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

tag_button

FMODB ID: 14R2Z

Calculation Name: 4EJS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EJS

Chain ID: A

ChEMBL ID:

UniProt ID: Q02884

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 OptAll
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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2879561.590968
FMO2-HF: Nuclear repulsion 2790916.854352
FMO2-HF: Total energy -88644.736616
FMO2-MP2: Total energy -88903.561025


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:67:GLY)


Summations of interaction energy for fragment #1(A:67:GLY)
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.
-13.031-10.6110.023-6.544-5.903-0.047
Interaction energy analysis for fragmet #1(A:67:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.019
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].
3A69ASP-1-0.794-0.8663.869-0.5341.382-0.008-1.116-0.7920.006
4A70SER00.0100.0066.8210.0380.0380.0000.0000.0000.000
5A71SER0-0.099-0.0549.6120.0610.0610.0000.0000.0000.000
6A72HIS00.0540.0209.3020.1740.1740.0000.0000.0000.000
7A73VAL0-0.052-0.04311.7820.0930.0930.0000.0000.0000.000
8A74GLY0-0.0020.00313.6790.0730.0730.0000.0000.0000.000
9A75VAL0-0.029-0.0219.540-0.017-0.0170.0000.0000.0000.000
10A76ARG10.8560.93212.7560.3200.3200.0000.0000.0000.000
11A77PRO00.0020.00413.979-0.025-0.0250.0000.0000.0000.000
12A78SER00.0360.00915.2520.0020.0020.0000.0000.0000.000
13A79PRO0-0.036-0.02918.0060.0300.0300.0000.0000.0000.000
14A80ALA00.0150.02320.8990.0210.0210.0000.0000.0000.000
15A81THR0-0.058-0.04616.6050.0140.0140.0000.0000.0000.000
16A82SER00.0090.00915.315-0.034-0.0340.0000.0000.0000.000
17A83GLN00.0070.01012.5600.0400.0400.0000.0000.0000.000
18A84PRO00.0180.0128.6020.0050.0050.0000.0000.0000.000
19A85THR00.000-0.01111.771-0.031-0.0310.0000.0000.0000.000
20A86THR00.0260.00713.034-0.093-0.0930.0000.0000.0000.000
21A87SER0-0.043-0.01514.8250.0500.0500.0000.0000.0000.000
22A88THR0-0.012-0.06418.121-0.057-0.0570.0000.0000.0000.000
23A89GLY00.008-0.00620.222-0.002-0.0020.0000.0000.0000.000
24A90SER00.0030.00922.4740.0270.0270.0000.0000.0000.000
25A91ALA00.0310.01724.638-0.004-0.0040.0000.0000.0000.000
26A92ASP-1-0.872-0.93025.982-0.157-0.1570.0000.0000.0000.000
27A93LEU00.0630.04123.3250.0030.0030.0000.0000.0000.000
28A94ASP-1-0.743-0.82921.142-0.329-0.3290.0000.0000.0000.000
29A95SER0-0.091-0.06422.8870.0110.0110.0000.0000.0000.000
30A96ILE00.0420.02325.5230.0120.0120.0000.0000.0000.000
31A97LEU00.0020.00420.3500.0090.0090.0000.0000.0000.000
32A98GLY0-0.031-0.01123.2480.0080.0080.0000.0000.0000.000
33A99HIS0-0.0070.00218.8230.0140.0140.0000.0000.0000.000
34A100MET0-0.0070.00319.426-0.010-0.0100.0000.0000.0000.000
35A101GLY00.0230.04218.161-0.026-0.0260.0000.0000.0000.000
36A102LEU00.0020.00716.1830.0380.0380.0000.0000.0000.000
37A103PRO0-0.046-0.03513.965-0.078-0.0780.0000.0000.0000.000
38A104LEU0-0.012-0.0017.553-0.029-0.0290.0000.0000.0000.000
39A105GLY00.0370.02210.5660.1420.1420.0000.0000.0000.000
40A106ASN0-0.054-0.02011.3960.1510.1510.0000.0000.0000.000
41A107SER0-0.016-0.03215.072-0.058-0.0580.0000.0000.0000.000
42A108VAL00.0010.01018.0170.0340.0340.0000.0000.0000.000
43A109LEU0-0.0190.00021.551-0.019-0.0190.0000.0000.0000.000
44A110VAL00.010-0.00424.6310.0160.0160.0000.0000.0000.000
45A111GLU-1-0.780-0.86427.146-0.134-0.1340.0000.0000.0000.000
46A112GLU-1-0.790-0.90130.511-0.158-0.1580.0000.0000.0000.000
47A113GLN00.0030.00333.6300.0030.0030.0000.0000.0000.000
48A114SER0-0.003-0.03336.529-0.005-0.0050.0000.0000.0000.000
49A115THR0-0.092-0.04738.795-0.001-0.0010.0000.0000.0000.000
50A116THR0-0.0320.00035.483-0.004-0.0040.0000.0000.0000.000
51A117GLU-1-0.744-0.85532.375-0.187-0.1870.0000.0000.0000.000
52A118PHE00.0550.03732.168-0.015-0.0150.0000.0000.0000.000
53A119HIS00.0400.01429.070-0.029-0.0290.0000.0000.0000.000
54A120SER0-0.074-0.05227.681-0.029-0.0290.0000.0000.0000.000
55A121ILE0-0.009-0.00128.097-0.020-0.0200.0000.0000.0000.000
56A122LEU00.0330.01425.936-0.021-0.0210.0000.0000.0000.000
57A123GLY00.0310.01623.753-0.029-0.0290.0000.0000.0000.000
58A124LYS10.7580.86223.3540.1770.1770.0000.0000.0000.000
59A125LEU00.0220.01624.289-0.025-0.0250.0000.0000.0000.000
60A126PHE00.0090.01916.624-0.038-0.0380.0000.0000.0000.000
61A127ALA0-0.023-0.02119.405-0.066-0.0660.0000.0000.0000.000
62A128ALA00.0130.00119.948-0.045-0.0450.0000.0000.0000.000
63A129GLN00.0430.01318.8070.0230.0230.0000.0000.0000.000
64A130GLY00.0260.01216.501-0.033-0.0330.0000.0000.0000.000
65A131ILE0-0.027-0.01116.791-0.055-0.0550.0000.0000.0000.000
66A132VAL0-0.014-0.00919.2180.0090.0090.0000.0000.0000.000
67A133HIS0-0.046-0.02315.063-0.059-0.0590.0000.0000.0000.000
68A134ASN0-0.042-0.02214.724-0.124-0.1240.0000.0000.0000.000
69A135ARG10.7000.82816.2940.3930.3930.0000.0000.0000.000
70A136ILE00.0190.01818.0930.0380.0380.0000.0000.0000.000
71A145ARG10.9290.97714.7750.3570.3570.0000.0000.0000.000
72A146ASN0-0.076-0.05910.510-0.152-0.1520.0000.0000.0000.000
73A147GLY00.0990.03013.0740.0380.0380.0000.0000.0000.000
74A148ASP-1-0.869-0.91910.728-0.927-0.9270.0000.0000.0000.000
75A149THR0-0.076-0.04810.813-0.264-0.2640.0000.0000.0000.000
76A150HIS0-0.019-0.00912.0830.1280.1280.0000.0000.0000.000
77A151VAL0-0.0060.00513.476-0.074-0.0740.0000.0000.0000.000
78A152ILE00.008-0.00112.7270.0460.0460.0000.0000.0000.000
79A153VAL0-0.014-0.00517.1170.0190.0190.0000.0000.0000.000
80A154LEU00.0070.00620.7710.0250.0250.0000.0000.0000.000
81A155SER00.012-0.01522.5150.0290.0290.0000.0000.0000.000
82A156LEU00.0200.00026.034-0.007-0.0070.0000.0000.0000.000
83A157ASN00.0070.00628.8530.0080.0080.0000.0000.0000.000
84A158GLN00.027-0.00726.403-0.027-0.0270.0000.0000.0000.000
85A159MET00.0030.00627.944-0.014-0.0140.0000.0000.0000.000
86A160PHE00.0610.03322.8550.0010.0010.0000.0000.0000.000
87A161ALA0-0.009-0.00424.448-0.009-0.0090.0000.0000.0000.000
88A162LYS10.7990.88425.9310.2660.2660.0000.0000.0000.000
89A163GLU-1-0.795-0.87029.234-0.174-0.1740.0000.0000.0000.000
90A164LEU0-0.054-0.00923.339-0.003-0.0030.0000.0000.0000.000
91A165PRO00.0490.02926.7590.0090.0090.0000.0000.0000.000
92A166GLY00.0050.02427.670-0.020-0.0200.0000.0000.0000.000
93A167ILE0-0.001-0.00225.2080.0020.0020.0000.0000.0000.000
94A168TYR0-0.063-0.03828.3360.0290.0290.0000.0000.0000.000
95A235LYS10.8670.90319.6870.2260.2260.0000.0000.0000.000
96A236ASP-1-0.853-0.90419.616-0.254-0.2540.0000.0000.0000.000
97A237TYR0-0.019-0.02315.490-0.040-0.0400.0000.0000.0000.000
98A238ASN0-0.026-0.02818.893-0.018-0.0180.0000.0000.0000.000
99A239HIS00.0020.01820.6060.0100.0100.0000.0000.0000.000
100A240GLN00.0660.03124.840-0.010-0.0100.0000.0000.0000.000
101A241PHE0-0.022-0.01923.185-0.012-0.0120.0000.0000.0000.000
102A242ASP-1-0.720-0.81029.143-0.146-0.1460.0000.0000.0000.000
103A243ILE00.0090.00531.320-0.011-0.0110.0000.0000.0000.000
104A244THR0-0.084-0.04633.2950.0050.0050.0000.0000.0000.000
105A245THR0-0.049-0.04533.258-0.003-0.0030.0000.0000.0000.000
106A246ARG10.7770.84030.7600.1780.1780.0000.0000.0000.000
107A247LEU0-0.034-0.02023.3710.0040.0040.0000.0000.0000.000
108A248MET00.0040.00028.036-0.002-0.0020.0000.0000.0000.000
109A249PRO0-0.0100.01925.6820.0100.0100.0000.0000.0000.000
110A250ALA00.0760.02526.149-0.022-0.0220.0000.0000.0000.000
111A251PRO0-0.0040.00121.931-0.008-0.0080.0000.0000.0000.000
112A252ILE0-0.0050.00421.4700.0300.0300.0000.0000.0000.000
113A253ALA00.0340.01120.532-0.038-0.0380.0000.0000.0000.000
114A254SER0-0.010-0.00817.033-0.019-0.0190.0000.0000.0000.000
115A255GLU-1-0.774-0.84915.805-0.534-0.5340.0000.0000.0000.000
116A256LEU00.0110.00616.858-0.057-0.0570.0000.0000.0000.000
117A257THR0-0.0140.00517.0250.0570.0570.0000.0000.0000.000
118A258PHE0-0.013-0.00119.620-0.017-0.0170.0000.0000.0000.000
119A259ILE0-0.001-0.00517.672-0.007-0.0070.0000.0000.0000.000
120A260ALA00.0370.02222.2100.0080.0080.0000.0000.0000.000
121A261PRO00.0340.01625.4530.0010.0010.0000.0000.0000.000
122A262THR00.0040.00426.5160.0120.0120.0000.0000.0000.000
123A263GLN0-0.075-0.04623.6160.0140.0140.0000.0000.0000.000
124A264PRO00.0480.01626.7420.0000.0000.0000.0000.0000.000
125A265VAL00.0850.05823.341-0.020-0.0200.0000.0000.0000.000
126A266SER00.007-0.00222.376-0.025-0.0250.0000.0000.0000.000
127A267THR0-0.029-0.01421.479-0.011-0.0110.0000.0000.0000.000
128A268ILE00.0230.02220.496-0.029-0.0290.0000.0000.0000.000
129A269LEU00.0030.00717.854-0.046-0.0460.0000.0000.0000.000
130A270SER0-0.035-0.00516.694-0.058-0.0580.0000.0000.0000.000
131A271GLN00.0210.00516.738-0.052-0.0520.0000.0000.0000.000
132A272ILE00.0370.03613.638-0.064-0.0640.0000.0000.0000.000
133A273GLU-1-0.704-0.82311.234-0.625-0.6250.0000.0000.0000.000
134A274GLN0-0.029-0.00211.813-0.137-0.1370.0000.0000.0000.000
135A275THR0-0.019-0.03312.850-0.033-0.0330.0000.0000.0000.000
136A276ILE00.0350.0197.596-0.119-0.1190.0000.0000.0000.000
137A277LYS10.8300.9168.1110.0890.0890.0000.0000.0000.000
138A278ARG10.8650.9378.5470.5070.5070.0000.0000.0000.000
139A279ASN0-0.061-0.0289.0800.1710.1710.0000.0000.0000.000
140A280ASP-1-0.760-0.8822.928-7.198-6.0100.124-0.650-0.662-0.007
141A281LYS10.7590.8643.2881.9492.3110.002-0.128-0.2370.000
142A282LYS10.8110.9264.5111.7271.822-0.001-0.014-0.0800.000
143A283LEU00.0000.0056.985-0.571-0.5710.0000.0000.0000.000
144A284ILE0-0.048-0.0328.3400.3010.3010.0000.0000.0000.000
145A285ARG10.8090.92010.7870.6980.6980.0000.0000.0000.000
146A286ILE00.0130.00413.0050.0560.0560.0000.0000.0000.000
147A287VAL00.0190.00115.9850.0340.0340.0000.0000.0000.000
148A288ILE0-0.011-0.01719.7510.0120.0120.0000.0000.0000.000
149A289PRO0-0.010-0.00822.8190.0180.0180.0000.0000.0000.000
150A290SER00.0220.00525.8580.0180.0180.0000.0000.0000.000
151A291LEU00.0000.00324.2270.0020.0020.0000.0000.0000.000
152A292LEU0-0.031-0.01827.6990.0110.0110.0000.0000.0000.000
153A293HIS00.1060.06230.5410.0150.0150.0000.0000.0000.000
154A294PRO00.0600.00832.560-0.004-0.0040.0000.0000.0000.000
155A295ALA0-0.048-0.01034.8270.0040.0040.0000.0000.0000.000
156A296MET0-0.072-0.02729.268-0.010-0.0100.0000.0000.0000.000
157A297TYR00.0270.02025.869-0.012-0.0120.0000.0000.0000.000
158A298PRO00.0320.01331.0090.0100.0100.0000.0000.0000.000
159A299PRO00.0600.01933.631-0.001-0.0010.0000.0000.0000.000
160A300LYS10.8360.89931.5300.1110.1110.0000.0000.0000.000
161A301MET0-0.0180.00127.3050.0010.0010.0000.0000.0000.000
162A302PHE00.001-0.01230.814-0.005-0.0050.0000.0000.0000.000
163A303GLU-1-0.860-0.87533.271-0.079-0.0790.0000.0000.0000.000
164A304SER00.0440.00231.258-0.010-0.0100.0000.0000.0000.000
165A305SER0-0.077-0.07429.437-0.010-0.0100.0000.0000.0000.000
166A306GLU-1-0.846-0.89727.896-0.137-0.1370.0000.0000.0000.000
167A307ILE00.0420.01525.978-0.016-0.0160.0000.0000.0000.000
168A308ILE00.0000.00225.533-0.016-0.0160.0000.0000.0000.000
169A309GLY00.0510.03924.362-0.006-0.0060.0000.0000.0000.000
170A310LEU0-0.040-0.03221.071-0.016-0.0160.0000.0000.0000.000
171A311MET0-0.010-0.00220.749-0.035-0.0350.0000.0000.0000.000
172A312HIS00.0340.01620.207-0.033-0.0330.0000.0000.0000.000
173A313GLY00.0170.00618.482-0.008-0.0080.0000.0000.0000.000
174A314VAL0-0.009-0.02616.354-0.042-0.0420.0000.0000.0000.000
175A315ARG10.8560.92515.3330.1320.1320.0000.0000.0000.000
176A316SER0-0.023-0.01515.098-0.020-0.0200.0000.0000.0000.000
177A317LEU0-0.043-0.02912.041-0.013-0.0130.0000.0000.0000.000
178A318VAL0-0.006-0.00210.583-0.153-0.1530.0000.0000.0000.000
179A319LYS10.8000.88110.7330.2060.2060.0000.0000.0000.000
180A320LYS10.8220.9119.0850.3280.3280.0000.0000.0000.000
181A321TYR0-0.037-0.0475.2910.3030.3030.0000.0000.0000.000
182A322TYR00.0720.0156.898-0.465-0.4650.0000.0000.0000.000
183A323GLU-1-0.887-0.9221.866-12.762-15.0539.658-3.993-3.375-0.049
184A324ARG10.7350.8482.4215.2486.3990.248-0.643-0.7570.003
185A325VAL00.0080.0176.4360.2520.2520.0000.0000.0000.000
186A326VAL0-0.0290.0009.3210.1810.1810.0000.0000.0000.000
187A327LEU0-0.032-0.01512.986-0.019-0.0190.0000.0000.0000.000
188A328PHE00.0410.02516.3770.0420.0420.0000.0000.0000.000
189A329ALA0-0.021-0.01619.946-0.012-0.0120.0000.0000.0000.000
190A330SER00.0400.02522.9340.0040.0040.0000.0000.0000.000
191A331ILE0-0.040-0.02226.6690.0000.0000.0000.0000.0000.000
192A332SER00.0440.03829.8900.0000.0000.0000.0000.0000.000
193A333ILE00.020-0.01132.0360.0040.0040.0000.0000.0000.000
194A334ASP-1-0.843-0.90735.185-0.110-0.1100.0000.0000.0000.000
195A335ILE0-0.049-0.01633.8560.0050.0050.0000.0000.0000.000
196A336ILE0-0.040-0.01432.271-0.003-0.0030.0000.0000.0000.000
197A337THR00.0100.00835.6810.0040.0040.0000.0000.0000.000
198A338PRO00.0670.01835.703-0.003-0.0030.0000.0000.0000.000
199A339PRO00.005-0.00935.168-0.003-0.0030.0000.0000.0000.000
200A340LEU00.0280.02031.003-0.001-0.0010.0000.0000.0000.000
201A341LEU00.0400.02130.651-0.008-0.0080.0000.0000.0000.000
202A342VAL0-0.011-0.00130.402-0.007-0.0070.0000.0000.0000.000
203A343LEU0-0.020-0.01229.419-0.003-0.0030.0000.0000.0000.000
204A344LEU0-0.006-0.01126.741-0.009-0.0090.0000.0000.0000.000
205A345ARG10.7240.79225.5670.1060.1060.0000.0000.0000.000
206A346ASN0-0.054-0.01525.455-0.006-0.0060.0000.0000.0000.000
207A347MET0-0.037-0.00721.9480.0000.0000.0000.0000.0000.000
208A348PHE00.0130.00420.700-0.035-0.0350.0000.0000.0000.000
209A349ASP-1-0.835-0.88017.665-0.243-0.2430.0000.0000.0000.000
210A350SER0-0.043-0.01620.9310.0180.0180.0000.0000.0000.000
211A351VAL00.0020.00123.417-0.021-0.0210.0000.0000.0000.000
212A352ILE00.007-0.00224.4710.0080.0080.0000.0000.0000.000
213A353ASN0-0.042-0.02528.311-0.003-0.0030.0000.0000.0000.000
214A354LEU00.0120.00830.0990.0040.0040.0000.0000.0000.000
215A355GLU-1-0.790-0.90433.369-0.095-0.0950.0000.0000.0000.000
216A356PRO00.0060.01237.1370.0000.0000.0000.0000.0000.000
217A357PHE0-0.049-0.02939.0190.0060.0060.0000.0000.0000.000
218A358ASN0-0.064-0.05041.086-0.001-0.0010.0000.0000.0000.000
219A359GLN0-0.094-0.02938.4030.0070.0070.0000.0000.0000.000
220A360GLU-1-0.877-0.93636.464-0.126-0.1260.0000.0000.0000.000
221A361MET0-0.033-0.01232.466-0.008-0.0080.0000.0000.0000.000
222A362THR0-0.038-0.01234.8840.0030.0030.0000.0000.0000.000
223A363GLU-1-0.842-0.94028.333-0.185-0.1850.0000.0000.0000.000
224A364PHE0-0.041-0.01132.2550.0070.0070.0000.0000.0000.000
225A365LEU0-0.033-0.00926.099-0.006-0.0060.0000.0000.0000.000
226A366GLU-1-0.827-0.87628.193-0.099-0.0990.0000.0000.0000.000
227A367ARG10.8630.93122.8300.1220.1220.0000.0000.0000.000