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: 22Z3R

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2410512.69982
FMO2-HF: Nuclear repulsion 2325902.440774
FMO2-HF: Total energy -84610.259046
FMO2-MP2: Total energy -84856.697028


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.
-40.629-36.85428.568-14.741-17.6-0.027
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 : -0.015
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].
3D4GLN00.0260.0162.644-2.1490.6540.832-1.494-2.141-0.013
4D5LEU0-0.003-0.0014.7380.3770.447-0.001-0.011-0.0580.000
5D6SER0-0.016-0.0238.0950.0440.0440.0000.0000.0000.000
6D7LEU00.0000.00710.9510.0820.0820.0000.0000.0000.000
7D8PHE00.018-0.00411.752-0.055-0.0550.0000.0000.0000.000
8D9GLY00.0560.02316.8790.0440.0440.0000.0000.0000.000
9D10SER0-0.077-0.02820.343-0.018-0.0180.0000.0000.0000.000
10D11ILE00.0190.02422.9820.0150.0150.0000.0000.0000.000
11D12GLY00.0660.03526.318-0.010-0.0100.0000.0000.0000.000
12D13ASP-1-0.801-0.90828.055-0.222-0.2220.0000.0000.0000.000
13D14ASP-1-0.927-0.96129.861-0.152-0.1520.0000.0000.0000.000
14D15GLY0-0.034-0.01329.9870.0080.0080.0000.0000.0000.000
15D16TYR0-0.019-0.01424.471-0.014-0.0140.0000.0000.0000.000
16D17ASP-1-0.845-0.93127.933-0.178-0.1780.0000.0000.0000.000
17D18LEU00.0030.02029.8260.0020.0020.0000.0000.0000.000
18D19LEU00.0450.04523.1460.0000.0000.0000.0000.0000.000
19D20ILE00.0170.00523.732-0.010-0.0100.0000.0000.0000.000
20D21SER0-0.021-0.01125.9240.0020.0020.0000.0000.0000.000
21D22THR0-0.038-0.02625.8750.0080.0080.0000.0000.0000.000
22D23LEU00.021-0.00320.3800.0020.0020.0000.0000.0000.000
23D24THR0-0.013-0.00122.964-0.006-0.0060.0000.0000.0000.000
24D25THR0-0.061-0.03225.1130.0100.0100.0000.0000.0000.000
25D26ILE0-0.050-0.00621.4790.0090.0090.0000.0000.0000.000
26D27SER0-0.057-0.04820.3110.0030.0030.0000.0000.0000.000
27D28GLY0-0.0280.00021.7460.0050.0050.0000.0000.0000.000
28D29ASN0-0.079-0.04721.4870.0140.0140.0000.0000.0000.000
29D30PRO00.0420.02123.403-0.008-0.0080.0000.0000.0000.000
30D31PRO0-0.0110.00621.858-0.016-0.0160.0000.0000.0000.000
31D32LEU0-0.012-0.01218.0660.0130.0130.0000.0000.0000.000
32D33LEU0-0.0010.00019.641-0.034-0.0340.0000.0000.0000.000
33D34TYR0-0.086-0.05714.3790.0160.0160.0000.0000.0000.000
34D35ASN0-0.003-0.02417.798-0.001-0.0010.0000.0000.0000.000
35D36SER0-0.021-0.00414.138-0.061-0.0610.0000.0000.0000.000
36D37LEU00.0360.03016.1680.0200.0200.0000.0000.0000.000
37D38CYS0-0.042-0.00713.338-0.124-0.1240.0000.0000.0000.000
38D39THR00.0350.02715.4790.0530.0530.0000.0000.0000.000
39D40VAL0-0.013-0.01015.272-0.069-0.0690.0000.0000.0000.000
40D41TRP00.002-0.01216.0350.0860.0860.0000.0000.0000.000
41D42LYS10.8870.92716.6580.1530.1530.0000.0000.0000.000
42D43PRO00.0710.03018.3690.0090.0090.0000.0000.0000.000
43D44ASN00.0230.01521.116-0.013-0.0130.0000.0000.0000.000
44D45PRO00.0140.01124.5790.0110.0110.0000.0000.0000.000
45D46SER0-0.059-0.03626.8770.0090.0090.0000.0000.0000.000
46D47TYR0-0.106-0.05825.3730.0070.0070.0000.0000.0000.000
47D48ASP-1-0.847-0.91726.075-0.036-0.0360.0000.0000.0000.000
48D49VAL0-0.063-0.03423.3970.0090.0090.0000.0000.0000.000
49D50GLU-1-0.905-0.94625.3700.0580.0580.0000.0000.0000.000
50D51ASN0-0.015-0.00121.663-0.001-0.0010.0000.0000.0000.000
51D52VAL0-0.029-0.01421.4150.0150.0150.0000.0000.0000.000
52D53ASN00.0360.02018.4170.0100.0100.0000.0000.0000.000
53D54SER0-0.005-0.00321.419-0.005-0.0050.0000.0000.0000.000
54D55ARG10.8790.93118.250-0.358-0.3580.0000.0000.0000.000
55D56ASN00.0400.01122.6590.0100.0100.0000.0000.0000.000
56D57GLN0-0.029-0.00518.2360.0070.0070.0000.0000.0000.000
57D58LEU00.0480.02118.881-0.003-0.0030.0000.0000.0000.000
58D59VAL0-0.046-0.03715.7510.0510.0510.0000.0000.0000.000
59D60GLU-1-0.840-0.89116.177-0.060-0.0600.0000.0000.0000.000
60D61PRO00.0240.02816.237-0.004-0.0040.0000.0000.0000.000
61D62ASN00.0280.01011.187-0.069-0.0690.0000.0000.0000.000
62D63ARG10.8170.89014.3120.3480.3480.0000.0000.0000.000
63D64ILE0-0.026-0.00811.794-0.053-0.0530.0000.0000.0000.000
64D65LYS10.8780.9359.2031.2091.2090.0000.0000.0000.000
65D66LEU0-0.0060.00411.278-0.112-0.1120.0000.0000.0000.000
66D67SER0-0.076-0.05811.1160.0130.0130.0000.0000.0000.000
67D68LYS10.8610.92112.9370.3320.3320.0000.0000.0000.000
68D69GLU-1-0.810-0.88914.641-0.404-0.4040.0000.0000.0000.000
69D70VAL00.0100.00317.1150.0280.0280.0000.0000.0000.000
70D71PRO0-0.0020.01920.845-0.003-0.0030.0000.0000.0000.000
71D72PHE00.1050.01921.4740.0080.0080.0000.0000.0000.000
72D73SER00.0000.02025.3750.0020.0020.0000.0000.0000.000
73D74TYR0-0.049-0.03525.1650.0080.0080.0000.0000.0000.000
74D75LEU0-0.029-0.00222.641-0.001-0.0010.0000.0000.0000.000
75D76ILE0-0.030-0.00427.3510.0080.0080.0000.0000.0000.000
76D160SER00.0150.01223.2110.0100.0100.0000.0000.0000.000
77D161CYS0-0.140-0.06620.616-0.011-0.0110.0000.0000.0000.000
78D162SER00.0480.01119.4250.0130.0130.0000.0000.0000.000
79D163PRO00.0350.00615.999-0.002-0.0020.0000.0000.0000.000
80D164TRP0-0.028-0.02014.148-0.002-0.0020.0000.0000.0000.000
81D165SER0-0.043-0.0257.7230.0490.0490.0000.0000.0000.000
82D166LEU00.0030.0029.8360.0750.0750.0000.0000.0000.000
83D167GLN0-0.016-0.0295.0930.2140.2140.0000.0000.0000.000
84D168ILE00.0400.0146.7680.3020.3020.0000.0000.0000.000
85D169SER0-0.0200.0056.618-0.393-0.3930.0000.0000.0000.000
86D170ASP-1-0.870-0.9237.4350.2570.2570.0000.0000.0000.000
87D171ILE0-0.014-0.0069.519-0.190-0.1900.0000.0000.0000.000
88D172PRO0-0.025-0.01210.3640.0520.0520.0000.0000.0000.000
89D173ALA00.0120.01211.1380.1560.1560.0000.0000.0000.000
90D174ALA0-0.017-0.01912.858-0.027-0.0270.0000.0000.0000.000
91D175GLY00.0290.01016.6440.0370.0370.0000.0000.0000.000
92D176ASN0-0.046-0.01819.076-0.032-0.0320.0000.0000.0000.000
93D177ASN00.010-0.01320.746-0.003-0.0030.0000.0000.0000.000
94D178ARG10.8560.94614.3880.3510.3510.0000.0000.0000.000
95D179SER00.004-0.02715.710-0.025-0.0250.0000.0000.0000.000
96D180VAL00.028-0.00111.616-0.025-0.0250.0000.0000.0000.000
97D181SER0-0.011-0.02311.9090.0640.0640.0000.0000.0000.000
98D182MET00.0150.0267.724-0.121-0.1210.0000.0000.0000.000
99D183GLN0-0.031-0.0236.5960.1800.1800.0000.0000.0000.000
100D184THR00.005-0.0034.330-1.241-1.105-0.001-0.045-0.0890.000
101D185ILE00.0230.0072.369-0.5040.5771.821-0.869-2.0330.001
102D186ALA0-0.0130.0041.913-6.942-8.6258.265-3.562-3.020-0.043
103D187GLU-1-0.818-0.8804.222-3.314-3.0130.000-0.041-0.2600.000
104D188THR0-0.037-0.0135.5980.5190.5190.0000.0000.0000.000
105D189ILE00.0160.0078.261-0.136-0.1360.0000.0000.0000.000
106D190ILE00.0070.01411.5000.1210.1210.0000.0000.0000.000
107D191LEU00.002-0.00414.964-0.037-0.0370.0000.0000.0000.000
108D192SER00.0370.01817.4330.0050.0050.0000.0000.0000.000
109D193SER0-0.058-0.04320.6040.0030.0030.0000.0000.0000.000
110D194ALA00.0390.01123.1660.0020.0020.0000.0000.0000.000
111D195GLY00.0310.01326.7530.0020.0020.0000.0000.0000.000
112D196LYS10.9230.93829.4260.0300.0300.0000.0000.0000.000
113D197ASN00.0060.00527.5420.0070.0070.0000.0000.0000.000
114D198SER00.0520.04725.200-0.008-0.0080.0000.0000.0000.000
115D199SER00.0380.03523.931-0.020-0.0200.0000.0000.0000.000
116D200VAL00.0940.02518.1730.0130.0130.0000.0000.0000.000
117D201SER00.0330.02320.562-0.010-0.0100.0000.0000.0000.000
118D202SER0-0.039-0.00722.7090.0070.0070.0000.0000.0000.000
119D203LEU0-0.017-0.00219.7500.0160.0160.0000.0000.0000.000
120D204MET00.0130.01915.6570.0150.0150.0000.0000.0000.000
121D205ASN0-0.036-0.03019.9690.0150.0150.0000.0000.0000.000
122D206GLY0-0.025-0.00423.3110.0150.0150.0000.0000.0000.000
123D207LEU0-0.039-0.02316.2720.0200.0200.0000.0000.0000.000
124D208GLY00.0060.01920.1960.0070.0070.0000.0000.0000.000
125D209TYR0-0.054-0.04216.0040.0110.0110.0000.0000.0000.000
126D210VAL0-0.038-0.02120.8860.0110.0110.0000.0000.0000.000
127D211PHE00.0300.01920.788-0.025-0.0250.0000.0000.0000.000
128D212GLU-1-0.829-0.87520.238-0.236-0.2360.0000.0000.0000.000
129D213PHE00.0310.00617.7610.0100.0100.0000.0000.0000.000
130D214GLN0-0.020-0.01719.257-0.041-0.0410.0000.0000.0000.000
131D215TYR00.0150.00513.4020.0150.0150.0000.0000.0000.000
132D216LEU00.0070.00818.303-0.032-0.0320.0000.0000.0000.000
133D217THR0-0.025-0.01714.9520.0350.0350.0000.0000.0000.000
134D218ILE00.021-0.00718.412-0.005-0.0050.0000.0000.0000.000
135D219GLY00.0400.02019.5310.0080.0080.0000.0000.0000.000
136D220VAL0-0.0190.00420.2740.0100.0100.0000.0000.0000.000
137D221LYS10.8450.91811.5750.6900.6900.0000.0000.0000.000
138D222PHE00.0410.02416.8500.0350.0350.0000.0000.0000.000
139D223PHE00.0040.00112.098-0.059-0.0590.0000.0000.0000.000
140D224MET00.0200.00714.9430.0400.0400.0000.0000.0000.000
141D225LYS10.9720.97615.1090.1200.1200.0000.0000.0000.000
142D226HIS00.0230.00313.798-0.018-0.0180.0000.0000.0000.000
143D227GLY00.0170.02310.5240.0000.0000.0000.0000.0000.000
144D228LEU0-0.032-0.00810.234-0.119-0.1190.0000.0000.0000.000
145D229ILE0-0.049-0.0159.5690.0500.0500.0000.0000.0000.000
146D230LEU00.0310.00212.517-0.035-0.0350.0000.0000.0000.000
147D231GLU-1-0.814-0.86612.482-0.799-0.7990.0000.0000.0000.000
148D232LEU00.0320.02016.7080.0050.0050.0000.0000.0000.000
149D233GLN0-0.007-0.00114.3210.0020.0020.0000.0000.0000.000
150D234LYS10.7820.87819.7350.2600.2600.0000.0000.0000.000
151D235ILE00.007-0.01617.296-0.024-0.0240.0000.0000.0000.000
152D236TRP0-0.028-0.01921.1210.0270.0270.0000.0000.0000.000
153D237GLN0-0.018-0.01722.012-0.050-0.0500.0000.0000.0000.000
154D238ILE0-0.063-0.03023.0260.0190.0190.0000.0000.0000.000
155D239GLU-1-0.843-0.90025.000-0.215-0.2150.0000.0000.0000.000
156D240GLU-1-0.893-0.95627.562-0.157-0.1570.0000.0000.0000.000
157D241ALA0-0.034-0.00630.9060.0090.0090.0000.0000.0000.000
158D242GLY0-0.015-0.00530.6960.0070.0070.0000.0000.0000.000
159D243ASN0-0.008-0.01127.501-0.015-0.0150.0000.0000.0000.000
160D244SER00.0280.00727.140-0.001-0.0010.0000.0000.0000.000
161D245GLN00.0280.00325.462-0.024-0.0240.0000.0000.0000.000
162D246ILE00.0340.01621.2490.0110.0110.0000.0000.0000.000
163D247THR0-0.031-0.00321.422-0.004-0.0040.0000.0000.0000.000
164D248SER0-0.017-0.00724.4660.0100.0100.0000.0000.0000.000
165D249GLY00.0130.01628.3030.0050.0050.0000.0000.0000.000
166D250GLY00.0250.00926.7490.0110.0110.0000.0000.0000.000
167D251PHE0-0.0170.01222.585-0.013-0.0130.0000.0000.0000.000
168D252LEU0-0.006-0.00116.3860.0080.0080.0000.0000.0000.000
169D253LEU0-0.0030.00018.815-0.015-0.0150.0000.0000.0000.000
170D254LYS10.8460.9278.6971.2151.2150.0000.0000.0000.000
171D255ALA00.0500.03013.9130.0160.0160.0000.0000.0000.000
172D256TYR0-0.067-0.0847.259-0.120-0.1200.0000.0000.0000.000
173D257ILE00.0720.0526.9560.0960.0960.0000.0000.0000.000
174D258ASN00.0020.0112.625-1.669-1.0640.362-0.234-0.7320.001
175D259VAL00.0300.0102.890-0.0090.7220.096-0.227-0.6000.000
176D260SER00.0330.0152.593-2.267-0.6911.963-1.508-2.031-0.016
177D261ARG10.8620.8991.944-22.771-24.38915.087-7.004-6.4650.043
178D262GLY00.0150.0273.222-1.552-1.7790.1440.254-0.1710.000
179D263THR0-0.096-0.0545.473-0.462-0.4620.0000.0000.0000.000
180D264ASP-1-0.855-0.9397.7100.3210.3210.0000.0000.0000.000
181D265ILE00.0690.02411.330-0.077-0.0770.0000.0000.0000.000
182D266ASP-1-0.831-0.89713.3960.1060.1060.0000.0000.0000.000
183D267ARG10.8990.9468.789-0.501-0.5010.0000.0000.0000.000
184D268ILE0-0.0130.0107.831-0.139-0.1390.0000.0000.0000.000
185D269ASN00.025-0.00511.046-0.067-0.0670.0000.0000.0000.000
186D270TYR0-0.025-0.00113.197-0.039-0.0390.0000.0000.0000.000
187D271THR0-0.020-0.0398.205-0.066-0.0660.0000.0000.0000.000
188D272GLU-1-0.827-0.87911.562-0.180-0.1800.0000.0000.0000.000
189D273THR0-0.044-0.02413.658-0.008-0.0080.0000.0000.0000.000
190D274VAL00.0090.00813.539-0.005-0.0050.0000.0000.0000.000
191D275LEU0-0.025-0.01210.907-0.009-0.0090.0000.0000.0000.000
192D276MET00.005-0.00314.9650.0080.0080.0000.0000.0000.000
193D277ASN0-0.075-0.03318.2030.0210.0210.0000.0000.0000.000
194D278LEU00.0710.04216.6100.0070.0070.0000.0000.0000.000
195D279LYS10.8000.88518.9480.2490.2490.0000.0000.0000.000
196D280LYS10.8020.88520.6100.1490.1490.0000.0000.0000.000
197D281GLU-1-0.918-0.95822.020-0.177-0.1770.0000.0000.0000.000
198D282LEU00.0350.01821.0800.0080.0080.0000.0000.0000.000
199D283GLN00.0420.02524.5320.0110.0110.0000.0000.0000.000
200D284GLY0-0.045-0.02126.3060.0100.0100.0000.0000.0000.000
201D285TYR0-0.076-0.03426.5710.0060.0060.0000.0000.0000.000
202D286ILE0-0.002-0.01823.267-0.004-0.0040.0000.0000.0000.000
203D287GLU-1-0.790-0.86022.876-0.233-0.2330.0000.0000.0000.000
204D288LEU00.0150.00517.537-0.021-0.0210.0000.0000.0000.000
205D289SER0-0.013-0.01719.6280.0140.0140.0000.0000.0000.000
206D290VAL0-0.034-0.01015.435-0.058-0.0580.0000.0000.0000.000
207D291PRO0-0.0160.00614.2910.0410.0410.0000.0000.0000.000
208D292ASP-1-0.749-0.87416.421-0.281-0.2810.0000.0000.0000.000
209D293ARG10.8680.93114.9620.1770.1770.0000.0000.0000.000
210D294GLN00.0340.00615.486-0.047-0.0470.0000.0000.0000.000
211D295SER0-0.061-0.04817.635-0.007-0.0070.0000.0000.0000.000
212D296MET0-0.074-0.01810.439-0.014-0.0140.0000.0000.0000.000
213D297ASP-1-0.781-0.87212.443-0.400-0.4000.0000.0000.0000.000
214D298SER0-0.007-0.00912.189-0.024-0.0240.0000.0000.0000.000
215D299ARG10.7790.84814.4650.1910.1910.0000.0000.0000.000
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