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: KGKK3

Calculation Name: 1TWD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TWD

Chain ID: A

ChEMBL ID:

UniProt ID: P67825

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2757326.970323
FMO2-HF: Nuclear repulsion 2666608.602471
FMO2-HF: Total energy -90718.367852
FMO2-MP2: Total energy -90975.657092


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-5.2141.4178.194-5.941-8.887-0.028
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / 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].
3A4LEU00.007-0.0123.702-0.7111.607-0.002-1.233-1.0830.007
4A5GLU-1-0.780-0.8855.960-0.288-0.2880.0000.0000.0000.000
5A6ILE0-0.013-0.0178.7690.1360.1360.0000.0000.0000.000
6A7CYS0-0.074-0.03711.8290.0330.0330.0000.0000.0000.000
7A8CYS0-0.062-0.01914.7390.0130.0130.0000.0000.0000.000
8A9TYR00.0450.00617.9070.0160.0160.0000.0000.0000.000
9A10SER00.0300.00921.3080.0140.0140.0000.0000.0000.000
10A11MET00.0210.02421.602-0.026-0.0260.0000.0000.0000.000
11A12GLU-1-0.915-0.96722.272-0.188-0.1880.0000.0000.0000.000
12A13CYS0-0.064-0.02019.482-0.009-0.0090.0000.0000.0000.000
13A14ALA00.0640.02617.757-0.033-0.0330.0000.0000.0000.000
14A15LEU0-0.019-0.01017.748-0.046-0.0460.0000.0000.0000.000
15A16THR00.0090.00718.138-0.018-0.0180.0000.0000.0000.000
16A17ALA00.0270.01014.035-0.023-0.0230.0000.0000.0000.000
17A18GLN00.0940.04614.307-0.079-0.0790.0000.0000.0000.000
18A19GLN0-0.084-0.05215.087-0.038-0.0380.0000.0000.0000.000
19A20ASN0-0.057-0.02814.6810.0410.0410.0000.0000.0000.000
20A21GLY00.0390.02311.216-0.025-0.0250.0000.0000.0000.000
21A22ALA0-0.029-0.0039.737-0.269-0.2690.0000.0000.0000.000
22A23ASP-1-0.842-0.9156.423-2.871-2.8710.0000.0000.0000.000
23A24ARG10.7500.8488.0920.9690.9690.0000.0000.0000.000
24A25VAL0-0.018-0.00711.403-0.008-0.0080.0000.0000.0000.000
25A26GLU-1-0.791-0.87113.607-0.218-0.2180.0000.0000.0000.000
26A27LEU0-0.049-0.03615.0740.0160.0160.0000.0000.0000.000
27A28CYS0-0.0020.00218.4250.0200.0200.0000.0000.0000.000
28A29ALA00.0200.01421.030-0.003-0.0030.0000.0000.0000.000
29A30ALA00.012-0.00423.9240.0030.0030.0000.0000.0000.000
30A31PRO00.0730.03222.7330.0060.0060.0000.0000.0000.000
31A32LYS10.8870.93223.7710.0730.0730.0000.0000.0000.000
32A33GLU-1-0.886-0.93425.899-0.054-0.0540.0000.0000.0000.000
33A34GLY0-0.038-0.01221.9670.0060.0060.0000.0000.0000.000
34A35GLY0-0.0120.00120.797-0.009-0.0090.0000.0000.0000.000
35A36LEU0-0.032-0.01122.0720.0090.0090.0000.0000.0000.000
36A37THR00.0850.02923.884-0.015-0.0150.0000.0000.0000.000
37A38PRO0-0.052-0.00622.8170.0090.0090.0000.0000.0000.000
38A39SER00.0540.02625.9030.0020.0020.0000.0000.0000.000
39A40LEU00.1060.04128.240-0.010-0.0100.0000.0000.0000.000
40A41GLY0-0.016-0.00629.536-0.007-0.0070.0000.0000.0000.000
41A42VAL0-0.005-0.00324.752-0.007-0.0070.0000.0000.0000.000
42A43LEU00.0330.02224.026-0.017-0.0170.0000.0000.0000.000
43A44LYS10.9950.98025.6330.1100.1100.0000.0000.0000.000
44A45SER0-0.026-0.00627.146-0.010-0.0100.0000.0000.0000.000
45A46VAL00.034-0.00220.855-0.008-0.0080.0000.0000.0000.000
46A47ARG10.8930.95522.3440.2210.2210.0000.0000.0000.000
47A48GLN0-0.061-0.02524.6990.0060.0060.0000.0000.0000.000
48A49ARG10.8860.94124.7290.2070.2070.0000.0000.0000.000
49A50VAL0-0.038-0.01018.482-0.008-0.0080.0000.0000.0000.000
50A51THR0-0.079-0.03518.8060.0140.0140.0000.0000.0000.000
51A52ILE0-0.0040.01713.6140.0050.0050.0000.0000.0000.000
52A53PRO00.015-0.00612.7280.0760.0760.0000.0000.0000.000
53A54VAL00.0280.01214.623-0.038-0.0380.0000.0000.0000.000
54A55HIS0-0.036-0.01313.7510.0060.0060.0000.0000.0000.000
55A56PRO0-0.011-0.00616.865-0.001-0.0010.0000.0000.0000.000
56A57ILE00.0090.02219.0140.0070.0070.0000.0000.0000.000
57A58ILE0-0.029-0.01820.2120.0070.0070.0000.0000.0000.000
58A59ARG10.8480.92222.4880.0870.0870.0000.0000.0000.000
59A60PRO00.0260.01424.959-0.004-0.0040.0000.0000.0000.000
60A61ARG10.8050.89627.8800.0420.0420.0000.0000.0000.000
61A62GLY00.0590.02926.401-0.003-0.0030.0000.0000.0000.000
62A63GLY0-0.044-0.02327.0350.0040.0040.0000.0000.0000.000
63A64ASP-1-0.814-0.89526.310-0.028-0.0280.0000.0000.0000.000
64A65PHE00.031-0.00221.931-0.007-0.0070.0000.0000.0000.000
65A66CYS0-0.0200.00526.8200.0000.0000.0000.0000.0000.000
66A67TYR0-0.008-0.00625.642-0.002-0.0020.0000.0000.0000.000
67A68SER00.0490.03031.3740.0030.0030.0000.0000.0000.000
68A69ASP-1-0.854-0.94734.010-0.032-0.0320.0000.0000.0000.000
69A70GLY0-0.034-0.01435.811-0.003-0.0030.0000.0000.0000.000
70A71GLU-1-0.827-0.92331.632-0.048-0.0480.0000.0000.0000.000
71A72PHE0-0.001-0.00228.513-0.005-0.0050.0000.0000.0000.000
72A73ALA00.0050.00431.585-0.004-0.0040.0000.0000.0000.000
73A74ALA0-0.014-0.00432.121-0.004-0.0040.0000.0000.0000.000
74A75ILE00.0480.02726.561-0.007-0.0070.0000.0000.0000.000
75A76LEU0-0.010-0.00928.151-0.008-0.0080.0000.0000.0000.000
76A77GLU-1-0.879-0.92129.869-0.084-0.0840.0000.0000.0000.000
77A78ASP-1-0.907-0.95326.976-0.108-0.1080.0000.0000.0000.000
78A79VAL0-0.051-0.01924.596-0.013-0.0130.0000.0000.0000.000
79A80ARG10.8780.92226.3630.0670.0670.0000.0000.0000.000
80A81THR00.0020.00428.497-0.004-0.0040.0000.0000.0000.000
81A82VAL0-0.047-0.02922.074-0.010-0.0100.0000.0000.0000.000
82A83ARG10.9470.97524.7010.0950.0950.0000.0000.0000.000
83A84GLU-1-0.952-0.97525.747-0.118-0.1180.0000.0000.0000.000
84A85LEU0-0.108-0.04926.164-0.003-0.0030.0000.0000.0000.000
85A86GLY00.0050.00924.715-0.010-0.0100.0000.0000.0000.000
86A87PHE0-0.093-0.04120.168-0.020-0.0200.0000.0000.0000.000
87A88PRO0-0.007-0.00316.7240.0120.0120.0000.0000.0000.000
88A89GLY00.0740.02116.9130.0020.0020.0000.0000.0000.000
89A90LEU0-0.038-0.01217.6970.0020.0020.0000.0000.0000.000
90A91VAL00.0010.00815.2180.0000.0000.0000.0000.0000.000
91A92THR0-0.014-0.02117.8860.0150.0150.0000.0000.0000.000
92A93GLY00.0290.00819.5360.0030.0030.0000.0000.0000.000
93A94VAL0-0.036-0.01621.974-0.001-0.0010.0000.0000.0000.000
94A95LEU0-0.039-0.01522.8730.0040.0040.0000.0000.0000.000
95A96ASP-1-0.775-0.87726.6910.0030.0030.0000.0000.0000.000
96A97VAL0-0.020-0.04729.5570.0000.0000.0000.0000.0000.000
97A98ASP-1-0.970-0.97331.2440.0160.0160.0000.0000.0000.000
98A99GLY0-0.035-0.00227.0190.0060.0060.0000.0000.0000.000
99A100ASN0-0.035-0.01825.8890.0130.0130.0000.0000.0000.000
100A101VAL00.0420.00922.248-0.007-0.0070.0000.0000.0000.000
101A102ASP-1-0.829-0.90525.241-0.018-0.0180.0000.0000.0000.000
102A103MET00.0400.01325.507-0.008-0.0080.0000.0000.0000.000
103A104PRO00.0050.00028.096-0.006-0.0060.0000.0000.0000.000
104A105ARG10.7890.88229.4660.0260.0260.0000.0000.0000.000
105A106MET00.0150.01221.939-0.009-0.0090.0000.0000.0000.000
106A107GLU-1-0.866-0.92425.886-0.046-0.0460.0000.0000.0000.000
107A108LYS10.9060.94927.9500.0300.0300.0000.0000.0000.000
108A109ILE0-0.013-0.00823.772-0.006-0.0060.0000.0000.0000.000
109A110MET00.0160.01520.619-0.016-0.0160.0000.0000.0000.000
110A111ALA00.0040.01025.033-0.007-0.0070.0000.0000.0000.000
111A112ALA0-0.075-0.04127.929-0.004-0.0040.0000.0000.0000.000
112A113ALA00.028-0.00522.752-0.008-0.0080.0000.0000.0000.000
113A114GLY0-0.028-0.01024.241-0.013-0.0130.0000.0000.0000.000
114A115PRO0-0.037-0.02722.4030.0020.0020.0000.0000.0000.000
115A116LEU0-0.0620.00120.007-0.020-0.0200.0000.0000.0000.000
116A117ALA00.0080.00614.9610.0160.0160.0000.0000.0000.000
117A118VAL00.002-0.00116.784-0.024-0.0240.0000.0000.0000.000
118A119THR00.006-0.00413.0210.0050.0050.0000.0000.0000.000
119A120PHE00.0460.01915.3090.0060.0060.0000.0000.0000.000
120A121HIS00.0770.02415.2350.0060.0060.0000.0000.0000.000
121A122ARG10.9210.93915.2950.0210.0210.0000.0000.0000.000
122A123ALA00.0150.02417.3240.0150.0150.0000.0000.0000.000
123A124PHE00.032-0.00116.1210.0100.0100.0000.0000.0000.000
124A125ASP-1-0.786-0.88816.2580.0720.0720.0000.0000.0000.000
125A126MET0-0.068-0.02319.1290.0060.0060.0000.0000.0000.000
126A127CYS0-0.042-0.00421.555-0.005-0.0050.0000.0000.0000.000
127A128ALA00.0310.02823.2270.0110.0110.0000.0000.0000.000
128A129ASN0-0.005-0.00323.7810.0190.0190.0000.0000.0000.000
129A130PRO00.0400.01518.602-0.004-0.0040.0000.0000.0000.000
130A131LEU00.0730.02918.648-0.002-0.0020.0000.0000.0000.000
131A132TYR0-0.046-0.02820.719-0.004-0.0040.0000.0000.0000.000
132A133THR00.0030.00019.524-0.013-0.0130.0000.0000.0000.000
133A134LEU00.0050.00315.191-0.014-0.0140.0000.0000.0000.000
134A135ASN00.0500.03818.7490.0000.0000.0000.0000.0000.000
135A136ASN00.0010.00121.635-0.008-0.0080.0000.0000.0000.000
136A137LEU0-0.026-0.01816.996-0.012-0.0120.0000.0000.0000.000
137A138ALA00.0170.00619.010-0.016-0.0160.0000.0000.0000.000
138A139GLU-1-0.993-0.98719.971-0.001-0.0010.0000.0000.0000.000
139A140LEU0-0.046-0.02221.950-0.008-0.0080.0000.0000.0000.000
140A141GLY00.0300.02820.468-0.011-0.0110.0000.0000.0000.000
141A142ILE0-0.095-0.04715.831-0.023-0.0230.0000.0000.0000.000
142A143ALA0-0.0020.00313.7930.0110.0110.0000.0000.0000.000
143A144ARG10.8140.8748.9420.4840.4840.0000.0000.0000.000
144A145VAL00.0080.00411.562-0.008-0.0080.0000.0000.0000.000
145A146LEU0-0.0370.00710.5530.0210.0210.0000.0000.0000.000
146A147THR0-0.031-0.03011.2540.0300.0300.0000.0000.0000.000
147A148SER0-0.008-0.03111.6320.0180.0180.0000.0000.0000.000
148A149GLY00.006-0.01013.9510.0220.0220.0000.0000.0000.000
149A150GLN0-0.086-0.04815.2110.0090.0090.0000.0000.0000.000
150A151LYS10.9170.98517.419-0.131-0.1310.0000.0000.0000.000
151A152SER0-0.0030.00518.202-0.010-0.0100.0000.0000.0000.000
152A153ASP-1-0.864-0.92715.8270.1000.1000.0000.0000.0000.000
153A154ALA00.0520.00310.9770.0200.0200.0000.0000.0000.000
154A155LEU0-0.0250.00012.5450.0460.0460.0000.0000.0000.000
155A156GLN0-0.078-0.05413.9020.0260.0260.0000.0000.0000.000
156A157GLY0-0.034-0.00715.5130.0010.0010.0000.0000.0000.000
157A158LEU00.0450.0209.2610.0060.0060.0000.0000.0000.000
158A159SER00.007-0.00312.8860.0410.0410.0000.0000.0000.000
159A160LYS10.9170.97215.450-0.176-0.1760.0000.0000.0000.000
160A161ILE00.017-0.0029.365-0.007-0.0070.0000.0000.0000.000
161A162MET0-0.031-0.00910.6800.0390.0390.0000.0000.0000.000
162A163GLU-1-0.936-0.96312.3910.2350.2350.0000.0000.0000.000
163A164LEU0-0.049-0.03513.460-0.021-0.0210.0000.0000.0000.000
164A165ILE0-0.011-0.0028.143-0.032-0.0320.0000.0000.0000.000
165A166ALA0-0.033-0.00312.2640.0090.0090.0000.0000.0000.000
166A167HIS0-0.095-0.04915.117-0.019-0.0190.0000.0000.0000.000
167A168ARG10.9310.95615.975-0.125-0.1250.0000.0000.0000.000
168A169ASP-1-0.951-0.97217.0700.0820.0820.0000.0000.0000.000
169A170ALA00.0310.01615.422-0.021-0.0210.0000.0000.0000.000
170A171PRO0-0.044-0.00313.9230.0040.0040.0000.0000.0000.000
171A172ILE00.003-0.0037.6230.0530.0530.0000.0000.0000.000
172A173ILE00.0190.0069.028-0.062-0.0620.0000.0000.0000.000
173A174MET0-0.070-0.0126.4990.0040.0040.0000.0000.0000.000
174A175ALA00.0300.0236.4190.0060.0060.0000.0000.0000.000
175A176GLY00.0570.0127.991-0.112-0.1120.0000.0000.0000.000
176A177ALA0-0.032-0.01210.7150.0360.0360.0000.0000.0000.000
177A178GLY00.012-0.00213.7990.0370.0370.0000.0000.0000.000
178A179VAL0-0.0110.0207.5390.0250.0250.0000.0000.0000.000
179A180ARG10.9410.96210.781-0.097-0.0970.0000.0000.0000.000
180A181ALA00.0710.02510.2820.0550.0550.0000.0000.0000.000
181A182GLU-1-0.980-0.99011.3040.1230.1230.0000.0000.0000.000
182A183ASN00.004-0.00410.9970.0300.0300.0000.0000.0000.000
183A184LEU00.0430.0244.2960.0250.092-0.001-0.006-0.0610.000
184A185HIS00.0390.0096.8340.2260.2260.0000.0000.0000.000
185A186HIS00.0390.0298.5570.2110.2110.0000.0000.0000.000
186A187PHE0-0.034-0.0266.0030.0040.0040.0000.0000.0000.000
187A188LEU0-0.005-0.0022.522-0.552-0.2871.361-0.420-1.2060.000
188A189ASP-1-0.903-0.9544.8661.3501.372-0.001-0.003-0.0170.000
189A190ALA0-0.073-0.0407.898-0.077-0.0770.0000.0000.0000.000
190A191GLY00.0000.0105.919-0.193-0.1930.0000.0000.0000.000
191A192VAL0-0.077-0.0354.089-0.256-0.122-0.001-0.033-0.1010.000
192A193LEU00.0390.0142.690-0.9170.7750.760-0.916-1.536-0.009
193A194GLU-1-0.725-0.8372.427-4.088-2.6843.555-2.423-2.536-0.024
194A195VAL0-0.0110.0003.0350.2090.6400.0870.106-0.6240.000
195A196HIS0-0.035-0.0314.910-0.258-0.296-0.001-0.0020.0410.000
196A197SER00.008-0.0128.5190.1230.1230.0000.0000.0000.000
197A198SER00.0350.00910.991-0.042-0.0420.0000.0000.0000.000
198A199ALA0-0.0040.00912.9640.0360.0360.0000.0000.0000.000
199A200GLY00.0710.02714.809-0.028-0.0280.0000.0000.0000.000
200A201ALA0-0.0130.00518.5320.0240.0240.0000.0000.0000.000
201A202TRP0-0.0190.00122.008-0.009-0.0090.0000.0000.0000.000
202A203GLN00.0320.01325.4770.0080.0080.0000.0000.0000.000
203A204ALA00.058-0.01127.5270.0030.0030.0000.0000.0000.000
204A205SER00.022-0.00631.288-0.006-0.0060.0000.0000.0000.000
205A206PRO00.0170.00832.9610.0030.0030.0000.0000.0000.000
206A207MET0-0.041-0.01935.5420.0020.0020.0000.0000.0000.000
207A208ARG10.9730.98438.7690.0580.0580.0000.0000.0000.000
208A209TYR0-0.023-0.02041.6970.0030.0030.0000.0000.0000.000
209A210ARG10.9560.96639.9570.0400.0400.0000.0000.0000.000
210A211ASN00.0790.07344.0960.0030.0030.0000.0000.0000.000
211A225TYR0-0.0130.00828.8440.0000.0000.0000.0000.0000.000
212A226SER0-0.099-0.03930.1110.0020.0020.0000.0000.0000.000
213A227ARG10.9450.96527.5980.1030.1030.0000.0000.0000.000
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