Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R9398

Calculation Name: 4IBN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IBN

Chain ID: A

ChEMBL ID:

UniProt ID: E0X765

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2324792.293124
FMO2-HF: Nuclear repulsion 2245270.86029
FMO2-HF: Total energy -79521.432834
FMO2-MP2: Total energy -79754.949824


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:10:SER)


Summations of interaction energy for fragment #1(A:10:SER)
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.
-1.9330.47-0.029-1.24-1.1340.005
Interaction energy analysis for fragmet #1(A:10:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.000
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].
3A12ILE0-0.0020.0103.750-2.455-0.052-0.029-1.240-1.1340.005
4A13PRO0-0.009-0.0206.6760.6880.6880.0000.0000.0000.000
5A14THR00.0380.0398.7590.0370.0370.0000.0000.0000.000
6A15PRO0-0.016-0.00211.0770.0240.0240.0000.0000.0000.000
7A16LEU0-0.011-0.00113.1310.0710.0710.0000.0000.0000.000
8A17VAL0-0.018-0.01014.790-0.043-0.0430.0000.0000.0000.000
9A18ALA00.0090.01517.9670.0390.0390.0000.0000.0000.000
10A19VAL0-0.011-0.01220.535-0.021-0.0210.0000.0000.0000.000
11A20TYR0-0.017-0.01022.9860.0200.0200.0000.0000.0000.000
12A21ALA0-0.013-0.00626.298-0.011-0.0110.0000.0000.0000.000
13A22ASP-1-0.828-0.91028.3080.0730.0730.0000.0000.0000.000
14A23GLU-1-0.847-0.91331.8060.0820.0820.0000.0000.0000.000
15A24SER00.0130.01234.525-0.001-0.0010.0000.0000.0000.000
16A25CYS00.0040.01038.235-0.001-0.0010.0000.0000.0000.000
17A26LEU0-0.026-0.00541.3800.0000.0000.0000.0000.0000.000
18A27GLY00.0280.01244.744-0.001-0.0010.0000.0000.0000.000
19A28ASN0-0.043-0.03347.4060.0010.0010.0000.0000.0000.000
20A29GLY00.0420.03448.923-0.001-0.0010.0000.0000.0000.000
21A30ARG10.7950.88548.217-0.031-0.0310.0000.0000.0000.000
22A31GLU-1-0.840-0.95741.1040.0560.0560.0000.0000.0000.000
23A32GLY0-0.030-0.01743.1630.0000.0000.0000.0000.0000.000
24A33GLU-1-0.844-0.90544.1810.0300.0300.0000.0000.0000.000
25A34ASN0-0.044-0.00744.351-0.004-0.0040.0000.0000.0000.000
26A35PRO00.0480.03743.6280.0020.0020.0000.0000.0000.000
27A36GLY00.007-0.02639.8700.0020.0020.0000.0000.0000.000
28A37GLY0-0.009-0.01437.370-0.004-0.0040.0000.0000.0000.000
29A38ALA0-0.022-0.00931.7910.0060.0060.0000.0000.0000.000
30A39GLY00.0200.00432.409-0.007-0.0070.0000.0000.0000.000
31A40VAL0-0.033-0.02125.8950.0100.0100.0000.0000.0000.000
32A41LEU00.0300.03027.195-0.009-0.0090.0000.0000.0000.000
33A42VAL0-0.038-0.03122.1450.0130.0130.0000.0000.0000.000
34A43GLU-1-0.762-0.86423.0800.0310.0310.0000.0000.0000.000
35A44TYR00.010-0.01717.8100.0020.0020.0000.0000.0000.000
36A45ALA00.0330.03220.024-0.010-0.0100.0000.0000.0000.000
37A46ARG10.9480.97619.2700.1060.1060.0000.0000.0000.000
38A47PRO00.0320.00315.7410.0040.0040.0000.0000.0000.000
39A48GLY0-0.017-0.00417.885-0.018-0.0180.0000.0000.0000.000
40A49GLY0-0.045-0.01719.8790.0020.0020.0000.0000.0000.000
41A50ALA00.0210.00322.8700.0020.0020.0000.0000.0000.000
42A51GLY0-0.0030.00223.5540.0070.0070.0000.0000.0000.000
43A52ASP-1-0.921-0.95124.595-0.039-0.0390.0000.0000.0000.000
44A53ILE0-0.085-0.03823.655-0.003-0.0030.0000.0000.0000.000
45A54VAL0-0.014-0.00124.810-0.004-0.0040.0000.0000.0000.000
46A55ARG10.8220.88225.362-0.006-0.0060.0000.0000.0000.000
47A56ARG10.8070.89526.4360.0260.0260.0000.0000.0000.000
48A57ASP-1-0.650-0.77128.0010.0220.0220.0000.0000.0000.000
49A58VAL0-0.039-0.02927.049-0.007-0.0070.0000.0000.0000.000
50A59TRP00.0140.00330.3730.0080.0080.0000.0000.0000.000
51A60VAL0-0.052-0.03232.585-0.006-0.0060.0000.0000.0000.000
52A61SER00.005-0.00135.0370.0040.0040.0000.0000.0000.000
53A62GLU-1-0.773-0.83436.6120.0410.0410.0000.0000.0000.000
54A63PRO00.0760.04140.2790.0010.0010.0000.0000.0000.000
55A64ALA0-0.027-0.00243.0560.0000.0000.0000.0000.0000.000
56A65THR0-0.045-0.04238.4530.0030.0030.0000.0000.0000.000
57A66THR00.0160.00738.3130.0010.0010.0000.0000.0000.000
58A67ASN00.0730.02737.0190.0000.0000.0000.0000.0000.000
59A68ASN00.0040.00134.2550.0030.0030.0000.0000.0000.000
60A69ARG10.8330.89733.257-0.043-0.0430.0000.0000.0000.000
61A70MET0-0.0010.01633.1870.0010.0010.0000.0000.0000.000
62A71ALA00.0320.03430.8940.0010.0010.0000.0000.0000.000
63A72LEU0-0.014-0.01127.9840.0060.0060.0000.0000.0000.000
64A73ARG10.8230.88628.464-0.034-0.0340.0000.0000.0000.000
65A74SER0-0.020-0.00228.615-0.002-0.0020.0000.0000.0000.000
66A75VAL0-0.002-0.00723.2890.0010.0010.0000.0000.0000.000
67A76ILE0-0.038-0.01224.656-0.001-0.0010.0000.0000.0000.000
68A77GLU-1-0.768-0.89925.6340.0230.0230.0000.0000.0000.000
69A78ALA0-0.037-0.00123.800-0.010-0.0100.0000.0000.0000.000
70A79PHE00.017-0.01817.760-0.004-0.0040.0000.0000.0000.000
71A80ARG10.8510.92821.521-0.047-0.0470.0000.0000.0000.000
72A81ALA0-0.0190.00623.886-0.017-0.0170.0000.0000.0000.000
73A82ILE0-0.016-0.01518.279-0.018-0.0180.0000.0000.0000.000
74A83GLY0-0.0110.00419.204-0.016-0.0160.0000.0000.0000.000
75A84HIS0-0.024-0.00620.288-0.036-0.0360.0000.0000.0000.000
76A85LYS10.8840.93819.6190.0930.0930.0000.0000.0000.000
77A86GLY00.0080.01218.584-0.020-0.0200.0000.0000.0000.000
78A87THR0-0.021-0.01913.635-0.098-0.0980.0000.0000.0000.000
79A88ARG10.7950.8827.6620.1930.1930.0000.0000.0000.000
80A89PHE00.037-0.00213.267-0.052-0.0520.0000.0000.0000.000
81A90ARG10.8490.9228.461-0.222-0.2220.0000.0000.0000.000
82A91VAL00.006-0.00712.839-0.077-0.0770.0000.0000.0000.000
83A92VAL00.0260.02416.2850.0510.0510.0000.0000.0000.000
84A93PHE00.004-0.00718.210-0.033-0.0330.0000.0000.0000.000
85A94THR00.0240.00821.3000.0220.0220.0000.0000.0000.000
86A95THR00.0170.01724.360-0.013-0.0130.0000.0000.0000.000
87A96ASH00.056-0.00227.5740.0090.0090.0000.0000.0000.000
88A97SER00.0150.00629.5670.0030.0030.0000.0000.0000.000
89A98ARG10.8180.87527.379-0.151-0.1510.0000.0000.0000.000
90A99TYR0-0.016-0.01229.1140.0130.0130.0000.0000.0000.000
91A100ILE00.0470.01525.0170.0090.0090.0000.0000.0000.000
92A101VAL00.0290.02123.5930.0160.0160.0000.0000.0000.000
93A102ASP-1-0.807-0.86624.3020.2000.2000.0000.0000.0000.000
94A103GLY00.0090.00426.0680.0100.0100.0000.0000.0000.000
95A104MET0-0.024-0.02021.3270.0110.0110.0000.0000.0000.000
96A105THR0-0.064-0.04120.2380.0280.0280.0000.0000.0000.000
97A106ARG10.8950.94822.020-0.213-0.2130.0000.0000.0000.000
98A107TRP00.0490.03924.562-0.002-0.0020.0000.0000.0000.000
99A108VAL0-0.012-0.00522.083-0.010-0.0100.0000.0000.0000.000
100A109HIS0-0.020-0.00218.537-0.015-0.0150.0000.0000.0000.000
101A110ASP-1-0.850-0.92223.6880.1930.1930.0000.0000.0000.000
102A111TRP0-0.085-0.06327.339-0.011-0.0110.0000.0000.0000.000
103A112ALA0-0.022-0.00624.088-0.012-0.0120.0000.0000.0000.000
104A113GLN00.0110.02425.652-0.020-0.0200.0000.0000.0000.000
105A114ARG10.8040.90027.052-0.124-0.1240.0000.0000.0000.000
106A115GLY0-0.014-0.02528.892-0.013-0.0130.0000.0000.0000.000
107A116TRP00.002-0.00224.222-0.014-0.0140.0000.0000.0000.000
108A117LYS10.8980.96530.370-0.106-0.1060.0000.0000.0000.000
109A118ARG10.9840.97834.053-0.058-0.0580.0000.0000.0000.000
110A119LYS10.9260.97936.295-0.079-0.0790.0000.0000.0000.000
111A120SER0-0.015-0.02938.700-0.002-0.0020.0000.0000.0000.000
112A121GLY00.019-0.00142.2440.0010.0010.0000.0000.0000.000
113A122ALA0-0.0220.01338.5560.0000.0000.0000.0000.0000.000
114A123ILE00.015-0.00838.557-0.002-0.0020.0000.0000.0000.000
115A124GLU-1-0.741-0.88433.8990.1030.1030.0000.0000.0000.000
116A125ASN00.0310.02632.9840.0080.0080.0000.0000.0000.000
117A126LEU00.0410.02230.9850.0010.0010.0000.0000.0000.000
118A127ALA00.0070.00730.2840.0040.0040.0000.0000.0000.000
119A128LEU00.0480.02430.0000.0000.0000.0000.0000.0000.000
120A129TRP00.0140.01025.7130.0080.0080.0000.0000.0000.000
121A130GLN0-0.040-0.02325.8560.0030.0030.0000.0000.0000.000
122A131GLU-1-0.860-0.92625.0600.0500.0500.0000.0000.0000.000
123A132ALA0-0.008-0.01324.807-0.001-0.0010.0000.0000.0000.000
124A133VAL0-0.031-0.01820.4700.0100.0100.0000.0000.0000.000
125A134GLN0-0.016-0.01420.2470.0110.0110.0000.0000.0000.000
126A135ALA0-0.0030.01220.431-0.010-0.0100.0000.0000.0000.000
127A136VAL0-0.0080.01117.047-0.009-0.0090.0000.0000.0000.000
128A137ASN0-0.097-0.05616.209-0.005-0.0050.0000.0000.0000.000
129A138GLY00.0320.01113.0430.0390.0390.0000.0000.0000.000
130A139HIS0-0.0010.01811.9270.0550.0550.0000.0000.0000.000
131A140ALA0-0.0110.00810.3620.0610.0610.0000.0000.0000.000
132A141VAL00.023-0.00612.469-0.059-0.0590.0000.0000.0000.000
133A142GLU-1-0.778-0.83915.3360.3800.3800.0000.0000.0000.000
134A143TRP00.009-0.00316.830-0.060-0.0600.0000.0000.0000.000
135A144ARG10.8200.89218.357-0.202-0.2020.0000.0000.0000.000
136A145TRP0-0.025-0.02323.002-0.011-0.0110.0000.0000.0000.000
137A146VAL0-0.011-0.00426.8020.0010.0010.0000.0000.0000.000
138A147ARG10.9070.95429.441-0.086-0.0860.0000.0000.0000.000
139A148GLY00.1000.04233.166-0.001-0.0010.0000.0000.0000.000
140A149HIS0-0.032-0.00234.8310.0000.0000.0000.0000.0000.000
141A150ALA0-0.040-0.03434.822-0.001-0.0010.0000.0000.0000.000
142A151GLY00.0250.01936.1430.0010.0010.0000.0000.0000.000
143A152HIS0-0.090-0.04026.970-0.009-0.0090.0000.0000.0000.000
144A153ALA00.0580.01232.090-0.001-0.0010.0000.0000.0000.000
145A154GLN00.0480.00626.610-0.001-0.0010.0000.0000.0000.000
146A155ASN0-0.065-0.03630.052-0.001-0.0010.0000.0000.0000.000
147A156GLU-1-0.796-0.91631.2300.0460.0460.0000.0000.0000.000
148A157TYR0-0.060-0.05031.725-0.003-0.0030.0000.0000.0000.000
149A158ALA00.0070.00430.478-0.003-0.0030.0000.0000.0000.000
150A159ASN0-0.023-0.02532.586-0.006-0.0060.0000.0000.0000.000
151A160HIS00.0340.01335.555-0.002-0.0020.0000.0000.0000.000
152A161LEU0-0.043-0.01032.208-0.003-0.0030.0000.0000.0000.000
153A162ALA0-0.022-0.00134.667-0.002-0.0020.0000.0000.0000.000
154A163VAL00.0210.00836.335-0.002-0.0020.0000.0000.0000.000
155A164THR0-0.032-0.02738.975-0.003-0.0030.0000.0000.0000.000
156A165ALA0-0.037-0.00937.020-0.003-0.0030.0000.0000.0000.000
157A166ALA0-0.007-0.00639.135-0.002-0.0020.0000.0000.0000.000
158A167GLY0-0.011-0.00641.269-0.001-0.0010.0000.0000.0000.000
159A168GLY0-0.021-0.00942.966-0.002-0.0020.0000.0000.0000.000
160A169GLN0-0.076-0.04341.996-0.003-0.0030.0000.0000.0000.000
161A170THR0-0.0050.01240.004-0.003-0.0030.0000.0000.0000.000
162A171GLN0-0.012-0.00835.7440.0070.0070.0000.0000.0000.000
163A172SER00.0220.00831.801-0.001-0.0010.0000.0000.0000.000
164A173GLY0-0.032-0.00333.412-0.005-0.0050.0000.0000.0000.000
165A174GLY0-0.009-0.01829.399-0.004-0.0040.0000.0000.0000.000
166A175LEU0-0.0260.00024.1740.0030.0030.0000.0000.0000.000
167A176VAL00.0020.00928.740-0.009-0.0090.0000.0000.0000.000
168A177ASP-1-0.901-0.95930.902-0.027-0.0270.0000.0000.0000.000
169A178SER0-0.054-0.05030.4410.0050.0050.0000.0000.0000.000
170A179GLY00.0510.02632.496-0.004-0.0040.0000.0000.0000.000
171A180TYR0-0.049-0.02631.9370.0050.0050.0000.0000.0000.000
172A181GLU-1-0.789-0.91031.6240.0000.0000.0000.0000.0000.000
173A182GLU-1-0.901-0.94235.365-0.008-0.0080.0000.0000.0000.000
174A183TRP0-0.030-0.02535.0010.0010.0010.0000.0000.0000.000
175A184ALA0-0.036-0.01335.4130.0020.0020.0000.0000.0000.000
176A185ALA00.0170.01637.5540.0010.0010.0000.0000.0000.000
177A186ARG10.8490.95940.639-0.017-0.0170.0000.0000.0000.000
178A187VAL00.0500.00542.9860.0020.0020.0000.0000.0000.000
179A188SER00.005-0.00543.0360.0010.0010.0000.0000.0000.000
180A189THR0-0.011-0.01638.1280.0030.0030.0000.0000.0000.000
181A190ALA00.0350.02440.9310.0020.0020.0000.0000.0000.000
182A191ALA0-0.060-0.02842.4360.0010.0010.0000.0000.0000.000
183A192SER00.000-0.00740.2990.0020.0020.0000.0000.0000.000
184A193ARG10.8380.93740.308-0.021-0.0210.0000.0000.0000.000
185A194MET0-0.0030.02835.5300.0030.0030.0000.0000.0000.000
186A195ARG10.9130.95131.913-0.065-0.0650.0000.0000.0000.000
187A196LEU00.0160.01428.9150.0030.0030.0000.0000.0000.000
188A197GLU-1-0.877-0.92723.5830.1220.1220.0000.0000.0000.000
189A198PRO00.0120.00224.043-0.005-0.0050.0000.0000.0000.000
190A199PHE00.009-0.00117.5850.0130.0130.0000.0000.0000.000
191A200PRO0-0.0060.00717.1650.0000.0000.0000.0000.0000.000
192A201ASP-1-0.836-0.90616.1200.0460.0460.0000.0000.0000.000
193A202ALA0-0.055-0.04911.0920.0390.0390.0000.0000.0000.000
194A203ALA00.009-0.00811.5140.0730.0730.0000.0000.0000.000
195A204ALA0-0.0010.01313.5720.0400.0400.0000.0000.0000.000
196A205PHE0-0.033-0.0149.9430.0480.0480.0000.0000.0000.000
197A206ARG10.8400.89911.939-0.345-0.3450.0000.0000.0000.000
198A207PRO0-0.0220.00210.094-0.055-0.0550.0000.0000.0000.000
199A208SER0-0.012-0.01513.2960.0190.0190.0000.0000.0000.000
200A209PRO0-0.020-0.01113.3730.0800.0800.0000.0000.0000.000
201A210ALA00.0380.01512.241-0.069-0.0690.0000.0000.0000.000
202A211LEU00.0160.00714.253-0.030-0.0300.0000.0000.0000.000
203A212PRO0-0.011-0.00417.2210.0010.0010.0000.0000.0000.000
204A213VAL00.0090.00917.327-0.020-0.0200.0000.0000.0000.000
205A214VAL00.001-0.00219.945-0.004-0.0040.0000.0000.0000.000
206A215ALA00.010-0.00123.650-0.012-0.0120.0000.0000.0000.000
207A216ALA0-0.012-0.01226.235-0.005-0.0050.0000.0000.0000.000
208A217GLY00.0300.00828.168-0.003-0.0030.0000.0000.0000.000
209A218ARG10.9240.98330.342-0.080-0.0800.0000.0000.0000.000
210A219PRO00.0070.01633.0470.0010.0010.0000.0000.0000.000
211A220SER00.0620.04035.0310.0030.0030.0000.0000.0000.000