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: 98MM2

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2211409.07827
FMO2-HF: Nuclear repulsion 2129379.122916
FMO2-HF: Total energy -82029.955354
FMO2-MP2: Total energy -82266.619261


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.
-8.201-15.97428.023-3.766-16.4830.007
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 : 0.002 / q_NPA : -0.004
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].
3A5PHE0-0.052-0.0192.675-8.064-3.2010.668-2.359-3.1710.021
4A6GLU-1-0.790-0.9012.768-8.315-7.6062.012-0.991-1.730-0.009
5A7SER0-0.030-0.0094.939-0.960-0.867-0.001-0.005-0.0870.000
6A8PRO00.0190.0035.5330.8150.8150.0000.0000.0000.000
7A9PHE0-0.036-0.0256.3380.7530.7530.0000.0000.0000.000
8A10ARG10.8960.9547.8810.7410.7410.0000.0000.0000.000
9A11GLY00.0550.0357.7500.0850.0850.0000.0000.0000.000
10A12LYS10.8020.9057.525-0.110-0.1100.0000.0000.0000.000
11A13LEU00.0430.01411.3350.1580.1580.0000.0000.0000.000
12A14LEU00.0230.02513.5620.1450.1450.0000.0000.0000.000
13A15SER00.041-0.00715.1850.0780.0780.0000.0000.0000.000
14A16GLU-1-0.981-0.97214.3400.3210.3210.0000.0000.0000.000
15A17GLN0-0.061-0.04710.0250.5790.5790.0000.0000.0000.000
16A18VAL0-0.0390.00213.0470.1750.1750.0000.0000.0000.000
17A19SER0-0.049-0.02714.827-0.094-0.0940.0000.0000.0000.000
18A20ASN0-0.0150.00616.704-0.205-0.2050.0000.0000.0000.000
19A21PRO00.0500.01418.735-0.024-0.0240.0000.0000.0000.000
20A22ASN0-0.098-0.05321.964-0.098-0.0980.0000.0000.0000.000
21A23ILE00.0250.01116.9340.0110.0110.0000.0000.0000.000
22A24ARG10.8760.94420.890-0.478-0.4780.0000.0000.0000.000
23A25VAL00.0320.01817.335-0.009-0.0090.0000.0000.0000.000
24A26GLY00.0390.03420.662-0.045-0.0450.0000.0000.0000.000
25A27ARG10.8660.92120.764-0.144-0.1440.0000.0000.0000.000
26A28TYR0-0.003-0.02519.958-0.011-0.0110.0000.0000.0000.000
27A29SER0-0.0090.01418.241-0.040-0.0400.0000.0000.0000.000
28A30TYR0-0.030-0.00712.6610.0390.0390.0000.0000.0000.000
29A31TYR00.0530.0357.588-0.284-0.2840.0000.0000.0000.000
30A32SER00.006-0.0128.254-0.130-0.1300.0000.0000.0000.000
31A33GLY00.0260.0076.251-0.724-0.7240.0000.0000.0000.000
32A34TYR00.0010.0102.3010.520-2.29611.933-3.109-6.0080.005
33A35TYR0-0.021-0.0302.511-3.789-2.1240.897-1.001-1.561-0.018
34A36HIS00.0120.0444.866-0.470-0.439-0.001-0.005-0.0250.000
35A37GLY0-0.0080.0022.1052.212-1.58712.440-5.995-2.6460.021
36A38HIS0-0.0050.0132.7916.226-2.2930.0759.699-1.255-0.013
37A39SER00.011-0.0095.635-0.274-0.2740.0000.0000.0000.000
38A40PHE00.045-0.0257.931-0.179-0.1790.0000.0000.0000.000
39A41ASP-1-0.705-0.84211.0231.2141.2140.0000.0000.0000.000
40A42ASP-1-0.930-0.95310.0422.4962.4960.0000.0000.0000.000
41A43CYS0-0.106-0.03911.3890.0630.0630.0000.0000.0000.000
42A44ALA00.0040.01613.253-0.261-0.2610.0000.0000.0000.000
43A45ARG10.9320.96714.306-1.390-1.3900.0000.0000.0000.000
44A46TYR0-0.001-0.01817.898-0.088-0.0880.0000.0000.0000.000
45A47LEU00.0170.02519.285-0.085-0.0850.0000.0000.0000.000
46A48MET0-0.014-0.01520.1410.0510.0510.0000.0000.0000.000
47A49PRO0-0.029-0.00319.476-0.031-0.0310.0000.0000.0000.000
48A50ASP-1-0.893-0.96121.9510.6200.6200.0000.0000.0000.000
49A51ARG10.8020.85825.240-0.446-0.4460.0000.0000.0000.000
50A52ASP-1-0.877-0.92027.1770.4010.4010.0000.0000.0000.000
51A53ASP-1-0.791-0.88429.5570.3780.3780.0000.0000.0000.000
52A54VAL0-0.082-0.02425.412-0.011-0.0110.0000.0000.0000.000
53A55ASP-1-0.794-0.89026.8070.4360.4360.0000.0000.0000.000
54A56LYS10.8220.89024.510-0.420-0.4200.0000.0000.0000.000
55A57LEU00.0000.01418.093-0.027-0.0270.0000.0000.0000.000
56A58VAL0-0.045-0.03222.2320.0140.0140.0000.0000.0000.000
57A59ILE0-0.019-0.01417.889-0.001-0.0010.0000.0000.0000.000
58A60GLY00.0360.02521.880-0.018-0.0180.0000.0000.0000.000
59A61SER00.006-0.00822.0550.0510.0510.0000.0000.0000.000
60A62PHE0-0.020-0.02121.607-0.014-0.0140.0000.0000.0000.000
61A63CYS0-0.0110.02819.158-0.027-0.0270.0000.0000.0000.000
62A64SER0-0.020-0.00816.390-0.002-0.0020.0000.0000.0000.000
63A65ILE0-0.029-0.02013.361-0.036-0.0360.0000.0000.0000.000
64A66GLY00.0100.00212.2130.1130.1130.0000.0000.0000.000
65A67SER00.022-0.0377.5640.3740.3740.0000.0000.0000.000
66A68GLY00.0600.0168.785-0.442-0.4420.0000.0000.0000.000
67A69ALA0-0.0240.00810.423-0.244-0.2440.0000.0000.0000.000
68A70ALA0-0.033-0.02413.0960.2310.2310.0000.0000.0000.000
69A71PHE00.008-0.00715.541-0.175-0.1750.0000.0000.0000.000
70A72ILE0-0.013-0.01018.7960.0510.0510.0000.0000.0000.000
71A73MET00.0170.01320.671-0.089-0.0890.0000.0000.0000.000
72A74ALA00.0020.00323.086-0.013-0.0130.0000.0000.0000.000
73A75GLY00.0800.04125.802-0.032-0.0320.0000.0000.0000.000
74A76ASN0-0.025-0.02027.6690.0400.0400.0000.0000.0000.000
75A77GLN0-0.024-0.01024.0780.0100.0100.0000.0000.0000.000
76A78GLY0-0.009-0.00528.692-0.006-0.0060.0000.0000.0000.000
77A79HIS10.7840.90328.712-0.439-0.4390.0000.0000.0000.000
78A80ARG10.8810.92133.049-0.269-0.2690.0000.0000.0000.000
79A81ALA00.012-0.00335.320-0.008-0.0080.0000.0000.0000.000
80A82GLU-1-0.850-0.89637.0940.2500.2500.0000.0000.0000.000
81A83TRP0-0.031-0.00238.800-0.009-0.0090.0000.0000.0000.000
82A84ALA00.006-0.00541.0840.0010.0010.0000.0000.0000.000
83A85SER00.011-0.00138.8690.0020.0020.0000.0000.0000.000
84A86THR0-0.0090.01334.2420.0060.0060.0000.0000.0000.000
85A87PHE00.0430.01833.4010.0300.0300.0000.0000.0000.000
86A88PRO00.0380.02930.900-0.014-0.0140.0000.0000.0000.000
87A89PHE00.012-0.00833.8280.0080.0080.0000.0000.0000.000
88A90HIS0-0.034-0.01934.5690.0150.0150.0000.0000.0000.000
89A91PHE00.000-0.01330.9690.0030.0030.0000.0000.0000.000
90A92MET0-0.097-0.02032.3610.0250.0250.0000.0000.0000.000
91A93HIS00.000-0.02432.087-0.030-0.0300.0000.0000.0000.000
92A94GLU-1-0.931-0.95134.1750.2850.2850.0000.0000.0000.000
93A95GLU-1-0.895-0.95136.2530.2100.2100.0000.0000.0000.000
94A96PRO00.0510.02138.6870.0000.0000.0000.0000.0000.000
95A97ALA0-0.031-0.01041.735-0.005-0.0050.0000.0000.0000.000
96A98PHE0-0.070-0.05137.150-0.005-0.0050.0000.0000.0000.000
97A99ALA00.0430.02740.0980.0090.0090.0000.0000.0000.000
98A100GLY0-0.042-0.01941.8250.0020.0020.0000.0000.0000.000
99A101ALA0-0.0310.00339.276-0.003-0.0030.0000.0000.0000.000
100A102VAL00.0420.01840.6270.0040.0040.0000.0000.0000.000
101A103ASN00.0290.01733.9720.0140.0140.0000.0000.0000.000
102A104GLY00.0450.00636.595-0.006-0.0060.0000.0000.0000.000
103A105TYR0-0.018-0.02329.1230.0120.0120.0000.0000.0000.000
104A106GLN0-0.076-0.04332.665-0.041-0.0410.0000.0000.0000.000
105A107PRO00.0000.01831.0540.0200.0200.0000.0000.0000.000
106A108ALA0-0.043-0.04029.093-0.020-0.0200.0000.0000.0000.000
107A109GLY0-0.037-0.00130.550-0.020-0.0200.0000.0000.0000.000
108A110ASP-1-0.833-0.91927.3170.4640.4640.0000.0000.0000.000
109A111THR0-0.0230.00722.677-0.034-0.0340.0000.0000.0000.000
110A112LEU0-0.046-0.02724.6730.0210.0210.0000.0000.0000.000
111A113ILE00.0010.00120.779-0.014-0.0140.0000.0000.0000.000
112A114GLY00.0180.01023.9110.0000.0000.0000.0000.0000.000
113A115HIS00.0930.01624.1040.0480.0480.0000.0000.0000.000
114A116GLU-1-0.828-0.91623.3580.1490.1490.0000.0000.0000.000
115A117VAL0-0.0180.00521.526-0.016-0.0160.0000.0000.0000.000
116A118TRP0-0.043-0.01716.9330.0180.0180.0000.0000.0000.000
117A119ILE00.007-0.00316.689-0.026-0.0260.0000.0000.0000.000
118A120GLY00.0080.01216.1360.0380.0380.0000.0000.0000.000
119A121THR0-0.032-0.03311.7530.0580.0580.0000.0000.0000.000
120A122GLU-1-0.849-0.95012.5250.6910.6910.0000.0000.0000.000
121A123ALA0-0.0440.01114.554-0.075-0.0750.0000.0000.0000.000
122A124MET0-0.034-0.01616.8730.1010.1010.0000.0000.0000.000
123A125PHE0-0.001-0.01518.201-0.108-0.1080.0000.0000.0000.000
124A126MET0-0.017-0.01021.6930.0410.0410.0000.0000.0000.000
125A127PRO00.011-0.01924.408-0.002-0.0020.0000.0000.0000.000
126A128GLY00.0580.04725.997-0.034-0.0340.0000.0000.0000.000
127A129VAL0-0.0700.00724.666-0.033-0.0330.0000.0000.0000.000
128A130ARG10.9540.96226.816-0.286-0.2860.0000.0000.0000.000
129A131VAL00.0010.00823.629-0.026-0.0260.0000.0000.0000.000
130A132GLY00.0340.01226.6740.0070.0070.0000.0000.0000.000
131A133HIS00.0740.03127.3330.0170.0170.0000.0000.0000.000
132A134GLY00.0470.04826.729-0.019-0.0190.0000.0000.0000.000
133A135ALA0-0.052-0.02025.878-0.014-0.0140.0000.0000.0000.000
134A136ILE0-0.006-0.00722.3540.0100.0100.0000.0000.0000.000
135A137ILE0-0.061-0.02820.589-0.015-0.0150.0000.0000.0000.000
136A138GLY00.0520.02520.2690.0140.0140.0000.0000.0000.000
137A139SER00.050-0.00316.4930.0550.0550.0000.0000.0000.000
138A140ARG10.7680.89115.578-0.593-0.5930.0000.0000.0000.000
139A141ALA0-0.065-0.01219.141-0.022-0.0220.0000.0000.0000.000
140A142LEU00.0140.01921.1310.0600.0600.0000.0000.0000.000
141A143VAL00.004-0.00622.923-0.054-0.0540.0000.0000.0000.000
142A144THR0-0.003-0.01324.9900.0310.0310.0000.0000.0000.000
143A145GLY00.0340.01427.822-0.013-0.0130.0000.0000.0000.000
144A146ASP-1-0.886-0.94128.5720.3310.3310.0000.0000.0000.000
145A147VAL0-0.056-0.01726.442-0.015-0.0150.0000.0000.0000.000
146A148GLU-1-0.913-0.97029.6360.1810.1810.0000.0000.0000.000
147A149PRO00.032-0.00330.2940.0050.0050.0000.0000.0000.000
148A150TYR00.013-0.00929.349-0.016-0.0160.0000.0000.0000.000
149A151ALA0-0.0110.02629.771-0.021-0.0210.0000.0000.0000.000
150A152ILE00.0160.01126.1310.0180.0180.0000.0000.0000.000
151A153VAL00.0270.01125.144-0.015-0.0150.0000.0000.0000.000
152A154GLY00.0260.00024.3470.0130.0130.0000.0000.0000.000
153A155GLY0-0.024-0.00924.278-0.026-0.0260.0000.0000.0000.000
154A156ASN00.0050.02923.9910.0280.0280.0000.0000.0000.000
155A157PRO00.0560.00226.464-0.018-0.0180.0000.0000.0000.000
156A158ALA0-0.044-0.01125.317-0.027-0.0270.0000.0000.0000.000
157A159ARG10.9710.97727.322-0.194-0.1940.0000.0000.0000.000
158A160THR00.004-0.01629.6680.0020.0020.0000.0000.0000.000
159A161ILE0-0.058-0.02227.644-0.014-0.0140.0000.0000.0000.000
160A162ARG10.9690.97529.077-0.094-0.0940.0000.0000.0000.000
161A163LYS10.9701.00131.164-0.141-0.1410.0000.0000.0000.000
162A164ARG10.7380.85826.789-0.153-0.1530.0000.0000.0000.000
163A165PHE0-0.018-0.00430.787-0.014-0.0140.0000.0000.0000.000
164A166SER00.0030.02434.6420.0090.0090.0000.0000.0000.000
165A167ASP-1-0.818-0.92437.5140.1130.1130.0000.0000.0000.000
166A168GLY0-0.0060.00539.5730.0050.0050.0000.0000.0000.000
167A169ASP-1-0.792-0.93236.5440.0610.0610.0000.0000.0000.000
168A170ILE0-0.034-0.01834.1950.0060.0060.0000.0000.0000.000
169A171GLN0-0.049-0.02636.3480.0030.0030.0000.0000.0000.000
170A172ASN00.0050.00738.8720.0050.0050.0000.0000.0000.000
171A173LEU0-0.027-0.01832.0960.0020.0020.0000.0000.0000.000
172A174LEU0-0.059-0.05333.4410.0100.0100.0000.0000.0000.000
173A175GLU-1-0.830-0.87435.7480.0910.0910.0000.0000.0000.000
174A176MET0-0.0180.00635.009-0.002-0.0020.0000.0000.0000.000
175A177ALA00.0280.02233.1290.0000.0000.0000.0000.0000.000
176A178TRP00.0820.01225.6370.0040.0040.0000.0000.0000.000
177A179TRP0-0.013-0.00427.591-0.003-0.0030.0000.0000.0000.000
178A180ASP-1-0.915-0.97328.7290.2210.2210.0000.0000.0000.000
179A181TRP0-0.118-0.02731.432-0.014-0.0140.0000.0000.0000.000
180A182PRO00.0370.02331.4990.0080.0080.0000.0000.0000.000
181A183LEU00.032-0.00227.506-0.004-0.0040.0000.0000.0000.000
182A184ALA00.0400.01731.063-0.011-0.0110.0000.0000.0000.000
183A185ASP-1-0.822-0.91433.9970.0390.0390.0000.0000.0000.000
184A186ILE0-0.042-0.00728.064-0.005-0.0050.0000.0000.0000.000
185A187GLU-1-0.957-0.98130.579-0.041-0.0410.0000.0000.0000.000
186A188ALA0-0.065-0.03531.462-0.011-0.0110.0000.0000.0000.000
187A189ALA0-0.003-0.01533.643-0.008-0.0080.0000.0000.0000.000
188A190MET00.0300.04026.5290.0050.0050.0000.0000.0000.000
189A191PRO0-0.016-0.02731.088-0.003-0.0030.0000.0000.0000.000
190A192LEU00.0140.01433.235-0.003-0.0030.0000.0000.0000.000
191A193LEU0-0.057-0.00329.0720.0070.0070.0000.0000.0000.000
192A194CYS0-0.077-0.02428.2130.0010.0010.0000.0000.0000.000
193A195THR0-0.028-0.02029.744-0.014-0.0140.0000.0000.0000.000
194A196GLY00.011-0.00431.7960.0110.0110.0000.0000.0000.000
195A197ASP-1-0.874-0.94633.6220.0160.0160.0000.0000.0000.000
196A198ILE00.0060.02033.3130.0010.0010.0000.0000.0000.000
197A199PRO0-0.001-0.00936.8410.0020.0020.0000.0000.0000.000
198A200ALA00.0170.03038.6710.0000.0000.0000.0000.0000.000
199A201LEU0-0.006-0.01833.3860.0010.0010.0000.0000.0000.000
200A202TYR0-0.037-0.07837.693-0.001-0.0010.0000.0000.0000.000
201A203GLN00.0010.00640.0080.0020.0020.0000.0000.0000.000
202A204HIS0-0.013-0.00136.976-0.003-0.0030.0000.0000.0000.000
203A205TRP0-0.034-0.01838.465-0.001-0.0010.0000.0000.0000.000
204A206LYS10.8280.91840.189-0.070-0.0700.0000.0000.0000.000
205A207GLN0-0.0060.00143.6820.0010.0010.0000.0000.0000.000
206A208ARG10.8640.93838.226-0.031-0.0310.0000.0000.0000.000
207A209GLN0-0.060-0.02340.5030.0060.0060.0000.0000.0000.000
208A210ALA0-0.066-0.02143.6460.0020.0020.0000.0000.0000.000