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: 4JR7N

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005692.987466
FMO2-HF: Nuclear repulsion 1931265.092159
FMO2-HF: Total energy -74427.895308
FMO2-MP2: Total energy -74645.97549


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.
-19.494-16.83621.808-9.46-15.003-0.029
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 : 0.033 / 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].
3A13ARG10.9170.9741.554-1.190-6.88915.040-4.564-4.7760.024
4A14ARG10.9240.9543.353-2.758-3.3170.0680.976-0.4850.002
5A15PRO00.0320.0105.6820.0000.0000.0000.0000.0000.000
6A16SER00.0080.0218.7500.0860.0860.0000.0000.0000.000
7A17THR00.0750.0329.587-0.297-0.2970.0000.0000.0000.000
8A18THR0-0.013-0.03211.9590.0010.0010.0000.0000.0000.000
9A19GLN00.0410.02012.085-0.063-0.0630.0000.0000.0000.000
10A20ASP-1-0.800-0.9117.8682.6922.6920.0000.0000.0000.000
11A21ARG10.8810.95110.821-0.660-0.6600.0000.0000.0000.000
12A22ILE0-0.039-0.01413.108-0.117-0.1170.0000.0000.0000.000
13A23SER0-0.020-0.01410.984-0.005-0.0050.0000.0000.0000.000
14A24THR0-0.007-0.00210.077-0.051-0.0510.0000.0000.0000.000
15A25VAL0-0.010-0.00211.831-0.126-0.1260.0000.0000.0000.000
16A26GLY00.0200.01015.325-0.083-0.0830.0000.0000.0000.000
17A27ILE0-0.018-0.0069.885-0.075-0.0750.0000.0000.0000.000
18A28GLU-1-0.839-0.89513.9590.1250.1250.0000.0000.0000.000
19A29LEU00.012-0.00115.659-0.053-0.0530.0000.0000.0000.000
20A30PHE0-0.060-0.04115.694-0.033-0.0330.0000.0000.0000.000
21A31THR0-0.053-0.03215.221-0.051-0.0510.0000.0000.0000.000
22A32GLU-1-0.961-0.97017.7960.0730.0730.0000.0000.0000.000
23A33GLN0-0.073-0.04220.751-0.022-0.0220.0000.0000.0000.000
24A34GLY00.0280.02121.322-0.017-0.0170.0000.0000.0000.000
25A35PHE00.011-0.00618.0260.0180.0180.0000.0000.0000.000
26A36ASP-1-0.940-0.97321.0000.1320.1320.0000.0000.0000.000
27A37ALA0-0.037-0.01124.5060.0010.0010.0000.0000.0000.000
28A38THR00.0360.05020.9920.0060.0060.0000.0000.0000.000
29A39SER0-0.057-0.02823.6210.0120.0120.0000.0000.0000.000
30A40VAL00.013-0.02922.0190.0190.0190.0000.0000.0000.000
31A41ASP-1-0.846-0.93423.3910.2400.2400.0000.0000.0000.000
32A42GLU-1-0.786-0.88823.9200.1960.1960.0000.0000.0000.000
33A43VAL00.0320.02718.2310.0170.0170.0000.0000.0000.000
34A44ALA0-0.053-0.02220.8150.0360.0360.0000.0000.0000.000
35A45GLU-1-0.930-0.97222.7910.2270.2270.0000.0000.0000.000
36A46ALA00.0150.02121.0120.0050.0050.0000.0000.0000.000
37A47SER0-0.060-0.04018.8760.0530.0530.0000.0000.0000.000
38A48GLY0-0.039-0.02120.5300.0280.0280.0000.0000.0000.000
39A49ILE0-0.102-0.04420.1070.0040.0040.0000.0000.0000.000
40A50ALA00.0410.02323.837-0.021-0.0210.0000.0000.0000.000
41A51ARG10.9940.97824.758-0.185-0.1850.0000.0000.0000.000
42A52ARG10.9420.97425.213-0.219-0.2190.0000.0000.0000.000
43A53THR0-0.015-0.02321.310-0.004-0.0040.0000.0000.0000.000
44A54LEU00.0550.03419.8480.0360.0360.0000.0000.0000.000
45A55PHE0-0.023-0.02020.5140.0260.0260.0000.0000.0000.000
46A56ARG10.8570.95220.912-0.430-0.4300.0000.0000.0000.000
47A57TYR0-0.052-0.03216.542-0.011-0.0110.0000.0000.0000.000
48A58PHE00.0710.04413.6400.0120.0120.0000.0000.0000.000
49A59PRO00.0450.02518.505-0.043-0.0430.0000.0000.0000.000
50A60SER0-0.045-0.03420.251-0.045-0.0450.0000.0000.0000.000
51A61LYS10.8940.92519.656-0.160-0.1600.0000.0000.0000.000
52A62ASN00.018-0.00318.3390.0310.0310.0000.0000.0000.000
53A63ALA00.0010.01616.0170.0080.0080.0000.0000.0000.000
54A64ILE0-0.0070.01014.3570.0900.0900.0000.0000.0000.000
55A65PRO00.0180.00712.3130.1570.1570.0000.0000.0000.000
56A66TRP00.0340.0229.5080.1300.1300.0000.0000.0000.000
57A67GLY0-0.041-0.0059.5190.2770.2770.0000.0000.0000.000
58A68ASP-1-0.909-0.9579.1710.8440.8440.0000.0000.0000.000
59A69PHE00.006-0.0137.8260.1660.1660.0000.0000.0000.000
60A70ASP-1-0.867-0.9339.5950.3370.3370.0000.0000.0000.000
61A71ALA0-0.038-0.0108.455-0.142-0.1420.0000.0000.0000.000
62A72HIS0-0.031-0.0103.507-0.3160.2870.010-0.116-0.4970.000
63A73LEU00.0220.0036.047-0.597-0.5970.0000.0000.0000.000
64A74ALA0-0.035-0.0188.739-0.178-0.1780.0000.0000.0000.000
65A75GLU-1-0.973-0.9872.799-0.9340.4360.334-0.632-1.072-0.009
66A76MET00.0030.0166.225-0.239-0.2390.0000.0000.0000.000
67A77ARG10.8900.9446.9330.0150.0150.0000.0000.0000.000
68A78ALA0-0.029-0.0189.3340.0040.0040.0000.0000.0000.000
69A79GLN0-0.046-0.0345.937-0.106-0.1060.0000.0000.0000.000
70A80LEU0-0.035-0.0318.8340.0340.0340.0000.0000.0000.000
71A81ALA0-0.042-0.01611.3200.0340.0340.0000.0000.0000.000
72A82ALA0-0.045-0.01611.7350.0400.0400.0000.0000.0000.000
73A83GLN0-0.059-0.02310.1030.0700.0700.0000.0000.0000.000
74A84PRO00.0080.00813.9900.0300.0300.0000.0000.0000.000
75A85ASP-1-0.942-0.97217.707-0.180-0.1800.0000.0000.0000.000
76A86ASP-1-0.945-0.97120.019-0.208-0.2080.0000.0000.0000.000
77A87ILE0-0.0040.01015.936-0.007-0.0070.0000.0000.0000.000
78A88PRO00.0040.00119.0580.0110.0110.0000.0000.0000.000
79A89ILE00.0340.00617.676-0.034-0.0340.0000.0000.0000.000
80A90VAL00.0310.01516.330-0.041-0.0410.0000.0000.0000.000
81A91ASP-1-0.843-0.91415.623-0.478-0.4780.0000.0000.0000.000
82A92GLY00.0010.00612.967-0.089-0.0890.0000.0000.0000.000
83A93LEU0-0.069-0.04511.538-0.107-0.1070.0000.0000.0000.000
84A94THR00.0300.00111.505-0.114-0.1140.0000.0000.0000.000
85A95ALA0-0.0170.0019.518-0.167-0.1670.0000.0000.0000.000
86A96ALA00.0270.0116.909-0.335-0.3350.0000.0000.0000.000
87A97LEU00.000-0.0026.650-0.428-0.4280.0000.0000.0000.000
88A98LEU00.0090.0147.756-0.296-0.2960.0000.0000.0000.000
89A99GLN00.0140.0123.669-0.752-0.5010.001-0.026-0.2250.000
90A100PHE0-0.048-0.0242.547-4.902-2.4502.088-1.208-3.332-0.009
91A101ASN0-0.0220.0033.5760.0270.3700.010-0.027-0.326-0.001
92A102ALA00.0100.0263.7290.2390.6410.002-0.125-0.2790.000
93A103PHE00.0100.0012.239-7.618-4.5574.249-3.667-3.642-0.036
94A104PRO0-0.035-0.0233.7640.8651.1900.007-0.058-0.2740.000
95A105ALA00.0850.0396.7900.0080.0080.0000.0000.0000.000
96A106SER0-0.057-0.0359.1980.0990.0990.0000.0000.0000.000
97A107GLU-1-0.967-0.9845.1091.0941.0940.0000.0000.0000.000
98A108GLU-1-0.905-0.9266.652-0.697-0.6970.0000.0000.0000.000
99A109ILE00.0310.0118.2980.1170.1170.0000.0000.0000.000
100A110ASN00.013-0.0137.900-0.050-0.0500.0000.0000.0000.000
101A111HIS00.001-0.0014.7570.5050.614-0.001-0.013-0.0950.000
102A112ARG10.9450.9746.6200.4630.4630.0000.0000.0000.000
103A113LYS10.8570.9209.927-0.093-0.0930.0000.0000.0000.000
104A114ARG10.8560.9296.298-1.605-1.6050.0000.0000.0000.000
105A115MET0-0.018-0.0116.5200.1140.1140.0000.0000.0000.000
106A116GLY00.0620.03910.648-0.017-0.0170.0000.0000.0000.000
107A117LEU0-0.035-0.02113.5420.0080.0080.0000.0000.0000.000
108A118ILE0-0.047-0.03410.186-0.013-0.0130.0000.0000.0000.000
109A119LEU00.009-0.00313.033-0.014-0.0140.0000.0000.0000.000
110A120ARG10.9250.96915.8070.1390.1390.0000.0000.0000.000
111A121VAL00.0080.02718.0650.0030.0030.0000.0000.0000.000
112A122PRO00.0570.02719.8560.0110.0110.0000.0000.0000.000
113A123ALA0-0.015-0.01922.107-0.001-0.0010.0000.0000.0000.000
114A124LEU0-0.042-0.01215.5820.0230.0230.0000.0000.0000.000
115A125GLN00.0420.02017.8550.0180.0180.0000.0000.0000.000
116A126ALA0-0.046-0.01319.111-0.008-0.0080.0000.0000.0000.000
117A127TYR0-0.012-0.02616.3570.0110.0110.0000.0000.0000.000
118A128SER00.0020.01114.8460.0160.0160.0000.0000.0000.000
119A129VAL00.0300.03116.253-0.023-0.0230.0000.0000.0000.000
120A130VAL00.015-0.00718.455-0.018-0.0180.0000.0000.0000.000
121A131MET0-0.0160.00412.9520.0300.0300.0000.0000.0000.000
122A132TYR00.0630.00512.217-0.018-0.0180.0000.0000.0000.000
123A133GLU-1-0.988-0.98614.933-0.039-0.0390.0000.0000.0000.000
124A134GLY00.0010.00815.462-0.024-0.0240.0000.0000.0000.000
125A135TRP00.0620.0158.6610.0500.0500.0000.0000.0000.000
126A136ARG10.9120.96213.2180.0540.0540.0000.0000.0000.000
127A137ASN0-0.024-0.01415.975-0.038-0.0380.0000.0000.0000.000
128A138VAL0-0.0060.02010.8270.0030.0030.0000.0000.0000.000
129A139ILE00.0230.02011.320-0.015-0.0150.0000.0000.0000.000
130A140ALA0-0.016-0.01214.7210.0080.0080.0000.0000.0000.000
131A141GLU-1-0.854-0.93315.901-0.061-0.0610.0000.0000.0000.000
132A142TYR00.0260.01714.3610.0050.0050.0000.0000.0000.000
133A143VAL00.006-0.00816.5110.0110.0110.0000.0000.0000.000
134A144ALA0-0.014-0.01419.0670.0140.0140.0000.0000.0000.000
135A145SER0-0.0150.00619.4320.0200.0200.0000.0000.0000.000
136A146ARG10.8530.93318.0630.2540.2540.0000.0000.0000.000
137A147LEU0-0.039-0.02021.3850.0050.0050.0000.0000.0000.000
138A148GLY0-0.0270.00723.9950.0110.0110.0000.0000.0000.000
139A149THR0-0.072-0.03524.4690.0120.0120.0000.0000.0000.000
140A150SER0-0.0040.00025.0880.0050.0050.0000.0000.0000.000
141A151PRO00.0670.02120.965-0.010-0.0100.0000.0000.0000.000
142A152THR0-0.062-0.03622.698-0.008-0.0080.0000.0000.0000.000
143A153ASP-1-0.802-0.90425.350-0.073-0.0730.0000.0000.0000.000
144A154HIS0-0.008-0.02625.373-0.008-0.0080.0000.0000.0000.000
145A155VAL00.0370.02123.819-0.009-0.0090.0000.0000.0000.000
146A156PRO00.0230.01321.182-0.019-0.0190.0000.0000.0000.000
147A157ARG10.9550.98520.4840.0570.0570.0000.0000.0000.000
148A158THR0-0.037-0.02121.616-0.007-0.0070.0000.0000.0000.000
149A159VAL00.0300.01117.805-0.015-0.0150.0000.0000.0000.000
150A160GLY00.0300.02216.927-0.040-0.0400.0000.0000.0000.000
151A161TYR0-0.041-0.05017.253-0.016-0.0160.0000.0000.0000.000
152A162LEU0-0.0210.00019.372-0.006-0.0060.0000.0000.0000.000
153A163LEU00.0240.01312.637-0.018-0.0180.0000.0000.0000.000
154A164LEU0-0.019-0.01413.597-0.053-0.0530.0000.0000.0000.000
155A165GLY0-0.0040.00115.399-0.007-0.0070.0000.0000.0000.000
156A166VAL00.0060.00814.4250.0010.0010.0000.0000.0000.000
157A167ALA0-0.003-0.00611.183-0.040-0.0400.0000.0000.0000.000
158A168MET0-0.029-0.01712.925-0.023-0.0230.0000.0000.0000.000
159A169SER00.0120.02214.9200.0150.0150.0000.0000.0000.000
160A170ALA00.0310.01913.0010.0170.0170.0000.0000.0000.000
161A171TYR0-0.019-0.0556.559-0.062-0.0620.0000.0000.0000.000
162A172GLU-1-1.006-1.00112.980-0.168-0.1680.0000.0000.0000.000
163A173GLN00.0160.00816.4760.0350.0350.0000.0000.0000.000
164A174TRP00.011-0.0038.397-0.035-0.0350.0000.0000.0000.000
165A175LEU0-0.083-0.05212.7300.0370.0370.0000.0000.0000.000
166A176ASP-1-1.029-1.00615.378-0.164-0.1640.0000.0000.0000.000
167A177ASP-1-0.842-0.90317.628-0.256-0.2560.0000.0000.0000.000
168A178ASP-1-0.946-0.98416.248-0.291-0.2910.0000.0000.0000.000
169A179SER0-0.153-0.07516.561-0.036-0.0360.0000.0000.0000.000
170A180LEU0-0.0220.00216.539-0.019-0.0190.0000.0000.0000.000
171A181GLU-1-0.871-0.93612.968-0.814-0.8140.0000.0000.0000.000
172A182LEU00.005-0.0047.4330.0180.0180.0000.0000.0000.000
173A183ASN00.009-0.0149.8260.0230.0230.0000.0000.0000.000
174A184GLU-1-0.913-0.94811.380-0.465-0.4650.0000.0000.0000.000
175A185LEU0-0.005-0.00114.2530.0600.0600.0000.0000.0000.000
176A186LEU0-0.037-0.0249.1390.0480.0480.0000.0000.0000.000
177A187ALA0-0.0080.00713.5280.0620.0620.0000.0000.0000.000
178A188SER00.0110.00715.3980.0820.0820.0000.0000.0000.000
179A189GLY0-0.014-0.00317.2000.0530.0530.0000.0000.0000.000
180A190MET0-0.039-0.02814.5420.0390.0390.0000.0000.0000.000
181A191GLN0-0.064-0.03017.1330.0140.0140.0000.0000.0000.000
182A192SER00.0220.01220.2010.0440.0440.0000.0000.0000.000
183A193LEU0-0.052-0.02717.8120.0310.0310.0000.0000.0000.000
184A194TYR0-0.109-0.05319.8180.0300.0300.0000.0000.0000.000
185A195ASP-1-0.852-0.92121.577-0.273-0.2730.0000.0000.0000.000
186A196GLY0-0.044-0.01024.5220.0250.0250.0000.0000.0000.000
187A197LEU0-0.005-0.02625.3020.0040.0040.0000.0000.0000.000
188A198SER0-0.048-0.02128.4940.0080.0080.0000.0000.0000.000
189A199SER00.0120.00629.9630.0090.0090.0000.0000.0000.000
190A200LEU00.0220.01827.988-0.001-0.0010.0000.0000.0000.000
191A201GLY0-0.026-0.01630.9640.0100.0100.0000.0000.0000.000
192A202GLU-1-0.933-0.95633.571-0.118-0.1180.0000.0000.0000.000
193A203PRO0-0.093-0.04235.368-0.006-0.0060.0000.0000.0000.000