FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: J3599

Calculation Name: 3VX8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX8

Chain ID: D

ChEMBL ID:

UniProt ID: Q0WWQ1

Base Structure: X-ray

Registration Date: 2023-06-20

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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4475933.772921
FMO2-HF: Nuclear repulsion 4357145.81594
FMO2-HF: Total energy -118787.956981
FMO2-MP2: Total energy -119138.226535


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:9:ILE)


Summations of interaction energy for fragment #1(D:9:ILE)
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.
-8.816-2.7481.748-2.819-4.997-0.013
Interaction energy analysis for fragmet #1(D:9:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.002
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].
3D11LEU00.0260.0052.749-3.620-0.8810.468-1.491-1.716-0.008
4D12GLN0-0.041-0.0224.6850.4800.635-0.001-0.005-0.1490.000
5D13PHE00.0480.0216.643-0.056-0.0560.0000.0000.0000.000
6D14ALA00.0270.01310.0970.1150.1150.0000.0000.0000.000
7D15PRO0-0.063-0.04512.6920.0070.0070.0000.0000.0000.000
8D16LEU00.0470.03115.859-0.011-0.0110.0000.0000.0000.000
9D17ASN0-0.073-0.02418.9720.0400.0400.0000.0000.0000.000
10D18SER0-0.029-0.04022.148-0.009-0.0090.0000.0000.0000.000
11D19SER0-0.020-0.01225.8820.0040.0040.0000.0000.0000.000
12D20VAL0-0.015-0.00928.907-0.002-0.0020.0000.0000.0000.000
13D21ASP-1-0.817-0.89832.483-0.052-0.0520.0000.0000.0000.000
14D22GLU-1-0.910-0.97035.550-0.032-0.0320.0000.0000.0000.000
15D23GLY00.0800.03738.8350.0040.0040.0000.0000.0000.000
16D24PHE00.0000.02335.6180.0030.0030.0000.0000.0000.000
17D25TRP00.0430.00834.3670.0040.0040.0000.0000.0000.000
18D26HIS0-0.0180.01939.7130.0030.0030.0000.0000.0000.000
19D27SER00.0130.00041.2180.0020.0020.0000.0000.0000.000
20D28PHE00.009-0.00739.5600.0020.0020.0000.0000.0000.000
21D29SER0-0.039-0.04041.7100.0040.0040.0000.0000.0000.000
22D30SER00.0190.00444.3380.0020.0020.0000.0000.0000.000
23D31LEU0-0.0040.00742.1110.0010.0010.0000.0000.0000.000
24D32LYS10.7770.85143.7420.0090.0090.0000.0000.0000.000
25D33LEU0-0.052-0.03445.7460.0020.0020.0000.0000.0000.000
26D34ASP-1-0.912-0.95249.268-0.018-0.0180.0000.0000.0000.000
27D35LYS10.8830.94645.9560.0240.0240.0000.0000.0000.000
28D36LEU0-0.045-0.00943.0660.0010.0010.0000.0000.0000.000
29D37GLY00.0580.03947.6920.0020.0020.0000.0000.0000.000
30D38ILE0-0.022-0.01448.1760.0000.0000.0000.0000.0000.000
31D39ASP-1-0.816-0.88045.223-0.007-0.0070.0000.0000.0000.000
32D40ASP-1-0.854-0.93241.7780.0010.0010.0000.0000.0000.000
33D41SER0-0.037-0.03240.9080.0020.0020.0000.0000.0000.000
34D42PRO0-0.091-0.04136.549-0.002-0.0020.0000.0000.0000.000
35D43ILE00.0080.00337.625-0.001-0.0010.0000.0000.0000.000
36D44SER0-0.018-0.01235.436-0.001-0.0010.0000.0000.0000.000
37D45ILE0-0.047-0.02432.3390.0010.0010.0000.0000.0000.000
38D46THR00.0040.00932.818-0.003-0.0030.0000.0000.0000.000
39D47GLY0-0.022-0.00429.4940.0030.0030.0000.0000.0000.000
40D48PHE00.007-0.00429.728-0.003-0.0030.0000.0000.0000.000
41D49TYR0-0.039-0.02121.5370.0090.0090.0000.0000.0000.000
42D50GLY00.0680.04125.0910.0070.0070.0000.0000.0000.000
43D51PRO00.0240.02422.017-0.008-0.0080.0000.0000.0000.000
44D52CYS0-0.067-0.01320.0110.0290.0290.0000.0000.0000.000
45D53GLY00.0520.04022.093-0.009-0.0090.0000.0000.0000.000
46D54HIS00.001-0.01223.5750.0050.0050.0000.0000.0000.000
47D55PRO00.0510.02320.758-0.011-0.0110.0000.0000.0000.000
48D56GLN0-0.047-0.03719.976-0.008-0.0080.0000.0000.0000.000
49D57VAL0-0.041-0.02221.9180.0130.0130.0000.0000.0000.000
50D58SER0-0.015-0.02119.155-0.002-0.0020.0000.0000.0000.000
51D59ASN0-0.023-0.00221.1950.0340.0340.0000.0000.0000.000
52D60HIS0-0.038-0.03521.881-0.003-0.0030.0000.0000.0000.000
53D61LEU0-0.0180.00723.856-0.002-0.0020.0000.0000.0000.000
54D62THR0-0.071-0.05725.4580.0130.0130.0000.0000.0000.000
55D63LEU0-0.005-0.01029.099-0.001-0.0010.0000.0000.0000.000
56D64LEU00.0370.01432.4770.0020.0020.0000.0000.0000.000
57D65SER00.023-0.00336.0430.0020.0020.0000.0000.0000.000
58D66GLU-1-0.857-0.94337.530-0.063-0.0630.0000.0000.0000.000
59D67SER0-0.032-0.00933.894-0.002-0.0020.0000.0000.0000.000
60D68LEU0-0.036-0.01036.2860.0030.0030.0000.0000.0000.000
61D69PRO0-0.0090.00539.3610.0000.0000.0000.0000.0000.000
62D82GLY00.0560.03335.4230.0030.0030.0000.0000.0000.000
63D83ASN0-0.118-0.09234.215-0.001-0.0010.0000.0000.0000.000
64D84ARG10.8620.91431.0070.1420.1420.0000.0000.0000.000
65D85ASN0-0.031-0.01329.921-0.015-0.0150.0000.0000.0000.000
66D86LYS10.8150.91230.2850.0830.0830.0000.0000.0000.000
67D87CYS00.0220.02127.4740.0040.0040.0000.0000.0000.000
68D88PRO00.017-0.00228.9920.0000.0000.0000.0000.0000.000
69D89VAL00.0080.01625.914-0.008-0.0080.0000.0000.0000.000
70D90PRO0-0.0050.01528.4730.0100.0100.0000.0000.0000.000
71D91GLY00.0510.00529.002-0.004-0.0040.0000.0000.0000.000
72D92ILE0-0.087-0.04030.5400.0050.0050.0000.0000.0000.000
73D93LEU00.0130.01431.8810.0000.0000.0000.0000.0000.000
74D94TYR0-0.005-0.01632.6100.0040.0040.0000.0000.0000.000
75D95ASN00.0340.02035.7470.0010.0010.0000.0000.0000.000
76D96THR0-0.009-0.00837.9950.0000.0000.0000.0000.0000.000
77D97ASN00.003-0.00640.473-0.003-0.0030.0000.0000.0000.000
78D98THR0-0.067-0.04342.7300.0000.0000.0000.0000.0000.000
79D99VAL00.0560.03339.3120.0000.0000.0000.0000.0000.000
80D100GLU-1-0.848-0.91639.2990.0190.0190.0000.0000.0000.000
81D101SER0-0.016-0.01539.9100.0040.0040.0000.0000.0000.000
82D102PHE00.0180.02632.4710.0030.0030.0000.0000.0000.000
83D103ASN0-0.023-0.01235.2830.0020.0020.0000.0000.0000.000
84D104LYS10.9340.95535.064-0.029-0.0290.0000.0000.0000.000
85D105LEU00.0310.04633.9580.0030.0030.0000.0000.0000.000
86D106ASP-1-0.760-0.84331.1530.0530.0530.0000.0000.0000.000
87D107LYS10.8370.90528.065-0.037-0.0370.0000.0000.0000.000
88D108GLN00.0040.00925.6780.0020.0020.0000.0000.0000.000
89D109SER0-0.020-0.04727.506-0.006-0.0060.0000.0000.0000.000
90D110LEU00.0410.02329.957-0.005-0.0050.0000.0000.0000.000
91D111LEU0-0.009-0.00322.083-0.008-0.0080.0000.0000.0000.000
92D112LYS10.8930.94023.820-0.101-0.1010.0000.0000.0000.000
93D113ALA00.0320.02226.598-0.005-0.0050.0000.0000.0000.000
94D114GLU-1-0.769-0.87227.507-0.028-0.0280.0000.0000.0000.000
95D115ALA00.0290.01723.387-0.011-0.0110.0000.0000.0000.000
96D116ASN0-0.042-0.02225.204-0.010-0.0100.0000.0000.0000.000
97D117LYS10.8830.93427.6040.0160.0160.0000.0000.0000.000
98D118ILE00.0330.02822.942-0.004-0.0040.0000.0000.0000.000
99D119TRP0-0.021-0.02220.810-0.015-0.0150.0000.0000.0000.000
100D120GLU-1-0.867-0.93025.771-0.034-0.0340.0000.0000.0000.000
101D121ASP-1-0.846-0.90028.059-0.063-0.0630.0000.0000.0000.000
102D122ILE0-0.056-0.01721.977-0.011-0.0110.0000.0000.0000.000
103D123GLN00.0120.00723.814-0.009-0.0090.0000.0000.0000.000
104D124SER0-0.065-0.05027.883-0.002-0.0020.0000.0000.0000.000
105D125GLY00.0290.02028.763-0.001-0.0010.0000.0000.0000.000
106D126LYS10.8500.90829.8130.0420.0420.0000.0000.0000.000
107D127ALA0-0.027-0.02325.586-0.004-0.0040.0000.0000.0000.000
108D128LEU0-0.077-0.02526.355-0.017-0.0170.0000.0000.0000.000
109D129GLU-1-0.877-0.93328.023-0.095-0.0950.0000.0000.0000.000
110D130ASP-1-0.783-0.87029.812-0.117-0.1170.0000.0000.0000.000
111D131PRO0-0.0070.01524.4790.0040.0040.0000.0000.0000.000
112D132SER0-0.063-0.06825.086-0.008-0.0080.0000.0000.0000.000
113D133VAL0-0.002-0.01326.6860.0030.0030.0000.0000.0000.000
114D134LEU0-0.0110.00621.1780.0070.0070.0000.0000.0000.000
115D135PRO0-0.072-0.03321.5110.0020.0020.0000.0000.0000.000
116D136ARG10.8960.94522.4860.0640.0640.0000.0000.0000.000
117D137PHE0-0.055-0.02323.8950.0010.0010.0000.0000.0000.000
118D138LEU0-0.034-0.00726.0940.0060.0060.0000.0000.0000.000
119D139VAL0-0.0100.00227.784-0.001-0.0010.0000.0000.0000.000
120D140ILE0-0.0050.01430.1730.0040.0040.0000.0000.0000.000
121D141SER0-0.024-0.06532.526-0.002-0.0020.0000.0000.0000.000
122D142PHE0-0.0140.00435.2700.0030.0030.0000.0000.0000.000
123D143ALA00.0620.02638.486-0.002-0.0020.0000.0000.0000.000
124D144ASP-1-0.804-0.88041.0620.0000.0000.0000.0000.0000.000
125D145LEU00.018-0.00743.949-0.001-0.0010.0000.0000.0000.000
126D146LYS10.8970.94846.4540.0010.0010.0000.0000.0000.000
127D147LYS10.8240.90445.212-0.002-0.0020.0000.0000.0000.000
128D148TRP00.0510.03244.5060.0000.0000.0000.0000.0000.000
129D149SER0-0.0190.00240.810-0.001-0.0010.0000.0000.0000.000
130D150PHE00.0300.02037.6480.0020.0020.0000.0000.0000.000
131D151ARG10.8660.92033.968-0.016-0.0160.0000.0000.0000.000
132D152TYR00.0450.01229.4530.0030.0030.0000.0000.0000.000
133D153TRP0-0.060-0.05124.9080.0080.0080.0000.0000.0000.000
134D154PHE00.0970.05125.3980.0020.0020.0000.0000.0000.000
135D155ALA0-0.011-0.01623.5910.0100.0100.0000.0000.0000.000
136D156PHE00.0410.01520.271-0.006-0.0060.0000.0000.0000.000
137D157PRO0-0.047-0.02020.135-0.004-0.0040.0000.0000.0000.000
138D158ALA00.0570.04016.762-0.013-0.0130.0000.0000.0000.000
139D159PHE00.0250.00217.6220.0330.0330.0000.0000.0000.000
140D160VAL0-0.072-0.02813.527-0.045-0.0450.0000.0000.0000.000
141D161LEU0-0.023-0.01212.8810.0240.0240.0000.0000.0000.000
142D162ASP-1-0.761-0.85413.4920.2310.2310.0000.0000.0000.000
143D163PRO00.0080.01311.0110.1170.1170.0000.0000.0000.000
144D164PRO0-0.059-0.0328.034-0.140-0.1400.0000.0000.0000.000
145D165VAL00.0350.0247.8320.2110.2110.0000.0000.0000.000
146D166SER00.0170.0162.944-0.1410.4370.042-0.194-0.4260.000
147D167LEU0-0.045-0.0242.580-0.4450.7661.187-0.484-1.914-0.001
148D168ILE0-0.039-0.0113.412-3.557-2.3010.053-0.642-0.668-0.004
149D169GLU-1-0.843-0.9294.843-1.140-1.011-0.001-0.003-0.1240.000
150D170LEU0-0.051-0.0296.7750.0640.0640.0000.0000.0000.000
151D171LYS10.8330.9308.9310.8430.8430.0000.0000.0000.000
152D172PRO00.0450.02312.1890.0110.0110.0000.0000.0000.000
153D173ALA00.0080.00415.477-0.018-0.0180.0000.0000.0000.000
154D174SER0-0.019-0.04817.8780.0080.0080.0000.0000.0000.000
155D175GLU-1-0.927-0.92715.138-0.408-0.4080.0000.0000.0000.000
156D176TYR0-0.066-0.03614.559-0.026-0.0260.0000.0000.0000.000
157D177PHE0-0.037-0.01617.0070.0160.0160.0000.0000.0000.000
158D178SER00.0360.01920.6950.0100.0100.0000.0000.0000.000
159D179SER00.019-0.01523.5630.0020.0020.0000.0000.0000.000
160D180GLU-1-0.868-0.92326.158-0.178-0.1780.0000.0000.0000.000
161D181GLU-1-0.756-0.86222.616-0.326-0.3260.0000.0000.0000.000
162D182ALA0-0.026-0.00723.8450.0000.0000.0000.0000.0000.000
163D183GLU-1-0.907-0.94425.169-0.173-0.1730.0000.0000.0000.000
164D184SER00.0120.01428.4080.0090.0090.0000.0000.0000.000
165D185VAL00.003-0.01323.3980.0080.0080.0000.0000.0000.000
166D186SER0-0.007-0.00926.569-0.002-0.0020.0000.0000.0000.000
167D187ALA0-0.040-0.01327.7960.0090.0090.0000.0000.0000.000
168D188ALA00.0650.03828.3800.0050.0050.0000.0000.0000.000
169D189CYS0-0.098-0.04825.402-0.006-0.0060.0000.0000.0000.000
170D190ASN00.021-0.00628.0490.0040.0040.0000.0000.0000.000
171D191ASP-1-0.872-0.93531.010-0.142-0.1420.0000.0000.0000.000
172D192TRP0-0.049-0.02527.9500.0100.0100.0000.0000.0000.000
173D193ARG10.7340.84227.3060.1810.1810.0000.0000.0000.000
174D194ASP-1-0.827-0.89831.369-0.128-0.1280.0000.0000.0000.000
175D195SER0-0.033-0.01134.6660.0130.0130.0000.0000.0000.000
176D196ASP-1-0.849-0.92334.835-0.100-0.1000.0000.0000.0000.000
177D197LEU0-0.056-0.03035.625-0.002-0.0020.0000.0000.0000.000
178D198THR0-0.028-0.01931.4290.0010.0010.0000.0000.0000.000
179D199THR0-0.0170.00630.671-0.010-0.0100.0000.0000.0000.000
180D200ASP-1-0.883-0.94929.540-0.126-0.1260.0000.0000.0000.000
181D201VAL00.0330.03527.7280.0020.0020.0000.0000.0000.000
182D202PRO0-0.021-0.01423.859-0.013-0.0130.0000.0000.0000.000
183D203PHE0-0.018-0.03619.249-0.029-0.0290.0000.0000.0000.000
184D204PHE00.0140.01622.8040.0150.0150.0000.0000.0000.000
185D205LEU00.0170.01021.788-0.032-0.0320.0000.0000.0000.000
186D206VAL0-0.002-0.00621.6930.0200.0200.0000.0000.0000.000
187D207SER0-0.017-0.01222.977-0.012-0.0120.0000.0000.0000.000
188D208VAL00.012-0.01323.6270.0140.0140.0000.0000.0000.000
189D209SER00.0520.03925.960-0.005-0.0050.0000.0000.0000.000
190D210SER0-0.019-0.05126.850-0.015-0.0150.0000.0000.0000.000
191D211ASP-1-0.923-0.95128.013-0.149-0.1490.0000.0000.0000.000
192D212SER0-0.025-0.01627.1650.0010.0010.0000.0000.0000.000
193D213LYS10.8420.92227.9480.1520.1520.0000.0000.0000.000
194D214ALA0-0.006-0.01026.452-0.003-0.0030.0000.0000.0000.000
195D215SER0-0.022-0.00527.9530.0190.0190.0000.0000.0000.000
196D216ILE0-0.0010.00925.515-0.015-0.0150.0000.0000.0000.000
197D217ARG10.8870.94427.2000.1840.1840.0000.0000.0000.000
198D218HIS00.0660.02727.181-0.019-0.0190.0000.0000.0000.000
199D219LEU00.003-0.01422.605-0.004-0.0040.0000.0000.0000.000
200D220LYS10.8160.89726.5160.1070.1070.0000.0000.0000.000
201D221ASP-1-0.817-0.90629.117-0.137-0.1370.0000.0000.0000.000
202D222LEU00.0040.02322.774-0.006-0.0060.0000.0000.0000.000
203D223GLU-1-0.768-0.88326.716-0.134-0.1340.0000.0000.0000.000
204D224ALA0-0.051-0.01528.6630.0100.0100.0000.0000.0000.000
205D225CYS0-0.112-0.05127.389-0.004-0.0040.0000.0000.0000.000
206D226GLN00.0100.01322.268-0.004-0.0040.0000.0000.0000.000
207D227GLY00.0170.00125.9620.0190.0190.0000.0000.0000.000
208D228ASP-1-0.920-0.95826.114-0.167-0.1670.0000.0000.0000.000
209D229HIS0-0.020-0.01026.888-0.006-0.0060.0000.0000.0000.000
210D230GLN0-0.056-0.00225.8880.0080.0080.0000.0000.0000.000
211D231LYS10.8450.92419.4600.3690.3690.0000.0000.0000.000
212D232LEU00.002-0.00520.6920.0190.0190.0000.0000.0000.000
213D233LEU0-0.033-0.01116.011-0.050-0.0500.0000.0000.0000.000
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