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: J3899

Calculation Name: 2HZS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: H

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661027.617839
FMO2-HF: Nuclear repulsion 2570393.6687
FMO2-HF: Total energy -90633.949138
FMO2-MP2: Total energy -90896.280776


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(H:2:VAL)


Summations of interaction energy for fragment #1(H: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.
-36.631-26.77618.59-12.088-16.359-0.056
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.066 / q_NPA : -0.042
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].
3H4GLN00.0400.0222.654-2.3710.4790.752-1.513-2.090-0.012
4H5LEU0-0.011-0.0084.9430.3760.435-0.001-0.007-0.0510.000
5H6SER0-0.013-0.0198.2020.0750.0750.0000.0000.0000.000
6H7LEU0-0.0040.00511.0120.0870.0870.0000.0000.0000.000
7H8PHE00.014-0.00812.048-0.054-0.0540.0000.0000.0000.000
8H9GLY00.0840.04017.0450.0430.0430.0000.0000.0000.000
9H10SER0-0.069-0.02420.654-0.018-0.0180.0000.0000.0000.000
10H11ILE00.0260.01723.3080.0170.0170.0000.0000.0000.000
11H12GLY00.0540.03026.725-0.011-0.0110.0000.0000.0000.000
12H13ASP-1-0.789-0.90428.348-0.223-0.2230.0000.0000.0000.000
13H14ASP-1-0.933-0.96130.155-0.152-0.1520.0000.0000.0000.000
14H15GLY0-0.027-0.01030.1790.0080.0080.0000.0000.0000.000
15H16TYR0-0.020-0.01025.165-0.012-0.0120.0000.0000.0000.000
16H17ASP-1-0.843-0.92828.317-0.168-0.1680.0000.0000.0000.000
17H18LEU00.0110.02830.3710.0030.0030.0000.0000.0000.000
18H19LEU0-0.0230.02023.5140.0010.0010.0000.0000.0000.000
19H20ILE00.0700.02324.849-0.009-0.0090.0000.0000.0000.000
20H21SER0-0.032-0.01326.5270.0020.0020.0000.0000.0000.000
21H22THR0-0.011-0.00925.8130.0090.0090.0000.0000.0000.000
22H23LEU00.009-0.00520.8440.0030.0030.0000.0000.0000.000
23H24THR0-0.022-0.01623.452-0.004-0.0040.0000.0000.0000.000
24H25THR0-0.090-0.04625.6950.0130.0130.0000.0000.0000.000
25H26ILE0-0.058-0.01621.7040.0080.0080.0000.0000.0000.000
26H27SER0-0.052-0.04220.8440.0060.0060.0000.0000.0000.000
27H28GLY0-0.0150.00622.4370.0070.0070.0000.0000.0000.000
28H29ASN0-0.086-0.05121.9670.0110.0110.0000.0000.0000.000
29H30PRO00.0360.01823.912-0.008-0.0080.0000.0000.0000.000
30H31PRO0-0.0120.00122.327-0.014-0.0140.0000.0000.0000.000
31H32LEU0-0.014-0.00918.5490.0130.0130.0000.0000.0000.000
32H33LEU0-0.002-0.00320.199-0.033-0.0330.0000.0000.0000.000
33H34TYR0-0.042-0.01915.1800.0110.0110.0000.0000.0000.000
34H35ASN0-0.021-0.03918.560-0.002-0.0020.0000.0000.0000.000
35H36SER00.0000.00514.720-0.047-0.0470.0000.0000.0000.000
36H37LEU00.0340.03316.678-0.006-0.0060.0000.0000.0000.000
37H38CYS0-0.049-0.01113.974-0.118-0.1180.0000.0000.0000.000
38H39THR00.0480.02316.0640.0460.0460.0000.0000.0000.000
39H40VAL0-0.012-0.00215.560-0.071-0.0710.0000.0000.0000.000
40H41TRP00.000-0.00716.2540.0960.0960.0000.0000.0000.000
41H42LYS10.8860.92516.8900.1900.1900.0000.0000.0000.000
42H43PRO00.0550.02318.4740.0140.0140.0000.0000.0000.000
43H44ASN00.0280.01521.245-0.005-0.0050.0000.0000.0000.000
44H45PRO00.0180.01424.6470.0120.0120.0000.0000.0000.000
45H46SER0-0.058-0.03227.1020.0120.0120.0000.0000.0000.000
46H47TYR0-0.116-0.06325.6060.0080.0080.0000.0000.0000.000
47H48ASP-1-0.864-0.93526.532-0.082-0.0820.0000.0000.0000.000
48H49VAL0-0.075-0.03423.1470.0100.0100.0000.0000.0000.000
49H50GLU-1-0.881-0.93025.256-0.001-0.0010.0000.0000.0000.000
50H51ASN00.0120.01521.303-0.006-0.0060.0000.0000.0000.000
51H52VAL0-0.035-0.02221.4040.0180.0180.0000.0000.0000.000
52H53ASN00.0240.01019.2500.0230.0230.0000.0000.0000.000
53H54SER00.0140.01021.5540.0020.0020.0000.0000.0000.000
54H55ARG10.9080.95717.229-0.307-0.3070.0000.0000.0000.000
55H56ASN00.0210.01022.361-0.014-0.0140.0000.0000.0000.000
56H57GLN0-0.048-0.03418.8350.0080.0080.0000.0000.0000.000
57H58LEU00.0380.01119.847-0.006-0.0060.0000.0000.0000.000
58H59VAL0-0.041-0.02515.6350.0380.0380.0000.0000.0000.000
59H60GLU-1-0.850-0.90115.922-0.136-0.1360.0000.0000.0000.000
60H61PRO00.0150.02616.112-0.021-0.0210.0000.0000.0000.000
61H62ASN00.0360.01311.239-0.035-0.0350.0000.0000.0000.000
62H63ARG10.8120.88514.4680.4190.4190.0000.0000.0000.000
63H64ILE0-0.023-0.00312.038-0.080-0.0800.0000.0000.0000.000
64H65LYS10.8800.9359.5281.2821.2820.0000.0000.0000.000
65H66LEU0-0.0040.00111.403-0.130-0.1300.0000.0000.0000.000
66H67SER0-0.084-0.06311.533-0.012-0.0120.0000.0000.0000.000
67H68LYS10.8440.90613.4550.3250.3250.0000.0000.0000.000
68H69GLU-1-0.869-0.92815.352-0.424-0.4240.0000.0000.0000.000
69H70VAL0-0.007-0.00117.5760.0230.0230.0000.0000.0000.000
70H71PRO00.0090.02021.3190.0030.0030.0000.0000.0000.000
71H72PHE00.0740.00922.1580.0090.0090.0000.0000.0000.000
72H73SER0-0.030-0.00825.9110.0030.0030.0000.0000.0000.000
73H74TYR00.001-0.00426.5260.0120.0120.0000.0000.0000.000
74H75LEU0-0.0070.01422.871-0.003-0.0030.0000.0000.0000.000
75H76ILE00.0300.01726.567-0.004-0.0040.0000.0000.0000.000
76H77ASP-1-0.788-0.89129.411-0.156-0.1560.0000.0000.0000.000
77H78GLU-1-0.847-0.92422.648-0.291-0.2910.0000.0000.0000.000
78H79THR0-0.068-0.03525.548-0.024-0.0240.0000.0000.0000.000
79H80MET0-0.052-0.03027.5130.0040.0040.0000.0000.0000.000
80H81MET0-0.072-0.03331.3010.0080.0080.0000.0000.0000.000
81H82ASP-1-0.844-0.87828.606-0.191-0.1910.0000.0000.0000.000
82H83LYS10.7750.86430.0400.1890.1890.0000.0000.0000.000
83H84PRO00.0130.00533.7500.0020.0020.0000.0000.0000.000
84H85LEU00.0860.02531.0020.0030.0030.0000.0000.0000.000
85H86ASN0-0.057-0.02734.531-0.006-0.0060.0000.0000.0000.000
86H87PHE0-0.053-0.00936.9930.0060.0060.0000.0000.0000.000
87H88ARG10.9210.95632.9790.1210.1210.0000.0000.0000.000
88H89ILE0-0.037-0.02633.7470.0090.0090.0000.0000.0000.000
89H160SER00.0070.01023.2510.0090.0090.0000.0000.0000.000
90H161CYS0-0.137-0.06720.763-0.010-0.0100.0000.0000.0000.000
91H162SER00.0650.01919.7520.0160.0160.0000.0000.0000.000
92H163PRO00.019-0.00216.169-0.007-0.0070.0000.0000.0000.000
93H164TRP0-0.008-0.00514.417-0.002-0.0020.0000.0000.0000.000
94H165SER0-0.047-0.0278.0330.0290.0290.0000.0000.0000.000
95H166LEU00.0090.0009.8760.0910.0910.0000.0000.0000.000
96H167GLN0-0.014-0.0245.3090.1500.1500.0000.0000.0000.000
97H168ILE00.0310.0126.9420.3380.3380.0000.0000.0000.000
98H169SER0-0.0240.0006.629-0.558-0.5580.0000.0000.0000.000
99H170ASP-1-0.869-0.9256.891-0.017-0.0170.0000.0000.0000.000
100H171ILE0-0.028-0.0129.190-0.171-0.1710.0000.0000.0000.000
101H172PRO0-0.028-0.01510.5150.0410.0410.0000.0000.0000.000
102H173ALA00.0150.01311.3010.1610.1610.0000.0000.0000.000
103H174ALA0-0.013-0.01612.895-0.027-0.0270.0000.0000.0000.000
104H175GLY00.0270.00716.5920.0390.0390.0000.0000.0000.000
105H176ASN0-0.037-0.01719.191-0.029-0.0290.0000.0000.0000.000
106H177ASN0-0.031-0.03221.2080.0160.0160.0000.0000.0000.000
107H178ARG10.9020.97414.3230.3830.3830.0000.0000.0000.000
108H179SER0-0.035-0.03716.076-0.014-0.0140.0000.0000.0000.000
109H180VAL00.0370.01311.613-0.035-0.0350.0000.0000.0000.000
110H181SER00.003-0.01012.1220.0710.0710.0000.0000.0000.000
111H182MET00.0260.0327.877-0.131-0.1310.0000.0000.0000.000
112H183GLN0-0.014-0.0157.0880.2110.2110.0000.0000.0000.000
113H184THR0-0.024-0.0063.535-1.237-0.9060.006-0.123-0.2130.000
114H185ILE00.0000.0002.3390.0670.9882.081-0.970-2.0320.001
115H186ALA0-0.018-0.0031.946-9.413-9.7217.418-3.870-3.240-0.050
116H187GLU-1-0.815-0.8854.335-2.710-2.473-0.001-0.029-0.2080.000
117H188THR0-0.050-0.0215.6530.4530.4530.0000.0000.0000.000
118H189ILE00.0190.0088.298-0.112-0.1120.0000.0000.0000.000
119H190ILE00.0020.01211.4560.1200.1200.0000.0000.0000.000
120H191LEU00.005-0.00314.869-0.025-0.0250.0000.0000.0000.000
121H192SER00.0370.01917.4290.0130.0130.0000.0000.0000.000
122H193SER0-0.061-0.04220.544-0.001-0.0010.0000.0000.0000.000
123H194ALA00.0370.00923.1810.0070.0070.0000.0000.0000.000
124H195GLY00.0250.01026.699-0.001-0.0010.0000.0000.0000.000
125H196LYS10.9360.95229.5020.0510.0510.0000.0000.0000.000
126H197ASN00.001-0.00127.5770.0060.0060.0000.0000.0000.000
127H198SER00.0420.04025.279-0.012-0.0120.0000.0000.0000.000
128H199SER00.0470.03724.075-0.022-0.0220.0000.0000.0000.000
129H200VAL00.0980.02918.4130.0100.0100.0000.0000.0000.000
130H201SER00.0360.02420.695-0.015-0.0150.0000.0000.0000.000
131H202SER0-0.046-0.01122.8300.0060.0060.0000.0000.0000.000
132H203LEU0-0.017-0.00219.8490.0160.0160.0000.0000.0000.000
133H204MET00.0090.01815.8050.0090.0090.0000.0000.0000.000
134H205ASN0-0.033-0.03120.0480.0170.0170.0000.0000.0000.000
135H206GLY0-0.023-0.00223.3330.0160.0160.0000.0000.0000.000
136H207LEU0-0.043-0.02516.1920.0190.0190.0000.0000.0000.000
137H208GLY00.0070.01920.2400.0020.0020.0000.0000.0000.000
138H209TYR0-0.056-0.04515.9990.0120.0120.0000.0000.0000.000
139H210VAL0-0.030-0.02120.9070.0140.0140.0000.0000.0000.000
140H211PHE00.0120.01721.072-0.026-0.0260.0000.0000.0000.000
141H212GLU-1-0.817-0.87120.379-0.291-0.2910.0000.0000.0000.000
142H213PHE00.0240.00118.0110.0140.0140.0000.0000.0000.000
143H214GLN0-0.002-0.00319.684-0.046-0.0460.0000.0000.0000.000
144H215TYR00.003-0.00713.8150.0130.0130.0000.0000.0000.000
145H216LEU00.0300.03018.644-0.038-0.0380.0000.0000.0000.000
146H217THR0-0.040-0.02615.4880.0330.0330.0000.0000.0000.000
147H218ILE00.026-0.00318.9050.0010.0010.0000.0000.0000.000
148H219GLY00.0310.01520.0210.0050.0050.0000.0000.0000.000
149H220VAL0-0.0170.00520.7770.0120.0120.0000.0000.0000.000
150H221LYS10.8400.91312.0910.6620.6620.0000.0000.0000.000
151H222PHE00.0460.02517.3570.0330.0330.0000.0000.0000.000
152H223PHE00.0040.00312.332-0.047-0.0470.0000.0000.0000.000
153H224MET00.0150.00215.2430.0420.0420.0000.0000.0000.000
154H225LYS10.9760.97815.4900.0970.0970.0000.0000.0000.000
155H226HIS00.0210.00213.947-0.014-0.0140.0000.0000.0000.000
156H227GLY00.0180.02210.7930.0120.0120.0000.0000.0000.000
157H228LEU0-0.034-0.00910.531-0.115-0.1150.0000.0000.0000.000
158H229ILE0-0.046-0.0149.5110.0470.0470.0000.0000.0000.000
159H230LEU00.0290.00612.955-0.048-0.0480.0000.0000.0000.000
160H231GLU-1-0.817-0.87812.813-0.807-0.8070.0000.0000.0000.000
161H232LEU00.0290.01216.9620.0060.0060.0000.0000.0000.000
162H233GLN0-0.031-0.00814.696-0.001-0.0010.0000.0000.0000.000
163H234LYS10.7740.87320.1650.2600.2600.0000.0000.0000.000
164H235ILE00.012-0.01117.541-0.024-0.0240.0000.0000.0000.000
165H236TRP0-0.033-0.02321.4550.0290.0290.0000.0000.0000.000
166H237GLN0-0.038-0.01922.555-0.050-0.0500.0000.0000.0000.000
167H238ILE0-0.028-0.02423.0060.0200.0200.0000.0000.0000.000
168H239GLU-1-0.878-0.92625.667-0.232-0.2320.0000.0000.0000.000
169H240GLU-1-0.834-0.91228.513-0.163-0.1630.0000.0000.0000.000
170H241ALA0-0.047-0.02031.9810.0080.0080.0000.0000.0000.000
171H242GLY00.0120.01431.6010.0080.0080.0000.0000.0000.000
172H243ASN0-0.015-0.01527.089-0.004-0.0040.0000.0000.0000.000
173H244SER00.0450.02527.480-0.003-0.0030.0000.0000.0000.000
174H245GLN00.0360.00925.802-0.022-0.0220.0000.0000.0000.000
175H246ILE00.0240.00621.6030.0130.0130.0000.0000.0000.000
176H247THR0-0.0160.00421.633-0.007-0.0070.0000.0000.0000.000
177H248SER0-0.017-0.00824.6460.0120.0120.0000.0000.0000.000
178H249GLY00.0120.01628.4920.0040.0040.0000.0000.0000.000
179H250GLY00.0300.01127.0030.0120.0120.0000.0000.0000.000
180H251PHE0-0.0250.01222.808-0.012-0.0120.0000.0000.0000.000
181H252LEU00.0000.00116.6480.0070.0070.0000.0000.0000.000
182H253LEU0-0.007-0.00119.119-0.015-0.0150.0000.0000.0000.000
183H254LYS10.8450.9289.0771.1821.1820.0000.0000.0000.000
184H255ALA00.0370.02614.0890.0250.0250.0000.0000.0000.000
185H256TYR0-0.069-0.0877.537-0.119-0.1190.0000.0000.0000.000
186H257ILE00.0690.0507.0100.1130.1130.0000.0000.0000.000
187H258ASN00.0100.0122.820-1.577-1.0640.211-0.159-0.5660.001
188H259VAL00.0180.0052.888-0.0300.7740.102-0.257-0.6490.000
189H260SER00.017-0.0022.617-1.672-0.2302.457-1.626-2.272-0.015
190H261ARG10.9871.0011.958-17.171-13.8055.346-4.000-4.7120.019
191H262GLY0-0.0080.0243.123-0.938-1.2980.2190.466-0.3260.000
192H263THR0-0.088-0.0695.670-0.855-0.8550.0000.0000.0000.000
193H264ASP-1-0.848-0.9237.9380.4250.4250.0000.0000.0000.000
194H265ILE00.0590.01611.210-0.042-0.0420.0000.0000.0000.000
195H266ASP-1-0.823-0.90513.2230.1540.1540.0000.0000.0000.000
196H267ARG10.8900.9478.512-0.720-0.7200.0000.0000.0000.000
197H268ILE00.0090.0237.623-0.165-0.1650.0000.0000.0000.000
198H269ASN00.0350.01211.002-0.138-0.1380.0000.0000.0000.000
199H270TYR0-0.030-0.00713.258-0.055-0.0550.0000.0000.0000.000
200H271THR0-0.015-0.0328.322-0.071-0.0710.0000.0000.0000.000
201H272GLU-1-0.865-0.91711.613-0.244-0.2440.0000.0000.0000.000
202H273THR0-0.022-0.01813.774-0.015-0.0150.0000.0000.0000.000
203H274VAL0-0.025-0.00413.570-0.004-0.0040.0000.0000.0000.000
204H275LEU0-0.001-0.00311.106-0.008-0.0080.0000.0000.0000.000
205H276MET00.0090.00515.0690.0010.0010.0000.0000.0000.000
206H277ASN0-0.065-0.03518.3380.0210.0210.0000.0000.0000.000
207H278LEU00.0460.03316.6450.0030.0030.0000.0000.0000.000
208H279LYS10.8640.92118.9980.2330.2330.0000.0000.0000.000
209H280LYS10.8140.89220.6650.1330.1330.0000.0000.0000.000
210H281GLU-1-0.926-0.96622.152-0.154-0.1540.0000.0000.0000.000
211H282LEU00.0300.01721.0200.0060.0060.0000.0000.0000.000
212H283GLN00.0080.00724.6550.0070.0070.0000.0000.0000.000
213H284GLY0-0.041-0.01926.4200.0120.0120.0000.0000.0000.000
214H285TYR0-0.035-0.01027.6440.0060.0060.0000.0000.0000.000
215H286ILE00.005-0.00723.160-0.004-0.0040.0000.0000.0000.000
216H287GLU-1-0.941-0.94423.515-0.225-0.2250.0000.0000.0000.000
217H288LEU00.0480.02717.517-0.023-0.0230.0000.0000.0000.000
218H289SER0-0.023-0.04219.3250.0200.0200.0000.0000.0000.000
219H290VAL0-0.012-0.00115.427-0.062-0.0620.0000.0000.0000.000
220H291PRO00.0090.01714.6990.0420.0420.0000.0000.0000.000
221H292ASP-1-0.833-0.92016.736-0.292-0.2920.0000.0000.0000.000
222H293ARG10.8930.93415.0600.2240.2240.0000.0000.0000.000
223H294GLN00.019-0.00415.461-0.041-0.0410.0000.0000.0000.000
224H295SER0-0.032-0.00817.6510.0100.0100.0000.0000.0000.000
225H296MET0-0.064-0.02610.681-0.008-0.0080.0000.0000.0000.000
226H297ASP-1-0.766-0.85512.620-0.475-0.4750.0000.0000.0000.000
227H298SER0-0.007-0.01212.3920.0010.0010.0000.0000.0000.000
228H299ARG10.7640.83814.5320.2730.2730.0000.0000.0000.000
229H300VAL0-0.030-0.01716.5380.0000.0000.0000.0000.0000.000
230H301ALA00.0060.01019.9440.0240.0240.0000.0000.0000.000