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: 145RZ

Calculation Name: 1I39-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I39

Chain ID: A

ChEMBL ID:

UniProt ID: O29634

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2274336.812085
FMO2-HF: Nuclear repulsion 2194750.681423
FMO2-HF: Total energy -79586.130662
FMO2-MP2: Total energy -79816.850394


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.
-12.907-4.2715.155-4.268-9.525-0.014
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 : 0.032 / q_NPA : 0.021
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].
3A3ALA00.039-0.0053.129-1.9911.3450.095-1.837-1.5950.002
4A4GLY0-0.020-0.0015.782-0.025-0.0250.0000.0000.0000.000
5A5ILE0-0.008-0.0109.3980.1290.1290.0000.0000.0000.000
6A6ASP-1-0.798-0.87512.467-0.146-0.1460.0000.0000.0000.000
7A7GLU-1-0.775-0.89315.959-0.112-0.1120.0000.0000.0000.000
8A8ALA0-0.0010.00819.1330.0240.0240.0000.0000.0000.000
9A9GLY00.0330.01222.1340.0120.0120.0000.0000.0000.000
10A10LYS10.8220.90621.5360.1740.1740.0000.0000.0000.000
11A11GLY00.0100.00026.127-0.004-0.0040.0000.0000.0000.000
12A12CYS0-0.093-0.01628.8610.0110.0110.0000.0000.0000.000
13A13VAL0-0.048-0.02430.719-0.007-0.0070.0000.0000.0000.000
14A14ILE0-0.010-0.00633.019-0.001-0.0010.0000.0000.0000.000
15A15GLY00.0640.04030.1090.0030.0030.0000.0000.0000.000
16A16PRO00.0070.00425.286-0.011-0.0110.0000.0000.0000.000
17A17LEU0-0.045-0.00522.7680.0030.0030.0000.0000.0000.000
18A18VAL0-0.013-0.00219.145-0.003-0.0030.0000.0000.0000.000
19A19VAL0-0.004-0.01116.318-0.013-0.0130.0000.0000.0000.000
20A20ALA00.0060.00214.2290.0240.0240.0000.0000.0000.000
21A21GLY00.0370.00710.639-0.107-0.1070.0000.0000.0000.000
22A22VAL0-0.049-0.0167.4000.1710.1710.0000.0000.0000.000
23A23ALA00.0280.0202.967-1.301-0.8100.114-0.159-0.4460.001
24A24CYS0-0.037-0.0482.7930.7392.3080.388-0.497-1.460-0.003
25A25SER00.0330.0102.338-5.471-3.1654.440-2.317-4.429-0.014
26A26ASP-1-0.879-0.9463.0841.1350.3870.1120.916-0.2810.000
27A27GLU-1-0.810-0.9076.750-0.199-0.1990.0000.0000.0000.000
28A28ASP-1-0.861-0.9118.5150.2850.2850.0000.0000.0000.000
29A29ARG10.9320.97110.454-1.551-1.5510.0000.0000.0000.000
30A30LEU00.0160.0068.572-0.094-0.0940.0000.0000.0000.000
31A31ARG10.7530.84510.876-0.355-0.3550.0000.0000.0000.000
32A32LYS10.9360.97114.362-0.607-0.6070.0000.0000.0000.000
33A33LEU0-0.0150.00113.575-0.045-0.0450.0000.0000.0000.000
34A34GLY00.0240.01616.878-0.045-0.0450.0000.0000.0000.000
35A35VAL00.001-0.00813.094-0.058-0.0580.0000.0000.0000.000
36A36LYS10.9540.99016.498-0.080-0.0800.0000.0000.0000.000
37A37ASP-1-0.800-0.88917.9580.1210.1210.0000.0000.0000.000
38A38SER00.003-0.01518.446-0.012-0.0120.0000.0000.0000.000
39A39LYS10.7950.87120.9020.0420.0420.0000.0000.0000.000
40A40LYS10.8140.91123.274-0.169-0.1690.0000.0000.0000.000
41A41LEU0-0.0390.00021.5150.0020.0020.0000.0000.0000.000
42A42SER00.0270.00925.481-0.008-0.0080.0000.0000.0000.000
43A43GLN00.016-0.00925.9160.0090.0090.0000.0000.0000.000
44A44GLY00.0730.03725.1960.0120.0120.0000.0000.0000.000
45A45ARG10.8520.90624.522-0.183-0.1830.0000.0000.0000.000
46A46ARG10.8230.89021.373-0.064-0.0640.0000.0000.0000.000
47A47GLU-1-0.830-0.90020.3780.2100.2100.0000.0000.0000.000
48A48GLU-1-0.818-0.89820.3580.2730.2730.0000.0000.0000.000
49A49LEU0-0.0050.00516.6720.0510.0510.0000.0000.0000.000
50A50ALA00.018-0.00216.1510.0800.0800.0000.0000.0000.000
51A51GLU-1-0.711-0.83015.2310.4370.4370.0000.0000.0000.000
52A52GLU-1-0.860-0.91315.5940.6390.6390.0000.0000.0000.000
53A53ILE0-0.026-0.02010.9660.1520.1520.0000.0000.0000.000
54A54ARG10.8020.87010.653-0.103-0.1030.0000.0000.0000.000
55A55LYS10.7810.89610.996-0.519-0.5190.0000.0000.0000.000
56A56ILE0-0.063-0.0369.1710.0800.0800.0000.0000.0000.000
57A57CYS0-0.0320.0225.8410.4680.577-0.001-0.006-0.1020.000
58A58ARG10.8600.9434.314-0.443-0.209-0.001-0.027-0.2060.000
59A59THR0-0.010-0.0176.135-0.134-0.1340.0000.0000.0000.000
60A60GLU-1-0.806-0.8778.790-0.202-0.2020.0000.0000.0000.000
61A61VAL00.004-0.01211.311-0.015-0.0150.0000.0000.0000.000
62A62LEU00.0270.03015.146-0.012-0.0120.0000.0000.0000.000
63A63LYS10.8330.89418.142-0.036-0.0360.0000.0000.0000.000
64A64VAL00.0060.01121.788-0.005-0.0050.0000.0000.0000.000
65A65SER00.016-0.01524.9050.0050.0050.0000.0000.0000.000
66A66PRO00.018-0.00628.382-0.011-0.0110.0000.0000.0000.000
67A67GLU-1-0.779-0.85931.440-0.060-0.0600.0000.0000.0000.000
68A68ASN0-0.004-0.00427.919-0.016-0.0160.0000.0000.0000.000
69A69LEU0-0.050-0.02326.421-0.015-0.0150.0000.0000.0000.000
70A70ASP-1-0.792-0.90529.879-0.078-0.0780.0000.0000.0000.000
71A71GLU-1-0.952-0.96231.895-0.102-0.1020.0000.0000.0000.000
72A72ARG10.9110.94023.1810.1880.1880.0000.0000.0000.000
73A73MET0-0.054-0.02930.313-0.008-0.0080.0000.0000.0000.000
74A74ALA0-0.080-0.03832.3530.0050.0050.0000.0000.0000.000
75A75ALA0-0.026-0.01233.0470.0030.0030.0000.0000.0000.000
76A76LYS10.8890.94726.8860.2140.2140.0000.0000.0000.000
77A77THR0-0.012-0.03629.4490.0100.0100.0000.0000.0000.000
78A78ILE00.0380.00726.520-0.012-0.0120.0000.0000.0000.000
79A79ASN00.0250.00224.9960.0020.0020.0000.0000.0000.000
80A80GLU-1-0.845-0.89324.011-0.242-0.2420.0000.0000.0000.000
81A81ILE00.0080.00923.993-0.021-0.0210.0000.0000.0000.000
82A82LEU00.0020.00320.809-0.009-0.0090.0000.0000.0000.000
83A83LYS10.8830.95119.9400.2870.2870.0000.0000.0000.000
84A84GLU-1-0.824-0.88719.221-0.292-0.2920.0000.0000.0000.000
85A85CYS0-0.059-0.03318.842-0.019-0.0190.0000.0000.0000.000
86A86TYR0-0.029-0.03915.693-0.007-0.0070.0000.0000.0000.000
87A87ALA00.0380.02114.346-0.098-0.0980.0000.0000.0000.000
88A88GLU-1-0.815-0.89814.527-0.382-0.3820.0000.0000.0000.000
89A89ILE00.0020.00111.187-0.058-0.0580.0000.0000.0000.000
90A90ILE00.0180.0009.995-0.126-0.1260.0000.0000.0000.000
91A91LEU0-0.009-0.0019.807-0.282-0.2820.0000.0000.0000.000
92A92ARG10.6920.83810.2890.2420.2420.0000.0000.0000.000
93A93LEU0-0.060-0.0445.9180.0030.0030.0000.0000.0000.000
94A94LYS10.8910.9565.2220.4410.4410.0000.0000.0000.000
95A95PRO0-0.0170.0093.742-0.842-0.5650.000-0.071-0.2060.000
96A96GLU-1-0.892-0.9613.403-3.123-2.2030.009-0.260-0.6690.000
97A97ILE0-0.030-0.0275.1701.1911.333-0.001-0.010-0.1310.000
98A98ALA0-0.0120.0066.966-0.465-0.4650.0000.0000.0000.000
99A99TYR00.0160.0088.4690.1170.1170.0000.0000.0000.000
100A100VAL00.027-0.00811.7180.0610.0610.0000.0000.0000.000
101A101ASP-1-0.787-0.88814.685-0.192-0.1920.0000.0000.0000.000
102A102SER00.0250.00317.954-0.017-0.0170.0000.0000.0000.000
103A103PRO0-0.057-0.02820.8040.0380.0380.0000.0000.0000.000
104A104ASP-1-0.905-0.95423.676-0.230-0.2300.0000.0000.0000.000
105A105VAL00.0130.00724.723-0.017-0.0170.0000.0000.0000.000
106A106ILE0-0.0190.01126.1690.0030.0030.0000.0000.0000.000
107A107PRO00.0640.03620.575-0.015-0.0150.0000.0000.0000.000
108A108GLU-1-0.866-0.93521.132-0.374-0.3740.0000.0000.0000.000
109A109ARG10.8130.87922.4760.2540.2540.0000.0000.0000.000
110A110LEU00.0190.01119.319-0.015-0.0150.0000.0000.0000.000
111A111SER00.004-0.01417.892-0.050-0.0500.0000.0000.0000.000
112A112ARG10.9760.99318.3920.3300.3300.0000.0000.0000.000
113A113GLU-1-0.748-0.84120.344-0.334-0.3340.0000.0000.0000.000
114A114LEU00.005-0.00615.5490.0050.0050.0000.0000.0000.000
115A115GLU-1-0.817-0.87115.034-0.958-0.9580.0000.0000.0000.000
116A116GLU-1-0.998-0.98816.666-0.425-0.4250.0000.0000.0000.000
117A117ILE0-0.033-0.01918.387-0.006-0.0060.0000.0000.0000.000
118A118THR0-0.076-0.06113.469-0.053-0.0530.0000.0000.0000.000
119A119GLY00.0190.02214.189-0.059-0.0590.0000.0000.0000.000
120A120LEU0-0.041-0.0138.324-0.106-0.1060.0000.0000.0000.000
121A121ARG10.8660.92010.1031.1391.1390.0000.0000.0000.000
122A122VAL0-0.029-0.03310.833-0.237-0.2370.0000.0000.0000.000
123A123VAL0-0.039-0.01813.2760.1150.1150.0000.0000.0000.000
124A124ALA00.0050.01214.6670.0020.0020.0000.0000.0000.000
125A125GLU-1-0.810-0.88516.364-0.465-0.4650.0000.0000.0000.000
126A126HIS00.017-0.00218.9870.0130.0130.0000.0000.0000.000
127A127LYS10.8200.89920.4990.1950.1950.0000.0000.0000.000
128A128ALA00.0920.04315.2340.0220.0220.0000.0000.0000.000
129A129ASP-1-0.823-0.90515.838-0.068-0.0680.0000.0000.0000.000
130A130GLU-1-0.932-0.95017.072-0.019-0.0190.0000.0000.0000.000
131A131LYS10.7730.88016.2110.4090.4090.0000.0000.0000.000
132A132TYR0-0.017-0.03511.383-0.045-0.0450.0000.0000.0000.000
133A133PRO00.0110.00410.8580.0200.0200.0000.0000.0000.000
134A134LEU00.0520.0265.4410.1310.1310.0000.0000.0000.000
135A135VAL0-0.0180.0039.3200.0250.0250.0000.0000.0000.000
136A136ALA00.0050.01112.3840.0450.0450.0000.0000.0000.000
137A137ALA00.004-0.00110.4970.0310.0310.0000.0000.0000.000
138A138ALA0-0.016-0.00211.2650.0340.0340.0000.0000.0000.000
139A139SER00.016-0.02112.8600.0120.0120.0000.0000.0000.000
140A140ILE0-0.058-0.02315.3810.0030.0030.0000.0000.0000.000
141A141ILE0-0.0070.00012.970-0.007-0.0070.0000.0000.0000.000
142A142ALA00.006-0.00116.222-0.015-0.0150.0000.0000.0000.000
143A143LYS10.9040.93118.2270.0100.0100.0000.0000.0000.000
144A144VAL00.0180.02919.706-0.007-0.0070.0000.0000.0000.000
145A145GLU-1-0.793-0.88618.2070.1340.1340.0000.0000.0000.000
146A146ARG10.8060.89221.306-0.016-0.0160.0000.0000.0000.000
147A147GLU-1-0.819-0.90324.1740.0440.0440.0000.0000.0000.000
148A148ARG10.7480.84519.456-0.214-0.2140.0000.0000.0000.000
149A149GLU-1-0.815-0.86725.9160.0190.0190.0000.0000.0000.000
150A150ILE0-0.041-0.02627.512-0.007-0.0070.0000.0000.0000.000
151A151GLU-1-0.776-0.89529.8140.0520.0520.0000.0000.0000.000
152A152ARG10.8730.91428.745-0.036-0.0360.0000.0000.0000.000
153A153LEU0-0.055-0.03530.817-0.007-0.0070.0000.0000.0000.000
154A154LYS10.7710.88533.502-0.039-0.0390.0000.0000.0000.000
155A155GLU-1-0.963-0.96633.5880.0580.0580.0000.0000.0000.000
156A156LYS10.8670.94735.871-0.019-0.0190.0000.0000.0000.000
157A157PHE0-0.066-0.05035.753-0.005-0.0050.0000.0000.0000.000
158A158GLY00.0550.03939.238-0.003-0.0030.0000.0000.0000.000
159A159ASP-1-0.802-0.90937.7290.0250.0250.0000.0000.0000.000
160A160PHE00.009-0.00433.168-0.004-0.0040.0000.0000.0000.000
161A161GLY00.0210.02637.166-0.006-0.0060.0000.0000.0000.000
162A162SER0-0.070-0.06832.3320.0000.0000.0000.0000.0000.000
163A163GLY00.0460.02631.8770.0000.0000.0000.0000.0000.000
164A164TYR00.0480.00827.477-0.014-0.0140.0000.0000.0000.000
165A165ALA00.0340.00634.1450.0040.0040.0000.0000.0000.000
166A166SER00.0240.00535.5210.0000.0000.0000.0000.0000.000
167A167ASP-1-0.777-0.84736.3310.0030.0030.0000.0000.0000.000
168A168PRO0-0.011-0.02138.335-0.003-0.0030.0000.0000.0000.000
169A169ARG10.9290.96639.987-0.004-0.0040.0000.0000.0000.000
170A170THR0-0.016-0.02236.451-0.001-0.0010.0000.0000.0000.000
171A171ARG10.8160.90139.3790.0190.0190.0000.0000.0000.000
172A172GLU-1-0.896-0.92742.077-0.005-0.0050.0000.0000.0000.000
173A173VAL00.0390.02741.070-0.001-0.0010.0000.0000.0000.000
174A174LEU00.0040.00038.190-0.002-0.0020.0000.0000.0000.000
175A175LYS10.9230.96542.3900.0150.0150.0000.0000.0000.000
176A176GLU-1-0.890-0.95145.785-0.003-0.0030.0000.0000.0000.000
177A177TRP00.0400.00338.357-0.002-0.0020.0000.0000.0000.000
178A178ILE0-0.039-0.02042.935-0.002-0.0020.0000.0000.0000.000
179A179ALA0-0.030-0.01246.331-0.001-0.0010.0000.0000.0000.000
180A180SER0-0.049-0.03047.0860.0010.0010.0000.0000.0000.000
181A181GLY00.0000.00048.6120.0010.0010.0000.0000.0000.000
182A182ARG10.8650.93345.9550.0060.0060.0000.0000.0000.000
183A183ILE00.0270.01440.5400.0020.0020.0000.0000.0000.000
184A184PRO00.0200.03438.602-0.002-0.0020.0000.0000.0000.000
185A185SER00.038-0.00135.670-0.002-0.0020.0000.0000.0000.000
186A186CYS0-0.0230.00533.692-0.004-0.0040.0000.0000.0000.000
187A187VAL0-0.003-0.00633.982-0.003-0.0030.0000.0000.0000.000
188A188ARG10.7920.91427.6870.0680.0680.0000.0000.0000.000
189A189MET00.003-0.01235.0750.0010.0010.0000.0000.0000.000
190A190ARG10.8440.92535.6320.0930.0930.0000.0000.0000.000
191A191TRP00.0210.01529.496-0.005-0.0050.0000.0000.0000.000
192A192LYS10.9740.99236.3840.0770.0770.0000.0000.0000.000
193A193THR00.002-0.01037.7830.0020.0020.0000.0000.0000.000
194A194VAL00.0650.03938.2430.0050.0050.0000.0000.0000.000
195A195SER00.0050.00740.2540.0030.0030.0000.0000.0000.000
196A196ASN0-0.009-0.03242.5080.0010.0010.0000.0000.0000.000
197A197LEU0-0.0430.00042.1380.0030.0030.0000.0000.0000.000
198A198ARG10.9840.99842.8290.0490.0490.0000.0000.0000.000
199A199GLN0-0.0130.00945.5420.0000.0000.0000.0000.0000.000
200A200LYS10.8540.92446.6300.0400.0400.0000.0000.0000.000