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: 49G3N

Calculation Name: 1LIL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LIL

Chain ID: A

ChEMBL ID:

UniProt ID: P0DOY2

Base Structure: X-ray

Registration Date: 2023-06-26

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134476.426497
FMO2-HF: Nuclear repulsion 2054457.928374
FMO2-HF: Total energy -80018.498123
FMO2-MP2: Total energy -80251.123539


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:TYR)


Summations of interaction energy for fragment #1(A:2:TYR)
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.
-34.576-21.9636.175-5.931-12.856-0.004
Interaction energy analysis for fragmet #1(A:2:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.019
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].
3A4VAL00.044-0.0043.420-2.017-0.1090.052-0.836-1.1240.000
4A5THR0-0.0030.0105.7210.5990.5990.0000.0000.0000.000
5A6GLN0-0.001-0.0409.158-0.283-0.2830.0000.0000.0000.000
6A7PRO0-0.0160.00412.1320.1360.1360.0000.0000.0000.000
7A8PRO00.0560.05015.866-0.042-0.0420.0000.0000.0000.000
8A9SER0-0.038-0.04618.204-0.004-0.0040.0000.0000.0000.000
9A11LEU0-0.025-0.01720.727-0.015-0.0150.0000.0000.0000.000
10A12SER0-0.005-0.02922.8710.0050.0050.0000.0000.0000.000
11A13VAL0-0.0310.00626.1580.0170.0170.0000.0000.0000.000
12A14SER00.0480.00527.9070.0220.0220.0000.0000.0000.000
13A15PRO0-0.001-0.01631.295-0.017-0.0170.0000.0000.0000.000
14A16GLY00.0320.03931.7950.0140.0140.0000.0000.0000.000
15A17GLN00.0050.00628.882-0.014-0.0140.0000.0000.0000.000
16A18THR0-0.030-0.00926.076-0.013-0.0130.0000.0000.0000.000
17A19ALA00.0230.02422.5720.0080.0080.0000.0000.0000.000
18A20ARG10.8920.91320.2310.4710.4710.0000.0000.0000.000
19A21ILE00.0200.03215.8470.0110.0110.0000.0000.0000.000
20A22THR00.007-0.00814.192-0.084-0.0840.0000.0000.0000.000
21A23CYS0-0.0110.0079.189-0.075-0.0750.0000.0000.0000.000
22A24SER0-0.002-0.0208.586-0.075-0.0750.0000.0000.0000.000
23A25GLY00.0580.0344.4740.0110.048-0.001-0.007-0.0280.000
24A26GLU-1-0.936-0.9752.503-0.4730.9630.512-0.544-1.405-0.001
25A27LYS10.8530.9302.793-8.757-5.3373.572-1.765-5.2280.023
26A28LEU00.0010.0243.403-4.394-3.4360.085-0.305-0.738-0.001
27A29GLY00.0220.0165.8180.1970.1970.0000.0000.0000.000
28A30ASP-1-0.940-0.9694.344-4.430-4.218-0.001-0.009-0.2010.000
29A31ALA0-0.0040.0054.364-1.696-1.561-0.001-0.011-0.1230.000
30A32TYR0-0.039-0.0166.0711.0381.0380.0000.0000.0000.000
31A33VAL00.007-0.0018.385-0.067-0.0670.0000.0000.0000.000
32A34CYS0-0.076-0.02810.5120.3560.3560.0000.0000.0000.000
33A35TRP00.0100.01513.199-0.088-0.0880.0000.0000.0000.000
34A36TYR0-0.023-0.03414.2600.2030.2030.0000.0000.0000.000
35A37GLN00.0220.01817.8410.0290.0290.0000.0000.0000.000
36A38GLN0-0.014-0.02520.735-0.013-0.0130.0000.0000.0000.000
37A39ARG10.9380.96922.3760.4080.4080.0000.0000.0000.000
38A40PRO0-0.009-0.02425.930-0.001-0.0010.0000.0000.0000.000
39A41GLY00.0310.04426.0690.0220.0220.0000.0000.0000.000
40A42GLN0-0.036-0.02126.1730.0150.0150.0000.0000.0000.000
41A43SER00.0170.01124.365-0.010-0.0100.0000.0000.0000.000
42A44PRO0-0.010-0.00219.8710.0100.0100.0000.0000.0000.000
43A45VAL0-0.009-0.00521.8960.0110.0110.0000.0000.0000.000
44A46VAL00.0000.01417.794-0.032-0.0320.0000.0000.0000.000
45A47VAL0-0.013-0.02019.2900.0680.0680.0000.0000.0000.000
46A48ILE0-0.054-0.01916.3120.0460.0460.0000.0000.0000.000
47A49TYR00.0440.01515.352-0.076-0.0760.0000.0000.0000.000
48A50GLN00.0650.01813.4950.2340.2340.0000.0000.0000.000
49A51ASP-1-0.772-0.85311.513-2.040-2.0400.0000.0000.0000.000
50A52ASN0-0.074-0.04814.0790.2270.2270.0000.0000.0000.000
51A53ARG10.9300.99417.8820.8910.8910.0000.0000.0000.000
52A54ARG10.8230.88619.5990.6330.6330.0000.0000.0000.000
53A55PRO0-0.0130.00320.8790.0170.0170.0000.0000.0000.000
54A56SER0-0.002-0.01223.2810.0300.0300.0000.0000.0000.000
55A57GLY00.0180.00727.0870.0080.0080.0000.0000.0000.000
56A58ILE0-0.0380.00123.7030.0270.0270.0000.0000.0000.000
57A59PRO00.0050.00426.862-0.003-0.0030.0000.0000.0000.000
58A60GLU-1-0.786-0.90725.188-0.566-0.5660.0000.0000.0000.000
59A61ARG10.7210.82927.2460.3840.3840.0000.0000.0000.000
60A62PHE0-0.013-0.00222.2980.0030.0030.0000.0000.0000.000
61A63SER00.0410.00821.506-0.003-0.0030.0000.0000.0000.000
62A64GLY00.0210.00717.329-0.010-0.0100.0000.0000.0000.000
63A65SER0-0.021-0.01216.0310.0360.0360.0000.0000.0000.000
64A66SER00.048-0.00611.475-0.070-0.0700.0000.0000.0000.000
65A67SER0-0.0250.00113.2310.0930.0930.0000.0000.0000.000
66A68GLY00.0110.00511.8400.0870.0870.0000.0000.0000.000
67A69ASN0-0.019-0.0196.617-0.223-0.2230.0000.0000.0000.000
68A70THR0-0.0140.0119.187-0.054-0.0540.0000.0000.0000.000
69A71ALA00.0380.04510.3470.1010.1010.0000.0000.0000.000
70A72THR0-0.075-0.05011.9250.1440.1440.0000.0000.0000.000
71A73LEU0-0.0110.00415.520-0.036-0.0360.0000.0000.0000.000
72A74THR0-0.046-0.01817.9920.0950.0950.0000.0000.0000.000
73A75ILE00.0290.01621.760-0.018-0.0180.0000.0000.0000.000
74A76SER0-0.022-0.01324.7660.0330.0330.0000.0000.0000.000
75A77GLY00.0180.00628.2460.0050.0050.0000.0000.0000.000
76A78THR0-0.050-0.02326.7900.0090.0090.0000.0000.0000.000
77A79GLN00.004-0.00829.6890.0250.0250.0000.0000.0000.000
78A80THR00.0430.00630.009-0.014-0.0140.0000.0000.0000.000
79A81LEU0-0.056-0.02330.437-0.008-0.0080.0000.0000.0000.000
80A82ASP-1-0.778-0.84426.070-0.406-0.4060.0000.0000.0000.000
81A83GLU-1-0.797-0.87925.402-0.303-0.3030.0000.0000.0000.000
82A84ALA0-0.010-0.01922.8830.0110.0110.0000.0000.0000.000
83A85ASP-1-0.809-0.86019.133-0.424-0.4240.0000.0000.0000.000
84A86TYR0-0.030-0.04317.660-0.026-0.0260.0000.0000.0000.000
85A87TYR00.0190.01913.6290.0210.0210.0000.0000.0000.000
86A89GLN00.0700.0469.978-0.070-0.0700.0000.0000.0000.000
87A90VAL00.016-0.0064.3040.3030.414-0.001-0.007-0.1030.000
88A91TRP00.0140.0126.782-0.222-0.2220.0000.0000.0000.000
89A92ASP-1-0.855-0.9232.503-17.886-14.5671.646-2.032-2.933-0.023
90A93SER0-0.023-0.0424.4850.6290.692-0.001-0.002-0.0590.000
91A94ASN0-0.096-0.0494.9462.0142.0140.0000.0000.0000.000
92A95ALA00.0230.0007.4640.5980.5980.0000.0000.0000.000
93A95SER0-0.0300.0064.8540.7380.7380.0000.0000.0000.000
94A96VAL0-0.017-0.0096.713-0.767-0.7670.0000.0000.0000.000
95A97VAL0-0.0030.0122.465-0.0051.0090.313-0.413-0.914-0.002
96A98PHE0-0.021-0.0245.8650.3100.3100.0000.0000.0000.000
97A99GLY00.0290.0208.7660.0810.0810.0000.0000.0000.000
98A100GLY0-0.022-0.0219.7090.2050.2050.0000.0000.0000.000
99A101GLY00.0080.00712.5190.1360.1360.0000.0000.0000.000
100A102THR0-0.065-0.04015.180-0.020-0.0200.0000.0000.0000.000
101A103LYS10.8490.90117.7380.3490.3490.0000.0000.0000.000
102A104LEU0-0.056-0.01321.3990.0350.0350.0000.0000.0000.000
103A105THR0-0.055-0.03723.2730.0190.0190.0000.0000.0000.000
104A106VAL00.000-0.00626.843-0.001-0.0010.0000.0000.0000.000
105A106LEU0-0.062-0.03829.9530.0180.0180.0000.0000.0000.000
106A107GLY00.0210.01932.1130.0070.0070.0000.0000.0000.000
107A108GLN0-0.014-0.01033.1380.0260.0260.0000.0000.0000.000
108A109PRO0-0.0270.00133.078-0.012-0.0120.0000.0000.0000.000
109A110LYS10.8300.90525.2500.2080.2080.0000.0000.0000.000
110A111ALA0-0.025-0.01329.8920.0130.0130.0000.0000.0000.000
111A112ALA00.0480.02627.736-0.010-0.0100.0000.0000.0000.000
112A113PRO0-0.020-0.00725.2670.0060.0060.0000.0000.0000.000
113A114SER00.005-0.00428.6050.0120.0120.0000.0000.0000.000
114A115VAL0-0.0150.00525.8040.0040.0040.0000.0000.0000.000
115A116THR0-0.024-0.01528.7590.0070.0070.0000.0000.0000.000
116A117LEU0-0.036-0.00426.2660.0000.0000.0000.0000.0000.000
117A118PHE0-0.009-0.00729.456-0.005-0.0050.0000.0000.0000.000
118A119PRO00.0090.00330.3750.0130.0130.0000.0000.0000.000
119A120PRO00.0050.02330.894-0.010-0.0100.0000.0000.0000.000
120A121SER0-0.025-0.03833.4210.0010.0010.0000.0000.0000.000
121A122SER00.022-0.01637.1860.0070.0070.0000.0000.0000.000
122A123GLU-1-0.823-0.87840.2230.0980.0980.0000.0000.0000.000
123A124GLU-1-0.782-0.85433.0150.1560.1560.0000.0000.0000.000
124A125LEU00.0340.00134.6650.0090.0090.0000.0000.0000.000
125A126GLN0-0.072-0.02837.7480.0010.0010.0000.0000.0000.000
126A127ALA0-0.056-0.01738.2060.0000.0000.0000.0000.0000.000
127A128ASN0-0.040-0.02036.4050.0110.0110.0000.0000.0000.000
128A129LYS10.8620.92432.540-0.138-0.1380.0000.0000.0000.000
129A130ALA00.012-0.01030.894-0.006-0.0060.0000.0000.0000.000
130A131THR0-0.063-0.05728.2040.0200.0200.0000.0000.0000.000
131A132LEU0-0.0080.02126.081-0.016-0.0160.0000.0000.0000.000
132A133VAL00.0320.00526.9880.0010.0010.0000.0000.0000.000
133A134CYS0-0.063-0.02621.9030.0120.0120.0000.0000.0000.000
134A135LEU00.0250.02826.562-0.011-0.0110.0000.0000.0000.000
135A136ILE00.003-0.00523.7090.0010.0010.0000.0000.0000.000
136A137SER00.001-0.02028.083-0.009-0.0090.0000.0000.0000.000
137A138ASP-1-0.800-0.89630.629-0.039-0.0390.0000.0000.0000.000
138A139PHE00.0030.02025.164-0.007-0.0070.0000.0000.0000.000
139A140TYR00.010-0.00828.865-0.001-0.0010.0000.0000.0000.000
140A141PRO00.0730.03524.9060.0110.0110.0000.0000.0000.000
141A142GLY00.018-0.00725.9760.0100.0100.0000.0000.0000.000
142A143ALA0-0.028-0.02020.475-0.019-0.0190.0000.0000.0000.000
143A144VAL0-0.012-0.00820.8020.0170.0170.0000.0000.0000.000
144A145THR0-0.0010.00614.599-0.058-0.0580.0000.0000.0000.000
145A146VAL0-0.008-0.00717.3910.0190.0190.0000.0000.0000.000
146A147ALA00.0120.01115.4700.0270.0270.0000.0000.0000.000
147A148TRP00.0270.00417.121-0.016-0.0160.0000.0000.0000.000
148A149LYS10.7810.86217.327-0.217-0.2170.0000.0000.0000.000
149A150ALA00.0230.01219.834-0.051-0.0510.0000.0000.0000.000
150A151ASP-1-0.772-0.87221.7430.3690.3690.0000.0000.0000.000
151A152SER0-0.020-0.01719.5620.0130.0130.0000.0000.0000.000
152A153SER0-0.0110.01617.7350.0540.0540.0000.0000.0000.000
153A154PRO0-0.007-0.01413.440-0.061-0.0610.0000.0000.0000.000
154A155VAL0-0.016-0.00215.9320.0610.0610.0000.0000.0000.000
155A156LYS10.8390.9108.432-1.231-1.2310.0000.0000.0000.000
156A157ALA00.0220.00014.9280.0740.0740.0000.0000.0000.000
157A158GLY00.0550.03618.047-0.036-0.0360.0000.0000.0000.000
158A159VAL0-0.046-0.01016.536-0.030-0.0300.0000.0000.0000.000
159A160GLU-1-0.888-0.94019.5220.1900.1900.0000.0000.0000.000
160A161THR0-0.019-0.00819.481-0.014-0.0140.0000.0000.0000.000
161A162THR0-0.047-0.03021.243-0.028-0.0280.0000.0000.0000.000
162A163THR00.004-0.00222.612-0.025-0.0250.0000.0000.0000.000
163A164PRO0-0.042-0.02022.7480.0160.0160.0000.0000.0000.000
164A165SER00.0110.01225.857-0.019-0.0190.0000.0000.0000.000
165A166LYS10.8850.94629.4330.1070.1070.0000.0000.0000.000
166A167GLN00.0380.00632.2950.0110.0110.0000.0000.0000.000
167A168SER00.018-0.00734.864-0.008-0.0080.0000.0000.0000.000
168A170ASN00.0010.02036.341-0.009-0.0090.0000.0000.0000.000
169A171ASN0-0.020-0.01835.596-0.005-0.0050.0000.0000.0000.000
170A172LYS10.8760.96732.4850.0790.0790.0000.0000.0000.000
171A173TYR0-0.043-0.03228.350-0.006-0.0060.0000.0000.0000.000
172A174ALA00.0030.01129.8400.0090.0090.0000.0000.0000.000
173A175ALA00.0180.00324.916-0.016-0.0160.0000.0000.0000.000
174A176SER0-0.016-0.01925.9730.0150.0150.0000.0000.0000.000
175A177SER00.0190.02221.1520.0020.0020.0000.0000.0000.000
176A178TYR0-0.009-0.00523.583-0.011-0.0110.0000.0000.0000.000
177A179LEU00.0300.02121.3080.0200.0200.0000.0000.0000.000
178A180SER0-0.0080.00124.010-0.022-0.0220.0000.0000.0000.000
179A181LEU0-0.070-0.03124.9600.0360.0360.0000.0000.0000.000
180A182THR00.032-0.00727.171-0.025-0.0250.0000.0000.0000.000
181A183PRO00.0360.01230.1570.0110.0110.0000.0000.0000.000
182A184GLU-1-0.847-0.92631.8960.2190.2190.0000.0000.0000.000
183A185GLN00.0370.05924.470-0.008-0.0080.0000.0000.0000.000
184A186TRP00.0160.03028.0980.0140.0140.0000.0000.0000.000
185A187LYS10.8530.89029.787-0.172-0.1720.0000.0000.0000.000
186A188SER0-0.056-0.03629.1550.0040.0040.0000.0000.0000.000
187A189HIS10.8180.90123.785-0.384-0.3840.0000.0000.0000.000
188A190ARG10.9720.98128.171-0.241-0.2410.0000.0000.0000.000
189A191SER0-0.067-0.05527.146-0.033-0.0330.0000.0000.0000.000
190A192TYR0-0.033-0.03023.8730.0430.0430.0000.0000.0000.000
191A193SER0-0.010-0.01422.355-0.020-0.0200.0000.0000.0000.000
192A195GLN0-0.019-0.01017.517-0.013-0.0130.0000.0000.0000.000
193A196VAL00.0480.00120.018-0.003-0.0030.0000.0000.0000.000
194A197THR00.0370.02416.9830.0090.0090.0000.0000.0000.000
195A198HIS00.0260.02719.787-0.023-0.0230.0000.0000.0000.000
196A199GLU-1-0.741-0.81920.547-0.294-0.2940.0000.0000.0000.000
197A200GLY00.0140.00021.0460.0060.0060.0000.0000.0000.000
198A203SER0-0.016-0.01222.0660.0190.0190.0000.0000.0000.000
199A204THR0-0.014-0.01819.328-0.014-0.0140.0000.0000.0000.000
200A205VAL0-0.0230.00022.2130.0120.0120.0000.0000.0000.000
201A206GLU-1-0.778-0.87121.5200.2220.2220.0000.0000.0000.000
202A207LYS10.8440.92124.657-0.067-0.0670.0000.0000.0000.000
203A208THR00.0320.00525.8780.0270.0270.0000.0000.0000.000
204A209VAL0-0.0070.01127.876-0.017-0.0170.0000.0000.0000.000
205A210ALA00.0150.00029.1840.0210.0210.0000.0000.0000.000
206A211PRO0-0.031-0.00530.747-0.016-0.0160.0000.0000.0000.000
207A212THR00.0160.01333.671-0.007-0.0070.0000.0000.0000.000
208A213GLU-1-0.814-0.86837.1930.1630.1630.0000.0000.0000.000
209A214CYS0-0.022-0.00740.284-0.003-0.0030.0000.0000.0000.000
210A215SER0-0.050-0.04042.615-0.008-0.0080.0000.0000.0000.000