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: NN5YQ

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2045163.630099
FMO2-HF: Nuclear repulsion 1967610.767947
FMO2-HF: Total energy -77552.862153
FMO2-MP2: Total energy -77782.301261


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.
-7.567-2.6240.646-2.13-3.459-0.003
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 : -0.003 / q_NPA : -0.023
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].
3A19VAL0-0.0110.0022.718-4.761-1.8550.442-1.404-1.944-0.008
4A20GLY0-0.003-0.0225.3910.2750.362-0.001-0.002-0.0840.000
5A21ALA0-0.021-0.0087.6110.1570.1570.0000.0000.0000.000
6A22ARG10.8130.89410.392-0.136-0.1360.0000.0000.0000.000
7A23ALA00.0100.02614.1200.0540.0540.0000.0000.0000.000
8A24GLU-1-0.798-0.88017.4170.1030.1030.0000.0000.0000.000
9A25VAL00.0530.01620.3000.0150.0150.0000.0000.0000.000
10A26GLY0-0.002-0.02023.942-0.010-0.0100.0000.0000.0000.000
11A27THR00.0490.03426.2830.0040.0040.0000.0000.0000.000
12A28THR00.0350.04223.586-0.001-0.0010.0000.0000.0000.000
13A29GLY00.0510.02824.8930.0160.0160.0000.0000.0000.000
14A30TYR0-0.042-0.03322.899-0.011-0.0110.0000.0000.0000.000
15A31GLY00.0250.01819.5500.0190.0190.0000.0000.0000.000
16A32GLY0-0.029-0.01516.122-0.045-0.0450.0000.0000.0000.000
17A33ALA00.0000.00813.1350.0620.0620.0000.0000.0000.000
18A34LEU0-0.014-0.0066.832-0.122-0.1220.0000.0000.0000.000
19A35LEU00.0270.0178.1890.1610.1610.0000.0000.0000.000
20A36TRP0-0.0090.0003.090-5.216-3.4850.205-0.690-1.2460.005
21A37GLN0-0.007-0.0246.3120.1770.1770.0000.0000.0000.000
22A38ALA0-0.0070.0167.226-0.276-0.2760.0000.0000.0000.000
23A39ASN00.030-0.0018.229-0.140-0.1400.0000.0000.0000.000
24A40PRO0-0.004-0.01311.3830.0340.0340.0000.0000.0000.000
25A41TYR0-0.0140.00014.1160.0090.0090.0000.0000.0000.000
26A42VAL0-0.0120.02411.5620.0440.0440.0000.0000.0000.000
27A43GLY00.010-0.0019.922-0.084-0.0840.0000.0000.0000.000
28A44LEU0-0.027-0.0118.8170.0960.0960.0000.0000.0000.000
29A45ALA00.0570.03310.314-0.054-0.0540.0000.0000.0000.000
30A46LEU0-0.0070.00210.2240.0620.0620.0000.0000.0000.000
31A47GLY00.000-0.01112.095-0.034-0.0340.0000.0000.0000.000
32A48TYR0-0.038-0.02614.7920.0250.0250.0000.0000.0000.000
33A49ASN0-0.136-0.08417.720-0.039-0.0390.0000.0000.0000.000
34A50GLY00.0740.02021.1410.0140.0140.0000.0000.0000.000
35A51GLY0-0.018-0.01223.997-0.013-0.0130.0000.0000.0000.000
36A52ASP-1-0.860-0.92627.2010.1020.1020.0000.0000.0000.000
37A53ILE0-0.103-0.03628.575-0.007-0.0070.0000.0000.0000.000
38A54SER00.0590.02432.6710.0020.0020.0000.0000.0000.000
39A55TRP0-0.108-0.05232.233-0.003-0.0030.0000.0000.0000.000
40A56THR00.0050.01238.5340.0010.0010.0000.0000.0000.000
41A57ASP-1-0.998-1.01241.9240.0180.0180.0000.0000.0000.000
42A65LYS10.8460.93547.824-0.019-0.0190.0000.0000.0000.000
43A66TYR00.006-0.01843.6610.0010.0010.0000.0000.0000.000
44A67ASP-1-0.831-0.89542.0960.0300.0300.0000.0000.0000.000
45A68LEU0-0.044-0.02835.9440.0010.0010.0000.0000.0000.000
46A69ASP-1-0.822-0.91035.9840.0480.0480.0000.0000.0000.000
47A70MET0-0.070-0.02130.4540.0020.0020.0000.0000.0000.000
48A71ASP-1-0.850-0.89530.6830.0790.0790.0000.0000.0000.000
49A72ASN0-0.009-0.03026.2410.0050.0050.0000.0000.0000.000
50A73ASN00.0220.02223.8000.0110.0110.0000.0000.0000.000
51A74ASN00.0020.00122.1720.0020.0020.0000.0000.0000.000
52A75VAL0-0.0010.00716.4950.0060.0060.0000.0000.0000.000
53A76TYR0-0.030-0.02415.848-0.008-0.0080.0000.0000.0000.000
54A77LEU0-0.010-0.00811.8450.0820.0820.0000.0000.0000.000
55A78ASN00.0230.01014.715-0.024-0.0240.0000.0000.0000.000
56A79ALA0-0.016-0.01313.6490.0560.0560.0000.0000.0000.000
57A80GLU-1-0.886-0.95213.9570.0190.0190.0000.0000.0000.000
58A81ILE0-0.011-0.01614.845-0.029-0.0290.0000.0000.0000.000
59A82ARG10.9140.97715.5260.1350.1350.0000.0000.0000.000
60A83PRO00.0340.00918.564-0.021-0.0210.0000.0000.0000.000
61A84TRP00.0130.00021.428-0.009-0.0090.0000.0000.0000.000
62A85GLY00.0200.00417.467-0.020-0.0200.0000.0000.0000.000
63A86ALA0-0.032-0.02717.655-0.048-0.0480.0000.0000.0000.000
64A87SER0-0.0290.00519.050-0.002-0.0020.0000.0000.0000.000
65A88THR00.004-0.00721.217-0.019-0.0190.0000.0000.0000.000
66A89ASN00.0250.01123.1790.0010.0010.0000.0000.0000.000
67A90PRO00.026-0.01121.9990.0030.0030.0000.0000.0000.000
68A91TRP00.0280.02522.6800.0020.0020.0000.0000.0000.000
69A92ALA00.0160.00324.5540.0070.0070.0000.0000.0000.000
70A93GLN0-0.037-0.02316.7940.0060.0060.0000.0000.0000.000
71A94GLY00.0140.01219.541-0.009-0.0090.0000.0000.0000.000
72A95LEU0-0.046-0.01920.5930.0140.0140.0000.0000.0000.000
73A96TYR0-0.081-0.08818.541-0.030-0.0300.0000.0000.0000.000
74A97ILE00.0220.02620.2430.0040.0040.0000.0000.0000.000
75A98ALA0-0.016-0.00218.6650.0080.0080.0000.0000.0000.000
76A99ALA00.0220.01218.485-0.014-0.0140.0000.0000.0000.000
77A100GLY0-0.0040.00017.9070.0480.0480.0000.0000.0000.000
78A101ALA0-0.0190.00418.603-0.042-0.0420.0000.0000.0000.000
79A102ALA00.0090.00219.1440.0430.0430.0000.0000.0000.000
80A103TYR0-0.0250.01920.877-0.017-0.0170.0000.0000.0000.000
81A104LEU0-0.029-0.03922.7610.0000.0000.0000.0000.0000.000
82A105ASP-1-0.910-0.96325.4800.1380.1380.0000.0000.0000.000
83A106ASN0-0.002-0.01626.543-0.002-0.0020.0000.0000.0000.000
84A107ASP-1-0.835-0.90329.8890.0980.0980.0000.0000.0000.000
85A108TYR0-0.054-0.04329.4760.0000.0000.0000.0000.0000.000
86A109ASP-1-0.826-0.91635.3870.0640.0640.0000.0000.0000.000
87A110LEU0-0.032-0.01538.751-0.004-0.0040.0000.0000.0000.000
88A111ALA0-0.013-0.01241.4660.0010.0010.0000.0000.0000.000
89A112LYS10.8750.95044.784-0.032-0.0320.0000.0000.0000.000
90A113ARG10.9420.96847.741-0.026-0.0260.0000.0000.0000.000
91A114ILE0-0.080-0.04650.692-0.002-0.0020.0000.0000.0000.000
92A115GLY00.0250.01154.0360.0010.0010.0000.0000.0000.000
93A116ASN00.034-0.01156.8730.0000.0000.0000.0000.0000.000
94A117GLY0-0.0250.00060.162-0.001-0.0010.0000.0000.0000.000
95A118ASP-1-0.918-0.93455.5140.0150.0150.0000.0000.0000.000
96A119THR0-0.043-0.04155.3730.0010.0010.0000.0000.0000.000
97A120LEU0-0.025-0.01950.8600.0000.0000.0000.0000.0000.000
98A121SER0-0.009-0.01450.4500.0000.0000.0000.0000.0000.000
99A122ILE00.014-0.00249.2350.0010.0010.0000.0000.0000.000
100A123ASP-1-0.794-0.87348.5740.0320.0320.0000.0000.0000.000
101A124GLY0-0.036-0.01849.556-0.001-0.0010.0000.0000.0000.000
102A125LYS10.8770.94751.414-0.029-0.0290.0000.0000.0000.000
103A126ASN00.0000.00353.5820.0010.0010.0000.0000.0000.000
104A127TYR0-0.026-0.02954.4300.0000.0000.0000.0000.0000.000
105A128GLN00.0090.00656.772-0.001-0.0010.0000.0000.0000.000
106A129GLN00.0460.02458.7960.0000.0000.0000.0000.0000.000
107A130ALA0-0.048-0.00659.861-0.001-0.0010.0000.0000.0000.000
108A131VAL0-0.025-0.03461.749-0.001-0.0010.0000.0000.0000.000
109A132PRO0-0.001-0.01162.1960.0010.0010.0000.0000.0000.000
110A133GLY0-0.047-0.00463.1320.0000.0000.0000.0000.0000.000
111A134GLN0-0.0090.00758.6850.0000.0000.0000.0000.0000.000
112A135GLU-1-0.902-0.95352.7200.0280.0280.0000.0000.0000.000
113A136GLY00.0800.05555.3650.0000.0000.0000.0000.0000.000
114A137GLY00.010-0.01251.344-0.001-0.0010.0000.0000.0000.000
115A138VAL0-0.031-0.01347.5960.0000.0000.0000.0000.0000.000
116A139ARG10.9240.97541.625-0.050-0.0500.0000.0000.0000.000
117A140GLY0-0.009-0.00943.4180.0000.0000.0000.0000.0000.000
118A141LYS10.9681.00337.338-0.074-0.0740.0000.0000.0000.000
119A142MET0-0.033-0.02236.3970.0000.0000.0000.0000.0000.000
120A143SER0-0.0010.00134.279-0.001-0.0010.0000.0000.0000.000
121A144TYR0-0.026-0.01730.548-0.002-0.0020.0000.0000.0000.000
122A145LYS10.9490.98027.943-0.170-0.1700.0000.0000.0000.000
123A146ASN0-0.080-0.04827.567-0.009-0.0090.0000.0000.0000.000
124A147ASP-1-0.888-0.94525.9240.2150.2150.0000.0000.0000.000
125A148ILE0-0.040-0.03322.3370.0300.0300.0000.0000.0000.000
126A149ALA00.0100.02324.256-0.021-0.0210.0000.0000.0000.000
127A150PRO0-0.025-0.01623.3940.0210.0210.0000.0000.0000.000
128A151TYR0-0.039-0.04120.623-0.020-0.0200.0000.0000.0000.000
129A152LEU0-0.037-0.02722.8330.0090.0090.0000.0000.0000.000
130A153GLY00.0290.02023.075-0.009-0.0090.0000.0000.0000.000
131A154PHE0-0.042-0.02823.356-0.001-0.0010.0000.0000.0000.000
132A155GLY00.0560.03621.8930.0020.0020.0000.0000.0000.000
133A156PHE0-0.086-0.04022.681-0.014-0.0140.0000.0000.0000.000
134A157ALA00.0440.01217.7210.0050.0050.0000.0000.0000.000
135A158PRO0-0.0280.01118.590-0.036-0.0360.0000.0000.0000.000
136A159LYS10.9410.96413.6070.4470.4470.0000.0000.0000.000
137A160ILE0-0.0070.00318.5790.0150.0150.0000.0000.0000.000
138A161SER0-0.008-0.01717.780-0.008-0.0080.0000.0000.0000.000
139A162LYS10.9340.95413.9450.4110.4110.0000.0000.0000.000
140A163ASN0-0.0140.00112.2780.0100.0100.0000.0000.0000.000
141A164TRP00.0820.05413.755-0.022-0.0220.0000.0000.0000.000
142A165GLY00.007-0.01116.310-0.010-0.0100.0000.0000.0000.000
143A166VAL00.0010.02717.8060.0070.0070.0000.0000.0000.000
144A167PHE0-0.035-0.02718.211-0.019-0.0190.0000.0000.0000.000
145A168GLY00.0310.02920.8530.0080.0080.0000.0000.0000.000
146A169GLU-1-0.835-0.87519.8080.0930.0930.0000.0000.0000.000
147A170VAL00.000-0.00723.6840.0030.0030.0000.0000.0000.000
148A171GLY00.0280.01125.696-0.001-0.0010.0000.0000.0000.000
149A172ALA0-0.035-0.00726.508-0.006-0.0060.0000.0000.0000.000
150A173TYR00.0310.01721.9060.0210.0210.0000.0000.0000.000
151A174TYR0-0.053-0.01127.291-0.009-0.0090.0000.0000.0000.000
152A175THR0-0.037-0.04228.9130.0110.0110.0000.0000.0000.000
153A176GLY00.0120.01830.9850.0020.0020.0000.0000.0000.000
154A177ASN0-0.053-0.02834.5470.0030.0030.0000.0000.0000.000
155A178PRO00.0110.03335.2070.0040.0040.0000.0000.0000.000
156A179LYS10.9140.94836.571-0.089-0.0890.0000.0000.0000.000
157A180VAL00.0360.01038.6320.0000.0000.0000.0000.0000.000
158A181GLU-1-0.999-0.98641.4090.0640.0640.0000.0000.0000.000
159A182LEU00.0230.00243.632-0.001-0.0010.0000.0000.0000.000
160A183THR0-0.044-0.00246.328-0.001-0.0010.0000.0000.0000.000
161A184GLN00.007-0.02849.214-0.002-0.0020.0000.0000.0000.000
162A185TYR00.0140.02148.4880.0000.0000.0000.0000.0000.000
163A186ASN0-0.029-0.04354.439-0.002-0.0020.0000.0000.0000.000
164A187LEU00.0280.01653.153-0.001-0.0010.0000.0000.0000.000
165A188ALA0-0.010-0.00957.7890.0010.0010.0000.0000.0000.000
166A189PRO00.0190.01559.3000.0000.0000.0000.0000.0000.000
167A190VAL0-0.0020.01459.055-0.001-0.0010.0000.0000.0000.000
168A191THR0-0.039-0.03561.7540.0000.0000.0000.0000.0000.000
169A192GLY00.0620.01763.9820.0000.0000.0000.0000.0000.000
170A193ASN0-0.050-0.00457.3700.0000.0000.0000.0000.0000.000
171A194PRO0-0.013-0.01460.7430.0000.0000.0000.0000.0000.000
172A195THR0-0.023-0.00756.2200.0010.0010.0000.0000.0000.000
173A196SER00.0630.04158.7200.0000.0000.0000.0000.0000.000
174A197ALA00.0720.02754.9110.0010.0010.0000.0000.0000.000
175A198GLN00.010-0.00352.9340.0010.0010.0000.0000.0000.000
176A199ASP-1-0.859-0.92253.9220.0320.0320.0000.0000.0000.000
177A200ALA0-0.083-0.03252.8600.0010.0010.0000.0000.0000.000
178A201VAL00.014-0.00449.5100.0010.0010.0000.0000.0000.000
179A202ASP-1-0.883-0.94449.1250.0420.0420.0000.0000.0000.000
180A203LYS10.7970.89449.747-0.031-0.0310.0000.0000.0000.000
181A204GLU-1-0.861-0.93645.5790.0400.0400.0000.0000.0000.000
182A205ALA00.009-0.00644.9470.0030.0030.0000.0000.0000.000
183A206ASN0-0.026-0.02944.6620.0060.0060.0000.0000.0000.000
184A207GLU-1-0.936-0.95245.3290.0410.0410.0000.0000.0000.000
185A208ILE00.0410.00739.7190.0030.0030.0000.0000.0000.000
186A209ARG10.8720.94140.643-0.053-0.0530.0000.0000.0000.000
187A210ASN0-0.038-0.01541.8140.0050.0050.0000.0000.0000.000
188A211ASP-1-0.870-0.92842.8690.0500.0500.0000.0000.0000.000
189A212ASN00.0260.02439.4040.0020.0020.0000.0000.0000.000
190A213LYS10.8570.92638.069-0.044-0.0440.0000.0000.0000.000
191A214TYR0-0.023-0.01136.8080.0020.0020.0000.0000.0000.000
192A215GLU-1-0.891-0.94035.0270.0860.0860.0000.0000.0000.000
193A216TRP0-0.032-0.02228.0810.0130.0130.0000.0000.0000.000
194A217MET00.0260.02727.583-0.005-0.0050.0000.0000.0000.000
195A218PRO0-0.034-0.00629.2430.0080.0080.0000.0000.0000.000
196A219VAL0-0.002-0.01524.7110.0020.0020.0000.0000.0000.000
197A220GLY00.011-0.00926.682-0.005-0.0050.0000.0000.0000.000
198A221LYS10.8870.96919.951-0.130-0.1300.0000.0000.0000.000
199A222VAL00.004-0.00723.049-0.010-0.0100.0000.0000.0000.000
200A223GLY00.0390.02120.1740.0140.0140.0000.0000.0000.000
201A224VAL0-0.067-0.03117.171-0.018-0.0180.0000.0000.0000.000
202A225ASN00.007-0.00213.6760.0400.0400.0000.0000.0000.000
203A226PHE0-0.006-0.01010.774-0.016-0.0160.0000.0000.0000.000
204A227TYR0-0.021-0.0179.2370.0010.0010.0000.0000.0000.000
205A228TRP0-0.032-0.0273.6750.4670.6860.000-0.034-0.1850.000