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: LJ539

Calculation Name: 2HZS-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: F

ChEMBL ID:

UniProt ID: P32585

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2726952.170034
FMO2-HF: Nuclear repulsion 2635085.519556
FMO2-HF: Total energy -91866.650478
FMO2-MP2: Total energy -92133.308724


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(F:2:VAL)


Summations of interaction energy for fragment #1(F:2:VAL)
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.
-15.896-7.268.406-5.96-11.08-0.047
Interaction energy analysis for fragmet #1(F:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.026
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].
3F4GLN00.0390.0223.251-0.8171.6180.085-1.039-1.481-0.001
4F5LEU0-0.009-0.0024.7280.1350.220-0.001-0.010-0.0750.000
5F6SER0-0.024-0.0348.1140.0280.0280.0000.0000.0000.000
6F7LEU0-0.007-0.00210.8380.0480.0480.0000.0000.0000.000
7F8PHE00.010-0.00812.312-0.028-0.0280.0000.0000.0000.000
8F9GLY00.0760.04116.9630.0350.0350.0000.0000.0000.000
9F10SER0-0.063-0.02020.546-0.019-0.0190.0000.0000.0000.000
10F11ILE00.0140.01123.1600.0150.0150.0000.0000.0000.000
11F12GLY00.0520.04326.319-0.010-0.0100.0000.0000.0000.000
12F13ASP-1-0.769-0.91128.536-0.140-0.1400.0000.0000.0000.000
13F14ASP-1-0.944-0.96130.158-0.089-0.0890.0000.0000.0000.000
14F15GLY0-0.066-0.03529.8280.0060.0060.0000.0000.0000.000
15F16TYR0-0.002-0.00924.327-0.003-0.0030.0000.0000.0000.000
16F17ASP-1-0.818-0.91827.885-0.091-0.0910.0000.0000.0000.000
17F18LEU0-0.028-0.00229.9540.0050.0050.0000.0000.0000.000
18F19LEU00.0050.00522.8700.0040.0040.0000.0000.0000.000
19F20ILE00.0620.03423.9530.0010.0010.0000.0000.0000.000
20F21SER00.0080.00525.8050.0040.0040.0000.0000.0000.000
21F22THR0-0.073-0.02626.0730.0100.0100.0000.0000.0000.000
22F23LEU00.010-0.00520.5040.0080.0080.0000.0000.0000.000
23F24THR0-0.022-0.00523.2680.0040.0040.0000.0000.0000.000
24F25THR0-0.081-0.03025.4080.0090.0090.0000.0000.0000.000
25F26ILE0-0.055-0.01521.7380.0070.0070.0000.0000.0000.000
26F27SER0-0.062-0.04620.2780.0090.0090.0000.0000.0000.000
27F28GLY0-0.038-0.01621.8590.0100.0100.0000.0000.0000.000
28F29ASN0-0.080-0.03421.6810.0050.0050.0000.0000.0000.000
29F30PRO00.0380.01523.461-0.004-0.0040.0000.0000.0000.000
30F31PRO00.0070.00521.581-0.002-0.0020.0000.0000.0000.000
31F32LEU0-0.044-0.01818.2210.0070.0070.0000.0000.0000.000
32F33LEU00.0230.01419.828-0.020-0.0200.0000.0000.0000.000
33F34TYR0-0.066-0.02914.6930.0160.0160.0000.0000.0000.000
34F35ASN00.028-0.00918.168-0.013-0.0130.0000.0000.0000.000
35F36SER0-0.040-0.01614.510-0.048-0.0480.0000.0000.0000.000
36F37LEU00.0490.03516.5380.0070.0070.0000.0000.0000.000
37F38CYS0-0.068-0.02513.893-0.097-0.0970.0000.0000.0000.000
38F39THR00.0420.02115.9020.0480.0480.0000.0000.0000.000
39F40VAL0-0.013-0.01715.363-0.069-0.0690.0000.0000.0000.000
40F41TRP00.006-0.00316.4720.0870.0870.0000.0000.0000.000
41F42LYS10.8620.91717.2560.1910.1910.0000.0000.0000.000
42F43PRO00.0420.01918.7630.0150.0150.0000.0000.0000.000
43F44ASN00.0360.00421.2470.0140.0140.0000.0000.0000.000
44F45PRO0-0.030-0.01424.6980.0070.0070.0000.0000.0000.000
45F46SER0-0.033-0.00826.9580.0140.0140.0000.0000.0000.000
46F47TYR0-0.106-0.04925.5010.0120.0120.0000.0000.0000.000
47F48ASP-1-0.866-0.94927.209-0.109-0.1090.0000.0000.0000.000
48F49VAL0-0.074-0.01523.2860.0070.0070.0000.0000.0000.000
49F50GLU-1-0.917-0.95825.420-0.063-0.0630.0000.0000.0000.000
50F51ASN00.0090.00421.574-0.023-0.0230.0000.0000.0000.000
51F52VAL00.017-0.00121.7340.0160.0160.0000.0000.0000.000
52F53ASN00.0000.02217.755-0.023-0.0230.0000.0000.0000.000
53F54SER0-0.001-0.00121.7680.0050.0050.0000.0000.0000.000
54F55ARG10.8840.90116.694-0.095-0.0950.0000.0000.0000.000
55F56ASN0-0.018-0.02222.3250.0060.0060.0000.0000.0000.000
56F57GLN00.0540.04419.0670.0100.0100.0000.0000.0000.000
57F58LEU00.0210.02419.866-0.012-0.0120.0000.0000.0000.000
58F59VAL0-0.033-0.01616.0030.0160.0160.0000.0000.0000.000
59F60GLU-1-0.859-0.91115.199-0.169-0.1690.0000.0000.0000.000
60F61PRO00.0260.02616.134-0.035-0.0350.0000.0000.0000.000
61F62ASN00.0390.01611.715-0.009-0.0090.0000.0000.0000.000
62F63ARG10.8400.90814.9940.3840.3840.0000.0000.0000.000
63F64ILE0-0.037-0.01112.394-0.091-0.0910.0000.0000.0000.000
64F65LYS10.8970.9439.3311.1731.1730.0000.0000.0000.000
65F66LEU00.0080.00511.408-0.128-0.1280.0000.0000.0000.000
66F67SER0-0.077-0.05111.1960.0440.0440.0000.0000.0000.000
67F68LYS10.9620.96313.0350.2730.2730.0000.0000.0000.000
68F69GLU-1-0.898-0.92814.939-0.338-0.3380.0000.0000.0000.000
69F70VAL0-0.011-0.00317.3770.0120.0120.0000.0000.0000.000
70F71PRO00.0030.01421.0740.0030.0030.0000.0000.0000.000
71F72PHE00.1100.01821.740-0.001-0.0010.0000.0000.0000.000
72F73SER0-0.0110.00925.4270.0020.0020.0000.0000.0000.000
73F74TYR0-0.044-0.02526.2000.0090.0090.0000.0000.0000.000
74F75LEU0-0.054-0.02922.141-0.012-0.0120.0000.0000.0000.000
75F76ILE0-0.049-0.02826.263-0.002-0.0020.0000.0000.0000.000
76F77ASP-1-0.876-0.91529.540-0.102-0.1020.0000.0000.0000.000
77F78GLU-1-1.056-1.01631.523-0.081-0.0810.0000.0000.0000.000
78F143ASP-1-0.795-0.88929.625-0.165-0.1650.0000.0000.0000.000
79F144ASP-1-0.997-1.00230.633-0.115-0.1150.0000.0000.0000.000
80F145ILE0-0.0090.00327.6030.0050.0050.0000.0000.0000.000
81F146ILE0-0.067-0.04525.853-0.004-0.0040.0000.0000.0000.000
82F147ASP-1-0.908-0.95329.040-0.121-0.1210.0000.0000.0000.000
83F148VAL0-0.068-0.03225.766-0.007-0.0070.0000.0000.0000.000
84F149ASP-1-0.915-0.94629.099-0.126-0.1260.0000.0000.0000.000
85F150MET0-0.084-0.04127.025-0.016-0.0160.0000.0000.0000.000
86F151ASP-1-0.854-0.91329.549-0.131-0.1310.0000.0000.0000.000
87F152ALA0-0.017-0.00229.967-0.009-0.0090.0000.0000.0000.000
88F153SER0-0.141-0.07832.1840.0090.0090.0000.0000.0000.000
89F154PRO0-0.052-0.03430.214-0.007-0.0070.0000.0000.0000.000
90F155ALA00.0500.02527.5050.0040.0040.0000.0000.0000.000
91F156PRO00.0290.02129.3770.0060.0060.0000.0000.0000.000
92F157SER00.0080.00629.647-0.008-0.0080.0000.0000.0000.000
93F158ASN0-0.107-0.05330.1530.0050.0050.0000.0000.0000.000
94F159GLU-1-0.925-0.95927.694-0.139-0.1390.0000.0000.0000.000
95F160SER0-0.0040.01623.171-0.008-0.0080.0000.0000.0000.000
96F161CYS0-0.077-0.02120.453-0.010-0.0100.0000.0000.0000.000
97F162SER00.0630.03118.9500.0170.0170.0000.0000.0000.000
98F163PRO00.017-0.01115.898-0.019-0.0190.0000.0000.0000.000
99F164TRP0-0.003-0.00214.2800.0050.0050.0000.0000.0000.000
100F165SER0-0.048-0.0237.828-0.015-0.0150.0000.0000.0000.000
101F166LEU00.0060.0009.8700.0670.0670.0000.0000.0000.000
102F167GLN0-0.016-0.0365.428-0.021-0.0210.0000.0000.0000.000
103F168ILE00.0360.0227.1450.3500.3500.0000.0000.0000.000
104F169SER0-0.0030.0127.000-0.474-0.4740.0000.0000.0000.000
105F170ASP-1-0.852-0.9167.756-0.007-0.0070.0000.0000.0000.000
106F171ILE0-0.045-0.0119.602-0.129-0.1290.0000.0000.0000.000
107F172PRO0-0.029-0.01410.6910.0640.0640.0000.0000.0000.000
108F173ALA00.0360.02311.1570.1020.1020.0000.0000.0000.000
109F174ALA0-0.023-0.01412.816-0.022-0.0220.0000.0000.0000.000
110F175GLY00.013-0.01016.4970.0330.0330.0000.0000.0000.000
111F176ASN0-0.037-0.01118.423-0.033-0.0330.0000.0000.0000.000
112F177ASN0-0.017-0.01021.4080.0070.0070.0000.0000.0000.000
113F178ARG10.8820.96414.6920.2210.2210.0000.0000.0000.000
114F179SER0-0.023-0.03016.357-0.028-0.0280.0000.0000.0000.000
115F180VAL00.029-0.01611.729-0.022-0.0220.0000.0000.0000.000
116F181SER0-0.012-0.00311.7860.0430.0430.0000.0000.0000.000
117F182MET00.0190.0167.9140.0050.0050.0000.0000.0000.000
118F183GLN0-0.012-0.0166.5610.1550.1550.0000.0000.0000.000
119F184THR00.0240.0263.991-0.869-0.6530.001-0.085-0.1320.000
120F185ILE0-0.031-0.0182.405-0.3681.0970.804-0.643-1.626-0.001
121F186ALA0-0.0160.0012.317-8.849-6.7363.012-2.314-2.811-0.034
122F187GLU-1-0.822-0.8923.969-2.029-1.7670.001-0.038-0.2250.000
123F188THR0-0.059-0.0245.4160.2950.2950.0000.0000.0000.000
124F189ILE00.0230.0088.023-0.029-0.0290.0000.0000.0000.000
125F190ILE0-0.0260.00411.2010.0920.0920.0000.0000.0000.000
126F191LEU00.014-0.00214.7390.0030.0030.0000.0000.0000.000
127F192SER00.0250.01117.1540.0180.0180.0000.0000.0000.000
128F193SER0-0.075-0.05320.330-0.009-0.0090.0000.0000.0000.000
129F194ALA00.0450.01722.9460.0120.0120.0000.0000.0000.000
130F195GLY00.0040.00426.443-0.003-0.0030.0000.0000.0000.000
131F196LYS10.9340.95729.1720.0930.0930.0000.0000.0000.000
132F197ASN00.0320.00327.4890.0060.0060.0000.0000.0000.000
133F198SER00.009-0.00425.203-0.005-0.0050.0000.0000.0000.000
134F199SER00.1120.07824.011-0.021-0.0210.0000.0000.0000.000
135F200VAL00.0610.00518.2130.0040.0040.0000.0000.0000.000
136F201SER00.0160.02120.798-0.010-0.0100.0000.0000.0000.000
137F202SER0-0.011-0.01123.1320.0040.0040.0000.0000.0000.000
138F203LEU0-0.007-0.00220.0870.0070.0070.0000.0000.0000.000
139F204MET00.0120.02216.062-0.009-0.0090.0000.0000.0000.000
140F205ASN00.0250.01620.119-0.006-0.0060.0000.0000.0000.000
141F206GLY0-0.074-0.02723.2060.0150.0150.0000.0000.0000.000
142F207LEU0-0.050-0.02916.4220.0130.0130.0000.0000.0000.000
143F208GLY0-0.0210.00320.5570.0020.0020.0000.0000.0000.000
144F209TYR0-0.111-0.07516.3720.0050.0050.0000.0000.0000.000
145F210VAL0-0.009-0.00721.0300.0200.0200.0000.0000.0000.000
146F211PHE00.0180.01721.274-0.030-0.0300.0000.0000.0000.000
147F212GLU-1-0.805-0.87320.502-0.276-0.2760.0000.0000.0000.000
148F213PHE00.0370.00617.8230.0160.0160.0000.0000.0000.000
149F214GLN00.0320.01919.451-0.058-0.0580.0000.0000.0000.000
150F215TYR0-0.0100.00013.7800.0050.0050.0000.0000.0000.000
151F216LEU00.0280.02118.690-0.039-0.0390.0000.0000.0000.000
152F217THR0-0.041-0.01615.5310.0230.0230.0000.0000.0000.000
153F218ILE00.0530.02518.715-0.007-0.0070.0000.0000.0000.000
154F219GLY00.0430.01219.7440.0020.0020.0000.0000.0000.000
155F220VAL0-0.022-0.00320.2950.0100.0100.0000.0000.0000.000
156F221LYS10.8400.91211.5550.3580.3580.0000.0000.0000.000
157F222PHE00.0270.01216.8060.0210.0210.0000.0000.0000.000
158F223PHE0-0.001-0.00112.237-0.014-0.0140.0000.0000.0000.000
159F224MET00.0340.01815.0720.0140.0140.0000.0000.0000.000
160F225LYS10.9460.95715.251-0.031-0.0310.0000.0000.0000.000
161F226HIS00.005-0.00913.5000.0110.0110.0000.0000.0000.000
162F227GLY00.0230.02010.3630.0470.0470.0000.0000.0000.000
163F228LEU0-0.0160.00610.230-0.037-0.0370.0000.0000.0000.000
164F229ILE0-0.037-0.0139.2480.0050.0050.0000.0000.0000.000
165F230LEU00.020-0.00812.772-0.030-0.0300.0000.0000.0000.000
166F231GLU-1-0.814-0.87712.518-0.491-0.4910.0000.0000.0000.000
167F232LEU00.0080.01116.400-0.002-0.0020.0000.0000.0000.000
168F233GLN0-0.041-0.03614.412-0.020-0.0200.0000.0000.0000.000
169F234LYS10.8420.92519.8460.1790.1790.0000.0000.0000.000
170F235ILE0-0.007-0.02417.396-0.024-0.0240.0000.0000.0000.000
171F236TRP0-0.005-0.03121.2470.0140.0140.0000.0000.0000.000
172F237GLN0-0.099-0.05822.429-0.046-0.0460.0000.0000.0000.000
173F238ILE0-0.018-0.02623.6810.0140.0140.0000.0000.0000.000
174F239GLU-1-0.906-0.94125.395-0.203-0.2030.0000.0000.0000.000
175F240GLU-1-0.840-0.92828.177-0.149-0.1490.0000.0000.0000.000
176F241ALA0-0.083-0.03231.4650.0090.0090.0000.0000.0000.000
177F242GLY00.0090.00432.1450.0020.0020.0000.0000.0000.000
178F243ASN00.0330.00727.531-0.017-0.0170.0000.0000.0000.000
179F244SER00.0350.01827.4750.0070.0070.0000.0000.0000.000
180F245GLN00.0170.00025.561-0.022-0.0220.0000.0000.0000.000
181F246ILE00.0110.00721.3740.0090.0090.0000.0000.0000.000
182F247THR0-0.063-0.02521.508-0.003-0.0030.0000.0000.0000.000
183F248SER0-0.021-0.00124.5000.0140.0140.0000.0000.0000.000
184F249GLY00.0250.02128.2590.0020.0020.0000.0000.0000.000
185F250GLY00.014-0.00127.1180.0120.0120.0000.0000.0000.000
186F251PHE0-0.0120.01522.498-0.013-0.0130.0000.0000.0000.000
187F252LEU0-0.0170.00016.7470.0080.0080.0000.0000.0000.000
188F253LEU0-0.031-0.02018.366-0.007-0.0070.0000.0000.0000.000
189F254LYS10.8750.9378.9460.8170.8170.0000.0000.0000.000
190F255ALA00.0410.03213.5640.0170.0170.0000.0000.0000.000
191F256TYR0-0.073-0.0857.053-0.076-0.0760.0000.0000.0000.000
192F257ILE00.0420.0277.0810.0860.0860.0000.0000.0000.000
193F258ASN00.0040.0222.516-1.496-1.0120.660-0.280-0.8630.002
194F259VAL0-0.004-0.0083.213-0.2880.5520.090-0.234-0.6960.000
195F260SER00.012-0.0032.297-1.426-0.3953.712-2.233-2.510-0.010
196F261ARG10.8700.9363.074-0.401-0.7790.0430.923-0.587-0.003
197F262GLY00.0970.0604.7540.7100.793-0.001-0.007-0.0740.000
198F263THR0-0.024-0.0346.186-0.434-0.4340.0000.0000.0000.000
199F264ASP-1-0.817-0.9039.2960.6310.6310.0000.0000.0000.000
200F265ILE00.0820.02611.176-0.018-0.0180.0000.0000.0000.000
201F266ASP-1-0.863-0.91013.4700.3160.3160.0000.0000.0000.000
202F267ARG10.8630.9158.376-0.819-0.8190.0000.0000.0000.000
203F268ILE0-0.0200.0177.3080.0040.0040.0000.0000.0000.000
204F269ASN00.0680.02710.735-0.099-0.0990.0000.0000.0000.000
205F270TYR0-0.069-0.02712.695-0.062-0.0620.0000.0000.0000.000
206F271THR0-0.004-0.0328.314-0.034-0.0340.0000.0000.0000.000
207F272GLU-1-0.849-0.89611.6990.0160.0160.0000.0000.0000.000
208F273THR0-0.054-0.02813.580-0.044-0.0440.0000.0000.0000.000
209F274VAL0-0.026-0.00513.531-0.026-0.0260.0000.0000.0000.000
210F275LEU00.0260.01410.698-0.022-0.0220.0000.0000.0000.000
211F276MET0-0.012-0.00614.849-0.026-0.0260.0000.0000.0000.000
212F277ASN0-0.040-0.02618.075-0.012-0.0120.0000.0000.0000.000
213F278LEU00.0450.04416.406-0.006-0.0060.0000.0000.0000.000
214F279LYS10.8700.93118.6500.0800.0800.0000.0000.0000.000
215F280LYS10.8080.88420.2670.0170.0170.0000.0000.0000.000
216F281GLU-1-0.946-0.97622.316-0.025-0.0250.0000.0000.0000.000
217F282LEU00.0250.01820.664-0.001-0.0010.0000.0000.0000.000
218F283GLN00.0310.00524.3300.0010.0010.0000.0000.0000.000
219F284GLY0-0.065-0.03126.0220.0050.0050.0000.0000.0000.000
220F285TYR0-0.046-0.01226.7060.0020.0020.0000.0000.0000.000
221F286ILE00.0280.00522.957-0.006-0.0060.0000.0000.0000.000
222F287GLU-1-0.932-0.94823.309-0.107-0.1070.0000.0000.0000.000
223F288LEU00.0410.03017.302-0.013-0.0130.0000.0000.0000.000
224F289SER0-0.017-0.03419.2210.0160.0160.0000.0000.0000.000
225F290VAL0-0.037-0.01315.378-0.037-0.0370.0000.0000.0000.000
226F291PRO00.0370.03514.9950.0250.0250.0000.0000.0000.000
227F292ASP-1-0.781-0.91217.026-0.212-0.2120.0000.0000.0000.000
228F293ARG10.8710.93815.3410.1400.1400.0000.0000.0000.000
229F294GLN00.001-0.01415.793-0.036-0.0360.0000.0000.0000.000
230F295SER0-0.023-0.00817.7780.0020.0020.0000.0000.0000.000
231F296MET0-0.091-0.03810.8500.0030.0030.0000.0000.0000.000
232F297ASP-1-0.777-0.87312.586-0.425-0.4250.0000.0000.0000.000
233F298SER0-0.001-0.00612.7210.0000.0000.0000.0000.0000.000
234F299ARG10.7830.84114.5900.2580.2580.0000.0000.0000.000
235F300VAL0-0.042-0.01416.6950.0240.0240.0000.0000.0000.000