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: 9G612

Calculation Name: 5E27-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E27

Chain ID: A

ChEMBL ID:

UniProt ID: P9WG29

Base Structure: X-ray

Registration Date: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894971.01373
FMO2-HF: Nuclear repulsion 1811922.921714
FMO2-HF: Total energy -83048.092017
FMO2-MP2: Total energy -83292.06999


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:137:SER)


Summations of interaction energy for fragment #1(A:137: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.
-1.4491.0025.134-3.864-3.719-0.01
Interaction energy analysis for fragmet #1(A:137:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.042
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].
3A139LYS10.9340.9792.0620.2862.5681.357-1.511-2.127-0.001
4A140THR0-0.042-0.0236.0590.2230.2230.0000.0000.0000.000
5A141VAL00.0530.0208.3100.2190.2190.0000.0000.0000.000
6A142GLN0-0.039-0.01710.108-0.141-0.1410.0000.0000.0000.000
7A143LEU00.0100.00913.3730.0520.0520.0000.0000.0000.000
8A144ASN0-0.026-0.01815.125-0.053-0.0530.0000.0000.0000.000
9A145ASP-1-0.798-0.88617.9880.2650.2650.0000.0000.0000.000
10A146GLY00.0580.02219.796-0.025-0.0250.0000.0000.0000.000
11A147GLY0-0.041-0.01522.706-0.019-0.0190.0000.0000.0000.000
12A148LEU0-0.044-0.02821.517-0.013-0.0130.0000.0000.0000.000
13A149VAL0-0.013-0.00417.9100.0200.0200.0000.0000.0000.000
14A150ARG10.9670.98914.385-0.213-0.2130.0000.0000.0000.000
15A151THR00.005-0.00211.8820.0360.0360.0000.0000.0000.000
16A152VAL0-0.063-0.0388.248-0.037-0.0370.0000.0000.0000.000
17A153HIS00.0450.0226.781-0.079-0.0790.0000.0000.0000.000
18A154LEU0-0.003-0.0045.125-0.601-0.509-0.001-0.007-0.0830.000
19A155PRO0-0.0070.0091.936-0.050-0.0593.744-2.386-1.349-0.008
20A156ALA00.008-0.0123.420-1.703-1.6170.0340.040-0.160-0.001
21A157PRO00.0030.0095.8780.9770.9770.0000.0000.0000.000
22A158ASN00.0090.0047.855-0.096-0.0960.0000.0000.0000.000
23A159VAL00.0730.04510.1930.0700.0700.0000.0000.0000.000
24A160ALA00.0290.01811.840-0.074-0.0740.0000.0000.0000.000
25A161GLY00.0180.01210.948-0.081-0.0810.0000.0000.0000.000
26A162LEU0-0.024-0.0187.371-0.064-0.0640.0000.0000.0000.000
27A163LEU00.0260.0029.808-0.160-0.1600.0000.0000.0000.000
28A164SER0-0.061-0.03112.991-0.124-0.1240.0000.0000.0000.000
29A165ALA00.0140.0229.222-0.100-0.1000.0000.0000.0000.000
30A166ALA0-0.087-0.02411.164-0.107-0.1070.0000.0000.0000.000
31A167GLY00.010-0.01112.646-0.056-0.0560.0000.0000.0000.000
32A168VAL0-0.052-0.02315.244-0.042-0.0420.0000.0000.0000.000
33A169PRO00.0570.03016.4330.0320.0320.0000.0000.0000.000
34A170LEU0-0.011-0.01117.172-0.027-0.0270.0000.0000.0000.000
35A171LEU0-0.058-0.02819.598-0.015-0.0150.0000.0000.0000.000
36A172GLN0-0.027-0.01923.105-0.004-0.0040.0000.0000.0000.000
37A173SER00.0280.02126.1580.0050.0050.0000.0000.0000.000
38A174ASP-1-0.758-0.85221.9420.2300.2300.0000.0000.0000.000
39A175HIS0-0.014-0.00122.2340.0270.0270.0000.0000.0000.000
40A176VAL00.001-0.02116.5840.0010.0010.0000.0000.0000.000
41A177VAL0-0.0280.01519.083-0.002-0.0020.0000.0000.0000.000
42A178PRO00.0510.01314.516-0.003-0.0030.0000.0000.0000.000
43A179ALA00.0550.02617.2200.0010.0010.0000.0000.0000.000
44A180ALA00.0820.02415.5670.0740.0740.0000.0000.0000.000
45A181THR0-0.037-0.02414.4320.0900.0900.0000.0000.0000.000
46A182ALA0-0.031-0.00313.6980.0350.0350.0000.0000.0000.000
47A183PRO00.0420.0059.4520.1430.1430.0000.0000.0000.000
48A184ILE0-0.0010.0095.880-0.264-0.2640.0000.0000.0000.000
49A185VAL0-0.015-0.0186.6300.3440.3440.0000.0000.0000.000
50A186GLU-1-0.790-0.8876.9880.1090.1090.0000.0000.0000.000
51A187GLY0-0.025-0.0188.723-0.067-0.0670.0000.0000.0000.000
52A188MET0-0.0570.0109.421-0.044-0.0440.0000.0000.0000.000
53A189GLN0-0.024-0.02012.497-0.049-0.0490.0000.0000.0000.000
54A190ILE00.0040.00411.2940.0560.0560.0000.0000.0000.000
55A191GLN0-0.030-0.01715.678-0.050-0.0500.0000.0000.0000.000
56A192VAL00.0280.01317.3970.0200.0200.0000.0000.0000.000
57A193THR0-0.034-0.00920.167-0.035-0.0350.0000.0000.0000.000
58A194ARG10.7110.82717.876-0.264-0.2640.0000.0000.0000.000
59A195ASN00.0330.02624.813-0.023-0.0230.0000.0000.0000.000
60A196ARG10.8420.90022.046-0.189-0.1890.0000.0000.0000.000
61A197ILE00.0560.03729.200-0.008-0.0080.0000.0000.0000.000
62A198LYS10.9080.94730.283-0.085-0.0850.0000.0000.0000.000
63A199LYS10.9500.99233.041-0.071-0.0710.0000.0000.0000.000
64A200VAL00.0140.01235.2340.0010.0010.0000.0000.0000.000
65A201THR0-0.029-0.01937.773-0.001-0.0010.0000.0000.0000.000
66A202GLU-1-0.872-0.92140.9640.0500.0500.0000.0000.0000.000
67A203ARG10.8940.95743.839-0.032-0.0320.0000.0000.0000.000
68A204LEU00.001-0.00446.793-0.001-0.0010.0000.0000.0000.000
69A205PRO00.0360.01249.783-0.001-0.0010.0000.0000.0000.000
70A206LEU0-0.0190.00053.1150.0020.0020.0000.0000.0000.000
71A207PRO00.0170.01055.047-0.001-0.0010.0000.0000.0000.000
72A208PRO00.0020.00758.2850.0000.0000.0000.0000.0000.000
73A209ASN00.0000.00260.3760.0010.0010.0000.0000.0000.000
74A210ALA00.0120.00362.710-0.001-0.0010.0000.0000.0000.000
75A211ARG10.8820.93165.967-0.018-0.0180.0000.0000.0000.000
76A212ARG10.9140.95668.918-0.023-0.0230.0000.0000.0000.000
77A213VAL0-0.032-0.01771.7100.0000.0000.0000.0000.0000.000
78A214GLU-1-0.940-0.97075.3950.0190.0190.0000.0000.0000.000
79A215ASP-1-0.811-0.92078.3290.0160.0160.0000.0000.0000.000
80A216PRO0-0.0230.00580.8340.0000.0000.0000.0000.0000.000
81A217GLU-1-0.958-0.98183.5810.0140.0140.0000.0000.0000.000
82A218MET0-0.106-0.05278.4820.0000.0000.0000.0000.0000.000
83A219ASN0-0.002-0.02081.1120.0000.0000.0000.0000.0000.000
84A220MET0-0.0150.00178.0740.0010.0010.0000.0000.0000.000
85A221SER0-0.081-0.05076.5260.0010.0010.0000.0000.0000.000
86A222ARG10.9120.96275.789-0.018-0.0180.0000.0000.0000.000
87A223GLU-1-0.870-0.94870.8720.0230.0230.0000.0000.0000.000
88A224VAL0-0.022-0.01973.1720.0000.0000.0000.0000.0000.000
89A225VAL0-0.043-0.02868.0370.0000.0000.0000.0000.0000.000
90A226GLU-1-0.881-0.92171.0910.0170.0170.0000.0000.0000.000
91A227ASP-1-0.845-0.93769.5270.0180.0180.0000.0000.0000.000
92A228PRO0-0.0430.00766.0390.0010.0010.0000.0000.0000.000
93A229GLY00.0840.03365.1450.0010.0010.0000.0000.0000.000
94A230VAL0-0.100-0.05161.3120.0000.0000.0000.0000.0000.000
95A231PRO0-0.005-0.00758.1190.0010.0010.0000.0000.0000.000
96A232GLY00.0490.03557.018-0.001-0.0010.0000.0000.0000.000
97A233THR0-0.094-0.05851.0290.0010.0010.0000.0000.0000.000
98A234GLN0-0.038-0.03950.1320.0000.0000.0000.0000.0000.000
99A235ASP-1-0.804-0.90645.0730.0370.0370.0000.0000.0000.000
100A236VAL0-0.0060.00545.2300.0010.0010.0000.0000.0000.000
101A237THR0-0.039-0.01439.8190.0010.0010.0000.0000.0000.000
102A238PHE00.0640.01940.3300.0000.0000.0000.0000.0000.000
103A239ALA0-0.043-0.02437.6480.0030.0030.0000.0000.0000.000
104A240VAL00.015-0.01035.005-0.002-0.0020.0000.0000.0000.000
105A241ALA00.0060.00334.0130.0060.0060.0000.0000.0000.000
106A242GLU-1-0.833-0.94330.1440.0980.0980.0000.0000.0000.000
107A243VAL0-0.003-0.00828.8650.0110.0110.0000.0000.0000.000
108A244ASN0-0.036-0.03125.5040.0070.0070.0000.0000.0000.000
109A245GLY00.0100.01827.251-0.004-0.0040.0000.0000.0000.000
110A246VAL00.0010.01829.004-0.010-0.0100.0000.0000.0000.000
111A247GLU-1-0.839-0.91432.4690.0750.0750.0000.0000.0000.000
112A248THR0-0.093-0.05433.888-0.001-0.0010.0000.0000.0000.000
113A249GLY00.0470.02336.801-0.003-0.0030.0000.0000.0000.000
114A250ARG10.7700.86638.037-0.058-0.0580.0000.0000.0000.000
115A251LEU00.0150.01440.412-0.002-0.0020.0000.0000.0000.000
116A252PRO00.0010.01942.0010.0020.0020.0000.0000.0000.000
117A253VAL0-0.051-0.04440.5980.0010.0010.0000.0000.0000.000
118A254ALA0-0.011-0.00643.852-0.001-0.0010.0000.0000.0000.000
119A255ASN00.002-0.00545.5880.0020.0020.0000.0000.0000.000
120A256VAL00.0000.02445.963-0.001-0.0010.0000.0000.0000.000
121A257VAL00.0360.01548.7570.0000.0000.0000.0000.0000.000
122A258VAL0-0.058-0.02348.671-0.001-0.0010.0000.0000.0000.000
123A259THR0-0.019-0.01551.706-0.001-0.0010.0000.0000.0000.000
124A260PRO00.0220.00755.1700.0010.0010.0000.0000.0000.000
125A261ALA00.0150.01757.713-0.001-0.0010.0000.0000.0000.000
126A262HIS0-0.055-0.02359.8950.0000.0000.0000.0000.0000.000
127A263GLU-1-0.842-0.92663.6380.0200.0200.0000.0000.0000.000
128A264ALA00.0220.03265.4570.0000.0000.0000.0000.0000.000
129A265VAL0-0.045-0.02467.1230.0000.0000.0000.0000.0000.000
130A266VAL0-0.010-0.01468.1390.0000.0000.0000.0000.0000.000
131A267ARG10.8500.91871.178-0.017-0.0170.0000.0000.0000.000
132A268VAL00.008-0.00472.9470.0000.0000.0000.0000.0000.000
133A269GLY00.0150.00575.610-0.001-0.0010.0000.0000.0000.000
134A270THR00.003-0.01278.6710.0000.0000.0000.0000.0000.000
135A271LYS10.9330.99580.979-0.016-0.0160.0000.0000.0000.000
136A272PRO00.0510.03884.1040.0000.0000.0000.0000.0000.000
137A273GLY0-0.0180.00285.7210.0000.0000.0000.0000.0000.000
138A274THR0-0.048-0.05782.7680.0000.0000.0000.0000.0000.000
139A275GLU-1-0.809-0.90880.4100.0190.0190.0000.0000.0000.000
140A276VAL0-0.0260.02977.8020.0000.0000.0000.0000.0000.000
141A277PRO0-0.044-0.00977.8860.0010.0010.0000.0000.0000.000
142A278PRO0-0.003-0.01174.1010.0000.0000.0000.0000.0000.000
143A279VAL00.0060.00474.9270.0000.0000.0000.0000.0000.000
144A280ILE0-0.0290.00174.2290.0010.0010.0000.0000.0000.000
145A281ASP-1-0.875-0.94975.5680.0230.0230.0000.0000.0000.000
146A282GLY00.033-0.01474.7470.0000.0000.0000.0000.0000.000
147A283SER00.0840.02872.7970.0000.0000.0000.0000.0000.000
148A284ILE0-0.0280.00374.7780.0000.0000.0000.0000.0000.000
149A285TRP00.002-0.00178.135-0.001-0.0010.0000.0000.0000.000
150A286ASP-1-0.883-0.93574.0450.0240.0240.0000.0000.0000.000
151A287ALA0-0.0270.00777.2090.0000.0000.0000.0000.0000.000
152A288ILE0-0.027-0.01378.8090.0000.0000.0000.0000.0000.000
153A289ALA00.0620.05378.909-0.001-0.0010.0000.0000.0000.000
154A290GLY0-0.030-0.03178.7720.0000.0000.0000.0000.0000.000
155A291CYS0-0.172-0.08679.4170.0000.0000.0000.0000.0000.000
156A292GLU-1-0.898-0.97282.8060.0180.0180.0000.0000.0000.000
157A293ALA0-0.005-0.00182.836-0.001-0.0010.0000.0000.0000.000
158A294GLY0-0.016-0.00580.8050.0000.0000.0000.0000.0000.000
159A295GLY0-0.028-0.01177.8020.0010.0010.0000.0000.0000.000
160A296ASN0-0.021-0.00778.1300.0010.0010.0000.0000.0000.000
161A297TRP00.0420.00077.377-0.001-0.0010.0000.0000.0000.000
162A298ALA00.0110.01181.1980.0000.0000.0000.0000.0000.000
163A299ILE0-0.089-0.02182.983-0.001-0.0010.0000.0000.0000.000
164A300ASN00.005-0.00685.3580.0000.0000.0000.0000.0000.000
165A301THR0-0.019-0.00188.8260.0000.0000.0000.0000.0000.000
166A302GLY00.0500.01990.0730.0000.0000.0000.0000.0000.000
167A303ASN0-0.026-0.03691.6760.0000.0000.0000.0000.0000.000
168A304GLY00.0110.02894.8150.0000.0000.0000.0000.0000.000
169A305TYR0-0.118-0.05491.7120.0000.0000.0000.0000.0000.000
170A306TYR0-0.029-0.02489.5750.0000.0000.0000.0000.0000.000
171A307GLY00.0550.02785.4140.0000.0000.0000.0000.0000.000
172A308GLY0-0.017-0.00682.5740.0000.0000.0000.0000.0000.000
173A309VAL0-0.040-0.02783.3070.0000.0000.0000.0000.0000.000
174A310GLN00.0010.01385.6450.0000.0000.0000.0000.0000.000
175A311PHE00.0510.04786.6860.0000.0000.0000.0000.0000.000
176A312ASP-1-0.820-0.88290.7200.0140.0140.0000.0000.0000.000
177A313GLN0-0.042-0.07493.5670.0000.0000.0000.0000.0000.000
178A314GLY00.0380.01595.4370.0000.0000.0000.0000.0000.000
179A315THR0-0.061-0.06093.3820.0000.0000.0000.0000.0000.000
180A316TRP00.0090.02685.9560.0000.0000.0000.0000.0000.000
181A317GLU-1-0.899-0.93992.0410.0140.0140.0000.0000.0000.000
182A318ALA0-0.047-0.02094.6860.0000.0000.0000.0000.0000.000
183A319ASN0-0.061-0.04391.0040.0000.0000.0000.0000.0000.000
184A320GLY00.0330.01890.5860.0000.0000.0000.0000.0000.000
185A321GLY00.0740.02488.6710.0000.0000.0000.0000.0000.000
186A322LEU0-0.042-0.01688.8610.0000.0000.0000.0000.0000.000
187A323ARG10.8390.94284.885-0.018-0.0180.0000.0000.0000.000
188A324TYR0-0.108-0.09282.9360.0000.0000.0000.0000.0000.000
189A325ALA00.0700.03085.8940.0000.0000.0000.0000.0000.000
190A326PRO0-0.006-0.01287.9020.0000.0000.0000.0000.0000.000
191A327ARG10.8990.95389.332-0.015-0.0150.0000.0000.0000.000
192A328ALA00.0430.03287.3580.0000.0000.0000.0000.0000.000
193A329ASP-1-0.791-0.89985.2700.0160.0160.0000.0000.0000.000
194A330LEU0-0.074-0.03984.5170.0000.0000.0000.0000.0000.000
195A331ALA00.0010.01883.2920.0000.0000.0000.0000.0000.000
196A332THR00.0130.00677.8260.0000.0000.0000.0000.0000.000
197A333ARG10.9220.96073.849-0.024-0.0240.0000.0000.0000.000
198A334GLU-1-0.880-0.95375.1220.0230.0230.0000.0000.0000.000
199A335GLU-1-0.774-0.86578.4200.0190.0190.0000.0000.0000.000
200A336GLN00.002-0.01781.745-0.001-0.0010.0000.0000.0000.000
201A337ILE0-0.012-0.00178.0490.0000.0000.0000.0000.0000.000
202A338ALA00.0010.01581.8520.0000.0000.0000.0000.0000.000
203A339VAL0-0.041-0.00383.2020.0000.0000.0000.0000.0000.000
204A340ALA00.0290.01984.6940.0000.0000.0000.0000.0000.000
205A341GLU-1-0.859-0.96580.4130.0220.0220.0000.0000.0000.000
206A342VAL00.0080.01485.3470.0000.0000.0000.0000.0000.000
207A343THR0-0.030-0.03288.7980.0000.0000.0000.0000.0000.000
208A344ARG10.8920.95881.286-0.021-0.0210.0000.0000.0000.000
209A345LEU0-0.067-0.01785.0140.0000.0000.0000.0000.0000.000
210A346ARG10.9110.97388.873-0.016-0.0160.0000.0000.0000.000
211A347GLN0-0.008-0.01291.6670.0000.0000.0000.0000.0000.000
212A348GLY00.0060.00888.2240.0000.0000.0000.0000.0000.000
213A349TRP0-0.022-0.04681.2150.0000.0000.0000.0000.0000.000
214A350GLY0-0.0090.00187.3510.0000.0000.0000.0000.0000.000
215A351ALA0-0.0040.00489.9410.0000.0000.0000.0000.0000.000
216A352TRP00.004-0.01287.3420.0000.0000.0000.0000.0000.000
217A353PRO0-0.0030.00888.5700.0000.0000.0000.0000.0000.000
218A354VAL00.035-0.01088.0240.0000.0000.0000.0000.0000.000
219A356ALA00.0390.03484.2520.0010.0010.0000.0000.0000.000
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