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: 9MYL2

Calculation Name: 1IUH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IUH

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHB1

Base Structure: X-ray

Registration Date: 2023-09-26

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1995043.428023
FMO2-HF: Nuclear repulsion 1924208.619496
FMO2-HF: Total energy -70834.808527
FMO2-MP2: Total energy -71048.800661


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.
-58.622-51.31730.119-14.447-22.973-0.057
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 : 0.003 / q_NPA : 0.012
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].
3A3LEU00.017-0.0032.4900.1114.3231.592-2.117-3.6880.011
4A4PHE0-0.072-0.0355.068-0.990-0.962-0.001-0.005-0.0210.000
5A5TYR00.1070.0548.7680.4950.4950.0000.0000.0000.000
6A6ALA0-0.073-0.04611.586-0.191-0.1910.0000.0000.0000.000
7A7VAL00.0730.05414.1140.0600.0600.0000.0000.0000.000
8A8PHE0-0.028-0.02712.530-0.019-0.0190.0000.0000.0000.000
9A9LEU0-0.005-0.01018.027-0.059-0.0590.0000.0000.0000.000
10A10PRO00.0490.04221.6690.0480.0480.0000.0000.0000.000
11A11GLU-1-0.805-0.90824.6810.4090.4090.0000.0000.0000.000
12A12GLU-1-0.810-0.92326.9450.3110.3110.0000.0000.0000.000
13A13VAL0-0.0040.01024.904-0.018-0.0180.0000.0000.0000.000
14A14ARG10.7740.87221.835-0.504-0.5040.0000.0000.0000.000
15A15ALA00.0400.01525.397-0.008-0.0080.0000.0000.0000.000
16A16ALA00.0820.05428.845-0.016-0.0160.0000.0000.0000.000
17A17LEU0-0.014-0.01424.308-0.018-0.0180.0000.0000.0000.000
18A18VAL0-0.034-0.01825.640-0.004-0.0040.0000.0000.0000.000
19A19GLU-1-0.917-0.94827.8360.2090.2090.0000.0000.0000.000
20A20ALA0-0.055-0.03128.875-0.019-0.0190.0000.0000.0000.000
21A21GLN0-0.065-0.07223.264-0.014-0.0140.0000.0000.0000.000
22A22THR00.0170.02028.735-0.009-0.0090.0000.0000.0000.000
23A23LYS10.8420.92532.010-0.175-0.1750.0000.0000.0000.000
24A24VAL00.013-0.01127.915-0.014-0.0140.0000.0000.0000.000
25A25ARG10.9560.99330.640-0.232-0.2320.0000.0000.0000.000
26A26PRO00.0080.01031.7890.0000.0000.0000.0000.0000.000
27A27PHE0-0.011-0.00931.649-0.011-0.0110.0000.0000.0000.000
28A28ARG11.0461.01929.948-0.130-0.1300.0000.0000.0000.000
29A29GLY00.0100.01328.4170.0070.0070.0000.0000.0000.000
30A30TRP0-0.064-0.05424.9970.0020.0020.0000.0000.0000.000
31A31LYS10.9300.97219.815-0.420-0.4200.0000.0000.0000.000
32A32PRO00.0250.01222.7490.0070.0070.0000.0000.0000.000
33A33VAL0-0.047-0.02218.0600.0270.0270.0000.0000.0000.000
34A34PRO00.0440.02618.204-0.039-0.0390.0000.0000.0000.000
35A35PRO00.1150.05019.6990.0450.0450.0000.0000.0000.000
36A36HIS00.0350.01418.5330.0100.0100.0000.0000.0000.000
37A37GLN0-0.067-0.03814.1710.0010.0010.0000.0000.0000.000
38A38LEU0-0.0360.00216.493-0.001-0.0010.0000.0000.0000.000
39A39HIS10.8480.92013.776-0.693-0.6930.0000.0000.0000.000
40A40LEU0-0.0180.00617.730-0.060-0.0600.0000.0000.0000.000
41A41THR0-0.071-0.04812.9230.1110.1110.0000.0000.0000.000
42A42LEU00.0390.02614.772-0.074-0.0740.0000.0000.0000.000
43A43LEU00.0460.02512.291-0.067-0.0670.0000.0000.0000.000
44A44PHE0-0.104-0.0429.1830.1630.1630.0000.0000.0000.000
45A45LEU00.0660.0296.9820.0330.0330.0000.0000.0000.000
46A46GLY0-0.014-0.0027.834-0.318-0.3180.0000.0000.0000.000
47A47GLU-1-0.929-0.9691.926-17.480-18.2958.071-3.837-3.419-0.046
48A48ARG10.8430.9052.9565.6676.8590.022-0.463-0.7510.000
49A49PRO00.0540.0422.051-12.000-11.2454.029-2.556-2.227-0.033
50A50GLU-1-0.911-0.9792.280-8.874-6.3772.941-2.040-3.397-0.023
51A51GLU-1-0.960-0.9724.194-0.414-0.2330.000-0.039-0.1430.000
52A52GLU-1-0.671-0.8166.558-2.249-2.2490.0000.0000.0000.000
53A53LEU0-0.069-0.0373.0180.5290.3613.181-0.642-2.371-0.001
54A54PRO00.0390.0096.9130.3610.3610.0000.0000.0000.000
55A55ASP-1-0.826-0.89310.229-0.365-0.3650.0000.0000.0000.000
56A56TYR0-0.042-0.0586.3180.3360.3360.0000.0000.0000.000
57A57LEU0-0.049-0.0197.7570.1800.1800.0000.0000.0000.000
58A58ALA00.0210.01011.255-0.036-0.0360.0000.0000.0000.000
59A59LEU0-0.0430.00112.863-0.008-0.0080.0000.0000.0000.000
60A60GLY00.0180.00013.442-0.017-0.0170.0000.0000.0000.000
61A61HIS0-0.043-0.03513.823-0.131-0.1310.0000.0000.0000.000
62A62ARG10.7780.87317.3270.0340.0340.0000.0000.0000.000
63A63LEU00.0060.00216.755-0.016-0.0160.0000.0000.0000.000
64A64ALA0-0.040-0.01518.654-0.015-0.0150.0000.0000.0000.000
65A65ARG10.9490.97020.472-0.131-0.1310.0000.0000.0000.000
66A66LEU0-0.0190.00322.421-0.026-0.0260.0000.0000.0000.000
67A67GLU-1-0.828-0.88523.2130.0980.0980.0000.0000.0000.000
68A68ALA00.0440.03624.9180.0290.0290.0000.0000.0000.000
69A69PRO00.006-0.00325.6270.0050.0050.0000.0000.0000.000
70A70PHE0-0.0070.01722.800-0.028-0.0280.0000.0000.0000.000
71A71ARG10.8620.91427.317-0.136-0.1360.0000.0000.0000.000
72A72ALA00.0040.01625.991-0.016-0.0160.0000.0000.0000.000
73A73ARG10.8750.92928.060-0.143-0.1430.0000.0000.0000.000
74A74LEU0-0.026-0.00126.161-0.001-0.0010.0000.0000.0000.000
75A75ARG10.8670.88929.153-0.107-0.1070.0000.0000.0000.000
76A76GLY00.0400.03331.181-0.012-0.0120.0000.0000.0000.000
77A77THR00.0250.01928.7840.0070.0070.0000.0000.0000.000
78A78GLY0-0.010-0.00728.420-0.018-0.0180.0000.0000.0000.000
79A79TYR00.0150.00327.2420.0200.0200.0000.0000.0000.000
80A80PHE00.0210.04922.910-0.012-0.0120.0000.0000.0000.000
81A81PRO00.0810.01825.4280.0140.0140.0000.0000.0000.000
82A82ASN00.001-0.01927.6560.0240.0240.0000.0000.0000.000
83A83GLU-1-0.801-0.86330.7330.0010.0010.0000.0000.0000.000
84A84GLY00.0590.03231.657-0.009-0.0090.0000.0000.0000.000
85A85THR0-0.019-0.01428.3680.0150.0150.0000.0000.0000.000
86A86PRO0-0.0140.01827.767-0.009-0.0090.0000.0000.0000.000
87A87ARG10.9360.94817.6250.0340.0340.0000.0000.0000.000
88A88VAL0-0.103-0.07220.7740.0280.0280.0000.0000.0000.000
89A89TRP00.0800.05523.739-0.011-0.0110.0000.0000.0000.000
90A90PHE0-0.032-0.02523.0220.0310.0310.0000.0000.0000.000
91A91ALA00.0950.04524.441-0.025-0.0250.0000.0000.0000.000
92A92LYS10.8220.89724.870-0.089-0.0890.0000.0000.0000.000
93A93ALA00.0270.03124.4350.0090.0090.0000.0000.0000.000
94A94GLU-1-0.876-0.93326.5400.0950.0950.0000.0000.0000.000
95A95ALA00.0820.01126.4590.0130.0130.0000.0000.0000.000
96A96GLU-1-0.844-0.93726.4350.0680.0680.0000.0000.0000.000
97A97GLY00.0610.04725.493-0.009-0.0090.0000.0000.0000.000
98A98PHE0-0.041-0.02621.3770.0130.0130.0000.0000.0000.000
99A99LEU0-0.038-0.01521.540-0.001-0.0010.0000.0000.0000.000
100A100ARG10.9140.93522.704-0.094-0.0940.0000.0000.0000.000
101A101LEU00.004-0.00318.918-0.008-0.0080.0000.0000.0000.000
102A102ALA0-0.059-0.03418.006-0.010-0.0100.0000.0000.0000.000
103A103GLU-1-0.927-0.96318.448-0.073-0.0730.0000.0000.0000.000
104A104GLY00.0270.01219.973-0.040-0.0400.0000.0000.0000.000
105A105LEU0-0.019-0.02613.510-0.012-0.0120.0000.0000.0000.000
106A106ARG10.8330.90815.4150.0340.0340.0000.0000.0000.000
107A107ALA00.0730.03916.987-0.068-0.0680.0000.0000.0000.000
108A108GLY00.0010.00316.294-0.033-0.0330.0000.0000.0000.000
109A109VAL0-0.019-0.02511.862-0.050-0.0500.0000.0000.0000.000
110A110GLU-1-0.887-0.94414.159-0.448-0.4480.0000.0000.0000.000
111A111GLU-1-0.914-0.92417.205-0.242-0.2420.0000.0000.0000.000
112A112LEU0-0.040-0.02011.022-0.012-0.0120.0000.0000.0000.000
113A113LEU00.007-0.00110.614-0.117-0.1170.0000.0000.0000.000
114A114GLY00.0070.00614.861-0.005-0.0050.0000.0000.0000.000
115A115GLU-1-0.852-0.92217.296-0.815-0.8150.0000.0000.0000.000
116A116GLU-1-0.817-0.90313.427-1.285-1.2850.0000.0000.0000.000
117A117ALA0-0.013-0.00713.643-0.145-0.1450.0000.0000.0000.000
118A118VAL0-0.052-0.02914.7220.0140.0140.0000.0000.0000.000
119A119ARG10.7430.84613.4491.0741.0740.0000.0000.0000.000
120A120ILE0-0.0380.02010.434-0.174-0.1740.0000.0000.0000.000
121A121PRO0-0.038-0.04510.4650.2510.2510.0000.0000.0000.000
122A122GLY0-0.120-0.08613.4250.0810.0810.0000.0000.0000.000
123A123TRP00.0650.05213.5460.0730.0730.0000.0000.0000.000
124A124ASP-1-0.818-0.90016.829-0.399-0.3990.0000.0000.0000.000
125A125LYS10.7890.91117.1620.3230.3230.0000.0000.0000.000
126A126PRO00.0270.01120.6820.0080.0080.0000.0000.0000.000
127A127PHE00.0350.00919.2180.0160.0160.0000.0000.0000.000
128A128LYS10.9430.96121.5610.0360.0360.0000.0000.0000.000
129A129PRO00.0490.04021.8080.0210.0210.0000.0000.0000.000
130A130HIS10.8570.93721.368-0.109-0.1090.0000.0000.0000.000
131A131ILE00.0680.04520.2910.0280.0280.0000.0000.0000.000
132A132THR0-0.118-0.06519.111-0.035-0.0350.0000.0000.0000.000
133A133LEU00.0580.03321.0510.0430.0430.0000.0000.0000.000
134A134ALA00.0450.01622.7610.0240.0240.0000.0000.0000.000
135A135ARG10.9010.95217.837-0.259-0.2590.0000.0000.0000.000
136A136ARG10.9621.00422.386-0.045-0.0450.0000.0000.0000.000
137A137LYS10.9570.97719.215-0.293-0.2930.0000.0000.0000.000
138A138ALA0-0.0110.00024.214-0.014-0.0140.0000.0000.0000.000
139A139PRO00.012-0.00327.8960.0030.0030.0000.0000.0000.000
140A140ALA00.0040.00929.6810.0110.0110.0000.0000.0000.000
141A141PRO00.0020.02531.671-0.009-0.0090.0000.0000.0000.000
142A142ARG10.7970.87630.869-0.029-0.0290.0000.0000.0000.000
143A143VAL00.0120.01032.976-0.002-0.0020.0000.0000.0000.000
144A144PRO00.0240.00834.439-0.001-0.0010.0000.0000.0000.000
145A145PRO00.005-0.00333.9910.0100.0100.0000.0000.0000.000
146A146VAL00.0150.00731.9830.0010.0010.0000.0000.0000.000
147A147LEU0-0.023-0.01632.8110.0040.0040.0000.0000.0000.000
148A148PHE0-0.009-0.02629.1900.0070.0070.0000.0000.0000.000
149A149GLY00.0080.02233.442-0.001-0.0010.0000.0000.0000.000
150A150LEU00.0340.01829.963-0.002-0.0020.0000.0000.0000.000
151A151GLU-1-0.815-0.88330.8460.1600.1600.0000.0000.0000.000
152A152TRP00.0300.00523.253-0.002-0.0020.0000.0000.0000.000
153A153PRO00.0470.01528.066-0.013-0.0130.0000.0000.0000.000
154A154VAL0-0.069-0.03021.9470.0390.0390.0000.0000.0000.000
155A155GLU-1-0.802-0.92123.3930.2890.2890.0000.0000.0000.000
156A156GLY00.0240.01920.046-0.002-0.0020.0000.0000.0000.000
157A157PHE0-0.097-0.03914.4700.0070.0070.0000.0000.0000.000
158A158ALA0-0.011-0.01112.2430.0300.0300.0000.0000.0000.000
159A159LEU00.0490.0507.059-0.103-0.1030.0000.0000.0000.000
160A160VAL0-0.058-0.0467.7320.3570.3570.0000.0000.0000.000
161A161ARG10.9860.9862.089-17.997-19.40010.118-2.513-6.2020.034
162A162SER0-0.089-0.0474.798-1.818-1.733-0.001-0.008-0.0740.000
163A163GLU-1-0.752-0.8605.0344.0764.0760.0000.0000.0000.000
164A164LEU0-0.048-0.0276.878-0.387-0.3870.0000.0000.0000.000
165A165LYS10.9330.9559.249-2.253-2.2530.0000.0000.0000.000
166A166PRO00.0830.02312.454-0.089-0.0890.0000.0000.0000.000
167A167LYS10.9210.96116.277-0.645-0.6450.0000.0000.0000.000
168A168GLY0-0.0130.00115.032-0.074-0.0740.0000.0000.0000.000
169A169PRO0-0.049-0.02311.1760.0620.0620.0000.0000.0000.000
170A170VAL00.0030.01410.302-0.158-0.1580.0000.0000.0000.000
171A171TYR0-0.020-0.0249.0350.2970.2970.0000.0000.0000.000
172A172THR00.0080.0117.171-0.363-0.3630.0000.0000.0000.000
173A173VAL0-0.038-0.0167.6740.8060.8060.0000.0000.0000.000
174A174LEU0-0.0170.0043.647-0.6500.0910.167-0.227-0.6800.001
175A175GLU-1-0.773-0.9027.9400.5150.5150.0000.0000.0000.000
176A176LYS10.9020.96211.227-0.979-0.9790.0000.0000.0000.000
177A177PHE00.0510.03211.618-0.022-0.0220.0000.0000.0000.000
178A178SER0-0.019-0.01917.1140.0000.0000.0000.0000.0000.000
179A179LEU0-0.067-0.02620.866-0.019-0.0190.0000.0000.0000.000
180A180ARG10.8380.89723.129-0.202-0.2020.0000.0000.0000.000
181A181GLY00.0320.02925.573-0.019-0.0190.0000.0000.0000.000
182A182GLU-1-0.910-0.95527.0530.1430.1430.0000.0000.0000.000
183A183HIS0-0.039-0.00628.504-0.010-0.0100.0000.0000.0000.000