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: 14KJZ

Calculation Name: 1WSC-A-Xray372

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: 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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2660432.70012
FMO2-HF: Nuclear repulsion 2572593.051617
FMO2-HF: Total energy -87839.648503
FMO2-MP2: Total energy -88098.368633


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-10.473-11.58522.242-9.415-11.7120.034
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.042
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].
3A5GLN0-0.037-0.0603.354-0.7592.9490.008-1.935-1.7800.007
4A6LEU0-0.051-0.0141.7720.525-0.2719.197-3.419-4.9820.005
5A7VAL00.0130.0012.502-4.254-3.5551.486-0.444-1.741-0.018
6A8ALA00.0080.0123.9180.2300.4690.000-0.036-0.2030.000
7A9VAL00.0910.0295.4430.1590.1590.0000.0000.0000.000
8A10ASN0-0.025-0.0037.746-0.008-0.0080.0000.0000.0000.000
9A11GLU-1-0.813-0.8895.491-4.575-4.5750.0000.0000.0000.000
10A12LEU0-0.079-0.0349.9700.0290.0290.0000.0000.0000.000
11A13ASN00.0610.02612.6360.2280.2280.0000.0000.0000.000
12A14GLU-1-0.839-0.94315.945-0.312-0.3120.0000.0000.0000.000
13A15ASN00.0100.00518.4540.0550.0550.0000.0000.0000.000
14A16LEU00.0170.00813.0700.0130.0130.0000.0000.0000.000
15A17GLY00.0230.02216.2460.0040.0040.0000.0000.0000.000
16A18LYS10.8270.91818.0370.3630.3630.0000.0000.0000.000
17A19VAL0-0.022-0.01017.5090.0320.0320.0000.0000.0000.000
18A20LEU0-0.010-0.00713.8860.0290.0290.0000.0000.0000.000
19A21ILE00.0370.01918.1770.0460.0460.0000.0000.0000.000
20A22LYS10.8840.92421.7250.4140.4140.0000.0000.0000.000
21A23ILE00.0000.01117.6000.0250.0250.0000.0000.0000.000
22A24ALA00.0130.01221.4420.0320.0320.0000.0000.0000.000
23A25ARG10.7680.86822.7980.2310.2310.0000.0000.0000.000
24A26ASP-1-0.784-0.87424.748-0.341-0.3410.0000.0000.0000.000
25A27SER00.0020.00422.9830.0070.0070.0000.0000.0000.000
26A28ILE00.0000.00825.5240.0230.0230.0000.0000.0000.000
27A29ALA00.0190.01728.2310.0190.0190.0000.0000.0000.000
28A30ASN0-0.047-0.01528.1090.0100.0100.0000.0000.0000.000
29A31LYS10.8740.92827.0090.2680.2680.0000.0000.0000.000
30A32LEU0-0.0190.01131.0550.0160.0160.0000.0000.0000.000
31A33GLY0-0.022-0.00833.3250.0150.0150.0000.0000.0000.000
32A34ILE0-0.073-0.02833.5200.0060.0060.0000.0000.0000.000
33A35LEU0-0.0030.00428.2690.0030.0030.0000.0000.0000.000
34A36LYS10.8920.92432.1730.1800.1800.0000.0000.0000.000
35A37ILE00.0060.00726.440-0.007-0.0070.0000.0000.0000.000
36A38ASN00.0170.00727.9000.0240.0240.0000.0000.0000.000
37A39LEU00.007-0.01323.230-0.021-0.0210.0000.0000.0000.000
38A40GLU-1-0.889-0.93522.609-0.444-0.4440.0000.0000.0000.000
39A41ASP-1-0.812-0.89922.306-0.452-0.4520.0000.0000.0000.000
40A42TYR0-0.121-0.07923.336-0.046-0.0460.0000.0000.0000.000
41A43LEU00.0250.01218.673-0.046-0.0460.0000.0000.0000.000
42A44SER0-0.033-0.01818.531-0.091-0.0910.0000.0000.0000.000
43A45SER0-0.067-0.03419.423-0.038-0.0380.0000.0000.0000.000
44A46LEU0-0.023-0.00117.402-0.017-0.0170.0000.0000.0000.000
45A47ASN0-0.008-0.02116.259-0.095-0.0950.0000.0000.0000.000
46A48ASP-1-0.833-0.90412.801-1.494-1.4940.0000.0000.0000.000
47A49PRO00.024-0.01810.040-0.076-0.0760.0000.0000.0000.000
48A50ILE0-0.0080.0098.382-0.443-0.4430.0000.0000.0000.000
49A51LEU0-0.0030.0049.261-0.141-0.1410.0000.0000.0000.000
50A52ASN0-0.029-0.02210.3780.3450.3450.0000.0000.0000.000
51A53LYS10.8370.9103.7475.9756.105-0.001-0.012-0.1170.000
52A54LYS10.8650.9236.1072.9362.9360.0000.0000.0000.000
53A55GLY00.0310.0126.524-0.459-0.4590.0000.0000.0000.000
54A56LEU0-0.0090.0019.0610.0870.0870.0000.0000.0000.000
55A57ALA00.0170.00612.260-0.070-0.0700.0000.0000.0000.000
56A58PHE00.0250.00815.2400.0580.0580.0000.0000.0000.000
57A59VAL0-0.033-0.01718.699-0.046-0.0460.0000.0000.0000.000
58A60THR0-0.034-0.01621.6320.0280.0280.0000.0000.0000.000
59A61LEU00.0150.00824.702-0.025-0.0250.0000.0000.0000.000
60A62GLU-1-0.775-0.85427.227-0.024-0.0240.0000.0000.0000.000
61A63THR0-0.013-0.02130.241-0.017-0.0170.0000.0000.0000.000
62A64TYR00.0400.00433.3220.0060.0060.0000.0000.0000.000
63A65TYR00.011-0.00334.600-0.001-0.0010.0000.0000.0000.000
64A66GLY0-0.038-0.01436.471-0.003-0.0030.0000.0000.0000.000
65A67ASN0-0.022-0.01736.624-0.006-0.0060.0000.0000.0000.000
66A68SER00.0000.00334.7470.0070.0070.0000.0000.0000.000
67A69THR0-0.009-0.02430.565-0.008-0.0080.0000.0000.0000.000
68A70SER00.0060.00533.6600.0150.0150.0000.0000.0000.000
69A71LEU0-0.048-0.00428.558-0.012-0.0120.0000.0000.0000.000
70A72ARG10.7820.86530.3880.0680.0680.0000.0000.0000.000
71A73GLY00.0270.02329.360-0.004-0.0040.0000.0000.0000.000
72A74CYS0-0.106-0.05623.695-0.003-0.0030.0000.0000.0000.000
73A75ILE00.0390.02322.4300.0170.0170.0000.0000.0000.000
74A76GLY00.0230.00919.593-0.038-0.0380.0000.0000.0000.000
75A77TYR0-0.073-0.02317.0170.0330.0330.0000.0000.0000.000
76A78VAL00.039-0.01114.833-0.040-0.0400.0000.0000.0000.000
77A79GLU-1-0.964-0.95915.0510.2590.2590.0000.0000.0000.000
78A80ALA00.0180.00113.1660.0990.0990.0000.0000.0000.000
79A81VAL0-0.047-0.0147.566-0.076-0.0760.0000.0000.0000.000
80A82ALA0-0.011-0.01010.755-0.040-0.0400.0000.0000.0000.000
81A83PRO00.0060.00810.296-0.141-0.1410.0000.0000.0000.000
82A84LEU00.0480.0219.2250.3090.3090.0000.0000.0000.000
83A85LYS10.8550.92912.2401.2681.2680.0000.0000.0000.000
84A86GLU-1-0.898-0.95914.720-0.814-0.8140.0000.0000.0000.000
85A87ILE0-0.073-0.02613.0440.1350.1350.0000.0000.0000.000
86A88VAL00.0430.01015.3470.1080.1080.0000.0000.0000.000
87A89SER0-0.022-0.01817.7620.0800.0800.0000.0000.0000.000
88A90LYS10.9470.96418.2150.3960.3960.0000.0000.0000.000
89A91ALA00.0290.01119.4260.0470.0470.0000.0000.0000.000
90A92ALA00.0240.02821.3010.0400.0400.0000.0000.0000.000
91A93ILE0-0.035-0.01723.6250.0320.0320.0000.0000.0000.000
92A94ALA00.0260.00624.0790.0240.0240.0000.0000.0000.000
93A95ALA0-0.0050.01024.6560.0270.0270.0000.0000.0000.000
94A96ALA0-0.015-0.01126.5910.0180.0180.0000.0000.0000.000
95A97PHE0-0.057-0.05229.1070.0110.0110.0000.0000.0000.000
96A98SER0-0.020-0.01127.6970.0000.0000.0000.0000.0000.000
97A99ASP-1-0.713-0.81329.0730.0140.0140.0000.0000.0000.000
98A100PRO0-0.011-0.01429.907-0.002-0.0020.0000.0000.0000.000
99A101ARG10.7950.87028.092-0.026-0.0260.0000.0000.0000.000
100A102PHE0-0.0180.00531.2400.0010.0010.0000.0000.0000.000
101A103PRO00.0100.01635.337-0.002-0.0020.0000.0000.0000.000
102A104PRO00.0430.02034.016-0.003-0.0030.0000.0000.0000.000
103A105LEU0-0.041-0.01431.2550.0020.0020.0000.0000.0000.000
104A106SER0-0.022-0.03434.525-0.006-0.0060.0000.0000.0000.000
105A107LYS10.9270.93336.3630.1270.1270.0000.0000.0000.000
106A108GLY00.0080.00437.464-0.005-0.0050.0000.0000.0000.000
107A109GLU-1-0.746-0.82435.943-0.075-0.0750.0000.0000.0000.000
108A110PHE00.0180.01329.666-0.002-0.0020.0000.0000.0000.000
109A111ASP-1-0.845-0.91733.132-0.160-0.1600.0000.0000.0000.000
110A112ASN0-0.068-0.03035.3580.0000.0000.0000.0000.0000.000
111A113ILE0-0.0180.00529.7100.0100.0100.0000.0000.0000.000
112A114ILE00.0060.01527.604-0.017-0.0170.0000.0000.0000.000
113A115ILE0-0.047-0.03723.5320.0110.0110.0000.0000.0000.000
114A116GLU-1-0.814-0.90821.373-0.048-0.0480.0000.0000.0000.000
115A117VAL0-0.023-0.02116.9790.0000.0000.0000.0000.0000.000
116A118THR00.0010.00915.4240.0140.0140.0000.0000.0000.000
117A119VAL0-0.034-0.01910.470-0.038-0.0380.0000.0000.0000.000
118A120LEU00.0090.00010.7500.0890.0890.0000.0000.0000.000
119A121THR0-0.0060.0055.058-0.100-0.1000.0000.0000.0000.000
120A122LYS10.9010.9445.473-3.972-3.9720.0000.0000.0000.000
121A123PRO00.0240.0176.0651.1671.1670.0000.0000.0000.000
122A124GLN0-0.042-0.0421.796-9.922-15.01411.552-3.569-2.8890.040
123A125GLU-1-0.817-0.9006.9461.5631.5630.0000.0000.0000.000
124A126ILE0-0.026-0.0108.1300.8870.8870.0000.0000.0000.000
125A127ASP-1-0.958-0.9749.8541.4491.4490.0000.0000.0000.000
126A128VAL00.004-0.00311.858-0.083-0.0830.0000.0000.0000.000
127A129GLU-1-0.861-0.91614.6830.9820.9820.0000.0000.0000.000
128A130ASN0-0.043-0.02717.956-0.171-0.1710.0000.0000.0000.000
129A131ARG10.8810.95517.109-1.190-1.1900.0000.0000.0000.000
130A132TRP00.0900.04119.5780.0220.0220.0000.0000.0000.000
131A133GLU-1-0.947-0.96417.3550.9680.9680.0000.0000.0000.000
132A134LEU0-0.030-0.01914.4680.1050.1050.0000.0000.0000.000
133A135PRO00.0310.01615.9670.1310.1310.0000.0000.0000.000
134A136LYS10.9370.97117.200-0.706-0.7060.0000.0000.0000.000
135A137LYS10.8280.91411.924-1.388-1.3880.0000.0000.0000.000
136A138ILE0-0.054-0.00611.7330.4560.4560.0000.0000.0000.000
137A139LYS10.8990.93513.740-0.734-0.7340.0000.0000.0000.000
138A140VAL00.0130.00715.0450.0180.0180.0000.0000.0000.000
139A141GLY00.0060.00517.116-0.068-0.0680.0000.0000.0000.000
140A142GLU-1-0.923-0.95912.0570.4990.4990.0000.0000.0000.000
141A143ASP-1-0.786-0.88710.0432.0362.0360.0000.0000.0000.000
142A144GLY0-0.0050.00211.734-0.167-0.1670.0000.0000.0000.000
143A145LEU0-0.019-0.02712.5300.3150.3150.0000.0000.0000.000
144A146ILE0-0.007-0.00912.851-0.173-0.1730.0000.0000.0000.000
145A147VAL00.0090.00515.1720.1630.1630.0000.0000.0000.000
146A148GLU-1-0.839-0.93115.2651.2211.2210.0000.0000.0000.000
147A149TYR0-0.020-0.01418.9770.0510.0510.0000.0000.0000.000
148A150GLY00.0170.01521.040-0.071-0.0710.0000.0000.0000.000
149A151ILE0-0.006-0.03022.5720.0100.0100.0000.0000.0000.000
150A152LEU0-0.036-0.01723.569-0.002-0.0020.0000.0000.0000.000
151A153TYR0-0.0080.02823.824-0.033-0.0330.0000.0000.0000.000
152A154SER00.0220.00319.0520.0710.0710.0000.0000.0000.000
153A155GLY00.0430.03219.838-0.082-0.0820.0000.0000.0000.000
154A156LEU0-0.040-0.00915.4140.1150.1150.0000.0000.0000.000
155A157LEU0-0.024-0.02317.141-0.125-0.1250.0000.0000.0000.000
156A158LEU0-0.012-0.00316.0340.1090.1090.0000.0000.0000.000
157A159PRO00.010-0.00713.138-0.024-0.0240.0000.0000.0000.000
158A160GLN00.0680.03215.8690.0410.0410.0000.0000.0000.000
159A161VAL0-0.029-0.00119.363-0.017-0.0170.0000.0000.0000.000
160A162PRO00.0630.02418.367-0.043-0.0430.0000.0000.0000.000
161A163MET0-0.0020.03019.949-0.032-0.0320.0000.0000.0000.000
162A164GLU-1-0.858-0.91522.3770.2270.2270.0000.0000.0000.000
163A165TYR0-0.041-0.02324.747-0.047-0.0470.0000.0000.0000.000
164A166CYS0-0.125-0.02725.692-0.006-0.0060.0000.0000.0000.000
165A167TRP00.0290.01422.5040.0080.0080.0000.0000.0000.000
166A168ASP-1-0.806-0.87023.2370.4950.4950.0000.0000.0000.000
167A169GLU-1-0.774-0.92318.1980.7750.7750.0000.0000.0000.000
168A170GLU-1-0.870-0.95120.4400.6910.6910.0000.0000.0000.000
169A171THR0-0.048-0.04022.6090.0020.0020.0000.0000.0000.000
170A172PHE0-0.007-0.00115.893-0.005-0.0050.0000.0000.0000.000
171A173LEU00.0060.00116.7670.0410.0410.0000.0000.0000.000
172A174ALA0-0.0060.00320.412-0.001-0.0010.0000.0000.0000.000
173A175GLU-1-0.896-0.96623.6580.4070.4070.0000.0000.0000.000
174A176THR0-0.070-0.04518.287-0.011-0.0110.0000.0000.0000.000
175A177CYS0-0.082-0.02321.6560.0700.0700.0000.0000.0000.000
176A178ILE00.0310.03023.099-0.028-0.0280.0000.0000.0000.000
177A179LYS10.8590.93322.101-0.510-0.5100.0000.0000.0000.000
178A180ALA0-0.028-0.00821.811-0.020-0.0200.0000.0000.0000.000
179A181GLY0-0.026-0.00623.817-0.017-0.0170.0000.0000.0000.000
180A182LEU0-0.081-0.04422.663-0.012-0.0120.0000.0000.0000.000
181A183GLU-1-0.865-0.93626.6500.3950.3950.0000.0000.0000.000
182A184PRO00.009-0.01026.0450.0490.0490.0000.0000.0000.000
183A185ASP-1-0.909-0.95125.1860.5280.5280.0000.0000.0000.000
184A187TRP00.0660.00919.3960.0800.0800.0000.0000.0000.000
185A188LEU0-0.021-0.00519.9180.0920.0920.0000.0000.0000.000
186A189ASN0-0.013-0.00722.355-0.003-0.0030.0000.0000.0000.000
187A190ASN00.019-0.02619.4320.0970.0970.0000.0000.0000.000
188A191LYS10.8820.95119.501-0.467-0.4670.0000.0000.0000.000
189A192VAL0-0.023-0.00118.949-0.005-0.0050.0000.0000.0000.000
190A193LYS10.8700.94214.523-1.411-1.4110.0000.0000.0000.000
191A194ILE00.0400.01913.744-0.122-0.1220.0000.0000.0000.000
192A195LYS10.8170.9119.885-1.472-1.4720.0000.0000.0000.000
193A196LYS10.8120.8968.204-3.047-3.0470.0000.0000.0000.000
194A197PHE0-0.015-0.0027.5620.7150.7150.0000.0000.0000.000
195A198GLN00.0280.0166.254-0.452-0.4520.0000.0000.0000.000
196A199GLY00.040-0.0059.565-0.112-0.1120.0000.0000.0000.000
197A200ILE0-0.056-0.01711.9410.0140.0140.0000.0000.0000.000
198A201ILE00.0100.01114.324-0.032-0.0320.0000.0000.0000.000
199A202PHE00.0160.02314.553-0.017-0.0170.0000.0000.0000.000
200A203ARG10.8640.90719.7750.0630.0630.0000.0000.0000.000
201A204GLU-1-0.739-0.84323.446-0.208-0.2080.0000.0000.0000.000
202A205GLU-1-0.801-0.87226.683-0.115-0.1150.0000.0000.0000.000
203A206LYS10.9280.94129.2900.1270.1270.0000.0000.0000.000
204A207PRO0-0.0100.00630.456-0.017-0.0170.0000.0000.0000.000
205A208LYS10.8400.91529.2860.1680.1680.0000.0000.0000.000
206A209SER0-0.079-0.02228.525-0.005-0.0050.0000.0000.0000.000
207A210GLU-1-0.843-0.95027.331-0.313-0.3130.0000.0000.0000.000
208A211LYS10.8320.90726.7160.1210.1210.0000.0000.0000.000
209A212ILE0-0.0190.00220.5540.0110.0110.0000.0000.0000.000
210A213LEU00.0200.00923.7740.0000.0000.0000.0000.0000.000
211A214ILE0-0.018-0.01617.639-0.020-0.0200.0000.0000.0000.000
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