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: N978Q

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 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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4749801.52569
FMO2-HF: Nuclear repulsion 4626850.535668
FMO2-HF: Total energy -122950.990021
FMO2-MP2: Total energy -123310.137981


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.
-2.196-0.518-0.018-0.765-0.8950.003
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 : 0.001 / q_NPA : -0.003
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].
3A16PRO00.0170.0353.8170.4292.107-0.018-0.765-0.8950.003
4A17ILE0-0.046-0.0376.308-0.040-0.0400.0000.0000.0000.000
5A18VAL0-0.045-0.0139.720-0.176-0.1760.0000.0000.0000.000
6A19ASP-1-0.771-0.88412.3610.3460.3460.0000.0000.0000.000
7A20TYR0-0.089-0.08714.2510.1640.1640.0000.0000.0000.000
8A21GLU-1-0.778-0.86316.2030.3170.3170.0000.0000.0000.000
9A22PHE0-0.018-0.01519.5990.0430.0430.0000.0000.0000.000
10A23ASN0-0.023-0.01821.827-0.009-0.0090.0000.0000.0000.000
11A24GLN00.0350.01024.6640.0120.0120.0000.0000.0000.000
12A25ASP-1-0.813-0.87127.6740.2720.2720.0000.0000.0000.000
13A26GLN0-0.014-0.01424.449-0.020-0.0200.0000.0000.0000.000
14A27SER0-0.015-0.01624.2540.0270.0270.0000.0000.0000.000
15A28CYS0-0.068-0.04021.1160.0180.0180.0000.0000.0000.000
16A29LEU00.0050.00014.800-0.011-0.0110.0000.0000.0000.000
17A30ILE0-0.018-0.00116.7640.0530.0530.0000.0000.0000.000
18A31VAL0-0.006-0.01411.3300.0270.0270.0000.0000.0000.000
19A32SER00.0280.00713.2970.0150.0150.0000.0000.0000.000
20A33THR0-0.038-0.0297.8750.1540.1540.0000.0000.0000.000
21A34PRO00.0240.0037.715-0.132-0.1320.0000.0000.0000.000
22A35LYS10.7980.8787.733-0.113-0.1130.0000.0000.0000.000
23A36SER0-0.0070.00210.099-0.011-0.0110.0000.0000.0000.000
24A37PHE00.0400.02612.0090.0650.0650.0000.0000.0000.000
25A38ASP-1-0.833-0.88811.3591.1091.1090.0000.0000.0000.000
26A39ILE00.0540.02114.030-0.004-0.0040.0000.0000.0000.000
27A40TYR00.001-0.01010.7120.1160.1160.0000.0000.0000.000
28A41ASN00.0320.01917.101-0.071-0.0710.0000.0000.0000.000
29A42VAL00.0010.00618.6260.0640.0640.0000.0000.0000.000
30A43HIS00.0150.01820.3330.0460.0460.0000.0000.0000.000
31A44PRO0-0.002-0.00521.604-0.033-0.0330.0000.0000.0000.000
32A45LEU00.004-0.00214.438-0.011-0.0110.0000.0000.0000.000
33A46LYS10.9340.96016.737-0.438-0.4380.0000.0000.0000.000
34A47ARG10.8940.9688.939-1.414-1.4140.0000.0000.0000.000
35A48ILE0-0.081-0.03515.917-0.070-0.0700.0000.0000.0000.000
36A49MET0-0.0290.00017.301-0.052-0.0520.0000.0000.0000.000
37A50SER0-0.041-0.04612.3750.0650.0650.0000.0000.0000.000
38A51GLN00.0300.00714.990-0.084-0.0840.0000.0000.0000.000
39A52GLU-1-0.806-0.88111.3620.1650.1650.0000.0000.0000.000
40A53MET0-0.014-0.00913.688-0.063-0.0630.0000.0000.0000.000
41A54PRO00.0260.03713.6850.0470.0470.0000.0000.0000.000
42A55ASP-1-0.845-0.92314.354-0.053-0.0530.0000.0000.0000.000
43A56ALA00.0070.00715.369-0.005-0.0050.0000.0000.0000.000
44A57GLY00.022-0.00215.5060.0390.0390.0000.0000.0000.000
45A58THR00.0130.01117.1100.0540.0540.0000.0000.0000.000
46A59ILE0-0.030-0.02116.701-0.036-0.0360.0000.0000.0000.000
47A60ARG10.8200.91119.977-0.296-0.2960.0000.0000.0000.000
48A61MET00.0340.00921.8050.0130.0130.0000.0000.0000.000
49A62LEU0-0.0010.02023.792-0.010-0.0100.0000.0000.0000.000
50A63HIS00.016-0.00527.388-0.001-0.0010.0000.0000.0000.000
51A64ARG10.8720.91523.525-0.311-0.3110.0000.0000.0000.000
52A65THR0-0.048-0.02127.015-0.012-0.0120.0000.0000.0000.000
53A66ASN0-0.008-0.00525.7900.0210.0210.0000.0000.0000.000
54A67TYR0-0.0040.00126.064-0.005-0.0050.0000.0000.0000.000
55A68ILE00.0040.00620.5420.0170.0170.0000.0000.0000.000
56A69ALA00.0180.02323.653-0.027-0.0270.0000.0000.0000.000
57A70PHE00.0090.00719.8000.0360.0360.0000.0000.0000.000
58A71VAL00.0680.03721.160-0.031-0.0310.0000.0000.0000.000
59A72SER0-0.066-0.01720.2480.0030.0030.0000.0000.0000.000
60A73THR00.0480.01017.039-0.017-0.0170.0000.0000.0000.000
61A74LYS10.8180.90417.5830.0790.0790.0000.0000.0000.000
62A75LYS10.8410.90521.080-0.063-0.0630.0000.0000.0000.000
63A76GLU-1-0.872-0.92123.7700.0760.0760.0000.0000.0000.000
64A77LEU0-0.019-0.00724.662-0.005-0.0050.0000.0000.0000.000
65A78LEU00.0420.03324.6860.0170.0170.0000.0000.0000.000
66A79HIS0-0.013-0.02623.876-0.027-0.0270.0000.0000.0000.000
67A80ILE00.0210.00925.7970.0210.0210.0000.0000.0000.000
68A81TRP00.0120.00221.318-0.022-0.0220.0000.0000.0000.000
69A82ASP-1-0.749-0.87825.1680.1650.1650.0000.0000.0000.000
70A83ASP-1-0.815-0.92421.6280.3040.3040.0000.0000.0000.000
71A84VAL0-0.042-0.02624.1330.0080.0080.0000.0000.0000.000
72A85LYS10.8530.91726.832-0.128-0.1280.0000.0000.0000.000
73A86LYS10.7740.90120.456-0.281-0.2810.0000.0000.0000.000
74A87GLN00.0080.00224.506-0.016-0.0160.0000.0000.0000.000
75A88ASP-1-0.799-0.87025.2290.1210.1210.0000.0000.0000.000
76A89ILE0-0.052-0.01927.282-0.010-0.0100.0000.0000.0000.000
77A90THR0-0.012-0.01829.896-0.009-0.0090.0000.0000.0000.000
78A91ARG10.8230.89727.322-0.051-0.0510.0000.0000.0000.000
79A92VAL00.0230.02129.435-0.010-0.0100.0000.0000.0000.000
80A93LYS10.8250.90428.632-0.035-0.0350.0000.0000.0000.000
81A94LEU0-0.0020.01526.6290.0050.0050.0000.0000.0000.000
82A95ASP-1-0.874-0.94630.5000.0440.0440.0000.0000.0000.000
83A96ALA0-0.057-0.02929.839-0.008-0.0080.0000.0000.0000.000
84A97ALA00.0370.02624.8740.0060.0060.0000.0000.0000.000
85A98VAL0-0.014-0.01724.1040.0020.0020.0000.0000.0000.000
86A99LYS10.8160.91724.194-0.100-0.1000.0000.0000.0000.000
87A100ASP-1-0.829-0.93024.8080.2550.2550.0000.0000.0000.000
88A101LEU0-0.079-0.02923.974-0.016-0.0160.0000.0000.0000.000
89A102PHE00.0300.01826.4050.0200.0200.0000.0000.0000.000
90A103LEU00.0010.00025.962-0.013-0.0130.0000.0000.0000.000
91A104SER0-0.003-0.00829.8580.0040.0040.0000.0000.0000.000
92A105ARG10.9620.95932.880-0.154-0.1540.0000.0000.0000.000
93A106GLU-1-0.907-0.92734.8610.1090.1090.0000.0000.0000.000
94A107PHE00.0290.01235.575-0.005-0.0050.0000.0000.0000.000
95A108ILE0-0.048-0.03029.9840.0140.0140.0000.0000.0000.000
96A109VAL00.0110.02131.727-0.011-0.0110.0000.0000.0000.000
97A110VAL00.018-0.00828.1740.0160.0160.0000.0000.0000.000
98A111SER00.0190.02328.858-0.015-0.0150.0000.0000.0000.000
99A112GLN00.0710.03928.4870.0100.0100.0000.0000.0000.000
100A113GLY00.0390.01829.180-0.010-0.0100.0000.0000.0000.000
101A114ASP-1-0.881-0.93430.9370.0720.0720.0000.0000.0000.000
102A115VAL0-0.001-0.00633.478-0.002-0.0020.0000.0000.0000.000
103A116ILE0-0.021-0.00633.1620.0090.0090.0000.0000.0000.000
104A117SER0-0.029-0.03933.474-0.007-0.0070.0000.0000.0000.000
105A118ILE00.009-0.00234.1150.0110.0110.0000.0000.0000.000
106A119PHE00.014-0.00432.735-0.009-0.0090.0000.0000.0000.000
107A120LYS10.9260.95736.097-0.075-0.0750.0000.0000.0000.000
108A121PHE0-0.036-0.02630.0480.0030.0030.0000.0000.0000.000
109A122GLY00.0480.01035.136-0.001-0.0010.0000.0000.0000.000
110A123ASN00.0050.02036.640-0.003-0.0030.0000.0000.0000.000
111A124PRO0-0.035-0.02538.7410.0010.0010.0000.0000.0000.000
112A125TRP00.0140.01632.2870.0000.0000.0000.0000.0000.000
113A126ASN00.0100.01336.3470.0020.0020.0000.0000.0000.000
114A127LYS10.8970.92136.930-0.062-0.0620.0000.0000.0000.000
115A128ILE0-0.035-0.02138.847-0.004-0.0040.0000.0000.0000.000
116A129THR0-0.0040.00840.212-0.004-0.0040.0000.0000.0000.000
117A130GLU-1-0.916-0.94141.1680.0540.0540.0000.0000.0000.000
118A131ASP-1-0.804-0.88037.5140.0780.0780.0000.0000.0000.000
119A132ILE0-0.024-0.00838.469-0.004-0.0040.0000.0000.0000.000
120A133LYS10.8620.93737.658-0.049-0.0490.0000.0000.0000.000
121A134PHE0-0.039-0.02631.4540.0020.0020.0000.0000.0000.000
122A135GLY00.0190.01336.500-0.003-0.0030.0000.0000.0000.000
123A136GLY0-0.072-0.03232.360-0.002-0.0020.0000.0000.0000.000
124A137VAL0-0.038-0.01730.7050.0110.0110.0000.0000.0000.000
125A138CYS0-0.035-0.03130.776-0.011-0.0110.0000.0000.0000.000
126A139GLU-1-0.796-0.88429.9590.2190.2190.0000.0000.0000.000
127A140PHE0-0.0160.00531.541-0.013-0.0130.0000.0000.0000.000
128A141ALA00.007-0.00131.7780.0150.0150.0000.0000.0000.000
129A142ASN0-0.057-0.03033.776-0.008-0.0080.0000.0000.0000.000
130A143GLY00.0640.03036.322-0.007-0.0070.0000.0000.0000.000
131A144LEU0-0.059-0.02637.399-0.009-0.0090.0000.0000.0000.000
132A145LEU0-0.0020.00235.3690.0100.0100.0000.0000.0000.000
133A146VAL00.011-0.00435.869-0.007-0.0070.0000.0000.0000.000
134A147TYR00.0350.02035.3590.0070.0070.0000.0000.0000.000
135A148SER00.0350.02635.696-0.005-0.0050.0000.0000.0000.000
136A149ASN00.0250.00037.952-0.004-0.0040.0000.0000.0000.000
137A150GLU-1-0.850-0.94638.9110.0600.0600.0000.0000.0000.000
138A151PHE0-0.0070.01139.919-0.002-0.0020.0000.0000.0000.000
139A152ASN0-0.064-0.02742.273-0.002-0.0020.0000.0000.0000.000
140A153LEU00.0660.02936.6710.0040.0040.0000.0000.0000.000
141A154GLY0-0.039-0.00738.5520.0060.0060.0000.0000.0000.000
142A155GLN0-0.043-0.04540.8610.0020.0020.0000.0000.0000.000
143A156ILE00.0120.00137.8550.0030.0030.0000.0000.0000.000
144A157HIS00.0090.01840.467-0.006-0.0060.0000.0000.0000.000
145A158VAL00.0180.00140.2410.0070.0070.0000.0000.0000.000
146A159THR00.0080.00640.821-0.007-0.0070.0000.0000.0000.000
147A160ARG10.9650.97641.046-0.099-0.0990.0000.0000.0000.000
148A161LEU0-0.0100.00537.652-0.004-0.0040.0000.0000.0000.000
149A162GLN0-0.061-0.03742.0240.0030.0030.0000.0000.0000.000
150A163THR0-0.037-0.02544.3480.0010.0010.0000.0000.0000.000
151A164ASP-1-0.856-0.91147.0360.0710.0710.0000.0000.0000.000
152A165ALA00.0110.01348.344-0.003-0.0030.0000.0000.0000.000
153A166GLU-1-0.811-0.90148.2470.0610.0610.0000.0000.0000.000
154A167GLN0-0.065-0.05546.6370.0020.0020.0000.0000.0000.000
155A168VAL0-0.026-0.02742.8880.0030.0030.0000.0000.0000.000
156A169VAL0-0.027-0.01641.4040.0060.0060.0000.0000.0000.000
157A170GLY00.0210.03243.9110.0000.0000.0000.0000.0000.000
158A171LYS10.8730.93145.658-0.062-0.0620.0000.0000.0000.000
159A172GLY00.0450.01145.9700.0010.0010.0000.0000.0000.000
160A173VAL0-0.0110.01245.457-0.004-0.0040.0000.0000.0000.000
161A174LEU0-0.0270.00444.7570.0040.0040.0000.0000.0000.000
162A175VAL00.0410.02143.154-0.002-0.0020.0000.0000.0000.000
163A176LYS10.8750.92943.590-0.069-0.0690.0000.0000.0000.000
164A177ALA00.0280.03840.339-0.001-0.0010.0000.0000.0000.000
165A178HIS00.0310.00038.8530.0040.0040.0000.0000.0000.000
166A179ALA0-0.021-0.00741.854-0.004-0.0040.0000.0000.0000.000
167A180ASN0-0.018-0.03138.328-0.007-0.0070.0000.0000.0000.000
168A181PRO00.011-0.00335.9470.0030.0030.0000.0000.0000.000
169A182VAL0-0.007-0.00734.6440.0050.0050.0000.0000.0000.000
170A183LYS10.8460.92927.870-0.153-0.1530.0000.0000.0000.000
171A184MET0-0.018-0.01027.5200.0080.0080.0000.0000.0000.000
172A185VAL00.0240.00131.121-0.010-0.0100.0000.0000.0000.000
173A186ARG10.8210.89925.773-0.232-0.2320.0000.0000.0000.000
174A187LEU00.0110.02932.461-0.011-0.0110.0000.0000.0000.000
175A188ASN0-0.032-0.02733.1840.0140.0140.0000.0000.0000.000
176A189ARG10.9260.95628.831-0.237-0.2370.0000.0000.0000.000
177A190LYS10.9340.97834.906-0.127-0.1270.0000.0000.0000.000
178A191GLY00.0520.02537.816-0.001-0.0010.0000.0000.0000.000
179A192ASP-1-0.834-0.89738.6810.1190.1190.0000.0000.0000.000
180A193MET0-0.023-0.00939.329-0.004-0.0040.0000.0000.0000.000
181A194VAL00.0110.00836.3800.0090.0090.0000.0000.0000.000
182A195ALA0-0.0190.00334.221-0.007-0.0070.0000.0000.0000.000
183A196THR0-0.011-0.01435.1130.0030.0030.0000.0000.0000.000
184A197CYS00.0200.01832.4170.0020.0020.0000.0000.0000.000
185A198SER00.0590.02735.055-0.003-0.0030.0000.0000.0000.000
186A199GLN00.016-0.00231.6390.0140.0140.0000.0000.0000.000
187A200ASP-1-0.831-0.89533.1380.0920.0920.0000.0000.0000.000
188A201GLY00.0550.03633.0950.0030.0030.0000.0000.0000.000
189A202THR0-0.043-0.03034.0740.0050.0050.0000.0000.0000.000
190A203LEU0-0.032-0.01637.1570.0000.0000.0000.0000.0000.000
191A204ILE0-0.014-0.00533.7450.0040.0040.0000.0000.0000.000
192A205ARG10.7920.88837.400-0.093-0.0930.0000.0000.0000.000
193A206VAL00.0120.00138.2860.0080.0080.0000.0000.0000.000
194A207PHE0-0.0020.00240.453-0.007-0.0070.0000.0000.0000.000
195A208GLN00.002-0.00741.7460.0050.0050.0000.0000.0000.000
196A209THR0-0.076-0.04940.047-0.005-0.0050.0000.0000.0000.000
197A210ASP-1-0.881-0.92043.2460.0920.0920.0000.0000.0000.000
198A211ASN00.008-0.02246.825-0.001-0.0010.0000.0000.0000.000
199A212GLY00.0120.00845.079-0.003-0.0030.0000.0000.0000.000
200A213VAL0-0.044-0.01446.160-0.001-0.0010.0000.0000.0000.000
201A214LEU0-0.024-0.02043.7230.0050.0050.0000.0000.0000.000
202A215VAL00.0090.01343.498-0.003-0.0030.0000.0000.0000.000
203A216ARG10.8480.90041.921-0.104-0.1040.0000.0000.0000.000
204A217GLU-1-0.780-0.86641.8260.0920.0920.0000.0000.0000.000
205A218PHE00.0160.02338.010-0.001-0.0010.0000.0000.0000.000
206A219ARG10.9320.96939.366-0.096-0.0960.0000.0000.0000.000
207A220ARG10.8560.94631.694-0.140-0.1400.0000.0000.0000.000
208A221GLY00.009-0.01035.7810.0040.0040.0000.0000.0000.000
209A222LEU0-0.040-0.01937.177-0.003-0.0030.0000.0000.0000.000
210A223ASP-1-0.802-0.88234.6410.1120.1120.0000.0000.0000.000
211A224ARG10.8890.93734.942-0.074-0.0740.0000.0000.0000.000
212A225THR0-0.057-0.01729.9060.0010.0010.0000.0000.0000.000
213A226SER0-0.050-0.05426.8570.0010.0010.0000.0000.0000.000
214A227ILE0-0.030-0.03827.6530.0100.0100.0000.0000.0000.000
215A228ILE0-0.036-0.00921.657-0.002-0.0020.0000.0000.0000.000
216A229ASP-1-0.680-0.82723.5840.3300.3300.0000.0000.0000.000
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