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

tag_button

FMODB ID: 76MMK

Calculation Name: 1XAT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAT

Chain ID: A

ChEMBL ID:

UniProt ID: P26841

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2214584.783385
FMO2-HF: Nuclear repulsion 2132552.952289
FMO2-HF: Total energy -82031.831096
FMO2-MP2: Total energy -82268.373022


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-35.801-27.6320.474-12.381-16.263-0.002
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.005
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].
3A5PHE0-0.054-0.0072.019-14.157-10.6156.016-4.436-5.1220.045
4A6GLU-1-0.782-0.8912.755-5.569-3.9681.298-0.947-1.952-0.011
5A7SER0-0.018-0.0265.163-0.830-0.774-0.001-0.002-0.0530.000
6A8PRO00.0230.0206.0500.8950.8950.0000.0000.0000.000
7A9PHE0-0.028-0.0196.7870.4230.4230.0000.0000.0000.000
8A10ARG10.8650.9438.413-0.577-0.5770.0000.0000.0000.000
9A11GLY00.0780.0388.0290.5880.5880.0000.0000.0000.000
10A12LYS10.7540.8566.513-1.901-1.9010.0000.0000.0000.000
11A13LEU00.0590.02410.7040.0980.0980.0000.0000.0000.000
12A14LEU00.0070.00612.8050.1610.1610.0000.0000.0000.000
13A15SER00.017-0.00214.4320.0300.0300.0000.0000.0000.000
14A16GLU-1-0.944-0.95713.2510.4220.4220.0000.0000.0000.000
15A17GLN0-0.032-0.0419.0440.6650.6650.0000.0000.0000.000
16A18VAL0-0.0430.00312.2180.0820.0820.0000.0000.0000.000
17A19SER0-0.052-0.03214.868-0.118-0.1180.0000.0000.0000.000
18A20ASN0-0.018-0.01916.536-0.147-0.1470.0000.0000.0000.000
19A21PRO00.0180.00718.4550.0080.0080.0000.0000.0000.000
20A22ASN0-0.048-0.01221.661-0.046-0.0460.0000.0000.0000.000
21A23ILE0-0.013-0.00316.4910.0080.0080.0000.0000.0000.000
22A24ARG10.8570.92420.463-0.367-0.3670.0000.0000.0000.000
23A25VAL00.0190.00117.1760.0150.0150.0000.0000.0000.000
24A26GLY00.0260.03020.438-0.037-0.0370.0000.0000.0000.000
25A27ARG10.8050.88220.327-0.189-0.1890.0000.0000.0000.000
26A28TYR00.002-0.02719.172-0.009-0.0090.0000.0000.0000.000
27A29SER00.0130.01317.7090.0070.0070.0000.0000.0000.000
28A30TYR0-0.065-0.03012.2950.0640.0640.0000.0000.0000.000
29A31TYR00.0080.0257.513-0.236-0.2360.0000.0000.0000.000
30A32SER0-0.012-0.0067.5990.4120.4120.0000.0000.0000.000
31A33GLY00.0340.0095.630-1.060-1.0600.0000.0000.0000.000
32A34TYR0-0.0060.0092.255-2.5620.3702.570-1.997-3.5050.008
33A35TYR0-0.007-0.0201.922-12.202-14.4047.644-2.739-2.704-0.043
34A36HIS00.0070.0244.515-0.178-0.098-0.001-0.008-0.0710.000
35A37GLY0-0.0220.0202.508-2.516-1.7292.365-1.729-1.4220.012
36A38HIS0-0.028-0.0242.8050.1911.5660.583-0.523-1.434-0.013
37A39SER00.0450.0165.5461.2011.2010.0000.0000.0000.000
38A40PHE00.048-0.0147.661-0.287-0.2870.0000.0000.0000.000
39A41ASP-1-0.707-0.84710.8180.6540.6540.0000.0000.0000.000
40A42ASP-1-0.896-0.9459.4881.4801.4800.0000.0000.0000.000
41A43CYS0-0.089-0.03611.5040.0360.0360.0000.0000.0000.000
42A44ALA00.0050.01113.373-0.176-0.1760.0000.0000.0000.000
43A45ARG10.9220.96412.810-1.078-1.0780.0000.0000.0000.000
44A46TYR00.000-0.01817.522-0.045-0.0450.0000.0000.0000.000
45A47LEU0-0.0160.01419.032-0.055-0.0550.0000.0000.0000.000
46A48MET00.0190.01519.8820.0190.0190.0000.0000.0000.000
47A49PRO00.0000.01419.255-0.006-0.0060.0000.0000.0000.000
48A50ASP-1-0.896-0.96121.6520.3160.3160.0000.0000.0000.000
49A51ARG10.7830.85324.837-0.254-0.2540.0000.0000.0000.000
50A52ASP-1-0.863-0.92626.9090.2370.2370.0000.0000.0000.000
51A53ASP-1-0.800-0.85829.5230.2330.2330.0000.0000.0000.000
52A54VAL0-0.0170.00625.136-0.003-0.0030.0000.0000.0000.000
53A55ASP-1-0.761-0.88526.3560.2910.2910.0000.0000.0000.000
54A56LYS10.7520.85624.356-0.276-0.2760.0000.0000.0000.000
55A57LEU0-0.018-0.00617.938-0.007-0.0070.0000.0000.0000.000
56A58VAL0-0.048-0.03122.2610.0000.0000.0000.0000.0000.000
57A59ILE0-0.003-0.00517.4140.0100.0100.0000.0000.0000.000
58A60GLY00.0500.04021.491-0.009-0.0090.0000.0000.0000.000
59A61SER00.0320.00321.4010.0560.0560.0000.0000.0000.000
60A62PHE0-0.027-0.02320.859-0.010-0.0100.0000.0000.0000.000
61A63CYS0-0.0490.01018.830-0.027-0.0270.0000.0000.0000.000
62A64SER00.0110.00816.1210.0690.0690.0000.0000.0000.000
63A65ILE00.0110.00613.034-0.074-0.0740.0000.0000.0000.000
64A66GLY00.0110.00111.4900.1920.1920.0000.0000.0000.000
65A67SER00.010-0.0366.6120.3190.3190.0000.0000.0000.000
66A68GLY00.0810.0388.800-0.465-0.4650.0000.0000.0000.000
67A69ALA0-0.041-0.00110.205-0.202-0.2020.0000.0000.0000.000
68A70ALA0-0.038-0.01513.0850.1710.1710.0000.0000.0000.000
69A71PHE00.021-0.00815.244-0.117-0.1170.0000.0000.0000.000
70A72ILE0-0.020-0.01518.8040.0300.0300.0000.0000.0000.000
71A73MET00.0190.01720.547-0.038-0.0380.0000.0000.0000.000
72A74ALA00.0070.00622.981-0.014-0.0140.0000.0000.0000.000
73A75GLY00.0720.03125.653-0.021-0.0210.0000.0000.0000.000
74A76ASN0-0.026-0.02327.6260.0210.0210.0000.0000.0000.000
75A77GLN0-0.055-0.02822.907-0.022-0.0220.0000.0000.0000.000
76A78GLY0-0.009-0.00328.315-0.007-0.0070.0000.0000.0000.000
77A79HIS10.8150.91427.905-0.250-0.2500.0000.0000.0000.000
78A80ARG10.8240.89732.738-0.156-0.1560.0000.0000.0000.000
79A81ALA00.0130.00235.518-0.005-0.0050.0000.0000.0000.000
80A82GLU-1-0.816-0.88637.2810.1430.1430.0000.0000.0000.000
81A83TRP0-0.030-0.00638.940-0.006-0.0060.0000.0000.0000.000
82A84ALA0-0.001-0.00840.9690.0010.0010.0000.0000.0000.000
83A85SER00.001-0.00638.1730.0000.0000.0000.0000.0000.000
84A86THR00.0180.02433.7960.0020.0020.0000.0000.0000.000
85A87PHE00.0110.01032.7730.0170.0170.0000.0000.0000.000
86A88PRO00.0230.02630.319-0.006-0.0060.0000.0000.0000.000
87A89PHE00.018-0.01933.5110.0030.0030.0000.0000.0000.000
88A90HIS0-0.012-0.00834.7120.0050.0050.0000.0000.0000.000
89A91PHE0-0.008-0.00530.3210.0020.0020.0000.0000.0000.000
90A92MET0-0.070-0.01731.7490.0110.0110.0000.0000.0000.000
91A93HIS00.026-0.01432.090-0.016-0.0160.0000.0000.0000.000
92A94GLU-1-0.944-0.95633.0750.1240.1240.0000.0000.0000.000
93A95GLU-1-0.901-0.93035.6070.0930.0930.0000.0000.0000.000
94A96PRO00.020-0.00738.5890.0010.0010.0000.0000.0000.000
95A97ALA0-0.038-0.01741.797-0.001-0.0010.0000.0000.0000.000
96A98PHE0-0.036-0.03736.7950.0000.0000.0000.0000.0000.000
97A99ALA00.0160.01940.1840.0050.0050.0000.0000.0000.000
98A100GLY0-0.017-0.00241.3370.0000.0000.0000.0000.0000.000
99A101ALA0-0.046-0.01539.173-0.001-0.0010.0000.0000.0000.000
100A102VAL00.0130.00440.1530.0040.0040.0000.0000.0000.000
101A103ASN0-0.0020.00033.9200.0110.0110.0000.0000.0000.000
102A104GLY00.0690.02935.837-0.004-0.0040.0000.0000.0000.000
103A105TYR0-0.048-0.02428.3650.0060.0060.0000.0000.0000.000
104A106GLN0-0.048-0.02532.654-0.022-0.0220.0000.0000.0000.000
105A107PRO00.0220.01930.6410.0130.0130.0000.0000.0000.000
106A108ALA0-0.050-0.03728.876-0.011-0.0110.0000.0000.0000.000
107A109GLY0-0.029-0.00830.139-0.012-0.0120.0000.0000.0000.000
108A110ASP-1-0.809-0.90827.1900.3280.3280.0000.0000.0000.000
109A111THR0-0.034-0.00123.027-0.010-0.0100.0000.0000.0000.000
110A112LEU0-0.021-0.01224.0460.0280.0280.0000.0000.0000.000
111A113ILE0-0.021-0.00620.373-0.010-0.0100.0000.0000.0000.000
112A114GLY00.0610.02423.5770.0050.0050.0000.0000.0000.000
113A115HIS00.0380.01423.6930.0640.0640.0000.0000.0000.000
114A116GLU-1-0.759-0.84223.1490.2020.2020.0000.0000.0000.000
115A117VAL0-0.0250.00421.214-0.015-0.0150.0000.0000.0000.000
116A118TRP0-0.068-0.02816.6730.0200.0200.0000.0000.0000.000
117A119ILE00.0170.00116.180-0.044-0.0440.0000.0000.0000.000
118A120GLY00.0210.01415.6720.0700.0700.0000.0000.0000.000
119A121THR0-0.045-0.04910.8110.0200.0200.0000.0000.0000.000
120A122GLU-1-0.797-0.88711.8000.2450.2450.0000.0000.0000.000
121A123ALA0-0.0390.00513.992-0.072-0.0720.0000.0000.0000.000
122A124MET0-0.024-0.01516.6960.0800.0800.0000.0000.0000.000
123A125PHE0-0.005-0.00618.044-0.074-0.0740.0000.0000.0000.000
124A126MET0-0.0020.00121.7240.0170.0170.0000.0000.0000.000
125A127PRO00.0360.01224.5800.0050.0050.0000.0000.0000.000
126A128GLY00.0070.01626.042-0.025-0.0250.0000.0000.0000.000
127A129VAL0-0.078-0.01224.680-0.018-0.0180.0000.0000.0000.000
128A130ARG10.8410.87526.402-0.207-0.2070.0000.0000.0000.000
129A131VAL0-0.024-0.00823.882-0.020-0.0200.0000.0000.0000.000
130A132GLY00.0370.01026.6560.0120.0120.0000.0000.0000.000
131A133HIS00.0680.02226.9600.0310.0310.0000.0000.0000.000
132A134GLY00.0420.02326.121-0.021-0.0210.0000.0000.0000.000
133A135ALA0-0.0230.00925.663-0.014-0.0140.0000.0000.0000.000
134A136ILE0-0.025-0.01721.9400.0240.0240.0000.0000.0000.000
135A137ILE0-0.0110.00220.425-0.030-0.0300.0000.0000.0000.000
136A138GLY00.0370.01319.7350.0310.0310.0000.0000.0000.000
137A139SER00.030-0.01115.9820.0570.0570.0000.0000.0000.000
138A140ARG10.7590.86014.048-0.326-0.3260.0000.0000.0000.000
139A141ALA0-0.054-0.00218.208-0.022-0.0220.0000.0000.0000.000
140A142LEU00.0110.01620.7340.0440.0440.0000.0000.0000.000
141A143VAL00.028-0.00122.505-0.039-0.0390.0000.0000.0000.000
142A144THR00.006-0.01024.6960.0190.0190.0000.0000.0000.000
143A145GLY00.0260.01427.703-0.014-0.0140.0000.0000.0000.000
144A146ASP-1-0.791-0.85828.1970.2540.2540.0000.0000.0000.000
145A147VAL0-0.052-0.02626.653-0.011-0.0110.0000.0000.0000.000
146A148GLU-1-0.827-0.91129.5930.1610.1610.0000.0000.0000.000
147A149PRO00.024-0.00329.8170.0120.0120.0000.0000.0000.000
148A150TYR0-0.059-0.04628.908-0.019-0.0190.0000.0000.0000.000
149A151ALA0-0.0150.01229.620-0.016-0.0160.0000.0000.0000.000
150A152ILE00.0000.00125.5890.0180.0180.0000.0000.0000.000
151A153VAL00.0220.00424.929-0.020-0.0200.0000.0000.0000.000
152A154GLY00.0450.01623.9160.0210.0210.0000.0000.0000.000
153A155GLY0-0.022-0.00423.695-0.022-0.0220.0000.0000.0000.000
154A156ASN00.0250.01523.5820.0280.0280.0000.0000.0000.000
155A157PRO00.0790.01825.789-0.016-0.0160.0000.0000.0000.000
156A158ALA0-0.069-0.01024.524-0.015-0.0150.0000.0000.0000.000
157A159ARG10.9050.94826.534-0.154-0.1540.0000.0000.0000.000
158A160THR00.019-0.01328.7560.0060.0060.0000.0000.0000.000
159A161ILE0-0.059-0.01627.050-0.012-0.0120.0000.0000.0000.000
160A162ARG10.8920.94530.413-0.128-0.1280.0000.0000.0000.000
161A163LYS10.8830.94131.072-0.126-0.1260.0000.0000.0000.000
162A164ARG10.7610.85826.352-0.221-0.2210.0000.0000.0000.000
163A165PHE0-0.006-0.00330.485-0.009-0.0090.0000.0000.0000.000
164A166SER0-0.013-0.02934.4710.0020.0020.0000.0000.0000.000
165A167ASP-1-0.815-0.92837.3780.1220.1220.0000.0000.0000.000
166A168GLY00.0170.02038.9210.0030.0030.0000.0000.0000.000
167A169ASP-1-0.803-0.88136.4310.0980.0980.0000.0000.0000.000
168A170ILE0-0.002-0.00633.6620.0070.0070.0000.0000.0000.000
169A171GLN0-0.046-0.01335.9090.0030.0030.0000.0000.0000.000
170A172ASN00.0110.00038.4810.0010.0010.0000.0000.0000.000
171A173LEU00.008-0.01531.7860.0020.0020.0000.0000.0000.000
172A174LEU0-0.070-0.04333.0110.0100.0100.0000.0000.0000.000
173A175GLU-1-0.829-0.86935.3270.1050.1050.0000.0000.0000.000
174A176MET0-0.0320.00034.774-0.001-0.0010.0000.0000.0000.000
175A177ALA00.0140.00532.7560.0010.0010.0000.0000.0000.000
176A178TRP00.0480.00525.2910.0080.0080.0000.0000.0000.000
177A179TRP0-0.0020.00726.8280.0020.0020.0000.0000.0000.000
178A180ASP-1-0.853-0.93527.7830.2520.2520.0000.0000.0000.000
179A181TRP0-0.040-0.00630.485-0.010-0.0100.0000.0000.0000.000
180A182PRO00.0490.02030.8050.0160.0160.0000.0000.0000.000
181A183LEU00.0240.01327.0020.0000.0000.0000.0000.0000.000
182A184ALA00.0680.02430.306-0.003-0.0030.0000.0000.0000.000
183A185ASP-1-0.885-0.94533.4330.0980.0980.0000.0000.0000.000
184A186ILE0-0.003-0.00527.709-0.003-0.0030.0000.0000.0000.000
185A187GLU-1-0.971-0.98630.4920.0920.0920.0000.0000.0000.000
186A188ALA0-0.031-0.02231.327-0.008-0.0080.0000.0000.0000.000
187A189ALA00.0090.00933.055-0.008-0.0080.0000.0000.0000.000
188A190MET00.0240.02625.7200.0040.0040.0000.0000.0000.000
189A191PRO0-0.001-0.01831.1230.0000.0000.0000.0000.0000.000
190A192LEU0-0.0080.00633.573-0.005-0.0050.0000.0000.0000.000
191A193LEU00.0090.01629.0260.0020.0020.0000.0000.0000.000
192A194CYS0-0.097-0.03128.7470.0100.0100.0000.0000.0000.000
193A195THR0-0.059-0.04529.786-0.015-0.0150.0000.0000.0000.000
194A196GLY00.0260.00531.5890.0110.0110.0000.0000.0000.000
195A197ASP-1-0.880-0.92833.6380.0700.0700.0000.0000.0000.000
196A198ILE00.0130.00232.9550.0020.0020.0000.0000.0000.000
197A199PRO00.0040.00236.8680.0010.0010.0000.0000.0000.000
198A200ALA00.0110.00939.263-0.001-0.0010.0000.0000.0000.000
199A201LEU0-0.002-0.00433.235-0.001-0.0010.0000.0000.0000.000
200A202TYR0-0.055-0.06637.5000.0000.0000.0000.0000.0000.000
201A203GLN00.005-0.00639.593-0.002-0.0020.0000.0000.0000.000
202A204HIS0-0.0160.00536.714-0.006-0.0060.0000.0000.0000.000
203A205TRP0-0.009-0.00437.735-0.002-0.0020.0000.0000.0000.000
204A206LYS10.7960.89639.584-0.095-0.0950.0000.0000.0000.000
205A207GLN0-0.040-0.01343.266-0.005-0.0050.0000.0000.0000.000
206A208ARG10.8500.92437.017-0.096-0.0960.0000.0000.0000.000
207A209GLN0-0.039-0.00939.8990.0070.0070.0000.0000.0000.000
208A210ALA0-0.048-0.00842.963-0.002-0.0020.0000.0000.0000.000