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: 6YY1Z

Calculation Name: 1SCZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SCZ

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFG6

Base Structure: X-ray

Registration Date: 2023-09-21

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2792780.721149
FMO2-HF: Nuclear repulsion 2700384.859034
FMO2-HF: Total energy -92395.862115
FMO2-MP2: Total energy -92661.413068


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:172:ALA)


Summations of interaction energy for fragment #1(A:172:ALA)
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.
-0.0141.327-0.004-0.673-0.6650.003
Interaction energy analysis for fragmet #1(A:172:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.005
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].
3A174SER00.0690.0363.8340.2851.626-0.004-0.673-0.6650.003
4A175GLU-1-0.927-0.9536.3560.2700.2700.0000.0000.0000.000
5A176LYS10.9400.9726.650-0.468-0.4680.0000.0000.0000.000
6A177ARG10.9880.9928.2070.0850.0850.0000.0000.0000.000
7A178VAL0-0.011-0.00911.535-0.018-0.0180.0000.0000.0000.000
8A179PRO00.0120.00413.7270.0080.0080.0000.0000.0000.000
9A180MET00.0050.01417.3430.0100.0100.0000.0000.0000.000
10A181THR00.0330.01020.103-0.009-0.0090.0000.0000.0000.000
11A182ARG11.0710.99922.478-0.006-0.0060.0000.0000.0000.000
12A183LEU0-0.0240.00225.989-0.001-0.0010.0000.0000.0000.000
13A184ARG11.0100.99020.163-0.086-0.0860.0000.0000.0000.000
14A185LYS10.9060.96723.922-0.012-0.0120.0000.0000.0000.000
15A186ARG11.0061.01725.833-0.019-0.0190.0000.0000.0000.000
16A187VAL0-0.041-0.01327.2320.0000.0000.0000.0000.0000.000
17A188ALA00.019-0.02425.2830.0020.0020.0000.0000.0000.000
18A189GLU-1-0.905-0.96427.4090.0180.0180.0000.0000.0000.000
19A190ARG10.9610.98229.830-0.029-0.0290.0000.0000.0000.000
20A191LEU00.0200.04728.352-0.001-0.0010.0000.0000.0000.000
21A192LEU0-0.020-0.00929.1320.0000.0000.0000.0000.0000.000
22A193GLU-1-0.910-0.95532.2370.0170.0170.0000.0000.0000.000
23A194ALA00.028-0.00235.325-0.001-0.0010.0000.0000.0000.000
24A195LYS10.9350.96633.392-0.035-0.0350.0000.0000.0000.000
25A196ASN0-0.057-0.03233.6670.0010.0010.0000.0000.0000.000
26A197SER0-0.0090.00837.571-0.002-0.0020.0000.0000.0000.000
27A198THR0-0.073-0.02339.4710.0000.0000.0000.0000.0000.000
28A199ALA00.0040.00640.8000.0010.0010.0000.0000.0000.000
29A200MET0-0.055-0.01035.9610.0010.0010.0000.0000.0000.000
30A201LEU0-0.0230.01340.8190.0000.0000.0000.0000.0000.000
31A202THR0-0.015-0.03439.5190.0010.0010.0000.0000.0000.000
32A203THR0-0.0140.01841.9930.0000.0000.0000.0000.0000.000
33A204PHE00.009-0.02439.2630.0020.0020.0000.0000.0000.000
34A205ASN00.0580.02944.620-0.001-0.0010.0000.0000.0000.000
35A206GLU-1-0.873-0.91845.1220.0340.0340.0000.0000.0000.000
36A207VAL0-0.029-0.02046.110-0.002-0.0020.0000.0000.0000.000
37A208ASN00.1010.03347.4400.0030.0030.0000.0000.0000.000
38A209MET00.004-0.00245.379-0.001-0.0010.0000.0000.0000.000
39A210LYS10.8820.94348.753-0.026-0.0260.0000.0000.0000.000
40A211PRO00.0370.02751.2630.0000.0000.0000.0000.0000.000
41A212ILE00.0580.03148.7790.0000.0000.0000.0000.0000.000
42A213MET0-0.094-0.05646.5830.0000.0000.0000.0000.0000.000
43A214ASP-1-0.834-0.91850.0300.0270.0270.0000.0000.0000.000
44A215LEU00.0260.02253.482-0.001-0.0010.0000.0000.0000.000
45A216ARG10.8170.89345.163-0.035-0.0350.0000.0000.0000.000
46A217LYS10.9020.94949.346-0.031-0.0310.0000.0000.0000.000
47A218GLN0-0.0030.01652.8300.0000.0000.0000.0000.0000.000
48A219TYR00.017-0.00155.458-0.001-0.0010.0000.0000.0000.000
49A220GLY00.0060.01152.2160.0000.0000.0000.0000.0000.000
50A221GLU-1-0.898-0.95152.9820.0230.0230.0000.0000.0000.000
51A222ALA00.029-0.00254.4910.0000.0000.0000.0000.0000.000
52A223PHE0-0.023-0.00851.555-0.001-0.0010.0000.0000.0000.000
53A224GLU-1-0.950-0.98249.0530.0290.0290.0000.0000.0000.000
54A225LYS10.8830.94853.114-0.022-0.0220.0000.0000.0000.000
55A226ARG10.9500.99156.223-0.019-0.0190.0000.0000.0000.000
56A227HIS0-0.031-0.02153.848-0.001-0.0010.0000.0000.0000.000
57A228GLY00.0090.01452.7460.0000.0000.0000.0000.0000.000
58A229ILE0-0.070-0.04046.2700.0010.0010.0000.0000.0000.000
59A230ARG11.0041.01643.682-0.037-0.0370.0000.0000.0000.000
60A231LEU00.0400.03848.1630.0000.0000.0000.0000.0000.000
61A232GLY0-0.029-0.01045.5210.0010.0010.0000.0000.0000.000
62A233PHE00.040-0.00343.748-0.001-0.0010.0000.0000.0000.000
63A234MET00.0380.01440.173-0.001-0.0010.0000.0000.0000.000
64A235SER0-0.0180.00444.872-0.001-0.0010.0000.0000.0000.000
65A236PHE00.0330.00548.380-0.001-0.0010.0000.0000.0000.000
66A237TYR00.024-0.00942.458-0.001-0.0010.0000.0000.0000.000
67A238VAL00.0160.01145.832-0.001-0.0010.0000.0000.0000.000
68A239LYS10.9130.95948.089-0.023-0.0230.0000.0000.0000.000
69A240ALA00.0320.02249.748-0.001-0.0010.0000.0000.0000.000
70A241VAL0-0.002-0.01046.051-0.001-0.0010.0000.0000.0000.000
71A242VAL0-0.017-0.00449.505-0.001-0.0010.0000.0000.0000.000
72A243GLU-1-0.840-0.91552.0370.0180.0180.0000.0000.0000.000
73A244ALA00.0150.00351.126-0.001-0.0010.0000.0000.0000.000
74A245LEU0-0.044-0.03948.5340.0000.0000.0000.0000.0000.000
75A246LYS10.8890.95752.515-0.019-0.0190.0000.0000.0000.000
76A247ARG10.8730.94156.082-0.020-0.0200.0000.0000.0000.000
77A248TYR0-0.028-0.00253.224-0.001-0.0010.0000.0000.0000.000
78A249PRO00.0320.01253.3180.0010.0010.0000.0000.0000.000
79A250GLU-1-0.782-0.86952.9450.0160.0160.0000.0000.0000.000
80A251VAL0-0.054-0.03647.9010.0010.0010.0000.0000.0000.000
81A252ASN0-0.030-0.00948.6650.0020.0020.0000.0000.0000.000
82A253ALA00.0280.04250.5360.0000.0000.0000.0000.0000.000
83A254SER0-0.022-0.01246.5570.0010.0010.0000.0000.0000.000
84A255ILE00.0010.00947.066-0.001-0.0010.0000.0000.0000.000
85A256ASP-1-1.017-1.00346.9600.0160.0160.0000.0000.0000.000
86A257GLY00.0160.00947.905-0.001-0.0010.0000.0000.0000.000
87A258ASP-1-0.985-0.99049.5890.0110.0110.0000.0000.0000.000
88A259ASP-1-0.911-0.94352.1860.0110.0110.0000.0000.0000.000
89A260VAL0-0.015-0.01151.7260.0010.0010.0000.0000.0000.000
90A261VAL0-0.025-0.02151.032-0.001-0.0010.0000.0000.0000.000
91A262TYR0-0.026-0.04552.0060.0010.0010.0000.0000.0000.000
92A263HIS10.8020.89348.608-0.020-0.0200.0000.0000.0000.000
93A264ASN0-0.025-0.01153.6640.0000.0000.0000.0000.0000.000
94A265TYR00.0560.02649.526-0.001-0.0010.0000.0000.0000.000
95A266PHE0-0.004-0.02351.1680.0000.0000.0000.0000.0000.000
96A267ASP-1-0.788-0.88646.7620.0220.0220.0000.0000.0000.000
97A268VAL0-0.023-0.01643.9660.0000.0000.0000.0000.0000.000
98A269SER00.0160.00739.8260.0000.0000.0000.0000.0000.000
99A270MET00.013-0.00538.8950.0000.0000.0000.0000.0000.000
100A271ALA0-0.024-0.01034.4410.0010.0010.0000.0000.0000.000
101A272VAL0-0.019-0.00633.9590.0010.0010.0000.0000.0000.000
102A273SER0-0.036-0.02529.3510.0010.0010.0000.0000.0000.000
103A274THR0-0.035-0.03928.256-0.001-0.0010.0000.0000.0000.000
104A275PRO00.013-0.00425.9380.0060.0060.0000.0000.0000.000
105A276ARG10.9070.95324.126-0.048-0.0480.0000.0000.0000.000
106A277GLY0-0.0090.00425.632-0.003-0.0030.0000.0000.0000.000
107A278LEU00.0020.00626.4980.0000.0000.0000.0000.0000.000
108A279VAL0-0.0100.00129.874-0.002-0.0020.0000.0000.0000.000
109A280THR00.019-0.00533.0170.0010.0010.0000.0000.0000.000
110A281PRO0-0.0170.00936.304-0.002-0.0020.0000.0000.0000.000
111A282VAL00.0000.00439.2190.0010.0010.0000.0000.0000.000
112A283LEU0-0.070-0.02342.781-0.001-0.0010.0000.0000.0000.000
113A284ARG10.8620.89644.216-0.024-0.0240.0000.0000.0000.000
114A285ASP-1-0.827-0.89448.7140.0190.0190.0000.0000.0000.000
115A286VAL0-0.016-0.01247.7890.0000.0000.0000.0000.0000.000
116A287ASP-1-0.948-0.98251.0840.0190.0190.0000.0000.0000.000
117A288THR0-0.058-0.02754.421-0.001-0.0010.0000.0000.0000.000
118A289LEU0-0.0190.00650.0730.0000.0000.0000.0000.0000.000
119A290GLY00.0340.01554.1300.0000.0000.0000.0000.0000.000
120A291MET00.023-0.01551.6390.0000.0000.0000.0000.0000.000
121A292ALA0-0.0030.00250.8350.0010.0010.0000.0000.0000.000
122A293ASP-1-0.867-0.94150.5350.0220.0220.0000.0000.0000.000
123A294ILE0-0.0050.00647.3830.0010.0010.0000.0000.0000.000
124A295GLU-1-0.829-0.92045.8860.0340.0340.0000.0000.0000.000
125A296LYS10.8750.94545.549-0.022-0.0220.0000.0000.0000.000
126A297LYS10.9700.99345.516-0.024-0.0240.0000.0000.0000.000
127A298ILE00.0270.02041.2800.0010.0010.0000.0000.0000.000
128A299LYS10.9310.96741.127-0.031-0.0310.0000.0000.0000.000
129A300GLU-1-0.899-0.95740.8800.0280.0280.0000.0000.0000.000
130A301LEU00.022-0.00239.8840.0010.0010.0000.0000.0000.000
131A302ALA0-0.008-0.00337.1220.0020.0020.0000.0000.0000.000
132A303VAL0-0.025-0.01236.0190.0030.0030.0000.0000.0000.000
133A304LYS10.9961.00436.159-0.027-0.0270.0000.0000.0000.000
134A305GLY0-0.0050.01134.2950.0010.0010.0000.0000.0000.000
135A306ARG10.9240.98332.141-0.051-0.0510.0000.0000.0000.000
136A307ASP-1-0.920-0.96231.5050.0480.0480.0000.0000.0000.000
137A308GLY0-0.054-0.02331.774-0.002-0.0020.0000.0000.0000.000
138A309LYS10.8930.93832.628-0.033-0.0330.0000.0000.0000.000
139A310LEU0-0.009-0.00435.116-0.002-0.0020.0000.0000.0000.000
140A311THR0-0.018-0.02536.3210.0000.0000.0000.0000.0000.000
141A312VAL00.027-0.00938.1780.0010.0010.0000.0000.0000.000
142A313GLU-1-0.911-0.95139.0400.0210.0210.0000.0000.0000.000
143A314ASP-1-0.842-0.90739.7850.0280.0280.0000.0000.0000.000
144A315LEU0-0.068-0.04635.6840.0020.0020.0000.0000.0000.000
145A316THR0-0.0350.01639.0680.0000.0000.0000.0000.0000.000
146A317GLY00.0430.03941.340-0.001-0.0010.0000.0000.0000.000
147A318GLY0-0.015-0.00642.4870.0020.0020.0000.0000.0000.000
148A319ASN0-0.024-0.01544.5760.0000.0000.0000.0000.0000.000
149A320PHE00.0300.01644.2670.0000.0000.0000.0000.0000.000
150A321THR0-0.009-0.03838.0630.0010.0010.0000.0000.0000.000
151A322ILE00.0130.02840.9220.0000.0000.0000.0000.0000.000
152A323THR0-0.022-0.02234.5370.0020.0020.0000.0000.0000.000
153A324ASN00.0400.00636.4300.0000.0000.0000.0000.0000.000
154A325GLY00.0580.03233.3740.0030.0030.0000.0000.0000.000
155A326GLY00.0360.00333.5350.0040.0040.0000.0000.0000.000
156A327VAL0-0.080-0.02632.8610.0010.0010.0000.0000.0000.000
157A328PHE0-0.038-0.03229.3040.0030.0030.0000.0000.0000.000
158A329GLY00.0090.01830.7330.0050.0050.0000.0000.0000.000
159A330SER0-0.038-0.00732.718-0.001-0.0010.0000.0000.0000.000
160A331LEU00.0440.02533.785-0.003-0.0030.0000.0000.0000.000
161A332MET00.028-0.00835.694-0.004-0.0040.0000.0000.0000.000
162A333SER0-0.075-0.02833.5340.0040.0040.0000.0000.0000.000
163A334THR00.0550.00134.355-0.003-0.0030.0000.0000.0000.000
164A335PRO0-0.0360.02134.5260.0030.0030.0000.0000.0000.000
165A336ILE00.0350.01532.515-0.002-0.0020.0000.0000.0000.000
166A337ILE00.0430.01435.5030.0010.0010.0000.0000.0000.000
167A338ASN0-0.059-0.01336.8440.0010.0010.0000.0000.0000.000
168A339PRO0-0.0210.01036.275-0.002-0.0020.0000.0000.0000.000
169A340PRO0-0.013-0.01439.1760.0010.0010.0000.0000.0000.000
170A341GLN00.0420.03841.5610.0000.0000.0000.0000.0000.000
171A342SER00.0810.02542.7540.0000.0000.0000.0000.0000.000
172A343ALA0-0.016-0.01443.0470.0000.0000.0000.0000.0000.000
173A344ILE0-0.081-0.02437.1030.0010.0010.0000.0000.0000.000
174A345LEU00.0200.01841.4540.0000.0000.0000.0000.0000.000
175A346GLY0-0.019-0.02138.5700.0020.0020.0000.0000.0000.000
176A347MET0-0.054-0.02338.896-0.002-0.0020.0000.0000.0000.000
177A348HIS0-0.028-0.03535.8540.0060.0060.0000.0000.0000.000
178A349ALA0-0.006-0.01036.362-0.001-0.0010.0000.0000.0000.000
179A350ILE0-0.039-0.00638.369-0.002-0.0020.0000.0000.0000.000
180A351LYS10.9110.94037.480-0.051-0.0510.0000.0000.0000.000
181A352ASP-1-0.896-0.93542.0790.0360.0360.0000.0000.0000.000
182A353ARG10.8160.88644.188-0.034-0.0340.0000.0000.0000.000
183A354PRO0-0.010-0.00446.372-0.001-0.0010.0000.0000.0000.000
184A355MET0-0.014-0.00948.5620.0010.0010.0000.0000.0000.000
185A356ALA00.0140.01252.002-0.001-0.0010.0000.0000.0000.000
186A357VAL00.010-0.00155.3540.0000.0000.0000.0000.0000.000
187A358ASN0-0.014-0.01257.923-0.001-0.0010.0000.0000.0000.000
188A359GLY00.0050.00560.569-0.001-0.0010.0000.0000.0000.000
189A360GLN0-0.0160.00359.434-0.001-0.0010.0000.0000.0000.000
190A361VAL0-0.0150.00453.0780.0010.0010.0000.0000.0000.000
191A362GLU-1-0.901-0.96454.2900.0240.0240.0000.0000.0000.000
192A363ILE0-0.033-0.01548.1010.0010.0010.0000.0000.0000.000
193A364LEU00.0080.01349.5120.0000.0000.0000.0000.0000.000
194A365PRO00.0320.01246.1560.0020.0020.0000.0000.0000.000
195A366MET0-0.0170.00745.378-0.001-0.0010.0000.0000.0000.000
196A367MET0-0.0100.00641.4980.0030.0030.0000.0000.0000.000
197A368TYR00.0010.00640.579-0.002-0.0020.0000.0000.0000.000
198A369LEU0-0.028-0.01241.6640.0020.0020.0000.0000.0000.000
199A370ALA00.0150.00439.491-0.001-0.0010.0000.0000.0000.000
200A371LEU00.0170.01741.5830.0010.0010.0000.0000.0000.000
201A372SER0-0.022-0.03438.247-0.001-0.0010.0000.0000.0000.000
202A373TYR00.000-0.01441.4350.0000.0000.0000.0000.0000.000
203A374ASP-1-0.692-0.85843.6070.0220.0220.0000.0000.0000.000
204A375HIS0-0.003-0.01244.5690.0000.0000.0000.0000.0000.000
205A376ARG10.8200.91344.626-0.019-0.0190.0000.0000.0000.000
206A377LEU0-0.017-0.00448.235-0.001-0.0010.0000.0000.0000.000
207A378ILE0-0.0020.02347.0840.0000.0000.0000.0000.0000.000
208A379ASP-1-0.766-0.88349.3970.0180.0180.0000.0000.0000.000
209A380GLY00.002-0.02950.2750.0010.0010.0000.0000.0000.000
210A381ARG10.9410.96651.330-0.015-0.0150.0000.0000.0000.000
211A382GLU-1-0.883-0.94452.6840.0180.0180.0000.0000.0000.000
212A383SER0-0.0210.00447.7760.0010.0010.0000.0000.0000.000
213A384VAL0-0.016-0.01649.5100.0010.0010.0000.0000.0000.000
214A385GLY00.0200.01151.0660.0000.0000.0000.0000.0000.000
215A386PHE00.0300.01847.3570.0000.0000.0000.0000.0000.000
216A387LEU0-0.033-0.02745.5760.0010.0010.0000.0000.0000.000
217A388VAL0-0.015-0.00849.4090.0010.0010.0000.0000.0000.000
218A389THR00.0170.01152.4840.0000.0000.0000.0000.0000.000
219A390ILE0-0.009-0.00747.3150.0000.0000.0000.0000.0000.000
220A391LYS10.8390.92250.103-0.026-0.0260.0000.0000.0000.000
221A392GLU-1-0.923-0.97251.0930.0210.0210.0000.0000.0000.000
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