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: 821VY

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661623.853565
FMO2-HF: Nuclear repulsion 2570992.196267
FMO2-HF: Total energy -90631.657298
FMO2-MP2: Total energy -90894.320382


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.
-30.293-19.91616.775-11.958-15.194-0.059
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 : -0.068 / q_NPA : -0.032
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].
3H4GLN00.0510.0333.207-1.3221.3210.085-1.184-1.543-0.004
4H5LEU0-0.0040.0014.8780.2550.340-0.001-0.009-0.0750.000
5H6SER0-0.009-0.0228.2290.0290.0290.0000.0000.0000.000
6H7LEU00.0170.01011.0300.0790.0790.0000.0000.0000.000
7H8PHE0-0.002-0.01311.670-0.047-0.0470.0000.0000.0000.000
8H9GLY00.0900.04016.7790.0450.0450.0000.0000.0000.000
9H10SER0-0.085-0.02120.223-0.026-0.0260.0000.0000.0000.000
10H11ILE00.0460.02922.9020.0180.0180.0000.0000.0000.000
11H12GLY00.0600.03326.165-0.014-0.0140.0000.0000.0000.000
12H13ASP-1-0.828-0.94828.860-0.196-0.1960.0000.0000.0000.000
13H14ASP-1-0.914-0.95329.990-0.131-0.1310.0000.0000.0000.000
14H15GLY0-0.067-0.02529.8110.0080.0080.0000.0000.0000.000
15H16TYR0-0.049-0.02624.9320.0000.0000.0000.0000.0000.000
16H17ASP-1-0.828-0.92628.235-0.142-0.1420.0000.0000.0000.000
17H18LEU0-0.0340.00130.2890.0040.0040.0000.0000.0000.000
18H19LEU00.0540.03122.9820.0020.0020.0000.0000.0000.000
19H20ILE00.0590.02624.952-0.004-0.0040.0000.0000.0000.000
20H21SER0-0.049-0.00426.4530.0070.0070.0000.0000.0000.000
21H22THR00.0090.00625.4840.0120.0120.0000.0000.0000.000
22H23LEU00.006-0.00720.9180.0060.0060.0000.0000.0000.000
23H24THR0-0.041-0.02923.4770.0010.0010.0000.0000.0000.000
24H25THR0-0.088-0.03625.6160.0120.0120.0000.0000.0000.000
25H26ILE0-0.068-0.02421.6640.0070.0070.0000.0000.0000.000
26H27SER0-0.091-0.05320.5070.0060.0060.0000.0000.0000.000
27H28GLY00.008-0.00222.2790.0090.0090.0000.0000.0000.000
28H29ASN0-0.072-0.02720.4970.0170.0170.0000.0000.0000.000
29H30PRO00.0280.00923.692-0.008-0.0080.0000.0000.0000.000
30H31PRO0-0.0090.00321.809-0.009-0.0090.0000.0000.0000.000
31H32LEU0-0.016-0.00818.3470.0100.0100.0000.0000.0000.000
32H33LEU0-0.0010.00320.037-0.030-0.0300.0000.0000.0000.000
33H34TYR0-0.051-0.02015.1690.0160.0160.0000.0000.0000.000
34H35ASN0-0.016-0.03018.300-0.014-0.0140.0000.0000.0000.000
35H36SER0-0.019-0.01614.368-0.055-0.0550.0000.0000.0000.000
36H37LEU00.0390.03816.4360.0030.0030.0000.0000.0000.000
37H38CYS0-0.047-0.03013.498-0.121-0.1210.0000.0000.0000.000
38H39THR00.0440.02615.7940.0590.0590.0000.0000.0000.000
39H40VAL0-0.010-0.01215.298-0.082-0.0820.0000.0000.0000.000
40H41TRP0-0.005-0.00816.3880.1070.1070.0000.0000.0000.000
41H42LYS10.9490.98417.0890.2130.2130.0000.0000.0000.000
42H43PRO00.0380.01618.5510.0180.0180.0000.0000.0000.000
43H44ASN00.022-0.00121.1610.0080.0080.0000.0000.0000.000
44H45PRO00.004-0.01024.6840.0090.0090.0000.0000.0000.000
45H46SER0-0.036-0.00526.9830.0150.0150.0000.0000.0000.000
46H47TYR0-0.103-0.04825.6300.0080.0080.0000.0000.0000.000
47H48ASP-1-0.867-0.94626.670-0.142-0.1420.0000.0000.0000.000
48H49VAL0-0.055-0.01323.2800.0100.0100.0000.0000.0000.000
49H50GLU-1-0.887-0.93325.630-0.055-0.0550.0000.0000.0000.000
50H51ASN0-0.012-0.00721.208-0.016-0.0160.0000.0000.0000.000
51H52VAL0-0.006-0.00921.7850.0180.0180.0000.0000.0000.000
52H53ASN0-0.0180.00519.7080.0280.0280.0000.0000.0000.000
53H54SER00.000-0.00621.8140.0050.0050.0000.0000.0000.000
54H55ARG10.9250.97017.410-0.166-0.1660.0000.0000.0000.000
55H56ASN00.0610.01922.244-0.015-0.0150.0000.0000.0000.000
56H57GLN0-0.051-0.02917.9890.0010.0010.0000.0000.0000.000
57H58LEU00.0370.00220.003-0.017-0.0170.0000.0000.0000.000
58H59VAL0-0.032-0.02015.6160.0250.0250.0000.0000.0000.000
59H60GLU-1-0.921-0.95416.338-0.158-0.1580.0000.0000.0000.000
60H61PRO00.0220.02716.137-0.041-0.0410.0000.0000.0000.000
61H62ASN00.0660.02111.857-0.003-0.0030.0000.0000.0000.000
62H63ARG10.7890.86514.5900.4740.4740.0000.0000.0000.000
63H64ILE0-0.0230.00212.430-0.110-0.1100.0000.0000.0000.000
64H65LYS10.9260.9589.2811.4271.4270.0000.0000.0000.000
65H66LEU00.0060.00311.513-0.134-0.1340.0000.0000.0000.000
66H67SER0-0.081-0.04011.1570.0410.0410.0000.0000.0000.000
67H68LYS10.9980.99313.0780.3450.3450.0000.0000.0000.000
68H69GLU-1-0.883-0.93215.022-0.443-0.4430.0000.0000.0000.000
69H70VAL00.0050.01817.4500.0260.0260.0000.0000.0000.000
70H71PRO00.0090.02021.0980.0070.0070.0000.0000.0000.000
71H72PHE00.1070.01422.1380.0070.0070.0000.0000.0000.000
72H73SER0-0.066-0.02025.5660.0010.0010.0000.0000.0000.000
73H74TYR00.0310.00526.2720.0140.0140.0000.0000.0000.000
74H75LEU00.0000.00922.867-0.004-0.0040.0000.0000.0000.000
75H76ILE0-0.010-0.01126.593-0.003-0.0030.0000.0000.0000.000
76H77ASP-1-0.817-0.93029.644-0.169-0.1690.0000.0000.0000.000
77H78GLU-1-0.970-0.98423.479-0.304-0.3040.0000.0000.0000.000
78H79THR0-0.046-0.01625.458-0.016-0.0160.0000.0000.0000.000
79H80MET0-0.020-0.01727.3180.0050.0050.0000.0000.0000.000
80H81MET0-0.099-0.02530.9820.0030.0030.0000.0000.0000.000
81H82ASP-1-0.903-0.91728.578-0.213-0.2130.0000.0000.0000.000
82H83LYS10.8640.95130.5790.2010.2010.0000.0000.0000.000
83H84PRO0-0.031-0.03933.6380.0040.0040.0000.0000.0000.000
84H85LEU00.0920.02831.3930.0010.0010.0000.0000.0000.000
85H86ASN0-0.108-0.06034.548-0.004-0.0040.0000.0000.0000.000
86H87PHE0-0.0290.00936.5750.0090.0090.0000.0000.0000.000
87H88ARG10.9880.99433.1910.1380.1380.0000.0000.0000.000
88H89ILE0-0.047-0.02433.7410.0090.0090.0000.0000.0000.000
89H160SER0-0.001-0.01523.7310.0030.0030.0000.0000.0000.000
90H161CYS0-0.081-0.02419.914-0.001-0.0010.0000.0000.0000.000
91H162SER0-0.007-0.00919.8570.0160.0160.0000.0000.0000.000
92H163PRO00.0280.00316.259-0.019-0.0190.0000.0000.0000.000
93H164TRP00.0080.00114.306-0.002-0.0020.0000.0000.0000.000
94H165SER0-0.0230.0158.094-0.060-0.0600.0000.0000.0000.000
95H166LEU00.0290.00910.0520.0630.0630.0000.0000.0000.000
96H167GLN0-0.021-0.0335.848-0.332-0.3320.0000.0000.0000.000
97H168ILE00.0320.0277.2050.3700.3700.0000.0000.0000.000
98H169SER0-0.016-0.0016.806-0.492-0.4920.0000.0000.0000.000
99H170ASP-1-0.879-0.9227.704-0.169-0.1690.0000.0000.0000.000
100H171ILE0-0.036-0.0049.509-0.169-0.1690.0000.0000.0000.000
101H172PRO0-0.029-0.01610.2790.0730.0730.0000.0000.0000.000
102H173ALA00.0410.03011.0850.1310.1310.0000.0000.0000.000
103H174ALA0-0.021-0.01912.889-0.042-0.0420.0000.0000.0000.000
104H175GLY00.0310.00716.5660.0400.0400.0000.0000.0000.000
105H176ASN0-0.042-0.00718.968-0.036-0.0360.0000.0000.0000.000
106H177ASN00.001-0.02421.6390.0120.0120.0000.0000.0000.000
107H178ARG10.9190.98014.1730.3000.3000.0000.0000.0000.000
108H179SER00.0020.00816.667-0.033-0.0330.0000.0000.0000.000
109H180VAL00.0630.01011.721-0.034-0.0340.0000.0000.0000.000
110H181SER0-0.080-0.02911.4140.0240.0240.0000.0000.0000.000
111H182MET00.0470.0158.094-0.034-0.0340.0000.0000.0000.000
112H183GLN0-0.029-0.0316.2900.1230.1230.0000.0000.0000.000
113H184THR0-0.022-0.0393.524-1.181-0.8450.005-0.109-0.2320.000
114H185ILE0-0.016-0.0142.0970.3740.8993.100-1.219-2.4060.000
115H186ALA0-0.011-0.0012.215-10.055-8.2594.297-2.892-3.201-0.045
116H187GLU-1-0.900-0.9824.410-2.460-2.267-0.001-0.014-0.1780.000
117H188THR0-0.057-0.0166.0040.3950.3950.0000.0000.0000.000
118H189ILE00.0170.0068.894-0.076-0.0760.0000.0000.0000.000
119H190ILE0-0.0290.00111.5280.1270.1270.0000.0000.0000.000
120H191LEU00.0300.00715.027-0.007-0.0070.0000.0000.0000.000
121H192SER0-0.044-0.01917.4780.0240.0240.0000.0000.0000.000
122H193SER00.010-0.00720.738-0.004-0.0040.0000.0000.0000.000
123H194ALA00.026-0.00123.3210.0110.0110.0000.0000.0000.000
124H195GLY00.0130.01026.995-0.002-0.0020.0000.0000.0000.000
125H196LYS10.9310.95829.7320.0950.0950.0000.0000.0000.000
126H197ASN00.0210.01227.8170.0020.0020.0000.0000.0000.000
127H198SER00.0350.02925.643-0.011-0.0110.0000.0000.0000.000
128H199SER00.0720.05624.249-0.023-0.0230.0000.0000.0000.000
129H200VAL00.1030.02818.4010.0100.0100.0000.0000.0000.000
130H201SER00.0160.00721.066-0.020-0.0200.0000.0000.0000.000
131H202SER00.0070.00623.2860.0110.0110.0000.0000.0000.000
132H203LEU0-0.021-0.01420.6080.0100.0100.0000.0000.0000.000
133H204MET00.0110.02416.155-0.004-0.0040.0000.0000.0000.000
134H205ASN0-0.041-0.02720.4070.0190.0190.0000.0000.0000.000
135H206GLY0-0.036-0.00623.6540.0160.0160.0000.0000.0000.000
136H207LEU0-0.050-0.03316.7830.0180.0180.0000.0000.0000.000
137H208GLY0-0.0080.00820.6860.0030.0030.0000.0000.0000.000
138H209TYR0-0.082-0.05316.1300.0020.0020.0000.0000.0000.000
139H210VAL0-0.018-0.00121.1130.0240.0240.0000.0000.0000.000
140H211PHE00.0020.00821.283-0.033-0.0330.0000.0000.0000.000
141H212GLU-1-0.844-0.90220.097-0.351-0.3510.0000.0000.0000.000
142H213PHE00.0280.00917.6610.0160.0160.0000.0000.0000.000
143H214GLN00.0540.02019.285-0.074-0.0740.0000.0000.0000.000
144H215TYR0-0.024-0.01213.8380.0130.0130.0000.0000.0000.000
145H216LEU00.0360.02618.451-0.044-0.0440.0000.0000.0000.000
146H217THR0-0.062-0.02315.4370.0280.0280.0000.0000.0000.000
147H218ILE00.0360.01018.747-0.003-0.0030.0000.0000.0000.000
148H219GLY00.0430.01319.4760.0020.0020.0000.0000.0000.000
149H220VAL0-0.0050.00820.2480.0120.0120.0000.0000.0000.000
150H221LYS10.9320.96411.9800.5320.5320.0000.0000.0000.000
151H222PHE00.0410.01516.9650.0310.0310.0000.0000.0000.000
152H223PHE0-0.002-0.00212.562-0.038-0.0380.0000.0000.0000.000
153H224MET00.0450.01915.2310.0340.0340.0000.0000.0000.000
154H225LYS10.9640.96715.6830.0160.0160.0000.0000.0000.000
155H226HIS00.0120.01313.5580.0060.0060.0000.0000.0000.000
156H227GLY00.0220.02510.4950.0340.0340.0000.0000.0000.000
157H228LEU0-0.019-0.00210.343-0.090-0.0900.0000.0000.0000.000
158H229ILE0-0.044-0.0119.6010.0240.0240.0000.0000.0000.000
159H230LEU00.016-0.01212.925-0.040-0.0400.0000.0000.0000.000
160H231GLU-1-0.930-0.97312.763-0.748-0.7480.0000.0000.0000.000
161H232LEU00.0220.02116.5310.0010.0010.0000.0000.0000.000
162H233GLN0-0.036-0.03913.8520.0090.0090.0000.0000.0000.000
163H234LYS10.8240.93319.5360.2610.2610.0000.0000.0000.000
164H235ILE0-0.008-0.01617.482-0.029-0.0290.0000.0000.0000.000
165H236TRP0-0.003-0.01421.1830.0290.0290.0000.0000.0000.000
166H237GLN0-0.0030.00822.384-0.044-0.0440.0000.0000.0000.000
167H238ILE0-0.041-0.02622.6580.0230.0230.0000.0000.0000.000
168H239GLU-1-0.916-0.96525.216-0.252-0.2520.0000.0000.0000.000
169H240GLU-1-0.887-0.95228.055-0.179-0.1790.0000.0000.0000.000
170H241ALA0-0.028-0.01431.4730.0080.0080.0000.0000.0000.000
171H242GLY00.0010.00731.0790.0100.0100.0000.0000.0000.000
172H243ASN00.020-0.00626.638-0.013-0.0130.0000.0000.0000.000
173H244SER00.0100.02326.8550.0100.0100.0000.0000.0000.000
174H245GLN00.0300.00125.429-0.027-0.0270.0000.0000.0000.000
175H246ILE00.0250.02121.3820.0140.0140.0000.0000.0000.000
176H247THR0-0.004-0.00721.234-0.003-0.0030.0000.0000.0000.000
177H248SER0-0.060-0.02524.1700.0140.0140.0000.0000.0000.000
178H249GLY00.0350.02427.9310.0020.0020.0000.0000.0000.000
179H250GLY00.0430.01926.7050.0150.0150.0000.0000.0000.000
180H251PHE0-0.058-0.00822.253-0.013-0.0130.0000.0000.0000.000
181H252LEU0-0.0030.00416.2700.0140.0140.0000.0000.0000.000
182H253LEU0-0.019-0.02018.532-0.018-0.0180.0000.0000.0000.000
183H254LYS10.8840.9498.5311.1791.1790.0000.0000.0000.000
184H255ALA00.0250.02513.7730.0180.0180.0000.0000.0000.000
185H256TYR0-0.046-0.0447.204-0.109-0.1090.0000.0000.0000.000
186H257ILE00.0750.0466.9300.0890.0890.0000.0000.0000.000
187H258ASN00.0080.0092.548-1.334-0.8530.637-0.266-0.8530.003
188H259VAL00.0190.0032.958-0.2090.6410.132-0.252-0.730-0.001
189H260SER0-0.003-0.0222.592-1.5720.9631.911-2.116-2.330-0.018
190H261ARG11.0301.0081.721-10.749-9.9836.472-3.921-3.3170.007
191H262GLY00.0060.0413.356-1.625-1.4580.1380.024-0.329-0.001
192H263THR0-0.103-0.0685.941-0.718-0.7180.0000.0000.0000.000
193H264ASP-1-0.861-0.9218.3700.6060.6060.0000.0000.0000.000
194H265ILE00.0450.00011.1900.0050.0050.0000.0000.0000.000
195H266ASP-1-0.852-0.90013.2510.3700.3700.0000.0000.0000.000
196H267ARG10.9440.9578.289-1.081-1.0810.0000.0000.0000.000
197H268ILE00.0130.0217.306-0.101-0.1010.0000.0000.0000.000
198H269ASN00.0820.02810.757-0.135-0.1350.0000.0000.0000.000
199H270TYR0-0.076-0.05012.950-0.077-0.0770.0000.0000.0000.000
200H271THR0-0.014-0.0358.295-0.070-0.0700.0000.0000.0000.000
201H272GLU-1-0.915-0.96311.549-0.021-0.0210.0000.0000.0000.000
202H273THR0-0.034-0.00613.499-0.047-0.0470.0000.0000.0000.000
203H274VAL0-0.031-0.00913.376-0.028-0.0280.0000.0000.0000.000
204H275LEU0-0.005-0.00110.658-0.028-0.0280.0000.0000.0000.000
205H276MET0-0.027-0.01214.895-0.023-0.0230.0000.0000.0000.000
206H277ASN0-0.029-0.02518.137-0.001-0.0010.0000.0000.0000.000
207H278LEU00.0460.03716.357-0.006-0.0060.0000.0000.0000.000
208H279LYS10.9010.94818.6790.1400.1400.0000.0000.0000.000
209H280LYS10.8640.93420.2590.0550.0550.0000.0000.0000.000
210H281GLU-1-0.937-0.97422.576-0.079-0.0790.0000.0000.0000.000
211H282LEU00.0210.02020.940-0.001-0.0010.0000.0000.0000.000
212H283GLN00.0200.00024.5560.0020.0020.0000.0000.0000.000
213H284GLY0-0.077-0.02226.2430.0080.0080.0000.0000.0000.000
214H285TYR0-0.027-0.01627.390-0.001-0.0010.0000.0000.0000.000
215H286ILE00.0120.00422.248-0.007-0.0070.0000.0000.0000.000
216H287GLU-1-1.000-0.99623.829-0.164-0.1640.0000.0000.0000.000
217H288LEU00.0100.00917.679-0.021-0.0210.0000.0000.0000.000
218H289SER00.016-0.01319.2330.0200.0200.0000.0000.0000.000
219H290VAL0-0.024-0.00914.917-0.053-0.0530.0000.0000.0000.000
220H291PRO00.0140.02814.4790.0350.0350.0000.0000.0000.000
221H292ASP-1-0.812-0.91616.653-0.260-0.2600.0000.0000.0000.000
222H293ARG10.9060.94114.9960.1830.1830.0000.0000.0000.000
223H294GLN00.011-0.00915.526-0.045-0.0450.0000.0000.0000.000
224H295SER0-0.057-0.02617.4010.0070.0070.0000.0000.0000.000
225H296MET0-0.082-0.03910.481-0.007-0.0070.0000.0000.0000.000
226H297ASP-1-0.783-0.88212.393-0.552-0.5520.0000.0000.0000.000
227H298SER0-0.012-0.00212.4410.0020.0020.0000.0000.0000.000
228H299ARG10.8730.92014.4940.3190.3190.0000.0000.0000.000
229H300VAL0-0.051-0.01716.4440.0130.0130.0000.0000.0000.000
230H301ALA00.0020.00519.8390.0230.0230.0000.0000.0000.000