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: YQ2G2

Calculation Name: 1WSC-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WSC

Chain ID: A

ChEMBL ID:

UniProt ID: Q976G0

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2670076.302857
FMO2-HF: Nuclear repulsion 2582067.77452
FMO2-HF: Total energy -88008.528337
FMO2-MP2: Total energy -88267.891115


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:2:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
9.619-0.44722.335-7.578-4.693-0.048
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.120 / q_NPA : 0.011
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].
3A4GLU -1-0.901-0.9303.846-0.7710.128-0.001-0.462-0.436-0.001
4A5GLN 0-0.070-0.0645.7970.4050.4050.0000.0000.0000.000
5A6LEU 0-0.043-0.0093.1510.0460.5170.074-0.244-0.3020.001
6A7VAL 00.0030.0462.21810.884-2.79820.432-4.622-2.128-0.028
7A8ALA 00.0230.0082.445-0.4020.0401.298-1.023-0.717-0.007
8A9VAL 00.0600.0213.879-0.734-0.8110.010-0.0100.0760.000
9A10ASN 0-0.050-0.0125.884-0.092-0.0920.0000.0000.0000.000
10A11GLU -1-0.809-0.9312.699-1.4550.2650.518-1.152-1.086-0.013
11A12LEU 0-0.082-0.0347.331-0.186-0.1860.0000.0000.0000.000
12A13ASN 00.0560.04510.195-0.024-0.0240.0000.0000.0000.000
13A14GLU -1-0.842-0.95313.4010.0990.0990.0000.0000.0000.000
14A15ASN 00.030-0.00416.140-0.014-0.0140.0000.0000.0000.000
15A16LEU 00.0170.00210.899-0.013-0.0130.0000.0000.0000.000
16A17GLY 00.0180.01914.184-0.007-0.0070.0000.0000.0000.000
17A18LYS 10.8810.95215.945-0.080-0.0800.0000.0000.0000.000
18A19VAL 0-0.013-0.00615.793-0.014-0.0140.0000.0000.0000.000
19A20LEU 0-0.014-0.00912.386-0.013-0.0130.0000.0000.0000.000
20A21ILE 00.0410.02216.719-0.011-0.0110.0000.0000.0000.000
21A22LYS 10.9100.96120.138-0.033-0.0330.0000.0000.0000.000
22A23ILE 0-0.0050.01316.386-0.009-0.0090.0000.0000.0000.000
23A24ALA 00.0170.01620.313-0.008-0.0080.0000.0000.0000.000
24A25ARG 10.7920.90321.772-0.051-0.0510.0000.0000.0000.000
25A26ASP -1-0.807-0.93524.0120.0170.0170.0000.0000.0000.000
26A27SER 0-0.022-0.01722.299-0.007-0.0070.0000.0000.0000.000
27A28ILE 00.0030.01024.923-0.005-0.0050.0000.0000.0000.000
28A29ALA 00.0140.01427.511-0.003-0.0030.0000.0000.0000.000
29A30ASN 0-0.058-0.02827.642-0.004-0.0040.0000.0000.0000.000
30A31LYS 10.9210.95727.107-0.004-0.0040.0000.0000.0000.000
31A32LEU 0-0.0320.00530.706-0.001-0.0010.0000.0000.0000.000
32A33GLY 0-0.045-0.01732.809-0.001-0.0010.0000.0000.0000.000
33A34ILE 0-0.098-0.04432.566-0.001-0.0010.0000.0000.0000.000
34A35LEU 0-0.007-0.00127.584-0.001-0.0010.0000.0000.0000.000
35A36LYS 10.9340.95331.641-0.003-0.0030.0000.0000.0000.000
36A37ILE 00.0190.00826.028-0.001-0.0010.0000.0000.0000.000
37A38ASN 00.0420.04527.3970.0010.0010.0000.0000.0000.000
38A39LEU 00.013-0.00822.793-0.002-0.0020.0000.0000.0000.000
39A40GLU -1-0.881-0.93623.109-0.039-0.0390.0000.0000.0000.000
40A41ASP -1-0.846-0.93322.592-0.042-0.0420.0000.0000.0000.000
41A42TYR 0-0.113-0.04721.906-0.003-0.0030.0000.0000.0000.000
42A43LEU 00.0230.01018.6230.0000.0000.0000.0000.0000.000
43A44SER 0-0.022-0.01218.479-0.008-0.0080.0000.0000.0000.000
44A45SER 0-0.075-0.04019.581-0.008-0.0080.0000.0000.0000.000
45A46LEU 0-0.034-0.00616.7850.0000.0000.0000.0000.0000.000
46A47ASN 0-0.011-0.02316.105-0.005-0.0050.0000.0000.0000.000
47A48ASP -1-0.848-0.91711.699-0.062-0.0620.0000.0000.0000.000
48A49PRO 00.017-0.0189.623-0.001-0.0010.0000.0000.0000.000
49A50ILE 0-0.0060.0106.787-0.078-0.0780.0000.0000.0000.000
50A51LEU 0-0.0040.0028.3750.0460.0460.0000.0000.0000.000
51A52ASN 0-0.010-0.00810.3470.0610.0610.0000.0000.0000.000
52A53LYS 10.9090.9833.2691.4551.6160.004-0.065-0.1000.000
53A54LYS 10.9080.9456.8900.3860.3860.0000.0000.0000.000
54A55GLY 00.0250.0126.3630.1610.1610.0000.0000.0000.000
55A56LEU 0-0.017-0.0018.654-0.084-0.0840.0000.0000.0000.000
56A57ALA 00.0340.01011.9950.0450.0450.0000.0000.0000.000
57A58PHE 00.0210.02414.595-0.028-0.0280.0000.0000.0000.000
58A59VAL 0-0.036-0.01518.1270.0100.0100.0000.0000.0000.000
59A60THR 00.0010.00220.751-0.013-0.0130.0000.0000.0000.000
60A61LEU 0-0.006-0.00423.9190.0020.0020.0000.0000.0000.000
61A62GLU -1-0.796-0.87126.5570.0720.0720.0000.0000.0000.000
62A63THR 0-0.038-0.02429.298-0.002-0.0020.0000.0000.0000.000
63A64TYR 00.029-0.01031.8820.0000.0000.0000.0000.0000.000
64A65TYR 00.000-0.00733.414-0.004-0.0040.0000.0000.0000.000
65A66GLY 0-0.040-0.01735.3220.0020.0020.0000.0000.0000.000
66A67ASN 00.0000.00035.6350.0030.0030.0000.0000.0000.000
67A68SER 0-0.011-0.00733.9640.0010.0010.0000.0000.0000.000
68A69THR 0-0.038-0.04829.662-0.002-0.0020.0000.0000.0000.000
69A70SER 00.0160.00832.8170.0000.0000.0000.0000.0000.000
70A71LEU 0-0.0040.02128.5420.0000.0000.0000.0000.0000.000
71A72ARG 10.7740.84629.660-0.036-0.0360.0000.0000.0000.000
72A73GLY 00.0110.02628.713-0.005-0.0050.0000.0000.0000.000
73A74CYS 0-0.077-0.04223.8260.0080.0080.0000.0000.0000.000
74A75ILE 00.0310.03421.892-0.005-0.0050.0000.0000.0000.000
75A76GLY 00.031-0.01219.2580.0090.0090.0000.0000.0000.000
76A77TYR 0-0.077-0.02016.959-0.015-0.0150.0000.0000.0000.000
77A78VAL 00.037-0.00615.2090.0150.0150.0000.0000.0000.000
78A79GLU -1-0.965-0.96215.8400.0120.0120.0000.0000.0000.000
79A80ALA 00.012-0.00214.296-0.010-0.0100.0000.0000.0000.000
80A81VAL 0-0.044-0.0179.0470.0110.0110.0000.0000.0000.000
81A82ALA 0-0.015-0.01511.598-0.045-0.0450.0000.0000.0000.000
82A83PRO 00.0170.01110.7500.0350.0350.0000.0000.0000.000
83A84LEU 00.0530.0208.3240.0310.0310.0000.0000.0000.000
84A85LYS 10.8600.92611.7990.0840.0840.0000.0000.0000.000
85A86GLU -1-0.915-0.96414.698-0.071-0.0710.0000.0000.0000.000
86A87ILE 0-0.061-0.02313.0220.0040.0040.0000.0000.0000.000
87A88VAL 00.0320.01014.4480.0070.0070.0000.0000.0000.000
88A89SER 0-0.022-0.00817.020-0.005-0.0050.0000.0000.0000.000
89A90LYS 10.9530.96719.3880.0030.0030.0000.0000.0000.000
90A91ALA 00.0080.00218.853-0.002-0.0020.0000.0000.0000.000
91A92ALA 00.0370.03220.7270.0000.0000.0000.0000.0000.000
92A93ILE 0-0.021-0.01422.727-0.003-0.0030.0000.0000.0000.000
93A94ALA 00.0140.00623.704-0.002-0.0020.0000.0000.0000.000
94A95ALA 00.0020.00423.872-0.001-0.0010.0000.0000.0000.000
95A96ALA 0-0.014-0.01325.794-0.001-0.0010.0000.0000.0000.000
96A97PHE 0-0.061-0.05228.511-0.003-0.0030.0000.0000.0000.000
97A98SER 0-0.017-0.01427.380-0.003-0.0030.0000.0000.0000.000
98A99ASP -1-0.709-0.79228.6320.0430.0430.0000.0000.0000.000
99A100PRO 0-0.007-0.01129.658-0.002-0.0020.0000.0000.0000.000
100A101ARG 10.7790.84428.142-0.048-0.0480.0000.0000.0000.000
101A102PHE 0-0.0120.00331.0380.0000.0000.0000.0000.0000.000
102A103PRO 0-0.0090.00634.783-0.001-0.0010.0000.0000.0000.000
103A104PRO 00.0370.01633.3240.0020.0020.0000.0000.0000.000
104A105LEU 0-0.034-0.01230.1110.0000.0000.0000.0000.0000.000
105A106SER 0-0.009-0.00833.565-0.003-0.0030.0000.0000.0000.000
106A107LYS 10.9340.93235.358-0.009-0.0090.0000.0000.0000.000
107A108GLY 00.0000.00136.3690.0010.0010.0000.0000.0000.000
108A109GLU -1-0.760-0.84634.9250.0290.0290.0000.0000.0000.000
109A110PHE 00.0140.01228.4630.0020.0020.0000.0000.0000.000
110A111ASP -1-0.870-0.94931.7630.0270.0270.0000.0000.0000.000
111A112ASN 0-0.055-0.02633.7500.0020.0020.0000.0000.0000.000
112A113ILE 0-0.026-0.00328.6430.0020.0020.0000.0000.0000.000
113A114ILE 0-0.027-0.00126.302-0.002-0.0020.0000.0000.0000.000
114A115ILE 0-0.024-0.03422.0280.0000.0000.0000.0000.0000.000
115A116GLU -1-0.841-0.91420.4480.1170.1170.0000.0000.0000.000
116A117VAL 0-0.018-0.01415.576-0.006-0.0060.0000.0000.0000.000
117A118THR 00.0080.01114.9570.0170.0170.0000.0000.0000.000
118A119VAL 0-0.034-0.0179.376-0.017-0.0170.0000.0000.0000.000
119A120LEU 00.007-0.00610.7170.0390.0390.0000.0000.0000.000
120A121THR 0-0.0090.0035.545-0.105-0.1050.0000.0000.0000.000
121A122LYS 10.9740.9826.4420.0050.0050.0000.0000.0000.000
122A123PRO 00.0230.0167.7610.0580.0580.0000.0000.0000.000
123A124GLN 0-0.142-0.1034.975-0.356-0.3560.0000.0000.0000.000
124A125GLU -1-0.904-0.96010.1670.0440.0440.0000.0000.0000.000
125A126ILE 0-0.046-0.01812.4650.0080.0080.0000.0000.0000.000
126A127ASP -1-0.951-0.96914.334-0.013-0.0130.0000.0000.0000.000
127A128VAL 00.0070.00216.4070.0000.0000.0000.0000.0000.000
128A129GLU -1-0.884-0.94718.8230.0080.0080.0000.0000.0000.000
129A130ASN 0-0.050-0.02621.976-0.007-0.0070.0000.0000.0000.000
130A131ARG 10.8780.92920.928-0.040-0.0400.0000.0000.0000.000
131A132TRP 00.0900.03723.4880.0070.0070.0000.0000.0000.000
132A133GLU -1-1.012-1.00920.1020.0640.0640.0000.0000.0000.000
133A134LEU 0-0.031-0.01618.2310.0110.0110.0000.0000.0000.000
134A135PRO 00.0250.00618.8320.0180.0180.0000.0000.0000.000
135A136LYS 10.9490.97919.283-0.075-0.0750.0000.0000.0000.000
136A137LYS 10.8440.93714.894-0.090-0.0900.0000.0000.0000.000
137A138ILE 0-0.061-0.01914.0370.0410.0410.0000.0000.0000.000
138A139LYS 10.9210.96814.861-0.248-0.2480.0000.0000.0000.000
139A140VAL 00.0180.01016.1950.0270.0270.0000.0000.0000.000
140A141GLY 0-0.002-0.00318.037-0.004-0.0040.0000.0000.0000.000
141A142GLU -1-0.995-1.01612.7260.3620.3620.0000.0000.0000.000
142A143ASP -1-0.837-0.93211.6420.4450.4450.0000.0000.0000.000
143A144GLY 0-0.0070.00413.039-0.042-0.0420.0000.0000.0000.000
144A145LEU 0-0.010-0.02714.2390.0150.0150.0000.0000.0000.000
145A146ILE 0-0.016-0.00714.689-0.010-0.0100.0000.0000.0000.000
146A147VAL 00.0100.00817.671-0.002-0.0020.0000.0000.0000.000
147A148GLU -1-0.903-0.96718.6330.0460.0460.0000.0000.0000.000
148A149TYR 0-0.020-0.00922.059-0.004-0.0040.0000.0000.0000.000
149A150GLY 00.0140.01224.460-0.003-0.0030.0000.0000.0000.000
150A151ILE 0-0.005-0.03025.3120.0040.0040.0000.0000.0000.000
151A152LEU 0-0.026-0.01526.3310.0030.0030.0000.0000.0000.000
152A153TYR 0-0.0190.02626.8620.0000.0000.0000.0000.0000.000
153A154SER 00.0410.00721.4640.0040.0040.0000.0000.0000.000
154A155GLY 00.0300.02822.153-0.002-0.0020.0000.0000.0000.000
155A156LEU 0-0.036-0.01616.5800.0080.0080.0000.0000.0000.000
156A157LEU 0-0.009-0.01518.729-0.009-0.0090.0000.0000.0000.000
157A158LEU 0-0.022-0.00616.6590.0210.0210.0000.0000.0000.000
158A159PRO 00.000-0.01114.161-0.012-0.0120.0000.0000.0000.000
159A160GLN 00.0910.03616.7120.0100.0100.0000.0000.0000.000
160A161VAL 0-0.0140.00719.958-0.011-0.0110.0000.0000.0000.000
161A162PRO 00.0320.01619.482-0.012-0.0120.0000.0000.0000.000
162A163MET 0-0.0140.01920.423-0.006-0.0060.0000.0000.0000.000
163A164GLU -1-0.897-0.94823.1870.0960.0960.0000.0000.0000.000
164A165TYR 0-0.063-0.02925.677-0.016-0.0160.0000.0000.0000.000
165A222CYS 0-0.086-0.00726.609-0.011-0.0110.0000.0000.0000.000
166A167TRP 00.0170.00924.091-0.004-0.0040.0000.0000.0000.000
167A168ASP -1-0.803-0.86724.5400.0920.0920.0000.0000.0000.000
168A169GLU -1-0.765-0.93319.7770.1520.1520.0000.0000.0000.000
169A170GLU -1-0.908-0.96422.3470.0770.0770.0000.0000.0000.000
170A171THR 0-0.038-0.03024.874-0.005-0.0050.0000.0000.0000.000
171A172PHE 0-0.013-0.00117.497-0.004-0.0040.0000.0000.0000.000
172A173LEU 0-0.005-0.00219.3020.0010.0010.0000.0000.0000.000
173A174ALA 00.0030.01122.777-0.006-0.0060.0000.0000.0000.000
174A175GLU -1-0.895-0.97025.3330.0610.0610.0000.0000.0000.000
175A176THR 0-0.059-0.04320.3210.0010.0010.0000.0000.0000.000
176A186CYS 0-0.059-0.01523.651-0.005-0.0050.0000.0000.0000.000
177A178ILE 00.0320.03325.679-0.006-0.0060.0000.0000.0000.000
178A179LYS 10.8300.92523.688-0.082-0.0820.0000.0000.0000.000
179A180ALA 0-0.024-0.00924.300-0.003-0.0030.0000.0000.0000.000
180A181GLY 0-0.030-0.00726.158-0.006-0.0060.0000.0000.0000.000
181A182LEU 0-0.078-0.04025.694-0.005-0.0050.0000.0000.0000.000
182A183GLU -1-0.867-0.94429.5600.0340.0340.0000.0000.0000.000
183A184PRO 00.005-0.00729.0160.0040.0040.0000.0000.0000.000
184A185ASP -1-0.919-0.95528.0190.0450.0450.0000.0000.0000.000
185A187TRP 00.0770.01322.666-0.001-0.0010.0000.0000.0000.000
186A188LEU 0-0.032-0.00323.6310.0000.0000.0000.0000.0000.000
187A189ASN 00.0010.00726.182-0.008-0.0080.0000.0000.0000.000
188A190ASN 00.0490.00324.0110.0040.0040.0000.0000.0000.000
189A191LYS 10.8820.94823.827-0.014-0.0140.0000.0000.0000.000
190A192VAL 0-0.0140.00822.305-0.003-0.0030.0000.0000.0000.000
191A193LYS 10.9140.97918.542-0.007-0.0070.0000.0000.0000.000
192A194ILE 00.0600.02816.6030.0050.0050.0000.0000.0000.000
193A195LYS 10.9020.96712.710-0.047-0.0470.0000.0000.0000.000
194A196LYS 10.9560.9939.685-0.359-0.3590.0000.0000.0000.000
195A197PHE 0-0.039-0.0159.0940.0140.0140.0000.0000.0000.000
196A198GLN 00.0480.0417.0520.1950.1950.0000.0000.0000.000
197A199GLY 00.044-0.00310.158-0.013-0.0130.0000.0000.0000.000
198A200ILE 0-0.061-0.01911.4720.0160.0160.0000.0000.0000.000
199A201ILE 00.0340.02513.606-0.014-0.0140.0000.0000.0000.000
200A202PHE 00.0140.01712.698-0.003-0.0030.0000.0000.0000.000
201A203ARG 10.8960.92918.408-0.112-0.1120.0000.0000.0000.000
202A204GLU -1-0.771-0.86022.0920.0570.0570.0000.0000.0000.000
203A205GLU -1-0.858-0.92625.0050.0660.0660.0000.0000.0000.000
204A206LYS 10.9260.93627.751-0.045-0.0450.0000.0000.0000.000
205A207PRO 0-0.0160.00028.5750.0020.0020.0000.0000.0000.000
206A208LYS 10.8750.94927.542-0.033-0.0330.0000.0000.0000.000
207A209SER 0-0.094-0.03326.486-0.003-0.0030.0000.0000.0000.000
208A210GLU -1-0.890-0.96325.3610.0500.0500.0000.0000.0000.000
209A211LYS 10.9030.95724.467-0.054-0.0540.0000.0000.0000.000
210A212ILE 0-0.0050.00918.221-0.003-0.0030.0000.0000.0000.000
211A213LEU 00.0190.00722.0630.0040.0040.0000.0000.0000.000
212A214ILE 0-0.028-0.01516.1400.0100.0100.0000.0000.0000.000
213A215ILE 00.0080.01018.374-0.006-0.0060.0000.0000.0000.000
214A216LYS 10.9410.95614.577-0.251-0.2510.0000.0000.0000.000
215A217PRO 0-0.011-0.00414.784-0.024-0.0240.0000.0000.0000.000
216A218SER 0-0.010-0.00416.657-0.020-0.0200.0000.0000.0000.000
217A219GLU -1-0.878-0.94418.4530.1610.1610.0000.0000.0000.000
218A220VAL 0-0.029-0.00820.944-0.015-0.0150.0000.0000.0000.000
219A221LYS 10.9650.98023.235-0.082-0.0820.0000.0000.0000.000
220A223LYS 10.9920.98328.164-0.077-0.0770.0000.0000.0000.000
221A224LYS 10.8640.91330.658-0.064-0.0640.0000.0000.0000.000
222A225GLU -1-0.964-0.98330.6880.0760.0760.0000.0000.0000.000
223A226GLU -1-0.943-0.97530.2440.0810.0810.0000.0000.0000.000
224A227ILE 0-0.066-0.03033.786-0.004-0.0040.0000.0000.0000.000
225A228NME 0-0.0020.00837.2530.0000.0000.0000.0000.0000.000