Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5JR2Z

Calculation Name: 5D1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1H

Chain ID: A

ChEMBL ID:

UniProt ID: C7Q5P8

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 OptAll
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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2143487.976618
FMO2-HF: Nuclear repulsion 2068427.288616
FMO2-HF: Total energy -75060.688002
FMO2-MP2: Total energy -75283.726868


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:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
0.152.160.013-0.76-1.2590.002
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.022
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].
3A7LEU00.0150.0243.8672.0423.393-0.005-0.649-0.6960.002
4A8LYS10.8320.8946.4400.1260.1260.0000.0000.0000.000
5A9VAL00.0620.0188.6570.1000.1000.0000.0000.0000.000
6A10LEU0-0.047-0.02512.003-0.023-0.0230.0000.0000.0000.000
7A11ALA00.0280.03215.505-0.017-0.0170.0000.0000.0000.000
8A12GLY0-0.004-0.01817.0970.0200.0200.0000.0000.0000.000
9A13LYS10.8950.93119.5950.0570.0570.0000.0000.0000.000
10A14LYS10.9380.97415.3420.2780.2780.0000.0000.0000.000
11A15LEU00.0270.01911.202-0.026-0.0260.0000.0000.0000.000
12A16THR0-0.057-0.03411.788-0.002-0.0020.0000.0000.0000.000
13A17ASP-1-0.834-0.8876.274-0.668-0.6680.0000.0000.0000.000
14A18LEU0-0.027-0.0108.424-0.026-0.0260.0000.0000.0000.000
15A19ASP-1-0.804-0.9186.990-1.718-1.7180.0000.0000.0000.000
16A20PRO0-0.008-0.0133.316-0.2310.0590.019-0.064-0.2450.000
17A21ASP-1-0.869-0.9175.780-0.528-0.5280.0000.0000.0000.000
18A22GLU-1-0.821-0.9059.157-0.288-0.2880.0000.0000.0000.000
19A23TRP0-0.037-0.0256.8290.1680.1680.0000.0000.0000.000
20A24ALA00.0090.0169.1160.1430.1430.0000.0000.0000.000
21A25LYS10.7930.86910.6520.4890.4890.0000.0000.0000.000
22A26ALA0-0.016-0.01113.1870.0650.0650.0000.0000.0000.000
23A27GLN0-0.014-0.0219.6170.1450.1450.0000.0000.0000.000
24A28ALA0-0.030-0.01114.6700.0460.0460.0000.0000.0000.000
25A29SER0-0.128-0.06516.6800.0290.0290.0000.0000.0000.000
26A30ALA0-0.0190.00118.6160.0160.0160.0000.0000.0000.000
27A31GLU-1-0.934-0.96920.305-0.075-0.0750.0000.0000.0000.000
28A32ARG10.7690.87021.5380.0430.0430.0000.0000.0000.000
29A33ILE00.0100.01214.981-0.018-0.0180.0000.0000.0000.000
30A34LEU0-0.027-0.00418.5310.0230.0230.0000.0000.0000.000
31A35VAL00.007-0.01315.235-0.015-0.0150.0000.0000.0000.000
32A36ASP-1-0.829-0.90118.0020.0070.0070.0000.0000.0000.000
33A37VAL00.004-0.01716.6800.0080.0080.0000.0000.0000.000
34A38GLY00.0070.00418.8330.0010.0010.0000.0000.0000.000
35A39THR0-0.060-0.03519.517-0.025-0.0250.0000.0000.0000.000
36A40GLY00.0570.02822.214-0.013-0.0130.0000.0000.0000.000
37A41ASP-1-0.843-0.92522.768-0.011-0.0110.0000.0000.0000.000
38A42ALA00.0100.00321.116-0.015-0.0150.0000.0000.0000.000
39A43ARG10.7980.86523.0970.0180.0180.0000.0000.0000.000
40A44THR00.009-0.00625.752-0.007-0.0070.0000.0000.0000.000
41A45ALA00.1170.07221.241-0.003-0.0030.0000.0000.0000.000
42A46TYR0-0.061-0.05423.374-0.008-0.0080.0000.0000.0000.000
43A47ARG10.8740.93424.9680.0100.0100.0000.0000.0000.000
44A48GLN0-0.034-0.02823.8890.0020.0020.0000.0000.0000.000
45A49ALA00.0200.01222.795-0.003-0.0030.0000.0000.0000.000
46A50ILE0-0.041-0.02424.556-0.005-0.0050.0000.0000.0000.000
47A51ALA0-0.065-0.03327.8370.0000.0000.0000.0000.0000.000
48A52HIS10.8060.89125.9250.0600.0600.0000.0000.0000.000
49A53PRO0-0.0020.00424.794-0.008-0.0080.0000.0000.0000.000
50A54GLU-1-0.760-0.85523.821-0.089-0.0890.0000.0000.0000.000
51A55TRP0-0.036-0.01921.9800.0020.0020.0000.0000.0000.000
52A56LEU00.0330.02714.035-0.007-0.0070.0000.0000.0000.000
53A57VAL0-0.036-0.00718.5320.0160.0160.0000.0000.0000.000
54A58VAL00.007-0.01113.308-0.028-0.0280.0000.0000.0000.000
55A59GLY00.0320.02016.5680.0340.0340.0000.0000.0000.000
56A60VAL0-0.014-0.01013.014-0.010-0.0100.0000.0000.0000.000
57A61ASP-1-0.757-0.88915.4960.1060.1060.0000.0000.0000.000
58A62PRO00.0400.03415.1240.0070.0070.0000.0000.0000.000
59A63ALA0-0.013-0.00216.173-0.008-0.0080.0000.0000.0000.000
60A64TRP00.0570.00615.131-0.060-0.0600.0000.0000.0000.000
61A65GLN00.0210.01417.564-0.034-0.0340.0000.0000.0000.000
62A66ARG10.8540.92920.278-0.061-0.0610.0000.0000.0000.000
63A67MET00.0640.06116.104-0.014-0.0140.0000.0000.0000.000
64A68THR0-0.040-0.03119.465-0.019-0.0190.0000.0000.0000.000
65A69GLU-1-0.797-0.84921.724-0.057-0.0570.0000.0000.0000.000
66A70THR00.014-0.01023.397-0.011-0.0110.0000.0000.0000.000
67A71ALA00.0410.03519.662-0.011-0.0110.0000.0000.0000.000
68A72VAL0-0.056-0.03921.654-0.019-0.0190.0000.0000.0000.000
69A73ARG10.7690.87923.9950.0480.0480.0000.0000.0000.000
70A74ALA00.0620.03222.410-0.001-0.0010.0000.0000.0000.000
71A75ALA00.0240.02721.587-0.012-0.0120.0000.0000.0000.000
72A76ARG10.8600.94023.3110.1090.1090.0000.0000.0000.000
73A77LYS11.0341.00326.0080.1150.1150.0000.0000.0000.000
74A78PRO00.0750.02626.8490.0080.0080.0000.0000.0000.000
75A79ALA0-0.009-0.00229.0650.0060.0060.0000.0000.0000.000
76A80LYS10.8930.94731.2130.0770.0770.0000.0000.0000.000
77A81GLY00.0220.01729.9520.0020.0020.0000.0000.0000.000
78A82GLY0-0.0240.02026.0830.0000.0000.0000.0000.0000.000
79A83ALA00.019-0.00623.9660.0080.0080.0000.0000.0000.000
80A84PRO0-0.020-0.01920.692-0.004-0.0040.0000.0000.0000.000
81A85ASN0-0.0020.01419.146-0.031-0.0310.0000.0000.0000.000
82A86LEU0-0.025-0.00219.3640.0100.0100.0000.0000.0000.000
83A87VAL0-0.018-0.00612.791-0.028-0.0280.0000.0000.0000.000
84A88LEU0-0.025-0.01615.5060.0420.0420.0000.0000.0000.000
85A89VAL00.0330.00610.012-0.030-0.0300.0000.0000.0000.000
86A90SER0-0.046-0.03311.5090.0080.0080.0000.0000.0000.000
87A91SER0-0.041-0.04110.4290.2170.2170.0000.0000.0000.000
88A92ALA0-0.0040.01412.143-0.095-0.0950.0000.0000.0000.000
89A93ILE00.0280.02313.0900.0590.0590.0000.0000.0000.000
90A94GLU-1-0.829-0.93414.2780.3110.3110.0000.0000.0000.000
91A95THR0-0.048-0.02911.028-0.030-0.0300.0000.0000.0000.000
92A96VAL0-0.0170.0199.8930.2040.2040.0000.0000.0000.000
93A97PRO00.0280.0024.4510.0600.150-0.001-0.004-0.0840.000
94A98ALA00.0550.0274.001-0.642-0.4880.000-0.018-0.1350.000
95A99ALA0-0.0040.0014.202-0.338-0.2130.000-0.025-0.0990.000
96A100LEU0-0.0010.0015.789-0.041-0.0410.0000.0000.0000.000
97A101HIS0-0.043-0.0328.5470.0510.0510.0000.0000.0000.000
98A102GLY0-0.014-0.00510.558-0.076-0.0760.0000.0000.0000.000
99A103VAL0-0.0040.00810.760-0.035-0.0350.0000.0000.0000.000
100A104ALA0-0.005-0.00213.735-0.016-0.0160.0000.0000.0000.000
101A105ASP-1-0.822-0.91617.009-0.051-0.0510.0000.0000.0000.000
102A106GLU-1-0.842-0.91320.1020.0000.0000.0000.0000.0000.000
103A107VAL00.0140.01418.253-0.008-0.0080.0000.0000.0000.000
104A108MET0-0.020-0.00420.762-0.002-0.0020.0000.0000.0000.000
105A109VAL00.0180.01321.6330.0070.0070.0000.0000.0000.000
106A110LEU0-0.008-0.01123.939-0.004-0.0040.0000.0000.0000.000
107A111MET0-0.046-0.01226.7800.0000.0000.0000.0000.0000.000
108A112PRO00.0140.02424.8980.0010.0010.0000.0000.0000.000
109A113TRP00.021-0.00325.583-0.005-0.0050.0000.0000.0000.000
110A114GLY0-0.006-0.01525.2480.0120.0120.0000.0000.0000.000
111A115LYS10.8030.87820.482-0.208-0.2080.0000.0000.0000.000
112A116LEU00.0080.02420.4480.0030.0030.0000.0000.0000.000
113A117LEU00.0010.01223.170-0.003-0.0030.0000.0000.0000.000
114A118ARG10.8050.85326.930-0.099-0.0990.0000.0000.0000.000
115A119GLY00.0240.00324.312-0.003-0.0030.0000.0000.0000.000
116A120VAL0-0.005-0.00824.1150.0000.0000.0000.0000.0000.000
117A121VAL0-0.034-0.01626.383-0.006-0.0060.0000.0000.0000.000
118A122LEU0-0.018-0.00528.535-0.004-0.0040.0000.0000.0000.000
119A123GLY00.0420.02226.507-0.002-0.0020.0000.0000.0000.000
120A124GLU-1-0.912-0.95023.9610.1560.1560.0000.0000.0000.000
121A125ALA00.0640.01522.7620.0080.0080.0000.0000.0000.000
122A126ASP-1-0.797-0.86918.3930.2440.2440.0000.0000.0000.000
123A127VAL0-0.002-0.00918.0500.0250.0250.0000.0000.0000.000
124A128LEU0-0.0130.00519.2800.0000.0000.0000.0000.0000.000
125A129SER00.007-0.01117.492-0.010-0.0100.0000.0000.0000.000
126A130GLY0-0.0030.00014.7750.0160.0160.0000.0000.0000.000
127A131LEU0-0.029-0.03515.261-0.010-0.0100.0000.0000.0000.000
128A132ARG10.7940.91117.713-0.151-0.1510.0000.0000.0000.000
129A133ALA00.0190.01912.682-0.019-0.0190.0000.0000.0000.000
130A134VAL0-0.013-0.00412.055-0.016-0.0160.0000.0000.0000.000
131A135ALA0-0.0210.00713.966-0.054-0.0540.0000.0000.0000.000
132A136LYS10.8250.91916.7300.0860.0860.0000.0000.0000.000
133A137PRO00.012-0.01618.3790.0050.0050.0000.0000.0000.000
134A138GLY0-0.023-0.00821.546-0.013-0.0130.0000.0000.0000.000
135A139ALA0-0.0060.01220.775-0.007-0.0070.0000.0000.0000.000
136A140PRO0-0.034-0.02522.7500.0130.0130.0000.0000.0000.000
137A141LEU00.0000.00821.7990.0010.0010.0000.0000.0000.000
138A142GLU-1-0.800-0.86924.2440.0260.0260.0000.0000.0000.000
139A143ILE00.005-0.00425.2760.0050.0050.0000.0000.0000.000
140A144SER0-0.018-0.01727.637-0.005-0.0050.0000.0000.0000.000
141A145ILE00.011-0.00829.2450.0030.0030.0000.0000.0000.000
142A146GLY00.0150.00932.042-0.003-0.0030.0000.0000.0000.000
143A147THR0-0.022-0.04535.2150.0020.0020.0000.0000.0000.000
144A148SER0-0.058-0.05037.6380.0020.0020.0000.0000.0000.000
145A149ILE0-0.0010.00532.8490.0000.0000.0000.0000.0000.000
146A150TRP00.0330.01033.3460.0020.0020.0000.0000.0000.000
147A151ARG10.7660.86239.021-0.033-0.0330.0000.0000.0000.000
148A152GLU-1-0.790-0.86940.9830.0400.0400.0000.0000.0000.000
149A153PRO0-0.099-0.04439.817-0.003-0.0030.0000.0000.0000.000
150A154ILE00.0430.01836.8240.0000.0000.0000.0000.0000.000
151A155PRO00.0000.00332.8550.0010.0010.0000.0000.0000.000
152A156LEU00.015-0.00332.9460.0020.0020.0000.0000.0000.000
153A157GLU-1-0.855-0.92929.0290.0770.0770.0000.0000.0000.000
154A158ILE00.0190.00430.9970.0070.0070.0000.0000.0000.000
155A159ARG10.8210.91533.479-0.049-0.0490.0000.0000.0000.000
156A160ASP-1-0.825-0.86934.5190.0760.0760.0000.0000.0000.000
157A161LEU0-0.032-0.01232.0570.0010.0010.0000.0000.0000.000
158A162PRO0-0.006-0.00436.659-0.003-0.0030.0000.0000.0000.000
159A163GLU-1-0.823-0.89937.1720.0380.0380.0000.0000.0000.000
160A164LEU00.0080.02032.121-0.001-0.0010.0000.0000.0000.000
161A165THR00.0280.01236.417-0.002-0.0020.0000.0000.0000.000
162A166PRO00.0450.00437.1640.0030.0030.0000.0000.0000.000
163A167GLU-1-0.917-0.94638.1360.0410.0410.0000.0000.0000.000
164A168THR0-0.016-0.00737.5530.0030.0030.0000.0000.0000.000
165A169VAL00.0290.02632.7150.0040.0040.0000.0000.0000.000
166A170VAL0-0.0080.02034.4310.0040.0040.0000.0000.0000.000
167A171SER0-0.002-0.01736.7870.0040.0040.0000.0000.0000.000
168A172THR0-0.035-0.03234.5440.0030.0030.0000.0000.0000.000
169A173GLY00.0570.03334.2790.0060.0060.0000.0000.0000.000
170A174LEU0-0.057-0.01028.3910.0060.0060.0000.0000.0000.000
171A175THR0-0.004-0.03429.8260.0040.0040.0000.0000.0000.000
172A176ASP-1-0.885-0.94130.6460.0780.0780.0000.0000.0000.000
173A177ARG10.7900.87927.411-0.095-0.0950.0000.0000.0000.000
174A178LEU00.001-0.00425.0830.0110.0110.0000.0000.0000.000
175A179ALA0-0.0150.00226.0320.0050.0050.0000.0000.0000.000
176A180ALA00.0280.00927.0930.0030.0030.0000.0000.0000.000
177A181LEU0-0.062-0.02821.8380.0150.0150.0000.0000.0000.000
178A182GLY00.0070.01422.0520.0080.0080.0000.0000.0000.000
179A183TRP00.0130.00719.937-0.015-0.0150.0000.0000.0000.000
180A184GLN0-0.001-0.00625.3300.0030.0030.0000.0000.0000.000
181A185VAL00.0200.01428.872-0.004-0.0040.0000.0000.0000.000
182A186ALA0-0.049-0.02630.837-0.002-0.0020.0000.0000.0000.000
183A187ASP-1-0.830-0.89832.6730.0230.0230.0000.0000.0000.000
184A188VAL00.0060.00833.1740.0040.0040.0000.0000.0000.000
185A189ARG10.8140.90035.472-0.025-0.0250.0000.0000.0000.000
186A190LEU00.0200.00736.8690.0020.0020.0000.0000.0000.000
187A191VAL0-0.029-0.02537.790-0.002-0.0020.0000.0000.0000.000
188A192PRO00.0030.02539.186-0.001-0.0010.0000.0000.0000.000
189A212THR0-0.016-0.01341.0000.0000.0000.0000.0000.0000.000
190A213GLU-1-0.845-0.91336.7900.0270.0270.0000.0000.0000.000
191A214THR0-0.007-0.00439.905-0.002-0.0020.0000.0000.0000.000
192A215VAL00.0270.03133.9750.0030.0030.0000.0000.0000.000
193A216LEU00.0150.01532.991-0.002-0.0020.0000.0000.0000.000
194A217HIS0-0.004-0.00132.3420.0030.0030.0000.0000.0000.000
195A218LEU00.0020.00328.592-0.001-0.0010.0000.0000.0000.000
196A219ARG10.8630.90928.205-0.019-0.0190.0000.0000.0000.000
197A220ALA00.019-0.00226.2010.0020.0020.0000.0000.0000.000
198A221VAL0-0.021-0.01025.738-0.006-0.0060.0000.0000.0000.000
199A222ALA00.0190.02521.2310.0090.0090.0000.0000.0000.000
200A223VAL0-0.046-0.02823.251-0.011-0.0110.0000.0000.0000.000
201A224ASP-1-0.854-0.92323.0900.1180.1180.0000.0000.0000.000
202A225PRO0-0.074-0.04922.376-0.007-0.0070.0000.0000.0000.000
203A226ARG10.8320.91525.226-0.091-0.0910.0000.0000.0000.000
204A227ASP-1-0.948-0.95628.7930.1000.1000.0000.0000.0000.000