FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: LZGL9

Calculation Name: 1VAV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I4H0

Base Structure: X-ray

Registration Date: 2023-06-22

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2811531.038539
FMO2-HF: Nuclear repulsion 2725048.001915
FMO2-HF: Total energy -86483.036624
FMO2-MP2: Total energy -86740.924476


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(A:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-14.893-6.3285.419-4.5-9.487-0.022
Interaction energy analysis for fragmet #1(A:2:PRO)
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 : -0.010
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].
3A4LEU0-0.007-0.0163.094-2.2770.0880.116-0.906-1.5760.003
4A5SER0-0.004-0.0065.5020.1370.1370.0000.0000.0000.000
5A6THR0-0.038-0.0227.9800.0280.0280.0000.0000.0000.000
6A7TRP0-0.0040.0114.8680.0880.0880.0000.0000.0000.000
7A8ASN0-0.0260.0019.3870.0710.0710.0000.0000.0000.000
8A9LEU00.0620.0109.747-0.046-0.0460.0000.0000.0000.000
9A10THR0-0.0280.01012.0640.0190.0190.0000.0000.0000.000
10A11ILE0-0.019-0.00214.172-0.008-0.0080.0000.0000.0000.000
11A12PRO0-0.0220.00516.236-0.010-0.0100.0000.0000.0000.000
12A13GLN00.1170.07719.2950.0040.0040.0000.0000.0000.000
13A14GLY00.0040.00721.1860.0020.0020.0000.0000.0000.000
14A15ARG10.9460.98823.883-0.037-0.0370.0000.0000.0000.000
15A16PRO00.018-0.02224.9410.0000.0000.0000.0000.0000.000
16A17ALA0-0.014-0.00420.1300.0060.0060.0000.0000.0000.000
17A18ILE00.0050.01418.730-0.005-0.0050.0000.0000.0000.000
18A19THR0-0.037-0.02615.776-0.004-0.0040.0000.0000.0000.000
19A20ILE0-0.037-0.01213.4910.0020.0020.0000.0000.0000.000
20A21SER00.015-0.00713.955-0.009-0.0090.0000.0000.0000.000
21A22THR00.1210.05410.8620.0410.0410.0000.0000.0000.000
22A23SER00.003-0.00612.0140.0570.0570.0000.0000.0000.000
23A24GLN0-0.034-0.02113.9890.0400.0400.0000.0000.0000.000
24A25LEU0-0.0080.0077.7310.0450.0450.0000.0000.0000.000
25A26GLN0-0.051-0.0548.4620.2380.2380.0000.0000.0000.000
26A27ARG10.8870.98010.908-0.155-0.1550.0000.0000.0000.000
27A28ASP-1-0.912-0.97010.1990.9320.9320.0000.0000.0000.000
28A29TYR0-0.030-0.00311.174-0.094-0.0940.0000.0000.0000.000
29A30ARG10.9170.9469.583-0.563-0.5630.0000.0000.0000.000
30A31SER0-0.035-0.01012.360-0.080-0.0800.0000.0000.0000.000
31A32ASP-1-0.841-0.93513.3920.1850.1850.0000.0000.0000.000
32A33TYR0-0.041-0.05014.203-0.018-0.0180.0000.0000.0000.000
33A34PHE00.0060.0065.813-0.036-0.0360.0000.0000.0000.000
34A35GLN00.0000.0018.9290.1000.1000.0000.0000.0000.000
35A36ARG11.0141.0334.226-4.935-4.5430.000-0.107-0.2850.000
36A37THR0-0.066-0.0535.602-0.342-0.3420.0000.0000.0000.000
37A38ALA00.0340.0096.1910.2590.2590.0000.0000.0000.000
38A39ASP-1-0.791-0.8776.914-0.141-0.1410.0000.0000.0000.000
39A40GLY00.0220.0102.888-0.944-0.5530.166-0.203-0.3540.000
40A41ILE0-0.039-0.0032.125-0.2170.2822.567-0.678-2.3880.000
41A42ARG10.9140.9724.697-0.518-0.444-0.001-0.011-0.0620.000
42A43PHE00.022-0.0016.1940.1090.1090.0000.0000.0000.000
43A44TRP0-0.007-0.02010.606-0.031-0.0310.0000.0000.0000.000
44A45VAL0-0.055-0.02414.4020.0150.0150.0000.0000.0000.000
45A46PRO00.0560.03917.203-0.013-0.0130.0000.0000.0000.000
46A47VAL00.059-0.00220.819-0.003-0.0030.0000.0000.0000.000
47A48ASN0-0.024-0.00723.043-0.001-0.0010.0000.0000.0000.000
48A49GLY0-0.0230.00021.9520.0060.0060.0000.0000.0000.000
49A50SER0-0.094-0.05422.563-0.006-0.0060.0000.0000.0000.000
50A51HIS00.0530.01921.980-0.003-0.0030.0000.0000.0000.000
51A52THR0-0.012-0.01220.0110.0050.0050.0000.0000.0000.000
52A53ARG10.9920.96622.968-0.009-0.0090.0000.0000.0000.000
53A54ASN00.0020.01525.1330.0020.0020.0000.0000.0000.000
54A55SER0-0.0110.01823.176-0.010-0.0100.0000.0000.0000.000
55A56GLU-1-0.828-0.90825.174-0.011-0.0110.0000.0000.0000.000
56A57PHE0-0.065-0.02622.3590.0020.0020.0000.0000.0000.000
57A58PRO0-0.0470.00920.390-0.001-0.0010.0000.0000.0000.000
58A59ARG10.8680.91615.8180.0420.0420.0000.0000.0000.000
59A60SER00.0190.00612.7660.0240.0240.0000.0000.0000.000
60A61GLU-1-0.858-0.92211.436-0.160-0.1600.0000.0000.0000.000
61A62LEU00.0150.0165.5870.0600.0600.0000.0000.0000.000
62A63ARG10.8060.89610.0930.0690.0690.0000.0000.0000.000
63A64GLU-1-0.710-0.82311.252-0.244-0.2440.0000.0000.0000.000
64A65THR0-0.022-0.02811.9450.0450.0450.0000.0000.0000.000
65A66LEU00.0090.01012.871-0.025-0.0250.0000.0000.0000.000
66A67SER00.0650.03513.0110.0100.0100.0000.0000.0000.000
67A68SER0-0.047-0.02914.0390.0320.0320.0000.0000.0000.000
68A69GLY00.0380.00214.8950.0180.0180.0000.0000.0000.000
69A70ARG10.8750.95415.8320.0150.0150.0000.0000.0000.000
70A71PRO0-0.0050.00216.619-0.015-0.0150.0000.0000.0000.000
71A72TYR0-0.020-0.01214.2040.0230.0230.0000.0000.0000.000
72A73ASN00.0520.02116.624-0.028-0.0280.0000.0000.0000.000
73A74TRP0-0.020-0.01914.8640.0200.0200.0000.0000.0000.000
74A75ARG10.9480.98819.8770.0710.0710.0000.0000.0000.000
75A76TYR00.0840.03620.6780.0000.0000.0000.0000.0000.000
76A77ALA0-0.0030.02221.739-0.004-0.0040.0000.0000.0000.000
77A78ARG10.8380.91821.4080.0890.0890.0000.0000.0000.000
78A79ALA0-0.030-0.01618.7440.0040.0040.0000.0000.0000.000
79A80ASP-1-0.835-0.89718.292-0.160-0.1600.0000.0000.0000.000
80A81ASN0-0.032-0.06315.375-0.006-0.0060.0000.0000.0000.000
81A82TRP00.0340.01212.5290.0090.0090.0000.0000.0000.000
82A83LEU0-0.0100.0067.830-0.052-0.0520.0000.0000.0000.000
83A84GLU-1-0.893-0.9568.172-0.461-0.4610.0000.0000.0000.000
84A85ALA00.0200.0036.642-0.242-0.2420.0000.0000.0000.000
85A86THR00.015-0.0046.4550.2020.2020.0000.0000.0000.000
86A87LEU0-0.046-0.0176.497-0.143-0.1430.0000.0000.0000.000
87A88ARG10.8250.9298.7520.1750.1750.0000.0000.0000.000
88A89ILE00.002-0.00311.4630.0080.0080.0000.0000.0000.000
89A90GLU-1-0.788-0.89811.978-0.022-0.0220.0000.0000.0000.000
90A91ALA0-0.016-0.00915.5600.0160.0160.0000.0000.0000.000
91A92VAL0-0.0060.00417.275-0.013-0.0130.0000.0000.0000.000
92A93PRO00.0280.00819.6220.0080.0080.0000.0000.0000.000
93A94SER00.0630.02222.749-0.006-0.0060.0000.0000.0000.000
94A95THR0-0.080-0.03824.906-0.003-0.0030.0000.0000.0000.000
95A96ARG10.8520.93422.7530.0460.0460.0000.0000.0000.000
96A97ARG10.9390.97520.9300.0730.0730.0000.0000.0000.000
97A98MET0-0.051-0.00614.8120.0180.0180.0000.0000.0000.000
98A99ILE0-0.0190.00415.766-0.014-0.0140.0000.0000.0000.000
99A100ILE00.0500.01211.9580.0070.0070.0000.0000.0000.000
100A101GLY00.0460.02211.337-0.065-0.0650.0000.0000.0000.000
101A102GLN0-0.081-0.06713.1580.0530.0530.0000.0000.0000.000
102A103ILE00.0370.05914.231-0.030-0.0300.0000.0000.0000.000
103A104HIS0-0.095-0.07316.6980.0210.0210.0000.0000.0000.000
104A105SER00.0490.03118.950-0.006-0.0060.0000.0000.0000.000
105A106ASP-1-0.839-0.93821.691-0.070-0.0700.0000.0000.0000.000
106A107GLY0-0.0020.00322.9440.0080.0080.0000.0000.0000.000
107A108SER0-0.102-0.04125.6370.0060.0060.0000.0000.0000.000
108A109ASN0-0.083-0.05127.8550.0090.0090.0000.0000.0000.000
109A110SER0-0.021-0.01128.740-0.003-0.0030.0000.0000.0000.000
110A111GLY00.0110.01930.9280.0030.0030.0000.0000.0000.000
111A112GLN0-0.080-0.04328.3470.0050.0050.0000.0000.0000.000
112A113ALA00.0330.03124.023-0.004-0.0040.0000.0000.0000.000
113A114ALA0-0.001-0.01124.1470.0010.0010.0000.0000.0000.000
114A115PRO0-0.045-0.02220.263-0.006-0.0060.0000.0000.0000.000
115A116LEU00.0600.03620.2920.0080.0080.0000.0000.0000.000
116A117VAL00.009-0.01518.7430.0050.0050.0000.0000.0000.000
117A118LYS10.9160.97618.0200.0900.0900.0000.0000.0000.000
118A119LEU00.0280.02013.8530.0140.0140.0000.0000.0000.000
119A120LEU0-0.044-0.03916.7230.0010.0010.0000.0000.0000.000
120A121TYR00.0340.03016.2240.0040.0040.0000.0000.0000.000
121A122GLN00.0330.00118.3000.0100.0100.0000.0000.0000.000
122A123LEU00.0280.02321.073-0.004-0.0040.0000.0000.0000.000
123A124ARG10.8330.91322.6600.0890.0890.0000.0000.0000.000
124A125LEU00.003-0.00226.309-0.001-0.0010.0000.0000.0000.000
125A126ASP-1-0.824-0.91825.038-0.050-0.0500.0000.0000.0000.000
126A127GLN0-0.027-0.01423.320-0.013-0.0130.0000.0000.0000.000
127A128GLY00.0170.00520.2980.0050.0050.0000.0000.0000.000
128A129ARG10.8460.94221.1590.0860.0860.0000.0000.0000.000
129A130VAL00.001-0.01116.3090.0000.0000.0000.0000.0000.000
130A131GLN0-0.060-0.04319.4000.0060.0060.0000.0000.0000.000
131A132ALA00.0510.03820.085-0.011-0.0110.0000.0000.0000.000
132A133LEU0-0.073-0.04021.2200.0140.0140.0000.0000.0000.000
133A134VAL00.0740.02922.347-0.007-0.0070.0000.0000.0000.000
134A135ARG10.8130.90624.2990.0920.0920.0000.0000.0000.000
135A136GLU-1-0.895-0.94826.458-0.089-0.0890.0000.0000.0000.000
136A137ARG10.9270.97829.0240.0560.0560.0000.0000.0000.000
137A138PRO00.0080.00527.3840.0000.0000.0000.0000.0000.000
138A139ASP-1-0.815-0.91028.408-0.053-0.0530.0000.0000.0000.000
139A140ASP-1-0.855-0.90529.978-0.062-0.0620.0000.0000.0000.000
140A141GLY00.0450.00830.299-0.002-0.0020.0000.0000.0000.000
141A142GLY0-0.035-0.01929.9290.0000.0000.0000.0000.0000.000
142A143THR0-0.053-0.02925.488-0.004-0.0040.0000.0000.0000.000
143A144ARG10.9510.97627.3820.0790.0790.0000.0000.0000.000
144A145ALA0-0.007-0.00925.578-0.008-0.0080.0000.0000.0000.000
145A146TYR00.0340.03124.3770.0070.0070.0000.0000.0000.000
146A147THR0-0.030-0.02623.506-0.008-0.0080.0000.0000.0000.000
147A148LEU00.0140.02819.1290.0040.0040.0000.0000.0000.000
148A149MET00.0110.01819.0680.0010.0010.0000.0000.0000.000
149A150ASP-1-0.810-0.90421.528-0.097-0.0970.0000.0000.0000.000
150A151GLY00.006-0.01022.322-0.006-0.0060.0000.0000.0000.000
151A152ILE0-0.039-0.01116.465-0.005-0.0050.0000.0000.0000.000
152A153PRO00.0270.03019.6970.0020.0020.0000.0000.0000.000
153A154LEU00.003-0.01017.698-0.015-0.0150.0000.0000.0000.000
154A155GLY0-0.038-0.01715.3950.0090.0090.0000.0000.0000.000
155A156GLN00.0000.00215.0860.0010.0010.0000.0000.0000.000
156A157PRO0-0.038-0.02911.710-0.014-0.0140.0000.0000.0000.000
157A158PHE0-0.037-0.01812.0120.0250.0250.0000.0000.0000.000
158A159SER00.0550.02610.952-0.047-0.0470.0000.0000.0000.000
159A160TYR0-0.020-0.03510.2800.0440.0440.0000.0000.0000.000
160A161ARG10.9340.97711.3920.2480.2480.0000.0000.0000.000
161A162ILE0-0.034-0.01712.9130.0500.0500.0000.0000.0000.000
162A163GLY00.0380.00613.875-0.040-0.0400.0000.0000.0000.000
163A164VAL0-0.041-0.00616.3330.0210.0210.0000.0000.0000.000
164A165SER00.0500.04619.306-0.005-0.0050.0000.0000.0000.000
165A166ARG11.0121.00321.3480.1200.1200.0000.0000.0000.000
166A167SER0-0.034-0.03523.2240.0070.0070.0000.0000.0000.000
167A168GLY00.008-0.01124.2700.0090.0090.0000.0000.0000.000
168A169LEU0-0.0100.00622.6590.0050.0050.0000.0000.0000.000
169A170LEU0-0.017-0.00619.696-0.015-0.0150.0000.0000.0000.000
170A171SER00.0470.02118.9910.0110.0110.0000.0000.0000.000
171A172VAL0-0.022-0.02017.400-0.024-0.0240.0000.0000.0000.000
172A173SER0-0.035-0.02216.7680.0140.0140.0000.0000.0000.000
173A174VAL00.0470.00215.520-0.033-0.0330.0000.0000.0000.000
174A175ASN00.011-0.00315.309-0.006-0.0060.0000.0000.0000.000
175A176GLY00.0040.00816.7340.0160.0160.0000.0000.0000.000
176A177SER0-0.061-0.02418.4380.0170.0170.0000.0000.0000.000
177A178ALA00.014-0.02520.268-0.015-0.0150.0000.0000.0000.000
178A179LEU0-0.0200.01021.7960.0140.0140.0000.0000.0000.000
179A180GLU-1-0.942-0.97922.373-0.160-0.1600.0000.0000.0000.000
180A181GLN00.000-0.00524.4450.0080.0080.0000.0000.0000.000
181A182GLN0-0.040-0.00125.392-0.009-0.0090.0000.0000.0000.000
182A183LEU0-0.044-0.02922.8060.0040.0040.0000.0000.0000.000
183A184ASP-1-0.785-0.89727.257-0.063-0.0630.0000.0000.0000.000
184A185PRO00.026-0.00529.217-0.004-0.0040.0000.0000.0000.000
185A186GLN0-0.033-0.02130.6790.0010.0010.0000.0000.0000.000
186A187TRP0-0.002-0.03024.092-0.002-0.0020.0000.0000.0000.000
187A188ALA0-0.025-0.00225.769-0.005-0.0050.0000.0000.0000.000
188A189TYR0-0.071-0.04127.039-0.001-0.0010.0000.0000.0000.000
189A190GLN0-0.0230.00624.9370.0060.0060.0000.0000.0000.000
190A191GLY0-0.024-0.00722.731-0.007-0.0070.0000.0000.0000.000
191A192LEU0-0.018-0.02018.9700.0010.0010.0000.0000.0000.000
192A193TYR0-0.027-0.00215.3450.0010.0010.0000.0000.0000.000
193A194PHE00.0240.01811.1490.0030.0030.0000.0000.0000.000
194A195LYS10.8350.91411.7720.1420.1420.0000.0000.0000.000
195A196ALA00.0460.0238.050-0.027-0.0270.0000.0000.0000.000
196A197GLY00.0250.0289.2440.0340.0340.0000.0000.0000.000
197A198LEU0-0.018-0.01110.136-0.015-0.0150.0000.0000.0000.000
198A199TYR0-0.026-0.03613.4390.0290.0290.0000.0000.0000.000
199A200LEU00.0150.00916.811-0.011-0.0110.0000.0000.0000.000
200A201GLN0-0.085-0.05219.692-0.005-0.0050.0000.0000.0000.000
201A202ASP-1-0.822-0.94723.009-0.028-0.0280.0000.0000.0000.000
202A203ASN0-0.031-0.01823.8400.0000.0000.0000.0000.0000.000
203A204ARG10.9510.99826.2350.0310.0310.0000.0000.0000.000
204A205GLY00.0760.03627.697-0.003-0.0030.0000.0000.0000.000
205A206PRO0-0.023-0.00727.5600.0040.0040.0000.0000.0000.000
206A207SER00.0490.01324.2840.0000.0000.0000.0000.0000.000
207A208SER0-0.007-0.00423.7280.0050.0050.0000.0000.0000.000
208A209GLU-1-0.845-0.90023.365-0.019-0.0190.0000.0000.0000.000
209A210GLY00.0430.00720.2170.0060.0060.0000.0000.0000.000
210A211GLY0-0.049-0.00717.037-0.008-0.0080.0000.0000.0000.000
211A212ARG10.8960.92413.5050.0120.0120.0000.0000.0000.000
212A213ALA00.0010.00810.720-0.019-0.0190.0000.0000.0000.000
213A214THR0-0.0060.0016.9380.0870.0870.0000.0000.0000.000
214A215PHE0-0.025-0.0113.965-0.1240.0260.000-0.020-0.1300.000
215A216SER00.0440.0113.593-0.805-0.2250.015-0.228-0.368-0.001
216A217GLU-1-0.881-0.9232.693-2.279-1.4420.300-0.375-0.762-0.002
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