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: JQJ59

Calculation Name: 4RL9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RL9

Chain ID: A

ChEMBL ID:

UniProt ID: A6XB80

Base Structure: X-ray

Registration Date: 2023-09-24

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046380.985295
FMO2-HF: Nuclear repulsion 1968826.883723
FMO2-HF: Total energy -77554.101571
FMO2-MP2: Total energy -77783.491331


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:17:ILE)


Summations of interaction energy for fragment #1(A:17:ILE)
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.
-8.529-3.4540.719-2.319-3.4750.003
Interaction energy analysis for fragmet #1(A:17:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.029
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].
3A19VAL00.0050.0032.890-4.040-1.2890.216-1.304-1.664-0.005
4A20GLY0-0.012-0.0225.4910.3260.3260.0000.0000.0000.000
5A21ALA0-0.024-0.0077.8220.1460.1460.0000.0000.0000.000
6A22ARG10.8160.90610.663-0.146-0.1460.0000.0000.0000.000
7A23ALA00.0070.02314.3880.0490.0490.0000.0000.0000.000
8A24GLU-1-0.760-0.85317.7020.1250.1250.0000.0000.0000.000
9A25VAL00.0500.01920.5830.0130.0130.0000.0000.0000.000
10A26GLY00.000-0.01724.154-0.008-0.0080.0000.0000.0000.000
11A27THR00.0470.03226.2590.0020.0020.0000.0000.0000.000
12A28THR00.0200.04223.508-0.003-0.0030.0000.0000.0000.000
13A29GLY00.0530.03224.8650.0150.0150.0000.0000.0000.000
14A30TYR0-0.023-0.02922.882-0.010-0.0100.0000.0000.0000.000
15A31GLY00.0230.01619.5320.0170.0170.0000.0000.0000.000
16A32GLY0-0.033-0.01816.203-0.042-0.0420.0000.0000.0000.000
17A33ALA00.0010.01013.0650.0570.0570.0000.0000.0000.000
18A34LEU0-0.017-0.0036.996-0.116-0.1160.0000.0000.0000.000
19A35LEU00.0310.0178.2860.1650.1650.0000.0000.0000.000
20A36TRP0-0.010-0.0012.897-6.599-4.4400.503-0.996-1.6650.008
21A37GLN0-0.019-0.0306.3790.1040.1040.0000.0000.0000.000
22A38ALA0-0.0070.0177.275-0.241-0.2410.0000.0000.0000.000
23A39ASN00.0300.0038.279-0.160-0.1600.0000.0000.0000.000
24A40PRO0-0.001-0.01111.4250.0420.0420.0000.0000.0000.000
25A41TYR0-0.0010.00814.1630.0050.0050.0000.0000.0000.000
26A42VAL0-0.0120.01812.1040.0380.0380.0000.0000.0000.000
27A43GLY00.0180.0019.994-0.063-0.0630.0000.0000.0000.000
28A44LEU0-0.045-0.0148.7400.0780.0780.0000.0000.0000.000
29A45ALA00.0670.03010.314-0.048-0.0480.0000.0000.0000.000
30A46LEU0-0.0110.0009.9330.0510.0510.0000.0000.0000.000
31A47GLY00.009-0.00812.066-0.038-0.0380.0000.0000.0000.000
32A48TYR0-0.035-0.02414.7620.0210.0210.0000.0000.0000.000
33A49ASN0-0.115-0.07517.693-0.035-0.0350.0000.0000.0000.000
34A50GLY00.0790.02821.1150.0130.0130.0000.0000.0000.000
35A51GLY00.003-0.00223.974-0.012-0.0120.0000.0000.0000.000
36A52ASP-1-0.888-0.94027.1800.0980.0980.0000.0000.0000.000
37A53ILE0-0.098-0.03828.549-0.006-0.0060.0000.0000.0000.000
38A54SER00.053-0.00332.6510.0030.0030.0000.0000.0000.000
39A55TRP0-0.124-0.06231.978-0.003-0.0030.0000.0000.0000.000
40A56THR0-0.010-0.01538.5190.0010.0010.0000.0000.0000.000
41A57ASP-1-1.002-1.01042.0460.0190.0190.0000.0000.0000.000
42A65LYS10.7860.90747.977-0.021-0.0210.0000.0000.0000.000
43A66TYR0-0.044-0.04943.7030.0020.0020.0000.0000.0000.000
44A67ASP-1-0.826-0.88042.1180.0310.0310.0000.0000.0000.000
45A68LEU0-0.028-0.02236.1120.0020.0020.0000.0000.0000.000
46A69ASP-1-0.812-0.88135.9110.0470.0470.0000.0000.0000.000
47A70MET0-0.080-0.02230.1880.0030.0030.0000.0000.0000.000
48A71ASP-1-0.841-0.89130.6650.0790.0790.0000.0000.0000.000
49A72ASN0-0.026-0.03526.2360.0060.0060.0000.0000.0000.000
50A73ASN00.0070.01023.8560.0110.0110.0000.0000.0000.000
51A74ASN0-0.036-0.01722.3000.0040.0040.0000.0000.0000.000
52A75VAL00.0050.01316.3240.0050.0050.0000.0000.0000.000
53A76TYR0-0.031-0.03616.195-0.003-0.0030.0000.0000.0000.000
54A77LEU0-0.010-0.01011.7210.0810.0810.0000.0000.0000.000
55A78ASN00.0210.00814.715-0.030-0.0300.0000.0000.0000.000
56A79ALA0-0.013-0.00513.7220.0620.0620.0000.0000.0000.000
57A80GLU-1-0.831-0.91214.0410.0200.0200.0000.0000.0000.000
58A81ILE0-0.020-0.02314.917-0.019-0.0190.0000.0000.0000.000
59A82ARG10.9030.96215.3080.0520.0520.0000.0000.0000.000
60A83PRO00.0390.01318.629-0.018-0.0180.0000.0000.0000.000
61A84TRP00.004-0.00621.489-0.009-0.0090.0000.0000.0000.000
62A85GLY00.0420.01317.522-0.019-0.0190.0000.0000.0000.000
63A86ALA0-0.043-0.02017.702-0.044-0.0440.0000.0000.0000.000
64A87SER0-0.038-0.00219.091-0.004-0.0040.0000.0000.0000.000
65A88THR00.0230.00121.187-0.017-0.0170.0000.0000.0000.000
66A89ASN00.0030.00423.1300.0000.0000.0000.0000.0000.000
67A90PRO00.035-0.00521.9390.0040.0040.0000.0000.0000.000
68A91TRP00.0190.01822.7380.0030.0030.0000.0000.0000.000
69A92ALA00.0270.00724.6240.0080.0080.0000.0000.0000.000
70A93GLN0-0.036-0.02216.609-0.003-0.0030.0000.0000.0000.000
71A94GLY00.0030.00619.601-0.005-0.0050.0000.0000.0000.000
72A95LEU0-0.045-0.02020.7030.0140.0140.0000.0000.0000.000
73A96TYR0-0.090-0.07618.582-0.025-0.0250.0000.0000.0000.000
74A97ILE00.0160.02320.3350.0010.0010.0000.0000.0000.000
75A98ALA0-0.016-0.00218.7440.0140.0140.0000.0000.0000.000
76A99ALA00.0240.01318.561-0.017-0.0170.0000.0000.0000.000
77A100GLY00.0030.00117.9820.0520.0520.0000.0000.0000.000
78A101ALA0-0.0220.00218.599-0.043-0.0430.0000.0000.0000.000
79A102ALA00.0130.00419.1110.0430.0430.0000.0000.0000.000
80A103TYR0-0.065-0.00820.826-0.015-0.0150.0000.0000.0000.000
81A104LEU0-0.026-0.03622.7260.0000.0000.0000.0000.0000.000
82A105ASP-1-0.815-0.92225.4450.1450.1450.0000.0000.0000.000
83A106ASN0-0.023-0.02726.242-0.001-0.0010.0000.0000.0000.000
84A107ASP-1-0.726-0.81129.8570.0920.0920.0000.0000.0000.000
85A108TYR0-0.060-0.04629.4180.0010.0010.0000.0000.0000.000
86A109ASP-1-0.749-0.86135.3570.0620.0620.0000.0000.0000.000
87A110LEU0-0.031-0.01338.723-0.003-0.0030.0000.0000.0000.000
88A111ALA0-0.005-0.00841.4390.0010.0010.0000.0000.0000.000
89A112LYS10.8760.94744.758-0.034-0.0340.0000.0000.0000.000
90A113ARG10.8580.90347.715-0.027-0.0270.0000.0000.0000.000
91A114ILE0-0.052-0.02950.667-0.001-0.0010.0000.0000.0000.000
92A115GLY00.0410.01254.0120.0010.0010.0000.0000.0000.000
93A116ASN0-0.015-0.02756.8500.0010.0010.0000.0000.0000.000
94A117GLY0-0.032-0.00460.140-0.001-0.0010.0000.0000.0000.000
95A118ASP-1-0.823-0.89954.2330.0180.0180.0000.0000.0000.000
96A119THR0-0.037-0.02755.4770.0010.0010.0000.0000.0000.000
97A120LEU0-0.003-0.00150.9360.0000.0000.0000.0000.0000.000
98A121SER00.002-0.00450.4200.0000.0000.0000.0000.0000.000
99A122ILE00.0190.00349.2810.0010.0010.0000.0000.0000.000
100A123ASP-1-0.743-0.82548.5320.0330.0330.0000.0000.0000.000
101A124GLY0-0.041-0.01949.523-0.001-0.0010.0000.0000.0000.000
102A125LYS10.8280.91351.382-0.032-0.0320.0000.0000.0000.000
103A126ASN00.001-0.00153.5510.0020.0020.0000.0000.0000.000
104A127TYR0-0.020-0.03154.1900.0000.0000.0000.0000.0000.000
105A128GLN00.0250.01956.744-0.001-0.0010.0000.0000.0000.000
106A129GLN00.0270.00058.8230.0000.0000.0000.0000.0000.000
107A130ALA0-0.045-0.00659.834-0.001-0.0010.0000.0000.0000.000
108A131VAL0-0.011-0.02761.730-0.001-0.0010.0000.0000.0000.000
109A132PRO00.002-0.00662.1710.0010.0010.0000.0000.0000.000
110A133GLY0-0.041-0.00663.1090.0000.0000.0000.0000.0000.000
111A134GLN00.0100.02158.5260.0000.0000.0000.0000.0000.000
112A135GLU-1-0.802-0.87652.5410.0270.0270.0000.0000.0000.000
113A136GLY00.0340.01855.3390.0010.0010.0000.0000.0000.000
114A137GLY00.015-0.00751.315-0.001-0.0010.0000.0000.0000.000
115A138VAL0-0.045-0.01947.2030.0000.0000.0000.0000.0000.000
116A139ARG10.8680.91641.330-0.052-0.0520.0000.0000.0000.000
117A140GLY0-0.019-0.01143.3890.0000.0000.0000.0000.0000.000
118A141LYS10.8750.94336.932-0.078-0.0780.0000.0000.0000.000
119A142MET0-0.038-0.01836.6230.0000.0000.0000.0000.0000.000
120A143SER0-0.002-0.03334.2560.0000.0000.0000.0000.0000.000
121A144TYR0-0.030-0.02530.546-0.003-0.0030.0000.0000.0000.000
122A145LYS10.8900.94327.535-0.171-0.1710.0000.0000.0000.000
123A146ASN0-0.091-0.05327.573-0.008-0.0080.0000.0000.0000.000
124A147ASP-1-0.846-0.91725.8810.2040.2040.0000.0000.0000.000
125A148ILE0-0.050-0.03221.9980.0300.0300.0000.0000.0000.000
126A149ALA00.0350.03224.232-0.021-0.0210.0000.0000.0000.000
127A150PRO0-0.022-0.01923.3930.0210.0210.0000.0000.0000.000
128A151TYR0-0.037-0.04620.757-0.021-0.0210.0000.0000.0000.000
129A152LEU0-0.048-0.02822.8700.0100.0100.0000.0000.0000.000
130A153GLY00.0430.02323.167-0.010-0.0100.0000.0000.0000.000
131A154PHE0-0.043-0.03023.4330.0010.0010.0000.0000.0000.000
132A155GLY00.0610.03421.9010.0010.0010.0000.0000.0000.000
133A156PHE0-0.085-0.04122.795-0.013-0.0130.0000.0000.0000.000
134A157ALA00.0290.00917.8730.0050.0050.0000.0000.0000.000
135A158PRO0-0.0300.00818.707-0.030-0.0300.0000.0000.0000.000
136A159LYS10.9080.94913.4350.3310.3310.0000.0000.0000.000
137A160ILE0-0.0100.00018.6650.0130.0130.0000.0000.0000.000
138A161SER0-0.011-0.01717.984-0.008-0.0080.0000.0000.0000.000
139A162LYS10.9470.96313.8980.3680.3680.0000.0000.0000.000
140A163ASN0-0.021-0.00812.1470.0040.0040.0000.0000.0000.000
141A164TRP00.0790.05413.882-0.018-0.0180.0000.0000.0000.000
142A165GLY00.009-0.01016.441-0.008-0.0080.0000.0000.0000.000
143A166VAL0-0.0050.02117.9530.0060.0060.0000.0000.0000.000
144A167PHE0-0.044-0.02818.599-0.017-0.0170.0000.0000.0000.000
145A168GLY00.0330.02921.0480.0060.0060.0000.0000.0000.000
146A169GLU-1-0.839-0.88319.6080.1210.1210.0000.0000.0000.000
147A170VAL00.009-0.00423.7160.0010.0010.0000.0000.0000.000
148A171GLY00.0350.01725.7190.0010.0010.0000.0000.0000.000
149A172ALA0-0.032-0.00726.504-0.008-0.0080.0000.0000.0000.000
150A173TYR00.0350.01822.0360.0220.0220.0000.0000.0000.000
151A174TYR0-0.090-0.05127.265-0.009-0.0090.0000.0000.0000.000
152A175THR0-0.025-0.02528.8910.0110.0110.0000.0000.0000.000
153A176GLY00.0080.01730.9450.0010.0010.0000.0000.0000.000
154A177ASN0-0.071-0.05034.5080.0040.0040.0000.0000.0000.000
155A178PRO00.0170.03435.1030.0040.0040.0000.0000.0000.000
156A179LYS10.9100.94736.534-0.091-0.0910.0000.0000.0000.000
157A180VAL00.0370.01238.5980.0000.0000.0000.0000.0000.000
158A181GLU-1-0.979-0.96941.3540.0640.0640.0000.0000.0000.000
159A182LEU00.028-0.00343.6000.0000.0000.0000.0000.0000.000
160A183THR0-0.0200.01746.296-0.002-0.0020.0000.0000.0000.000
161A184GLN0-0.011-0.03649.184-0.002-0.0020.0000.0000.0000.000
162A185TYR0-0.018-0.00548.7110.0000.0000.0000.0000.0000.000
163A186ASN0-0.025-0.02054.411-0.001-0.0010.0000.0000.0000.000
164A187LEU00.0410.02053.119-0.001-0.0010.0000.0000.0000.000
165A188ALA0-0.011-0.00957.7600.0010.0010.0000.0000.0000.000
166A189PRO00.0120.01759.2690.0000.0000.0000.0000.0000.000
167A190VAL00.0090.01359.209-0.001-0.0010.0000.0000.0000.000
168A191THR0-0.001-0.01861.7240.0000.0000.0000.0000.0000.000
169A192GLY00.004-0.01063.9520.0000.0000.0000.0000.0000.000
170A193ASN0-0.059-0.01257.3940.0010.0010.0000.0000.0000.000
171A194PRO0-0.017-0.01760.7930.0000.0000.0000.0000.0000.000
172A195THR0-0.0230.00556.0910.0010.0010.0000.0000.0000.000
173A196SER00.005-0.02058.6880.0000.0000.0000.0000.0000.000
174A197ALA00.0670.02054.9920.0010.0010.0000.0000.0000.000
175A198GLN00.0000.00152.8330.0010.0010.0000.0000.0000.000
176A199ASP-1-0.818-0.87853.8880.0320.0320.0000.0000.0000.000
177A200ALA0-0.050-0.01552.8810.0010.0010.0000.0000.0000.000
178A201VAL00.0140.00249.4180.0010.0010.0000.0000.0000.000
179A202ASP-1-0.870-0.93349.0900.0430.0430.0000.0000.0000.000
180A203LYS10.7280.83949.568-0.035-0.0350.0000.0000.0000.000
181A204GLU-1-0.878-0.95145.6140.0410.0410.0000.0000.0000.000
182A205ALA00.0280.00444.9060.0030.0030.0000.0000.0000.000
183A206ASN0-0.003-0.01044.6250.0060.0060.0000.0000.0000.000
184A207GLU-1-0.848-0.89945.3810.0430.0430.0000.0000.0000.000
185A208ILE00.0280.00139.7040.0030.0030.0000.0000.0000.000
186A209ARG10.8530.92740.606-0.054-0.0540.0000.0000.0000.000
187A210ASN0-0.069-0.03641.7750.0040.0040.0000.0000.0000.000
188A211ASP-1-0.823-0.88642.6330.0540.0540.0000.0000.0000.000
189A212ASN00.0520.03039.4800.0010.0010.0000.0000.0000.000
190A213LYS10.8000.88538.069-0.048-0.0480.0000.0000.0000.000
191A214TYR0-0.043-0.02136.8080.0020.0020.0000.0000.0000.000
192A215GLU-1-0.847-0.89634.9410.0920.0920.0000.0000.0000.000
193A216TRP0-0.032-0.01927.8510.0130.0130.0000.0000.0000.000
194A217MET0-0.0080.01628.549-0.004-0.0040.0000.0000.0000.000
195A218PRO0-0.028-0.01029.2070.0080.0080.0000.0000.0000.000
196A219VAL00.007-0.00824.8670.0010.0010.0000.0000.0000.000
197A220GLY00.0140.00226.652-0.005-0.0050.0000.0000.0000.000
198A221LYS10.8450.93119.595-0.143-0.1430.0000.0000.0000.000
199A222VAL00.004-0.00923.262-0.008-0.0080.0000.0000.0000.000
200A223GLY00.0360.01820.4340.0120.0120.0000.0000.0000.000
201A224VAL0-0.066-0.03117.645-0.016-0.0160.0000.0000.0000.000
202A225ASN00.002-0.00213.8830.0340.0340.0000.0000.0000.000
203A226PHE00.007-0.00510.779-0.015-0.0150.0000.0000.0000.000
204A227TYR0-0.016-0.0179.3820.0050.0050.0000.0000.0000.000
205A228TRP0-0.017-0.0113.8900.3860.5510.000-0.019-0.1460.000