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: QY9YY

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2327028.802659
FMO2-HF: Nuclear repulsion 2247506.727147
FMO2-HF: Total energy -79522.075512
FMO2-MP2: Total energy -79756.771113


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.
-2.1310.2990.014-1.414-1.0290.003
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 : 0.023 / q_NPA : 0.006
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].
3A12ILE0-0.008-0.0053.496-3.374-0.9440.014-1.414-1.0290.003
4A13PRO0-0.021-0.0276.1940.6690.6690.0000.0000.0000.000
5A14THR00.0480.0438.0320.1700.1700.0000.0000.0000.000
6A15PRO0-0.023-0.00510.4340.0290.0290.0000.0000.0000.000
7A16LEU0-0.030-0.00712.3180.0540.0540.0000.0000.0000.000
8A17VAL0-0.022-0.01313.966-0.033-0.0330.0000.0000.0000.000
9A18ALA00.0050.01717.1910.0410.0410.0000.0000.0000.000
10A19VAL0-0.008-0.00619.935-0.024-0.0240.0000.0000.0000.000
11A20TYR0-0.027-0.02722.5490.0260.0260.0000.0000.0000.000
12A21ALA00.0140.00825.922-0.013-0.0130.0000.0000.0000.000
13A22ASP-1-0.779-0.87927.8430.0480.0480.0000.0000.0000.000
14A23GLU-1-0.814-0.86631.3970.0490.0490.0000.0000.0000.000
15A24SER00.0080.00834.3020.0010.0010.0000.0000.0000.000
16A25CYS00.0070.00638.124-0.002-0.0020.0000.0000.0000.000
17A26LEU0-0.040-0.01141.3390.0010.0010.0000.0000.0000.000
18A27GLY00.0250.00144.663-0.002-0.0020.0000.0000.0000.000
19A28ASN0-0.038-0.01947.4810.0010.0010.0000.0000.0000.000
20A29GLY00.0350.03349.0810.0000.0000.0000.0000.0000.000
21A30ARG10.8080.88348.150-0.015-0.0150.0000.0000.0000.000
22A31GLU-1-0.774-0.90540.7430.0320.0320.0000.0000.0000.000
23A32GLY0-0.042-0.01643.3430.0000.0000.0000.0000.0000.000
24A33GLU-1-0.828-0.90444.3440.0130.0130.0000.0000.0000.000
25A34ASN0-0.032-0.01244.256-0.004-0.0040.0000.0000.0000.000
26A35PRO00.0530.04443.6200.0010.0010.0000.0000.0000.000
27A36GLY00.009-0.02540.0140.0030.0030.0000.0000.0000.000
28A37GLY00.000-0.01137.149-0.005-0.0050.0000.0000.0000.000
29A38ALA0-0.033-0.01031.6800.0060.0060.0000.0000.0000.000
30A39GLY00.0140.00232.293-0.008-0.0080.0000.0000.0000.000
31A40VAL0-0.031-0.02225.7510.0090.0090.0000.0000.0000.000
32A41LEU00.0090.02526.698-0.010-0.0100.0000.0000.0000.000
33A42VAL0-0.023-0.01921.6320.0120.0120.0000.0000.0000.000
34A43GLU-1-0.759-0.85922.559-0.020-0.0200.0000.0000.0000.000
35A44TYR00.010-0.01916.995-0.001-0.0010.0000.0000.0000.000
36A45ALA00.0340.03919.220-0.003-0.0030.0000.0000.0000.000
37A46ARG10.9660.98318.6270.1640.1640.0000.0000.0000.000
38A47PRO00.006-0.00315.2820.0090.0090.0000.0000.0000.000
39A48GLY0-0.012-0.00517.370-0.012-0.0120.0000.0000.0000.000
40A49GLY0-0.036-0.01019.5810.0110.0110.0000.0000.0000.000
41A50ALA0-0.005-0.00922.5850.0030.0030.0000.0000.0000.000
42A51GLY00.0210.01623.1900.0110.0110.0000.0000.0000.000
43A52ASP-1-0.949-0.97624.240-0.089-0.0890.0000.0000.0000.000
44A53ILE0-0.057-0.02522.857-0.012-0.0120.0000.0000.0000.000
45A54VAL0-0.015-0.00323.8110.0030.0030.0000.0000.0000.000
46A55ARG10.8240.89124.5720.0380.0380.0000.0000.0000.000
47A56ARG10.7670.87225.5560.0810.0810.0000.0000.0000.000
48A57ASP-1-0.660-0.77727.084-0.026-0.0260.0000.0000.0000.000
49A58VAL0-0.033-0.02726.761-0.009-0.0090.0000.0000.0000.000
50A59TRP00.008-0.00129.9730.0080.0080.0000.0000.0000.000
51A60VAL0-0.048-0.02032.497-0.006-0.0060.0000.0000.0000.000
52A61SER0-0.003-0.01334.9540.0060.0060.0000.0000.0000.000
53A62GLU-1-0.753-0.83036.8940.0080.0080.0000.0000.0000.000
54A63PRO00.0510.03940.4630.0020.0020.0000.0000.0000.000
55A64ALA0-0.016-0.00643.4640.0010.0010.0000.0000.0000.000
56A65THR0-0.040-0.04138.7840.0020.0020.0000.0000.0000.000
57A66THR0-0.022-0.01038.4340.0020.0020.0000.0000.0000.000
58A67ASN00.0440.00337.155-0.002-0.0020.0000.0000.0000.000
59A68ASN0-0.003-0.00734.2200.0000.0000.0000.0000.0000.000
60A69ARG10.8120.88633.337-0.012-0.0120.0000.0000.0000.000
61A70MET0-0.0020.02633.225-0.001-0.0010.0000.0000.0000.000
62A71ALA00.0330.02531.120-0.001-0.0010.0000.0000.0000.000
63A72LEU0-0.027-0.00728.0230.0030.0030.0000.0000.0000.000
64A73ARG10.8250.88628.2820.0030.0030.0000.0000.0000.000
65A74SER0-0.031-0.01728.387-0.005-0.0050.0000.0000.0000.000
66A75VAL0-0.0070.00022.977-0.002-0.0020.0000.0000.0000.000
67A76ILE0-0.028-0.01424.547-0.010-0.0100.0000.0000.0000.000
68A77GLU-1-0.742-0.86825.580-0.032-0.0320.0000.0000.0000.000
69A78ALA00.0060.01423.924-0.015-0.0150.0000.0000.0000.000
70A79PHE0-0.009-0.02217.550-0.013-0.0130.0000.0000.0000.000
71A80ARG10.8190.89321.3990.0030.0030.0000.0000.0000.000
72A81ALA0-0.019-0.00323.639-0.022-0.0220.0000.0000.0000.000
73A82ILE0-0.015-0.00518.001-0.019-0.0190.0000.0000.0000.000
74A83GLY00.0260.01619.306-0.032-0.0320.0000.0000.0000.000
75A84HIS0-0.014-0.00120.379-0.047-0.0470.0000.0000.0000.000
76A85LYS10.8550.92219.4470.1870.1870.0000.0000.0000.000
77A86GLY00.0020.01419.039-0.029-0.0290.0000.0000.0000.000
78A87THR0-0.043-0.02813.389-0.119-0.1190.0000.0000.0000.000
79A88ARG10.8040.8798.1490.5730.5730.0000.0000.0000.000
80A89PHE00.024-0.00613.000-0.082-0.0820.0000.0000.0000.000
81A90ARG10.8670.9397.8180.1900.1900.0000.0000.0000.000
82A91VAL00.0230.00112.382-0.073-0.0730.0000.0000.0000.000
83A92VAL00.0190.01815.8600.0570.0570.0000.0000.0000.000
84A93PHE00.014-0.01517.913-0.034-0.0340.0000.0000.0000.000
85A94THR00.0090.01321.0900.0250.0250.0000.0000.0000.000
86A95THR0-0.022-0.01324.053-0.015-0.0150.0000.0000.0000.000
87A96ASH00.032-0.02327.3540.0110.0110.0000.0000.0000.000
88A97SER0-0.008-0.02329.1530.0080.0080.0000.0000.0000.000
89A98ARG10.8080.86927.543-0.131-0.1310.0000.0000.0000.000
90A99TYR0-0.028-0.01628.8830.0140.0140.0000.0000.0000.000
91A100ILE00.0450.02024.7440.0070.0070.0000.0000.0000.000
92A101VAL00.0290.02023.5750.0150.0150.0000.0000.0000.000
93A102ASP-1-0.819-0.87424.2980.1780.1780.0000.0000.0000.000
94A103GLY00.0260.00726.2420.0100.0100.0000.0000.0000.000
95A104MET0-0.024-0.01421.2600.0100.0100.0000.0000.0000.000
96A105THR0-0.064-0.04720.4060.0280.0280.0000.0000.0000.000
97A106ARG10.9040.96222.178-0.200-0.2000.0000.0000.0000.000
98A107TRP00.0460.04124.856-0.002-0.0020.0000.0000.0000.000
99A108VAL0-0.012-0.00622.195-0.013-0.0130.0000.0000.0000.000
100A109HIS0-0.025-0.00118.736-0.013-0.0130.0000.0000.0000.000
101A110ASP-1-0.853-0.92623.7960.1720.1720.0000.0000.0000.000
102A111TRP0-0.083-0.07227.503-0.011-0.0110.0000.0000.0000.000
103A112ALA0-0.0210.00524.357-0.012-0.0120.0000.0000.0000.000
104A113GLN0-0.0010.00826.048-0.016-0.0160.0000.0000.0000.000
105A114ARG10.8100.90727.310-0.101-0.1010.0000.0000.0000.000
106A115GLY0-0.012-0.02229.128-0.012-0.0120.0000.0000.0000.000
107A116TRP00.006-0.01824.434-0.016-0.0160.0000.0000.0000.000
108A117LYS10.9030.96730.626-0.085-0.0850.0000.0000.0000.000
109A118ARG10.9580.97134.327-0.035-0.0350.0000.0000.0000.000
110A119LYS10.9230.96836.562-0.063-0.0630.0000.0000.0000.000
111A120SER0-0.017-0.02938.887-0.003-0.0030.0000.0000.0000.000
112A121GLY00.0200.00542.4840.0020.0020.0000.0000.0000.000
113A122ALA0-0.0170.01038.9590.0000.0000.0000.0000.0000.000
114A123ILE00.0190.00038.994-0.002-0.0020.0000.0000.0000.000
115A124GLU-1-0.746-0.86634.1300.0790.0790.0000.0000.0000.000
116A125ASN00.0400.02233.2800.0080.0080.0000.0000.0000.000
117A126LEU00.0350.01631.116-0.004-0.0040.0000.0000.0000.000
118A127ALA00.0160.02030.3360.0020.0020.0000.0000.0000.000
119A128LEU00.0560.03330.125-0.002-0.0020.0000.0000.0000.000
120A129TRP00.0050.00525.8130.0040.0040.0000.0000.0000.000
121A130GLN0-0.034-0.01926.005-0.001-0.0010.0000.0000.0000.000
122A131GLU-1-0.868-0.93325.339-0.003-0.0030.0000.0000.0000.000
123A132ALA00.008-0.00225.137-0.007-0.0070.0000.0000.0000.000
124A133VAL0-0.020-0.01420.5820.0040.0040.0000.0000.0000.000
125A134GLN0-0.022-0.01620.5880.0000.0000.0000.0000.0000.000
126A135ALA0-0.029-0.00621.304-0.021-0.0210.0000.0000.0000.000
127A136VAL0-0.0030.00317.255-0.020-0.0200.0000.0000.0000.000
128A137ASN0-0.053-0.02316.556-0.033-0.0330.0000.0000.0000.000
129A138GLY00.0120.00013.2120.0430.0430.0000.0000.0000.000
130A139HIS0-0.0080.00312.254-0.001-0.0010.0000.0000.0000.000
131A140ALA0-0.0130.00810.2720.0650.0650.0000.0000.0000.000
132A141VAL00.0320.00012.389-0.057-0.0570.0000.0000.0000.000
133A142GLU-1-0.786-0.85115.2910.3220.3220.0000.0000.0000.000
134A143TRP00.000-0.01016.853-0.064-0.0640.0000.0000.0000.000
135A144ARG10.8370.89518.082-0.147-0.1470.0000.0000.0000.000
136A145TRP0-0.039-0.02922.674-0.011-0.0110.0000.0000.0000.000
137A146VAL0-0.009-0.00426.4400.0030.0030.0000.0000.0000.000
138A147ARG10.9100.95629.136-0.071-0.0710.0000.0000.0000.000
139A148GLY00.1150.05732.942-0.003-0.0030.0000.0000.0000.000
140A149HIS0-0.054-0.02734.3950.0020.0020.0000.0000.0000.000
141A150ALA0-0.068-0.03634.7980.0020.0020.0000.0000.0000.000
142A151GLY00.0030.00535.8540.0020.0020.0000.0000.0000.000
143A152HIS0-0.056-0.02526.716-0.008-0.0080.0000.0000.0000.000
144A153ALA00.0610.02331.570-0.002-0.0020.0000.0000.0000.000
145A154GLN00.0280.00126.0440.0030.0030.0000.0000.0000.000
146A155ASN0-0.058-0.03729.3490.0000.0000.0000.0000.0000.000
147A156GLU-1-0.763-0.90430.6160.0280.0280.0000.0000.0000.000
148A157TYR0-0.057-0.04731.137-0.002-0.0020.0000.0000.0000.000
149A158ALA00.0130.00629.874-0.004-0.0040.0000.0000.0000.000
150A159ASN0-0.038-0.03331.973-0.005-0.0050.0000.0000.0000.000
151A160HIS00.0400.01635.1650.0000.0000.0000.0000.0000.000
152A161LEU0-0.0350.00431.713-0.003-0.0030.0000.0000.0000.000
153A162ALA00.0080.01134.352-0.003-0.0030.0000.0000.0000.000
154A163VAL00.001-0.00236.018-0.001-0.0010.0000.0000.0000.000
155A164THR0-0.034-0.03338.386-0.002-0.0020.0000.0000.0000.000
156A165ALA0-0.046-0.01536.648-0.002-0.0020.0000.0000.0000.000
157A166ALA0-0.012-0.00838.789-0.001-0.0010.0000.0000.0000.000
158A167GLY0-0.009-0.00641.0090.0000.0000.0000.0000.0000.000
159A168GLY0-0.022-0.00842.696-0.001-0.0010.0000.0000.0000.000
160A169GLN0-0.077-0.05441.924-0.003-0.0030.0000.0000.0000.000
161A170THR00.0080.02239.613-0.004-0.0040.0000.0000.0000.000
162A171GLN00.0040.00335.9290.0060.0060.0000.0000.0000.000
163A172SER00.0130.00731.5220.0000.0000.0000.0000.0000.000
164A173GLY0-0.026-0.00633.531-0.006-0.0060.0000.0000.0000.000
165A174GLY0-0.007-0.01929.380-0.005-0.0050.0000.0000.0000.000
166A175LEU0-0.0200.00523.7410.0070.0070.0000.0000.0000.000
167A176VAL0-0.032-0.00728.221-0.010-0.0100.0000.0000.0000.000
168A177ASP-1-0.862-0.94330.115-0.077-0.0770.0000.0000.0000.000
169A178SER0-0.061-0.05329.8800.0070.0070.0000.0000.0000.000
170A179GLY00.0590.03131.936-0.002-0.0020.0000.0000.0000.000
171A180TYR0-0.056-0.03031.4420.0080.0080.0000.0000.0000.000
172A181GLU-1-0.782-0.89731.325-0.037-0.0370.0000.0000.0000.000
173A182GLU-1-0.883-0.94334.883-0.030-0.0300.0000.0000.0000.000
174A183TRP0-0.042-0.02434.4640.0040.0040.0000.0000.0000.000
175A184ALA0-0.023-0.01434.9290.0050.0050.0000.0000.0000.000
176A185ALA00.0090.01437.0810.0030.0030.0000.0000.0000.000
177A186ARG10.8360.94640.1370.0060.0060.0000.0000.0000.000
178A187VAL00.0650.01642.2250.0030.0030.0000.0000.0000.000
179A188SER00.004-0.00242.2240.0010.0010.0000.0000.0000.000
180A189THR0-0.029-0.02137.4410.0040.0040.0000.0000.0000.000
181A190ALA00.0560.03140.0340.0030.0030.0000.0000.0000.000
182A191ALA0-0.052-0.02441.6130.0030.0030.0000.0000.0000.000
183A192SER0-0.012-0.01039.8460.0030.0030.0000.0000.0000.000
184A193ARG10.8420.92939.989-0.010-0.0100.0000.0000.0000.000
185A194MET0-0.0330.01335.1100.0030.0030.0000.0000.0000.000
186A195ARG10.9160.95531.701-0.051-0.0510.0000.0000.0000.000
187A196LEU00.0040.01428.0210.0020.0020.0000.0000.0000.000
188A197GLU-1-0.813-0.89223.1280.0910.0910.0000.0000.0000.000
189A198PRO0-0.001-0.01223.424-0.010-0.0100.0000.0000.0000.000
190A199PHE00.0210.01416.9500.0130.0130.0000.0000.0000.000
191A200PRO0-0.0130.00516.6760.0020.0020.0000.0000.0000.000
192A201ASP-1-0.847-0.92715.7160.0030.0030.0000.0000.0000.000
193A202ALA0-0.030-0.03810.3540.0410.0410.0000.0000.0000.000
194A203ALA00.0120.00711.1640.0740.0740.0000.0000.0000.000
195A204ALA00.0010.00413.0970.0740.0740.0000.0000.0000.000
196A205PHE0-0.0210.0019.5600.0520.0520.0000.0000.0000.000
197A206ARG10.8120.88711.942-0.335-0.3350.0000.0000.0000.000
198A207PRO0-0.024-0.00110.158-0.058-0.0580.0000.0000.0000.000
199A208SER00.010-0.00513.3620.0520.0520.0000.0000.0000.000
200A209PRO0-0.015-0.01113.4070.0710.0710.0000.0000.0000.000
201A210ALA00.0060.00112.461-0.078-0.0780.0000.0000.0000.000
202A211LEU00.0270.01514.381-0.019-0.0190.0000.0000.0000.000
203A212PRO0-0.026-0.00217.699-0.012-0.0120.0000.0000.0000.000
204A213VAL00.025-0.00318.044-0.024-0.0240.0000.0000.0000.000
205A214VAL00.0030.01520.5860.0040.0040.0000.0000.0000.000
206A215ALA0-0.0030.00424.296-0.013-0.0130.0000.0000.0000.000
207A216ALA00.022-0.00526.862-0.002-0.0020.0000.0000.0000.000
208A217GLY00.0030.00228.838-0.002-0.0020.0000.0000.0000.000
209A218ARG10.9200.97330.587-0.042-0.0420.0000.0000.0000.000
210A219PRO00.0140.01933.2820.0000.0000.0000.0000.0000.000
211A220SER00.0450.02835.3230.0040.0040.0000.0000.0000.000