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: VKQ61

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1955937.70818
FMO2-HF: Nuclear repulsion 1880198.857391
FMO2-HF: Total energy -75738.850789
FMO2-MP2: Total energy -75964.152874


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.
-20.743-17.52120.175-6.936-16.462-0.002
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 : -0.024 / q_NPA : -0.029
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].
3A17ARG10.9961.0093.8690.5671.603-0.006-0.462-0.5690.002
4A18GLU-1-0.815-0.9316.7290.1020.1020.0000.0000.0000.000
5A19ARG10.8880.9422.109-17.041-17.4988.650-3.321-4.8720.015
6A20ILE0-0.034-0.0102.276-0.823-0.1320.820-0.307-1.204-0.002
7A21VAL00.0100.0036.1300.1530.1530.0000.0000.0000.000
8A22GLY00.0370.0288.8630.0160.0160.0000.0000.0000.000
9A23ALA00.0250.0077.256-0.045-0.0450.0000.0000.0000.000
10A24ALA0-0.019-0.0199.178-0.078-0.0780.0000.0000.0000.000
11A25VAL00.0300.01211.436-0.022-0.0220.0000.0000.0000.000
12A26GLU-1-0.794-0.86911.6710.7200.7200.0000.0000.0000.000
13A27LEU0-0.053-0.00811.098-0.038-0.0380.0000.0000.0000.000
14A28LEU0-0.054-0.02514.678-0.034-0.0340.0000.0000.0000.000
15A29ASP-1-0.779-0.85617.0850.1800.1800.0000.0000.0000.000
16A30THR0-0.073-0.04616.639-0.003-0.0030.0000.0000.0000.000
17A31VAL0-0.048-0.02116.675-0.015-0.0150.0000.0000.0000.000
18A32GLY00.0540.04519.469-0.025-0.0250.0000.0000.0000.000
19A33GLU-1-0.848-0.95118.556-0.048-0.0480.0000.0000.0000.000
20A34ARG10.9100.93618.5190.0030.0030.0000.0000.0000.000
21A35GLY00.0520.04217.932-0.010-0.0100.0000.0000.0000.000
22A36LEU0-0.0060.01012.0250.0060.0060.0000.0000.0000.000
23A37THR0-0.024-0.02013.647-0.042-0.0420.0000.0000.0000.000
24A38PHE00.019-0.0018.7550.0310.0310.0000.0000.0000.000
25A39ARG10.9440.9799.540-0.022-0.0220.0000.0000.0000.000
26A40ALA00.0920.05410.1920.0320.0320.0000.0000.0000.000
27A41LEU00.0200.0155.8970.0810.0810.0000.0000.0000.000
28A42ALA00.011-0.0085.5700.1330.1330.0000.0000.0000.000
29A43GLU-1-0.925-0.9736.3980.2820.2820.0000.0000.0000.000
30A44ARG10.8280.8918.912-0.518-0.5180.0000.0000.0000.000
31A45LEU0-0.046-0.0062.2850.036-0.7453.825-0.460-2.585-0.001
32A46ALA0-0.0090.0074.3300.5540.7470.000-0.029-0.1640.000
33A47THR0-0.046-0.0362.317-1.242-1.1663.992-1.125-2.942-0.009
34A48GLY00.0400.0164.737-0.091-0.049-0.001-0.009-0.0320.000
35A49PRO00.0340.0005.859-0.126-0.1260.0000.0000.0000.000
36A50GLY0-0.019-0.0097.514-0.055-0.0550.0000.0000.0000.000
37A51ALA00.0070.0054.986-0.016-0.0160.0000.0000.0000.000
38A52ILE00.001-0.0052.426-1.241-0.2580.978-0.475-1.4860.001
39A53TYR0-0.016-0.0033.524-0.164-0.216-0.0010.162-0.1090.000
40A54TRP0-0.0150.0014.185-0.0960.032-0.001-0.013-0.1140.000
41A55HIS0-0.011-0.0042.387-2.377-1.0141.919-0.897-2.385-0.008
42A56ILE0-0.062-0.0265.7080.1940.1940.0000.0000.0000.000
43A57THR00.0090.0018.2460.0140.0140.0000.0000.0000.000
44A58GLY00.0500.02111.6990.0470.0470.0000.0000.0000.000
45A59LYS10.8200.91913.1330.0390.0390.0000.0000.0000.000
46A60ALA00.0290.02015.0330.0210.0210.0000.0000.0000.000
47A61GLU-1-0.859-0.93613.815-0.261-0.2610.0000.0000.0000.000
48A62LEU0-0.033-0.0089.544-0.016-0.0160.0000.0000.0000.000
49A63LEU0-0.0070.00112.8150.0430.0430.0000.0000.0000.000
50A64GLY00.0240.02716.1970.0330.0330.0000.0000.0000.000
51A65ALA0-0.017-0.01412.3800.0200.0200.0000.0000.0000.000
52A66ALA00.001-0.00513.9900.0370.0370.0000.0000.0000.000
53A67THR00.027-0.01514.9950.0450.0450.0000.0000.0000.000
54A68ASP-1-0.829-0.89216.639-0.112-0.1120.0000.0000.0000.000
55A69ALA00.0000.01714.2440.0180.0180.0000.0000.0000.000
56A70VAL0-0.010-0.00116.2920.0340.0340.0000.0000.0000.000
57A71VAL00.0220.01218.5250.0110.0110.0000.0000.0000.000
58A72THR0-0.044-0.03618.8390.0000.0000.0000.0000.0000.000
59A73ALA0-0.0190.00417.9000.0070.0070.0000.0000.0000.000
60A74ALA00.0110.00820.0070.0060.0060.0000.0000.0000.000
61A75VAL0-0.040-0.02823.127-0.001-0.0010.0000.0000.0000.000
62A76THR0-0.085-0.05722.230-0.003-0.0030.0000.0000.0000.000
63A77ALA0-0.0200.01022.9410.0060.0060.0000.0000.0000.000
64A78GLY0-0.0080.00724.4330.0080.0080.0000.0000.0000.000
65A79PRO0-0.051-0.02428.262-0.007-0.0070.0000.0000.0000.000
66A80THR00.0100.00530.437-0.003-0.0030.0000.0000.0000.000
67A81GLY00.0120.00133.3220.0040.0040.0000.0000.0000.000
68A82ALA0-0.072-0.05536.815-0.004-0.0040.0000.0000.0000.000
69A83ALA0-0.046-0.03239.465-0.003-0.0030.0000.0000.0000.000
70A84ASP-1-0.846-0.89435.6110.0390.0390.0000.0000.0000.000
71A85SER0-0.043-0.04339.099-0.005-0.0050.0000.0000.0000.000
72A86PRO00.0330.00238.1700.0020.0020.0000.0000.0000.000
73A87GLN00.0610.00937.819-0.001-0.0010.0000.0000.0000.000
74A88ASP-1-0.786-0.84237.9710.0290.0290.0000.0000.0000.000
75A89ALA00.0260.02534.1390.0040.0040.0000.0000.0000.000
76A90VAL0-0.028-0.02033.3790.0000.0000.0000.0000.0000.000
77A91ARG10.8650.90934.167-0.025-0.0250.0000.0000.0000.000
78A92ALA00.0270.02431.4210.0040.0040.0000.0000.0000.000
79A93VAL0-0.014-0.01129.0760.0040.0040.0000.0000.0000.000
80A94ALA0-0.023-0.01629.6430.0010.0010.0000.0000.0000.000
81A95LEU00.0270.01031.2090.0020.0020.0000.0000.0000.000
82A96GLY00.0240.02427.3930.0070.0070.0000.0000.0000.000
83A97LEU0-0.036-0.04225.8710.0050.0050.0000.0000.0000.000
84A98TRP0-0.002-0.00227.457-0.002-0.0020.0000.0000.0000.000
85A99ASP-1-0.760-0.84827.5080.0870.0870.0000.0000.0000.000
86A100ALA0-0.057-0.02423.1970.0140.0140.0000.0000.0000.000
87A101THR0-0.082-0.07424.0190.0030.0030.0000.0000.0000.000
88A102GLU-1-0.830-0.89726.3110.0840.0840.0000.0000.0000.000
89A103ALA0-0.035-0.01023.3130.0080.0080.0000.0000.0000.000
90A104HIS10.7610.85919.073-0.155-0.1550.0000.0000.0000.000
91A105PRO00.1200.06222.759-0.018-0.0180.0000.0000.0000.000
92A106TRP0-0.084-0.06117.790-0.034-0.0340.0000.0000.0000.000
93A107LEU0-0.0070.00020.719-0.021-0.0210.0000.0000.0000.000
94A108ALA00.0910.05023.101-0.016-0.0160.0000.0000.0000.000
95A109THR0-0.005-0.00724.869-0.009-0.0090.0000.0000.0000.000
96A110GLN0-0.005-0.00220.078-0.027-0.0270.0000.0000.0000.000
97A111LEU00.0490.02723.108-0.019-0.0190.0000.0000.0000.000
98A112ALA00.0460.03725.060-0.009-0.0090.0000.0000.0000.000
99A113THR0-0.097-0.05723.880-0.011-0.0110.0000.0000.0000.000
100A114GLN0-0.024-0.01920.360-0.025-0.0250.0000.0000.0000.000
101A115LEU00.0290.00224.595-0.010-0.0100.0000.0000.0000.000
102A116SER0-0.040-0.01628.1630.0000.0000.0000.0000.0000.000
103A117ARG10.8920.94023.2700.0820.0820.0000.0000.0000.000
104A118THR0-0.049-0.00721.299-0.014-0.0140.0000.0000.0000.000
105A119PRO00.0180.00624.576-0.002-0.0020.0000.0000.0000.000
106A120TRP0-0.0030.00222.1110.0010.0010.0000.0000.0000.000
107A121GLY00.0100.01020.661-0.021-0.0210.0000.0000.0000.000
108A122THR0-0.040-0.05418.6520.0070.0070.0000.0000.0000.000
109A123VAL00.0430.01420.8360.0120.0120.0000.0000.0000.000
110A124ALA00.0200.02222.4330.0140.0140.0000.0000.0000.000
111A125PRO0-0.004-0.00224.3840.0100.0100.0000.0000.0000.000
112A126ARG10.8780.93918.0970.1330.1330.0000.0000.0000.000
113A127ILE00.0570.04725.6850.0100.0100.0000.0000.0000.000
114A128PHE00.005-0.00828.0220.0060.0060.0000.0000.0000.000
115A129GLU-1-0.835-0.88928.778-0.046-0.0460.0000.0000.0000.000
116A130SER0-0.066-0.04527.9340.0070.0070.0000.0000.0000.000
117A131LEU00.0030.00130.6120.0060.0060.0000.0000.0000.000
118A132GLY00.0460.02333.5910.0030.0030.0000.0000.0000.000
119A133ARG10.8340.89230.5440.0390.0390.0000.0000.0000.000
120A134GLN0-0.013-0.00133.5220.0040.0040.0000.0000.0000.000
121A135VAL0-0.002-0.00837.4860.0010.0010.0000.0000.0000.000
122A136GLN0-0.056-0.03137.4400.0010.0010.0000.0000.0000.000
123A137ALA00.0000.00739.6370.0010.0010.0000.0000.0000.000
124A138MET0-0.083-0.02841.4000.0020.0020.0000.0000.0000.000
125A139GLY00.0120.01543.5860.0010.0010.0000.0000.0000.000
126A140VAL0-0.0270.00043.249-0.001-0.0010.0000.0000.0000.000
127A141PRO00.015-0.00444.676-0.002-0.0020.0000.0000.0000.000
128A142GLU-1-0.868-0.94242.133-0.036-0.0360.0000.0000.0000.000
129A143ALA0-0.050-0.02842.697-0.002-0.0020.0000.0000.0000.000
130A144HIS0-0.011-0.01143.520-0.001-0.0010.0000.0000.0000.000
131A145TRP00.0480.03438.9200.0000.0000.0000.0000.0000.000
132A146PHE00.0390.02934.1340.0010.0010.0000.0000.0000.000
133A147THR00.0160.01438.1410.0000.0000.0000.0000.0000.000
134A148ALA00.0400.01740.2320.0020.0020.0000.0000.0000.000
135A149SER00.014-0.01134.9390.0030.0030.0000.0000.0000.000
136A150SER0-0.020-0.02435.5600.0000.0000.0000.0000.0000.000
137A151ALA0-0.054-0.01536.6720.0020.0020.0000.0000.0000.000
138A152LEU00.0130.00736.0270.0030.0030.0000.0000.0000.000
139A153MET0-0.0010.00828.1270.0050.0050.0000.0000.0000.000
140A154HIS00.000-0.01433.3100.0040.0040.0000.0000.0000.000
141A155TYR0-0.044-0.01235.4600.0010.0010.0000.0000.0000.000
142A156ILE00.0110.00631.1180.0040.0040.0000.0000.0000.000
143A157LEU0-0.029-0.02728.9880.0030.0030.0000.0000.0000.000
144A158GLY0-0.026-0.00132.1990.0020.0020.0000.0000.0000.000
145A159ALA0-0.0040.00135.4270.0030.0030.0000.0000.0000.000
146A160ALA00.0440.01830.2910.0040.0040.0000.0000.0000.000
147A161GLY0-0.040-0.02130.8710.0050.0050.0000.0000.0000.000
148A162GLN0-0.045-0.02731.915-0.002-0.0020.0000.0000.0000.000
149A163ASN0-0.009-0.01831.7580.0020.0020.0000.0000.0000.000
150A164ALA0-0.058-0.02528.4250.0060.0060.0000.0000.0000.000
151A165ALA0-0.089-0.03430.1240.0030.0030.0000.0000.0000.000
152A166ASN00.0020.01832.773-0.001-0.0010.0000.0000.0000.000
153A180ASP-1-0.910-0.97339.5200.0550.0550.0000.0000.0000.000
154A181GLU-1-0.858-0.92638.8230.0570.0570.0000.0000.0000.000
155A182PHE0-0.042-0.01840.255-0.004-0.0040.0000.0000.0000.000
156A183LEU00.0110.01741.283-0.004-0.0040.0000.0000.0000.000
157A184ASP-1-0.821-0.90144.1370.0360.0360.0000.0000.0000.000
158A185THR0-0.040-0.02645.180-0.003-0.0030.0000.0000.0000.000
159A186VAL0-0.026-0.01344.386-0.003-0.0030.0000.0000.0000.000
160A187SER0-0.0140.00047.407-0.002-0.0020.0000.0000.0000.000
161A188THR0-0.029-0.03050.002-0.002-0.0020.0000.0000.0000.000
162A189ALA0-0.036-0.01149.859-0.002-0.0020.0000.0000.0000.000
163A190TRP0-0.012-0.02747.727-0.002-0.0020.0000.0000.0000.000
164A191GLU-1-0.824-0.89552.9350.0270.0270.0000.0000.0000.000
165A192GLY0-0.046-0.01255.114-0.001-0.0010.0000.0000.0000.000
166A193LEU0-0.076-0.02353.092-0.001-0.0010.0000.0000.0000.000
167A194ASP-1-0.857-0.93057.2940.0120.0120.0000.0000.0000.000
168A195PRO0-0.009-0.02260.4320.0000.0000.0000.0000.0000.000
169A196ASP-1-0.918-0.94962.3130.0110.0110.0000.0000.0000.000
170A197ALA0-0.070-0.03760.842-0.001-0.0010.0000.0000.0000.000
171A198TYR0-0.047-0.02655.436-0.001-0.0010.0000.0000.0000.000
172A199PRO00.0260.02758.1410.0010.0010.0000.0000.0000.000
173A200PHE0-0.031-0.02352.2960.0010.0010.0000.0000.0000.000
174A201THR00.0370.00652.2770.0010.0010.0000.0000.0000.000
175A202ARG10.9090.94954.624-0.017-0.0170.0000.0000.0000.000
176A203ALA0-0.059-0.02457.2460.0010.0010.0000.0000.0000.000
177A204VAL0-0.0070.00051.3340.0000.0000.0000.0000.0000.000
178A205ALA0-0.041-0.01352.1280.0010.0010.0000.0000.0000.000
179A206ASP-1-0.871-0.93751.2630.0280.0280.0000.0000.0000.000
180A207GLN0-0.039-0.02050.4430.0010.0010.0000.0000.0000.000
181A208VAL0-0.017-0.00245.8270.0010.0010.0000.0000.0000.000
182A209ARG10.7640.84446.032-0.031-0.0310.0000.0000.0000.000
183A210GLY00.0140.01444.4770.0000.0000.0000.0000.0000.000
184A211HIS0-0.048-0.01041.938-0.002-0.0020.0000.0000.0000.000
185A212ASP-1-0.823-0.91139.1830.0580.0580.0000.0000.0000.000
186A213ASP-1-0.847-0.93737.6370.0400.0400.0000.0000.0000.000
187A214ARG10.8420.89631.453-0.076-0.0760.0000.0000.0000.000
188A215GLU-1-0.917-0.97437.0530.0480.0480.0000.0000.0000.000
189A216GLN0-0.066-0.02740.189-0.006-0.0060.0000.0000.0000.000
190A217PHE0-0.0060.00033.323-0.006-0.0060.0000.0000.0000.000
191A218LEU00.0540.01936.542-0.005-0.0050.0000.0000.0000.000
192A219ALA0-0.0100.01339.324-0.004-0.0040.0000.0000.0000.000
193A220GLY00.0360.01141.707-0.003-0.0030.0000.0000.0000.000
194A221ILE0-0.011-0.00936.478-0.004-0.0040.0000.0000.0000.000
195A222THR0-0.020-0.00539.788-0.003-0.0030.0000.0000.0000.000
196A223LEU0-0.0020.02442.648-0.003-0.0030.0000.0000.0000.000
197A224VAL0-0.004-0.00640.427-0.003-0.0030.0000.0000.0000.000
198A225LEU0-0.013-0.01438.849-0.003-0.0030.0000.0000.0000.000
199A226THR0-0.031-0.02142.768-0.002-0.0020.0000.0000.0000.000
200A227GLY0-0.0010.00746.332-0.001-0.0010.0000.0000.0000.000
201A228ILE0-0.011-0.01340.775-0.002-0.0020.0000.0000.0000.000
202A229THR0-0.031-0.02845.084-0.001-0.0010.0000.0000.0000.000
203A230ALA0-0.0070.01047.113-0.001-0.0010.0000.0000.0000.000
204A231LEU0-0.031-0.01744.919-0.001-0.0010.0000.0000.0000.000
205A232HIS0-0.056-0.01548.029-0.001-0.0010.0000.0000.0000.000
206A233ARG10.8350.90149.6510.0080.0080.0000.0000.0000.000
207A234PRO00.0160.02653.150-0.001-0.0010.0000.0000.0000.000