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

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FMODB ID: 14G6Z

Calculation Name: 4RLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5DL42

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144537.123515
FMO2-HF: Nuclear repulsion 2065320.915924
FMO2-HF: Total energy -79216.207592
FMO2-MP2: Total energy -79451.581295


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:14:ASN)


Summations of interaction energy for fragment #1(A:14:ASN)
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.
-12.358-10.6047.518-4.028-5.2420.035
Interaction energy analysis for fragmet #1(A:14:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.006
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].
3A16LEU00.014-0.0093.7460.4132.071-0.022-0.632-1.0030.004
4A17ILE0-0.0100.0095.9420.0040.0040.0000.0000.0000.000
5A18PRO00.0010.0058.296-0.047-0.0470.0000.0000.0000.000
6A19VAL0-0.044-0.03910.6860.1370.1370.0000.0000.0000.000
7A20GLY00.0320.01613.448-0.020-0.0200.0000.0000.0000.000
8A21ALA0-0.028-0.00616.968-0.047-0.0470.0000.0000.0000.000
9A22ARG10.7970.88017.760-0.181-0.1810.0000.0000.0000.000
10A23ALA00.0040.02821.550-0.034-0.0340.0000.0000.0000.000
11A24GLU-1-0.762-0.83422.6110.1550.1550.0000.0000.0000.000
12A25VAL00.0420.01026.375-0.014-0.0140.0000.0000.0000.000
13A26GLY00.028-0.00228.8890.0090.0090.0000.0000.0000.000
14A27THR00.0090.01130.254-0.002-0.0020.0000.0000.0000.000
15A28THR0-0.0010.00627.715-0.003-0.0030.0000.0000.0000.000
16A29GLY00.0510.02830.884-0.005-0.0050.0000.0000.0000.000
17A30TYR0-0.033-0.02729.5470.0090.0090.0000.0000.0000.000
18A31GLY00.0190.00227.332-0.016-0.0160.0000.0000.0000.000
19A32GLY0-0.0030.00223.8770.0250.0250.0000.0000.0000.000
20A33ALA0-0.022-0.00518.870-0.036-0.0360.0000.0000.0000.000
21A34LEU0-0.0050.00416.8710.0580.0580.0000.0000.0000.000
22A35LEU00.0180.00714.251-0.048-0.0480.0000.0000.0000.000
23A36TRP0-0.014-0.0179.3270.0460.0460.0000.0000.0000.000
24A37GLN0-0.024-0.0198.055-0.506-0.5060.0000.0000.0000.000
25A38ALA0-0.0060.0093.094-0.505-0.1780.084-0.150-0.2600.000
26A39ASN0-0.015-0.0291.940-6.787-7.0317.457-3.243-3.9700.031
27A40PRO0-0.016-0.0075.035-1.727-1.714-0.001-0.003-0.0090.000
28A41TYR00.0100.0105.972-0.766-0.7660.0000.0000.0000.000
29A42VAL00.0100.0255.470-0.746-0.7460.0000.0000.0000.000
30A43GLY00.0520.0247.3320.8180.8180.0000.0000.0000.000
31A44LEU0-0.060-0.0289.422-0.390-0.3900.0000.0000.0000.000
32A45ALA00.0640.04211.6110.1690.1690.0000.0000.0000.000
33A46LEU0-0.004-0.00815.322-0.104-0.1040.0000.0000.0000.000
34A47GLY00.0230.00817.6960.0630.0630.0000.0000.0000.000
35A48TYR0-0.0240.01121.321-0.038-0.0380.0000.0000.0000.000
36A49ASN0-0.098-0.05925.0070.0090.0090.0000.0000.0000.000
37A50GLY00.0600.01627.621-0.018-0.0180.0000.0000.0000.000
38A51GLY0-0.021-0.01331.2320.0140.0140.0000.0000.0000.000
39A52ASP-1-0.898-0.93934.6770.0130.0130.0000.0000.0000.000
40A53ILE0-0.087-0.03834.3020.0100.0100.0000.0000.0000.000
41A54SER00.1170.07838.711-0.007-0.0070.0000.0000.0000.000
42A55TRP0-0.115-0.07234.1050.0080.0080.0000.0000.0000.000
43A56SER0-0.079-0.05939.5440.0020.0020.0000.0000.0000.000
44A57ASP-1-0.872-0.92142.9190.0310.0310.0000.0000.0000.000
45A58ASP-1-0.856-0.92146.4950.0270.0270.0000.0000.0000.000
46A59LEU0-0.025-0.00343.8580.0020.0020.0000.0000.0000.000
47A60SER0-0.078-0.04347.822-0.006-0.0060.0000.0000.0000.000
48A61ILE00.014-0.00845.5720.0020.0020.0000.0000.0000.000
49A62ASN0-0.056-0.03350.062-0.003-0.0030.0000.0000.0000.000
50A63GLY00.0180.00653.005-0.003-0.0030.0000.0000.0000.000
51A64THR00.001-0.00249.925-0.002-0.0020.0000.0000.0000.000
52A65LYS10.9260.98650.251-0.014-0.0140.0000.0000.0000.000
53A66TYR0-0.039-0.02145.003-0.007-0.0070.0000.0000.0000.000
54A67ASP-1-0.849-0.92645.5440.0190.0190.0000.0000.0000.000
55A68MET0-0.088-0.06337.717-0.005-0.0050.0000.0000.0000.000
56A69ASP-1-0.799-0.88341.1060.0210.0210.0000.0000.0000.000
57A70MET0-0.110-0.07034.858-0.007-0.0070.0000.0000.0000.000
58A71ASP-1-0.839-0.91237.1730.0050.0050.0000.0000.0000.000
59A72ASN0-0.073-0.02831.853-0.017-0.0170.0000.0000.0000.000
60A73LYS10.9280.96730.8300.0230.0230.0000.0000.0000.000
61A74LEU0-0.0140.01724.743-0.016-0.0160.0000.0000.0000.000
62A75ALA00.001-0.00523.6520.0260.0260.0000.0000.0000.000
63A76TYR0-0.082-0.08818.913-0.025-0.0250.0000.0000.0000.000
64A77LEU00.0040.00114.3660.0340.0340.0000.0000.0000.000
65A78ASN0-0.026-0.02415.295-0.024-0.0240.0000.0000.0000.000
66A79ALA00.0100.01510.7370.0630.0630.0000.0000.0000.000
67A80GLU-1-0.864-0.93411.4320.3480.3480.0000.0000.0000.000
68A81ILE0-0.025-0.0209.8650.0740.0740.0000.0000.0000.000
69A82ARG10.8810.93411.274-0.700-0.7000.0000.0000.0000.000
70A83PRO0-0.010-0.00511.7250.0690.0690.0000.0000.0000.000
71A84TRP00.0240.00812.9210.0000.0000.0000.0000.0000.000
72A85GLY00.0280.01311.3890.0440.0440.0000.0000.0000.000
73A86ALA0-0.022-0.01410.4390.2360.2360.0000.0000.0000.000
74A87SER0-0.058-0.01612.325-0.067-0.0670.0000.0000.0000.000
75A88THR00.0290.00416.0240.0550.0550.0000.0000.0000.000
76A89ASN00.0480.01918.545-0.015-0.0150.0000.0000.0000.000
77A90PRO00.0370.01419.3540.0280.0280.0000.0000.0000.000
78A91TRP0-0.010-0.01220.3250.0020.0020.0000.0000.0000.000
79A92ALA00.0200.00318.592-0.027-0.0270.0000.0000.0000.000
80A93GLN00.0000.00513.831-0.072-0.0720.0000.0000.0000.000
81A94GLY0-0.005-0.00115.5660.0770.0770.0000.0000.0000.000
82A95LEU0-0.0310.00618.094-0.027-0.0270.0000.0000.0000.000
83A96TYR0-0.077-0.08415.0090.0730.0730.0000.0000.0000.000
84A97VAL00.0070.02015.529-0.024-0.0240.0000.0000.0000.000
85A98ALA00.0210.01215.0230.0020.0020.0000.0000.0000.000
86A99ALA0-0.004-0.01415.038-0.024-0.0240.0000.0000.0000.000
87A100GLY0-0.031-0.02515.159-0.049-0.0490.0000.0000.0000.000
88A101ALA0-0.0160.00117.323-0.003-0.0030.0000.0000.0000.000
89A102ALA0-0.034-0.02220.3590.0190.0190.0000.0000.0000.000
90A103TYR00.0410.06123.189-0.016-0.0160.0000.0000.0000.000
91A104VAL0-0.081-0.06826.0810.0210.0210.0000.0000.0000.000
92A105ASP-1-0.808-0.88228.949-0.058-0.0580.0000.0000.0000.000
93A106ASN00.019-0.00230.4390.0120.0120.0000.0000.0000.000
94A107GLN00.0060.01133.998-0.008-0.0080.0000.0000.0000.000
95A108TYR00.004-0.00132.7630.0030.0030.0000.0000.0000.000
96A109ASP-1-0.798-0.88339.269-0.021-0.0210.0000.0000.0000.000
97A110LEU0-0.061-0.04040.6710.0040.0040.0000.0000.0000.000
98A111THR0-0.001-0.01044.212-0.004-0.0040.0000.0000.0000.000
99A112LYS10.9370.98446.3270.0210.0210.0000.0000.0000.000
100A113ASN00.017-0.00149.363-0.004-0.0040.0000.0000.0000.000
101A114VAL0-0.021-0.01852.7160.0020.0020.0000.0000.0000.000
102A115GLY00.0540.02954.5220.0000.0000.0000.0000.0000.000
103A116THR0-0.004-0.05257.370-0.001-0.0010.0000.0000.0000.000
104A117ASN0-0.110-0.04960.3030.0000.0000.0000.0000.0000.000
105A118ALA00.0040.02855.5010.0000.0000.0000.0000.0000.000
106A119SER0-0.056-0.03655.432-0.003-0.0030.0000.0000.0000.000
107A120VAL00.0350.01850.1840.0010.0010.0000.0000.0000.000
108A121GLU-1-0.851-0.93449.895-0.026-0.0260.0000.0000.0000.000
109A122ILE0-0.037-0.01748.1160.0000.0000.0000.0000.0000.000
110A123ASP-1-0.779-0.87547.723-0.057-0.0570.0000.0000.0000.000
111A124GLY0-0.0010.00148.735-0.001-0.0010.0000.0000.0000.000
112A125ASN00.0130.03850.8420.0030.0030.0000.0000.0000.000
113A126ARG10.8560.92053.1160.0230.0230.0000.0000.0000.000
114A127PHE00.0030.01153.6230.0000.0000.0000.0000.0000.000
115A128ASN0-0.028-0.02956.5380.0030.0030.0000.0000.0000.000
116A129GLY00.0330.02658.406-0.001-0.0010.0000.0000.0000.000
117A130GLY00.0090.01859.4150.0000.0000.0000.0000.0000.000
118A131ALA00.036-0.00362.7950.0020.0020.0000.0000.0000.000
119A132ASN0-0.049-0.01562.9330.0010.0010.0000.0000.0000.000
120A133GLY00.0410.04458.9220.0010.0010.0000.0000.0000.000
121A134VAL0-0.038-0.02455.536-0.001-0.0010.0000.0000.0000.000
122A135SER0-0.061-0.02853.3730.0020.0020.0000.0000.0000.000
123A136ILE00.000-0.00949.285-0.002-0.0020.0000.0000.0000.000
124A137ALA00.0140.00848.3770.0030.0030.0000.0000.0000.000
125A138GLY00.004-0.01045.085-0.004-0.0040.0000.0000.0000.000
126A139ASN0-0.0390.00442.836-0.002-0.0020.0000.0000.0000.000
127A140LEU0-0.017-0.02238.190-0.007-0.0070.0000.0000.0000.000
128A141LYS10.8250.90735.6040.0630.0630.0000.0000.0000.000
129A142TYR0-0.020-0.02532.716-0.009-0.0090.0000.0000.0000.000
130A143ASP-1-0.853-0.94332.908-0.070-0.0700.0000.0000.0000.000
131A144ASN0-0.075-0.06228.511-0.020-0.0200.0000.0000.0000.000
132A145ASP-1-0.852-0.91427.711-0.144-0.1440.0000.0000.0000.000
133A146ILE0-0.078-0.04321.462-0.014-0.0140.0000.0000.0000.000
134A147ALA00.0280.02325.172-0.017-0.0170.0000.0000.0000.000
135A148PRO0-0.027-0.01521.871-0.001-0.0010.0000.0000.0000.000
136A149TYR0-0.049-0.05819.4310.0310.0310.0000.0000.0000.000
137A150ILE0-0.012-0.00419.031-0.050-0.0500.0000.0000.0000.000
138A151GLY00.0500.02419.8650.0330.0330.0000.0000.0000.000
139A152PHE0-0.050-0.02319.711-0.029-0.0290.0000.0000.0000.000
140A153GLY00.0540.02919.8260.0070.0070.0000.0000.0000.000
141A154PHE0-0.063-0.02820.2980.0160.0160.0000.0000.0000.000
142A155ALA00.0530.01117.802-0.005-0.0050.0000.0000.0000.000
143A156PRO0-0.0240.00817.8880.0940.0940.0000.0000.0000.000
144A157LYS10.9150.96413.937-1.091-1.0910.0000.0000.0000.000
145A158PHE00.0230.00618.2750.0010.0010.0000.0000.0000.000
146A159SER00.0040.01019.848-0.006-0.0060.0000.0000.0000.000
147A160LYS10.9220.95315.337-1.198-1.1980.0000.0000.0000.000
148A161ASN00.0140.00418.0840.0820.0820.0000.0000.0000.000
149A162TRP00.0250.01420.629-0.022-0.0220.0000.0000.0000.000
150A163GLY0-0.006-0.00520.8290.0490.0490.0000.0000.0000.000
151A164VAL00.0250.02921.758-0.024-0.0240.0000.0000.0000.000
152A165PHE0-0.041-0.02320.8330.0450.0450.0000.0000.0000.000
153A166GLY00.0340.02122.749-0.020-0.0200.0000.0000.0000.000
154A167GLU-1-0.826-0.85319.7690.0720.0720.0000.0000.0000.000
155A168VAL00.0010.00423.549-0.004-0.0040.0000.0000.0000.000
156A169GLY00.0470.01323.794-0.012-0.0120.0000.0000.0000.000
157A170ALA0-0.043-0.01924.4060.0140.0140.0000.0000.0000.000
158A171TYR00.0390.01622.722-0.016-0.0160.0000.0000.0000.000
159A172TYR0-0.0180.00525.7120.0160.0160.0000.0000.0000.000
160A173SER0-0.022-0.03427.630-0.014-0.0140.0000.0000.0000.000
161A174GLY00.0180.02229.824-0.005-0.0050.0000.0000.0000.000
162A175ASN0-0.070-0.04132.762-0.001-0.0010.0000.0000.0000.000
163A176PRO0-0.0020.02036.261-0.003-0.0030.0000.0000.0000.000
164A177LYS10.9480.97137.3610.0750.0750.0000.0000.0000.000
165A178VAL0-0.015-0.01840.5770.0040.0040.0000.0000.0000.000
166A179SER0-0.0240.00142.915-0.001-0.0010.0000.0000.0000.000
167A180LEU0-0.049-0.02645.0450.0040.0040.0000.0000.0000.000
168A181ALA00.0250.02148.395-0.001-0.0010.0000.0000.0000.000
169A182SER0-0.031-0.04851.6160.0030.0030.0000.0000.0000.000
170A183ASN00.0280.02054.402-0.002-0.0020.0000.0000.0000.000
171A184ASN0-0.027-0.03957.4750.0000.0000.0000.0000.0000.000
172A185ASP-1-0.763-0.84256.296-0.028-0.0280.0000.0000.0000.000
173A186ALA0-0.003-0.01158.607-0.002-0.0020.0000.0000.0000.000
174A187LEU0-0.026-0.00258.5300.0000.0000.0000.0000.0000.000
175A188ILE0-0.023-0.01759.746-0.002-0.0020.0000.0000.0000.000
176A189GLY00.0300.02757.7070.0020.0020.0000.0000.0000.000
177A190SER0-0.039-0.01856.7530.0000.0000.0000.0000.0000.000
178A191ASP-1-0.855-0.93755.094-0.040-0.0400.0000.0000.0000.000
179A192GLY0-0.003-0.00858.502-0.002-0.0020.0000.0000.0000.000
180A193ARG10.7010.84451.4940.0460.0460.0000.0000.0000.000
181A194THR00.0500.02258.4960.0010.0010.0000.0000.0000.000
182A195LEU00.0310.04153.397-0.003-0.0030.0000.0000.0000.000
183A196GLY00.0450.01154.387-0.002-0.0020.0000.0000.0000.000
184A197LYS10.8810.95154.2790.0470.0470.0000.0000.0000.000
185A198THR0-0.034-0.04951.460-0.004-0.0040.0000.0000.0000.000
186A199LEU00.0020.00449.582-0.003-0.0030.0000.0000.0000.000
187A200ASP-1-0.864-0.92449.390-0.054-0.0540.0000.0000.0000.000
188A201ASP-1-0.879-0.94849.373-0.059-0.0590.0000.0000.0000.000
189A202GLN0-0.035-0.02543.554-0.004-0.0040.0000.0000.0000.000
190A203GLU-1-0.852-0.92844.940-0.055-0.0550.0000.0000.0000.000
191A204ARG10.9340.97644.5450.0620.0620.0000.0000.0000.000
192A205LYS10.8800.93643.0290.0610.0610.0000.0000.0000.000
193A206ILE0-0.018-0.00239.563-0.007-0.0070.0000.0000.0000.000
194A207ALA00.0470.02839.540-0.007-0.0070.0000.0000.0000.000
195A208ASN0-0.095-0.06240.036-0.010-0.0100.0000.0000.0000.000
196A209ASP-1-0.916-0.95539.100-0.104-0.1040.0000.0000.0000.000
197A210ASP-1-0.858-0.94934.625-0.156-0.1560.0000.0000.0000.000
198A211LYS10.8740.93834.2270.0840.0840.0000.0000.0000.000
199A212TYR0-0.001-0.02234.2910.0020.0020.0000.0000.0000.000
200A213LYS10.8640.97032.1530.1500.1500.0000.0000.0000.000
201A214TRP0-0.035-0.00225.461-0.015-0.0150.0000.0000.0000.000
202A215LEU00.0180.01929.5670.0110.0110.0000.0000.0000.000
203A216PRO0-0.028-0.01128.750-0.005-0.0050.0000.0000.0000.000
204A217VAL0-0.003-0.01225.5700.0080.0080.0000.0000.0000.000
205A218GLY00.0230.01327.349-0.004-0.0040.0000.0000.0000.000
206A219LYS10.8960.96122.008-0.048-0.0480.0000.0000.0000.000
207A220VAL00.0140.01025.8680.0090.0090.0000.0000.0000.000
208A221GLY00.0420.01225.225-0.014-0.0140.0000.0000.0000.000
209A222VAL0-0.060-0.02524.0890.0210.0210.0000.0000.0000.000
210A223ASN0-0.012-0.01218.789-0.040-0.0400.0000.0000.0000.000
211A224PHE00.003-0.00820.2690.0050.0050.0000.0000.0000.000
212A225TYR0-0.046-0.02715.5130.0260.0260.0000.0000.0000.000
213A226TRP00.0130.00817.2580.0010.0010.0000.0000.0000.000