Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LNGK9

Calculation Name: 1VF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VF7

Chain ID: A

ChEMBL ID:

UniProt ID: P52477

Base Structure: X-ray

Registration Date: 2023-09-23

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2356289.698158
FMO2-HF: Nuclear repulsion 2266921.864673
FMO2-HF: Total energy -89367.833485
FMO2-MP2: Total energy -89633.022689


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:26:THR)


Summations of interaction energy for fragment #1(A:26:THR)
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.
-5.822-0.2273.427-3.569-5.454-0.016
Interaction energy analysis for fragmet #1(A:26:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.000
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].
3A28ASN0-0.0110.0002.947-0.2052.2360.295-1.074-1.664-0.002
4A29THR0-0.037-0.0265.0260.3870.460-0.001-0.006-0.0660.000
5A30GLU-1-0.757-0.8688.541-0.801-0.8010.0000.0000.0000.000
6A31LEU0-0.034-0.01211.9210.0680.0680.0000.0000.0000.000
7A32PRO00.0050.01615.0240.0210.0210.0000.0000.0000.000
8A33GLY00.0410.00118.4670.0230.0230.0000.0000.0000.000
9A34ARG10.8420.92020.9860.1860.1860.0000.0000.0000.000
10A35THR00.0120.00223.6790.0040.0040.0000.0000.0000.000
11A36ASN0-0.072-0.04325.2670.0250.0250.0000.0000.0000.000
12A37ALA00.0290.01327.876-0.003-0.0030.0000.0000.0000.000
13A38PHE0-0.0200.00727.9970.0030.0030.0000.0000.0000.000
14A39ARG10.8880.92330.3230.0980.0980.0000.0000.0000.000
15A40ILE00.0140.00633.989-0.001-0.0010.0000.0000.0000.000
16A41ALA0-0.0020.00436.9140.0030.0030.0000.0000.0000.000
17A42GLU-1-0.811-0.87340.651-0.067-0.0670.0000.0000.0000.000
18A43VAL0-0.022-0.01143.9470.0020.0020.0000.0000.0000.000
19A44ARG10.7960.85246.5720.0600.0600.0000.0000.0000.000
20A45PRO00.0000.01449.8030.0000.0000.0000.0000.0000.000
21A46GLN00.0200.00250.6190.0010.0010.0000.0000.0000.000
22A47VAL0-0.020-0.00454.9690.0010.0010.0000.0000.0000.000
23A48ASN00.0560.03157.928-0.002-0.0020.0000.0000.0000.000
24A49GLY00.0420.02860.5600.0010.0010.0000.0000.0000.000
25A50ILE00.0370.02960.385-0.001-0.0010.0000.0000.0000.000
26A51ILE0-0.005-0.00254.1350.0000.0000.0000.0000.0000.000
27A52LEU00.0250.03258.0780.0000.0000.0000.0000.0000.000
28A53LYS10.7950.86355.5560.0390.0390.0000.0000.0000.000
29A54ARG10.8650.92648.7370.0540.0540.0000.0000.0000.000
30A55LEU0-0.013-0.00150.572-0.002-0.0020.0000.0000.0000.000
31A56PHE00.0000.01645.544-0.001-0.0010.0000.0000.0000.000
32A57LYS10.9420.96342.0930.0700.0700.0000.0000.0000.000
33A58GLU-1-0.772-0.85744.089-0.062-0.0620.0000.0000.0000.000
34A59GLY0-0.0170.00639.8130.0000.0000.0000.0000.0000.000
35A60SER0-0.102-0.06939.7350.0000.0000.0000.0000.0000.000
36A61ASP-1-0.784-0.87635.751-0.096-0.0960.0000.0000.0000.000
37A62VAL0-0.030-0.00838.9430.0050.0050.0000.0000.0000.000
38A63LYS10.9570.96539.2800.0590.0590.0000.0000.0000.000
39A64ALA00.0230.00640.3640.0030.0030.0000.0000.0000.000
40A65GLY00.0120.00542.1190.0020.0020.0000.0000.0000.000
41A66GLN00.0150.01743.6350.0010.0010.0000.0000.0000.000
42A67GLN0-0.044-0.05046.6650.0000.0000.0000.0000.0000.000
43A68LEU0-0.055-0.03044.576-0.001-0.0010.0000.0000.0000.000
44A69TYR00.0860.02048.917-0.001-0.0010.0000.0000.0000.000
45A70GLN0-0.0300.01052.5520.0000.0000.0000.0000.0000.000
46A71ILE00.0040.01155.7690.0000.0000.0000.0000.0000.000
47A72ASP-1-0.863-0.94158.413-0.031-0.0310.0000.0000.0000.000
48A73PRO0-0.015-0.01061.2660.0000.0000.0000.0000.0000.000
49A74ALA00.0050.01163.0380.0010.0010.0000.0000.0000.000
50A75THR00.003-0.00666.8030.0010.0010.0000.0000.0000.000
51A76TYR00.000-0.02062.3340.0010.0010.0000.0000.0000.000
52A77GLU-1-0.851-0.91764.929-0.028-0.0280.0000.0000.0000.000
53A78ALA00.0170.01266.7300.0010.0010.0000.0000.0000.000
54A79ASP-1-0.872-0.92767.676-0.027-0.0270.0000.0000.0000.000
55A80TYR0-0.040-0.03164.8380.0000.0000.0000.0000.0000.000
56A81GLN0-0.070-0.04267.5460.0010.0010.0000.0000.0000.000
57A82SER0-0.044-0.03470.5870.0010.0010.0000.0000.0000.000
58A83ALA00.0160.00769.5610.0010.0010.0000.0000.0000.000
59A84GLN00.001-0.01367.5920.0000.0000.0000.0000.0000.000
60A85ALA00.0060.01571.3360.0010.0010.0000.0000.0000.000
61A86ASN0-0.0010.01674.3720.0010.0010.0000.0000.0000.000
62A87LEU00.0270.02569.6490.0010.0010.0000.0000.0000.000
63A88ALA0-0.004-0.00273.7480.0000.0000.0000.0000.0000.000
64A89SER0-0.026-0.00475.6480.0010.0010.0000.0000.0000.000
65A90THR00.002-0.02075.8730.0000.0000.0000.0000.0000.000
66A91GLN00.0150.01572.8030.0000.0000.0000.0000.0000.000
67A92GLU-1-0.840-0.90076.778-0.016-0.0160.0000.0000.0000.000
68A93GLN00.0630.04480.0210.0010.0010.0000.0000.0000.000
69A94ALA0-0.0060.00078.0590.0000.0000.0000.0000.0000.000
70A95GLN0-0.018-0.01276.6170.0000.0000.0000.0000.0000.000
71A96ARG10.8450.90280.4120.0160.0160.0000.0000.0000.000
72A97TYR00.002-0.02083.2570.0010.0010.0000.0000.0000.000
73A98LYS10.8810.94177.6100.0170.0170.0000.0000.0000.000
74A99LEU0-0.0100.00682.7370.0000.0000.0000.0000.0000.000
75A100LEU00.0530.01885.3140.0000.0000.0000.0000.0000.000
76A101VAL0-0.056-0.02284.1190.0000.0000.0000.0000.0000.000
77A102ALA0-0.059-0.02585.6920.0000.0000.0000.0000.0000.000
78A103ASP-1-0.896-0.94287.566-0.012-0.0120.0000.0000.0000.000
79A104GLN0-0.147-0.07390.0600.0010.0010.0000.0000.0000.000
80A105ALA00.0260.02691.4460.0000.0000.0000.0000.0000.000
81A106VAL0-0.059-0.02187.1310.0000.0000.0000.0000.0000.000
82A107SER00.024-0.01789.4300.0000.0000.0000.0000.0000.000
83A108LYS10.9900.96085.4770.0140.0140.0000.0000.0000.000
84A109GLN0-0.056-0.01883.4080.0000.0000.0000.0000.0000.000
85A110GLN00.1230.08584.3960.0000.0000.0000.0000.0000.000
86A111TYR00.014-0.00378.1110.0000.0000.0000.0000.0000.000
87A112ALA00.0000.00180.392-0.001-0.0010.0000.0000.0000.000
88A113ASP-1-0.814-0.90179.734-0.017-0.0170.0000.0000.0000.000
89A114ALA00.0010.00280.078-0.001-0.0010.0000.0000.0000.000
90A115ASN0-0.020-0.00374.9760.0000.0000.0000.0000.0000.000
91A116ALA00.0010.00175.675-0.001-0.0010.0000.0000.0000.000
92A117ALA00.0260.01075.169-0.001-0.0010.0000.0000.0000.000
93A118TYR0-0.016-0.02471.865-0.001-0.0010.0000.0000.0000.000
94A119LEU0-0.025-0.01270.433-0.001-0.0010.0000.0000.0000.000
95A120GLN00.0100.00170.4880.0000.0000.0000.0000.0000.000
96A121SER00.002-0.00770.858-0.001-0.0010.0000.0000.0000.000
97A122LYS10.8920.93867.4220.0220.0220.0000.0000.0000.000
98A123ALA0-0.005-0.00266.350-0.001-0.0010.0000.0000.0000.000
99A124ALA00.0050.00466.115-0.001-0.0010.0000.0000.0000.000
100A125VAL00.0070.00566.295-0.001-0.0010.0000.0000.0000.000
101A126GLU-1-0.793-0.85159.994-0.033-0.0330.0000.0000.0000.000
102A127GLN0-0.020-0.02060.549-0.001-0.0010.0000.0000.0000.000
103A128ALA00.0220.00962.698-0.001-0.0010.0000.0000.0000.000
104A129ARG10.8290.88058.1520.0310.0310.0000.0000.0000.000
105A130ILE0-0.067-0.02657.044-0.001-0.0010.0000.0000.0000.000
106A131ASN00.0110.00358.352-0.002-0.0020.0000.0000.0000.000
107A132LEU00.0350.02159.677-0.001-0.0010.0000.0000.0000.000
108A133ARG10.8830.96654.1560.0390.0390.0000.0000.0000.000
109A134TYR0-0.012-0.03252.827-0.001-0.0010.0000.0000.0000.000
110A135THR0-0.023-0.01055.816-0.001-0.0010.0000.0000.0000.000
111A136LYS10.8430.93053.6550.0370.0370.0000.0000.0000.000
112A137VAL00.0300.02149.762-0.001-0.0010.0000.0000.0000.000
113A138LEU00.002-0.00447.9080.0000.0000.0000.0000.0000.000
114A139SER00.010-0.01041.875-0.001-0.0010.0000.0000.0000.000
115A140PRO0-0.0200.00242.2240.0010.0010.0000.0000.0000.000
116A141ILE0-0.006-0.01036.668-0.001-0.0010.0000.0000.0000.000
117A142SER00.0130.00536.6430.0040.0040.0000.0000.0000.000
118A143GLY00.001-0.00235.422-0.005-0.0050.0000.0000.0000.000
119A144ARG10.8800.95034.1240.1010.1010.0000.0000.0000.000
120A145ILE0-0.025-0.00237.0360.0000.0000.0000.0000.0000.000
121A146GLY00.0360.01140.509-0.001-0.0010.0000.0000.0000.000
122A147ARG10.9510.95041.2640.0750.0750.0000.0000.0000.000
123A148SER0-0.041-0.02344.6040.0000.0000.0000.0000.0000.000
124A149ALA0-0.041-0.00947.8730.0010.0010.0000.0000.0000.000
125A150VAL0-0.028-0.01249.5110.0020.0020.0000.0000.0000.000
126A151THR00.005-0.00152.396-0.001-0.0010.0000.0000.0000.000
127A152GLU-1-0.776-0.89254.886-0.042-0.0420.0000.0000.0000.000
128A153GLY00.001-0.00256.8250.0000.0000.0000.0000.0000.000
129A154ALA0-0.0180.00556.8470.0010.0010.0000.0000.0000.000
130A155LEU00.0020.00358.9350.0000.0000.0000.0000.0000.000
131A156VAL0-0.007-0.00455.122-0.001-0.0010.0000.0000.0000.000
132A157THR0-0.044-0.03157.1180.0020.0020.0000.0000.0000.000
133A158ASN00.0180.00056.176-0.003-0.0030.0000.0000.0000.000
134A159GLY00.0310.01853.9440.0010.0010.0000.0000.0000.000
135A160GLN0-0.023-0.00552.7240.0020.0020.0000.0000.0000.000
136A161ALA00.0470.01752.396-0.002-0.0020.0000.0000.0000.000
137A162ASN0-0.0010.01049.995-0.003-0.0030.0000.0000.0000.000
138A163ALA00.0270.02246.6650.0020.0020.0000.0000.0000.000
139A164MET0-0.033-0.00748.6030.0020.0020.0000.0000.0000.000
140A165ALA00.0330.01145.0430.0000.0000.0000.0000.0000.000
141A166THR00.0040.00239.9300.0020.0020.0000.0000.0000.000
142A167VAL0-0.0010.00538.327-0.001-0.0010.0000.0000.0000.000
143A168GLN00.0410.00734.197-0.005-0.0050.0000.0000.0000.000
144A169GLN00.0350.02732.0440.0040.0040.0000.0000.0000.000
145A170LEU00.003-0.01729.870-0.004-0.0040.0000.0000.0000.000
146A171ASP-1-0.828-0.89128.464-0.137-0.1370.0000.0000.0000.000
147A172PRO0-0.026-0.00326.463-0.009-0.0090.0000.0000.0000.000
148A173ILE0-0.042-0.02124.0060.0100.0100.0000.0000.0000.000
149A174TYR00.001-0.00524.086-0.010-0.0100.0000.0000.0000.000
150A175VAL00.015-0.01219.0700.0020.0020.0000.0000.0000.000
151A176ASP-1-0.876-0.92521.454-0.207-0.2070.0000.0000.0000.000
152A177VAL00.0420.03217.284-0.004-0.0040.0000.0000.0000.000
153A178THR00.0090.00920.6670.0200.0200.0000.0000.0000.000
154A179GLN0-0.007-0.00716.924-0.055-0.0550.0000.0000.0000.000
155A180PRO00.0660.02919.7220.0230.0230.0000.0000.0000.000
156A181SER00.0760.03820.855-0.017-0.0170.0000.0000.0000.000
157A182THR00.010-0.00719.197-0.002-0.0020.0000.0000.0000.000
158A183ALA0-0.045-0.02016.567-0.003-0.0030.0000.0000.0000.000
159A184LEU00.0580.04616.800-0.015-0.0150.0000.0000.0000.000
160A185LEU0-0.025-0.01918.7080.0080.0080.0000.0000.0000.000
161A186ARG10.8280.91211.3500.4990.4990.0000.0000.0000.000
162A187LEU00.0190.01512.0900.0260.0260.0000.0000.0000.000
163A188ARG10.9070.94714.9870.1540.1540.0000.0000.0000.000
164A189ARG10.9040.95613.8170.1100.1100.0000.0000.0000.000
165A190GLH0-0.047-0.05710.5380.0460.0460.0000.0000.0000.000
166A191LEU00.0220.02613.5710.0180.0180.0000.0000.0000.000
167A192ALA0-0.068-0.03215.5320.0180.0180.0000.0000.0000.000
168A193SER0-0.046-0.04614.1730.0020.0020.0000.0000.0000.000
169A194GLY00.0080.01214.6790.0280.0280.0000.0000.0000.000
170A195GLN0-0.0260.0019.938-0.041-0.0410.0000.0000.0000.000
171A196LEU0-0.0240.0039.286-0.016-0.0160.0000.0000.0000.000
172A197GLU-1-0.852-0.92810.660-0.314-0.3140.0000.0000.0000.000
173A198ARG10.8240.89812.6140.0700.0700.0000.0000.0000.000
174A199ALA00.0390.02516.2310.0070.0070.0000.0000.0000.000
175A200GLY0-0.015-0.01818.2420.0170.0170.0000.0000.0000.000
176A201ASP-1-0.893-0.93520.521-0.095-0.0950.0000.0000.0000.000
177A202ASN0-0.043-0.02921.6540.0010.0010.0000.0000.0000.000
178A203ALA00.0190.01819.131-0.009-0.0090.0000.0000.0000.000
179A204ALA00.0360.02113.4700.0180.0180.0000.0000.0000.000
180A205LYS10.8270.90012.8540.3060.3060.0000.0000.0000.000
181A206VAL0-0.070-0.02712.404-0.051-0.0510.0000.0000.0000.000
182A207SER00.0210.01511.6710.0730.0730.0000.0000.0000.000
183A208LEU0-0.020-0.01613.595-0.013-0.0130.0000.0000.0000.000
184A209LYS10.8270.92312.4480.7250.7250.0000.0000.0000.000
185A210LEU00.004-0.00816.0590.0210.0210.0000.0000.0000.000
186A211GLU-1-0.845-0.92319.494-0.230-0.2300.0000.0000.0000.000
187A212ASP-1-0.861-0.90021.498-0.251-0.2510.0000.0000.0000.000
188A213GLY0-0.044-0.01917.6180.0040.0040.0000.0000.0000.000
189A214SER0-0.085-0.06316.693-0.041-0.0410.0000.0000.0000.000
190A215GLN0-0.019-0.03712.495-0.009-0.0090.0000.0000.0000.000
191A216TYR00.012-0.03316.7020.0460.0460.0000.0000.0000.000
192A217PRO0-0.028-0.00817.400-0.030-0.0300.0000.0000.0000.000
193A218LEU0-0.042-0.03718.5650.0260.0260.0000.0000.0000.000
194A219GLU-1-0.883-0.91313.926-0.331-0.3310.0000.0000.0000.000
195A220GLY00.0520.01316.3550.0380.0380.0000.0000.0000.000
196A221ARG10.7470.85116.7240.1480.1480.0000.0000.0000.000
197A222LEU00.0250.00814.984-0.001-0.0010.0000.0000.0000.000
198A223GLU-1-0.762-0.85718.146-0.166-0.1660.0000.0000.0000.000
199A224PHE00.0030.00115.244-0.006-0.0060.0000.0000.0000.000
200A225SER0-0.065-0.04321.5330.0130.0130.0000.0000.0000.000
201A226GLU-1-0.867-0.92023.744-0.157-0.1570.0000.0000.0000.000
202A227VAL0-0.018-0.02326.3210.0050.0050.0000.0000.0000.000
203A228SER0-0.0330.00127.3170.0120.0120.0000.0000.0000.000
204A229VAL0-0.001-0.01627.058-0.012-0.0120.0000.0000.0000.000
205A230ASP-1-0.819-0.88128.529-0.124-0.1240.0000.0000.0000.000
206A231GLU-1-0.964-0.98030.336-0.079-0.0790.0000.0000.0000.000
207A232GLY0-0.037-0.00932.9780.0050.0050.0000.0000.0000.000
208A233THR0-0.060-0.04328.637-0.004-0.0040.0000.0000.0000.000
209A234GLY00.0350.02027.6730.0020.0020.0000.0000.0000.000
210A235SER0-0.088-0.05924.921-0.017-0.0170.0000.0000.0000.000
211A236VAL0-0.009-0.01723.2600.0150.0150.0000.0000.0000.000
212A237THR0-0.048-0.01623.350-0.014-0.0140.0000.0000.0000.000
213A238ILE00.010-0.00417.9930.0170.0170.0000.0000.0000.000
214A239ARG10.8920.94121.8230.1430.1430.0000.0000.0000.000
215A240ALA00.0370.01218.406-0.004-0.0040.0000.0000.0000.000
216A241VAL0-0.049-0.02920.4670.0150.0150.0000.0000.0000.000
217A242PHE00.0160.01416.249-0.013-0.0130.0000.0000.0000.000
218A243PRO00.0540.03321.5520.0180.0180.0000.0000.0000.000
219A244ASN0-0.0030.01923.765-0.021-0.0210.0000.0000.0000.000
220A245PRO00.0290.02726.0950.0100.0100.0000.0000.0000.000
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