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: M3K1Z

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413261.566322
FMO2-HF: Nuclear repulsion 2328653.57482
FMO2-HF: Total energy -84607.991502
FMO2-MP2: Total energy -84854.750993


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.
-31.907-23.99120.192-10.976-17.132-0.045
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 : -0.048 / q_NPA : -0.034
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].
3D4GLN00.0430.0253.188-1.3101.2040.088-1.120-1.482-0.004
4D5LEU00.0000.0064.9570.2920.377-0.001-0.008-0.0770.000
5D6SER0-0.013-0.0218.2570.0110.0110.0000.0000.0000.000
6D7LEU00.0100.00211.0470.0920.0920.0000.0000.0000.000
7D8PHE00.001-0.01111.779-0.056-0.0560.0000.0000.0000.000
8D9GLY00.0740.03716.9070.0490.0490.0000.0000.0000.000
9D10SER0-0.071-0.01520.353-0.025-0.0250.0000.0000.0000.000
10D11ILE00.0570.03223.0970.0190.0190.0000.0000.0000.000
11D12GLY00.0440.03026.384-0.014-0.0140.0000.0000.0000.000
12D13ASP-1-0.822-0.92728.985-0.208-0.2080.0000.0000.0000.000
13D14ASP-1-0.898-0.95030.116-0.142-0.1420.0000.0000.0000.000
14D15GLY0-0.079-0.03230.2280.0090.0090.0000.0000.0000.000
15D16TYR0-0.048-0.02924.753-0.005-0.0050.0000.0000.0000.000
16D17ASP-1-0.835-0.92428.013-0.163-0.1630.0000.0000.0000.000
17D18LEU0-0.018-0.00629.559-0.001-0.0010.0000.0000.0000.000
18D19LEU00.0330.02123.3230.0020.0020.0000.0000.0000.000
19D20ILE00.0420.01824.094-0.008-0.0080.0000.0000.0000.000
20D21SER0-0.030-0.02126.1390.0030.0030.0000.0000.0000.000
21D22THR0-0.029-0.00625.1090.0100.0100.0000.0000.0000.000
22D23LEU00.023-0.00320.8230.0060.0060.0000.0000.0000.000
23D24THR0-0.019-0.00523.320-0.001-0.0010.0000.0000.0000.000
24D25THR0-0.042-0.01325.2550.0090.0090.0000.0000.0000.000
25D26ILE0-0.050-0.00121.3960.0070.0070.0000.0000.0000.000
26D27SER0-0.098-0.05820.3430.0020.0020.0000.0000.0000.000
27D28GLY0-0.035-0.01921.9210.0090.0090.0000.0000.0000.000
28D29ASN0-0.072-0.03321.0070.0160.0160.0000.0000.0000.000
29D30PRO00.0400.02123.729-0.008-0.0080.0000.0000.0000.000
30D31PRO0-0.0130.00121.776-0.013-0.0130.0000.0000.0000.000
31D32LEU0-0.008-0.00118.2720.0130.0130.0000.0000.0000.000
32D33LEU0-0.0040.00219.961-0.033-0.0330.0000.0000.0000.000
33D34TYR0-0.044-0.02015.0230.0160.0160.0000.0000.0000.000
34D35ASN00.013-0.01718.161-0.016-0.0160.0000.0000.0000.000
35D36SER0-0.015-0.00914.396-0.058-0.0580.0000.0000.0000.000
36D37LEU00.0280.01316.4200.0180.0180.0000.0000.0000.000
37D38CYS0-0.049-0.02413.555-0.120-0.1200.0000.0000.0000.000
38D39THR00.0220.01215.7300.0690.0690.0000.0000.0000.000
39D40VAL00.005-0.00115.378-0.074-0.0740.0000.0000.0000.000
40D41TRP0-0.031-0.02016.2330.0990.0990.0000.0000.0000.000
41D42LYS10.9720.99117.0600.1890.1890.0000.0000.0000.000
42D43PRO00.0440.02018.4220.0140.0140.0000.0000.0000.000
43D44ASN0-0.007-0.01721.0100.0020.0020.0000.0000.0000.000
44D45PRO0-0.012-0.00424.5770.0070.0070.0000.0000.0000.000
45D46SER0-0.0190.00326.8570.0140.0140.0000.0000.0000.000
46D47TYR0-0.094-0.04925.4650.0070.0070.0000.0000.0000.000
47D48ASP-1-0.842-0.92426.260-0.110-0.1100.0000.0000.0000.000
48D49VAL0-0.049-0.02623.5600.0120.0120.0000.0000.0000.000
49D50GLU-1-0.925-0.96124.9210.0100.0100.0000.0000.0000.000
50D51ASN0-0.0030.01721.168-0.003-0.0030.0000.0000.0000.000
51D52VAL0-0.031-0.02421.6590.0180.0180.0000.0000.0000.000
52D53ASN00.0630.03817.810-0.008-0.0080.0000.0000.0000.000
53D54SER0-0.048-0.03221.1360.0050.0050.0000.0000.0000.000
54D55ARG10.9000.95718.111-0.297-0.2970.0000.0000.0000.000
55D56ASN00.0630.01423.051-0.002-0.0020.0000.0000.0000.000
56D57GLN0-0.063-0.02218.634-0.007-0.0070.0000.0000.0000.000
57D58LEU00.0640.03218.309-0.012-0.0120.0000.0000.0000.000
58D59VAL0-0.026-0.02615.7680.0390.0390.0000.0000.0000.000
59D60GLU-1-0.887-0.94216.379-0.102-0.1020.0000.0000.0000.000
60D61PRO00.0130.02715.987-0.032-0.0320.0000.0000.0000.000
61D62ASN00.0790.03811.867-0.017-0.0170.0000.0000.0000.000
62D63ARG10.7780.87214.6100.4240.4240.0000.0000.0000.000
63D64ILE0-0.0200.00912.246-0.092-0.0920.0000.0000.0000.000
64D65LYS10.9310.9629.4651.3851.3850.0000.0000.0000.000
65D66LEU00.0060.00311.398-0.130-0.1300.0000.0000.0000.000
66D67SER0-0.065-0.03811.0900.0370.0370.0000.0000.0000.000
67D68LYS10.9850.99213.0910.3620.3620.0000.0000.0000.000
68D69GLU-1-0.884-0.91514.936-0.459-0.4590.0000.0000.0000.000
69D70VAL0-0.035-0.02117.4100.0270.0270.0000.0000.0000.000
70D71PRO0-0.0010.01621.1230.0000.0000.0000.0000.0000.000
71D72PHE00.1090.02021.6970.0020.0020.0000.0000.0000.000
72D73SER00.0110.01825.4090.0030.0030.0000.0000.0000.000
73D74TYR0-0.100-0.05325.5670.0090.0090.0000.0000.0000.000
74D75LEU0-0.022-0.01523.127-0.006-0.0060.0000.0000.0000.000
75D76ILE00.0150.03227.7700.0020.0020.0000.0000.0000.000
76D160SER00.0420.02123.9210.0100.0100.0000.0000.0000.000
77D161CYS0-0.130-0.06019.759-0.004-0.0040.0000.0000.0000.000
78D162SER0-0.010-0.01419.6190.0140.0140.0000.0000.0000.000
79D163PRO00.0340.00816.205-0.015-0.0150.0000.0000.0000.000
80D164TRP0-0.003-0.00414.3550.0020.0020.0000.0000.0000.000
81D165SER0-0.0150.0168.039-0.037-0.0370.0000.0000.0000.000
82D166LEU00.0210.00810.0860.0440.0440.0000.0000.0000.000
83D167GLN0-0.025-0.0335.671-0.294-0.2940.0000.0000.0000.000
84D168ILE00.0400.0236.9990.3680.3680.0000.0000.0000.000
85D169SER0-0.0070.0036.792-0.429-0.4290.0000.0000.0000.000
86D170ASP-1-0.893-0.9287.6650.1610.1610.0000.0000.0000.000
87D171ILE0-0.032-0.0049.494-0.191-0.1910.0000.0000.0000.000
88D172PRO0-0.033-0.01910.2570.0800.0800.0000.0000.0000.000
89D173ALA00.0530.02810.9080.1420.1420.0000.0000.0000.000
90D174ALA0-0.028-0.03212.685-0.061-0.0610.0000.0000.0000.000
91D175GLY00.0230.00516.4460.0450.0450.0000.0000.0000.000
92D176ASN0-0.038-0.01018.790-0.028-0.0280.0000.0000.0000.000
93D177ASN00.012-0.00421.3150.0080.0080.0000.0000.0000.000
94D178ARG10.9170.97314.3780.2820.2820.0000.0000.0000.000
95D179SER00.0060.00016.390-0.023-0.0230.0000.0000.0000.000
96D180VAL00.041-0.00411.649-0.034-0.0340.0000.0000.0000.000
97D181SER0-0.060-0.00811.3030.0160.0160.0000.0000.0000.000
98D182MET00.0490.0198.172-0.096-0.0960.0000.0000.0000.000
99D183GLN0-0.039-0.0316.2730.1330.1330.0000.0000.0000.000
100D184THR0-0.012-0.0303.503-1.408-1.0670.006-0.122-0.2250.000
101D185ILE0-0.009-0.0122.2070.1060.4953.528-1.355-2.5620.000
102D186ALA0-0.038-0.0162.207-8.856-8.4306.210-3.141-3.495-0.047
103D187GLU-1-0.882-0.9714.304-2.606-2.399-0.001-0.018-0.1890.000
104D188THR0-0.052-0.0165.7510.4770.4770.0000.0000.0000.000
105D189ILE00.0100.0058.894-0.094-0.0940.0000.0000.0000.000
106D190ILE0-0.031-0.00211.5780.1320.1320.0000.0000.0000.000
107D191LEU00.0370.00715.089-0.015-0.0150.0000.0000.0000.000
108D192SER0-0.041-0.01917.4950.0190.0190.0000.0000.0000.000
109D193SER00.002-0.01620.724-0.003-0.0030.0000.0000.0000.000
110D194ALA00.0320.00723.3270.0080.0080.0000.0000.0000.000
111D195GLY00.0140.01126.8350.0000.0000.0000.0000.0000.000
112D196LYS10.9330.95729.5950.0750.0750.0000.0000.0000.000
113D197ASN00.0240.01627.635-0.001-0.0010.0000.0000.0000.000
114D198SER00.0480.03425.475-0.010-0.0100.0000.0000.0000.000
115D199SER00.0700.07824.310-0.022-0.0220.0000.0000.0000.000
116D200VAL00.1050.03118.4830.0120.0120.0000.0000.0000.000
117D201SER00.014-0.00220.924-0.016-0.0160.0000.0000.0000.000
118D202SER0-0.023-0.02323.1550.0130.0130.0000.0000.0000.000
119D203LEU0-0.013-0.01520.3960.0110.0110.0000.0000.0000.000
120D204MET00.0180.03215.8980.0020.0020.0000.0000.0000.000
121D205ASN0-0.037-0.03020.1730.0210.0210.0000.0000.0000.000
122D206GLY0-0.052-0.01823.5160.0160.0160.0000.0000.0000.000
123D207LEU0-0.039-0.02416.6990.0190.0190.0000.0000.0000.000
124D208GLY0-0.0190.00320.5640.0080.0080.0000.0000.0000.000
125D209TYR0-0.065-0.04016.0280.0060.0060.0000.0000.0000.000
126D210VAL0-0.020-0.00321.0080.0170.0170.0000.0000.0000.000
127D211PHE00.0070.00521.132-0.032-0.0320.0000.0000.0000.000
128D212GLU-1-0.863-0.90820.115-0.319-0.3190.0000.0000.0000.000
129D213PHE00.0540.01217.6360.0130.0130.0000.0000.0000.000
130D214GLN00.0280.00319.268-0.063-0.0630.0000.0000.0000.000
131D215TYR0-0.015-0.00313.8790.0090.0090.0000.0000.0000.000
132D216LEU00.0190.01518.413-0.045-0.0450.0000.0000.0000.000
133D217THR0-0.065-0.01515.4430.0230.0230.0000.0000.0000.000
134D218ILE00.0400.01518.560-0.010-0.0100.0000.0000.0000.000
135D219GLY00.0350.00819.5270.0070.0070.0000.0000.0000.000
136D220VAL0-0.0060.00720.2500.0080.0080.0000.0000.0000.000
137D221LYS10.9270.96612.0160.6020.6020.0000.0000.0000.000
138D222PHE00.0360.01416.8650.0340.0340.0000.0000.0000.000
139D223PHE0-0.008-0.00812.551-0.046-0.0460.0000.0000.0000.000
140D224MET00.0410.02015.2080.0420.0420.0000.0000.0000.000
141D225LYS10.9640.96615.2260.0560.0560.0000.0000.0000.000
142D226HIS00.0130.02213.5120.0000.0000.0000.0000.0000.000
143D227GLY00.0250.02610.3930.0150.0150.0000.0000.0000.000
144D228LEU0-0.0160.00410.201-0.109-0.1090.0000.0000.0000.000
145D229ILE0-0.047-0.0119.9160.0430.0430.0000.0000.0000.000
146D230LEU00.023-0.01612.867-0.031-0.0310.0000.0000.0000.000
147D231GLU-1-0.941-0.97812.800-0.801-0.8010.0000.0000.0000.000
148D232LEU00.0230.01516.5790.0070.0070.0000.0000.0000.000
149D233GLN0-0.040-0.03913.9720.0160.0160.0000.0000.0000.000
150D234LYS10.8290.93519.5500.2740.2740.0000.0000.0000.000
151D235ILE00.002-0.01617.476-0.033-0.0330.0000.0000.0000.000
152D236TRP0-0.005-0.02021.0590.0320.0320.0000.0000.0000.000
153D237GLN00.0110.00622.195-0.049-0.0490.0000.0000.0000.000
154D238ILE0-0.059-0.03523.0500.0210.0210.0000.0000.0000.000
155D239GLU-1-0.914-0.96025.102-0.248-0.2480.0000.0000.0000.000
156D240GLU-1-0.894-0.95427.727-0.186-0.1860.0000.0000.0000.000
157D241ALA0-0.070-0.02631.2750.0090.0090.0000.0000.0000.000
158D242GLY00.0080.01130.9960.0090.0090.0000.0000.0000.000
159D243ASN0-0.022-0.02327.513-0.019-0.0190.0000.0000.0000.000
160D244SER00.0350.02427.3220.0080.0080.0000.0000.0000.000
161D245GLN00.0110.00225.464-0.027-0.0270.0000.0000.0000.000
162D246ILE00.0470.03121.4320.0130.0130.0000.0000.0000.000
163D247THR0-0.020-0.00321.230-0.003-0.0030.0000.0000.0000.000
164D248SER0-0.029-0.02224.2410.0130.0130.0000.0000.0000.000
165D249GLY00.0040.01427.9840.0040.0040.0000.0000.0000.000
166D250GLY00.0560.02626.8910.0140.0140.0000.0000.0000.000
167D251PHE0-0.048-0.01122.376-0.014-0.0140.0000.0000.0000.000
168D252LEU0-0.012-0.00216.3390.0130.0130.0000.0000.0000.000
169D253LEU0-0.021-0.01518.461-0.020-0.0200.0000.0000.0000.000
170D254LYS10.8750.9488.7811.2411.2410.0000.0000.0000.000
171D255ALA00.0320.03213.8290.0110.0110.0000.0000.0000.000
172D256TYR0-0.033-0.0397.201-0.102-0.1020.0000.0000.0000.000
173D257ILE00.0580.0386.9910.0960.0960.0000.0000.0000.000
174D258ASN00.0260.0182.608-1.248-0.7610.546-0.243-0.7890.002
175D259VAL00.0290.0123.220-0.0010.6580.054-0.175-0.537-0.001
176D260SER0-0.0030.0042.564-1.6900.2451.447-1.509-1.872-0.011
177D261ARG10.9560.9612.170-14.094-12.6178.104-3.856-5.7250.016
178D262GLY0-0.0030.0223.075-1.575-2.1790.2110.571-0.1790.000
179D263THR0-0.080-0.0555.502-0.574-0.5740.0000.0000.0000.000
180D264ASP-1-0.834-0.9147.6320.4900.4900.0000.0000.0000.000
181D265ILE00.0610.00711.221-0.065-0.0650.0000.0000.0000.000
182D266ASP-1-0.834-0.88612.7820.3060.3060.0000.0000.0000.000
183D267ARG10.9030.9438.580-0.798-0.7980.0000.0000.0000.000
184D268ILE00.0010.0167.280-0.096-0.0960.0000.0000.0000.000
185D269ASN00.0660.01610.841-0.090-0.0900.0000.0000.0000.000
186D270TYR0-0.055-0.04413.053-0.066-0.0660.0000.0000.0000.000
187D271THR0-0.009-0.0428.397-0.070-0.0700.0000.0000.0000.000
188D272GLU-1-0.892-0.94411.601-0.089-0.0890.0000.0000.0000.000
189D273THR0-0.052-0.01013.540-0.034-0.0340.0000.0000.0000.000
190D274VAL00.0210.01713.472-0.022-0.0220.0000.0000.0000.000
191D275LEU0-0.021-0.00810.578-0.024-0.0240.0000.0000.0000.000
192D276MET0-0.017-0.01314.913-0.011-0.0110.0000.0000.0000.000
193D277ASN0-0.068-0.04518.1430.0110.0110.0000.0000.0000.000
194D278LEU00.1090.06216.4860.0020.0020.0000.0000.0000.000
195D279LYS10.8870.95918.9350.1780.1780.0000.0000.0000.000
196D280LYS10.8290.91120.5430.0940.0940.0000.0000.0000.000
197D281GLU-1-0.957-0.98022.386-0.118-0.1180.0000.0000.0000.000
198D282LEU00.0230.01020.9630.0050.0050.0000.0000.0000.000
199D283GLN00.0140.00024.5710.0060.0060.0000.0000.0000.000
200D284GLY0-0.039-0.01626.2750.0070.0070.0000.0000.0000.000
201D285TYR0-0.021-0.00226.7230.0030.0030.0000.0000.0000.000
202D286ILE00.008-0.00922.766-0.008-0.0080.0000.0000.0000.000
203D287GLU-1-1.009-0.99023.810-0.188-0.1880.0000.0000.0000.000
204D288LEU00.0240.01917.711-0.019-0.0190.0000.0000.0000.000
205D289SER00.002-0.02119.3860.0200.0200.0000.0000.0000.000
206D290VAL0-0.023-0.00415.164-0.055-0.0550.0000.0000.0000.000
207D291PRO00.0020.01714.5060.0390.0390.0000.0000.0000.000
208D292ASP-1-0.818-0.92316.515-0.256-0.2560.0000.0000.0000.000
209D293ARG10.8850.94314.9660.1450.1450.0000.0000.0000.000
210D294GLN00.0320.00215.478-0.067-0.0670.0000.0000.0000.000
211D295SER0-0.053-0.02317.3570.0050.0050.0000.0000.0000.000
212D296MET0-0.086-0.04010.599-0.014-0.0140.0000.0000.0000.000
213D297ASP-1-0.772-0.88912.368-0.478-0.4780.0000.0000.0000.000
214D298SER0-0.016-0.01312.579-0.013-0.0130.0000.0000.0000.000
215D299ARG10.8500.91214.3560.2370.2370.0000.0000.0000.000
216D300VAL0-0.070-0.03616.4360.0020.0020.0000.0000.0000.000
217D301ALA00.0120.01619.8490.0390.0390.0000.0000.0000.000