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: KG4K3

Calculation Name: 1A21-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A21

Chain ID: A

ChEMBL ID:

UniProt ID: P24055

Base Structure: X-ray

Registration Date: 2023-09-24

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2179037.876729
FMO2-HF: Nuclear repulsion 2097042.332934
FMO2-HF: Total energy -81995.543795
FMO2-MP2: Total energy -82236.033625


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:4:THR)


Summations of interaction energy for fragment #1(A:4: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.
-20.617-14.9385.249-4.311-6.6160.017
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / 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].
3A6ARG10.8420.9151.951-13.579-9.1845.049-3.975-5.4690.014
4A7ALA00.0710.0623.527-0.657-0.5720.0010.157-0.2430.000
5A8TYR0-0.033-0.0226.2680.4920.4920.0000.0000.0000.000
6A9ASN00.0390.0128.650-0.117-0.1170.0000.0000.0000.000
7A10LEU0-0.0310.00511.205-0.116-0.1160.0000.0000.0000.000
8A11THR0-0.038-0.02213.669-0.096-0.0960.0000.0000.0000.000
9A12TRP00.0110.00017.408-0.019-0.0190.0000.0000.0000.000
10A13LYS10.8470.93819.642-0.534-0.5340.0000.0000.0000.000
11A14SER00.0190.00323.297-0.022-0.0220.0000.0000.0000.000
12A15THR00.0170.00526.6070.0030.0030.0000.0000.0000.000
13A16ASN00.0270.01230.262-0.002-0.0020.0000.0000.0000.000
14A17PHE00.024-0.00130.199-0.011-0.0110.0000.0000.0000.000
15A18LYS10.9351.00428.030-0.205-0.2050.0000.0000.0000.000
16A19THR0-0.024-0.03323.4630.0110.0110.0000.0000.0000.000
17A20ILE00.0440.03420.788-0.009-0.0090.0000.0000.0000.000
18A21LEU0-0.051-0.00315.0290.0210.0210.0000.0000.0000.000
19A22GLU-1-0.792-0.90816.6510.4550.4550.0000.0000.0000.000
20A23TRP0-0.070-0.03710.3880.0600.0600.0000.0000.0000.000
21A24GLU-1-0.892-0.91810.9380.7830.7830.0000.0000.0000.000
22A25PRO00.0300.0127.2980.3510.3510.0000.0000.0000.000
23A26LYS10.9900.98610.331-0.421-0.4210.0000.0000.0000.000
24A27SER0-0.023-0.0129.278-0.049-0.0490.0000.0000.0000.000
25A28ILE00.0310.02012.133-0.027-0.0270.0000.0000.0000.000
26A29ASP-1-0.873-0.9338.566-0.680-0.6800.0000.0000.0000.000
27A30HIS0-0.045-0.0245.3860.3460.390-0.001-0.012-0.0310.000
28A31VAL00.0090.02310.5450.1160.1160.0000.0000.0000.000
29A32TYR0-0.021-0.0357.9290.1030.1030.0000.0000.0000.000
30A33THR0-0.027-0.00612.409-0.138-0.1380.0000.0000.0000.000
31A34VAL0-0.0060.00913.4540.1350.1350.0000.0000.0000.000
32A35GLN00.010-0.00415.533-0.053-0.0530.0000.0000.0000.000
33A36ILE0-0.011-0.00417.6410.0680.0680.0000.0000.0000.000
34A37SER0-0.014-0.00219.672-0.035-0.0350.0000.0000.0000.000
35A38THR00.0770.03222.0430.0140.0140.0000.0000.0000.000
36A39ARG10.9360.96424.538-0.216-0.2160.0000.0000.0000.000
37A40LEU0-0.012-0.00826.542-0.016-0.0160.0000.0000.0000.000
38A41GLU-1-0.930-0.95325.9160.1480.1480.0000.0000.0000.000
39A42ASN00.0400.01522.1840.0430.0430.0000.0000.0000.000
40A43TRP0-0.023-0.01316.1310.0110.0110.0000.0000.0000.000
41A44LYS10.9720.99920.035-0.227-0.2270.0000.0000.0000.000
42A45SER00.000-0.00818.1340.0550.0550.0000.0000.0000.000
43A46LYS10.8110.92919.699-0.267-0.2670.0000.0000.0000.000
44A47CYS0-0.030-0.00917.878-0.088-0.0880.0000.0000.0000.000
45A48PHE00.026-0.01117.9040.0420.0420.0000.0000.0000.000
46A49LEU0-0.010-0.00614.592-0.017-0.0170.0000.0000.0000.000
47A50THR00.0490.04415.915-0.055-0.0550.0000.0000.0000.000
48A51ALA00.0610.02214.9040.0410.0410.0000.0000.0000.000
49A52GLU-1-0.957-0.96915.6910.3220.3220.0000.0000.0000.000
50A53THR0-0.035-0.03412.6650.0340.0340.0000.0000.0000.000
51A54GLU-1-0.904-0.96215.3180.4180.4180.0000.0000.0000.000
52A56ASP-1-0.854-0.92619.6360.2720.2720.0000.0000.0000.000
53A57LEU0-0.008-0.01819.397-0.014-0.0140.0000.0000.0000.000
54A58THR00.0230.01423.779-0.012-0.0120.0000.0000.0000.000
55A59ASP-1-0.930-0.96827.0670.1940.1940.0000.0000.0000.000
56A60GLU-1-0.821-0.91424.6720.2010.2010.0000.0000.0000.000
57A61VAL00.0480.01725.110-0.009-0.0090.0000.0000.0000.000
58A62VAL0-0.044-0.02927.735-0.011-0.0110.0000.0000.0000.000
59A63LYS10.8040.91828.816-0.196-0.1960.0000.0000.0000.000
60A64ASP-1-0.762-0.88231.3880.1600.1600.0000.0000.0000.000
61A65VAL0-0.0270.00730.8740.0160.0160.0000.0000.0000.000
62A66GLY00.0250.00031.6020.0100.0100.0000.0000.0000.000
63A67GLN0-0.069-0.02829.0720.0110.0110.0000.0000.0000.000
64A68THR0-0.021-0.01024.3280.0020.0020.0000.0000.0000.000
65A69TYR0-0.050-0.04923.053-0.002-0.0020.0000.0000.0000.000
66A70MET0-0.0140.00317.3380.0480.0480.0000.0000.0000.000
67A71ALA00.0190.00417.180-0.047-0.0470.0000.0000.0000.000
68A72ARG10.8840.93712.204-0.523-0.5230.0000.0000.0000.000
69A73VAL0-0.0100.00210.102-0.156-0.1560.0000.0000.0000.000
70A74LEU0-0.030-0.0149.0840.4090.4090.0000.0000.0000.000
71A75SER00.0220.0006.221-0.097-0.0970.0000.0000.0000.000
72A76TYR00.0220.0007.932-0.271-0.2710.0000.0000.0000.000
73A77PRO00.0110.0027.6470.1420.1420.0000.0000.0000.000
74A78ALA00.0180.01210.0040.1140.1140.0000.0000.0000.000
75A79ARG10.8810.93411.9200.4530.4530.0000.0000.0000.000
76A80ASN00.014-0.01712.530-0.086-0.0860.0000.0000.0000.000
77A81GLY0-0.0050.01012.386-0.055-0.0550.0000.0000.0000.000
78A82ASN0-0.019-0.00813.0180.1770.1770.0000.0000.0000.000
79A83THR00.0010.00210.2830.1120.1120.0000.0000.0000.000
80A84THR00.0050.01812.3200.0490.0490.0000.0000.0000.000
81A85GLY00.0060.00214.7400.0440.0440.0000.0000.0000.000
82A86PHE0-0.036-0.02714.0010.0950.0950.0000.0000.0000.000
83A87PRO0-0.035-0.00611.795-0.183-0.1830.0000.0000.0000.000
84A88GLU-1-0.924-0.9675.796-4.053-4.0530.0000.0000.0000.000
85A89GLU-1-0.927-0.9568.058-0.146-0.1460.0000.0000.0000.000
86A90PRO0-0.028-0.0106.548-0.345-0.3450.0000.0000.0000.000
87A91PRO00.0140.0152.965-0.0831.0460.201-0.479-0.8510.003
88A92PHE00.011-0.0085.017-0.091-0.065-0.001-0.002-0.0220.000
89A93ARG10.8110.8945.667-2.321-2.3210.0000.0000.0000.000
90A94ASN00.0480.0139.195-0.226-0.2260.0000.0000.0000.000
91A95SER00.005-0.00612.7720.0900.0900.0000.0000.0000.000
92A96PRO0-0.018-0.01115.070-0.034-0.0340.0000.0000.0000.000
93A97GLU-1-0.887-0.94617.9350.3930.3930.0000.0000.0000.000
94A98PHE0-0.009-0.00921.243-0.006-0.0060.0000.0000.0000.000
95A99THR00.0510.02823.726-0.018-0.0180.0000.0000.0000.000
96A100PRO0-0.0230.00327.066-0.010-0.0100.0000.0000.0000.000
97A101TYR00.0330.00528.991-0.001-0.0010.0000.0000.0000.000
98A102LEU0-0.042-0.00930.272-0.011-0.0110.0000.0000.0000.000
99A103ASP-1-0.855-0.94226.0410.3260.3260.0000.0000.0000.000
100A104THR0-0.041-0.00928.0070.0060.0060.0000.0000.0000.000
101A105ASN0-0.013-0.02027.712-0.018-0.0180.0000.0000.0000.000
102A106LEU00.0250.01531.055-0.005-0.0050.0000.0000.0000.000
103A107GLY00.010-0.01034.4670.0060.0060.0000.0000.0000.000
104A108GLN0-0.089-0.04135.426-0.006-0.0060.0000.0000.0000.000
105A109PRO0-0.0190.00638.148-0.002-0.0020.0000.0000.0000.000
106A110THR00.012-0.00841.4900.0000.0000.0000.0000.0000.000
107A111ILE0-0.0270.00444.126-0.001-0.0010.0000.0000.0000.000
108A112GLN0-0.005-0.00347.870-0.002-0.0020.0000.0000.0000.000
109A113SER00.005-0.00149.233-0.004-0.0040.0000.0000.0000.000
110A114PHE00.004-0.00252.8280.0030.0030.0000.0000.0000.000
111A115GLU-1-0.901-0.93955.2430.0600.0600.0000.0000.0000.000
112A116GLN00.013-0.00358.9750.0010.0010.0000.0000.0000.000
113A117VAL00.0460.02461.620-0.002-0.0020.0000.0000.0000.000
114A118GLY0-0.070-0.07064.772-0.001-0.0010.0000.0000.0000.000
115A119THR0-0.027-0.02965.6950.0000.0000.0000.0000.0000.000
116A120LYS10.9120.96162.691-0.060-0.0600.0000.0000.0000.000
117A121LEU0-0.0070.02556.3150.0000.0000.0000.0000.0000.000
118A122ASN0-0.024-0.02356.8020.0010.0010.0000.0000.0000.000
119A123VAL0-0.0120.00251.0390.0000.0000.0000.0000.0000.000
120A124THR00.013-0.00650.7390.0000.0000.0000.0000.0000.000
121A125VAL0-0.043-0.02445.1390.0020.0020.0000.0000.0000.000
122A126GLN00.0340.02042.630-0.006-0.0060.0000.0000.0000.000
123A127ASP-1-0.936-0.98243.9000.1170.1170.0000.0000.0000.000
124A128ALA0-0.0120.01238.9010.0020.0020.0000.0000.0000.000
125A129ARG10.9420.96338.834-0.116-0.1160.0000.0000.0000.000
126A130THR0-0.0060.01032.4130.0040.0040.0000.0000.0000.000
127A131LEU00.0350.01233.707-0.007-0.0070.0000.0000.0000.000
128A132VAL00.0080.00331.5160.0130.0130.0000.0000.0000.000
129A133ARG10.8720.95631.361-0.152-0.1520.0000.0000.0000.000
130A134ARG10.9340.94827.908-0.181-0.1810.0000.0000.0000.000
131A135ASN0-0.051-0.04132.0990.0040.0040.0000.0000.0000.000
132A136GLY00.0280.00035.444-0.002-0.0020.0000.0000.0000.000
133A137THR00.0160.03636.526-0.001-0.0010.0000.0000.0000.000
134A138PHE00.003-0.00336.3530.0070.0070.0000.0000.0000.000
135A139LEU00.005-0.00234.048-0.004-0.0040.0000.0000.0000.000
136A140SER0-0.008-0.00837.3630.0050.0050.0000.0000.0000.000
137A141LEU00.0680.02736.5260.0040.0040.0000.0000.0000.000
138A142ARG10.8980.95539.364-0.111-0.1110.0000.0000.0000.000
139A143ALA0-0.041-0.02540.857-0.002-0.0020.0000.0000.0000.000
140A144VAL0-0.0260.00535.9760.0000.0000.0000.0000.0000.000
141A145PHE00.019-0.00434.9210.0020.0020.0000.0000.0000.000
142A146GLY00.0260.02640.593-0.004-0.0040.0000.0000.0000.000
143A147LYS10.9160.91644.350-0.097-0.0970.0000.0000.0000.000
144A148ASP-1-0.879-0.91241.0110.1340.1340.0000.0000.0000.000
145A149LEU0-0.073-0.02440.2370.0060.0060.0000.0000.0000.000
146A150ASN0-0.018-0.01242.803-0.003-0.0030.0000.0000.0000.000
147A151TYR00.0190.00542.1770.0070.0070.0000.0000.0000.000
148A152THR0-0.050-0.02845.512-0.004-0.0040.0000.0000.0000.000
149A153LEU00.0030.01246.9260.0030.0030.0000.0000.0000.000
150A154TYR0-0.022-0.00944.159-0.003-0.0030.0000.0000.0000.000
151A155TYR00.0050.00249.919-0.001-0.0010.0000.0000.0000.000
152A156TRP00.002-0.00648.9550.0010.0010.0000.0000.0000.000
153A157ARG10.9070.96555.424-0.064-0.0640.0000.0000.0000.000
154A158ALA00.0480.03057.5530.0020.0020.0000.0000.0000.000
155A159SER0-0.013-0.00158.414-0.003-0.0030.0000.0000.0000.000
156A160SER00.0230.01759.4570.0020.0020.0000.0000.0000.000
157A161THR0-0.050-0.05256.9500.0000.0000.0000.0000.0000.000
158A162GLY00.0230.02655.2920.0020.0020.0000.0000.0000.000
159A163LYS10.8880.93946.792-0.111-0.1110.0000.0000.0000.000
160A164LYS10.9460.99552.954-0.073-0.0730.0000.0000.0000.000
161A165THR0-0.006-0.01948.6940.0010.0010.0000.0000.0000.000
162A166ALA00.0030.02951.661-0.002-0.0020.0000.0000.0000.000
163A167THR0-0.012-0.02548.7040.0060.0060.0000.0000.0000.000
164A168THR00.0230.01849.186-0.005-0.0050.0000.0000.0000.000
165A169ASN00.021-0.00847.9280.0090.0090.0000.0000.0000.000
166A170THR0-0.0240.00348.5390.0020.0020.0000.0000.0000.000
167A171ASN00.033-0.01345.5650.0060.0060.0000.0000.0000.000
168A172GLU-1-0.856-0.89849.1970.0820.0820.0000.0000.0000.000
169A173PHE0-0.013-0.00848.5750.0010.0010.0000.0000.0000.000
170A174LEU0-0.021-0.02353.993-0.002-0.0020.0000.0000.0000.000
171A175ILE0-0.0260.00956.1640.0000.0000.0000.0000.0000.000
172A176ASP-1-0.848-0.94558.9160.0600.0600.0000.0000.0000.000
173A177VAL0-0.070-0.01459.8890.0020.0020.0000.0000.0000.000
174A178ASP-1-0.833-0.90562.7540.0590.0590.0000.0000.0000.000
175A179LYS10.9960.99765.170-0.049-0.0490.0000.0000.0000.000
176A180GLY0-0.072-0.02366.678-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.839-0.91762.9260.0610.0610.0000.0000.0000.000
178A182ASN0-0.023-0.01059.7070.0020.0020.0000.0000.0000.000
179A183TYR0-0.008-0.02156.8260.0020.0020.0000.0000.0000.000
180A184CYS0-0.050-0.01851.3430.0000.0000.0000.0000.0000.000
181A185PHE00.045-0.01250.8470.0000.0000.0000.0000.0000.000
182A186SER00.003-0.00245.838-0.001-0.0010.0000.0000.0000.000
183A187VAL00.0400.01944.592-0.001-0.0010.0000.0000.0000.000
184A188GLN00.002-0.00840.2010.0010.0010.0000.0000.0000.000
185A189ALA00.0380.02439.420-0.005-0.0050.0000.0000.0000.000
186A190VAL0-0.031-0.04040.0430.0070.0070.0000.0000.0000.000
187A191ILE00.0340.03336.804-0.004-0.0040.0000.0000.0000.000
188A192PRO00.016-0.00139.0700.0090.0090.0000.0000.0000.000
189A193SER00.0180.02240.0230.0030.0030.0000.0000.0000.000
190A194ARG10.7880.91232.569-0.206-0.2060.0000.0000.0000.000
191A195LYS10.9950.98233.565-0.203-0.2030.0000.0000.0000.000
192A196ARG10.9280.96627.800-0.281-0.2810.0000.0000.0000.000
193A197LYS10.9260.96326.962-0.303-0.3030.0000.0000.0000.000
194A198GLN0-0.005-0.00333.056-0.008-0.0080.0000.0000.0000.000
195A199ARG10.9190.97636.445-0.148-0.1480.0000.0000.0000.000
196A200SER00.0180.02935.8210.0090.0090.0000.0000.0000.000
197A201PRO0-0.015-0.01435.100-0.005-0.0050.0000.0000.0000.000
198A202GLU-1-0.872-0.93537.8330.1210.1210.0000.0000.0000.000
199A203SER00.014-0.00240.8620.0040.0040.0000.0000.0000.000
200A204LEU0-0.0030.00342.2400.0000.0000.0000.0000.0000.000
201A205THR0-0.052-0.03944.655-0.001-0.0010.0000.0000.0000.000
202A206GLU-1-0.883-0.92048.0810.0880.0880.0000.0000.0000.000
203A208THR0-0.0090.00054.905-0.002-0.0020.0000.0000.0000.000