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: 2N7RR

Calculation Name: 2CW5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CW5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLF5

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2632960.618775
FMO2-HF: Nuclear repulsion 2547698.430828
FMO2-HF: Total energy -85262.187947
FMO2-MP2: Total energy -85518.048733


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-6.0280.7669.777-4.285-12.288-0.037
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.024
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].
3A3PRO0-0.037-0.0083.877-0.6621.631-0.007-1.009-1.2770.003
4A4VAL00.0460.0185.7940.0200.0200.0000.0000.0000.000
5A5TYR00.0060.0028.809-0.160-0.1600.0000.0000.0000.000
6A6PHE00.006-0.01012.302-0.009-0.0090.0000.0000.0000.000
7A7LEU00.0210.01114.758-0.056-0.0560.0000.0000.0000.000
8A8SER0-0.022-0.00418.5090.0110.0110.0000.0000.0000.000
9A9ASP-1-0.760-0.87521.3800.1760.1760.0000.0000.0000.000
10A10PHE0-0.018-0.00622.049-0.011-0.0110.0000.0000.0000.000
11A11GLY00.0520.03824.296-0.016-0.0160.0000.0000.0000.000
12A12LEU0-0.048-0.06020.1480.0080.0080.0000.0000.0000.000
13A13GLU-1-0.966-0.97422.6770.0840.0840.0000.0000.0000.000
14A14ASP-1-0.865-0.90523.7490.1170.1170.0000.0000.0000.000
15A15PRO00.0490.00422.4100.0130.0130.0000.0000.0000.000
16A16TYR0-0.0070.00118.5770.0190.0190.0000.0000.0000.000
17A17VAL0-0.011-0.01318.0520.0300.0300.0000.0000.0000.000
18A18ALA00.0100.00017.0400.0290.0290.0000.0000.0000.000
19A19VAL00.0090.00616.323-0.002-0.0020.0000.0000.0000.000
20A20VAL0-0.0090.00213.5230.0020.0020.0000.0000.0000.000
21A21LYS10.8420.89012.413-0.231-0.2310.0000.0000.0000.000
22A22ALA00.0040.01011.5610.0030.0030.0000.0000.0000.000
23A23VAL00.0190.00911.247-0.050-0.0500.0000.0000.0000.000
24A24LEU0-0.033-0.0238.414-0.063-0.0630.0000.0000.0000.000
25A25ALA0-0.0090.0016.8400.0360.0360.0000.0000.0000.000
26A26GLU-1-0.889-0.9008.572-0.324-0.3240.0000.0000.0000.000
27A27ARG10.7750.8564.0380.2710.4370.000-0.026-0.1400.000
28A28ALA0-0.0610.0045.7760.1060.1060.0000.0000.0000.000
29A29PRO0-0.029-0.0382.422-0.4330.2360.542-0.228-0.9830.001
30A30GLY00.0690.0172.605-3.552-2.3791.194-0.808-1.559-0.009
31A31PRO0-0.009-0.0013.0980.7442.0242.881-0.984-3.177-0.004
32A32ALA0-0.0010.0083.776-0.384-2.1430.0772.008-0.3260.000
33A33VAL00.002-0.0056.8430.1290.1290.0000.0000.0000.000
34A34VAL0-0.013-0.0029.693-0.181-0.1810.0000.0000.0000.000
35A35ASP-1-0.779-0.85412.5660.3580.3580.0000.0000.0000.000
36A36LEU0-0.036-0.01415.631-0.029-0.0290.0000.0000.0000.000
37A37ALA00.017-0.01517.766-0.038-0.0380.0000.0000.0000.000
38A38HIS10.8040.87017.063-0.280-0.2800.0000.0000.0000.000
39A39ALA00.0210.02022.266-0.012-0.0120.0000.0000.0000.000
40A40LEU0-0.0160.01223.401-0.010-0.0100.0000.0000.0000.000
41A41PRO00.013-0.00326.727-0.004-0.0040.0000.0000.0000.000
42A42PRO00.0440.01429.1380.0090.0090.0000.0000.0000.000
43A43GLN0-0.052-0.05028.233-0.014-0.0140.0000.0000.0000.000
44A44ASP-1-0.844-0.90229.6790.1440.1440.0000.0000.0000.000
45A45LEU00.007-0.01726.4040.0110.0110.0000.0000.0000.000
46A46ARG10.8170.90127.445-0.118-0.1180.0000.0000.0000.000
47A47ARG10.9100.96526.173-0.162-0.1620.0000.0000.0000.000
48A48ALA0-0.002-0.00623.9560.0080.0080.0000.0000.0000.000
49A49ALA00.0250.01423.7590.0200.0200.0000.0000.0000.000
50A50TYR00.016-0.00524.2990.0160.0160.0000.0000.0000.000
51A51ALA0-0.0080.00722.6310.0040.0040.0000.0000.0000.000
52A52LEU0-0.049-0.02318.3880.0180.0180.0000.0000.0000.000
53A53PHE0-0.040-0.01720.4600.0200.0200.0000.0000.0000.000
54A54GLU-1-0.940-0.98822.6390.1870.1870.0000.0000.0000.000
55A55ALA0-0.010-0.00817.861-0.005-0.0050.0000.0000.0000.000
56A56LEU0-0.0080.00316.0570.0060.0060.0000.0000.0000.000
57A57PRO0-0.024-0.01117.0360.0290.0290.0000.0000.0000.000
58A58TYR0-0.028-0.01117.406-0.018-0.0180.0000.0000.0000.000
59A59LEU0-0.054-0.00612.755-0.003-0.0030.0000.0000.0000.000
60A60PRO00.0010.0009.205-0.002-0.0020.0000.0000.0000.000
61A61GLU-1-0.833-0.93511.1710.5540.5540.0000.0000.0000.000
62A62GLY0-0.031-0.0188.5730.1010.1010.0000.0000.0000.000
63A63ALA0-0.068-0.0258.0270.3530.3530.0000.0000.0000.000
64A64VAL00.0270.0147.031-0.066-0.0660.0000.0000.0000.000
65A65VAL0-0.012-0.0169.622-0.071-0.0710.0000.0000.0000.000
66A66LEU0-0.0060.00812.699-0.032-0.0320.0000.0000.0000.000
67A67ALA00.003-0.00714.454-0.043-0.0430.0000.0000.0000.000
68A68VAL0-0.023-0.02417.932-0.013-0.0130.0000.0000.0000.000
69A69VAL00.0200.02420.576-0.019-0.0190.0000.0000.0000.000
70A70ASP-1-0.777-0.89124.1620.1960.1960.0000.0000.0000.000
71A71PRO00.0710.02526.027-0.009-0.0090.0000.0000.0000.000
72A72GLY0-0.0370.01028.730-0.011-0.0110.0000.0000.0000.000
73A73VAL00.0220.01728.1840.0010.0010.0000.0000.0000.000
74A74GLY0-0.018-0.00429.429-0.008-0.0080.0000.0000.0000.000
75A75THR0-0.060-0.04230.582-0.008-0.0080.0000.0000.0000.000
76A76ALA0-0.008-0.00930.1760.0070.0070.0000.0000.0000.000
77A77ARG10.8660.90424.086-0.192-0.1920.0000.0000.0000.000
78A78ARG10.8500.93524.162-0.218-0.2180.0000.0000.0000.000
79A79ALA00.0130.02820.3580.0060.0060.0000.0000.0000.000
80A80VAL00.003-0.01219.414-0.014-0.0140.0000.0000.0000.000
81A81ALA00.0330.01914.2050.0320.0320.0000.0000.0000.000
82A82ALA0-0.008-0.00915.639-0.050-0.0500.0000.0000.0000.000
83A83LEU00.007-0.00811.8080.0870.0870.0000.0000.0000.000
84A84GLY00.0540.02114.281-0.106-0.1060.0000.0000.0000.000
85A85ARG10.7870.91213.686-0.309-0.3090.0000.0000.0000.000
86A86TRP0-0.009-0.01012.1120.1050.1050.0000.0000.0000.000
87A87THR0-0.004-0.00110.078-0.023-0.0230.0000.0000.0000.000
88A88TYR0-0.046-0.04012.194-0.012-0.0120.0000.0000.0000.000
89A89VAL00.0180.01712.262-0.012-0.0120.0000.0000.0000.000
90A90GLY00.0430.00815.193-0.008-0.0080.0000.0000.0000.000
91A91PRO0-0.055-0.01818.709-0.008-0.0080.0000.0000.0000.000
92A92ASP-1-0.777-0.87022.3830.2510.2510.0000.0000.0000.000
93A93ASN0-0.007-0.02224.112-0.009-0.0090.0000.0000.0000.000
94A94GLY00.0540.03125.482-0.013-0.0130.0000.0000.0000.000
95A95LEU0-0.0010.02721.132-0.003-0.0030.0000.0000.0000.000
96A96PHE00.0290.00317.3420.0050.0050.0000.0000.0000.000
97A97THR0-0.016-0.02422.0700.0050.0050.0000.0000.0000.000
98A98LEU00.0280.00325.072-0.002-0.0020.0000.0000.0000.000
99A99ALA00.0360.02619.497-0.003-0.0030.0000.0000.0000.000
100A100TRP0-0.007-0.01818.516-0.011-0.0110.0000.0000.0000.000
101A101LEU0-0.053-0.01022.312-0.010-0.0100.0000.0000.0000.000
102A102LEU0-0.042-0.01321.634-0.011-0.0110.0000.0000.0000.000
103A103ASP-1-0.803-0.87816.8430.5380.5380.0000.0000.0000.000
104A104PRO0-0.0040.00520.0310.0220.0220.0000.0000.0000.000
105A105PRO0-0.023-0.00618.7400.0220.0220.0000.0000.0000.000
106A106ARG10.9240.95815.403-0.547-0.5470.0000.0000.0000.000
107A107ARG10.7720.85615.159-0.462-0.4620.0000.0000.0000.000
108A108ALA00.0180.01318.0970.0440.0440.0000.0000.0000.000
109A109PHE00.0300.01415.738-0.008-0.0080.0000.0000.0000.000
110A110LEU0-0.039-0.00819.0630.0140.0140.0000.0000.0000.000
111A111LEU0-0.030-0.03015.8700.0040.0040.0000.0000.0000.000
112A112GLU-1-0.904-0.96419.3840.1310.1310.0000.0000.0000.000
113A113PRO0-0.063-0.01820.4800.0050.0050.0000.0000.0000.000
114A114PRO00.0190.01019.638-0.012-0.0120.0000.0000.0000.000
115A134GLY00.0390.01324.352-0.001-0.0010.0000.0000.0000.000
116A135ARG10.8780.91121.166-0.157-0.1570.0000.0000.0000.000
117A136ASP-1-0.953-0.96719.1560.1660.1660.0000.0000.0000.000
118A137VAL00.0690.03417.9290.0000.0000.0000.0000.0000.000
119A138PHE0-0.039-0.01616.3630.0310.0310.0000.0000.0000.000
120A139ALA00.0210.01013.3930.0760.0760.0000.0000.0000.000
121A140PRO00.0350.01111.7040.0940.0940.0000.0000.0000.000
122A141ALA00.0550.03811.3650.0350.0350.0000.0000.0000.000
123A142ALA0-0.002-0.00310.3710.1410.1410.0000.0000.0000.000
124A143ALA00.007-0.0027.3310.3870.3870.0000.0000.0000.000
125A144HIS0-0.028-0.0306.6840.0970.0970.0000.0000.0000.000
126A145LEU00.016-0.0077.3060.0990.0990.0000.0000.0000.000
127A146ALA0-0.0270.0024.4750.4730.7630.006-0.090-0.2070.000
128A147LEU0-0.043-0.0352.307-1.5290.4225.070-2.843-4.179-0.026
129A148GLY0-0.032-0.0043.523-1.924-1.2390.015-0.300-0.400-0.002
130A149LEU0-0.042-0.0074.580-0.763-0.717-0.001-0.005-0.0400.000
131A150PRO00.0230.0027.8810.2140.2140.0000.0000.0000.000
132A151PRO00.0410.04110.820-0.049-0.0490.0000.0000.0000.000
133A152GLU-1-0.829-0.91012.7840.3520.3520.0000.0000.0000.000
134A153GLY0-0.068-0.02614.145-0.052-0.0520.0000.0000.0000.000
135A154LEU0-0.062-0.02812.249-0.018-0.0180.0000.0000.0000.000
136A155GLY00.0620.03215.953-0.028-0.0280.0000.0000.0000.000
137A156PRO0-0.0260.00619.3090.0200.0200.0000.0000.0000.000
138A157GLU-1-0.800-0.88919.7740.3530.3530.0000.0000.0000.000
139A158VAL0-0.081-0.04621.188-0.035-0.0350.0000.0000.0000.000
140A159PRO00.012-0.00222.9220.0200.0200.0000.0000.0000.000
141A160VAL00.0710.03721.295-0.001-0.0010.0000.0000.0000.000
142A161GLU-1-0.940-0.98024.0060.1970.1970.0000.0000.0000.000
143A162THR0-0.086-0.04826.053-0.009-0.0090.0000.0000.0000.000
144A163LEU0-0.059-0.00821.352-0.004-0.0040.0000.0000.0000.000
145A164ALA00.0270.01125.586-0.012-0.0120.0000.0000.0000.000
146A165ARG10.8900.93625.299-0.223-0.2230.0000.0000.0000.000
147A166LEU0-0.008-0.00728.241-0.014-0.0140.0000.0000.0000.000
148A167PRO0-0.0250.00530.5960.0030.0030.0000.0000.0000.000
149A168LEU0-0.011-0.02429.968-0.006-0.0060.0000.0000.0000.000
150A169ALA00.0190.00431.9640.0070.0070.0000.0000.0000.000
151A170LEU0-0.0280.00528.572-0.008-0.0080.0000.0000.0000.000
152A171THR00.0330.01432.842-0.001-0.0010.0000.0000.0000.000
153A172GLU-1-0.768-0.85135.5480.1160.1160.0000.0000.0000.000
154A173GLY0-0.0350.01637.983-0.005-0.0050.0000.0000.0000.000
155A174PRO0-0.082-0.06140.8580.0000.0000.0000.0000.0000.000
156A175GLU-1-0.858-0.93942.8110.0800.0800.0000.0000.0000.000
157A176GLY00.016-0.00139.3040.0050.0050.0000.0000.0000.000
158A177GLU-1-0.862-0.91936.8300.1150.1150.0000.0000.0000.000
159A178VAL0-0.0130.00237.0740.0050.0050.0000.0000.0000.000
160A179LEU00.0090.00429.8100.0010.0010.0000.0000.0000.000
161A180THR00.0430.00729.9690.0040.0040.0000.0000.0000.000
162A181PHE00.0140.01932.813-0.007-0.0070.0000.0000.0000.000
163A182ASP-1-0.780-0.87030.7370.1190.1190.0000.0000.0000.000
164A183ARG10.9170.93229.125-0.119-0.1190.0000.0000.0000.000
165A184PHE0-0.038-0.02032.115-0.005-0.0050.0000.0000.0000.000
166A185GLY00.0240.02435.278-0.006-0.0060.0000.0000.0000.000
167A186ASN0-0.033-0.02834.002-0.009-0.0090.0000.0000.0000.000
168A187ALA0-0.009-0.02535.2180.0060.0060.0000.0000.0000.000
169A188ILE00.0040.01930.786-0.002-0.0020.0000.0000.0000.000
170A189THR0-0.024-0.03434.084-0.001-0.0010.0000.0000.0000.000
171A190THR00.0150.00533.4710.0050.0050.0000.0000.0000.000
172A191LEU00.0080.01234.7390.0030.0030.0000.0000.0000.000
173A192LEU00.0460.02331.1220.0020.0020.0000.0000.0000.000
174A193ARG10.7620.84433.857-0.120-0.1200.0000.0000.0000.000
175A194ALA00.0610.02337.568-0.002-0.0020.0000.0000.0000.000
176A195PRO0-0.038-0.00939.285-0.002-0.0020.0000.0000.0000.000
177A196VAL00.0670.01640.927-0.003-0.0030.0000.0000.0000.000
178A197GLY0-0.060-0.01643.420-0.002-0.0020.0000.0000.0000.000
179A198GLY0-0.0080.00545.633-0.002-0.0020.0000.0000.0000.000
180A199PHE0-0.038-0.04446.769-0.002-0.0020.0000.0000.0000.000
181A200VAL00.0380.02142.2560.0020.0020.0000.0000.0000.000
182A201GLU-1-0.962-0.97545.4460.0600.0600.0000.0000.0000.000
183A202VAL00.0510.01743.0830.0040.0040.0000.0000.0000.000
184A203GLY00.0330.01045.922-0.002-0.0020.0000.0000.0000.000
185A204GLY0-0.022-0.00148.246-0.003-0.0030.0000.0000.0000.000
186A205ARG10.9310.96949.177-0.059-0.0590.0000.0000.0000.000
187A206ARG10.9410.97348.758-0.050-0.0500.0000.0000.0000.000
188A207VAL00.0120.01743.983-0.002-0.0020.0000.0000.0000.000
189A208PRO0-0.024-0.00946.3080.0010.0010.0000.0000.0000.000
190A209VAL00.0360.03441.2610.0020.0020.0000.0000.0000.000
191A210ARG10.8530.91542.088-0.062-0.0620.0000.0000.0000.000
192A211ARG10.9640.97738.956-0.063-0.0630.0000.0000.0000.000
193A212THR00.0090.01238.0430.0050.0050.0000.0000.0000.000
194A213PHE00.0380.01535.526-0.003-0.0030.0000.0000.0000.000
195A214GLY00.0420.01640.317-0.002-0.0020.0000.0000.0000.000
196A215GLU-1-0.919-0.96742.2950.0570.0570.0000.0000.0000.000
197A216VAL0-0.041-0.02244.334-0.001-0.0010.0000.0000.0000.000
198A217PRO00.0290.00546.4420.0000.0000.0000.0000.0000.000
199A218GLU-1-0.904-0.96746.0050.0480.0480.0000.0000.0000.000
200A219GLY00.0030.00045.962-0.002-0.0020.0000.0000.0000.000
201A220ALA0-0.052-0.02047.2510.0000.0000.0000.0000.0000.000
202A221PRO0-0.008-0.01944.7970.0020.0020.0000.0000.0000.000
203A222VAL0-0.042-0.01641.299-0.002-0.0020.0000.0000.0000.000
204A223ALA00.0300.02040.3470.0030.0030.0000.0000.0000.000
205A224TYR0-0.051-0.03634.206-0.008-0.0080.0000.0000.0000.000
206A225LEU0-0.019-0.00633.0590.0030.0030.0000.0000.0000.000
207A226GLY00.0420.01632.048-0.004-0.0040.0000.0000.0000.000
208A227SER0-0.051-0.02827.2300.0010.0010.0000.0000.0000.000
209A228ALA00.0360.02326.3990.0070.0070.0000.0000.0000.000
210A229GLY0-0.022-0.00727.5100.0070.0070.0000.0000.0000.000
211A230LEU0-0.009-0.00129.638-0.001-0.0010.0000.0000.0000.000
212A231LEU0-0.045-0.00932.490-0.005-0.0050.0000.0000.0000.000
213A232GLU-1-0.827-0.89631.7540.1250.1250.0000.0000.0000.000
214A233VAL0-0.021-0.01936.279-0.007-0.0070.0000.0000.0000.000
215A234ALA00.0290.01338.1510.0030.0030.0000.0000.0000.000
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