Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQKR1

Calculation Name: 5V89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V89

Chain ID: A

ChEMBL ID:

UniProt ID: Q13616

Base Structure: X-ray

Registration Date: 2023-09-21

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200782.564244
FMO2-HF: Nuclear repulsion 2121108.052625
FMO2-HF: Total energy -79674.511619
FMO2-MP2: Total energy -79904.081399


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:101:SER)


Summations of interaction energy for fragment #1(A:101: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.
-1.6040.298-0.023-0.913-0.968-0.001
Interaction energy analysis for fragmet #1(A:101:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015
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].
3A103SER00.0760.0353.811-1.0650.837-0.023-0.913-0.968-0.001
4A104LYS10.7900.8866.2800.9740.9740.0000.0000.0000.000
5A105ARG10.8830.9346.3420.0920.0920.0000.0000.0000.000
6A106CYS00.0030.0037.8890.1280.1280.0000.0000.0000.000
7A107LEU00.0100.0059.6710.1080.1080.0000.0000.0000.000
8A108GLU-1-0.811-0.89711.922-0.257-0.2570.0000.0000.0000.000
9A109TRP00.0090.00611.9270.0350.0350.0000.0000.0000.000
10A110PHE0-0.0020.00814.0010.0430.0430.0000.0000.0000.000
11A111TYR0-0.051-0.06715.8210.0190.0190.0000.0000.0000.000
12A112GLU-1-0.948-0.95817.112-0.128-0.1280.0000.0000.0000.000
13A113TYR0-0.124-0.08617.2480.0270.0270.0000.0000.0000.000
14A114ALA0-0.022-0.00919.7900.0170.0170.0000.0000.0000.000
15A115GLY00.0330.03421.7730.0110.0110.0000.0000.0000.000
16A116THR0-0.051-0.03923.429-0.007-0.0070.0000.0000.0000.000
17A117ASP-1-0.921-0.96524.136-0.237-0.2370.0000.0000.0000.000
18A118ASP-1-0.859-0.91019.719-0.433-0.4330.0000.0000.0000.000
19A119VAL0-0.057-0.05120.831-0.036-0.0360.0000.0000.0000.000
20A120VAL00.0110.03219.5880.0170.0170.0000.0000.0000.000
21A121GLY00.0500.01922.547-0.002-0.0020.0000.0000.0000.000
22A122PRO00.032-0.00225.8770.0000.0000.0000.0000.0000.000
23A123GLU-1-0.912-0.94628.170-0.117-0.1170.0000.0000.0000.000
24A124GLY00.0350.01824.5210.0070.0070.0000.0000.0000.000
25A125MET0-0.036-0.02622.419-0.003-0.0030.0000.0000.0000.000
26A126GLU-1-0.914-0.95024.641-0.101-0.1010.0000.0000.0000.000
27A127LYS10.8600.94020.9580.1510.1510.0000.0000.0000.000
28A128PHE0-0.013-0.02417.1690.0040.0040.0000.0000.0000.000
29A129CYS0-0.075-0.05021.8310.0070.0070.0000.0000.0000.000
30A130GLU-1-0.904-0.94324.126-0.055-0.0550.0000.0000.0000.000
31A131ASP-1-0.790-0.86120.493-0.095-0.0950.0000.0000.0000.000
32A132ILE0-0.103-0.06218.6690.0260.0260.0000.0000.0000.000
33A133GLY0-0.058-0.02321.4050.0130.0130.0000.0000.0000.000
34A134VAL0-0.108-0.05724.1610.0080.0080.0000.0000.0000.000
35A135GLU-1-0.874-0.93626.614-0.067-0.0670.0000.0000.0000.000
36A136PRO00.045-0.00527.189-0.006-0.0060.0000.0000.0000.000
37A137GLU-1-0.892-0.92228.254-0.100-0.1000.0000.0000.0000.000
38A138ASN00.0350.00427.2970.0070.0070.0000.0000.0000.000
39A139VAL00.0470.02027.552-0.013-0.0130.0000.0000.0000.000
40A140VAL0-0.028-0.01722.203-0.012-0.0120.0000.0000.0000.000
41A141MET00.0280.02322.322-0.022-0.0220.0000.0000.0000.000
42A142LEU0-0.0010.00723.516-0.022-0.0220.0000.0000.0000.000
43A143VAL0-0.042-0.01821.218-0.020-0.0200.0000.0000.0000.000
44A144LEU00.0070.00116.836-0.026-0.0260.0000.0000.0000.000
45A145ALA00.0310.01519.138-0.043-0.0430.0000.0000.0000.000
46A146TRP0-0.016-0.00420.818-0.033-0.0330.0000.0000.0000.000
47A147LYS10.9010.95116.1540.3260.3260.0000.0000.0000.000
48A148LEU0-0.071-0.02915.277-0.074-0.0740.0000.0000.0000.000
49A149ASP-1-0.959-0.97817.428-0.420-0.4200.0000.0000.0000.000
50A150ALA00.0010.02420.3320.0000.0000.0000.0000.0000.000
51A151GLN0-0.057-0.04121.9000.0510.0510.0000.0000.0000.000
52A152ASN0-0.049-0.02025.0830.0340.0340.0000.0000.0000.000
53A153MET00.0210.00025.951-0.010-0.0100.0000.0000.0000.000
54A154GLY00.0020.00026.4800.0100.0100.0000.0000.0000.000
55A155TYR0-0.050-0.03024.6220.0050.0050.0000.0000.0000.000
56A156PHE0-0.010-0.00118.866-0.013-0.0130.0000.0000.0000.000
57A157THR0-0.005-0.02219.939-0.015-0.0150.0000.0000.0000.000
58A158LEU00.0480.02714.939-0.052-0.0520.0000.0000.0000.000
59A159GLN0-0.017-0.02714.799-0.161-0.1610.0000.0000.0000.000
60A160GLU-1-0.776-0.85214.915-0.448-0.4480.0000.0000.0000.000
61A161TRP00.0500.03212.626-0.027-0.0270.0000.0000.0000.000
62A162LEU0-0.0020.0068.752-0.097-0.0970.0000.0000.0000.000
63A163LYS10.9050.96510.0570.3310.3310.0000.0000.0000.000
64A164GLY00.0370.01211.386-0.064-0.0640.0000.0000.0000.000
65A165MET0-0.0050.01210.9140.0560.0560.0000.0000.0000.000
66A166THR0-0.054-0.0415.598-0.182-0.1820.0000.0000.0000.000
67A167SER0-0.125-0.0607.8410.0590.0590.0000.0000.0000.000
68A168LEU0-0.023-0.02110.3970.1180.1180.0000.0000.0000.000
69A169GLN0-0.049-0.0076.2570.4370.4370.0000.0000.0000.000
70A170CYS0-0.054-0.0118.2910.3320.3320.0000.0000.0000.000
71A171ASP-1-0.751-0.8796.972-0.244-0.2440.0000.0000.0000.000
72A172THR00.0410.0099.4170.0210.0210.0000.0000.0000.000
73A173THR00.1140.05712.437-0.005-0.0050.0000.0000.0000.000
74A174GLU-1-0.960-0.96713.4960.2830.2830.0000.0000.0000.000
75A175LYS10.8790.9267.205-0.630-0.6300.0000.0000.0000.000
76A176LEU00.0400.02113.414-0.010-0.0100.0000.0000.0000.000
77A177ARG10.8870.94015.4250.0220.0220.0000.0000.0000.000
78A178ASN0-0.064-0.02915.843-0.012-0.0120.0000.0000.0000.000
79A179THR0-0.006-0.01014.6600.0170.0170.0000.0000.0000.000
80A180LEU0-0.0010.01017.152-0.027-0.0270.0000.0000.0000.000
81A181ASP-1-0.833-0.91120.559-0.027-0.0270.0000.0000.0000.000
82A182TYR00.0060.00716.154-0.020-0.0200.0000.0000.0000.000
83A183LEU00.0180.01617.452-0.017-0.0170.0000.0000.0000.000
84A184ARG10.9080.92720.8280.0430.0430.0000.0000.0000.000
85A185SER0-0.084-0.04422.1770.0010.0010.0000.0000.0000.000
86A186PHE00.000-0.00618.903-0.006-0.0060.0000.0000.0000.000
87A187LEU0-0.038-0.01724.520-0.002-0.0020.0000.0000.0000.000
88A188ASN0-0.024-0.01427.5760.0050.0050.0000.0000.0000.000
89A189ASP-1-0.781-0.87027.119-0.105-0.1050.0000.0000.0000.000
90A190SER00.0020.01129.136-0.009-0.0090.0000.0000.0000.000
91A191THR00.021-0.00228.537-0.002-0.0020.0000.0000.0000.000
92A192ASN0-0.014-0.04624.051-0.027-0.0270.0000.0000.0000.000
93A193PHE00.0150.02926.971-0.011-0.0110.0000.0000.0000.000
94A194LYS10.8270.89929.3140.0960.0960.0000.0000.0000.000
95A195LEU0-0.041-0.02025.332-0.003-0.0030.0000.0000.0000.000
96A196ILE00.0280.02624.185-0.007-0.0070.0000.0000.0000.000
97A197TYR0-0.008-0.02827.318-0.002-0.0020.0000.0000.0000.000
98A198ARG10.8590.91130.8630.1190.1190.0000.0000.0000.000
99A199TYR0-0.005-0.01523.8030.0070.0070.0000.0000.0000.000
100A200ALA00.0210.01028.465-0.004-0.0040.0000.0000.0000.000
101A201PHE0-0.024-0.00629.7890.0020.0020.0000.0000.0000.000
102A202ASP-1-0.841-0.92229.583-0.159-0.1590.0000.0000.0000.000
103A203PHE00.0270.02824.6450.0010.0010.0000.0000.0000.000
104A204ALA00.0250.00928.707-0.002-0.0020.0000.0000.0000.000
105A205ARG10.8350.93931.5450.1690.1690.0000.0000.0000.000
106A206GLU-1-0.835-0.90532.685-0.127-0.1270.0000.0000.0000.000
107A207LYS10.8790.90132.9850.1510.1510.0000.0000.0000.000
108A208ASP-1-0.919-0.95334.870-0.131-0.1310.0000.0000.0000.000
109A209GLN00.0360.04437.3580.0110.0110.0000.0000.0000.000
110A210ARG10.8640.91237.8230.1170.1170.0000.0000.0000.000
111A211SER0-0.018-0.02339.4710.0040.0040.0000.0000.0000.000
112A212LEU00.0180.04334.731-0.003-0.0030.0000.0000.0000.000
113A213ASP-1-0.751-0.85538.682-0.087-0.0870.0000.0000.0000.000
114A214ILE00.025-0.00840.072-0.003-0.0030.0000.0000.0000.000
115A215ASN00.003-0.00440.9620.0040.0040.0000.0000.0000.000
116A216THR00.0390.00234.925-0.001-0.0010.0000.0000.0000.000
117A217ALA0-0.035-0.02136.522-0.003-0.0030.0000.0000.0000.000
118A218LYS10.8010.88737.9720.0650.0650.0000.0000.0000.000
119A219CYS0-0.044-0.01535.3180.0020.0020.0000.0000.0000.000
120A220MET00.0180.00430.7900.0000.0000.0000.0000.0000.000
121A221LEU0-0.017-0.00934.003-0.001-0.0010.0000.0000.0000.000
122A222GLY00.0230.01836.4780.0030.0030.0000.0000.0000.000
123A223LEU0-0.055-0.02230.3720.0030.0030.0000.0000.0000.000
124A224LEU0-0.058-0.02629.7760.0010.0010.0000.0000.0000.000
125A225LEU0-0.007-0.02532.9550.0030.0030.0000.0000.0000.000
126A226GLY00.0110.02236.0790.0060.0060.0000.0000.0000.000
127A227LYS10.8670.92434.3750.0460.0460.0000.0000.0000.000
128A228ILE00.0120.00533.6560.0050.0050.0000.0000.0000.000
129A229TRP00.0410.03737.1420.0010.0010.0000.0000.0000.000
130A230PRO00.014-0.00140.1970.0000.0000.0000.0000.0000.000
131A231LEU00.0270.01943.4490.0010.0010.0000.0000.0000.000
132A232PHE00.0130.03039.980-0.001-0.0010.0000.0000.0000.000
133A233PRO00.0130.00342.716-0.001-0.0010.0000.0000.0000.000
134A234VAL00.0410.02344.7610.0000.0000.0000.0000.0000.000
135A235PHE00.0070.00642.198-0.001-0.0010.0000.0000.0000.000
136A236HIS0-0.036-0.02542.7550.0000.0000.0000.0000.0000.000
137A237GLN00.0150.00044.6510.0000.0000.0000.0000.0000.000
138A238PHE00.0040.00947.7170.0000.0000.0000.0000.0000.000
139A239LEU00.0110.00043.081-0.001-0.0010.0000.0000.0000.000
140A240GLU-1-0.855-0.89544.784-0.058-0.0580.0000.0000.0000.000
141A241GLN0-0.065-0.02047.9310.0030.0030.0000.0000.0000.000
142A242SER0-0.054-0.01748.7620.0010.0010.0000.0000.0000.000
143A243LYS10.8370.89051.1180.0520.0520.0000.0000.0000.000
144A244TYR0-0.064-0.06946.777-0.003-0.0030.0000.0000.0000.000
145A245LYS10.9140.94746.7290.0590.0590.0000.0000.0000.000
146A246VAL0-0.015-0.00142.805-0.003-0.0030.0000.0000.0000.000
147A247ILE00.0110.01940.2920.0040.0040.0000.0000.0000.000
148A248ASN00.0390.01140.368-0.008-0.0080.0000.0000.0000.000
149A249LYS10.8470.89932.9430.1450.1450.0000.0000.0000.000
150A250ASP-1-0.857-0.93238.970-0.084-0.0840.0000.0000.0000.000
151A251GLN00.0680.03941.618-0.001-0.0010.0000.0000.0000.000
152A252TRP0-0.005-0.00233.4750.0040.0040.0000.0000.0000.000
153A253CYS0-0.091-0.04836.913-0.003-0.0030.0000.0000.0000.000
154A254ASN00.024-0.00538.3810.0040.0040.0000.0000.0000.000
155A255VAL00.0290.03339.7310.0040.0040.0000.0000.0000.000
156A256LEU0-0.0230.00934.4960.0030.0030.0000.0000.0000.000
157A257GLU-1-0.765-0.86737.769-0.090-0.0900.0000.0000.0000.000
158A258PHE00.0680.04840.7500.0040.0040.0000.0000.0000.000
159A259SER0-0.088-0.07139.4570.0030.0030.0000.0000.0000.000
160A260ARG10.8160.90633.0300.0890.0890.0000.0000.0000.000
161A261THR0-0.072-0.04140.9760.0030.0030.0000.0000.0000.000
162A262ILE0-0.0220.01944.3340.0030.0030.0000.0000.0000.000
163A263ASN0-0.042-0.02646.354-0.001-0.0010.0000.0000.0000.000
164A264LEU00.023-0.01144.4750.0000.0000.0000.0000.0000.000
165A265ASP-1-0.832-0.89248.438-0.032-0.0320.0000.0000.0000.000
166A266LEU0-0.041-0.03349.3790.0000.0000.0000.0000.0000.000
167A267SER0-0.063-0.04652.021-0.001-0.0010.0000.0000.0000.000
168A268ASN0-0.038-0.01948.6580.0010.0010.0000.0000.0000.000
169A269TYR0-0.067-0.06449.054-0.002-0.0020.0000.0000.0000.000
170A270ASP-1-0.892-0.94652.279-0.042-0.0420.0000.0000.0000.000
171A271GLU-1-0.900-0.96953.625-0.040-0.0400.0000.0000.0000.000
172A272ASP-1-0.968-0.95955.958-0.040-0.0400.0000.0000.0000.000
173A273GLY0-0.019-0.00152.307-0.001-0.0010.0000.0000.0000.000
174A274ALA0-0.074-0.05349.3210.0000.0000.0000.0000.0000.000
175A275TRP0-0.0110.00044.130-0.006-0.0060.0000.0000.0000.000
176A276PRO0-0.002-0.00245.1720.0010.0010.0000.0000.0000.000
177A277VAL00.0970.04648.4830.0010.0010.0000.0000.0000.000
178A278LEU0-0.070-0.01545.5660.0010.0010.0000.0000.0000.000
179A279LEU0-0.038-0.03344.4920.0010.0010.0000.0000.0000.000
180A280ASP-1-0.731-0.83648.911-0.050-0.0500.0000.0000.0000.000
181A281GLU-1-0.768-0.85452.029-0.051-0.0510.0000.0000.0000.000
182A282PHE0-0.060-0.02447.3060.0020.0020.0000.0000.0000.000
183A283VAL00.0350.01250.7230.0020.0020.0000.0000.0000.000
184A284GLU-1-0.938-0.96352.883-0.038-0.0380.0000.0000.0000.000
185A285TRP0-0.046-0.03251.1640.0020.0020.0000.0000.0000.000
186A286TYR0-0.015-0.02351.5160.0010.0010.0000.0000.0000.000
187A287LYS10.8890.93554.2140.0390.0390.0000.0000.0000.000
188A288ASP-1-0.886-0.92057.340-0.031-0.0310.0000.0000.0000.000
189A289LYS10.8090.89955.5650.0370.0370.0000.0000.0000.000
190A290GLN0-0.128-0.03454.6830.0040.0040.0000.0000.0000.000