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: QY51Y

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134145.762437
FMO2-HF: Nuclear repulsion 2054132.855261
FMO2-HF: Total energy -80012.907176
FMO2-MP2: Total energy -80246.292443


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.
-30.834-25.17419.023-8.334-16.346-0.028
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 : -0.065 / q_NPA : -0.042
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].
3A4VAL00.0580.0033.779-1.479-0.027-0.009-0.526-0.9170.002
4A5THR00.0190.0035.8590.6100.6100.0000.0000.0000.000
5A6GLN0-0.090-0.0559.109-0.045-0.0450.0000.0000.0000.000
6A7PRO0-0.034-0.00712.0270.1230.1230.0000.0000.0000.000
7A8PRO00.0930.07015.560-0.062-0.0620.0000.0000.0000.000
8A9SER0-0.041-0.02718.435-0.007-0.0070.0000.0000.0000.000
9A11LEU0-0.033-0.03120.258-0.004-0.0040.0000.0000.0000.000
10A12SER0-0.014-0.01522.860-0.009-0.0090.0000.0000.0000.000
11A13VAL0-0.0510.00526.5700.0230.0230.0000.0000.0000.000
12A14SER00.005-0.02228.0960.0180.0180.0000.0000.0000.000
13A15PRO00.008-0.01831.442-0.015-0.0150.0000.0000.0000.000
14A16GLY00.0640.06131.7260.0170.0170.0000.0000.0000.000
15A17GLN0-0.0030.01228.674-0.007-0.0070.0000.0000.0000.000
16A18THR0-0.031-0.00325.800-0.009-0.0090.0000.0000.0000.000
17A19ALA00.0280.03122.4000.0110.0110.0000.0000.0000.000
18A20ARG10.9000.93920.1830.4340.4340.0000.0000.0000.000
19A21ILE00.0000.01615.8880.0210.0210.0000.0000.0000.000
20A22THR00.023-0.00213.708-0.067-0.0670.0000.0000.0000.000
21A23CYS00.0130.0229.297-0.104-0.1040.0000.0000.0000.000
22A24SER00.0370.0408.8690.0590.0590.0000.0000.0000.000
23A25GLY00.0400.0284.576-0.0120.015-0.001-0.005-0.0210.000
24A26GLU-1-0.914-0.9712.290-0.8320.1010.986-0.524-1.3950.000
25A27LYS10.9240.9471.745-9.631-9.8428.339-2.310-5.8180.017
26A28LEU0-0.0300.0094.692-0.884-0.737-0.001-0.008-0.1380.000
27A29GLY0-0.0270.0056.624-0.047-0.0470.0000.0000.0000.000
28A30ASP-1-0.913-0.9715.162-0.303-0.3030.0000.0000.0000.000
29A31ALA00.063-0.0075.960-1.695-1.6950.0000.0000.0000.000
30A32TYR0-0.067-0.0167.7640.6890.6890.0000.0000.0000.000
31A33VAL00.007-0.0079.297-0.250-0.2500.0000.0000.0000.000
32A34CYS0-0.062-0.04711.4820.3580.3580.0000.0000.0000.000
33A35TRP00.0130.01413.472-0.123-0.1230.0000.0000.0000.000
34A36TYR0-0.067-0.02414.1240.2290.2290.0000.0000.0000.000
35A37GLN00.0190.03017.8370.0280.0280.0000.0000.0000.000
36A38GLN0-0.017-0.03720.514-0.016-0.0160.0000.0000.0000.000
37A39ARG10.9881.00422.4440.4130.4130.0000.0000.0000.000
38A40PRO0-0.031-0.03425.991-0.001-0.0010.0000.0000.0000.000
39A41GLY00.0210.03625.2870.0220.0220.0000.0000.0000.000
40A42GLN0-0.022-0.01824.9980.0420.0420.0000.0000.0000.000
41A43SER0-0.016-0.00924.214-0.018-0.0180.0000.0000.0000.000
42A44PRO00.0120.00919.8600.0240.0240.0000.0000.0000.000
43A45VAL00.0150.01221.5090.0320.0320.0000.0000.0000.000
44A46VAL00.0020.00818.409-0.030-0.0300.0000.0000.0000.000
45A47VAL0-0.006-0.02619.5810.0610.0610.0000.0000.0000.000
46A48ILE0-0.050-0.03117.4170.0800.0800.0000.0000.0000.000
47A49TYR00.0750.06115.914-0.109-0.1090.0000.0000.0000.000
48A50GLN0-0.040-0.01914.6420.1430.1430.0000.0000.0000.000
49A51ASP-1-0.746-0.88613.342-1.557-1.5570.0000.0000.0000.000
50A52ASN0-0.090-0.06115.5070.1480.1480.0000.0000.0000.000
51A53ARG10.9170.98819.0400.7880.7880.0000.0000.0000.000
52A54ARG10.9511.00720.0020.5100.5100.0000.0000.0000.000
53A55PRO0-0.0110.00221.3520.0230.0230.0000.0000.0000.000
54A56SER00.027-0.01423.6720.0160.0160.0000.0000.0000.000
55A57GLY0-0.028-0.00827.482-0.004-0.0040.0000.0000.0000.000
56A58ILE0-0.027-0.00824.6940.0280.0280.0000.0000.0000.000
57A59PRO00.0060.00427.8070.0070.0070.0000.0000.0000.000
58A60GLU-1-0.925-0.98626.655-0.481-0.4810.0000.0000.0000.000
59A61ARG10.8570.92827.8690.3880.3880.0000.0000.0000.000
60A62PHE0-0.0160.00922.850-0.001-0.0010.0000.0000.0000.000
61A63SER00.062-0.00122.0970.0130.0130.0000.0000.0000.000
62A64GLY0-0.0140.00517.7850.0070.0070.0000.0000.0000.000
63A65SER0-0.035-0.03516.4340.0490.0490.0000.0000.0000.000
64A66SER00.0850.04512.322-0.120-0.1200.0000.0000.0000.000
65A67SER0-0.0250.00814.2460.0620.0620.0000.0000.0000.000
66A68GLY00.0150.00912.593-0.030-0.0300.0000.0000.0000.000
67A69ASN0-0.0070.0077.398-0.143-0.1430.0000.0000.0000.000
68A70THR0-0.071-0.0459.296-0.110-0.1100.0000.0000.0000.000
69A71ALA00.0780.04210.4060.0910.0910.0000.0000.0000.000
70A72THR0-0.067-0.04412.3200.0400.0400.0000.0000.0000.000
71A73LEU0-0.021-0.00115.678-0.020-0.0200.0000.0000.0000.000
72A74THR0-0.051-0.02118.1650.0630.0630.0000.0000.0000.000
73A75ILE00.004-0.01221.837-0.019-0.0190.0000.0000.0000.000
74A76SER0-0.014-0.01624.8540.0370.0370.0000.0000.0000.000
75A77GLY00.002-0.00828.487-0.007-0.0070.0000.0000.0000.000
76A78THR0-0.053-0.03726.8620.0060.0060.0000.0000.0000.000
77A79GLN00.0440.01730.0550.0080.0080.0000.0000.0000.000
78A80THR00.0800.03730.667-0.013-0.0130.0000.0000.0000.000
79A81LEU0-0.062-0.03330.593-0.015-0.0150.0000.0000.0000.000
80A82ASP-1-0.836-0.90727.008-0.427-0.4270.0000.0000.0000.000
81A83GLU-1-0.906-0.93725.966-0.337-0.3370.0000.0000.0000.000
82A84ALA0-0.055-0.03323.0400.0030.0030.0000.0000.0000.000
83A85ASP-1-0.867-0.92019.022-0.487-0.4870.0000.0000.0000.000
84A86TYR0-0.040-0.04817.882-0.034-0.0340.0000.0000.0000.000
85A87TYR0-0.0300.01713.860-0.034-0.0340.0000.0000.0000.000
86A89GLN00.0820.02610.162-0.074-0.0740.0000.0000.0000.000
87A90VAL00.0680.0354.6690.6760.790-0.001-0.001-0.1110.000
88A91TRP0-0.066-0.0336.429-0.995-0.9950.0000.0000.0000.000
89A92ASP-1-0.802-0.8992.305-18.638-17.0926.964-3.211-5.298-0.038
90A93SER0-0.031-0.0144.368-1.010-0.857-0.001-0.031-0.1210.000
91A94ASN0-0.099-0.0592.9573.1023.4450.006-0.095-0.2540.000
92A95ALA00.0120.0025.8790.9520.9520.0000.0000.0000.000
93A95SER0-0.056-0.0143.452-0.5960.0910.015-0.296-0.405-0.002
94A96VAL00.0140.0104.968-1.513-1.412-0.001-0.004-0.0960.000
95A97VAL0-0.0170.0131.8430.9531.2472.728-1.321-1.702-0.007
96A98PHE0-0.039-0.0435.2800.2940.368-0.001-0.002-0.0700.000
97A99GLY00.0530.0278.3620.2220.2220.0000.0000.0000.000
98A100GLY00.0430.0129.9190.1110.1110.0000.0000.0000.000
99A101GLY0-0.007-0.00612.6220.1370.1370.0000.0000.0000.000
100A102THR0-0.041-0.05315.680-0.015-0.0150.0000.0000.0000.000
101A103LYS10.8410.92418.3360.4250.4250.0000.0000.0000.000
102A104LEU00.0070.01521.7860.0430.0430.0000.0000.0000.000
103A105THR0-0.044-0.04123.5870.0130.0130.0000.0000.0000.000
104A106VAL00.0080.01327.2180.0030.0030.0000.0000.0000.000
105A106LEU0-0.056-0.03730.0530.0110.0110.0000.0000.0000.000
106A107GLY00.0360.01032.1260.0000.0000.0000.0000.0000.000
107A108GLN0-0.075-0.04434.1860.0220.0220.0000.0000.0000.000
108A109PRO00.0210.02033.481-0.013-0.0130.0000.0000.0000.000
109A110LYS10.9781.00426.9860.1890.1890.0000.0000.0000.000
110A111ALA0-0.057-0.04330.4560.0150.0150.0000.0000.0000.000
111A112ALA00.0370.00527.793-0.011-0.0110.0000.0000.0000.000
112A113PRO0-0.044-0.01025.3380.0090.0090.0000.0000.0000.000
113A114SER00.0220.03728.5490.0160.0160.0000.0000.0000.000
114A115VAL00.0120.00125.824-0.004-0.0040.0000.0000.0000.000
115A116THR0-0.034-0.01628.9230.0110.0110.0000.0000.0000.000
116A117LEU0-0.044-0.02626.333-0.003-0.0030.0000.0000.0000.000
117A118PHE0-0.010-0.00929.5300.0010.0010.0000.0000.0000.000
118A119PRO00.0080.00730.4140.0080.0080.0000.0000.0000.000
119A120PRO00.0150.02231.131-0.010-0.0100.0000.0000.0000.000
120A121SER00.0490.01333.6530.0010.0010.0000.0000.0000.000
121A122SER00.0360.00437.3040.0070.0070.0000.0000.0000.000
122A123GLU-1-0.901-0.95439.7050.0690.0690.0000.0000.0000.000
123A124GLU-1-0.895-0.93433.0170.1130.1130.0000.0000.0000.000
124A125LEU00.055-0.00734.3510.0090.0090.0000.0000.0000.000
125A126GLN0-0.0250.00837.6490.0040.0040.0000.0000.0000.000
126A127ALA0-0.074-0.02738.1890.0010.0010.0000.0000.0000.000
127A128ASN0-0.026-0.02137.0760.0090.0090.0000.0000.0000.000
128A129LYS10.8780.96433.259-0.082-0.0820.0000.0000.0000.000
129A130ALA0-0.012-0.03630.8790.0020.0020.0000.0000.0000.000
130A131THR0-0.041-0.01527.8000.0180.0180.0000.0000.0000.000
131A132LEU0-0.059-0.01626.052-0.010-0.0100.0000.0000.0000.000
132A133VAL00.0720.02826.998-0.002-0.0020.0000.0000.0000.000
133A134CYS0-0.088-0.03921.8770.0130.0130.0000.0000.0000.000
134A135LEU00.0080.00826.570-0.015-0.0150.0000.0000.0000.000
135A136ILE0-0.0090.00323.6590.0040.0040.0000.0000.0000.000
136A137SER0-0.014-0.04527.906-0.011-0.0110.0000.0000.0000.000
137A138ASP-1-0.862-0.93830.606-0.057-0.0570.0000.0000.0000.000
138A139PHE0-0.0050.00525.533-0.005-0.0050.0000.0000.0000.000
139A140TYR0-0.021-0.01329.023-0.005-0.0050.0000.0000.0000.000
140A141PRO00.0970.04425.6000.0180.0180.0000.0000.0000.000
141A142GLY00.0010.01125.9490.0140.0140.0000.0000.0000.000
142A143ALA0-0.024-0.01620.629-0.022-0.0220.0000.0000.0000.000
143A144VAL00.0060.01420.8190.0150.0150.0000.0000.0000.000
144A145THR00.0360.01614.707-0.074-0.0740.0000.0000.0000.000
145A146VAL0-0.027-0.00117.5590.0220.0220.0000.0000.0000.000
146A147ALA0-0.0110.01115.7850.0230.0230.0000.0000.0000.000
147A148TRP00.037-0.01316.984-0.015-0.0150.0000.0000.0000.000
148A149LYS10.9270.93116.179-0.265-0.2650.0000.0000.0000.000
149A150ALA0-0.013-0.01619.427-0.053-0.0530.0000.0000.0000.000
150A151ASP-1-0.765-0.89121.5310.3520.3520.0000.0000.0000.000
151A152SER00.0200.00020.6250.0230.0230.0000.0000.0000.000
152A153SER0-0.0550.00117.4010.0530.0530.0000.0000.0000.000
153A154PRO00.0240.03013.251-0.076-0.0760.0000.0000.0000.000
154A155VAL0-0.018-0.00815.7500.0560.0560.0000.0000.0000.000
155A156LYS10.9440.9729.311-1.186-1.1860.0000.0000.0000.000
156A157ALA00.010-0.01414.9720.0770.0770.0000.0000.0000.000
157A158GLY00.0800.04918.263-0.026-0.0260.0000.0000.0000.000
158A159VAL0-0.083-0.02616.595-0.029-0.0290.0000.0000.0000.000
159A160GLU-1-0.910-0.96619.3480.1200.1200.0000.0000.0000.000
160A161THR0-0.049-0.03118.9010.0020.0020.0000.0000.0000.000
161A162THR0-0.037-0.02421.609-0.023-0.0230.0000.0000.0000.000
162A163THR00.014-0.01421.965-0.029-0.0290.0000.0000.0000.000
163A164PRO0-0.031-0.01122.9340.0190.0190.0000.0000.0000.000
164A165SER0-0.017-0.00125.917-0.015-0.0150.0000.0000.0000.000
165A166LYS10.9110.97129.4720.1450.1450.0000.0000.0000.000
166A167GLN00.0420.01932.2140.0100.0100.0000.0000.0000.000
167A168SER00.011-0.01934.660-0.009-0.0090.0000.0000.0000.000
168A170ASN00.002-0.00636.602-0.004-0.0040.0000.0000.0000.000
169A171ASN0-0.012-0.02535.399-0.005-0.0050.0000.0000.0000.000
170A172LYS10.9441.01432.4490.0840.0840.0000.0000.0000.000
171A173TYR0-0.052-0.02627.770-0.005-0.0050.0000.0000.0000.000
172A174ALA00.0090.00429.5840.0110.0110.0000.0000.0000.000
173A175ALA00.0500.03024.917-0.021-0.0210.0000.0000.0000.000
174A176SER0-0.029-0.00825.6400.0180.0180.0000.0000.0000.000
175A177SER00.0640.05921.192-0.005-0.0050.0000.0000.0000.000
176A178TYR00.0160.01923.323-0.010-0.0100.0000.0000.0000.000
177A179LEU00.0260.03021.1880.0140.0140.0000.0000.0000.000
178A180SER00.0330.02923.821-0.030-0.0300.0000.0000.0000.000
179A181LEU0-0.038-0.00624.5640.0330.0330.0000.0000.0000.000
180A182THR00.0610.02426.674-0.020-0.0200.0000.0000.0000.000
181A183PRO00.0610.02529.8520.0170.0170.0000.0000.0000.000
182A184GLU-1-0.863-0.93831.6280.1930.1930.0000.0000.0000.000
183A185GLN0-0.008-0.01424.3240.0060.0060.0000.0000.0000.000
184A186TRP00.0400.01828.4600.0100.0100.0000.0000.0000.000
185A187LYS10.9210.96429.612-0.153-0.1530.0000.0000.0000.000
186A188SER0-0.062-0.00128.1510.0040.0040.0000.0000.0000.000
187A189HIS10.8210.91123.236-0.346-0.3460.0000.0000.0000.000
188A190ARG10.9560.97228.074-0.226-0.2260.0000.0000.0000.000
189A191SER0-0.083-0.06226.899-0.029-0.0290.0000.0000.0000.000
190A192TYR00.0170.02223.2340.0310.0310.0000.0000.0000.000
191A193SER00.0290.02421.751-0.013-0.0130.0000.0000.0000.000
192A195GLN0-0.017-0.00517.571-0.009-0.0090.0000.0000.0000.000
193A196VAL00.019-0.00419.571-0.009-0.0090.0000.0000.0000.000
194A197THR00.0160.01217.3440.0220.0220.0000.0000.0000.000
195A198HIS0-0.044-0.04419.767-0.028-0.0280.0000.0000.0000.000
196A199GLU-1-0.757-0.87020.777-0.317-0.3170.0000.0000.0000.000
197A200GLY0-0.027-0.01321.2800.0210.0210.0000.0000.0000.000
198A203SER0-0.035-0.02022.5770.0160.0160.0000.0000.0000.000
199A204THR00.0090.00019.814-0.020-0.0200.0000.0000.0000.000
200A205VAL0-0.040-0.02422.5590.0150.0150.0000.0000.0000.000
201A206GLU-1-0.864-0.95321.2710.1790.1790.0000.0000.0000.000
202A207LYS10.9120.99224.556-0.037-0.0370.0000.0000.0000.000
203A208THR00.040-0.01525.9240.0210.0210.0000.0000.0000.000
204A209VAL0-0.039-0.00328.260-0.012-0.0120.0000.0000.0000.000
205A210ALA00.009-0.00129.3340.0180.0180.0000.0000.0000.000
206A211PRO0-0.052-0.02830.681-0.015-0.0150.0000.0000.0000.000
207A212THR00.016-0.00333.703-0.004-0.0040.0000.0000.0000.000
208A213GLU-1-0.885-0.94337.3060.1360.1360.0000.0000.0000.000
209A214CYS0-0.0290.00640.324-0.004-0.0040.0000.0000.0000.000
210A215SER0-0.048-0.02443.293-0.008-0.0080.0000.0000.0000.000