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: M37QZ

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1895248.711656
FMO2-HF: Nuclear repulsion 1812198.765825
FMO2-HF: Total energy -83049.945831
FMO2-MP2: Total energy -83293.787672


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.
-15.633-11.9716.396-4.916-5.140.005
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 : -0.044 / 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].
3A139LYS10.9200.9722.210-13.816-10.6513.500-3.079-3.5850.011
4A140THR0-0.040-0.0196.0600.2470.2470.0000.0000.0000.000
5A141VAL00.0390.0157.698-0.042-0.0420.0000.0000.0000.000
6A142GLN0-0.0180.01110.0220.0360.0360.0000.0000.0000.000
7A143LEU00.0130.00313.143-0.004-0.0040.0000.0000.0000.000
8A144ASN0-0.031-0.01915.025-0.004-0.0040.0000.0000.0000.000
9A145ASP-1-0.751-0.85817.8920.1050.1050.0000.0000.0000.000
10A146GLY00.0420.02619.693-0.003-0.0030.0000.0000.0000.000
11A147GLY0-0.023-0.00822.641-0.005-0.0050.0000.0000.0000.000
12A148LEU0-0.057-0.03521.4160.0000.0000.0000.0000.0000.000
13A149VAL0-0.023-0.00818.0370.0080.0080.0000.0000.0000.000
14A150ARG10.9420.98314.487-0.161-0.1610.0000.0000.0000.000
15A151THR0-0.002-0.01211.809-0.003-0.0030.0000.0000.0000.000
16A152VAL0-0.059-0.0418.1360.0190.0190.0000.0000.0000.000
17A153HIS00.0410.0156.7850.0610.0610.0000.0000.0000.000
18A154LEU0-0.0010.0055.161-0.207-0.117-0.001-0.007-0.0810.000
19A155PRO0-0.0220.0042.035-0.722-0.3602.855-1.925-1.292-0.005
20A156ALA00.016-0.0113.332-1.053-1.0080.0420.095-0.182-0.001
21A157PRO00.0050.0045.7810.5400.5400.0000.0000.0000.000
22A158ASN00.0010.0077.765-0.071-0.0710.0000.0000.0000.000
23A159VAL00.0760.04310.1930.0870.0870.0000.0000.0000.000
24A160ALA00.0230.02711.8400.0000.0000.0000.0000.0000.000
25A161GLY00.0310.01310.847-0.013-0.0130.0000.0000.0000.000
26A162LEU0-0.018-0.0136.8830.0070.0070.0000.0000.0000.000
27A163LEU00.0240.0009.678-0.043-0.0430.0000.0000.0000.000
28A164SER0-0.072-0.04312.893-0.040-0.0400.0000.0000.0000.000
29A165ALA00.0110.0219.143-0.030-0.0300.0000.0000.0000.000
30A166ALA0-0.077-0.01811.095-0.013-0.0130.0000.0000.0000.000
31A167GLY00.025-0.00812.586-0.020-0.0200.0000.0000.0000.000
32A168VAL0-0.052-0.02815.205-0.016-0.0160.0000.0000.0000.000
33A169PRO00.0580.03516.3250.0030.0030.0000.0000.0000.000
34A170LEU0-0.021-0.00917.282-0.008-0.0080.0000.0000.0000.000
35A171LEU0-0.040-0.02419.467-0.008-0.0080.0000.0000.0000.000
36A172GLN0-0.011-0.01322.980-0.002-0.0020.0000.0000.0000.000
37A173SER00.0200.02126.018-0.003-0.0030.0000.0000.0000.000
38A174ASP-1-0.751-0.82721.8240.0660.0660.0000.0000.0000.000
39A175HIS0-0.0090.00222.141-0.001-0.0010.0000.0000.0000.000
40A176VAL00.001-0.01916.4140.0090.0090.0000.0000.0000.000
41A177VAL0-0.0140.01719.120-0.012-0.0120.0000.0000.0000.000
42A178PRO00.0440.01514.4720.0090.0090.0000.0000.0000.000
43A179ALA00.0560.02117.2200.0130.0130.0000.0000.0000.000
44A180ALA00.0740.02115.5670.0200.0200.0000.0000.0000.000
45A181THR0-0.021-0.02114.4320.0380.0380.0000.0000.0000.000
46A182ALA0-0.043-0.00613.678-0.025-0.0250.0000.0000.0000.000
47A183PRO00.0460.0089.3230.0850.0850.0000.0000.0000.000
48A184ILE0-0.008-0.0025.665-0.097-0.0970.0000.0000.0000.000
49A185VAL0-0.012-0.0086.549-0.124-0.1240.0000.0000.0000.000
50A186GLU-1-0.804-0.9046.567-0.401-0.4010.0000.0000.0000.000
51A187GLY0-0.001-0.0098.6990.0560.0560.0000.0000.0000.000
52A188MET0-0.0630.0079.6640.0070.0070.0000.0000.0000.000
53A189GLN0-0.027-0.02312.4540.0390.0390.0000.0000.0000.000
54A190ILE00.0030.00310.9230.0020.0020.0000.0000.0000.000
55A191GLN0-0.023-0.01015.544-0.001-0.0010.0000.0000.0000.000
56A192VAL00.0180.00917.108-0.003-0.0030.0000.0000.0000.000
57A193THR0-0.025-0.00220.034-0.004-0.0040.0000.0000.0000.000
58A194ARG10.6750.78617.743-0.099-0.0990.0000.0000.0000.000
59A195ASN00.0430.02524.690-0.004-0.0040.0000.0000.0000.000
60A196ARG10.8100.87722.013-0.063-0.0630.0000.0000.0000.000
61A197ILE00.0350.02029.081-0.002-0.0020.0000.0000.0000.000
62A198LYS10.8120.88630.262-0.042-0.0420.0000.0000.0000.000
63A199LYS10.9660.99432.942-0.026-0.0260.0000.0000.0000.000
64A200VAL00.0310.02035.1510.0030.0030.0000.0000.0000.000
65A201THR0-0.018-0.01937.690-0.002-0.0020.0000.0000.0000.000
66A202GLU-1-0.867-0.90540.8890.0260.0260.0000.0000.0000.000
67A203ARG10.8780.92943.766-0.023-0.0230.0000.0000.0000.000
68A204LEU00.0000.00346.8910.0000.0000.0000.0000.0000.000
69A205PRO00.0520.01849.7090.0000.0000.0000.0000.0000.000
70A206LEU0-0.0180.00453.0340.0000.0000.0000.0000.0000.000
71A207PRO00.008-0.00455.0070.0000.0000.0000.0000.0000.000
72A208PRO0-0.0020.01058.2010.0000.0000.0000.0000.0000.000
73A209ASN0-0.0060.00660.2550.0000.0000.0000.0000.0000.000
74A210ALA00.0060.00262.6230.0000.0000.0000.0000.0000.000
75A211ARG10.8840.93665.876-0.008-0.0080.0000.0000.0000.000
76A212ARG10.8010.87068.829-0.006-0.0060.0000.0000.0000.000
77A213VAL0-0.021-0.01371.6150.0000.0000.0000.0000.0000.000
78A214GLU-1-0.925-0.95975.3020.0050.0050.0000.0000.0000.000
79A215ASP-1-0.768-0.87778.2330.0060.0060.0000.0000.0000.000
80A216PRO0-0.0010.01480.7370.0000.0000.0000.0000.0000.000
81A217GLU-1-0.883-0.95383.4240.0040.0040.0000.0000.0000.000
82A218MET0-0.071-0.03478.6290.0000.0000.0000.0000.0000.000
83A219ASN0-0.025-0.03880.9890.0000.0000.0000.0000.0000.000
84A220MET0-0.0160.00177.8890.0000.0000.0000.0000.0000.000
85A221SER0-0.071-0.03776.4320.0000.0000.0000.0000.0000.000
86A222ARG10.9070.95675.678-0.006-0.0060.0000.0000.0000.000
87A223GLU-1-0.778-0.86870.7760.0060.0060.0000.0000.0000.000
88A224VAL0-0.024-0.02273.0950.0000.0000.0000.0000.0000.000
89A225VAL0-0.037-0.02467.8090.0000.0000.0000.0000.0000.000
90A226GLU-1-0.894-0.91971.0010.0070.0070.0000.0000.0000.000
91A227ASP-1-0.852-0.93769.4520.0100.0100.0000.0000.0000.000
92A228PRO0-0.0360.00165.9690.0000.0000.0000.0000.0000.000
93A229GLY00.0850.04065.0690.0000.0000.0000.0000.0000.000
94A230VAL0-0.100-0.04861.3070.0000.0000.0000.0000.0000.000
95A231PRO00.004-0.00758.0890.0000.0000.0000.0000.0000.000
96A232GLY00.0460.03956.9510.0000.0000.0000.0000.0000.000
97A233THR0-0.112-0.06750.7440.0010.0010.0000.0000.0000.000
98A234GLN0-0.034-0.03850.001-0.001-0.0010.0000.0000.0000.000
99A235ASP-1-0.778-0.88744.9700.0230.0230.0000.0000.0000.000
100A236VAL00.0030.00845.041-0.001-0.0010.0000.0000.0000.000
101A237THR0-0.045-0.01639.6300.0010.0010.0000.0000.0000.000
102A238PHE00.0660.01840.365-0.002-0.0020.0000.0000.0000.000
103A239ALA0-0.053-0.02437.5430.0020.0020.0000.0000.0000.000
104A240VAL00.018-0.01035.317-0.001-0.0010.0000.0000.0000.000
105A241ALA00.0080.00633.8990.0020.0020.0000.0000.0000.000
106A242GLU-1-0.793-0.89030.5210.0430.0430.0000.0000.0000.000
107A243VAL00.0250.00128.3480.0010.0010.0000.0000.0000.000
108A244ASN0-0.041-0.03625.6010.0030.0030.0000.0000.0000.000
109A245GLY00.0070.00927.1430.0020.0020.0000.0000.0000.000
110A246VAL00.0070.01928.910-0.001-0.0010.0000.0000.0000.000
111A247GLU-1-0.811-0.88532.3720.0270.0270.0000.0000.0000.000
112A248THR0-0.075-0.05134.145-0.001-0.0010.0000.0000.0000.000
113A249GLY00.0270.01836.685-0.002-0.0020.0000.0000.0000.000
114A250ARG10.7430.83537.924-0.024-0.0240.0000.0000.0000.000
115A251LEU00.0130.01340.301-0.002-0.0020.0000.0000.0000.000
116A252PRO0-0.0140.01841.8930.0010.0010.0000.0000.0000.000
117A253VAL0-0.034-0.04240.454-0.001-0.0010.0000.0000.0000.000
118A254ALA0-0.016-0.00843.735-0.001-0.0010.0000.0000.0000.000
119A255ASN0-0.010-0.01345.4930.0010.0010.0000.0000.0000.000
120A256VAL00.0040.02746.177-0.001-0.0010.0000.0000.0000.000
121A257VAL00.0270.01748.6810.0010.0010.0000.0000.0000.000
122A258VAL0-0.057-0.02948.4670.0000.0000.0000.0000.0000.000
123A259THR00.010-0.00251.6450.0000.0000.0000.0000.0000.000
124A260PRO00.004-0.00655.1110.0000.0000.0000.0000.0000.000
125A261ALA00.0060.01957.6470.0000.0000.0000.0000.0000.000
126A262HIS0-0.044-0.01759.824-0.001-0.0010.0000.0000.0000.000
127A263GLU-1-0.851-0.93463.5680.0080.0080.0000.0000.0000.000
128A264ALA00.0250.03165.3790.0000.0000.0000.0000.0000.000
129A265VAL0-0.039-0.02367.0410.0000.0000.0000.0000.0000.000
130A266VAL0-0.009-0.01667.9110.0000.0000.0000.0000.0000.000
131A267ARG10.7790.85971.086-0.007-0.0070.0000.0000.0000.000
132A268VAL00.002-0.01272.5150.0000.0000.0000.0000.0000.000
133A269GLY00.0220.01775.5090.0000.0000.0000.0000.0000.000
134A270THR00.002-0.02278.5650.0000.0000.0000.0000.0000.000
135A271LYS10.8110.94480.873-0.005-0.0050.0000.0000.0000.000
136A272PRO00.0550.02083.9940.0000.0000.0000.0000.0000.000
137A273GLY0-0.0170.00685.5970.0000.0000.0000.0000.0000.000
138A274THR0-0.034-0.02882.5970.0000.0000.0000.0000.0000.000
139A275GLU-1-0.802-0.91280.2900.0040.0040.0000.0000.0000.000
140A276VAL0-0.0150.00977.9470.0000.0000.0000.0000.0000.000
141A277PRO0-0.046-0.00577.7630.0000.0000.0000.0000.0000.000
142A278PRO0-0.001-0.01273.9360.0000.0000.0000.0000.0000.000
143A279VAL00.0070.00474.7810.0000.0000.0000.0000.0000.000
144A280ILE0-0.023-0.00474.2170.0000.0000.0000.0000.0000.000
145A281ASP-1-0.815-0.90175.4400.0020.0020.0000.0000.0000.000
146A282GLY00.0510.00274.6130.0000.0000.0000.0000.0000.000
147A283SER00.0610.02772.7230.0000.0000.0000.0000.0000.000
148A284ILE0-0.0050.00174.6420.0000.0000.0000.0000.0000.000
149A285TRP00.0530.01978.0060.0000.0000.0000.0000.0000.000
150A286ASP-1-0.833-0.88474.2120.0040.0040.0000.0000.0000.000
151A287ALA0-0.0100.01977.0780.0000.0000.0000.0000.0000.000
152A288ILE0-0.011-0.00378.6750.0000.0000.0000.0000.0000.000
153A289ALA00.0600.05078.8470.0000.0000.0000.0000.0000.000
154A290GLY0-0.029-0.03078.6430.0000.0000.0000.0000.0000.000
155A291CYS0-0.177-0.09279.2880.0000.0000.0000.0000.0000.000
156A292GLU-1-0.868-0.96482.6760.0030.0030.0000.0000.0000.000
157A293ALA00.0050.02182.6210.0000.0000.0000.0000.0000.000
158A294GLY0-0.017-0.00480.6810.0000.0000.0000.0000.0000.000
159A295GLY0-0.028-0.01177.6790.0000.0000.0000.0000.0000.000
160A296ASN0-0.039-0.01578.0100.0000.0000.0000.0000.0000.000
161A297TRP00.0510.00177.2410.0000.0000.0000.0000.0000.000
162A298ALA00.0290.02881.0800.0000.0000.0000.0000.0000.000
163A299ILE0-0.059-0.01982.8690.0000.0000.0000.0000.0000.000
164A300ASN0-0.046-0.03985.2430.0000.0000.0000.0000.0000.000
165A301THR0-0.0120.00888.6890.0000.0000.0000.0000.0000.000
166A302GLY00.0520.02189.9600.0000.0000.0000.0000.0000.000
167A303ASN0-0.018-0.03491.5870.0000.0000.0000.0000.0000.000
168A304GLY0-0.020-0.01394.4680.0000.0000.0000.0000.0000.000
169A305TYR0-0.091-0.02691.5610.0000.0000.0000.0000.0000.000
170A306TYR0-0.024-0.01389.4800.0000.0000.0000.0000.0000.000
171A307GLY00.0490.03085.2990.0000.0000.0000.0000.0000.000
172A308GLY0-0.016-0.00682.4510.0000.0000.0000.0000.0000.000
173A309VAL0-0.041-0.02983.1650.0000.0000.0000.0000.0000.000
174A310GLN0-0.060-0.02985.5180.0000.0000.0000.0000.0000.000
175A311PHE00.0380.04586.7910.0000.0000.0000.0000.0000.000
176A312ASP-1-0.788-0.85890.5950.0030.0030.0000.0000.0000.000
177A313GLN0-0.065-0.06893.4440.0000.0000.0000.0000.0000.000
178A314GLY00.0450.01895.3160.0000.0000.0000.0000.0000.000
179A315THR0-0.069-0.09093.8060.0000.0000.0000.0000.0000.000
180A316TRP00.0020.03185.8580.0000.0000.0000.0000.0000.000
181A317GLU-1-0.885-0.93091.9190.0030.0030.0000.0000.0000.000
182A318ALA0-0.061-0.02894.5640.0000.0000.0000.0000.0000.000
183A319ASN0-0.059-0.04090.3030.0000.0000.0000.0000.0000.000
184A320GLY00.0260.01390.4600.0000.0000.0000.0000.0000.000
185A321GLY00.0660.01888.5500.0000.0000.0000.0000.0000.000
186A322LEU0-0.039-0.01588.7430.0000.0000.0000.0000.0000.000
187A323ARG10.8280.93684.638-0.003-0.0030.0000.0000.0000.000
188A324TYR0-0.088-0.06182.7300.0000.0000.0000.0000.0000.000
189A325ALA00.0760.03385.7530.0000.0000.0000.0000.0000.000
190A326PRO0-0.016-0.00987.7900.0000.0000.0000.0000.0000.000
191A327ARG10.8940.92789.165-0.004-0.0040.0000.0000.0000.000
192A328ALA00.0420.02887.3210.0000.0000.0000.0000.0000.000
193A329ASP-1-0.766-0.87685.1650.0040.0040.0000.0000.0000.000
194A330LEU0-0.064-0.03584.4050.0000.0000.0000.0000.0000.000
195A331ALA0-0.0130.01683.1680.0000.0000.0000.0000.0000.000
196A332THR0-0.005-0.03177.6460.0000.0000.0000.0000.0000.000
197A333ARG10.8150.86474.072-0.005-0.0050.0000.0000.0000.000
198A334GLU-1-0.858-0.93074.9860.0050.0050.0000.0000.0000.000
199A335GLU-1-0.747-0.82278.2970.0040.0040.0000.0000.0000.000
200A336GLN0-0.035-0.03781.6240.0000.0000.0000.0000.0000.000
201A337ILE00.003-0.00177.9480.0000.0000.0000.0000.0000.000
202A338ALA0-0.0040.01681.6380.0000.0000.0000.0000.0000.000
203A339VAL0-0.0230.00483.0740.0000.0000.0000.0000.0000.000
204A340ALA00.0310.01484.5290.0000.0000.0000.0000.0000.000
205A341GLU-1-0.830-0.92880.4410.0020.0020.0000.0000.0000.000
206A342VAL0-0.0010.00785.2140.0000.0000.0000.0000.0000.000
207A343THR0-0.014-0.02588.6650.0000.0000.0000.0000.0000.000
208A344ARG10.7610.86580.775-0.002-0.0020.0000.0000.0000.000
209A345LEU0-0.046-0.00185.1590.0000.0000.0000.0000.0000.000
210A346ARG10.9040.96988.734-0.002-0.0020.0000.0000.0000.000
211A347GLN0-0.025-0.02091.5020.0000.0000.0000.0000.0000.000
212A348GLY00.0290.02188.0830.0000.0000.0000.0000.0000.000
213A349TRP0-0.024-0.04580.7240.0000.0000.0000.0000.0000.000
214A350GLY0-0.0050.00287.2110.0000.0000.0000.0000.0000.000
215A351ALA0-0.0110.00089.8050.0000.0000.0000.0000.0000.000
216A352TRP00.0230.00687.3240.0000.0000.0000.0000.0000.000
217A353PRO0-0.0110.00088.4330.0000.0000.0000.0000.0000.000
218A354VAL00.0380.00187.8570.0000.0000.0000.0000.0000.000
219A356ALA00.0310.03384.1150.0000.0000.0000.0000.0000.000
220A357ALA0-0.008-0.00484.5030.0000.0000.0000.0000.0000.000
221A358ARG10.9080.93382.043-0.003-0.0030.0000.0000.0000.000
222A359ALA0-0.0160.00680.2320.0000.0000.0000.0000.0000.000
223A360GLY0-0.0090.01779.5030.0000.0000.0000.0000.0000.000
224A361ALA0-0.053-0.03480.5710.0000.0000.0000.0000.0000.000
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