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: 5JZMZ

Calculation Name: 2RAE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RAE

Chain ID: A

ChEMBL ID:

UniProt ID: Q0S3N9

Base Structure: X-ray

Registration Date: 2023-09-20

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005776.313386
FMO2-HF: Nuclear repulsion 1931347.33579
FMO2-HF: Total energy -74428.977596
FMO2-MP2: Total energy -74647.030138


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:11:ILE)


Summations of interaction energy for fragment #1(A:11: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.
-22.434-15.14717.356-8.709-15.933-0.048
Interaction energy analysis for fragmet #1(A:11:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / 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].
3A13ARG10.9420.9831.894-3.601-4.1107.512-2.973-4.0290.007
4A14ARG10.8040.8823.138-2.299-2.8850.0750.957-0.4460.001
5A15PRO00.0270.0036.1480.0070.0070.0000.0000.0000.000
6A16SER00.0060.0239.5400.1000.1000.0000.0000.0000.000
7A17THR00.0330.01310.251-0.311-0.3110.0000.0000.0000.000
8A18THR0-0.014-0.03512.710-0.014-0.0140.0000.0000.0000.000
9A19GLN00.0040.00312.405-0.168-0.1680.0000.0000.0000.000
10A20ASP-1-0.774-0.8948.7952.2342.2340.0000.0000.0000.000
11A21ARG10.8630.93710.909-0.588-0.5880.0000.0000.0000.000
12A22ILE0-0.044-0.01713.472-0.112-0.1120.0000.0000.0000.000
13A23SER0-0.023-0.01010.9510.0070.0070.0000.0000.0000.000
14A24THR0-0.001-0.00610.135-0.039-0.0390.0000.0000.0000.000
15A25VAL0-0.008-0.00411.820-0.124-0.1240.0000.0000.0000.000
16A26GLY00.0170.01115.320-0.080-0.0800.0000.0000.0000.000
17A27ILE0-0.018-0.0069.798-0.070-0.0700.0000.0000.0000.000
18A28GLU-1-0.818-0.87313.9500.1110.1110.0000.0000.0000.000
19A29LEU0-0.011-0.01515.650-0.053-0.0530.0000.0000.0000.000
20A30PHE0-0.044-0.03615.716-0.032-0.0320.0000.0000.0000.000
21A31THR0-0.046-0.03015.224-0.050-0.0500.0000.0000.0000.000
22A32GLU-1-0.966-0.97017.7890.0590.0590.0000.0000.0000.000
23A33GLN0-0.094-0.05720.743-0.024-0.0240.0000.0000.0000.000
24A34GLY00.0320.02321.315-0.016-0.0160.0000.0000.0000.000
25A35PHE00.011-0.01218.2150.0200.0200.0000.0000.0000.000
26A36ASP-1-0.937-0.97920.9930.1350.1350.0000.0000.0000.000
27A37ALA0-0.033-0.01224.4990.0010.0010.0000.0000.0000.000
28A38THR00.0260.04720.9180.0060.0060.0000.0000.0000.000
29A39SER0-0.075-0.07023.6120.0120.0120.0000.0000.0000.000
30A40VAL00.011-0.02922.0940.0190.0190.0000.0000.0000.000
31A41ASP-1-0.828-0.91123.3810.2390.2390.0000.0000.0000.000
32A42GLU-1-0.705-0.80123.9370.1910.1910.0000.0000.0000.000
33A43VAL00.0320.02718.1790.0150.0150.0000.0000.0000.000
34A44ALA0-0.054-0.01620.8040.0340.0340.0000.0000.0000.000
35A45GLU-1-0.919-0.96422.7800.2170.2170.0000.0000.0000.000
36A46ALA00.0130.02121.0250.0030.0030.0000.0000.0000.000
37A47SER0-0.057-0.03918.9970.0490.0490.0000.0000.0000.000
38A48GLY0-0.030-0.01720.5190.0290.0290.0000.0000.0000.000
39A49ILE0-0.101-0.04520.1510.0050.0050.0000.0000.0000.000
40A50ALA00.0380.02324.138-0.020-0.0200.0000.0000.0000.000
41A51ARG10.9580.94124.750-0.186-0.1860.0000.0000.0000.000
42A52ARG10.9450.97225.213-0.217-0.2170.0000.0000.0000.000
43A53THR0-0.005-0.01421.461-0.003-0.0030.0000.0000.0000.000
44A54LEU00.0440.02619.7730.0350.0350.0000.0000.0000.000
45A55PHE0-0.031-0.01720.4770.0280.0280.0000.0000.0000.000
46A56ARG10.8400.93620.307-0.447-0.4470.0000.0000.0000.000
47A57TYR0-0.039-0.01816.577-0.018-0.0180.0000.0000.0000.000
48A58PHE00.0580.04113.5200.0210.0210.0000.0000.0000.000
49A59PRO00.0350.01918.547-0.045-0.0450.0000.0000.0000.000
50A60SER0-0.035-0.03320.250-0.035-0.0350.0000.0000.0000.000
51A61LYS10.8820.92819.648-0.155-0.1550.0000.0000.0000.000
52A62ASN00.007-0.00818.3310.0340.0340.0000.0000.0000.000
53A63ALA00.0090.01516.0220.0140.0140.0000.0000.0000.000
54A64ILE0-0.0020.01714.3570.0960.0960.0000.0000.0000.000
55A65PRO00.0180.00812.2970.1550.1550.0000.0000.0000.000
56A66TRP00.0340.0279.5700.1390.1390.0000.0000.0000.000
57A67GLY0-0.036-0.0069.5260.3050.3050.0000.0000.0000.000
58A68ASP-1-0.871-0.9389.1470.8920.8920.0000.0000.0000.000
59A69PHE00.017-0.0087.5570.1980.1980.0000.0000.0000.000
60A70ASP-1-0.870-0.9369.2470.4510.4510.0000.0000.0000.000
61A71ALA0-0.0210.0008.418-0.127-0.1270.0000.0000.0000.000
62A72HIS0-0.034-0.0142.806-0.4410.6200.102-0.221-0.9420.000
63A73LEU00.003-0.0045.734-0.554-0.5540.0000.0000.0000.000
64A74ALA0-0.017-0.0098.410-0.197-0.1970.0000.0000.0000.000
65A75GLU-1-0.860-0.9122.9910.1991.4890.163-0.625-0.828-0.007
66A76MET0-0.0030.0125.767-0.267-0.2670.0000.0000.0000.000
67A77ARG10.8420.8836.588-0.110-0.1100.0000.0000.0000.000
68A78ALA0-0.035-0.0219.197-0.021-0.0210.0000.0000.0000.000
69A79GLN0-0.036-0.0345.777-0.124-0.1240.0000.0000.0000.000
70A80LEU0-0.036-0.0338.8900.0070.0070.0000.0000.0000.000
71A81ALA0-0.041-0.01611.2230.0210.0210.0000.0000.0000.000
72A82ALA0-0.045-0.01611.8870.0310.0310.0000.0000.0000.000
73A83GLN0-0.066-0.02210.2560.0190.0190.0000.0000.0000.000
74A84PRO00.0020.00614.1510.0270.0270.0000.0000.0000.000
75A85ASP-1-0.927-0.96117.844-0.157-0.1570.0000.0000.0000.000
76A86ASP-1-0.940-0.97320.099-0.185-0.1850.0000.0000.0000.000
77A87ILE00.0140.01716.173-0.010-0.0100.0000.0000.0000.000
78A88PRO00.0140.01819.2550.0130.0130.0000.0000.0000.000
79A89ILE00.017-0.00317.611-0.035-0.0350.0000.0000.0000.000
80A90VAL00.0360.01416.176-0.040-0.0400.0000.0000.0000.000
81A91ASP-1-0.817-0.90115.553-0.449-0.4490.0000.0000.0000.000
82A92GLY0-0.010-0.00212.961-0.084-0.0840.0000.0000.0000.000
83A93LEU0-0.048-0.03411.423-0.096-0.0960.0000.0000.0000.000
84A94THR00.0280.00011.255-0.111-0.1110.0000.0000.0000.000
85A95ALA0-0.0110.0039.759-0.181-0.1810.0000.0000.0000.000
86A96ALA00.0170.0066.747-0.339-0.3390.0000.0000.0000.000
87A97LEU0-0.006-0.0026.323-0.426-0.4260.0000.0000.0000.000
88A98LEU00.0220.0097.745-0.309-0.3090.0000.0000.0000.000
89A99GLN00.0080.0144.012-0.604-0.428-0.001-0.021-0.1550.000
90A100PHE0-0.050-0.0172.282-5.357-4.1435.299-1.912-4.601-0.010
91A101ASN0-0.0260.0023.2970.2030.4620.0310.201-0.491-0.002
92A102ALA00.0190.0283.4460.2920.7370.004-0.139-0.3100.000
93A103PHE00.0070.0012.240-8.511-5.1064.164-3.851-3.718-0.037
94A104PRO0-0.039-0.0243.7560.8671.1840.007-0.056-0.2680.000
95A105ALA00.0660.0276.798-0.013-0.0130.0000.0000.0000.000
96A106SER0-0.045-0.0299.1580.0830.0830.0000.0000.0000.000
97A107GLU-1-0.907-0.9505.2020.7010.7010.0000.0000.0000.000
98A108GLU-1-0.892-0.9276.648-0.632-0.6320.0000.0000.0000.000
99A109ILE00.0700.0318.2980.1160.1160.0000.0000.0000.000
100A110ASN0-0.043-0.0417.655-0.008-0.0080.0000.0000.0000.000
101A111HIS0-0.032-0.0244.2580.3520.5670.000-0.069-0.1450.000
102A112ARG10.8620.9276.6160.5210.5210.0000.0000.0000.000
103A113LYS10.8690.9209.925-0.033-0.0330.0000.0000.0000.000
104A114ARG10.8340.9166.202-1.651-1.6510.0000.0000.0000.000
105A115MET00.001-0.0046.7680.0900.0900.0000.0000.0000.000
106A116GLY00.0560.03510.646-0.012-0.0120.0000.0000.0000.000
107A117LEU0-0.039-0.02413.3300.0130.0130.0000.0000.0000.000
108A118ILE0-0.047-0.03310.189-0.008-0.0080.0000.0000.0000.000
109A119LEU00.009-0.00312.970-0.012-0.0120.0000.0000.0000.000
110A120ARG10.8180.89815.8060.1380.1380.0000.0000.0000.000
111A121VAL00.0130.03018.0570.0030.0030.0000.0000.0000.000
112A122PRO00.0540.02519.8530.0130.0130.0000.0000.0000.000
113A123ALA0-0.018-0.01922.1050.0010.0010.0000.0000.0000.000
114A124LEU0-0.029-0.00715.6880.0250.0250.0000.0000.0000.000
115A125GLN00.0490.02617.8550.0180.0180.0000.0000.0000.000
116A126ALA0-0.040-0.01119.109-0.006-0.0060.0000.0000.0000.000
117A127TYR0-0.015-0.02316.7070.0100.0100.0000.0000.0000.000
118A128SER0-0.0110.00214.9740.0090.0090.0000.0000.0000.000
119A129VAL00.0200.01316.255-0.017-0.0170.0000.0000.0000.000
120A130VAL00.001-0.00818.464-0.017-0.0170.0000.0000.0000.000
121A131MET0-0.0040.01012.9450.0360.0360.0000.0000.0000.000
122A132TYR00.0630.00812.429-0.027-0.0270.0000.0000.0000.000
123A133GLU-1-0.889-0.91914.936-0.047-0.0470.0000.0000.0000.000
124A134GLY0-0.0040.00115.096-0.023-0.0230.0000.0000.0000.000
125A135TRP00.0620.0178.2210.0400.0400.0000.0000.0000.000
126A136ARG10.8270.90412.6340.0060.0060.0000.0000.0000.000
127A137ASN0-0.023-0.01915.353-0.042-0.0420.0000.0000.0000.000
128A138VAL0-0.0030.02310.364-0.001-0.0010.0000.0000.0000.000
129A139ILE00.0160.01810.881-0.020-0.0200.0000.0000.0000.000
130A140ALA0-0.015-0.01214.2430.0040.0040.0000.0000.0000.000
131A141GLU-1-0.799-0.87015.4610.0080.0080.0000.0000.0000.000
132A142TYR00.0280.02214.0770.0120.0120.0000.0000.0000.000
133A143VAL00.009-0.00816.2050.0050.0050.0000.0000.0000.000
134A144ALA0-0.014-0.01018.7470.0100.0100.0000.0000.0000.000
135A145SER0-0.027-0.00219.1820.0170.0170.0000.0000.0000.000
136A146ARG10.8110.90417.6600.2300.2300.0000.0000.0000.000
137A147LEU0-0.044-0.01821.2100.0030.0030.0000.0000.0000.000
138A148GLY0-0.0260.00723.7680.0090.0090.0000.0000.0000.000
139A149THR0-0.083-0.06124.2810.0100.0100.0000.0000.0000.000
140A150SER0-0.054-0.06624.7490.0080.0080.0000.0000.0000.000
141A151PRO00.0720.02320.527-0.010-0.0100.0000.0000.0000.000
142A152THR0-0.032-0.01522.239-0.003-0.0030.0000.0000.0000.000
143A153ASP-1-0.768-0.82924.831-0.057-0.0570.0000.0000.0000.000
144A154HIS00.011-0.01324.873-0.003-0.0030.0000.0000.0000.000
145A155VAL00.0370.02523.443-0.008-0.0080.0000.0000.0000.000
146A156PRO00.0250.01420.643-0.018-0.0180.0000.0000.0000.000
147A157ARG10.9230.96319.9900.0350.0350.0000.0000.0000.000
148A158THR0-0.038-0.03121.055-0.007-0.0070.0000.0000.0000.000
149A159VAL00.0240.00917.378-0.015-0.0150.0000.0000.0000.000
150A160GLY00.0290.02116.392-0.039-0.0390.0000.0000.0000.000
151A161TYR0-0.026-0.03916.711-0.016-0.0160.0000.0000.0000.000
152A162LEU0-0.026-0.00119.097-0.008-0.0080.0000.0000.0000.000
153A163LEU00.0150.00911.847-0.021-0.0210.0000.0000.0000.000
154A164LEU0-0.008-0.00913.844-0.058-0.0580.0000.0000.0000.000
155A165GLY0-0.006-0.00215.314-0.011-0.0110.0000.0000.0000.000
156A166VAL00.0010.00414.461-0.002-0.0020.0000.0000.0000.000
157A167ALA0-0.005-0.00411.222-0.044-0.0440.0000.0000.0000.000
158A168MET0-0.017-0.01012.917-0.023-0.0230.0000.0000.0000.000
159A169SER0-0.0030.01514.9140.0100.0100.0000.0000.0000.000
160A170ALA00.0260.01413.0560.0160.0160.0000.0000.0000.000
161A171TYR00.005-0.0306.487-0.070-0.0700.0000.0000.0000.000
162A172GLU-1-0.886-0.92212.985-0.153-0.1530.0000.0000.0000.000
163A173GLN0-0.020-0.00216.4800.0410.0410.0000.0000.0000.000
164A174TRP00.015-0.0058.455-0.052-0.0520.0000.0000.0000.000
165A175LEU0-0.074-0.04512.4490.0310.0310.0000.0000.0000.000
166A176ASP-1-0.998-0.98215.380-0.172-0.1720.0000.0000.0000.000
167A177ASP-1-0.842-0.90117.608-0.277-0.2770.0000.0000.0000.000
168A178ASP-1-0.893-0.95516.233-0.318-0.3180.0000.0000.0000.000
169A179SER0-0.151-0.07716.565-0.037-0.0370.0000.0000.0000.000
170A180LEU0-0.0190.00316.666-0.019-0.0190.0000.0000.0000.000
171A181GLU-1-0.880-0.94512.528-0.924-0.9240.0000.0000.0000.000
172A182LEU00.002-0.0017.5660.0210.0210.0000.0000.0000.000
173A183ASN00.003-0.0209.7870.0590.0590.0000.0000.0000.000
174A184GLU-1-0.907-0.94311.260-0.476-0.4760.0000.0000.0000.000
175A185LEU00.0060.00814.2620.0680.0680.0000.0000.0000.000
176A186LEU0-0.035-0.0249.1470.0530.0530.0000.0000.0000.000
177A187ALA0-0.0150.00413.4370.0700.0700.0000.0000.0000.000
178A188SER0-0.002-0.00515.1540.0880.0880.0000.0000.0000.000
179A189GLY00.0000.00517.1060.0560.0560.0000.0000.0000.000
180A190MET0-0.045-0.03414.6180.0490.0490.0000.0000.0000.000
181A191GLN0-0.062-0.03716.9490.0160.0160.0000.0000.0000.000
182A192SER00.0310.01720.0350.0450.0450.0000.0000.0000.000
183A193LEU0-0.081-0.04317.3030.0350.0350.0000.0000.0000.000
184A194TYR0-0.095-0.04519.3420.0330.0330.0000.0000.0000.000
185A195ASP-1-0.857-0.91821.371-0.269-0.2690.0000.0000.0000.000
186A196GLY0-0.038-0.00324.2390.0250.0250.0000.0000.0000.000
187A197LEU0-0.009-0.03024.9950.0030.0030.0000.0000.0000.000
188A198SER0-0.047-0.01928.2860.0070.0070.0000.0000.0000.000
189A199SER00.0280.01429.6120.0080.0080.0000.0000.0000.000
190A200LEU00.0060.00927.960-0.001-0.0010.0000.0000.0000.000
191A201GLY0-0.023-0.01530.9750.0100.0100.0000.0000.0000.000
192A202GLU-1-0.930-0.95833.545-0.115-0.1150.0000.0000.0000.000
193A203PRO0-0.096-0.03935.249-0.007-0.0070.0000.0000.0000.000