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: N9QYQ

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2423760.066762
FMO2-HF: Nuclear repulsion 2340128.74669
FMO2-HF: Total energy -83631.320073
FMO2-MP2: Total energy -83871.879585


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.
20.33115.09115.157-5.606-4.312-0.027
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 : -0.948 / q_NPA : -1.004
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].
3A89MET0-0.040-0.0043.545-7.761-5.6510.006-0.900-1.2160.002
4A90SER0-0.0070.0021.780-0.350-8.13115.152-4.525-2.847-0.028
5A91GLY00.0090.0103.977-0.803-0.5210.000-0.175-0.107-0.001
6A92PRO0-0.010-0.0147.200-0.089-0.0890.0000.0000.0000.000
7A93LEU00.0100.02510.0760.5890.5890.0000.0000.0000.000
8A94HIS10.8190.89612.376-15.522-15.5220.0000.0000.0000.000
9A95ILE00.0540.01914.1290.0690.0690.0000.0000.0000.000
10A96GLY0-0.0090.00117.990-0.420-0.4200.0000.0000.0000.000
11A97LEU00.004-0.00220.6970.2670.2670.0000.0000.0000.000
12A98ILE00.0510.03624.166-0.257-0.2570.0000.0000.0000.000
13A99PRO00.028-0.00827.9310.1380.1380.0000.0000.0000.000
14A100THR0-0.050-0.02730.1850.0830.0830.0000.0000.0000.000
15A101VAL00.0250.02025.454-0.038-0.0380.0000.0000.0000.000
16A102GLY00.0010.00124.8540.1700.1700.0000.0000.0000.000
17A103PRO00.0320.00825.4450.3370.3370.0000.0000.0000.000
18A104TYR0-0.058-0.05327.8370.0340.0340.0000.0000.0000.000
19A105LEU00.0480.03522.8760.0760.0760.0000.0000.0000.000
20A106LEU00.0090.00520.4550.5450.5450.0000.0000.0000.000
21A107PRO0-0.028-0.01021.8450.5990.5990.0000.0000.0000.000
22A108HIS0-0.0040.00123.6580.4050.4050.0000.0000.0000.000
23A109ILE0-0.008-0.01018.7550.5010.5010.0000.0000.0000.000
24A110ILE00.0160.01517.3410.9170.9170.0000.0000.0000.000
25A111PRO0-0.013-0.01816.7210.9370.9370.0000.0000.0000.000
26A112MET00.0380.03816.1531.0291.0290.0000.0000.0000.000
27A113LEU00.0400.02213.4141.5251.5250.0000.0000.0000.000
28A114HIS0-0.015-0.00812.2012.2942.2940.0000.0000.0000.000
29A115GLN0-0.064-0.03112.5921.2171.2170.0000.0000.0000.000
30A116THR0-0.039-0.03110.6781.1211.1210.0000.0000.0000.000
31A117PHE0-0.039-0.0287.6363.4163.4160.0000.0000.0000.000
32A118PRO00.0280.0168.057-0.656-0.6560.0000.0000.0000.000
33A119LYS10.9140.9504.379-44.928-44.779-0.001-0.006-0.1420.000
34A120LEU0-0.0040.0146.5090.3400.3400.0000.0000.0000.000
35A121GLU-1-0.882-0.9177.90816.76916.7690.0000.0000.0000.000
36A122MET0-0.021-0.02210.939-0.220-0.2200.0000.0000.0000.000
37A123TYR0-0.086-0.04713.777-1.102-1.1020.0000.0000.0000.000
38A124LEU00.0150.00216.9080.1090.1090.0000.0000.0000.000
39A125HIS0-0.0040.00719.8080.0420.0420.0000.0000.0000.000
40A126GLU-1-0.867-0.93322.81810.65410.6540.0000.0000.0000.000
41A127ALA0-0.041-0.03126.127-0.272-0.2720.0000.0000.0000.000
42A128GLN00.0610.02228.6890.1260.1260.0000.0000.0000.000
43A129THR00.042-0.01129.2220.3340.3340.0000.0000.0000.000
44A130HIS00.0290.01929.2810.3400.3400.0000.0000.0000.000
45A131GLN0-0.036-0.02729.664-0.060-0.0600.0000.0000.0000.000
46A132LEU0-0.009-0.00124.1800.2940.2940.0000.0000.0000.000
47A133LEU00.0440.02125.0470.4310.4310.0000.0000.0000.000
48A134ALA00.0210.02626.6540.1320.1320.0000.0000.0000.000
49A135GLN0-0.060-0.04423.9470.1800.1800.0000.0000.0000.000
50A136LEU00.0070.03220.4320.4680.4680.0000.0000.0000.000
51A137ASP-1-0.928-0.95922.30211.18511.1850.0000.0000.0000.000
52A138SER0-0.087-0.04024.768-0.057-0.0570.0000.0000.0000.000
53A139GLY0-0.024-0.00720.6150.0700.0700.0000.0000.0000.000
54A140LYS10.8670.93119.555-10.070-10.0700.0000.0000.0000.000
55A141LEU0-0.0050.00818.7470.2300.2300.0000.0000.0000.000
56A142ASP-1-0.839-0.89913.84717.63917.6390.0000.0000.0000.000
57A143ALA00.012-0.00616.4610.0800.0800.0000.0000.0000.000
58A144VAL0-0.026-0.00918.308-0.191-0.1910.0000.0000.0000.000
59A145ILE0-0.0050.01619.1610.1810.1810.0000.0000.0000.000
60A146LEU0-0.021-0.02622.892-0.324-0.3240.0000.0000.0000.000
61A147ALA00.0140.01926.6600.1960.1960.0000.0000.0000.000
62A148LEU0-0.020-0.01126.311-0.060-0.0600.0000.0000.0000.000
63A149VAL00.0120.01429.941-0.328-0.3280.0000.0000.0000.000
64A150LYS11.0050.99932.082-7.657-7.6570.0000.0000.0000.000
65A151GLU-1-0.932-0.98432.1648.7798.7790.0000.0000.0000.000
66A152SER0-0.095-0.08827.5000.1290.1290.0000.0000.0000.000
67A153GLU-1-0.885-0.93428.0779.3559.3550.0000.0000.0000.000
68A154ALA0-0.107-0.03429.2980.0950.0950.0000.0000.0000.000
69A155PHE0-0.051-0.04424.0680.3290.3290.0000.0000.0000.000
70A156ILE0-0.042-0.00620.446-0.182-0.1820.0000.0000.0000.000
71A157GLU-1-0.778-0.87322.57010.93810.9380.0000.0000.0000.000
72A158VAL0-0.015-0.00519.0320.0470.0470.0000.0000.0000.000
73A159PRO0-0.007-0.01122.2770.1200.1200.0000.0000.0000.000
74A160LEU0-0.069-0.02320.1720.5270.5270.0000.0000.0000.000
75A161PHE00.031-0.00423.6350.1360.1360.0000.0000.0000.000
76A162ASP-1-0.853-0.87726.8919.8509.8500.0000.0000.0000.000
77A163GLU-1-0.792-0.90530.4429.7619.7610.0000.0000.0000.000
78A164PRO00.0020.00632.159-0.198-0.1980.0000.0000.0000.000
79A165MET0-0.027-0.01835.4930.1520.1520.0000.0000.0000.000
80A166LEU0-0.006-0.00537.985-0.165-0.1650.0000.0000.0000.000
81A167LEU0-0.004-0.00840.7190.0020.0020.0000.0000.0000.000
82A168ALA0-0.0050.00642.3360.0200.0200.0000.0000.0000.000
83A169ILE00.002-0.00644.389-0.077-0.0770.0000.0000.0000.000
84A170TYR00.0590.02547.9450.0430.0430.0000.0000.0000.000
85A171GLU-1-0.917-0.97649.9475.9885.9880.0000.0000.0000.000
86A172ASP-1-0.958-0.96651.7515.5785.5780.0000.0000.0000.000
87A173HIS0-0.028-0.00252.470-0.096-0.0960.0000.0000.0000.000
88A174PRO00.033-0.00454.4790.0120.0120.0000.0000.0000.000
89A175TRP0-0.024-0.03350.1420.0130.0130.0000.0000.0000.000
90A176ALA00.0330.03551.5770.0950.0950.0000.0000.0000.000
91A177ASN0-0.058-0.04252.0280.1150.1150.0000.0000.0000.000
92A178ARG10.7930.90051.878-5.917-5.9170.0000.0000.0000.000
93A179GLU-1-0.922-0.96649.2846.3676.3670.0000.0000.0000.000
94A180ALA0-0.034-0.02047.6180.1740.1740.0000.0000.0000.000
95A181VAL0-0.0150.00247.844-0.170-0.1700.0000.0000.0000.000
96A182PRO0-0.065-0.02848.0450.1580.1580.0000.0000.0000.000
97A183MET00.0560.02445.026-0.024-0.0240.0000.0000.0000.000
98A184ALA00.0320.01948.366-0.043-0.0430.0000.0000.0000.000
99A185ASP-1-0.842-0.91351.6845.7405.7400.0000.0000.0000.000
100A186LEU0-0.067-0.02746.374-0.051-0.0510.0000.0000.0000.000
101A187ALA00.0050.00451.017-0.004-0.0040.0000.0000.0000.000
102A188GLY0-0.033-0.02953.801-0.066-0.0660.0000.0000.0000.000
103A189GLU-1-0.871-0.90851.6245.7345.7340.0000.0000.0000.000
104A190LYS10.9070.95351.074-5.821-5.8210.0000.0000.0000.000
105A191LEU00.004-0.00646.1360.0860.0860.0000.0000.0000.000
106A192LEU0-0.042-0.01244.948-0.026-0.0260.0000.0000.0000.000
107A193MET0-0.0030.00442.2450.1290.1290.0000.0000.0000.000
108A194LEU0-0.021-0.00736.766-0.055-0.0550.0000.0000.0000.000
109A195GLU-1-0.937-0.99338.3087.4187.4180.0000.0000.0000.000
110A196ASP-1-0.803-0.88832.8199.0429.0420.0000.0000.0000.000
111A197GLY0-0.0120.00133.0560.0190.0190.0000.0000.0000.000
112A198HIS0-0.059-0.03233.7820.0860.0860.0000.0000.0000.000
113A199CYS0-0.066-0.02236.8740.1640.1640.0000.0000.0000.000
114A200LEU00.0200.01637.7700.1570.1570.0000.0000.0000.000
115A201ARG10.8040.90539.256-6.980-6.9800.0000.0000.0000.000
116A202ASP-1-0.818-0.90839.3837.4187.4180.0000.0000.0000.000
117A203GLN00.001-0.02739.762-0.308-0.3080.0000.0000.0000.000
118A204ALA0-0.048-0.00942.750-0.140-0.1400.0000.0000.0000.000
119A205MET0-0.078-0.04444.448-0.132-0.1320.0000.0000.0000.000
120A206GLY0-0.030-0.00546.558-0.140-0.1400.0000.0000.0000.000
121A207PHE0-0.015-0.00246.568-0.080-0.0800.0000.0000.0000.000
122A209PHE0-0.025-0.04040.1860.1790.1790.0000.0000.0000.000
123A210GLU-1-0.904-0.94744.7476.3196.3190.0000.0000.0000.000
124A211ALA00.0110.01048.377-0.057-0.0570.0000.0000.0000.000
125A212GLY00.0000.00250.899-0.085-0.0850.0000.0000.0000.000
126A213ALA0-0.0240.01149.875-0.103-0.1030.0000.0000.0000.000
127A214ASP-1-0.944-0.96252.0125.7165.7160.0000.0000.0000.000
128A215GLU-1-0.750-0.88247.0356.6806.6800.0000.0000.0000.000
129A216ASP-1-0.795-0.88148.3286.1256.1250.0000.0000.0000.000
130A217THR00.007-0.01046.6430.1190.1190.0000.0000.0000.000
131A218HIS10.7750.85246.714-5.883-5.8830.0000.0000.0000.000
132A219PHE00.0180.01544.0530.0080.0080.0000.0000.0000.000
133A220ARG11.0101.03242.133-6.572-6.5720.0000.0000.0000.000
134A221ALA0-0.0040.00740.1790.1650.1650.0000.0000.0000.000
135A222THR0-0.057-0.03639.8110.0470.0470.0000.0000.0000.000
136A223SER00.0310.00135.7870.1550.1550.0000.0000.0000.000
137A224LEU00.0930.03834.144-0.173-0.1730.0000.0000.0000.000
138A225GLU-1-0.761-0.84435.3308.0728.0720.0000.0000.0000.000
139A226THR0-0.050-0.01538.084-0.210-0.2100.0000.0000.0000.000
140A227LEU00.001-0.00240.007-0.186-0.1860.0000.0000.0000.000
141A228ARG10.7740.86136.002-8.199-8.1990.0000.0000.0000.000
142A229ASN00.023-0.00341.002-0.128-0.1280.0000.0000.0000.000
143A230MET0-0.039-0.01144.030-0.165-0.1650.0000.0000.0000.000
144A231VAL0-0.0240.00244.753-0.161-0.1610.0000.0000.0000.000
145A232ALA00.0170.01446.091-0.139-0.1390.0000.0000.0000.000
146A233ALA0-0.071-0.02547.922-0.124-0.1240.0000.0000.0000.000
147A234GLY00.0210.01150.127-0.134-0.1340.0000.0000.0000.000
148A235SER0-0.087-0.04649.351-0.104-0.1040.0000.0000.0000.000
149A236GLY00.006-0.00649.934-0.063-0.0630.0000.0000.0000.000
150A237ILE00.0340.02547.3490.0560.0560.0000.0000.0000.000
151A238THR0-0.023-0.04541.9270.0710.0710.0000.0000.0000.000
152A239LEU00.0230.02540.694-0.027-0.0270.0000.0000.0000.000
153A240LEU0-0.0100.01137.4730.0840.0840.0000.0000.0000.000
154A241PRO00.0180.01333.152-0.060-0.0600.0000.0000.0000.000
155A242ALA00.0580.02633.686-0.041-0.0410.0000.0000.0000.000
156A243LEU0-0.029-0.01427.685-0.029-0.0290.0000.0000.0000.000
157A244ALA0-0.0370.00031.7810.0640.0640.0000.0000.0000.000
158A245VAL0-0.0140.00034.023-0.316-0.3160.0000.0000.0000.000
159A246PRO0-0.069-0.01835.8510.1970.1970.0000.0000.0000.000
160A247PRO00.018-0.00635.641-0.047-0.0470.0000.0000.0000.000
161A248GLU-1-0.860-0.91638.0747.5197.5190.0000.0000.0000.000
162A249ARG10.9340.96841.730-6.522-6.5220.0000.0000.0000.000
163A250LYS10.9070.94544.193-6.241-6.2410.0000.0000.0000.000
164A251ARG10.8740.93037.183-7.746-7.7460.0000.0000.0000.000
165A252ASP-1-0.924-0.95842.6877.0677.0670.0000.0000.0000.000
166A253GLY00.0470.02145.899-0.038-0.0380.0000.0000.0000.000
167A254VAL0-0.049-0.01843.745-0.080-0.0800.0000.0000.0000.000
168A255VAL0-0.014-0.01345.8580.0700.0700.0000.0000.0000.000
169A256TYR00.0280.00140.5750.0800.0800.0000.0000.0000.000
170A257LEU0-0.043-0.02544.024-0.014-0.0140.0000.0000.0000.000
171A258PRO00.0310.01642.8140.0710.0710.0000.0000.0000.000
172A259ALA00.0600.04843.102-0.191-0.1910.0000.0000.0000.000
173A260ILE0-0.014-0.02843.5470.1350.1350.0000.0000.0000.000
174A261LYS10.8950.96645.757-6.272-6.2720.0000.0000.0000.000
175A262PRO00.0430.01443.036-0.145-0.1450.0000.0000.0000.000
176A263GLU-1-0.820-0.92338.4108.1228.1220.0000.0000.0000.000
177A264PRO0-0.015-0.00440.1410.1230.1230.0000.0000.0000.000
178A265ARG10.8810.92534.814-8.628-8.6280.0000.0000.0000.000
179A266ARG10.7930.90130.947-9.532-9.5320.0000.0000.0000.000
180A267THR00.015-0.03028.5970.0520.0520.0000.0000.0000.000
181A268ILE0-0.051-0.01425.084-0.038-0.0380.0000.0000.0000.000
182A269GLY00.0590.01624.3820.2690.2690.0000.0000.0000.000
183A270LEU0-0.048-0.01817.018-0.011-0.0110.0000.0000.0000.000
184A271VAL00.0380.00821.4860.0380.0380.0000.0000.0000.000
185A272TYR0-0.066-0.09017.7480.4410.4410.0000.0000.0000.000
186A273ARG10.9110.94517.569-14.391-14.3910.0000.0000.0000.000
187A274PRO00.0940.04620.0020.8120.8120.0000.0000.0000.000
188A275GLY0-0.022-0.01720.251-0.204-0.2040.0000.0000.0000.000
189A276SER0-0.061-0.02015.7750.3450.3450.0000.0000.0000.000
190A277PRO00.027-0.00813.9120.6570.6570.0000.0000.0000.000
191A278LEU0-0.026-0.0099.6351.5181.5180.0000.0000.0000.000
192A279ARG11.0081.00512.055-16.402-16.4020.0000.0000.0000.000
193A280SER0-0.0160.0018.604-0.602-0.6020.0000.0000.0000.000
194A281ARG10.9700.9865.129-30.404-30.4040.0000.0000.0000.000
195A282TYR0-0.027-0.03610.002-0.376-0.3760.0000.0000.0000.000
196A283GLU-1-0.839-0.88513.15116.17916.1790.0000.0000.0000.000
197A284GLN0-0.018-0.0146.7340.2660.2660.0000.0000.0000.000
198A285LEU0-0.022-0.00312.020-0.247-0.2470.0000.0000.0000.000
199A286ALA00.0280.00713.528-0.795-0.7950.0000.0000.0000.000
200A287GLU-1-0.846-0.92814.79116.09616.0960.0000.0000.0000.000
201A288ALA0-0.028-0.01913.615-0.535-0.5350.0000.0000.0000.000
202A289ILE0-0.031-0.02115.734-0.770-0.7700.0000.0000.0000.000
203A290ARG10.9270.98118.765-15.317-15.3170.0000.0000.0000.000
204A291ALA0-0.025-0.01918.463-0.594-0.5940.0000.0000.0000.000
205A292ARG10.8670.94919.599-13.536-13.5360.0000.0000.0000.000
206A293MET0-0.040-0.02621.270-0.453-0.4530.0000.0000.0000.000
207A294ASP-1-0.944-0.95623.74611.48411.4840.0000.0000.0000.000
208A295GLY00.0320.02425.6040.0050.0050.0000.0000.0000.000
209A296HIS0-0.067-0.02927.236-0.069-0.0690.0000.0000.0000.000
210A297PHE0-0.044-0.03829.174-0.248-0.2480.0000.0000.0000.000
211A298ASP-1-0.975-0.97332.2289.3279.3270.0000.0000.0000.000