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: JLG59

Calculation Name: 1I6A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I6A

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACQ4

Base Structure: X-ray

Registration Date: 2023-09-20

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2426345.31916
FMO2-HF: Nuclear repulsion 2342713.052182
FMO2-HF: Total energy -83632.266977
FMO2-MP2: Total energy -83872.815506


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:87:GLU)


Summations of interaction energy for fragment #1(A:87:GLU)
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.
-48.387-48.92218.214-9.537-8.1390.081
Interaction energy analysis for fragmet #1(A:87:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.872 / q_NPA : -0.938
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].
3A89MET0-0.0360.0053.420-7.991-5.407-0.007-1.230-1.3460.005
4A90SER00.0140.0072.0640.8370.5984.605-2.086-2.279-0.006
5A91GLY00.0100.0164.376-2.545-2.466-0.001-0.026-0.0520.000
6A92PRO0-0.003-0.0087.1810.1290.1290.0000.0000.0000.000
7A93LEU0-0.0020.01410.2060.3210.3210.0000.0000.0000.000
8A94HIS10.8140.90012.595-16.031-16.0310.0000.0000.0000.000
9A95ILE00.0490.01314.497-0.025-0.0250.0000.0000.0000.000
10A96GLY00.0000.00518.352-0.377-0.3770.0000.0000.0000.000
11A97LEU0-0.0050.00321.3820.2590.2590.0000.0000.0000.000
12A98ILE00.0560.03424.598-0.258-0.2580.0000.0000.0000.000
13A99PRO00.029-0.00528.3200.1610.1610.0000.0000.0000.000
14A100THR0-0.050-0.02830.5980.1020.1020.0000.0000.0000.000
15A101VAL00.0100.01125.777-0.052-0.0520.0000.0000.0000.000
16A102GLY00.0110.01225.1730.2010.2010.0000.0000.0000.000
17A103PRO00.0180.00225.7160.3800.3800.0000.0000.0000.000
18A104TYR0-0.071-0.06428.0510.0720.0720.0000.0000.0000.000
19A105LEU00.0330.02723.0430.0900.0900.0000.0000.0000.000
20A106LEU00.0100.00520.6490.6210.6210.0000.0000.0000.000
21A107PRO0-0.022-0.00621.9580.6950.6950.0000.0000.0000.000
22A108HIS00.0020.00423.6660.4920.4920.0000.0000.0000.000
23A109ILE00.010-0.00718.8810.5380.5380.0000.0000.0000.000
24A110ILE00.0140.01317.4451.0501.0500.0000.0000.0000.000
25A111PRO0-0.001-0.00616.7311.1311.1310.0000.0000.0000.000
26A112MET00.0180.02716.1911.3231.3230.0000.0000.0000.000
27A113LEU00.0430.01513.4571.7401.7400.0000.0000.0000.000
28A114HIS0-0.008-0.00412.1232.8002.8000.0000.0000.0000.000
29A115GLN0-0.063-0.03112.3961.4721.4720.0000.0000.0000.000
30A116THR0-0.041-0.02410.6251.5371.5370.0000.0000.0000.000
31A117PHE0-0.040-0.0327.5513.8253.8250.0000.0000.0000.000
32A118PRO00.0290.0167.695-0.495-0.4950.0000.0000.0000.000
33A119LYS10.8460.9221.749-120.054-123.11313.618-6.171-4.3880.082
34A120LEU0-0.0210.0026.752-0.526-0.5260.0000.0000.0000.000
35A121GLU-1-0.876-0.9078.21218.37318.3730.0000.0000.0000.000
36A122MET0-0.017-0.02011.358-0.463-0.4630.0000.0000.0000.000
37A123TYR0-0.086-0.05613.983-1.214-1.2140.0000.0000.0000.000
38A124LEU00.008-0.00317.2300.0410.0410.0000.0000.0000.000
39A125HIS00.0110.01119.8730.0760.0760.0000.0000.0000.000
40A126GLU-1-0.838-0.92523.14011.10011.1000.0000.0000.0000.000
41A127ALA0-0.043-0.02926.503-0.270-0.2700.0000.0000.0000.000
42A128GLN00.0560.02329.0280.1040.1040.0000.0000.0000.000
43A129THR00.032-0.02329.5560.3330.3330.0000.0000.0000.000
44A130HIS00.0270.01529.5240.3740.3740.0000.0000.0000.000
45A131GLN0-0.019-0.01929.6710.0980.0980.0000.0000.0000.000
46A132LEU0-0.014-0.00324.4250.2890.2890.0000.0000.0000.000
47A133LEU00.0330.01725.1920.4200.4200.0000.0000.0000.000
48A134ALA00.0220.02526.7100.1000.1000.0000.0000.0000.000
49A135GLN0-0.043-0.02623.9270.2990.2990.0000.0000.0000.000
50A136LEU00.0010.02520.3020.4630.4630.0000.0000.0000.000
51A137ASP-1-0.902-0.95222.24710.97910.9790.0000.0000.0000.000
52A138SER0-0.114-0.05924.579-0.088-0.0880.0000.0000.0000.000
53A139GLY0-0.022-0.00520.4390.0420.0420.0000.0000.0000.000
54A140LYS10.8710.93319.353-10.134-10.1340.0000.0000.0000.000
55A141LEU00.0100.02018.8010.3250.3250.0000.0000.0000.000
56A142ASP-1-0.841-0.88413.82017.57317.5730.0000.0000.0000.000
57A143ALA00.007-0.01016.555-0.025-0.0250.0000.0000.0000.000
58A144VAL0-0.013-0.00518.584-0.104-0.1040.0000.0000.0000.000
59A145ILE0-0.0110.00919.2740.1390.1390.0000.0000.0000.000
60A146LEU0-0.016-0.02423.260-0.281-0.2810.0000.0000.0000.000
61A147ALA00.0070.01527.0250.1830.1830.0000.0000.0000.000
62A148LEU0-0.027-0.00826.103-0.065-0.0650.0000.0000.0000.000
63A149VAL00.0020.00730.067-0.325-0.3250.0000.0000.0000.000
64A150LYS10.9310.94832.283-7.541-7.5410.0000.0000.0000.000
65A151GLU-1-0.942-0.97932.4408.7268.7260.0000.0000.0000.000
66A152SER0-0.078-0.07027.7730.1230.1230.0000.0000.0000.000
67A153GLU-1-0.874-0.93528.1729.1409.1400.0000.0000.0000.000
68A154ALA0-0.104-0.03429.4180.0640.0640.0000.0000.0000.000
69A155PHE0-0.058-0.04324.2780.3020.3020.0000.0000.0000.000
70A156ILE0-0.040-0.00620.684-0.183-0.1830.0000.0000.0000.000
71A157GLU-1-0.799-0.89322.77710.83410.8340.0000.0000.0000.000
72A158VAL0-0.019-0.01019.1870.0070.0070.0000.0000.0000.000
73A159PRO0-0.002-0.00722.3540.1800.1800.0000.0000.0000.000
74A160LEU0-0.066-0.02019.8800.5190.5190.0000.0000.0000.000
75A161PHE00.037-0.00223.4660.1480.1480.0000.0000.0000.000
76A162ASP-1-0.869-0.91026.7379.8029.8020.0000.0000.0000.000
77A163GLU-1-0.796-0.90330.3109.9869.9860.0000.0000.0000.000
78A164PRO00.0100.00932.033-0.209-0.2090.0000.0000.0000.000
79A165MET0-0.034-0.02135.4770.1860.1860.0000.0000.0000.000
80A166LEU0-0.006-0.00437.901-0.178-0.1780.0000.0000.0000.000
81A167LEU0-0.006-0.01040.805-0.001-0.0010.0000.0000.0000.000
82A168ALA0-0.0030.00342.4970.0300.0300.0000.0000.0000.000
83A169ILE00.004-0.00644.567-0.085-0.0850.0000.0000.0000.000
84A170TYR00.0730.03848.1110.0510.0510.0000.0000.0000.000
85A171GLU-1-0.821-0.91850.0376.2316.2310.0000.0000.0000.000
86A172ASP-1-0.966-0.97051.8915.7025.7020.0000.0000.0000.000
87A173HIS0-0.019-0.00452.646-0.105-0.1050.0000.0000.0000.000
88A174PRO00.028-0.00654.6480.0160.0160.0000.0000.0000.000
89A175TRP0-0.028-0.02950.3920.0190.0190.0000.0000.0000.000
90A176ALA00.0350.04151.6700.0970.0970.0000.0000.0000.000
91A177ASN0-0.049-0.03652.0840.1180.1180.0000.0000.0000.000
92A178ARG10.7780.89452.067-6.011-6.0110.0000.0000.0000.000
93A179GLU-1-0.915-0.96349.1876.4566.4560.0000.0000.0000.000
94A180ALA0-0.029-0.01947.5490.1750.1750.0000.0000.0000.000
95A181VAL0-0.015-0.00247.738-0.174-0.1740.0000.0000.0000.000
96A182PRO0-0.069-0.02447.9250.1620.1620.0000.0000.0000.000
97A183MET00.0530.02145.009-0.030-0.0300.0000.0000.0000.000
98A184ALA00.0070.00648.250-0.044-0.0440.0000.0000.0000.000
99A185ASP-1-0.781-0.89151.6025.8285.8280.0000.0000.0000.000
100A186LEU0-0.065-0.02646.546-0.054-0.0540.0000.0000.0000.000
101A187ALA00.0090.00651.210-0.003-0.0030.0000.0000.0000.000
102A188GLY0-0.032-0.02854.019-0.064-0.0640.0000.0000.0000.000
103A189GLU-1-0.884-0.92151.7325.8545.8540.0000.0000.0000.000
104A190LYS10.8810.95351.393-5.961-5.9610.0000.0000.0000.000
105A191LEU0-0.001-0.00647.0650.0990.0990.0000.0000.0000.000
106A192LEU0-0.055-0.02045.283-0.029-0.0290.0000.0000.0000.000
107A193MET00.0090.00542.6090.1150.1150.0000.0000.0000.000
108A194LEU00.0000.00337.272-0.047-0.0470.0000.0000.0000.000
109A195GLU-1-0.836-0.92138.9587.3527.3520.0000.0000.0000.000
110A196ASP-1-0.781-0.87633.2009.1499.1490.0000.0000.0000.000
111A197GLY0-0.0080.00133.4540.0290.0290.0000.0000.0000.000
112A198HIS0-0.050-0.01734.1750.0760.0760.0000.0000.0000.000
113A199CYS0-0.075-0.03037.2210.1590.1590.0000.0000.0000.000
114A200LEU00.0250.02238.0960.1500.1500.0000.0000.0000.000
115A201ARG10.8260.92839.362-6.959-6.9590.0000.0000.0000.000
116A202ASP-1-0.772-0.86739.5197.4637.4630.0000.0000.0000.000
117A203GLN00.005-0.02939.823-0.292-0.2920.0000.0000.0000.000
118A204ALA0-0.044-0.00743.134-0.139-0.1390.0000.0000.0000.000
119A205MET0-0.081-0.04644.455-0.119-0.1190.0000.0000.0000.000
120A206GLY0-0.019-0.00246.939-0.137-0.1370.0000.0000.0000.000
121A207PHE0-0.030-0.00946.930-0.073-0.0730.0000.0000.0000.000
122A209PHE0-0.039-0.04340.3360.1730.1730.0000.0000.0000.000
123A210GLU-1-0.865-0.94745.0386.3046.3040.0000.0000.0000.000
124A211ALA00.0030.01448.590-0.048-0.0480.0000.0000.0000.000
125A212GLY0-0.016-0.00551.154-0.087-0.0870.0000.0000.0000.000
126A213ALA0-0.0330.00550.182-0.100-0.1000.0000.0000.0000.000
127A214ASP-1-0.934-0.96052.3325.7915.7910.0000.0000.0000.000
128A215GLU-1-0.727-0.86347.2246.7646.7640.0000.0000.0000.000
129A216ASP-1-0.806-0.89348.7116.1646.1640.0000.0000.0000.000
130A217THR00.037-0.00647.0690.1140.1140.0000.0000.0000.000
131A218HIS10.7810.86847.113-5.970-5.9700.0000.0000.0000.000
132A219PHE00.0150.00844.5500.0120.0120.0000.0000.0000.000
133A220ARG10.9050.95342.482-6.736-6.7360.0000.0000.0000.000
134A221ALA00.0020.01140.5480.1780.1780.0000.0000.0000.000
135A222THR0-0.059-0.03440.2200.0670.0670.0000.0000.0000.000
136A223SER00.0270.00536.1640.1670.1670.0000.0000.0000.000
137A224LEU00.0870.03634.600-0.189-0.1890.0000.0000.0000.000
138A225GLU-1-0.754-0.82235.6088.3818.3810.0000.0000.0000.000
139A226THR0-0.051-0.02338.406-0.211-0.2110.0000.0000.0000.000
140A227LEU00.0080.00340.713-0.197-0.1970.0000.0000.0000.000
141A228ARG10.7750.86036.250-8.463-8.4630.0000.0000.0000.000
142A229ASN00.013-0.00741.150-0.134-0.1340.0000.0000.0000.000
143A230MET0-0.037-0.01044.320-0.167-0.1670.0000.0000.0000.000
144A231VAL0-0.0250.00145.196-0.169-0.1690.0000.0000.0000.000
145A232ALA00.0170.01546.261-0.145-0.1450.0000.0000.0000.000
146A233ALA0-0.074-0.02848.160-0.128-0.1280.0000.0000.0000.000
147A234GLY00.0190.01050.389-0.140-0.1400.0000.0000.0000.000
148A235SER0-0.081-0.04449.672-0.107-0.1070.0000.0000.0000.000
149A236GLY00.013-0.00350.242-0.068-0.0680.0000.0000.0000.000
150A237ILE00.0280.02247.5980.0710.0710.0000.0000.0000.000
151A238THR0-0.017-0.03742.1850.0710.0710.0000.0000.0000.000
152A239LEU00.0170.02440.901-0.029-0.0290.0000.0000.0000.000
153A240LEU0-0.0150.00037.7260.0840.0840.0000.0000.0000.000
154A241PRO00.0210.01233.279-0.072-0.0720.0000.0000.0000.000
155A242ALA00.0510.02133.617-0.025-0.0250.0000.0000.0000.000
156A243LEU0-0.034-0.01527.791-0.005-0.0050.0000.0000.0000.000
157A244ALA0-0.038-0.00331.8880.0930.0930.0000.0000.0000.000
158A245VAL0-0.023-0.00634.188-0.321-0.3210.0000.0000.0000.000
159A246PRO0-0.054-0.01335.9140.2130.2130.0000.0000.0000.000
160A247PRO00.008-0.00935.631-0.053-0.0530.0000.0000.0000.000
161A248GLU-1-0.849-0.90138.0547.8527.8520.0000.0000.0000.000
162A249ARG10.9070.95541.758-6.618-6.6180.0000.0000.0000.000
163A250LYS10.8000.87344.207-6.387-6.3870.0000.0000.0000.000
164A251ARG10.8500.91237.497-8.015-8.0150.0000.0000.0000.000
165A252ASP-1-0.907-0.95942.6997.3337.3330.0000.0000.0000.000
166A253GLY00.0390.02846.047-0.047-0.0470.0000.0000.0000.000
167A254VAL0-0.049-0.02044.032-0.093-0.0930.0000.0000.0000.000
168A255VAL0-0.013-0.00945.9720.0740.0740.0000.0000.0000.000
169A256TYR00.024-0.00341.3780.0730.0730.0000.0000.0000.000
170A257LEU0-0.042-0.01944.117-0.014-0.0140.0000.0000.0000.000
171A258PRO00.0380.01842.7210.0650.0650.0000.0000.0000.000
172A259ALA00.0460.04242.949-0.199-0.1990.0000.0000.0000.000
173A260ILE0-0.008-0.03043.4220.1300.1300.0000.0000.0000.000
174A261LYS10.9000.97245.623-6.321-6.3210.0000.0000.0000.000
175A262PRO00.0450.01542.809-0.150-0.1500.0000.0000.0000.000
176A263GLU-1-0.800-0.90538.4468.1958.1950.0000.0000.0000.000
177A264PRO0-0.014-0.00140.0300.1120.1120.0000.0000.0000.000
178A265ARG10.8460.90034.526-8.634-8.6340.0000.0000.0000.000
179A266ARG10.7770.88731.221-9.746-9.7460.0000.0000.0000.000
180A267THR00.029-0.00228.3560.0780.0780.0000.0000.0000.000
181A268ILE0-0.045-0.01125.158-0.042-0.0420.0000.0000.0000.000
182A269GLY00.0660.01824.1980.2530.2530.0000.0000.0000.000
183A270LEU0-0.052-0.02117.2890.0370.0370.0000.0000.0000.000
184A271VAL00.0360.00621.622-0.031-0.0310.0000.0000.0000.000
185A272TYR0-0.042-0.05718.0280.5350.5350.0000.0000.0000.000
186A273ARG10.8970.93317.201-14.283-14.2830.0000.0000.0000.000
187A274PRO00.0940.04820.0020.7100.7100.0000.0000.0000.000
188A275GLY0-0.024-0.01820.365-0.187-0.1870.0000.0000.0000.000
189A276SER0-0.058-0.01615.7730.3670.3670.0000.0000.0000.000
190A277PRO00.024-0.01013.8140.5230.5230.0000.0000.0000.000
191A278LEU0-0.028-0.0089.4341.2021.2020.0000.0000.0000.000
192A279ARG10.9170.94012.055-14.987-14.9870.0000.0000.0000.000
193A280SER0-0.0060.0049.037-0.281-0.2810.0000.0000.0000.000
194A281ARG10.9210.9524.659-28.189-28.089-0.001-0.024-0.0740.000
195A282TYR0-0.033-0.05410.168-0.187-0.1870.0000.0000.0000.000
196A283GLU-1-0.773-0.84513.59215.48215.4820.0000.0000.0000.000
197A284GLN0-0.030-0.0186.8170.0520.0520.0000.0000.0000.000
198A285LEU0-0.016-0.00211.9350.0240.0240.0000.0000.0000.000
199A286ALA00.0230.00513.373-0.660-0.6600.0000.0000.0000.000
200A287GLU-1-0.834-0.91414.69815.81415.8140.0000.0000.0000.000
201A288ALA0-0.025-0.01213.485-0.436-0.4360.0000.0000.0000.000
202A289ILE0-0.025-0.02215.611-0.691-0.6910.0000.0000.0000.000
203A290ARG10.8210.90318.653-15.048-15.0480.0000.0000.0000.000
204A291ALA0-0.016-0.00818.311-0.606-0.6060.0000.0000.0000.000
205A292ARG10.8130.91419.558-13.826-13.8260.0000.0000.0000.000
206A293MET0-0.040-0.01821.194-0.437-0.4370.0000.0000.0000.000
207A294ASP-1-0.841-0.90023.63511.80511.8050.0000.0000.0000.000
208A295GLY00.0150.02025.4870.0400.0400.0000.0000.0000.000
209A296HIS0-0.054-0.01927.1020.0560.0560.0000.0000.0000.000
210A297PHE0-0.032-0.03629.031-0.226-0.2260.0000.0000.0000.000
211A298ASP-1-0.970-0.96932.1309.3859.3850.0000.0000.0000.000