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: VQM21

Calculation Name: 1XKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X006

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309110.836523
FMO2-HF: Nuclear repulsion 2229019.325994
FMO2-HF: Total energy -80091.510529
FMO2-MP2: Total energy -80320.831279


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-17.59-16.5568.632-4.786-4.881-0.035
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.002
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].
3A2LYS10.9100.9591.870-13.443-12.7598.629-4.706-4.608-0.035
4A3ILE00.0430.0373.9562.2962.6460.003-0.080-0.2730.000
5A4SER0-0.074-0.0566.9270.2590.2590.0000.0000.0000.000
6A5GLU-1-0.772-0.8949.797-1.809-1.8090.0000.0000.0000.000
7A6ARG10.8590.92712.7621.1651.1650.0000.0000.0000.000
8A7GLN00.0390.03310.428-0.178-0.1780.0000.0000.0000.000
9A8LYS10.8750.9239.4042.2182.2180.0000.0000.0000.000
10A9ASP-1-0.793-0.88913.996-0.681-0.6810.0000.0000.0000.000
11A10LEU00.0050.01216.7650.0740.0740.0000.0000.0000.000
12A11LEU00.013-0.00113.7670.0700.0700.0000.0000.0000.000
13A12LYS10.8360.91417.7790.7980.7980.0000.0000.0000.000
14A13GLU-1-0.961-0.97519.948-0.571-0.5710.0000.0000.0000.000
15A14ILE00.0020.00519.6290.0560.0560.0000.0000.0000.000
16A15GLY00.0280.00921.5380.0500.0500.0000.0000.0000.000
17A16ASN0-0.060-0.04822.9020.0930.0930.0000.0000.0000.000
18A17ILE0-0.0040.01325.6760.0490.0490.0000.0000.0000.000
19A18GLY00.0320.02126.0770.0370.0370.0000.0000.0000.000
20A19ALA00.0040.00326.9520.0360.0360.0000.0000.0000.000
21A20GLY00.0600.02828.6940.0320.0320.0000.0000.0000.000
22A21ASN0-0.077-0.04530.5250.0480.0480.0000.0000.0000.000
23A22ALA00.0350.01130.7040.0250.0250.0000.0000.0000.000
24A23ALA00.0010.00232.6120.0220.0220.0000.0000.0000.000
25A24THR0-0.038-0.00734.4610.0270.0270.0000.0000.0000.000
26A25ALA0-0.007-0.00935.7920.0170.0170.0000.0000.0000.000
27A26ILE00.031-0.00333.6500.0160.0160.0000.0000.0000.000
28A27SER0-0.004-0.01437.7010.0160.0160.0000.0000.0000.000
29A28TYR0-0.070-0.03040.0770.0180.0180.0000.0000.0000.000
30A29MET0-0.057-0.00939.3010.0060.0060.0000.0000.0000.000
31A30ILE0-0.012-0.01539.0050.0090.0090.0000.0000.0000.000
32A31ASN0-0.080-0.03142.6350.0120.0120.0000.0000.0000.000
33A32LYS10.8610.91742.3730.1740.1740.0000.0000.0000.000
34A33LYS10.7540.86939.4570.2100.2100.0000.0000.0000.000
35A34VAL00.006-0.00635.3720.0050.0050.0000.0000.0000.000
36A35GLU-1-0.783-0.86933.697-0.257-0.2570.0000.0000.0000.000
37A36ILE0-0.032-0.01829.0940.0000.0000.0000.0000.0000.000
38A37SER0-0.045-0.01027.761-0.008-0.0080.0000.0000.0000.000
39A38VAL00.0330.00821.519-0.002-0.0020.0000.0000.0000.000
40A39PRO00.0000.01723.336-0.025-0.0250.0000.0000.0000.000
41A40ASN0-0.071-0.05018.468-0.065-0.0650.0000.0000.0000.000
42A41VAL00.0210.02214.8450.0320.0320.0000.0000.0000.000
43A42GLU-1-0.935-0.95713.389-1.083-1.0830.0000.0000.0000.000
44A43ILE0-0.053-0.0359.047-0.079-0.0790.0000.0000.0000.000
45A44VAL00.0140.0129.917-0.292-0.2920.0000.0000.0000.000
46A45PRO0-0.0060.0029.114-0.031-0.0310.0000.0000.0000.000
47A46ILE00.0510.02111.1280.1610.1610.0000.0000.0000.000
48A47SER0-0.002-0.00112.5960.1120.1120.0000.0000.0000.000
49A48LYS10.7940.88112.7660.4590.4590.0000.0000.0000.000
50A49VAL00.0730.04915.4920.0250.0250.0000.0000.0000.000
51A50ILE0-0.0060.01817.3610.0370.0370.0000.0000.0000.000
52A51PHE0-0.077-0.04517.6020.0570.0570.0000.0000.0000.000
53A52ILE0-0.0050.01116.4240.0240.0240.0000.0000.0000.000
54A53ALA0-0.041-0.00820.5830.0170.0170.0000.0000.0000.000
55A54LYS10.8930.93324.0040.3590.3590.0000.0000.0000.000
56A55ASP-1-0.837-0.91326.870-0.155-0.1550.0000.0000.0000.000
57A56PRO0-0.017-0.00924.906-0.019-0.0190.0000.0000.0000.000
58A57GLU-1-0.922-0.98626.630-0.129-0.1290.0000.0000.0000.000
59A58GLU-1-0.807-0.86629.612-0.239-0.2390.0000.0000.0000.000
60A59ILE0-0.042-0.01830.337-0.011-0.0110.0000.0000.0000.000
61A60VAL0-0.011-0.00627.793-0.001-0.0010.0000.0000.0000.000
62A61VAL00.002-0.00231.2910.0080.0080.0000.0000.0000.000
63A62GLY00.0180.00628.252-0.024-0.0240.0000.0000.0000.000
64A63VAL0-0.044-0.02627.8890.0260.0260.0000.0000.0000.000
65A64LYS10.8900.95022.1090.4210.4210.0000.0000.0000.000
66A65MET0-0.0070.00025.3260.0290.0290.0000.0000.0000.000
67A66PRO00.008-0.00123.989-0.049-0.0490.0000.0000.0000.000
68A67VAL0-0.049-0.02021.4300.0210.0210.0000.0000.0000.000
69A68THR0-0.026-0.03222.851-0.003-0.0030.0000.0000.0000.000
70A69GLY00.0240.01323.7390.0090.0090.0000.0000.0000.000
71A70ASP-1-0.860-0.95721.433-0.598-0.5980.0000.0000.0000.000
72A71ILE0-0.072-0.05617.336-0.101-0.1010.0000.0000.0000.000
73A72GLU-1-0.778-0.84118.713-0.445-0.4450.0000.0000.0000.000
74A73GLY00.0170.00217.981-0.108-0.1080.0000.0000.0000.000
75A74SER0-0.041-0.01419.4350.0950.0950.0000.0000.0000.000
76A75VAL0-0.0060.00820.079-0.085-0.0850.0000.0000.0000.000
77A76LEU0-0.006-0.00321.6040.0610.0610.0000.0000.0000.000
78A77LEU00.0290.01723.203-0.040-0.0400.0000.0000.0000.000
79A78ILE0-0.001-0.00924.0170.0290.0290.0000.0000.0000.000
80A79MET0-0.006-0.00626.853-0.007-0.0070.0000.0000.0000.000
81A80GLY00.0780.04330.0010.0140.0140.0000.0000.0000.000
82A81THR0-0.024-0.06031.1210.0100.0100.0000.0000.0000.000
83A82THR0-0.026-0.02334.5360.0100.0100.0000.0000.0000.000
84A83VAL00.0210.02331.8540.0100.0100.0000.0000.0000.000
85A84VAL00.0060.00733.5650.0070.0070.0000.0000.0000.000
86A85LYS10.8100.88536.0950.1650.1650.0000.0000.0000.000
87A86LYS10.8470.90738.3380.1800.1800.0000.0000.0000.000
88A87ILE00.0250.01334.6370.0050.0050.0000.0000.0000.000
89A88LEU00.0090.00439.0520.0070.0070.0000.0000.0000.000
90A89GLU-1-0.919-0.93341.628-0.148-0.1480.0000.0000.0000.000
91A90ILE0-0.028-0.01340.5390.0080.0080.0000.0000.0000.000
92A91LEU0-0.044-0.01241.1640.0050.0050.0000.0000.0000.000
93A92THR0-0.054-0.05044.2820.0070.0070.0000.0000.0000.000
94A93GLY0-0.0030.01246.9010.0080.0080.0000.0000.0000.000
95A94ARG10.7310.81546.8820.1310.1310.0000.0000.0000.000
96A95ALA00.0610.04843.147-0.005-0.0050.0000.0000.0000.000
97A96PRO00.0040.03041.1690.0100.0100.0000.0000.0000.000
98A97ASP-1-0.789-0.86642.718-0.123-0.1230.0000.0000.0000.000
99A98ASN0-0.045-0.02740.663-0.005-0.0050.0000.0000.0000.000
100A99LEU00.0710.02235.0230.0000.0000.0000.0000.0000.000
101A100LEU00.0460.03436.961-0.004-0.0040.0000.0000.0000.000
102A101ASN0-0.095-0.05939.6790.0100.0100.0000.0000.0000.000
103A102LEU0-0.0050.02338.3430.0040.0040.0000.0000.0000.000
104A103ASP-1-0.783-0.87042.368-0.150-0.1500.0000.0000.0000.000
105A104GLU-1-0.896-0.95042.753-0.151-0.1510.0000.0000.0000.000
106A105PHE0-0.040-0.00342.608-0.011-0.0110.0000.0000.0000.000
107A106SER00.003-0.03741.344-0.010-0.0100.0000.0000.0000.000
108A107ALA00.0010.00138.464-0.012-0.0120.0000.0000.0000.000
109A108SER0-0.031-0.03437.758-0.016-0.0160.0000.0000.0000.000
110A109ALA00.0030.00238.444-0.012-0.0120.0000.0000.0000.000
111A110LEU0-0.009-0.00535.085-0.014-0.0140.0000.0000.0000.000
112A111ARG10.8680.93733.8940.2350.2350.0000.0000.0000.000
113A112GLU-1-0.863-0.91433.791-0.287-0.2870.0000.0000.0000.000
114A113ILE00.022-0.00232.615-0.013-0.0130.0000.0000.0000.000
115A114GLY00.0180.00330.413-0.022-0.0220.0000.0000.0000.000
116A115ASN0-0.052-0.05030.085-0.044-0.0440.0000.0000.0000.000
117A116ILE0-0.0170.00831.337-0.021-0.0210.0000.0000.0000.000
118A117MET00.0080.01127.905-0.014-0.0140.0000.0000.0000.000
119A118CYS0-0.032-0.01426.399-0.041-0.0410.0000.0000.0000.000
120A119GLY00.0660.03326.804-0.034-0.0340.0000.0000.0000.000
121A120THR0-0.060-0.05228.915-0.018-0.0180.0000.0000.0000.000
122A121TYR00.0120.00819.216-0.034-0.0340.0000.0000.0000.000
123A122VAL00.0050.00123.940-0.046-0.0460.0000.0000.0000.000
124A123SER0-0.021-0.01125.352-0.012-0.0120.0000.0000.0000.000
125A124ALA0-0.0060.00425.266-0.011-0.0110.0000.0000.0000.000
126A125LEU0-0.007-0.02118.479-0.033-0.0330.0000.0000.0000.000
127A126ALA00.002-0.00422.141-0.047-0.0470.0000.0000.0000.000
128A127ASP-1-0.885-0.94124.496-0.462-0.4620.0000.0000.0000.000
129A128PHE0-0.048-0.03523.0920.0170.0170.0000.0000.0000.000
130A129LEU0-0.029-0.00318.163-0.047-0.0470.0000.0000.0000.000
131A130GLY00.0010.01122.039-0.011-0.0110.0000.0000.0000.000
132A131PHE0-0.076-0.02617.8130.0200.0200.0000.0000.0000.000
133A132LYS10.8490.91523.9930.5010.5010.0000.0000.0000.000
134A133ILE0-0.0050.00521.889-0.020-0.0200.0000.0000.0000.000
135A134ASP-1-0.897-0.92525.474-0.349-0.3490.0000.0000.0000.000
136A135THR0-0.007-0.02826.419-0.032-0.0320.0000.0000.0000.000
137A136LEU0-0.025-0.00827.7150.0360.0360.0000.0000.0000.000
138A137PRO0-0.013-0.01729.838-0.009-0.0090.0000.0000.0000.000
139A138PRO00.0180.01630.065-0.001-0.0010.0000.0000.0000.000
140A139GLN0-0.003-0.01527.5420.0110.0110.0000.0000.0000.000
141A140LEU0-0.040-0.00930.033-0.017-0.0170.0000.0000.0000.000
142A141VAL00.0250.01028.6570.0150.0150.0000.0000.0000.000
143A142ILE0-0.021-0.02832.063-0.010-0.0100.0000.0000.0000.000
144A143ASP-1-0.840-0.90830.501-0.186-0.1860.0000.0000.0000.000
145A144MET0-0.069-0.01728.981-0.011-0.0110.0000.0000.0000.000
146A145ILE0-0.007-0.00124.646-0.014-0.0140.0000.0000.0000.000
147A146SER00.011-0.03024.260-0.023-0.0230.0000.0000.0000.000
148A147ALA0-0.0160.01024.481-0.006-0.0060.0000.0000.0000.000
149A148ILE00.0320.01624.452-0.015-0.0150.0000.0000.0000.000
150A149PHE00.012-0.01419.610-0.034-0.0340.0000.0000.0000.000
151A150ALA0-0.0340.01220.564-0.028-0.0280.0000.0000.0000.000
152A151GLU-1-0.932-0.97121.485-0.245-0.2450.0000.0000.0000.000
153A152ALA0-0.019-0.01620.127-0.016-0.0160.0000.0000.0000.000
154A153SER0-0.035-0.04317.130-0.070-0.0700.0000.0000.0000.000
155A154ILE0-0.022-0.00717.100-0.004-0.0040.0000.0000.0000.000
156A155GLU-1-0.761-0.85218.774-0.439-0.4390.0000.0000.0000.000
157A156GLU-1-0.856-0.91614.299-0.709-0.7090.0000.0000.0000.000
158A157LEU0-0.106-0.06211.925-0.044-0.0440.0000.0000.0000.000
159A158GLU-1-0.954-0.96815.294-0.182-0.1820.0000.0000.0000.000
160A159ASP-1-0.919-0.94817.190-0.137-0.1370.0000.0000.0000.000
161A160ASN0-0.090-0.06711.820-0.089-0.0890.0000.0000.0000.000
162A161SER0-0.023-0.0229.0420.1410.1410.0000.0000.0000.000
163A162GLU-1-0.931-0.9437.224-1.734-1.7340.0000.0000.0000.000
164A163ASP-1-0.718-0.8658.538-1.071-1.0710.0000.0000.0000.000
165A164GLN0-0.126-0.0535.427-1.214-1.2140.0000.0000.0000.000
166A165ILE00.0130.0159.9170.0590.0590.0000.0000.0000.000
167A166VAL0-0.026-0.01212.731-0.192-0.1920.0000.0000.0000.000
168A167PHE00.030-0.00114.8450.1720.1720.0000.0000.0000.000
169A168VAL00.0340.00817.003-0.053-0.0530.0000.0000.0000.000
170A169GLU-1-0.829-0.87820.117-0.392-0.3920.0000.0000.0000.000
171A170THR0-0.047-0.03823.046-0.007-0.0070.0000.0000.0000.000
172A171LEU0-0.004-0.01226.0530.0310.0310.0000.0000.0000.000
173A172LEU00.0130.01628.7190.0030.0030.0000.0000.0000.000
174A173LYS10.8510.90132.1330.2240.2240.0000.0000.0000.000
175A174VAL00.0340.02135.2490.0020.0020.0000.0000.0000.000
176A175GLU-1-0.890-0.93838.734-0.189-0.1890.0000.0000.0000.000
177A176GLU-1-0.894-0.93640.900-0.157-0.1570.0000.0000.0000.000
178A177GLU-1-0.836-0.90739.093-0.173-0.1730.0000.0000.0000.000
179A178GLU-1-0.950-0.97539.470-0.170-0.1700.0000.0000.0000.000
180A179GLU-1-0.896-0.95835.248-0.215-0.2150.0000.0000.0000.000
181A180PRO0-0.085-0.03631.512-0.003-0.0030.0000.0000.0000.000
182A181LEU00.0140.00332.305-0.006-0.0060.0000.0000.0000.000
183A182THR0-0.035-0.00926.992-0.013-0.0130.0000.0000.0000.000
184A183SER0-0.041-0.02327.7490.0280.0280.0000.0000.0000.000
185A184TYR0-0.026-0.03522.258-0.004-0.0040.0000.0000.0000.000
186A185MET0-0.024-0.00322.4660.0430.0430.0000.0000.0000.000
187A186MET0-0.0140.00217.842-0.053-0.0530.0000.0000.0000.000
188A187MET0-0.051-0.00917.4060.0360.0360.0000.0000.0000.000
189A188ILE00.0360.01715.786-0.174-0.1740.0000.0000.0000.000
190A189PRO0-0.026-0.01612.8430.0970.0970.0000.0000.0000.000
191A190LYS10.8430.89414.1620.5330.5330.0000.0000.0000.000
192A191PRO00.0390.00811.545-0.138-0.1380.0000.0000.0000.000
193A192GLY0-0.007-0.01210.7520.1400.1400.0000.0000.0000.000
194A193TYR0-0.066-0.04411.961-0.063-0.0630.0000.0000.0000.000
195A194LEU00.0560.0308.890-0.045-0.0450.0000.0000.0000.000
196A195VAL0-0.014-0.0138.277-0.224-0.2240.0000.0000.0000.000
197A196LYS10.9320.98310.8850.9700.9700.0000.0000.0000.000
198A197ILE00.0200.01814.1820.1020.1020.0000.0000.0000.000
199A198PHE00.010-0.0229.8380.0130.0130.0000.0000.0000.000
200A199GLU-1-0.964-0.97712.919-0.961-0.9610.0000.0000.0000.000
201A200ARG10.8340.91814.7570.8710.8710.0000.0000.0000.000
202A201MET0-0.0060.03114.9220.0300.0300.0000.0000.0000.000
203A202GLY00.0150.02416.8150.0700.0700.0000.0000.0000.000
204A203ILE0-0.004-0.01315.447-0.124-0.1240.0000.0000.0000.000
205A204GLN0-0.039-0.00912.7480.0600.0600.0000.0000.0000.000