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: 7G8VK

Calculation Name: 2HZS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: D

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413150.862672
FMO2-HF: Nuclear repulsion 2328541.452461
FMO2-HF: Total energy -84609.410211
FMO2-MP2: Total energy -84855.933537


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(D:2:VAL)


Summations of interaction energy for fragment #1(D: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.
-36.579-31.34624.93-13.097-17.065-0.026
Interaction energy analysis for fragmet #1(D:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.025
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].
3D4GLN00.0220.0143.208-1.4041.0990.076-1.119-1.460-0.003
4D5LEU00.0070.0065.0110.3470.431-0.001-0.007-0.0750.000
5D6SER0-0.020-0.0278.287-0.015-0.0150.0000.0000.0000.000
6D7LEU00.0070.00711.0810.0940.0940.0000.0000.0000.000
7D8PHE0-0.005-0.01612.051-0.062-0.0620.0000.0000.0000.000
8D9GLY00.0880.04317.0420.0470.0470.0000.0000.0000.000
9D10SER0-0.072-0.01920.442-0.021-0.0210.0000.0000.0000.000
10D11ILE00.0410.03323.1780.0170.0170.0000.0000.0000.000
11D12GLY00.0560.03526.435-0.012-0.0120.0000.0000.0000.000
12D13ASP-1-0.803-0.91028.546-0.216-0.2160.0000.0000.0000.000
13D14ASP-1-0.908-0.95230.107-0.146-0.1460.0000.0000.0000.000
14D15GLY0-0.064-0.02630.2450.0080.0080.0000.0000.0000.000
15D16TYR0-0.032-0.02824.629-0.017-0.0170.0000.0000.0000.000
16D17ASP-1-0.839-0.92328.020-0.176-0.1760.0000.0000.0000.000
17D18LEU00.0050.00729.557-0.003-0.0030.0000.0000.0000.000
18D19LEU00.0380.03723.2290.0000.0000.0000.0000.0000.000
19D20ILE00.0370.01624.025-0.011-0.0110.0000.0000.0000.000
20D21SER0-0.027-0.01226.1250.0000.0000.0000.0000.0000.000
21D22THR0-0.044-0.02925.8000.0080.0080.0000.0000.0000.000
22D23LEU00.0470.01220.5990.0040.0040.0000.0000.0000.000
23D24THR0-0.018-0.01223.293-0.005-0.0050.0000.0000.0000.000
24D25THR0-0.048-0.01025.2460.0070.0070.0000.0000.0000.000
25D26ILE0-0.060-0.01321.5010.0070.0070.0000.0000.0000.000
26D27SER0-0.070-0.04220.368-0.001-0.0010.0000.0000.0000.000
27D28GLY0-0.038-0.02521.8800.0060.0060.0000.0000.0000.000
28D29ASN0-0.096-0.04521.6370.0120.0120.0000.0000.0000.000
29D30PRO00.0510.02923.736-0.006-0.0060.0000.0000.0000.000
30D31PRO0-0.008-0.00221.826-0.015-0.0150.0000.0000.0000.000
31D32LEU0-0.016-0.00518.3680.0140.0140.0000.0000.0000.000
32D33LEU0-0.0060.00020.019-0.033-0.0330.0000.0000.0000.000
33D34TYR0-0.086-0.05414.5830.0150.0150.0000.0000.0000.000
34D35ASN00.004-0.02618.104-0.004-0.0040.0000.0000.0000.000
35D36SER0-0.007-0.00813.530-0.014-0.0140.0000.0000.0000.000
36D37LEU00.0030.01516.4500.0220.0220.0000.0000.0000.000
37D38CYS0-0.053-0.01913.890-0.109-0.1090.0000.0000.0000.000
38D39THR00.0350.01415.9030.0620.0620.0000.0000.0000.000
39D40VAL0-0.010-0.00815.268-0.059-0.0590.0000.0000.0000.000
40D41TRP0-0.008-0.01216.3030.0900.0900.0000.0000.0000.000
41D42LYS10.8810.92917.1740.1640.1640.0000.0000.0000.000
42D43PRO00.0660.03218.7190.0070.0070.0000.0000.0000.000
43D44ASN0-0.017-0.01921.147-0.002-0.0020.0000.0000.0000.000
44D45PRO00.0120.00824.6940.0090.0090.0000.0000.0000.000
45D46SER0-0.042-0.01527.0140.0110.0110.0000.0000.0000.000
46D47TYR0-0.086-0.04525.5340.0060.0060.0000.0000.0000.000
47D48ASP-1-0.866-0.93826.279-0.041-0.0410.0000.0000.0000.000
48D49VAL0-0.048-0.02123.6450.0090.0090.0000.0000.0000.000
49D50GLU-1-0.918-0.95324.9580.0570.0570.0000.0000.0000.000
50D51ASN00.0070.02121.3260.0050.0050.0000.0000.0000.000
51D52VAL0-0.036-0.03521.7010.0210.0210.0000.0000.0000.000
52D53ASN00.0330.02117.796-0.008-0.0080.0000.0000.0000.000
53D54SER0-0.020-0.00721.185-0.001-0.0010.0000.0000.0000.000
54D55ARG10.8910.95017.928-0.364-0.3640.0000.0000.0000.000
55D56ASN00.0490.01323.1130.0020.0020.0000.0000.0000.000
56D57GLN0-0.035-0.01418.4300.0070.0070.0000.0000.0000.000
57D58LEU00.0590.02818.620-0.012-0.0120.0000.0000.0000.000
58D59VAL0-0.027-0.02915.7260.0530.0530.0000.0000.0000.000
59D60GLU-1-0.863-0.91016.354-0.003-0.0030.0000.0000.0000.000
60D61PRO00.0160.02616.034-0.015-0.0150.0000.0000.0000.000
61D62ASN00.0430.02211.587-0.065-0.0650.0000.0000.0000.000
62D63ARG10.8310.91014.8740.3290.3290.0000.0000.0000.000
63D64ILE0-0.028-0.00112.089-0.066-0.0660.0000.0000.0000.000
64D65LYS10.8910.9399.3161.3151.3150.0000.0000.0000.000
65D66LEU00.0010.00611.364-0.116-0.1160.0000.0000.0000.000
66D67SER0-0.074-0.04911.1820.0280.0280.0000.0000.0000.000
67D68LYS10.9820.98713.0700.3430.3430.0000.0000.0000.000
68D69GLU-1-0.886-0.92014.895-0.473-0.4730.0000.0000.0000.000
69D70VAL0-0.020-0.01617.3420.0310.0310.0000.0000.0000.000
70D71PRO00.0060.02121.071-0.002-0.0020.0000.0000.0000.000
71D72PHE00.1040.02021.5260.0050.0050.0000.0000.0000.000
72D73SER00.0130.01725.3440.0040.0040.0000.0000.0000.000
73D74TYR0-0.099-0.05325.3950.0100.0100.0000.0000.0000.000
74D75LEU0-0.027-0.01423.082-0.004-0.0040.0000.0000.0000.000
75D76ILE00.0050.02827.7900.0070.0070.0000.0000.0000.000
76D160SER00.0440.02323.6920.0100.0100.0000.0000.0000.000
77D161CYS0-0.156-0.07320.532-0.014-0.0140.0000.0000.0000.000
78D162SER00.019-0.00219.4160.0100.0100.0000.0000.0000.000
79D163PRO00.0500.01716.056-0.007-0.0070.0000.0000.0000.000
80D164TRP0-0.014-0.01414.3260.0020.0020.0000.0000.0000.000
81D165SER0-0.053-0.0307.8400.0290.0290.0000.0000.0000.000
82D166LEU00.0090.0019.9850.0470.0470.0000.0000.0000.000
83D167GLN0-0.020-0.0395.4270.1140.1140.0000.0000.0000.000
84D168ILE00.0530.0287.0990.3010.3010.0000.0000.0000.000
85D169SER0-0.0180.0056.937-0.313-0.3130.0000.0000.0000.000
86D170ASP-1-0.881-0.9267.5620.5190.5190.0000.0000.0000.000
87D171ILE0-0.023-0.0019.560-0.207-0.2070.0000.0000.0000.000
88D172PRO0-0.027-0.01410.6150.0890.0890.0000.0000.0000.000
89D173ALA00.0340.02611.2820.1330.1330.0000.0000.0000.000
90D174ALA0-0.017-0.02212.782-0.072-0.0720.0000.0000.0000.000
91D175GLY00.0270.00516.5450.0410.0410.0000.0000.0000.000
92D176ASN0-0.052-0.01718.993-0.034-0.0340.0000.0000.0000.000
93D177ASN00.0200.00021.4020.0040.0040.0000.0000.0000.000
94D178ARG10.9110.96914.6710.2470.2470.0000.0000.0000.000
95D179SER0-0.011-0.01716.170-0.029-0.0290.0000.0000.0000.000
96D180VAL00.035-0.00711.697-0.036-0.0360.0000.0000.0000.000
97D181SER0-0.046-0.01111.8270.0650.0650.0000.0000.0000.000
98D182MET00.0410.0228.020-0.078-0.0780.0000.0000.0000.000
99D183GLN0-0.038-0.0266.5560.1620.1620.0000.0000.0000.000
100D184THR00.008-0.0043.816-1.506-1.2580.002-0.099-0.1510.000
101D185ILE0-0.008-0.0142.434-0.4680.9361.223-0.785-1.8430.000
102D186ALA0-0.035-0.0152.203-8.787-6.9244.243-2.925-3.180-0.044
103D187GLU-1-0.810-0.8804.214-2.980-2.7470.000-0.026-0.2060.000
104D188THR0-0.041-0.0165.6190.4290.4290.0000.0000.0000.000
105D189ILE00.0110.0038.374-0.097-0.0970.0000.0000.0000.000
106D190ILE0-0.0270.00211.4080.1280.1280.0000.0000.0000.000
107D191LEU00.0310.00914.934-0.024-0.0240.0000.0000.0000.000
108D192SER00.0300.01117.2880.0080.0080.0000.0000.0000.000
109D193SER0-0.066-0.04620.4990.0000.0000.0000.0000.0000.000
110D194ALA00.0300.00823.1130.0050.0050.0000.0000.0000.000
111D195GLY00.0200.01326.6570.0020.0020.0000.0000.0000.000
112D196LYS10.9310.95929.4200.0560.0560.0000.0000.0000.000
113D197ASN00.0220.01127.7090.0030.0030.0000.0000.0000.000
114D198SER00.0560.04125.327-0.007-0.0070.0000.0000.0000.000
115D199SER00.0660.06524.143-0.019-0.0190.0000.0000.0000.000
116D200VAL00.0970.02718.2020.0140.0140.0000.0000.0000.000
117D201SER00.0310.01120.835-0.009-0.0090.0000.0000.0000.000
118D202SER0-0.054-0.02823.0810.0150.0150.0000.0000.0000.000
119D203LEU0-0.008-0.01120.2080.0130.0130.0000.0000.0000.000
120D204MET00.0160.03015.8910.0050.0050.0000.0000.0000.000
121D205ASN0-0.029-0.02420.1410.0190.0190.0000.0000.0000.000
122D206GLY0-0.048-0.01623.4790.0170.0170.0000.0000.0000.000
123D207LEU0-0.025-0.01716.6190.0190.0190.0000.0000.0000.000
124D208GLY0-0.0250.00220.6160.0140.0140.0000.0000.0000.000
125D209TYR0-0.068-0.05216.1980.0100.0100.0000.0000.0000.000
126D210VAL0-0.024-0.01121.0710.0100.0100.0000.0000.0000.000
127D211PHE00.0200.01521.167-0.025-0.0250.0000.0000.0000.000
128D212GLU-1-0.801-0.86320.363-0.241-0.2410.0000.0000.0000.000
129D213PHE00.0400.00917.8760.0120.0120.0000.0000.0000.000
130D214GLN00.0110.00319.428-0.050-0.0500.0000.0000.0000.000
131D215TYR0-0.004-0.00213.8160.0170.0170.0000.0000.0000.000
132D216LEU00.0140.01118.592-0.044-0.0440.0000.0000.0000.000
133D217THR00.0030.00615.4320.0280.0280.0000.0000.0000.000
134D218ILE00.001-0.00218.629-0.014-0.0140.0000.0000.0000.000
135D219GLY00.0430.01419.5860.0090.0090.0000.0000.0000.000
136D220VAL0-0.0040.00520.2220.0050.0050.0000.0000.0000.000
137D221LYS10.8420.91611.7290.7350.7350.0000.0000.0000.000
138D222PHE00.0330.01616.9100.0360.0360.0000.0000.0000.000
139D223PHE00.001-0.00212.453-0.052-0.0520.0000.0000.0000.000
140D224MET00.0280.01415.1720.0450.0450.0000.0000.0000.000
141D225LYS10.9630.96515.1500.1050.1050.0000.0000.0000.000
142D226HIS00.0170.00013.547-0.013-0.0130.0000.0000.0000.000
143D227GLY00.0210.02110.284-0.003-0.0030.0000.0000.0000.000
144D228LEU0-0.0100.00810.152-0.124-0.1240.0000.0000.0000.000
145D229ILE0-0.052-0.01610.1260.0500.0500.0000.0000.0000.000
146D230LEU00.033-0.00612.843-0.027-0.0270.0000.0000.0000.000
147D231GLU-1-0.813-0.87312.475-0.851-0.8510.0000.0000.0000.000
148D232LEU00.0360.02716.5780.0110.0110.0000.0000.0000.000
149D233GLN0-0.062-0.04614.165-0.006-0.0060.0000.0000.0000.000
150D234LYS10.8200.90819.5580.2720.2720.0000.0000.0000.000
151D235ILE00.021-0.00917.227-0.028-0.0280.0000.0000.0000.000
152D236TRP0-0.018-0.02321.1090.0320.0320.0000.0000.0000.000
153D237GLN0-0.051-0.03622.393-0.053-0.0530.0000.0000.0000.000
154D238ILE0-0.059-0.03823.2120.0190.0190.0000.0000.0000.000
155D239GLU-1-0.869-0.92325.331-0.219-0.2190.0000.0000.0000.000
156D240GLU-1-0.889-0.94927.942-0.168-0.1680.0000.0000.0000.000
157D241ALA0-0.060-0.02331.4460.0070.0070.0000.0000.0000.000
158D242GLY00.0120.01331.2330.0080.0080.0000.0000.0000.000
159D243ASN0-0.028-0.02627.778-0.018-0.0180.0000.0000.0000.000
160D244SER00.0330.02427.4390.0070.0070.0000.0000.0000.000
161D245GLN00.0230.00425.525-0.024-0.0240.0000.0000.0000.000
162D246ILE00.0590.03521.2830.0110.0110.0000.0000.0000.000
163D247THR0-0.0140.00121.216-0.001-0.0010.0000.0000.0000.000
164D248SER0-0.036-0.02224.2750.0090.0090.0000.0000.0000.000
165D249GLY00.0040.01428.0080.0050.0050.0000.0000.0000.000
166D250GLY00.0420.01826.9260.0130.0130.0000.0000.0000.000
167D251PHE0-0.044-0.00122.396-0.014-0.0140.0000.0000.0000.000
168D252LEU0-0.014-0.00316.6080.0120.0120.0000.0000.0000.000
169D253LEU0-0.026-0.01418.747-0.024-0.0240.0000.0000.0000.000
170D254LYS10.8930.9458.7181.2471.2470.0000.0000.0000.000
171D255ALA00.0440.03813.8400.0010.0010.0000.0000.0000.000
172D256TYR0-0.073-0.0847.278-0.106-0.1060.0000.0000.0000.000
173D257ILE00.0480.0376.9420.0840.0840.0000.0000.0000.000
174D258ASN0-0.0040.0152.638-1.324-0.8170.484-0.223-0.7680.002
175D259VAL00.0340.0133.179-0.0540.6700.071-0.202-0.592-0.001
176D260SER00.0110.0062.410-1.772-0.3692.264-1.570-2.098-0.011
177D261ARG10.9230.9391.939-18.995-22.14716.372-6.730-6.4900.031
178D262GLY00.0020.0173.054-1.096-1.6800.1960.589-0.2020.000
179D263THR0-0.086-0.0555.529-0.603-0.6030.0000.0000.0000.000
180D264ASP-1-0.845-0.9307.5040.4420.4420.0000.0000.0000.000
181D265ILE00.0640.01311.195-0.080-0.0800.0000.0000.0000.000
182D266ASP-1-0.806-0.87312.7520.2030.2030.0000.0000.0000.000
183D267ARG10.8940.9428.425-0.618-0.6180.0000.0000.0000.000
184D268ILE0-0.017-0.0037.237-0.128-0.1280.0000.0000.0000.000
185D269ASN00.025-0.00510.814-0.078-0.0780.0000.0000.0000.000
186D270TYR0-0.043-0.01012.880-0.054-0.0540.0000.0000.0000.000
187D271THR0-0.006-0.0348.260-0.080-0.0800.0000.0000.0000.000
188D272GLU-1-0.830-0.88811.565-0.077-0.0770.0000.0000.0000.000
189D273THR0-0.048-0.01813.530-0.024-0.0240.0000.0000.0000.000
190D274VAL00.0090.01213.475-0.015-0.0150.0000.0000.0000.000
191D275LEU0-0.018-0.00710.727-0.017-0.0170.0000.0000.0000.000
192D276MET0-0.003-0.01414.9030.0010.0010.0000.0000.0000.000
193D277ASN0-0.066-0.03618.1380.0110.0110.0000.0000.0000.000
194D278LEU00.0930.05316.6030.0050.0050.0000.0000.0000.000
195D279LYS10.8460.93119.0390.1980.1980.0000.0000.0000.000
196D280LYS10.7960.88020.5470.1190.1190.0000.0000.0000.000
197D281GLU-1-0.933-0.96422.097-0.154-0.1540.0000.0000.0000.000
198D282LEU00.0180.01121.0350.0070.0070.0000.0000.0000.000
199D283GLN00.0340.01624.5700.0080.0080.0000.0000.0000.000
200D284GLY0-0.044-0.02026.2820.0070.0070.0000.0000.0000.000
201D285TYR0-0.052-0.02226.5910.0050.0050.0000.0000.0000.000
202D286ILE00.013-0.00422.936-0.006-0.0060.0000.0000.0000.000
203D287GLU-1-0.928-0.94523.579-0.208-0.2080.0000.0000.0000.000
204D288LEU00.0400.03417.659-0.018-0.0180.0000.0000.0000.000
205D289SER0-0.019-0.03319.5330.0190.0190.0000.0000.0000.000
206D290VAL0-0.036-0.01815.347-0.057-0.0570.0000.0000.0000.000
207D291PRO00.0100.02214.8080.0380.0380.0000.0000.0000.000
208D292ASP-1-0.815-0.93816.802-0.203-0.2030.0000.0000.0000.000
209D293ARG10.8830.94515.0960.0700.0700.0000.0000.0000.000
210D294GLN00.0280.00215.780-0.052-0.0520.0000.0000.0000.000
211D295SER0-0.057-0.01917.6880.0030.0030.0000.0000.0000.000
212D296MET0-0.090-0.03810.608-0.017-0.0170.0000.0000.0000.000
213D297ASP-1-0.769-0.87712.639-0.320-0.3200.0000.0000.0000.000
214D298SER0-0.020-0.01912.737-0.017-0.0170.0000.0000.0000.000
215D299ARG10.8210.86514.4510.1150.1150.0000.0000.0000.000
216D300VAL0-0.075-0.03916.474-0.009-0.0090.0000.0000.0000.000
217D301ALA00.0160.01819.9470.0360.0360.0000.0000.0000.000