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: 39R1L

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2435386.457348
FMO2-HF: Nuclear repulsion 2351753.931142
FMO2-HF: Total energy -83632.526205
FMO2-MP2: Total energy -83873.172178


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.
-81.158-102.92655.079-20.84-12.4730.158
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 : -0.816 / q_NPA : -0.866
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].
3A89MET0-0.0470.0043.454-6.680-5.0870.002-0.660-0.9360.002
4A90SER00.033-0.0251.710-9.992-23.67826.521-9.230-3.6050.023
5A91GLY00.0150.0114.726-4.453-4.3500.000-0.054-0.0490.000
6A92PRO0-0.018-0.0078.052-0.389-0.3890.0000.0000.0000.000
7A93LEU0-0.022-0.00110.6120.5540.5540.0000.0000.0000.000
8A94HIS10.8100.89913.112-17.818-17.8180.0000.0000.0000.000
9A95ILE00.0600.03514.526-0.323-0.3230.0000.0000.0000.000
10A96GLY00.0110.00418.546-0.397-0.3970.0000.0000.0000.000
11A97LEU0-0.020-0.00921.0970.2500.2500.0000.0000.0000.000
12A98ILE00.0660.04024.498-0.284-0.2840.0000.0000.0000.000
13A99PRO00.0340.00928.2830.1040.1040.0000.0000.0000.000
14A100THR0-0.060-0.03230.4740.0630.0630.0000.0000.0000.000
15A101VAL00.0180.01325.681-0.097-0.0970.0000.0000.0000.000
16A102GLY00.0190.01524.9950.2190.2190.0000.0000.0000.000
17A103PRO0-0.009-0.01225.5430.3860.3860.0000.0000.0000.000
18A104TYR0-0.078-0.05627.928-0.035-0.0350.0000.0000.0000.000
19A105LEU00.0150.00422.7030.1140.1140.0000.0000.0000.000
20A106LEU00.0170.01020.4990.6290.6290.0000.0000.0000.000
21A107PRO0-0.008-0.00621.5140.7760.7760.0000.0000.0000.000
22A108HIS00.0040.00623.0420.5080.5080.0000.0000.0000.000
23A109ILE00.0170.00318.5390.4770.4770.0000.0000.0000.000
24A110ILE00.0200.01417.0731.1301.1300.0000.0000.0000.000
25A111PRO0-0.012-0.00916.4151.2221.2220.0000.0000.0000.000
26A112MET00.0180.03515.8971.4211.4210.0000.0000.0000.000
27A113LEU00.0370.00913.2021.7541.7540.0000.0000.0000.000
28A114HIS0-0.002-0.00211.7223.2043.2040.0000.0000.0000.000
29A115GLN0-0.055-0.02811.9921.4961.4960.0000.0000.0000.000
30A116THR0-0.051-0.03010.7951.3921.3920.0000.0000.0000.000
31A117PHE0-0.020-0.0227.3903.2563.2560.0000.0000.0000.000
32A118PRO00.0190.0107.5080.7540.7540.0000.0000.0000.000
33A119LYS10.7970.8901.770-139.602-149.44628.557-10.879-7.8350.133
34A120LEU0-0.0160.0046.4800.3280.3280.0000.0000.0000.000
35A121GLU-1-0.880-0.9228.27820.28620.2860.0000.0000.0000.000
36A122MET0-0.006-0.01511.675-0.866-0.8660.0000.0000.0000.000
37A123TYR0-0.075-0.05014.194-1.663-1.6630.0000.0000.0000.000
38A124LEU0-0.005-0.00217.4460.1410.1410.0000.0000.0000.000
39A125HIS00.0220.01620.2940.1720.1720.0000.0000.0000.000
40A126GLU-1-0.833-0.92423.46411.64911.6490.0000.0000.0000.000
41A127ALA0-0.048-0.03026.787-0.289-0.2890.0000.0000.0000.000
42A128GLN00.0610.01929.4180.0970.0970.0000.0000.0000.000
43A129THR00.025-0.01929.8050.3540.3540.0000.0000.0000.000
44A130HIS00.0320.01429.8080.4360.4360.0000.0000.0000.000
45A131GLN0-0.015-0.00430.5280.1490.1490.0000.0000.0000.000
46A132LEU0-0.0110.00224.8870.3220.3220.0000.0000.0000.000
47A133LEU00.0290.02125.7930.4410.4410.0000.0000.0000.000
48A134ALA00.0380.02326.9670.1560.1560.0000.0000.0000.000
49A135GLN0-0.060-0.02924.7590.4110.4110.0000.0000.0000.000
50A136LEU0-0.0140.01520.7080.4840.4840.0000.0000.0000.000
51A137ASP-1-0.904-0.94522.82511.25511.2550.0000.0000.0000.000
52A138SER0-0.117-0.07124.848-0.001-0.0010.0000.0000.0000.000
53A139GLY0-0.034-0.01621.0250.0820.0820.0000.0000.0000.000
54A140LYS10.8720.93820.129-10.577-10.5770.0000.0000.0000.000
55A141LEU00.0130.01619.5750.2760.2760.0000.0000.0000.000
56A142ASP-1-0.841-0.88714.39519.39219.3920.0000.0000.0000.000
57A143ALA00.020-0.00417.079-0.193-0.1930.0000.0000.0000.000
58A144VAL0-0.026-0.00819.0940.0100.0100.0000.0000.0000.000
59A145ILE0-0.004-0.00218.9140.1390.1390.0000.0000.0000.000
60A146LEU0-0.017-0.02023.185-0.253-0.2530.0000.0000.0000.000
61A147ALA00.0160.01126.9550.1660.1660.0000.0000.0000.000
62A148LEU0-0.034-0.00726.067-0.029-0.0290.0000.0000.0000.000
63A149VAL0-0.009-0.00130.107-0.351-0.3510.0000.0000.0000.000
64A150LYS10.9020.93432.228-7.635-7.6350.0000.0000.0000.000
65A151GLU-1-0.947-0.98232.5088.9488.9480.0000.0000.0000.000
66A152SER0-0.073-0.07127.7170.1530.1530.0000.0000.0000.000
67A153GLU-1-0.858-0.93128.2579.1879.1870.0000.0000.0000.000
68A154ALA0-0.079-0.02529.7750.0100.0100.0000.0000.0000.000
69A155PHE0-0.067-0.04024.3620.2860.2860.0000.0000.0000.000
70A156ILE0-0.046-0.01220.820-0.211-0.2110.0000.0000.0000.000
71A157GLU-1-0.790-0.88922.85211.09111.0910.0000.0000.0000.000
72A158VAL0-0.032-0.02019.0420.0180.0180.0000.0000.0000.000
73A159PRO00.015-0.00122.2040.2690.2690.0000.0000.0000.000
74A160LEU0-0.087-0.02719.9080.5330.5330.0000.0000.0000.000
75A161PHE00.0580.00023.5990.1210.1210.0000.0000.0000.000
76A162ASP-1-0.847-0.89527.0059.9389.9380.0000.0000.0000.000
77A163GLU-1-0.767-0.86730.1669.9819.9810.0000.0000.0000.000
78A164PRO00.0190.01631.812-0.215-0.2150.0000.0000.0000.000
79A165MET0-0.037-0.02435.1130.2360.2360.0000.0000.0000.000
80A166LEU00.0050.00737.708-0.208-0.2080.0000.0000.0000.000
81A167LEU00.000-0.00140.6030.0150.0150.0000.0000.0000.000
82A168ALA0-0.002-0.00242.1670.0470.0470.0000.0000.0000.000
83A169ILE00.001-0.00244.278-0.077-0.0770.0000.0000.0000.000
84A170TYR00.0860.04447.8740.0490.0490.0000.0000.0000.000
85A171GLU-1-0.820-0.90449.4906.4026.4020.0000.0000.0000.000
86A172ASP-1-0.939-0.96651.5975.7955.7950.0000.0000.0000.000
87A173HIS0-0.019-0.00752.116-0.099-0.0990.0000.0000.0000.000
88A174PRO00.005-0.01354.1390.0170.0170.0000.0000.0000.000
89A175TRP0-0.026-0.02150.2570.0020.0020.0000.0000.0000.000
90A176ALA00.0400.03750.8540.1000.1000.0000.0000.0000.000
91A177ASN0-0.033-0.02351.3590.1210.1210.0000.0000.0000.000
92A178ARG10.7800.88751.939-6.104-6.1040.0000.0000.0000.000
93A179GLU-1-0.921-0.95648.9266.5026.5020.0000.0000.0000.000
94A180ALA0-0.003-0.01147.0690.1820.1820.0000.0000.0000.000
95A181VAL0-0.0080.00047.424-0.182-0.1820.0000.0000.0000.000
96A182PRO0-0.065-0.02947.5660.1660.1660.0000.0000.0000.000
97A183MET00.0330.01244.889-0.037-0.0370.0000.0000.0000.000
98A184ALA00.0170.01448.204-0.035-0.0350.0000.0000.0000.000
99A185ASP-1-0.790-0.88851.7065.9135.9130.0000.0000.0000.000
100A186LEU0-0.027-0.01646.545-0.044-0.0440.0000.0000.0000.000
101A187ALA0-0.0120.00051.180-0.010-0.0100.0000.0000.0000.000
102A188GLY0-0.033-0.01954.145-0.085-0.0850.0000.0000.0000.000
103A189GLU-1-0.874-0.90751.3065.9625.9620.0000.0000.0000.000
104A190LYS10.8140.90151.159-6.111-6.1110.0000.0000.0000.000
105A191LEU00.0050.00446.2340.1040.1040.0000.0000.0000.000
106A192LEU0-0.064-0.02145.159-0.063-0.0630.0000.0000.0000.000
107A193MET0-0.0070.00242.5110.1300.1300.0000.0000.0000.000
108A194LEU00.0130.00237.491-0.028-0.0280.0000.0000.0000.000
109A195GLU-1-0.825-0.89939.1657.5617.5610.0000.0000.0000.000
110A196ASP-1-0.792-0.87633.2309.5149.5140.0000.0000.0000.000
111A197GLY00.0090.00433.211-0.024-0.0240.0000.0000.0000.000
112A198HIS0-0.055-0.01833.8740.1130.1130.0000.0000.0000.000
113A199CYS0-0.064-0.02536.8730.0950.0950.0000.0000.0000.000
114A200LEU00.0280.01637.9120.1630.1630.0000.0000.0000.000
115A201ARG10.8190.92639.896-7.091-7.0910.0000.0000.0000.000
116A202ASP-1-0.779-0.87339.1687.6857.6850.0000.0000.0000.000
117A203GLN00.015-0.02339.629-0.322-0.3220.0000.0000.0000.000
118A204ALA0-0.0290.00042.866-0.181-0.1810.0000.0000.0000.000
119A205MET0-0.074-0.03444.133-0.126-0.1260.0000.0000.0000.000
120A206GLY0-0.023-0.00646.545-0.150-0.1500.0000.0000.0000.000
121A207PHE0-0.046-0.01846.710-0.089-0.0890.0000.0000.0000.000
122A209PHE0-0.028-0.04340.0860.1660.1660.0000.0000.0000.000
123A210GLU-1-0.876-0.96244.7066.4216.4210.0000.0000.0000.000
124A211ALA00.0070.02448.361-0.054-0.0540.0000.0000.0000.000
125A212GLY0-0.009-0.00551.087-0.117-0.1170.0000.0000.0000.000
126A213ALA0-0.0220.00549.929-0.098-0.0980.0000.0000.0000.000
127A214ASP-1-0.910-0.96052.0495.9155.9150.0000.0000.0000.000
128A215GLU-1-0.723-0.86246.9786.9196.9190.0000.0000.0000.000
129A216ASP-1-0.801-0.87748.6626.3266.3260.0000.0000.0000.000
130A217THR00.0370.00047.0280.1330.1330.0000.0000.0000.000
131A218HIS10.7820.87047.244-6.098-6.0980.0000.0000.0000.000
132A219PHE00.0410.01644.5720.0340.0340.0000.0000.0000.000
133A220ARG10.8660.93842.520-6.924-6.9240.0000.0000.0000.000
134A221ALA00.0160.02140.8280.1860.1860.0000.0000.0000.000
135A222THR0-0.061-0.05340.1270.0380.0380.0000.0000.0000.000
136A223SER00.004-0.01036.0920.2870.2870.0000.0000.0000.000
137A224LEU00.0790.03134.511-0.215-0.2150.0000.0000.0000.000
138A225GLU-1-0.739-0.80935.6128.5888.5880.0000.0000.0000.000
139A226THR0-0.047-0.01138.429-0.134-0.1340.0000.0000.0000.000
140A227LEU00.0130.01240.388-0.207-0.2070.0000.0000.0000.000
141A228ARG10.7820.86536.258-8.642-8.6420.0000.0000.0000.000
142A229ASN00.006-0.00741.159-0.173-0.1730.0000.0000.0000.000
143A230MET0-0.041-0.01844.262-0.175-0.1750.0000.0000.0000.000
144A231VAL0-0.0350.00045.191-0.170-0.1700.0000.0000.0000.000
145A232ALA00.0160.00545.896-0.151-0.1510.0000.0000.0000.000
146A233ALA0-0.075-0.03047.806-0.140-0.1400.0000.0000.0000.000
147A234GLY00.0240.00950.377-0.134-0.1340.0000.0000.0000.000
148A235SER0-0.072-0.03449.926-0.103-0.1030.0000.0000.0000.000
149A236GLY0-0.003-0.00749.918-0.040-0.0400.0000.0000.0000.000
150A237ILE00.0170.01447.5670.0500.0500.0000.0000.0000.000
151A238THR00.001-0.03441.8990.0970.0970.0000.0000.0000.000
152A239LEU00.0100.01940.708-0.061-0.0610.0000.0000.0000.000
153A240LEU00.0070.00137.6430.1020.1020.0000.0000.0000.000
154A241PRO00.0140.00333.199-0.062-0.0620.0000.0000.0000.000
155A242ALA00.0420.02233.350-0.001-0.0010.0000.0000.0000.000
156A243LEU0-0.051-0.02327.3880.0350.0350.0000.0000.0000.000
157A244ALA0-0.0190.00131.4590.1310.1310.0000.0000.0000.000
158A245VAL0-0.022-0.00233.996-0.341-0.3410.0000.0000.0000.000
159A246PRO0-0.047-0.00635.5420.2390.2390.0000.0000.0000.000
160A247PRO00.005-0.01535.262-0.091-0.0910.0000.0000.0000.000
161A248GLU-1-0.838-0.89837.8118.0108.0100.0000.0000.0000.000
162A249ARG10.8640.92441.583-6.761-6.7610.0000.0000.0000.000
163A250LYS10.7850.86843.907-6.575-6.5750.0000.0000.0000.000
164A251ARG10.8010.87738.065-8.129-8.1290.0000.0000.0000.000
165A252ASP-1-0.866-0.93041.9687.5967.5960.0000.0000.0000.000
166A253GLY00.0350.02745.417-0.024-0.0240.0000.0000.0000.000
167A254VAL0-0.043-0.02043.950-0.110-0.1100.0000.0000.0000.000
168A255VAL0-0.014-0.01246.0560.0430.0430.0000.0000.0000.000
169A256TYR00.0330.00941.1290.0860.0860.0000.0000.0000.000
170A257LEU0-0.042-0.01843.613-0.021-0.0210.0000.0000.0000.000
171A258PRO00.0200.00142.3690.0790.0790.0000.0000.0000.000
172A259ALA00.0460.04342.414-0.216-0.2160.0000.0000.0000.000
173A260ILE0-0.013-0.02843.0790.1260.1260.0000.0000.0000.000
174A261LYS10.9080.96345.409-6.371-6.3710.0000.0000.0000.000
175A262PRO00.0490.02642.742-0.151-0.1510.0000.0000.0000.000
176A263GLU-1-0.810-0.90338.5598.2438.2430.0000.0000.0000.000
177A264PRO0-0.030-0.00939.8110.1060.1060.0000.0000.0000.000
178A265ARG10.8270.89133.575-8.803-8.8030.0000.0000.0000.000
179A266ARG10.7600.85730.993-10.011-10.0110.0000.0000.0000.000
180A267THR00.016-0.00728.4220.1300.1300.0000.0000.0000.000
181A268ILE0-0.032-0.00325.0390.0180.0180.0000.0000.0000.000
182A269GLY00.0550.01124.1050.1570.1570.0000.0000.0000.000
183A270LEU0-0.046-0.01217.1310.0820.0820.0000.0000.0000.000
184A271VAL00.0210.00921.603-0.181-0.1810.0000.0000.0000.000
185A272TYR0-0.037-0.05717.9520.4310.4310.0000.0000.0000.000
186A273ARG10.8900.93717.383-15.252-15.2520.0000.0000.0000.000
187A274PRO00.0680.02820.3640.6800.6800.0000.0000.0000.000
188A275GLY0-0.004-0.00820.265-0.134-0.1340.0000.0000.0000.000
189A276SER0-0.038-0.00515.9800.2660.2660.0000.0000.0000.000
190A277PRO00.023-0.00614.0660.6070.6070.0000.0000.0000.000
191A278LEU0-0.017-0.0029.7581.0871.0870.0000.0000.0000.000
192A279ARG10.8960.93811.831-14.695-14.6950.0000.0000.0000.000
193A280SER0-0.0120.0039.103-0.185-0.1850.0000.0000.0000.000
194A281ARG10.8840.9304.999-34.302-34.236-0.001-0.017-0.0480.000
195A282TYR0-0.040-0.05710.353-0.307-0.3070.0000.0000.0000.000
196A283GLU-1-0.750-0.84313.27315.71115.7110.0000.0000.0000.000
197A284GLN0-0.039-0.0276.7390.4150.4150.0000.0000.0000.000
198A285LEU0-0.0060.00011.787-0.025-0.0250.0000.0000.0000.000
199A286ALA00.0270.00913.570-0.718-0.7180.0000.0000.0000.000
200A287GLU-1-0.826-0.90614.57115.60715.6070.0000.0000.0000.000
201A288ALA0-0.016-0.01013.476-0.512-0.5120.0000.0000.0000.000
202A289ILE0-0.011-0.01315.592-0.737-0.7370.0000.0000.0000.000
203A290ARG10.7990.88418.624-14.940-14.9400.0000.0000.0000.000
204A291ALA0-0.017-0.01218.007-0.612-0.6120.0000.0000.0000.000
205A292ARG10.7740.88219.440-13.732-13.7320.0000.0000.0000.000
206A293MET0-0.045-0.01921.117-0.489-0.4890.0000.0000.0000.000
207A294ASP-1-0.797-0.88723.70911.96711.9670.0000.0000.0000.000
208A295GLY0-0.031-0.00325.6230.0910.0910.0000.0000.0000.000
209A296HIS0-0.030-0.00226.9020.0310.0310.0000.0000.0000.000
210A297PHE0-0.019-0.02328.368-0.170-0.1700.0000.0000.0000.000
211A298ASP-1-0.970-0.96831.7479.4559.4550.0000.0000.0000.000