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: K3KN3

Calculation Name: 1I8D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I8D

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFU8

Base Structure: X-ray

Registration Date: 2023-03-13

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2272751.345266
FMO2-HF: Nuclear repulsion 2192010.078688
FMO2-HF: Total energy -80741.266578
FMO2-MP2: Total energy -80973.669809


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
3.793-7.01528.848-4.163-13.879-0.012
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.027
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].
3A3THR00.005-0.0123.794-0.0342.727-0.025-1.432-1.3050.007
4A4GLY00.029-0.0086.3660.6910.6910.0000.0000.0000.000
5A5ILE0-0.049-0.0079.2100.3470.3470.0000.0000.0000.000
6A6VAL0-0.017-0.01611.061-0.224-0.2240.0000.0000.0000.000
7A7GLN00.0210.0218.8700.2990.2990.0000.0000.0000.000
8A8GLY00.0410.01013.8750.1420.1420.0000.0000.0000.000
9A9THR0-0.0110.00915.303-0.056-0.0560.0000.0000.0000.000
10A10ALA00.0160.01716.8500.0310.0310.0000.0000.0000.000
11A11LYS10.9370.97118.4870.3960.3960.0000.0000.0000.000
12A12LEU0-0.059-0.02319.713-0.022-0.0220.0000.0000.0000.000
13A13VAL00.0140.00321.7380.0460.0460.0000.0000.0000.000
14A14SER0-0.024-0.01723.1990.0430.0430.0000.0000.0000.000
15A15ILE00.002-0.01622.744-0.030-0.0300.0000.0000.0000.000
16A16ASP-1-0.889-0.92623.567-0.214-0.2140.0000.0000.0000.000
17A17GLU-1-0.875-0.94424.169-0.236-0.2360.0000.0000.0000.000
18A18LYS10.9240.96324.5280.2070.2070.0000.0000.0000.000
19A19PRO00.003-0.01926.0290.0000.0000.0000.0000.0000.000
20A20ASN0-0.012-0.01523.2690.0150.0150.0000.0000.0000.000
21A21PHE00.012-0.01819.8410.0060.0060.0000.0000.0000.000
22A22ARG10.8580.93320.2820.3250.3250.0000.0000.0000.000
23A23THR00.011-0.00119.653-0.023-0.0230.0000.0000.0000.000
24A24HIS0-0.048-0.00417.3260.0760.0760.0000.0000.0000.000
25A25VAL00.0470.03118.317-0.046-0.0460.0000.0000.0000.000
26A26VAL00.007-0.01315.9410.0310.0310.0000.0000.0000.000
27A27GLU-1-0.969-0.96419.249-0.432-0.4320.0000.0000.0000.000
28A28LEU0-0.015-0.02914.085-0.032-0.0320.0000.0000.0000.000
29A29PRO00.015-0.00816.6180.0490.0490.0000.0000.0000.000
30A30ASP-1-0.784-0.89718.128-0.560-0.5600.0000.0000.0000.000
31A31HIS0-0.079-0.03216.0080.0620.0620.0000.0000.0000.000
32A32MET0-0.061-0.04312.136-0.034-0.0340.0000.0000.0000.000
33A33LEU0-0.0040.02314.416-0.130-0.1300.0000.0000.0000.000
34A34ASP-1-0.871-0.92816.451-0.664-0.6640.0000.0000.0000.000
35A35GLY00.0340.02014.473-0.126-0.1260.0000.0000.0000.000
36A36LEU0-0.139-0.06811.925-0.118-0.1180.0000.0000.0000.000
37A37GLU-1-0.871-0.93313.272-0.472-0.4720.0000.0000.0000.000
38A38THR0-0.052-0.04313.543-0.115-0.1150.0000.0000.0000.000
39A39GLY0-0.007-0.00612.6580.0260.0260.0000.0000.0000.000
40A40ALA0-0.0240.0019.401-0.102-0.1020.0000.0000.0000.000
41A41SER00.0170.0095.1610.3490.3490.0000.0000.0000.000
42A42VAL0-0.032-0.0246.599-0.671-0.6710.0000.0000.0000.000
43A43ALA0-0.0020.0156.4980.3100.3100.0000.0000.0000.000
44A44HIS00.014-0.0018.1670.3600.3600.0000.0000.0000.000
45A45ASN0-0.057-0.04111.8000.0690.0690.0000.0000.0000.000
46A46GLY00.0610.0178.9120.1830.1830.0000.0000.0000.000
47A47CYS0-0.036-0.0108.4280.0250.0250.0000.0000.0000.000
48A48CYS0-0.044-0.0074.717-0.561-0.493-0.001-0.006-0.0610.000
49A49LEU0-0.021-0.0117.1470.4980.4980.0000.0000.0000.000
50A50THR00.007-0.0558.613-0.295-0.2950.0000.0000.0000.000
51A51VAL0-0.0470.03110.6710.1590.1590.0000.0000.0000.000
52A52THR0-0.001-0.00213.3550.0420.0420.0000.0000.0000.000
53A53GLU-1-0.926-0.96816.741-0.303-0.3030.0000.0000.0000.000
54A54ILE00.0280.00816.106-0.064-0.0640.0000.0000.0000.000
55A55ASN0-0.046-0.01619.8250.0610.0610.0000.0000.0000.000
56A56GLY00.0360.03023.1690.0090.0090.0000.0000.0000.000
57A57ASN00.0250.01420.804-0.026-0.0260.0000.0000.0000.000
58A58HIS0-0.038-0.02020.467-0.015-0.0150.0000.0000.0000.000
59A59VAL0-0.0020.00415.0010.0070.0070.0000.0000.0000.000
60A60SER00.005-0.00817.784-0.003-0.0030.0000.0000.0000.000
61A61PHE00.0680.02711.161-0.095-0.0950.0000.0000.0000.000
62A62ASP-1-0.802-0.88315.521-0.316-0.3160.0000.0000.0000.000
63A63LEU0-0.042-0.02515.026-0.022-0.0220.0000.0000.0000.000
64A64MET00.0390.02616.3580.0730.0730.0000.0000.0000.000
65A65LYS10.8830.92618.2090.1750.1750.0000.0000.0000.000
66A66GLU-1-0.880-0.92816.4320.0140.0140.0000.0000.0000.000
67A67THR00.0660.02313.8700.0420.0420.0000.0000.0000.000
68A68LEU0-0.0570.00216.376-0.013-0.0130.0000.0000.0000.000
69A69ARG10.9000.96419.2880.0190.0190.0000.0000.0000.000
70A70ILE0-0.077-0.04115.3070.0160.0160.0000.0000.0000.000
71A71THR0-0.0060.00613.687-0.020-0.0200.0000.0000.0000.000
72A72ASN0-0.069-0.05016.818-0.032-0.0320.0000.0000.0000.000
73A73LEU00.0580.01513.3070.0120.0120.0000.0000.0000.000
74A74GLY00.014-0.00817.9020.0030.0030.0000.0000.0000.000
75A75ASP-1-0.945-0.95620.831-0.168-0.1680.0000.0000.0000.000
76A76LEU0-0.139-0.04317.9820.0040.0040.0000.0000.0000.000
77A77LYS10.9250.94422.3830.2320.2320.0000.0000.0000.000
78A78VAL00.0380.02024.373-0.022-0.0220.0000.0000.0000.000
79A79GLY0-0.076-0.03924.8830.0220.0220.0000.0000.0000.000
80A80ASP-1-0.866-0.92022.628-0.303-0.3030.0000.0000.0000.000
81A81TRP0-0.008-0.01820.661-0.023-0.0230.0000.0000.0000.000
82A82VAL0-0.049-0.01314.7470.0260.0260.0000.0000.0000.000
83A83ASN00.008-0.00913.7360.0450.0450.0000.0000.0000.000
84A84VAL00.008-0.00711.652-0.067-0.0670.0000.0000.0000.000
85A85GLU-1-0.766-0.8817.528-2.804-2.8040.0000.0000.0000.000
86A86ARG10.8150.9037.8071.1331.1330.0000.0000.0000.000
87A87ALA0-0.006-0.0102.834-0.640-0.1710.073-0.176-0.3660.000
88A88ALA00.0090.0222.6631.2292.2410.216-0.370-0.858-0.001
89A89LYS10.9040.9564.2971.1591.294-0.001-0.049-0.0850.000
90A90PHE0-0.007-0.0196.5170.1910.1910.0000.0000.0000.000
91A91SER0-0.043-0.0188.1560.1720.1720.0000.0000.0000.000
92A92ASP-1-0.858-0.9197.544-1.809-1.8090.0000.0000.0000.000
93A93GLU-1-0.973-0.9778.953-0.323-0.3230.0000.0000.0000.000
94A94ILE0-0.003-0.0336.529-0.224-0.2240.0000.0000.0000.000
95A95GLY0-0.001-0.0018.9000.1710.1710.0000.0000.0000.000
96A96GLY0-0.025-0.0109.6430.0790.0790.0000.0000.0000.000
97A97HIS0-0.041-0.0358.3290.2360.2360.0000.0000.0000.000
98A98LEU0-0.018-0.0202.2681.212-3.42510.457-1.874-3.9460.000
99A99MET0-0.0090.0444.0980.3990.9270.003-0.109-0.4220.000
100A100SER00.007-0.0261.859-2.896-5.77818.185-9.598-5.706-0.010
101A101GLY00.0080.0082.7346.586-1.784-0.0589.459-1.031-0.008
102A102HIS0-0.057-0.0265.5620.2320.2320.0000.0000.0000.000
103A103ILE0-0.0010.0067.2420.1410.1410.0000.0000.0000.000
104A104MET0-0.007-0.00210.7180.0030.0030.0000.0000.0000.000
105A105THR00.0160.00113.129-0.012-0.0120.0000.0000.0000.000
106A106THR0-0.0110.01814.817-0.055-0.0550.0000.0000.0000.000
107A107ALA0-0.017-0.01217.5810.0470.0470.0000.0000.0000.000
108A108GLU-1-0.842-0.92320.008-0.098-0.0980.0000.0000.0000.000
109A109VAL0-0.0070.01522.9930.0230.0230.0000.0000.0000.000
110A110ALA0-0.010-0.00924.8300.0050.0050.0000.0000.0000.000
111A111LYS10.9220.93227.4240.0250.0250.0000.0000.0000.000
112A112ILE00.0160.00726.932-0.002-0.0020.0000.0000.0000.000
113A113LEU0-0.0210.00129.2450.0030.0030.0000.0000.0000.000
114A114THR0-0.013-0.01730.431-0.010-0.0100.0000.0000.0000.000
115A115SER0-0.007-0.00231.9300.0090.0090.0000.0000.0000.000
116A116GLU-1-0.874-0.94133.137-0.085-0.0850.0000.0000.0000.000
117A117ASN0-0.029-0.01031.518-0.002-0.0020.0000.0000.0000.000
118A118ASN0-0.033-0.01228.755-0.003-0.0030.0000.0000.0000.000
119A119ARG10.9710.98125.8310.1730.1730.0000.0000.0000.000
120A120GLN00.0420.04125.8070.0100.0100.0000.0000.0000.000
121A121ILE0-0.040-0.01722.8220.0020.0020.0000.0000.0000.000
122A122TRP00.0030.02724.0670.0150.0150.0000.0000.0000.000
123A123PHE00.016-0.00120.366-0.022-0.0220.0000.0000.0000.000
124A124LYS10.8150.90422.9590.0620.0620.0000.0000.0000.000
125A125VAL00.0140.01019.296-0.020-0.0200.0000.0000.0000.000
126A126GLN00.0170.01719.828-0.014-0.0140.0000.0000.0000.000
127A127ASP-1-0.771-0.91418.5980.2050.2050.0000.0000.0000.000
128A128SER0-0.047-0.01019.8030.0240.0240.0000.0000.0000.000
129A129GLN0-0.034-0.01920.0780.0260.0260.0000.0000.0000.000
130A130LEU00.0700.01014.9570.0390.0390.0000.0000.0000.000
131A131MET0-0.096-0.02317.1160.0210.0210.0000.0000.0000.000
132A132LYS10.8920.95517.516-0.361-0.3610.0000.0000.0000.000
133A133TYR0-0.045-0.02013.6220.0220.0220.0000.0000.0000.000
134A134ILE0-0.047-0.01114.7740.0290.0290.0000.0000.0000.000
135A135LEU00.0310.01217.076-0.038-0.0380.0000.0000.0000.000
136A136TYR0-0.036-0.02319.066-0.017-0.0170.0000.0000.0000.000
137A137LYS10.8930.94120.482-0.058-0.0580.0000.0000.0000.000
138A138GLY00.0270.03316.7700.0200.0200.0000.0000.0000.000
139A139PHE00.0180.02012.048-0.081-0.0810.0000.0000.0000.000
140A140ILE0-0.027-0.02912.6600.0720.0720.0000.0000.0000.000
141A141GLY00.0500.02610.780-0.094-0.0940.0000.0000.0000.000
142A142ILE0-0.039-0.04711.7030.0430.0430.0000.0000.0000.000
143A143ASP-1-0.750-0.84713.694-0.508-0.5080.0000.0000.0000.000
144A144GLY00.0480.0169.615-0.111-0.1110.0000.0000.0000.000
145A145ILE0-0.076-0.01910.130-0.161-0.1610.0000.0000.0000.000
146A146SER00.0560.06210.0070.2000.2000.0000.0000.0000.000
147A147LEU0-0.083-0.04711.975-0.003-0.0030.0000.0000.0000.000
148A148THR00.0410.02015.2300.0530.0530.0000.0000.0000.000
149A149VAL0-0.055-0.01516.709-0.043-0.0430.0000.0000.0000.000
150A150GLY0-0.002-0.00519.3410.0140.0140.0000.0000.0000.000
151A151GLU-1-0.890-0.96822.9030.0640.0640.0000.0000.0000.000
152A152VAL00.0320.00620.906-0.014-0.0140.0000.0000.0000.000
153A153THR0-0.081-0.03924.153-0.003-0.0030.0000.0000.0000.000
154A154PRO00.0660.01224.2480.0090.0090.0000.0000.0000.000
155A155THR00.0060.00124.6390.0030.0030.0000.0000.0000.000
156A156ARG10.9600.97123.392-0.016-0.0160.0000.0000.0000.000
157A157PHE00.0620.05118.0040.0240.0240.0000.0000.0000.000
158A158CYS0-0.015-0.00522.773-0.021-0.0210.0000.0000.0000.000
159A159VAL00.0270.01318.8120.0190.0190.0000.0000.0000.000
160A160HIS0-0.006-0.00722.154-0.026-0.0260.0000.0000.0000.000
161A161LEU0-0.030-0.02320.627-0.012-0.0120.0000.0000.0000.000
162A162ILE00.0280.02520.1350.0180.0180.0000.0000.0000.000
163A163PRO00.0680.00023.084-0.025-0.0250.0000.0000.0000.000
164A164GLU-1-0.734-0.86020.412-0.371-0.3710.0000.0000.0000.000
165A165THR0-0.015-0.00318.245-0.040-0.0400.0000.0000.0000.000
166A166LEU0-0.103-0.04820.150-0.030-0.0300.0000.0000.0000.000
167A167GLU-1-0.963-0.96822.824-0.275-0.2750.0000.0000.0000.000
168A168ARG10.8700.93917.8500.5020.5020.0000.0000.0000.000
169A169THR0-0.034-0.00216.261-0.051-0.0510.0000.0000.0000.000
170A170THR0-0.010-0.01218.3670.0720.0720.0000.0000.0000.000
171A171LEU00.0270.00918.4380.0560.0560.0000.0000.0000.000
172A172GLY00.015-0.01220.5950.0420.0420.0000.0000.0000.000
173A173LYS10.8940.94223.4900.3320.3320.0000.0000.0000.000
174A174LYS10.8480.93518.9410.3930.3930.0000.0000.0000.000
175A175LYS10.9500.97724.6070.1670.1670.0000.0000.0000.000
176A176LEU00.0300.00726.574-0.003-0.0030.0000.0000.0000.000
177A177GLY0-0.024-0.01027.606-0.004-0.0040.0000.0000.0000.000
178A178ALA0-0.032-0.00423.404-0.003-0.0030.0000.0000.0000.000
179A179ARG10.9580.97220.6500.1700.1700.0000.0000.0000.000
180A180VAL0-0.078-0.03517.417-0.040-0.0400.0000.0000.0000.000
181A181ASN00.024-0.01113.3010.1550.1550.0000.0000.0000.000
182A182ILE0-0.041-0.03313.525-0.036-0.0360.0000.0000.0000.000
183A183GLU-1-0.771-0.9015.9720.2360.2360.0000.0000.0000.000
184A184ILE00.0000.00110.277-0.031-0.0310.0000.0000.0000.000
185A185ASP-1-0.761-0.8828.4661.4541.4540.0000.0000.0000.000
186A186PRO00.0440.0244.559-0.195-0.087-0.001-0.008-0.0990.000
187A187GLN0-0.013-0.0057.074-0.330-0.3300.0000.0000.0000.000
188A188THR0-0.013-0.0189.336-0.256-0.2560.0000.0000.0000.000
189A189GLN0-0.012-0.0039.755-0.039-0.0390.0000.0000.0000.000
190A190ALA0-0.0130.0049.827-0.110-0.1100.0000.0000.0000.000
191A191VAL0-0.0090.01311.711-0.147-0.1470.0000.0000.0000.000
192A192VAL0-0.002-0.00614.660-0.098-0.0980.0000.0000.0000.000
193A193ASP-1-0.817-0.91413.7530.6390.6390.0000.0000.0000.000
194A194THR0-0.117-0.08414.839-0.051-0.0510.0000.0000.0000.000
195A195VAL0-0.015-0.01417.273-0.062-0.0620.0000.0000.0000.000
196A196GLU-1-0.883-0.93219.6210.3550.3550.0000.0000.0000.000
197A197ARG10.9660.98514.051-0.777-0.7770.0000.0000.0000.000
198A198VAL0-0.0160.00621.234-0.039-0.0390.0000.0000.0000.000
199A199LEU0-0.014-0.03023.364-0.035-0.0350.0000.0000.0000.000
200A200ALA00.0220.02524.445-0.026-0.0260.0000.0000.0000.000
201A201ALA0-0.026-0.01625.049-0.022-0.0220.0000.0000.0000.000
202A202ARG10.8640.91326.764-0.326-0.3260.0000.0000.0000.000
203A203GLU-1-0.938-0.95928.9810.1960.1960.0000.0000.0000.000
204A204ASN0-0.014-0.00528.696-0.023-0.0230.0000.0000.0000.000
205A205ALA0-0.096-0.02731.225-0.012-0.0120.0000.0000.0000.000
206A206MET0-0.039-0.01032.929-0.013-0.0130.0000.0000.0000.000