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: 5NJ8Z

Calculation Name: 2HXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HXO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K463

Base Structure: X-ray

Registration Date: 2023-09-27

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1952749.888898
FMO2-HF: Nuclear repulsion 1877012.275793
FMO2-HF: Total energy -75737.613105
FMO2-MP2: Total energy -75963.167605


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:15:LEU)


Summations of interaction energy for fragment #1(A:15:LEU)
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.
-13.965-12.13321.729-6.813-16.748-0.005
Interaction energy analysis for fragmet #1(A:15:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.033
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].
3A17ARG11.0181.0193.804-1.2700.397-0.026-0.818-0.8230.003
4A18GLU-1-0.823-0.9346.5670.2370.2370.0000.0000.0000.000
5A19ARG10.9290.9902.263-10.150-8.0673.202-1.978-3.3080.004
6A20ILE00.0010.0082.0220.170-1.0684.402-0.689-2.475-0.004
7A21VAL00.000-0.0095.1100.1390.205-0.001-0.003-0.0620.000
8A22GLY00.0240.0088.1310.0560.0560.0000.0000.0000.000
9A23ALA00.0230.0146.4710.0120.0120.0000.0000.0000.000
10A24ALA0-0.018-0.0258.411-0.010-0.0100.0000.0000.0000.000
11A25VAL00.0180.01710.7470.0140.0140.0000.0000.0000.000
12A26GLU-1-0.877-0.93710.2240.3890.3890.0000.0000.0000.000
13A27LEU0-0.071-0.03910.382-0.008-0.0080.0000.0000.0000.000
14A28LEU0-0.064-0.02714.127-0.010-0.0100.0000.0000.0000.000
15A29ASP-1-0.791-0.86516.2930.0460.0460.0000.0000.0000.000
16A30THR0-0.074-0.02716.2970.0000.0000.0000.0000.0000.000
17A31VAL0-0.032-0.00516.018-0.008-0.0080.0000.0000.0000.000
18A32GLY00.0470.03718.560-0.013-0.0130.0000.0000.0000.000
19A33GLU-1-0.876-0.97117.655-0.161-0.1610.0000.0000.0000.000
20A34ARG10.8890.93817.7140.0870.0870.0000.0000.0000.000
21A35GLY00.0500.02817.609-0.010-0.0100.0000.0000.0000.000
22A36LEU0-0.0210.00811.489-0.007-0.0070.0000.0000.0000.000
23A37THR0-0.033-0.03713.418-0.029-0.0290.0000.0000.0000.000
24A38PHE00.0310.0048.429-0.005-0.0050.0000.0000.0000.000
25A39ARG10.9730.9889.5740.1070.1070.0000.0000.0000.000
26A40ALA00.0760.05210.3840.0050.0050.0000.0000.0000.000
27A41LEU00.0260.0095.4890.0430.0430.0000.0000.0000.000
28A42ALA00.003-0.0115.780-0.004-0.0040.0000.0000.0000.000
29A43GLU-1-0.952-0.9876.408-0.053-0.0530.0000.0000.0000.000
30A44ARG10.9260.9698.460-0.136-0.1360.0000.0000.0000.000
31A45LEU0-0.035-0.0102.0400.622-1.2464.952-0.581-2.5030.002
32A46ALA0-0.037-0.0044.4210.1820.347-0.001-0.017-0.1470.000
33A47THR0-0.055-0.0292.123-1.444-0.7192.367-0.881-2.211-0.004
34A48GLY00.0240.0104.8440.0440.085-0.001-0.004-0.0360.000
35A49PRO00.035-0.0145.370-0.139-0.1390.0000.0000.0000.000
36A50GLY0-0.0030.0057.435-0.010-0.0100.0000.0000.0000.000
37A51ALA0-0.008-0.0055.3640.0140.0140.0000.0000.0000.000
38A52ILE00.0110.0132.738-1.031-0.2440.339-0.218-0.9080.001
39A53TYR0-0.017-0.0043.984-0.307-0.259-0.0010.016-0.0630.000
40A54TRP0-0.019-0.0045.0760.0400.0400.0000.0000.0000.000
41A55HIS0-0.023-0.0102.151-1.831-2.5526.498-1.638-4.139-0.007
42A56ILE0-0.037-0.0094.7350.0590.136-0.001-0.002-0.0730.000
43A57THR00.0240.0137.1580.0500.0500.0000.0000.0000.000
44A58GLY00.0450.02210.7640.0380.0380.0000.0000.0000.000
45A59LYS10.8880.94512.4850.1820.1820.0000.0000.0000.000
46A60ALA00.0200.01014.0570.0110.0110.0000.0000.0000.000
47A61GLU-1-0.851-0.93813.305-0.368-0.3680.0000.0000.0000.000
48A62LEU0-0.032-0.0049.061-0.018-0.0180.0000.0000.0000.000
49A63LEU0-0.005-0.00312.3120.0330.0330.0000.0000.0000.000
50A64GLY00.0190.01815.5280.0400.0400.0000.0000.0000.000
51A65ALA0-0.011-0.00611.8370.0260.0260.0000.0000.0000.000
52A66ALA0-0.003-0.00313.0910.0370.0370.0000.0000.0000.000
53A67THR00.019-0.01014.1680.0560.0560.0000.0000.0000.000
54A68ASP-1-0.851-0.89616.089-0.150-0.1500.0000.0000.0000.000
55A69ALA00.0060.00513.7020.0290.0290.0000.0000.0000.000
56A70VAL0-0.007-0.00115.7550.0450.0450.0000.0000.0000.000
57A71VAL00.0170.00717.9030.0190.0190.0000.0000.0000.000
58A72THR0-0.027-0.00918.5270.0130.0130.0000.0000.0000.000
59A73ALA0-0.0350.00117.7780.0160.0160.0000.0000.0000.000
60A74ALA00.0110.00919.8870.0150.0150.0000.0000.0000.000
61A75VAL0-0.031-0.02122.8790.0050.0050.0000.0000.0000.000
62A76THR0-0.101-0.07322.3650.0050.0050.0000.0000.0000.000
63A77ALA0-0.0170.00423.3840.0110.0110.0000.0000.0000.000
64A78GLY0-0.0220.00224.6190.0070.0070.0000.0000.0000.000
65A79PRO0-0.025-0.00328.150-0.003-0.0030.0000.0000.0000.000
66A80THR00.0250.00630.349-0.004-0.0040.0000.0000.0000.000
67A81GLY0-0.012-0.01433.0280.0060.0060.0000.0000.0000.000
68A82ALA0-0.059-0.04536.637-0.003-0.0030.0000.0000.0000.000
69A83ALA0-0.052-0.02839.214-0.002-0.0020.0000.0000.0000.000
70A84ASP-1-0.835-0.89135.6640.0270.0270.0000.0000.0000.000
71A85SER0-0.069-0.03039.119-0.003-0.0030.0000.0000.0000.000
72A86PRO00.027-0.01238.3410.0010.0010.0000.0000.0000.000
73A87GLN00.0470.00237.827-0.001-0.0010.0000.0000.0000.000
74A88ASP-1-0.809-0.89337.6240.0160.0160.0000.0000.0000.000
75A89ALA00.0200.01834.1830.0010.0010.0000.0000.0000.000
76A90VAL0-0.026-0.01633.321-0.002-0.0020.0000.0000.0000.000
77A91ARG10.9210.95233.748-0.011-0.0110.0000.0000.0000.000
78A92ALA00.0240.02931.1930.0010.0010.0000.0000.0000.000
79A93VAL0-0.028-0.01428.6890.0000.0000.0000.0000.0000.000
80A94ALA0-0.011-0.01529.113-0.003-0.0030.0000.0000.0000.000
81A95LEU00.0130.00530.497-0.001-0.0010.0000.0000.0000.000
82A96GLY00.0340.04327.0730.0040.0040.0000.0000.0000.000
83A97LEU0-0.046-0.04625.146-0.002-0.0020.0000.0000.0000.000
84A98TRP00.0190.00326.736-0.007-0.0070.0000.0000.0000.000
85A99ASP-1-0.745-0.88526.8370.0400.0400.0000.0000.0000.000
86A100ALA0-0.055-0.02522.3830.0060.0060.0000.0000.0000.000
87A101THR0-0.114-0.07823.220-0.003-0.0030.0000.0000.0000.000
88A102GLU-1-0.871-0.91325.2160.0280.0280.0000.0000.0000.000
89A103ALA0-0.045-0.01922.1510.0050.0050.0000.0000.0000.000
90A104HIS10.7570.86217.397-0.041-0.0410.0000.0000.0000.000
91A105PRO00.1300.06221.664-0.017-0.0170.0000.0000.0000.000
92A106TRP0-0.094-0.06716.826-0.027-0.0270.0000.0000.0000.000
93A107LEU0-0.014-0.01020.044-0.019-0.0190.0000.0000.0000.000
94A108ALA00.0930.04122.234-0.012-0.0120.0000.0000.0000.000
95A109THR0-0.004-0.00724.095-0.003-0.0030.0000.0000.0000.000
96A110GLN00.0110.00419.379-0.025-0.0250.0000.0000.0000.000
97A111LEU00.0440.02822.593-0.017-0.0170.0000.0000.0000.000
98A112ALA00.0560.04224.747-0.004-0.0040.0000.0000.0000.000
99A113THR0-0.051-0.03623.077-0.005-0.0050.0000.0000.0000.000
100A114GLN0-0.048-0.02919.573-0.027-0.0270.0000.0000.0000.000
101A115LEU0-0.002-0.00523.905-0.007-0.0070.0000.0000.0000.000
102A116SER0-0.032-0.00627.1630.0070.0070.0000.0000.0000.000
103A117ARG10.8840.92722.8630.1540.1540.0000.0000.0000.000
104A118THR0-0.0560.00020.785-0.019-0.0190.0000.0000.0000.000
105A119PRO00.0110.01123.9440.0010.0010.0000.0000.0000.000
106A120TRP00.006-0.00421.5500.0040.0040.0000.0000.0000.000
107A121GLY00.0160.01720.486-0.021-0.0210.0000.0000.0000.000
108A122THR0-0.065-0.06618.2080.0020.0020.0000.0000.0000.000
109A123VAL00.0570.02320.5640.0160.0160.0000.0000.0000.000
110A124ALA00.0460.02221.9830.0160.0160.0000.0000.0000.000
111A125PRO00.0020.00323.8810.0140.0140.0000.0000.0000.000
112A126ARG10.9120.95217.7330.1800.1800.0000.0000.0000.000
113A127ILE00.0280.03524.8740.0140.0140.0000.0000.0000.000
114A128PHE00.003-0.02227.3310.0090.0090.0000.0000.0000.000
115A129GLU-1-0.886-0.91828.055-0.055-0.0550.0000.0000.0000.000
116A130SER0-0.060-0.04227.5510.0100.0100.0000.0000.0000.000
117A131LEU0-0.013-0.01030.2100.0070.0070.0000.0000.0000.000
118A132GLY00.0620.02632.9690.0040.0040.0000.0000.0000.000
119A133ARG10.8700.93029.3810.0410.0410.0000.0000.0000.000
120A134GLN00.0290.02133.8230.0060.0060.0000.0000.0000.000
121A135VAL00.0060.00737.1610.0020.0020.0000.0000.0000.000
122A136GLN0-0.053-0.03637.1490.0020.0020.0000.0000.0000.000
123A137ALA0-0.0020.00939.3800.0020.0020.0000.0000.0000.000
124A138MET0-0.083-0.03441.1120.0030.0030.0000.0000.0000.000
125A139GLY00.0080.01643.2680.0000.0000.0000.0000.0000.000
126A140VAL0-0.0050.00842.5310.0000.0000.0000.0000.0000.000
127A141PRO00.000-0.00444.023-0.002-0.0020.0000.0000.0000.000
128A142GLU-1-0.842-0.95141.727-0.043-0.0430.0000.0000.0000.000
129A143ALA0-0.067-0.02742.471-0.003-0.0030.0000.0000.0000.000
130A144HIS0-0.009-0.01743.279-0.003-0.0030.0000.0000.0000.000
131A145TRP00.0240.03738.440-0.001-0.0010.0000.0000.0000.000
132A146PHE00.0350.02033.5210.0000.0000.0000.0000.0000.000
133A147THR00.0250.00637.671-0.002-0.0020.0000.0000.0000.000
134A148ALA00.0240.00839.5920.0000.0000.0000.0000.0000.000
135A149SER00.008-0.00934.5300.0020.0020.0000.0000.0000.000
136A150SER0-0.004-0.01434.832-0.002-0.0020.0000.0000.0000.000
137A151ALA0-0.0350.00335.9130.0000.0000.0000.0000.0000.000
138A152LEU00.0160.01235.4800.0020.0020.0000.0000.0000.000
139A153MET0-0.0060.00527.6780.0030.0030.0000.0000.0000.000
140A154HIS00.006-0.01433.0200.0000.0000.0000.0000.0000.000
141A155TYR0-0.045-0.00635.1090.0000.0000.0000.0000.0000.000
142A156ILE00.009-0.00430.5260.0020.0020.0000.0000.0000.000
143A157LEU0-0.042-0.03529.0870.0010.0010.0000.0000.0000.000
144A158GLY0-0.0160.00931.8050.0000.0000.0000.0000.0000.000
145A159ALA00.0090.00934.9330.0020.0020.0000.0000.0000.000
146A160ALA00.0350.01029.6080.0030.0030.0000.0000.0000.000
147A161GLY0-0.031-0.01330.1610.0010.0010.0000.0000.0000.000
148A162GLN0-0.042-0.02031.223-0.003-0.0030.0000.0000.0000.000
149A163ASN00.002-0.00230.1520.0040.0040.0000.0000.0000.000
150A164ALA0-0.042-0.01527.8150.0030.0030.0000.0000.0000.000
151A165ALA0-0.106-0.03829.6030.0010.0010.0000.0000.0000.000
152A166ASN00.0070.00731.9460.0020.0020.0000.0000.0000.000
153A180ASP-1-0.951-0.97238.3770.0250.0250.0000.0000.0000.000
154A181GLU-1-0.881-0.95337.5270.0220.0220.0000.0000.0000.000
155A182PHE0-0.040-0.02639.500-0.003-0.0030.0000.0000.0000.000
156A183LEU00.0510.01740.572-0.002-0.0020.0000.0000.0000.000
157A184ASP-1-0.887-0.94643.3280.0120.0120.0000.0000.0000.000
158A185THR0-0.017-0.01844.511-0.001-0.0010.0000.0000.0000.000
159A186VAL0-0.039-0.00843.613-0.002-0.0020.0000.0000.0000.000
160A187SER0-0.045-0.00746.794-0.001-0.0010.0000.0000.0000.000
161A188THR00.0190.00049.241-0.001-0.0010.0000.0000.0000.000
162A189ALA0-0.040-0.01549.296-0.001-0.0010.0000.0000.0000.000
163A190TRP00.008-0.01746.779-0.001-0.0010.0000.0000.0000.000
164A191GLU-1-0.950-0.97452.1420.0060.0060.0000.0000.0000.000
165A192GLY0-0.030-0.01354.5770.0000.0000.0000.0000.0000.000
166A193LEU0-0.101-0.04352.475-0.001-0.0010.0000.0000.0000.000
167A194ASP-1-0.856-0.94256.724-0.003-0.0030.0000.0000.0000.000
168A195PRO0-0.019-0.03859.6970.0000.0000.0000.0000.0000.000
169A196ASP-1-0.919-0.93861.349-0.003-0.0030.0000.0000.0000.000
170A197ALA0-0.088-0.03459.918-0.001-0.0010.0000.0000.0000.000
171A198TYR0-0.056-0.03553.878-0.001-0.0010.0000.0000.0000.000
172A199PRO00.0250.01757.5830.0010.0010.0000.0000.0000.000
173A200PHE0-0.007-0.00751.2000.0010.0010.0000.0000.0000.000
174A201THR00.0380.00151.5340.0010.0010.0000.0000.0000.000
175A202ARG10.9310.98153.724-0.001-0.0010.0000.0000.0000.000
176A203ALA0-0.052-0.02056.3790.0010.0010.0000.0000.0000.000
177A204VAL0-0.0130.00950.3510.0010.0010.0000.0000.0000.000
178A205ALA0-0.011-0.00451.4850.0010.0010.0000.0000.0000.000
179A206ASP-1-0.823-0.91250.5620.0080.0080.0000.0000.0000.000
180A207GLN0-0.065-0.04149.2600.0010.0010.0000.0000.0000.000
181A208VAL0-0.044-0.01045.2820.0010.0010.0000.0000.0000.000
182A209ARG10.9260.95645.236-0.011-0.0110.0000.0000.0000.000
183A210GLY0-0.0010.00644.2380.0000.0000.0000.0000.0000.000
184A211HIS0-0.043-0.00840.7640.0000.0000.0000.0000.0000.000
185A212ASP-1-0.828-0.93338.2270.0250.0250.0000.0000.0000.000
186A213ASP-1-0.886-0.94036.1700.0080.0080.0000.0000.0000.000
187A214ARG10.8900.94531.229-0.040-0.0400.0000.0000.0000.000
188A215GLU-1-0.920-0.97136.2930.0220.0220.0000.0000.0000.000
189A216GLN0-0.054-0.00539.593-0.005-0.0050.0000.0000.0000.000
190A217PHE0-0.026-0.01532.516-0.004-0.0040.0000.0000.0000.000
191A218LEU00.0480.00235.725-0.004-0.0040.0000.0000.0000.000
192A219ALA00.0040.02338.456-0.002-0.0020.0000.0000.0000.000
193A220GLY00.0450.01440.801-0.002-0.0020.0000.0000.0000.000
194A221ILE00.002-0.00136.026-0.003-0.0030.0000.0000.0000.000
195A222THR0-0.036-0.02239.210-0.001-0.0010.0000.0000.0000.000
196A223LEU00.0170.01742.088-0.001-0.0010.0000.0000.0000.000
197A224VAL0-0.016-0.00540.067-0.002-0.0020.0000.0000.0000.000
198A225LEU0-0.019-0.02138.665-0.002-0.0020.0000.0000.0000.000
199A226THR0-0.030-0.01142.4650.0000.0000.0000.0000.0000.000
200A227GLY0-0.0010.00645.6570.0000.0000.0000.0000.0000.000
201A228ILE0-0.018-0.01840.264-0.001-0.0010.0000.0000.0000.000
202A229THR0-0.044-0.01944.5420.0000.0000.0000.0000.0000.000
203A230ALA0-0.0090.00646.4600.0000.0000.0000.0000.0000.000
204A231LEU0-0.065-0.04244.342-0.001-0.0010.0000.0000.0000.000
205A232HIS0-0.078-0.02347.6330.0000.0000.0000.0000.0000.000
206A233ARG10.8750.93749.1760.0170.0170.0000.0000.0000.000
207A234PRO00.0340.02252.757-0.001-0.0010.0000.0000.0000.000