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: Z6M6N

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 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 -2325366.145574
FMO2-HF: Nuclear repulsion 2245846.57721
FMO2-HF: Total energy -79519.568364
FMO2-MP2: Total energy -79752.842331


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.
-1.5720.678-0.027-1.142-1.080.005
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 : 0.016 / q_NPA : -0.004
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].
3A12ILE0-0.0010.0103.750-2.331-0.081-0.027-1.142-1.0800.005
4A13PRO0-0.005-0.0156.5060.6330.6330.0000.0000.0000.000
5A14THR00.0290.0418.7410.0490.0490.0000.0000.0000.000
6A15PRO0-0.012-0.00511.1840.0310.0310.0000.0000.0000.000
7A16LEU00.0070.00613.3160.0600.0600.0000.0000.0000.000
8A17VAL0-0.022-0.01114.862-0.035-0.0350.0000.0000.0000.000
9A18ALA00.0040.01018.0510.0360.0360.0000.0000.0000.000
10A19VAL0-0.003-0.00620.620-0.020-0.0200.0000.0000.0000.000
11A20TYR00.0000.00223.0930.0200.0200.0000.0000.0000.000
12A21ALA0-0.008-0.01026.391-0.010-0.0100.0000.0000.0000.000
13A22ASP-1-0.817-0.88328.4090.0590.0590.0000.0000.0000.000
14A23GLU-1-0.902-0.95931.9040.0600.0600.0000.0000.0000.000
15A24SER00.0600.02534.6210.0020.0020.0000.0000.0000.000
16A25CYS0-0.045-0.01338.331-0.003-0.0030.0000.0000.0000.000
17A26LEU0-0.028-0.00941.4740.0010.0010.0000.0000.0000.000
18A27GLY00.0340.01744.840-0.001-0.0010.0000.0000.0000.000
19A28ASN0-0.050-0.03347.4980.0010.0010.0000.0000.0000.000
20A29GLY00.0500.03949.0300.0000.0000.0000.0000.0000.000
21A30ARG10.9110.95548.303-0.021-0.0210.0000.0000.0000.000
22A31GLU-1-0.880-0.97141.0340.0440.0440.0000.0000.0000.000
23A32GLY0-0.032-0.02343.1530.0000.0000.0000.0000.0000.000
24A33GLU-1-0.941-0.96944.1710.0190.0190.0000.0000.0000.000
25A34ASN0-0.042-0.00344.468-0.004-0.0040.0000.0000.0000.000
26A35PRO00.0350.03343.7240.0010.0010.0000.0000.0000.000
27A36GLY00.008-0.01939.9680.0030.0030.0000.0000.0000.000
28A37GLY0-0.011-0.01737.467-0.004-0.0040.0000.0000.0000.000
29A38ALA0-0.023-0.00831.8590.0050.0050.0000.0000.0000.000
30A39GLY00.0210.00432.514-0.007-0.0070.0000.0000.0000.000
31A40VAL0-0.036-0.01226.0980.0090.0090.0000.0000.0000.000
32A41LEU00.0320.02427.329-0.009-0.0090.0000.0000.0000.000
33A42VAL0-0.045-0.03222.3020.0110.0110.0000.0000.0000.000
34A43GLU-1-0.782-0.89423.1680.0140.0140.0000.0000.0000.000
35A44TYR00.000-0.02517.668-0.002-0.0020.0000.0000.0000.000
36A45ALA00.0500.03320.057-0.007-0.0070.0000.0000.0000.000
37A46ARG10.9410.97419.3230.1130.1130.0000.0000.0000.000
38A47PRO00.0370.00915.7950.0090.0090.0000.0000.0000.000
39A48GLY0-0.019-0.00717.920-0.017-0.0170.0000.0000.0000.000
40A49GLY0-0.047-0.01919.9030.0030.0030.0000.0000.0000.000
41A50ALA00.0200.00022.9020.0040.0040.0000.0000.0000.000
42A51GLY0-0.0050.00323.6060.0080.0080.0000.0000.0000.000
43A52ASP-1-0.922-0.95124.646-0.040-0.0400.0000.0000.0000.000
44A53ILE0-0.083-0.03423.796-0.005-0.0050.0000.0000.0000.000
45A54VAL0-0.017-0.00524.815-0.004-0.0040.0000.0000.0000.000
46A55ARG10.8410.90925.4280.0040.0040.0000.0000.0000.000
47A56ARG10.8810.93726.5090.0490.0490.0000.0000.0000.000
48A57ASP-1-0.642-0.77428.1130.0050.0050.0000.0000.0000.000
49A58VAL0-0.031-0.02627.191-0.007-0.0070.0000.0000.0000.000
50A59TRP00.011-0.00530.4810.0080.0080.0000.0000.0000.000
51A60VAL0-0.032-0.02232.657-0.006-0.0060.0000.0000.0000.000
52A61SER00.0210.00335.1390.0040.0040.0000.0000.0000.000
53A62GLU-1-0.783-0.84836.6550.0210.0210.0000.0000.0000.000
54A63PRO00.0730.03740.2690.0020.0020.0000.0000.0000.000
55A64ALA0-0.0190.00443.0360.0000.0000.0000.0000.0000.000
56A65THR0-0.040-0.02638.4190.0020.0020.0000.0000.0000.000
57A66THR00.0260.00738.3580.0010.0010.0000.0000.0000.000
58A67ASN00.0710.02436.8910.0000.0000.0000.0000.0000.000
59A68ASN00.0170.00534.2770.0030.0030.0000.0000.0000.000
60A69ARG10.8220.89533.244-0.025-0.0250.0000.0000.0000.000
61A70MET0-0.0010.01933.1760.0000.0000.0000.0000.0000.000
62A71ALA00.0480.03630.8890.0000.0000.0000.0000.0000.000
63A72LEU0-0.015-0.01327.8860.0040.0040.0000.0000.0000.000
64A73ARG10.8510.91128.453-0.015-0.0150.0000.0000.0000.000
65A74SER0-0.0020.00928.804-0.003-0.0030.0000.0000.0000.000
66A75VAL00.002-0.00323.3080.0000.0000.0000.0000.0000.000
67A76ILE0-0.034-0.02024.654-0.004-0.0040.0000.0000.0000.000
68A77GLU-1-0.882-0.96125.626-0.011-0.0110.0000.0000.0000.000
69A78ALA0-0.0280.00623.814-0.011-0.0110.0000.0000.0000.000
70A79PHE00.010-0.02117.864-0.006-0.0060.0000.0000.0000.000
71A80ARG10.9080.95821.515-0.017-0.0170.0000.0000.0000.000
72A81ALA00.0040.01423.882-0.018-0.0180.0000.0000.0000.000
73A82ILE0-0.030-0.02018.386-0.018-0.0180.0000.0000.0000.000
74A83GLY0-0.0140.00519.201-0.021-0.0210.0000.0000.0000.000
75A84HIS0-0.018-0.00720.287-0.039-0.0390.0000.0000.0000.000
76A85LYS10.8920.94419.7200.1300.1300.0000.0000.0000.000
77A86GLY00.0040.01018.584-0.020-0.0200.0000.0000.0000.000
78A87THR0-0.024-0.02013.806-0.104-0.1040.0000.0000.0000.000
79A88ARG10.8310.9257.7330.4390.4390.0000.0000.0000.000
80A89PHE00.0400.01013.371-0.049-0.0490.0000.0000.0000.000
81A90ARG10.8520.9208.725-0.113-0.1130.0000.0000.0000.000
82A91VAL00.013-0.00112.948-0.065-0.0650.0000.0000.0000.000
83A92VAL00.0320.02316.3900.0500.0500.0000.0000.0000.000
84A93PHE0-0.004-0.00618.304-0.031-0.0310.0000.0000.0000.000
85A94THR00.0210.00821.3970.0220.0220.0000.0000.0000.000
86A95THR00.0160.01624.456-0.014-0.0140.0000.0000.0000.000
87A96ASH00.0470.00627.6670.0110.0110.0000.0000.0000.000
88A97SER00.0400.02429.6920.0040.0040.0000.0000.0000.000
89A98ARG10.8230.87927.603-0.138-0.1380.0000.0000.0000.000
90A99TYR0-0.0070.00729.1840.0110.0110.0000.0000.0000.000
91A100ILE00.0350.00625.0600.0070.0070.0000.0000.0000.000
92A101VAL00.0260.01923.7620.0140.0140.0000.0000.0000.000
93A102ASP-1-0.794-0.87224.3670.1800.1800.0000.0000.0000.000
94A103GLY00.004-0.00126.0510.0090.0090.0000.0000.0000.000
95A104MET0-0.033-0.02221.2900.0090.0090.0000.0000.0000.000
96A105THR0-0.062-0.03520.3460.0250.0250.0000.0000.0000.000
97A106ARG10.8980.94622.006-0.195-0.1950.0000.0000.0000.000
98A107TRP00.0570.03624.548-0.004-0.0040.0000.0000.0000.000
99A108VAL00.0020.00622.171-0.010-0.0100.0000.0000.0000.000
100A109HIS0-0.015-0.00618.533-0.023-0.0230.0000.0000.0000.000
101A110ASP-1-0.851-0.91423.6870.1640.1640.0000.0000.0000.000
102A111TRP0-0.071-0.05227.338-0.012-0.0120.0000.0000.0000.000
103A112ALA0-0.017-0.00924.125-0.012-0.0120.0000.0000.0000.000
104A113GLN00.0200.02926.026-0.014-0.0140.0000.0000.0000.000
105A114ARG10.7850.89127.060-0.099-0.0990.0000.0000.0000.000
106A115GLY0-0.011-0.01928.906-0.011-0.0110.0000.0000.0000.000
107A116TRP00.005-0.00124.524-0.013-0.0130.0000.0000.0000.000
108A117LYS10.9080.96430.379-0.082-0.0820.0000.0000.0000.000
109A118ARG11.0060.98734.063-0.039-0.0390.0000.0000.0000.000
110A119LYS10.9230.98136.300-0.066-0.0660.0000.0000.0000.000
111A120SER0-0.016-0.03538.703-0.003-0.0030.0000.0000.0000.000
112A121GLY00.007-0.00142.2470.0020.0020.0000.0000.0000.000
113A122ALA0-0.0200.01538.5740.0000.0000.0000.0000.0000.000
114A123ILE00.027-0.00238.448-0.003-0.0030.0000.0000.0000.000
115A124GLU-1-0.795-0.91533.7520.0780.0780.0000.0000.0000.000
116A125ASN00.0130.01232.9140.0070.0070.0000.0000.0000.000
117A126LEU00.0330.01430.9450.0000.0000.0000.0000.0000.000
118A127ALA00.0230.01130.2870.0030.0030.0000.0000.0000.000
119A128LEU00.0460.02030.004-0.002-0.0020.0000.0000.0000.000
120A129TRP00.0100.01625.5390.0040.0040.0000.0000.0000.000
121A130GLN0-0.038-0.01925.8640.0010.0010.0000.0000.0000.000
122A131GLU-1-0.893-0.95125.0650.0170.0170.0000.0000.0000.000
123A132ALA00.000-0.01124.808-0.004-0.0040.0000.0000.0000.000
124A133VAL0-0.029-0.01320.3520.0070.0070.0000.0000.0000.000
125A134GLN0-0.021-0.01620.2480.0030.0030.0000.0000.0000.000
126A135ALA0-0.0250.00020.436-0.014-0.0140.0000.0000.0000.000
127A136VAL00.0200.00717.128-0.010-0.0100.0000.0000.0000.000
128A137ASN0-0.063-0.04315.666-0.027-0.0270.0000.0000.0000.000
129A138GLY00.0130.01213.0470.0330.0330.0000.0000.0000.000
130A139HIS0-0.0200.01211.9240.0320.0320.0000.0000.0000.000
131A140ALA0-0.0060.01110.5030.0600.0600.0000.0000.0000.000
132A141VAL00.015-0.00712.558-0.051-0.0510.0000.0000.0000.000
133A142GLU-1-0.807-0.87215.5180.3700.3700.0000.0000.0000.000
134A143TRP00.002-0.00516.913-0.058-0.0580.0000.0000.0000.000
135A144ARG10.8790.93418.345-0.191-0.1910.0000.0000.0000.000
136A145TRP0-0.008-0.00723.101-0.011-0.0110.0000.0000.0000.000
137A146VAL0-0.014-0.00426.9010.0020.0020.0000.0000.0000.000
138A147ARG10.9100.95129.540-0.082-0.0820.0000.0000.0000.000
139A148GLY00.0760.03133.265-0.001-0.0010.0000.0000.0000.000
140A149HIS00.0030.01434.9280.0010.0010.0000.0000.0000.000
141A150ALA0-0.045-0.03534.9440.0000.0000.0000.0000.0000.000
142A151GLY00.0160.01836.2360.0020.0020.0000.0000.0000.000
143A152HIS0-0.090-0.03927.070-0.007-0.0070.0000.0000.0000.000
144A153ALA00.0660.01332.130-0.001-0.0010.0000.0000.0000.000
145A154GLN00.0280.00027.0290.0000.0000.0000.0000.0000.000
146A155ASN0-0.025-0.01330.257-0.004-0.0040.0000.0000.0000.000
147A156GLU-1-0.818-0.92431.3230.0380.0380.0000.0000.0000.000
148A157TYR0-0.072-0.04231.893-0.003-0.0030.0000.0000.0000.000
149A158ALA00.0110.00430.601-0.004-0.0040.0000.0000.0000.000
150A159ASN0-0.034-0.03932.692-0.006-0.0060.0000.0000.0000.000
151A160HIS00.0120.00835.657-0.001-0.0010.0000.0000.0000.000
152A161LEU0-0.054-0.02532.197-0.003-0.0030.0000.0000.0000.000
153A162ALA0-0.0110.00434.842-0.003-0.0030.0000.0000.0000.000
154A163VAL00.0090.00236.439-0.002-0.0020.0000.0000.0000.000
155A164THR0-0.029-0.01439.026-0.003-0.0030.0000.0000.0000.000
156A165ALA0-0.032-0.01237.157-0.002-0.0020.0000.0000.0000.000
157A166ALA0-0.006-0.00939.240-0.002-0.0020.0000.0000.0000.000
158A167GLY0-0.030-0.01041.370-0.001-0.0010.0000.0000.0000.000
159A168GLY0-0.019-0.00843.076-0.001-0.0010.0000.0000.0000.000
160A169GLN0-0.081-0.04542.071-0.003-0.0030.0000.0000.0000.000
161A170THR00.0160.03040.086-0.003-0.0030.0000.0000.0000.000
162A171GLN0-0.031-0.03335.7270.0060.0060.0000.0000.0000.000
163A172SER00.0190.01831.969-0.001-0.0010.0000.0000.0000.000
164A173GLY0-0.032-0.00233.476-0.005-0.0050.0000.0000.0000.000
165A174GLY0-0.001-0.01429.506-0.006-0.0060.0000.0000.0000.000
166A175LEU0-0.034-0.00824.4330.0040.0040.0000.0000.0000.000
167A176VAL0-0.0030.00428.850-0.008-0.0080.0000.0000.0000.000
168A177ASP-1-0.947-0.99031.015-0.038-0.0380.0000.0000.0000.000
169A178SER0-0.056-0.04130.5320.0050.0050.0000.0000.0000.000
170A179GLY00.0560.03232.577-0.003-0.0030.0000.0000.0000.000
171A180TYR0-0.046-0.02431.9770.0050.0050.0000.0000.0000.000
172A181GLU-1-0.812-0.93331.446-0.013-0.0130.0000.0000.0000.000
173A182GLU-1-0.899-0.94235.437-0.015-0.0150.0000.0000.0000.000
174A183TRP0-0.036-0.02235.1550.0020.0020.0000.0000.0000.000
175A184ALA0-0.032-0.01935.5410.0030.0030.0000.0000.0000.000
176A185ALA00.0150.01537.6330.0020.0020.0000.0000.0000.000
177A186ARG10.8830.96740.714-0.008-0.0080.0000.0000.0000.000
178A187VAL00.0520.00843.0670.0020.0020.0000.0000.0000.000
179A188SER0-0.003-0.01343.2190.0010.0010.0000.0000.0000.000
180A189THR0-0.015-0.00938.2550.0030.0030.0000.0000.0000.000
181A190ALA00.0380.02141.0170.0020.0020.0000.0000.0000.000
182A191ALA0-0.061-0.02842.5190.0020.0020.0000.0000.0000.000
183A192SER0-0.009-0.01140.3580.0020.0020.0000.0000.0000.000
184A193ARG10.8570.94340.404-0.018-0.0180.0000.0000.0000.000
185A194MET00.0180.03335.6900.0030.0030.0000.0000.0000.000
186A195ARG10.9270.96232.206-0.062-0.0620.0000.0000.0000.000
187A196LEU00.0050.00629.0120.0020.0020.0000.0000.0000.000
188A197GLU-1-0.914-0.94124.1060.1090.1090.0000.0000.0000.000
189A198PRO00.0090.00224.067-0.007-0.0070.0000.0000.0000.000
190A199PHE0-0.007-0.00917.7000.0110.0110.0000.0000.0000.000
191A200PRO0-0.0160.00217.2410.0030.0030.0000.0000.0000.000
192A201ASP-1-0.818-0.89516.1070.0570.0570.0000.0000.0000.000
193A202ALA0-0.061-0.05611.1640.0340.0340.0000.0000.0000.000
194A203ALA0-0.014-0.02111.5950.0750.0750.0000.0000.0000.000
195A204ALA0-0.0110.00713.6480.0390.0390.0000.0000.0000.000
196A205PHE0-0.049-0.02110.3430.0370.0370.0000.0000.0000.000
197A206ARG10.8860.93012.034-0.366-0.3660.0000.0000.0000.000
198A207PRO0-0.0240.00610.186-0.056-0.0560.0000.0000.0000.000
199A208SER00.008-0.01313.3670.0330.0330.0000.0000.0000.000
200A209PRO0-0.033-0.01713.3680.0670.0670.0000.0000.0000.000
201A210ALA00.0450.01612.320-0.066-0.0660.0000.0000.0000.000
202A211LEU00.0100.00714.249-0.021-0.0210.0000.0000.0000.000
203A212PRO0-0.0200.00217.228-0.003-0.0030.0000.0000.0000.000
204A213VAL00.0170.00717.469-0.017-0.0170.0000.0000.0000.000
205A214VAL0-0.004-0.00419.9610.0000.0000.0000.0000.0000.000
206A215ALA00.018-0.00323.666-0.013-0.0130.0000.0000.0000.000
207A216ALA0-0.012-0.01526.252-0.001-0.0010.0000.0000.0000.000
208A217GLY00.0260.01028.188-0.003-0.0030.0000.0000.0000.000
209A218ARG10.9300.98330.074-0.048-0.0480.0000.0000.0000.000
210A219PRO00.0020.01633.0670.0010.0010.0000.0000.0000.000
211A220SER00.0580.04035.0400.0040.0040.0000.0000.0000.000