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: K9Q33

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 OptHSide
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 -2133048.516393
FMO2-HF: Nuclear repulsion 2053032.608501
FMO2-HF: Total energy -80015.907892
FMO2-MP2: Total energy -80248.998894


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.
-35.374-23.9379.138-7.049-13.52-0.018
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 : -0.025 / q_NPA : -0.024
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].
3A4VAL00.0700.0243.779-1.5540.005-0.007-0.608-0.9430.002
4A5THR0-0.012-0.0185.6860.7100.7100.0000.0000.0000.000
5A6GLN0-0.065-0.0769.017-0.034-0.0340.0000.0000.0000.000
6A7PRO0-0.0170.00011.8750.1310.1310.0000.0000.0000.000
7A8PRO00.0590.05615.436-0.052-0.0520.0000.0000.0000.000
8A9SER0-0.034-0.02618.283-0.003-0.0030.0000.0000.0000.000
9A11LEU0-0.040-0.03720.650-0.010-0.0100.0000.0000.0000.000
10A12SER0-0.015-0.02522.714-0.006-0.0060.0000.0000.0000.000
11A13VAL0-0.0380.00726.2470.0180.0180.0000.0000.0000.000
12A14SER00.0380.01327.9530.0210.0210.0000.0000.0000.000
13A15PRO00.010-0.02031.294-0.017-0.0170.0000.0000.0000.000
14A16GLY00.0560.05431.5650.0150.0150.0000.0000.0000.000
15A17GLN0-0.046-0.01428.739-0.013-0.0130.0000.0000.0000.000
16A18THR0-0.0010.00125.951-0.005-0.0050.0000.0000.0000.000
17A19ALA00.0240.02722.2330.0090.0090.0000.0000.0000.000
18A20ARG10.9030.93319.9330.4700.4700.0000.0000.0000.000
19A21ILE0-0.0150.01315.7020.0160.0160.0000.0000.0000.000
20A22THR00.017-0.00313.583-0.102-0.1020.0000.0000.0000.000
21A23CYS0-0.0050.0189.220-0.054-0.0540.0000.0000.0000.000
22A24SER00.0370.0188.811-0.049-0.0490.0000.0000.0000.000
23A25GLY00.0280.0214.5090.0900.119-0.001-0.005-0.0220.000
24A26GLU-1-0.911-0.9602.161-0.0270.5651.411-0.533-1.4690.001
25A27LYS10.9100.9482.760-10.025-5.8952.549-1.760-4.9190.021
26A28LEU0-0.0380.0084.683-1.810-1.568-0.001-0.011-0.2290.000
27A29GLY0-0.0240.0126.1590.2290.2290.0000.0000.0000.000
28A30ASP-1-0.917-0.9734.454-3.788-3.597-0.001-0.007-0.1830.000
29A31ALA00.039-0.0264.897-1.950-1.841-0.001-0.009-0.0990.000
30A32TYR0-0.095-0.0266.8300.8320.8320.0000.0000.0000.000
31A33VAL00.014-0.0118.591-0.109-0.1090.0000.0000.0000.000
32A34CYS0-0.072-0.04910.8770.3400.3400.0000.0000.0000.000
33A35TRP00.0170.01813.242-0.093-0.0930.0000.0000.0000.000
34A36TYR0-0.040-0.02414.3970.2070.2070.0000.0000.0000.000
35A37GLN00.0320.03117.8350.0290.0290.0000.0000.0000.000
36A38GLN0-0.016-0.03520.662-0.009-0.0090.0000.0000.0000.000
37A39ARG10.9840.99322.4430.3870.3870.0000.0000.0000.000
38A40PRO0-0.036-0.03425.9890.0030.0030.0000.0000.0000.000
39A41GLY00.0210.03625.2850.0190.0190.0000.0000.0000.000
40A42GLN0-0.012-0.01324.9990.0200.0200.0000.0000.0000.000
41A43SER0-0.0100.00624.213-0.008-0.0080.0000.0000.0000.000
42A44PRO00.0050.00219.8390.0110.0110.0000.0000.0000.000
43A45VAL00.0180.01021.4890.0280.0280.0000.0000.0000.000
44A46VAL0-0.0090.00218.271-0.030-0.0300.0000.0000.0000.000
45A47VAL00.000-0.02219.4000.0520.0520.0000.0000.0000.000
46A48ILE0-0.078-0.03916.2400.0590.0590.0000.0000.0000.000
47A49TYR00.0780.04315.426-0.082-0.0820.0000.0000.0000.000
48A50GLN0-0.040-0.02013.9830.2360.2360.0000.0000.0000.000
49A51ASP-1-0.696-0.81511.870-2.134-2.1340.0000.0000.0000.000
50A52ASN0-0.081-0.05514.6380.1870.1870.0000.0000.0000.000
51A53ARG10.9280.99318.2160.8790.8790.0000.0000.0000.000
52A54ARG10.8330.90119.3750.5860.5860.0000.0000.0000.000
53A55PRO00.0160.01720.8990.0160.0160.0000.0000.0000.000
54A56SER00.008-0.02123.2790.0150.0150.0000.0000.0000.000
55A57GLY0-0.0110.00127.1150.0020.0020.0000.0000.0000.000
56A58ILE0-0.043-0.01324.1180.0280.0280.0000.0000.0000.000
57A59PRO00.0150.01227.4260.0000.0000.0000.0000.0000.000
58A60GLU-1-0.840-0.92425.603-0.551-0.5510.0000.0000.0000.000
59A61ARG10.7490.85827.3320.3810.3810.0000.0000.0000.000
60A62PHE0-0.012-0.00322.4810.0040.0040.0000.0000.0000.000
61A63SER00.0830.03021.5610.0160.0160.0000.0000.0000.000
62A64GLY0-0.003-0.00217.2420.0180.0180.0000.0000.0000.000
63A65SER0-0.053-0.04416.1050.0340.0340.0000.0000.0000.000
64A66SER00.0510.00512.062-0.117-0.1170.0000.0000.0000.000
65A67SER0-0.0190.02313.7910.0770.0770.0000.0000.0000.000
66A68GLY00.0400.00912.441-0.015-0.0150.0000.0000.0000.000
67A69ASN0-0.040-0.0226.785-0.205-0.2050.0000.0000.0000.000
68A70THR0-0.066-0.0379.339-0.059-0.0590.0000.0000.0000.000
69A71ALA00.0920.05110.2870.0860.0860.0000.0000.0000.000
70A72THR0-0.081-0.04312.2310.1090.1090.0000.0000.0000.000
71A73LEU0-0.0170.00015.576-0.029-0.0290.0000.0000.0000.000
72A74THR0-0.025-0.01118.0100.0900.0900.0000.0000.0000.000
73A75ILE00.0240.00421.696-0.018-0.0180.0000.0000.0000.000
74A76SER0-0.011-0.00524.6860.0350.0350.0000.0000.0000.000
75A77GLY00.029-0.00228.331-0.002-0.0020.0000.0000.0000.000
76A78THR0-0.066-0.03226.8450.0080.0080.0000.0000.0000.000
77A79GLN00.008-0.00129.8710.0200.0200.0000.0000.0000.000
78A80THR00.0780.03830.454-0.011-0.0110.0000.0000.0000.000
79A81LEU0-0.056-0.03330.413-0.012-0.0120.0000.0000.0000.000
80A82ASP-1-0.757-0.84226.668-0.389-0.3890.0000.0000.0000.000
81A83GLU-1-0.852-0.91925.729-0.299-0.2990.0000.0000.0000.000
82A84ALA0-0.042-0.03223.0870.0050.0050.0000.0000.0000.000
83A85ASP-1-0.832-0.87719.077-0.385-0.3850.0000.0000.0000.000
84A86TYR0-0.025-0.03517.652-0.031-0.0310.0000.0000.0000.000
85A87TYR00.0250.03413.6800.0160.0160.0000.0000.0000.000
86A89GLN00.0530.02610.244-0.092-0.0920.0000.0000.0000.000
87A90VAL00.0420.0184.4440.4690.568-0.001-0.004-0.0930.000
88A91TRP0-0.025-0.0106.539-0.511-0.5110.0000.0000.0000.000
89A92ASP-1-0.836-0.9132.372-21.800-17.7232.346-2.769-3.653-0.034
90A93SER0-0.016-0.0124.3090.8590.950-0.001-0.006-0.0830.000
91A94ASN0-0.076-0.0454.3052.1762.276-0.001-0.007-0.0910.000
92A95ALA00.002-0.0046.7780.7010.7010.0000.0000.0000.000
93A95SER0-0.037-0.0064.4120.8430.960-0.001-0.007-0.1100.000
94A96VAL00.0200.0145.921-1.290-1.2900.0000.0000.0000.000
95A97VAL0-0.0090.0191.8301.2261.2532.848-1.321-1.555-0.008
96A98PHE0-0.050-0.0355.279-0.0420.032-0.001-0.002-0.0710.000
97A99GLY00.0380.0168.3600.2370.2370.0000.0000.0000.000
98A100GLY00.0240.0069.9170.1230.1230.0000.0000.0000.000
99A101GLY0-0.0160.00012.6200.1290.1290.0000.0000.0000.000
100A102THR0-0.040-0.04215.673-0.033-0.0330.0000.0000.0000.000
101A103LYS10.8340.90418.1360.3200.3200.0000.0000.0000.000
102A104LEU0-0.0300.00221.7230.0340.0340.0000.0000.0000.000
103A105THR0-0.085-0.05223.3870.0190.0190.0000.0000.0000.000
104A106VAL00.0100.01227.023-0.002-0.0020.0000.0000.0000.000
105A106LEU0-0.073-0.04629.8710.0150.0150.0000.0000.0000.000
106A107GLY00.0360.00731.962-0.001-0.0010.0000.0000.0000.000
107A108GLN0-0.016-0.00333.6210.0230.0230.0000.0000.0000.000
108A109PRO00.0080.01133.334-0.012-0.0120.0000.0000.0000.000
109A110LYS10.8550.93425.7900.1810.1810.0000.0000.0000.000
110A111ALA0-0.056-0.04030.3360.0120.0120.0000.0000.0000.000
111A112ALA00.0290.00628.160-0.007-0.0070.0000.0000.0000.000
112A113PRO0-0.018-0.00225.2320.0070.0070.0000.0000.0000.000
113A114SER00.0180.03828.5490.0120.0120.0000.0000.0000.000
114A115VAL00.0200.00325.9020.0000.0000.0000.0000.0000.000
115A116THR0-0.0090.00528.9820.0070.0070.0000.0000.0000.000
116A117LEU0-0.042-0.02126.1460.0010.0010.0000.0000.0000.000
117A118PHE0-0.012-0.01729.591-0.004-0.0040.0000.0000.0000.000
118A119PRO00.0190.02130.4780.0120.0120.0000.0000.0000.000
119A120PRO00.0200.01731.097-0.011-0.0110.0000.0000.0000.000
120A121SER00.0240.00833.717-0.001-0.0010.0000.0000.0000.000
121A122SER00.018-0.00937.3690.0060.0060.0000.0000.0000.000
122A123GLU-1-0.889-0.94339.7070.1060.1060.0000.0000.0000.000
123A124GLU-1-0.799-0.85533.0900.1720.1720.0000.0000.0000.000
124A125LEU00.0650.00634.5370.0090.0090.0000.0000.0000.000
125A126GLN0-0.052-0.00537.7120.0030.0030.0000.0000.0000.000
126A127ALA0-0.056-0.02438.3180.0010.0010.0000.0000.0000.000
127A128ASN0-0.027-0.01336.8470.0100.0100.0000.0000.0000.000
128A129LYS10.8290.91332.996-0.146-0.1460.0000.0000.0000.000
129A130ALA0-0.001-0.03530.976-0.002-0.0020.0000.0000.0000.000
130A131THR0-0.074-0.05128.0630.0240.0240.0000.0000.0000.000
131A132LEU0-0.0370.00225.959-0.015-0.0150.0000.0000.0000.000
132A133VAL00.0580.01327.0660.0030.0030.0000.0000.0000.000
133A134CYS0-0.041-0.01321.9380.0150.0150.0000.0000.0000.000
134A135LEU0-0.0090.00526.638-0.011-0.0110.0000.0000.0000.000
135A136ILE00.005-0.00223.5370.0000.0000.0000.0000.0000.000
136A137SER0-0.021-0.04827.970-0.008-0.0080.0000.0000.0000.000
137A138ASP-1-0.834-0.91630.606-0.023-0.0230.0000.0000.0000.000
138A139PHE0-0.0320.00925.197-0.007-0.0070.0000.0000.0000.000
139A140TYR00.007-0.01129.026-0.001-0.0010.0000.0000.0000.000
140A141PRO00.0840.04225.2510.0130.0130.0000.0000.0000.000
141A142GLY00.0170.00525.9470.0140.0140.0000.0000.0000.000
142A143ALA0-0.016-0.00920.595-0.014-0.0140.0000.0000.0000.000
143A144VAL0-0.012-0.00320.8190.0070.0070.0000.0000.0000.000
144A145THR00.0380.02415.076-0.051-0.0510.0000.0000.0000.000
145A146VAL0-0.0160.00017.6430.0050.0050.0000.0000.0000.000
146A147ALA0-0.0150.00315.7820.0350.0350.0000.0000.0000.000
147A148TRP00.0460.00017.035-0.039-0.0390.0000.0000.0000.000
148A149LYS10.7910.84617.215-0.255-0.2550.0000.0000.0000.000
149A150ALA0-0.010-0.01519.475-0.054-0.0540.0000.0000.0000.000
150A151ASP-1-0.772-0.87821.5700.3840.3840.0000.0000.0000.000
151A152SER0-0.016-0.01419.4540.0100.0100.0000.0000.0000.000
152A153SER0-0.0390.00417.4100.0550.0550.0000.0000.0000.000
153A154PRO00.0370.03813.142-0.078-0.0780.0000.0000.0000.000
154A155VAL0-0.029-0.01615.7960.0490.0490.0000.0000.0000.000
155A156LYS10.9010.9658.484-1.483-1.4830.0000.0000.0000.000
156A157ALA00.020-0.01515.0360.0780.0780.0000.0000.0000.000
157A158GLY00.0610.04118.328-0.039-0.0390.0000.0000.0000.000
158A159VAL0-0.071-0.02416.695-0.038-0.0380.0000.0000.0000.000
159A160GLU-1-0.915-0.96119.4210.2650.2650.0000.0000.0000.000
160A161THR0-0.055-0.03019.183-0.018-0.0180.0000.0000.0000.000
161A162THR0-0.025-0.00921.608-0.021-0.0210.0000.0000.0000.000
162A163THR0-0.008-0.01721.964-0.023-0.0230.0000.0000.0000.000
163A164PRO0-0.018-0.00322.9010.0120.0120.0000.0000.0000.000
164A165SER0-0.0080.00125.916-0.016-0.0160.0000.0000.0000.000
165A166LYS10.8690.94329.4710.0920.0920.0000.0000.0000.000
166A167GLN00.0340.00032.2130.0120.0120.0000.0000.0000.000
167A168SER00.002-0.02734.659-0.009-0.0090.0000.0000.0000.000
168A170ASN00.0100.01336.569-0.005-0.0050.0000.0000.0000.000
169A171ASN0-0.019-0.02035.414-0.003-0.0030.0000.0000.0000.000
170A172LYS10.9140.99232.6160.0640.0640.0000.0000.0000.000
171A173TYR0-0.046-0.03228.399-0.002-0.0020.0000.0000.0000.000
172A174ALA00.0110.01429.6510.0080.0080.0000.0000.0000.000
173A175ALA00.0570.03624.849-0.017-0.0170.0000.0000.0000.000
174A176SER0-0.035-0.02625.7230.0110.0110.0000.0000.0000.000
175A177SER00.0450.02821.1480.0040.0040.0000.0000.0000.000
176A178TYR00.0160.02023.391-0.019-0.0190.0000.0000.0000.000
177A179LEU00.0300.03021.2890.0230.0230.0000.0000.0000.000
178A180SER00.0420.03423.889-0.037-0.0370.0000.0000.0000.000
179A181LEU0-0.060-0.02524.6290.0380.0380.0000.0000.0000.000
180A182THR00.0450.00626.735-0.027-0.0270.0000.0000.0000.000
181A183PRO00.0540.02229.9070.0160.0160.0000.0000.0000.000
182A184GLU-1-0.867-0.93831.7640.2270.2270.0000.0000.0000.000
183A185GLN00.0410.03224.505-0.007-0.0070.0000.0000.0000.000
184A186TRP00.0120.02128.5080.0110.0110.0000.0000.0000.000
185A187LYS10.8700.91129.664-0.176-0.1760.0000.0000.0000.000
186A188SER0-0.064-0.01928.5250.0030.0030.0000.0000.0000.000
187A189HIS10.8000.87323.378-0.393-0.3930.0000.0000.0000.000
188A190ARG10.9460.97528.116-0.246-0.2460.0000.0000.0000.000
189A191SER0-0.021-0.02826.777-0.032-0.0320.0000.0000.0000.000
190A192TYR0-0.0240.00223.6430.0450.0450.0000.0000.0000.000
191A193SER0-0.0180.00621.994-0.020-0.0200.0000.0000.0000.000
192A195GLN0-0.034-0.02117.6520.0100.0100.0000.0000.0000.000
193A196VAL00.0380.00719.6280.0030.0030.0000.0000.0000.000
194A197THR00.011-0.00817.4950.0150.0150.0000.0000.0000.000
195A198HIS0-0.027-0.02719.767-0.022-0.0220.0000.0000.0000.000
196A199GLU-1-0.697-0.80020.681-0.285-0.2850.0000.0000.0000.000
197A200GLY0-0.015-0.01421.2260.0150.0150.0000.0000.0000.000
198A203SER0-0.033-0.02222.4860.0120.0120.0000.0000.0000.000
199A204THR00.0150.01219.738-0.015-0.0150.0000.0000.0000.000
200A205VAL0-0.024-0.00222.4970.0080.0080.0000.0000.0000.000
201A206GLU-1-0.762-0.87821.1450.2390.2390.0000.0000.0000.000
202A207LYS10.8980.96724.604-0.066-0.0660.0000.0000.0000.000
203A208THR00.009-0.03226.2080.0260.0260.0000.0000.0000.000
204A209VAL0-0.0220.00528.310-0.015-0.0150.0000.0000.0000.000
205A210ALA00.0060.00129.3840.0200.0200.0000.0000.0000.000
206A211PRO0-0.024-0.01230.743-0.016-0.0160.0000.0000.0000.000
207A212THR00.0150.00133.753-0.008-0.0080.0000.0000.0000.000
208A213GLU-1-0.806-0.85737.3580.1650.1650.0000.0000.0000.000
209A214CYS0-0.0100.02740.375-0.003-0.0030.0000.0000.0000.000
210A215SER0-0.066-0.07742.886-0.009-0.0090.0000.0000.0000.000