192A193ILE 0-0.0070.00729.168-0.008-0.0080.0000.0000.0000.000
193A194GLU -1-0.919-0.96330.8860.0730.0730.0000.0000.0000.000
194A195GLY 0-0.043-0.02033.458-0.002-0.0020.0000.0000.0000.000
195A196ALA 00.0050.00628.839-0.001-0.0010.0000.0000.0000.000
196A197HIS 0-0.053-0.02126.667-0.003-0.0030.0000.0000.0000.000
197A198VAL 00.0360.01121.8770.0040.0040.0000.0000.0000.000
198A199ALA 0-0.0180.00120.2330.0000.0000.0000.0000.0000.000
199A200ARG 10.8640.92916.685-0.226-0.2260.0000.0000.0000.000
200A201LEU 0-0.007-0.01214.6840.0060.0060.0000.0000.0000.000
201A202PRO 00.0090.0109.4270.0260.0260.0000.0000.0000.000
202A203LEU 00.000-0.00210.5250.0170.0170.0000.0000.0000.000
203A204GLY 00.0320.02811.772-0.006-0.0060.0000.0000.0000.000
204A205ALA 00.0240.02910.4480.1120.1120.0000.0000.0000.000
205A206GLY 0-0.010-0.02512.1060.0140.0140.0000.0000.0000.000
206A207LEU 0-0.023-0.00513.545-0.056-0.0560.0000.0000.0000.000
207A208THR 00.0450.01216.7380.0020.0020.0000.0000.0000.000
208A209VAL 0-0.025-0.01019.762-0.016-0.0160.0000.0000.0000.000
209A210VAL 00.0260.00622.4910.0000.0000.0000.0000.0000.000
210A211THR 0-0.028-0.02425.675-0.008-0.0080.0000.0000.0000.000
211A212LYS 10.8500.92628.450-0.065-0.0650.0000.0000.0000.000
212A213ALA 00.0370.03032.051-0.004-0.0040.0000.0000.0000.000
213A214LEU 00.006-0.01533.174-0.003-0.0030.0000.0000.0000.000
214A215GLU -1-1.027-1.01136.3240.0410.0410.0000.0000.0000.000
215A216HIS 00.0210.00433.897-0.003-0.0030.0000.0000.0000.000
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