FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8567Y

Calculation Name: 4V16-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4V16

Chain ID: A

ChEMBL ID:

UniProt ID: Q6CN23

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4743867.958406
FMO2-HF: Nuclear repulsion 4620918.218257
FMO2-HF: Total energy -122949.740149
FMO2-MP2: Total energy -123308.845523


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:14:SER)


Summations of interaction energy for fragment #1(A:14: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.
-3.604-1.9-0.019-0.798-0.8860.003
Interaction energy analysis for fragmet #1(A:14:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.002
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].
3A16PRO00.0020.0163.817-0.3911.313-0.019-0.798-0.8860.003
4A17ILE0-0.041-0.0356.3080.1760.1760.0000.0000.0000.000
5A18VAL0-0.057-0.0169.720-0.237-0.2370.0000.0000.0000.000
6A19ASP-1-0.787-0.90312.3610.3120.3120.0000.0000.0000.000
7A20TYR0-0.072-0.06514.2560.1840.1840.0000.0000.0000.000
8A21GLU-1-0.801-0.88816.2030.2750.2750.0000.0000.0000.000
9A22PHE0-0.026-0.00719.5630.0560.0560.0000.0000.0000.000
10A23ASN0-0.0170.00321.827-0.006-0.0060.0000.0000.0000.000
11A24GLN00.0460.00524.7430.0070.0070.0000.0000.0000.000
12A25ASP-1-0.831-0.89827.4840.2890.2890.0000.0000.0000.000
13A26GLN0-0.011-0.00724.474-0.020-0.0200.0000.0000.0000.000
14A27SER0-0.019-0.00224.3080.0280.0280.0000.0000.0000.000
15A28CYS0-0.058-0.04921.3410.0280.0280.0000.0000.0000.000
16A29LEU00.0020.00214.875-0.020-0.0200.0000.0000.0000.000
17A30ILE0-0.0190.00216.9930.0750.0750.0000.0000.0000.000
18A31VAL0-0.009-0.01411.582-0.010-0.0100.0000.0000.0000.000
19A32SER00.0260.00613.3800.0480.0480.0000.0000.0000.000
20A33THR0-0.024-0.0218.0720.1870.1870.0000.0000.0000.000
21A34PRO00.018-0.0037.738-0.152-0.1520.0000.0000.0000.000
22A35LYS10.8110.8867.595-0.438-0.4380.0000.0000.0000.000
23A36SER0-0.022-0.0049.978-0.008-0.0080.0000.0000.0000.000
24A37PHE00.0240.02311.9020.0500.0500.0000.0000.0000.000
25A38ASP-1-0.850-0.91611.7481.5521.5520.0000.0000.0000.000
26A39ILE00.0430.01114.487-0.039-0.0390.0000.0000.0000.000
27A40TYR0-0.023-0.01810.7400.0940.0940.0000.0000.0000.000
28A41ASN00.0460.03317.462-0.092-0.0920.0000.0000.0000.000
29A42VAL00.0010.00718.8800.0670.0670.0000.0000.0000.000
30A43HIS00.0060.01420.4120.0370.0370.0000.0000.0000.000
31A44PRO0-0.002-0.00721.889-0.032-0.0320.0000.0000.0000.000
32A45LEU0-0.0010.00014.342-0.001-0.0010.0000.0000.0000.000
33A46LYS10.9370.96517.055-0.534-0.5340.0000.0000.0000.000
34A47ARG10.9500.9959.396-1.801-1.8010.0000.0000.0000.000
35A48ILE0-0.086-0.04116.326-0.073-0.0730.0000.0000.0000.000
36A49MET0-0.0330.00117.076-0.062-0.0620.0000.0000.0000.000
37A50SER0-0.044-0.03812.3300.0550.0550.0000.0000.0000.000
38A51GLN00.0320.02414.896-0.101-0.1010.0000.0000.0000.000
39A52GLU-1-0.809-0.88411.1060.4570.4570.0000.0000.0000.000
40A53MET0-0.014-0.02313.549-0.099-0.0990.0000.0000.0000.000
41A54PRO00.0290.03913.7230.0600.0600.0000.0000.0000.000
42A55ASP-1-0.853-0.92614.3960.0010.0010.0000.0000.0000.000
43A56ALA00.0120.00915.409-0.023-0.0230.0000.0000.0000.000
44A57GLY00.021-0.00615.5060.0410.0410.0000.0000.0000.000
45A58THR0-0.0050.00117.1100.0600.0600.0000.0000.0000.000
46A59ILE0-0.008-0.00516.866-0.029-0.0290.0000.0000.0000.000
47A60ARG10.8520.93519.977-0.317-0.3170.0000.0000.0000.000
48A61MET00.0400.01022.0250.0210.0210.0000.0000.0000.000
49A62LEU00.0030.02223.984-0.017-0.0170.0000.0000.0000.000
50A63HIS00.006-0.01027.6130.0040.0040.0000.0000.0000.000
51A64ARG10.8650.89824.388-0.338-0.3380.0000.0000.0000.000
52A65THR0-0.040-0.01427.373-0.009-0.0090.0000.0000.0000.000
53A66ASN00.008-0.00126.1070.0230.0230.0000.0000.0000.000
54A67TYR0-0.012-0.00226.229-0.002-0.0020.0000.0000.0000.000
55A68ILE00.0190.00920.7700.0150.0150.0000.0000.0000.000
56A69ALA00.0200.02323.857-0.028-0.0280.0000.0000.0000.000
57A70PHE00.0060.00519.8390.0360.0360.0000.0000.0000.000
58A71VAL00.0660.03521.163-0.033-0.0330.0000.0000.0000.000
59A72SER0-0.065-0.01420.3030.0090.0090.0000.0000.0000.000
60A73THR00.0410.00517.058-0.022-0.0220.0000.0000.0000.000
61A74LYS10.8220.91217.7870.0150.0150.0000.0000.0000.000
62A75LYS10.8410.90321.118-0.118-0.1180.0000.0000.0000.000
63A76GLU-1-0.871-0.91023.8120.0800.0800.0000.0000.0000.000
64A77LEU0-0.030-0.02124.701-0.005-0.0050.0000.0000.0000.000
65A78LEU00.0460.03424.7250.0210.0210.0000.0000.0000.000
66A79HIS00.009-0.00223.637-0.028-0.0280.0000.0000.0000.000
67A80ILE00.0240.01225.7300.0200.0200.0000.0000.0000.000
68A81TRP00.0150.00721.530-0.019-0.0190.0000.0000.0000.000
69A82ASP-1-0.784-0.91225.0630.2200.2200.0000.0000.0000.000
70A83ASP-1-0.877-0.96222.0680.4020.4020.0000.0000.0000.000
71A84VAL0-0.073-0.03524.0410.0130.0130.0000.0000.0000.000
72A85LYS10.8870.94626.740-0.161-0.1610.0000.0000.0000.000
73A86LYS10.8570.95820.715-0.371-0.3710.0000.0000.0000.000
74A87GLN00.003-0.00524.331-0.020-0.0200.0000.0000.0000.000
75A88ASP-1-0.896-0.94824.9060.1850.1850.0000.0000.0000.000
76A89ILE0-0.051-0.01527.173-0.013-0.0130.0000.0000.0000.000
77A90THR0-0.014-0.02029.783-0.012-0.0120.0000.0000.0000.000
78A91ARG10.9080.95027.359-0.083-0.0830.0000.0000.0000.000
79A92VAL00.0330.02529.481-0.012-0.0120.0000.0000.0000.000
80A93LYS10.8330.91828.768-0.051-0.0510.0000.0000.0000.000
81A94LEU0-0.0090.00526.6330.0040.0040.0000.0000.0000.000
82A95ASP-1-0.897-0.95630.5380.0460.0460.0000.0000.0000.000
83A96ALA0-0.054-0.02529.836-0.010-0.0100.0000.0000.0000.000
84A97ALA00.0350.02224.8370.0080.0080.0000.0000.0000.000
85A98VAL0-0.021-0.02124.0360.0000.0000.0000.0000.0000.000
86A99LYS10.8140.91224.194-0.084-0.0840.0000.0000.0000.000
87A100ASP-1-0.884-0.93824.8080.2070.2070.0000.0000.0000.000
88A101LEU0-0.052-0.03024.006-0.011-0.0110.0000.0000.0000.000
89A102PHE00.0130.00826.4050.0220.0220.0000.0000.0000.000
90A103LEU00.000-0.00826.248-0.010-0.0100.0000.0000.0000.000
91A104SER00.0140.00729.9260.0060.0060.0000.0000.0000.000
92A105ARG10.9490.95932.994-0.170-0.1700.0000.0000.0000.000
93A106GLU-1-0.926-0.93835.0690.1160.1160.0000.0000.0000.000
94A107PHE00.0320.00835.636-0.005-0.0050.0000.0000.0000.000
95A108ILE0-0.040-0.01830.0010.0150.0150.0000.0000.0000.000
96A109VAL00.0090.01831.717-0.013-0.0130.0000.0000.0000.000
97A110VAL00.018-0.01228.1300.0170.0170.0000.0000.0000.000
98A111SER00.0270.03228.827-0.017-0.0170.0000.0000.0000.000
99A112GLN00.0830.03228.4870.0080.0080.0000.0000.0000.000
100A113GLY00.0300.01129.179-0.010-0.0100.0000.0000.0000.000
101A114ASP-1-0.939-0.97930.9370.0590.0590.0000.0000.0000.000
102A115VAL0-0.003-0.00733.489-0.002-0.0020.0000.0000.0000.000
103A116ILE0-0.013-0.00133.1620.0090.0090.0000.0000.0000.000
104A117SER0-0.023-0.00833.501-0.007-0.0070.0000.0000.0000.000
105A118ILE00.0310.01234.1150.0110.0110.0000.0000.0000.000
106A119PHE00.010-0.00532.698-0.009-0.0090.0000.0000.0000.000
107A120LYS10.9230.95536.097-0.091-0.0910.0000.0000.0000.000
108A121PHE0-0.040-0.02430.2280.0050.0050.0000.0000.0000.000
109A122GLY00.0470.01235.336-0.001-0.0010.0000.0000.0000.000
110A123ASN00.0010.02436.726-0.003-0.0030.0000.0000.0000.000
111A124PRO0-0.032-0.02838.640-0.001-0.0010.0000.0000.0000.000
112A125TRP00.0150.01132.3870.0000.0000.0000.0000.0000.000
113A126ASN00.0260.01736.3470.0030.0030.0000.0000.0000.000
114A127LYS10.8870.92636.625-0.069-0.0690.0000.0000.0000.000
115A128ILE0-0.027-0.01239.097-0.004-0.0040.0000.0000.0000.000
116A129THR0-0.0040.00040.371-0.005-0.0050.0000.0000.0000.000
117A130GLU-1-0.930-0.94141.1680.0560.0560.0000.0000.0000.000
118A131ASP-1-0.832-0.92737.1740.0800.0800.0000.0000.0000.000
119A132ILE0-0.022-0.00838.477-0.005-0.0050.0000.0000.0000.000
120A133LYS10.9430.98937.658-0.040-0.0400.0000.0000.0000.000
121A134PHE0-0.058-0.03431.6220.0020.0020.0000.0000.0000.000
122A135GLY00.0310.02136.526-0.004-0.0040.0000.0000.0000.000
123A136GLY0-0.074-0.03332.384-0.004-0.0040.0000.0000.0000.000
124A137VAL0-0.037-0.01130.7330.0090.0090.0000.0000.0000.000
125A138CYS0-0.061-0.04630.739-0.009-0.0090.0000.0000.0000.000
126A139GLU-1-0.841-0.92929.9730.2060.2060.0000.0000.0000.000
127A140PHE0-0.0130.00831.545-0.013-0.0130.0000.0000.0000.000
128A141ALA00.011-0.00131.7780.0160.0160.0000.0000.0000.000
129A142ASN0-0.041-0.01933.776-0.005-0.0050.0000.0000.0000.000
130A143GLY00.0410.01736.315-0.008-0.0080.0000.0000.0000.000
131A144LEU0-0.056-0.02337.412-0.010-0.0100.0000.0000.0000.000
132A145LEU00.0170.00835.4220.0100.0100.0000.0000.0000.000
133A146VAL0-0.003-0.00935.833-0.008-0.0080.0000.0000.0000.000
134A147TYR00.0330.01735.3590.0080.0080.0000.0000.0000.000
135A148SER00.0390.02835.740-0.004-0.0040.0000.0000.0000.000
136A149ASN00.0230.01537.973-0.004-0.0040.0000.0000.0000.000
137A150GLU-1-0.851-0.94338.9380.0490.0490.0000.0000.0000.000
138A151PHE0-0.0010.01239.943-0.003-0.0030.0000.0000.0000.000
139A152ASN0-0.065-0.03342.298-0.004-0.0040.0000.0000.0000.000
140A153LEU00.0690.02936.6400.0040.0040.0000.0000.0000.000
141A154GLY0-0.037-0.00738.5840.0050.0050.0000.0000.0000.000
142A155GLN0-0.046-0.05040.8950.0030.0030.0000.0000.0000.000
143A156ILE00.0140.00637.9520.0020.0020.0000.0000.0000.000
144A157HIS00.0080.00640.453-0.006-0.0060.0000.0000.0000.000
145A158VAL00.0180.00240.2410.0070.0070.0000.0000.0000.000
146A159THR00.0000.00041.062-0.005-0.0050.0000.0000.0000.000
147A160ARG10.9660.98441.046-0.098-0.0980.0000.0000.0000.000
148A161LEU0-0.0210.00137.643-0.004-0.0040.0000.0000.0000.000
149A162GLN0-0.059-0.02542.0240.0020.0020.0000.0000.0000.000
150A163THR0-0.051-0.03744.3840.0020.0020.0000.0000.0000.000
151A164ASP-1-0.851-0.91247.1000.0750.0750.0000.0000.0000.000
152A165ALA00.0130.01648.577-0.004-0.0040.0000.0000.0000.000
153A166GLU-1-0.811-0.90248.4880.0630.0630.0000.0000.0000.000
154A167GLN0-0.050-0.04646.8830.0020.0020.0000.0000.0000.000
155A168VAL0-0.040-0.03543.1360.0020.0020.0000.0000.0000.000
156A169VAL0-0.025-0.00641.3270.0060.0060.0000.0000.0000.000
157A170GLY00.0200.02343.9110.0000.0000.0000.0000.0000.000
158A171LYS10.8890.94145.658-0.060-0.0600.0000.0000.0000.000
159A172GLY00.0430.00045.9740.0020.0020.0000.0000.0000.000
160A173VAL0-0.0130.01245.459-0.004-0.0040.0000.0000.0000.000
161A174LEU0-0.0240.00644.7570.0030.0030.0000.0000.0000.000
162A175VAL00.0350.01743.130-0.002-0.0020.0000.0000.0000.000
163A176LYS10.8830.93543.547-0.053-0.0530.0000.0000.0000.000
164A177ALA00.0300.03840.209-0.001-0.0010.0000.0000.0000.000
165A178HIS00.012-0.00238.5080.0040.0040.0000.0000.0000.000
166A179ALA0-0.017-0.00541.773-0.003-0.0030.0000.0000.0000.000
167A180ASN0-0.013-0.01138.331-0.006-0.0060.0000.0000.0000.000
168A181PRO00.012-0.00535.9200.0040.0040.0000.0000.0000.000
169A182VAL0-0.010-0.00634.5740.0020.0020.0000.0000.0000.000
170A183LYS10.8700.94927.829-0.106-0.1060.0000.0000.0000.000
171A184MET0-0.014-0.01327.4980.0070.0070.0000.0000.0000.000
172A185VAL00.0500.01231.099-0.009-0.0090.0000.0000.0000.000
173A186ARG10.8220.90325.652-0.203-0.2030.0000.0000.0000.000
174A187LEU00.0330.04132.434-0.011-0.0110.0000.0000.0000.000
175A188ASN00.0000.01333.1840.0150.0150.0000.0000.0000.000
176A189ARG10.9710.97629.851-0.227-0.2270.0000.0000.0000.000
177A190LYS10.9310.97734.906-0.121-0.1210.0000.0000.0000.000
178A191GLY00.0590.02237.8150.0000.0000.0000.0000.0000.000
179A192ASP-1-0.861-0.92538.6810.1130.1130.0000.0000.0000.000
180A193MET0-0.015-0.01339.321-0.005-0.0050.0000.0000.0000.000
181A194VAL00.0100.00936.1340.0090.0090.0000.0000.0000.000
182A195ALA0-0.0190.00334.118-0.007-0.0070.0000.0000.0000.000
183A196THR0-0.016-0.01335.0090.0040.0040.0000.0000.0000.000
184A197CYS00.0300.01831.327-0.001-0.0010.0000.0000.0000.000
185A198SER00.0360.01634.916-0.002-0.0020.0000.0000.0000.000
186A199GLN00.003-0.01131.8700.0050.0050.0000.0000.0000.000
187A200ASP-1-0.868-0.92733.1380.0580.0580.0000.0000.0000.000
188A201GLY00.0430.02332.8210.0010.0010.0000.0000.0000.000
189A202THR0-0.042-0.02833.8030.0050.0050.0000.0000.0000.000
190A203LEU0-0.015-0.01236.7800.0010.0010.0000.0000.0000.000
191A204ILE0-0.011-0.00133.1870.0030.0030.0000.0000.0000.000
192A205ARG10.8660.94837.101-0.073-0.0730.0000.0000.0000.000
193A206VAL00.0210.00838.1490.0070.0070.0000.0000.0000.000
194A207PHE0-0.007-0.00140.332-0.007-0.0070.0000.0000.0000.000
195A208GLN00.0290.01441.6900.0060.0060.0000.0000.0000.000
196A209THR0-0.071-0.04440.085-0.005-0.0050.0000.0000.0000.000
197A210ASP-1-0.919-0.94643.2460.0880.0880.0000.0000.0000.000
198A211ASN00.009-0.01546.8250.0000.0000.0000.0000.0000.000
199A212GLY00.0120.00045.060-0.003-0.0030.0000.0000.0000.000
200A213VAL0-0.048-0.01546.141-0.002-0.0020.0000.0000.0000.000
201A214LEU0-0.014-0.01843.5010.0040.0040.0000.0000.0000.000
202A215VAL0-0.0040.00843.357-0.003-0.0030.0000.0000.0000.000
203A216ARG10.8810.91641.712-0.092-0.0920.0000.0000.0000.000
204A217GLU-1-0.887-0.94641.5510.0710.0710.0000.0000.0000.000
205A218PHE0-0.0020.01737.825-0.001-0.0010.0000.0000.0000.000
206A219ARG10.9390.97338.982-0.068-0.0680.0000.0000.0000.000
207A220ARG10.8450.93931.265-0.093-0.0930.0000.0000.0000.000
208A221GLY00.005-0.01435.2470.0020.0020.0000.0000.0000.000
209A222LEU0-0.035-0.01836.627-0.002-0.0020.0000.0000.0000.000
210A223ASP-1-0.799-0.87434.4240.0650.0650.0000.0000.0000.000
211A224ARG10.9400.96134.757-0.036-0.0360.0000.0000.0000.000
212A225THR0-0.044-0.01629.476-0.001-0.0010.0000.0000.0000.000
213A226SER0-0.012-0.00626.8990.0050.0050.0000.0000.0000.000
214A227ILE0-0.039-0.04027.3920.0050.0050.0000.0000.0000.000
215A228ILE0-0.036-0.00621.273-0.003-0.0030.0000.0000.0000.000
216A229ASP-1-0.718-0.85423.3540.2920.2920.0000.0000.0000.000
217A230MET0-0.053-0.02425.479-0.016-0.0160.0000.0000.0000.000
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