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: R8878

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 OptAll
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 -2797960.200686
FMO2-HF: Nuclear repulsion 2705562.507094
FMO2-HF: Total energy -92397.693591
FMO2-MP2: Total energy -92663.082354


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.
-2.841-1.592-0.009-0.663-0.5770.002
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 : 0.037 / q_NPA : 0.002
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].
3A174SER00.0680.0333.790-1.485-0.236-0.009-0.663-0.5770.002
4A175GLU-1-0.863-0.9166.4330.1710.1710.0000.0000.0000.000
5A176LYS10.9400.9616.436-0.715-0.7150.0000.0000.0000.000
6A177ARG10.9110.9538.343-0.335-0.3350.0000.0000.0000.000
7A178VAL00.012-0.00111.5200.1320.1320.0000.0000.0000.000
8A179PRO00.0120.00614.015-0.069-0.0690.0000.0000.0000.000
9A180MET00.0050.01317.778-0.006-0.0060.0000.0000.0000.000
10A181THR00.0580.02320.258-0.012-0.0120.0000.0000.0000.000
11A182ARG11.0070.99022.763-0.163-0.1630.0000.0000.0000.000
12A183LEU0-0.0010.02125.848-0.011-0.0110.0000.0000.0000.000
13A184ARG11.0080.98620.354-0.120-0.1200.0000.0000.0000.000
14A185LYS10.8180.89923.494-0.115-0.1150.0000.0000.0000.000
15A186ARG11.0221.02625.822-0.103-0.1030.0000.0000.0000.000
16A187VAL0-0.0110.00027.064-0.003-0.0030.0000.0000.0000.000
17A188ALA00.0390.01525.062-0.008-0.0080.0000.0000.0000.000
18A189GLU-1-0.808-0.90827.2190.0810.0810.0000.0000.0000.000
19A190ARG10.8810.92229.866-0.063-0.0630.0000.0000.0000.000
20A191LEU00.0210.02728.043-0.003-0.0030.0000.0000.0000.000
21A192LEU0-0.022-0.00428.870-0.005-0.0050.0000.0000.0000.000
22A193GLU-1-0.893-0.94531.6980.0290.0290.0000.0000.0000.000
23A194ALA00.0260.00834.911-0.003-0.0030.0000.0000.0000.000
24A195LYS10.9040.95932.906-0.009-0.0090.0000.0000.0000.000
25A196ASN0-0.035-0.02633.555-0.007-0.0070.0000.0000.0000.000
26A197SER0-0.0100.00437.286-0.001-0.0010.0000.0000.0000.000
27A198THR0-0.055-0.02638.907-0.001-0.0010.0000.0000.0000.000
28A199ALA0-0.014-0.00140.188-0.001-0.0010.0000.0000.0000.000
29A200MET0-0.063-0.01435.1280.0000.0000.0000.0000.0000.000
30A201LEU0-0.0170.01039.840-0.002-0.0020.0000.0000.0000.000
31A202THR0-0.036-0.04338.5740.0010.0010.0000.0000.0000.000
32A203THR0-0.0060.01741.053-0.002-0.0020.0000.0000.0000.000
33A204PHE00.019-0.01738.2670.0010.0010.0000.0000.0000.000
34A205ASN00.015-0.00743.7400.0000.0000.0000.0000.0000.000
35A206GLU-1-0.781-0.85944.112-0.021-0.0210.0000.0000.0000.000
36A207VAL00.0230.01945.1760.0010.0010.0000.0000.0000.000
37A208ASN00.0890.01546.375-0.002-0.0020.0000.0000.0000.000
38A209MET0-0.002-0.00344.3780.0020.0020.0000.0000.0000.000
39A210LYS10.8610.92647.6980.0130.0130.0000.0000.0000.000
40A211PRO00.0500.03250.2280.0010.0010.0000.0000.0000.000
41A212ILE00.0390.02548.1850.0010.0010.0000.0000.0000.000
42A213MET0-0.061-0.03745.0850.0010.0010.0000.0000.0000.000
43A214ASP-1-0.780-0.85848.967-0.010-0.0100.0000.0000.0000.000
44A215LEU00.0430.02352.5240.0010.0010.0000.0000.0000.000
45A216ARG10.7920.88744.8400.0040.0040.0000.0000.0000.000
46A217LYS10.8020.89849.1380.0110.0110.0000.0000.0000.000
47A218GLN0-0.0140.00552.1000.0010.0010.0000.0000.0000.000
48A219TYR00.0280.01054.5170.0010.0010.0000.0000.0000.000
49A220GLY0-0.0010.00551.2790.0010.0010.0000.0000.0000.000
50A221GLU-1-0.835-0.90152.1590.0020.0020.0000.0000.0000.000
51A222ALA00.0700.02453.5000.0010.0010.0000.0000.0000.000
52A223PHE0-0.012-0.01051.1660.0010.0010.0000.0000.0000.000
53A224GLU-1-0.898-0.95848.0870.0080.0080.0000.0000.0000.000
54A225LYS10.8050.88052.273-0.001-0.0010.0000.0000.0000.000
55A226ARG10.8940.95755.451-0.005-0.0050.0000.0000.0000.000
56A227HIS0-0.0100.00153.2760.0010.0010.0000.0000.0000.000
57A228GLY00.0290.02252.0180.0010.0010.0000.0000.0000.000
58A229ILE0-0.094-0.05845.5550.0010.0010.0000.0000.0000.000
59A230ARG10.9540.98942.399-0.003-0.0030.0000.0000.0000.000
60A231LEU00.0140.02247.1640.0010.0010.0000.0000.0000.000
61A232GLY00.0050.01545.008-0.002-0.0020.0000.0000.0000.000
62A233PHE00.0640.00442.317-0.001-0.0010.0000.0000.0000.000
63A234MET00.0260.01739.307-0.001-0.0010.0000.0000.0000.000
64A235SER0-0.043-0.03444.3210.0000.0000.0000.0000.0000.000
65A236PHE00.0200.00747.9380.0000.0000.0000.0000.0000.000
66A237TYR00.036-0.00341.7230.0000.0000.0000.0000.0000.000
67A238VAL00.0140.00444.9220.0000.0000.0000.0000.0000.000
68A239LYS10.8160.90247.241-0.009-0.0090.0000.0000.0000.000
69A240ALA00.0370.02448.9350.0000.0000.0000.0000.0000.000
70A241VAL0-0.012-0.01245.1540.0000.0000.0000.0000.0000.000
71A242VAL0-0.021-0.01148.5720.0000.0000.0000.0000.0000.000
72A243GLU-1-0.833-0.91251.1640.0050.0050.0000.0000.0000.000
73A244ALA00.0040.00450.1420.0000.0000.0000.0000.0000.000
74A245LEU0-0.040-0.04447.5990.0000.0000.0000.0000.0000.000
75A246LYS10.8220.91251.684-0.007-0.0070.0000.0000.0000.000
76A247ARG10.7990.88355.322-0.001-0.0010.0000.0000.0000.000
77A248TYR0-0.0200.00452.444-0.001-0.0010.0000.0000.0000.000
78A249PRO00.0420.02652.5870.0010.0010.0000.0000.0000.000
79A250GLU-1-0.795-0.88651.8640.0090.0090.0000.0000.0000.000
80A251VAL0-0.071-0.04747.1700.0010.0010.0000.0000.0000.000
81A252ASN0-0.023-0.00147.9260.0010.0010.0000.0000.0000.000
82A253ALA00.0330.04049.9320.0020.0020.0000.0000.0000.000
83A254SER0-0.029-0.01445.6090.0000.0000.0000.0000.0000.000
84A255ILE0-0.035-0.00747.0440.0000.0000.0000.0000.0000.000
85A256ASP-1-0.985-0.99946.6710.0260.0260.0000.0000.0000.000
86A257GLY0-0.0010.00647.620-0.001-0.0010.0000.0000.0000.000
87A258ASP-1-0.999-0.99749.1870.0160.0160.0000.0000.0000.000
88A259ASP-1-0.888-0.93551.5610.0140.0140.0000.0000.0000.000
89A260VAL0-0.034-0.02951.3770.0000.0000.0000.0000.0000.000
90A261VAL00.0030.00850.3820.0000.0000.0000.0000.0000.000
91A262TYR0-0.035-0.05651.3820.0000.0000.0000.0000.0000.000
92A263HIS10.7840.89748.127-0.016-0.0160.0000.0000.0000.000
93A264ASN0-0.003-0.00553.297-0.001-0.0010.0000.0000.0000.000
94A265TYR00.0200.01048.9480.0000.0000.0000.0000.0000.000
95A266PHE00.015-0.00850.7940.0000.0000.0000.0000.0000.000
96A267ASP-1-0.773-0.87746.1790.0230.0230.0000.0000.0000.000
97A268VAL0-0.022-0.00643.626-0.001-0.0010.0000.0000.0000.000
98A269SER00.0200.01239.3780.0010.0010.0000.0000.0000.000
99A270MET0-0.016-0.00637.560-0.004-0.0040.0000.0000.0000.000
100A271ALA0-0.017-0.01433.7600.0030.0030.0000.0000.0000.000
101A272VAL0-0.031-0.01733.703-0.003-0.0030.0000.0000.0000.000
102A273SER0-0.0100.00028.7530.0020.0020.0000.0000.0000.000
103A274THR0-0.017-0.02528.1060.0030.0030.0000.0000.0000.000
104A275PRO00.0150.00225.4790.0010.0010.0000.0000.0000.000
105A276ARG10.9060.95723.973-0.110-0.1100.0000.0000.0000.000
106A277GLY0-0.015-0.00424.9820.0070.0070.0000.0000.0000.000
107A278LEU0-0.011-0.00325.833-0.006-0.0060.0000.0000.0000.000
108A279VAL0-0.021-0.00429.1310.0050.0050.0000.0000.0000.000
109A280THR00.025-0.00232.439-0.004-0.0040.0000.0000.0000.000
110A281PRO00.0040.00935.6600.0000.0000.0000.0000.0000.000
111A282VAL00.0000.01738.764-0.003-0.0030.0000.0000.0000.000
112A283LEU0-0.046-0.02042.3410.0000.0000.0000.0000.0000.000
113A284ARG10.8320.88044.240-0.031-0.0310.0000.0000.0000.000
114A285ASP-1-0.816-0.90547.9690.0170.0170.0000.0000.0000.000
115A286VAL0-0.0050.00947.164-0.001-0.0010.0000.0000.0000.000
116A287ASP-1-0.843-0.91550.4630.0100.0100.0000.0000.0000.000
117A288THR0-0.013-0.00653.753-0.001-0.0010.0000.0000.0000.000
118A289LEU0-0.0210.00549.5330.0000.0000.0000.0000.0000.000
119A290GLY00.0730.04753.522-0.001-0.0010.0000.0000.0000.000
120A291MET00.013-0.01551.0890.0010.0010.0000.0000.0000.000
121A292ALA00.0120.00149.9960.0000.0000.0000.0000.0000.000
122A293ASP-1-0.813-0.91149.6440.0130.0130.0000.0000.0000.000
123A294ILE00.0430.03346.4840.0020.0020.0000.0000.0000.000
124A295GLU-1-0.811-0.88744.8410.0080.0080.0000.0000.0000.000
125A296LYS10.8090.90444.787-0.012-0.0120.0000.0000.0000.000
126A297LYS10.8900.92645.033-0.024-0.0240.0000.0000.0000.000
127A298ILE00.0330.02040.5040.0020.0020.0000.0000.0000.000
128A299LYS10.9280.96740.523-0.014-0.0140.0000.0000.0000.000
129A300GLU-1-0.828-0.90140.4780.0300.0300.0000.0000.0000.000
130A301LEU00.0310.00639.5760.0030.0030.0000.0000.0000.000
131A302ALA00.0090.00836.4880.0030.0030.0000.0000.0000.000
132A303VAL0-0.035-0.01135.5390.0030.0030.0000.0000.0000.000
133A304LYS10.8310.91635.819-0.033-0.0330.0000.0000.0000.000
134A305GLY00.0130.01033.7910.0050.0050.0000.0000.0000.000
135A306ARG10.8890.95431.509-0.024-0.0240.0000.0000.0000.000
136A307ASP-1-0.881-0.95330.9030.0500.0500.0000.0000.0000.000
137A308GLY0-0.056-0.02431.6480.0050.0050.0000.0000.0000.000
138A309LYS10.8800.94432.362-0.053-0.0530.0000.0000.0000.000
139A310LEU0-0.0030.00434.432-0.004-0.0040.0000.0000.0000.000
140A311THR0-0.013-0.02636.0820.0040.0040.0000.0000.0000.000
141A312VAL00.036-0.00638.192-0.001-0.0010.0000.0000.0000.000
142A313GLU-1-0.889-0.92239.0340.0340.0340.0000.0000.0000.000
143A314ASP-1-0.756-0.85139.1960.0360.0360.0000.0000.0000.000
144A315LEU0-0.040-0.02035.392-0.002-0.0020.0000.0000.0000.000
145A316THR0-0.044-0.03538.867-0.002-0.0020.0000.0000.0000.000
146A317GLY00.0370.02041.382-0.001-0.0010.0000.0000.0000.000
147A318GLY0-0.031-0.00342.1010.0000.0000.0000.0000.0000.000
148A319ASN0-0.013-0.01244.1900.0020.0020.0000.0000.0000.000
149A320PHE00.0360.02243.615-0.001-0.0010.0000.0000.0000.000
150A321THR0-0.025-0.03437.3510.0030.0030.0000.0000.0000.000
151A322ILE00.0220.02539.984-0.003-0.0030.0000.0000.0000.000
152A323THR0-0.012-0.01633.7190.0030.0030.0000.0000.0000.000
153A324ASN00.0300.00235.125-0.005-0.0050.0000.0000.0000.000
154A325GLY00.0610.03632.2870.0010.0010.0000.0000.0000.000
155A326GLY00.0230.00832.565-0.004-0.0040.0000.0000.0000.000
156A327VAL0-0.086-0.03431.622-0.003-0.0030.0000.0000.0000.000
157A328PHE0-0.028-0.02128.2760.0000.0000.0000.0000.0000.000
158A329GLY00.0110.01529.643-0.005-0.0050.0000.0000.0000.000
159A330SER0-0.043-0.01031.270-0.005-0.0050.0000.0000.0000.000
160A331LEU00.0250.00832.5170.0030.0030.0000.0000.0000.000
161A332MET00.0320.00034.7960.0030.0030.0000.0000.0000.000
162A333SER0-0.080-0.03632.593-0.002-0.0020.0000.0000.0000.000
163A334THR00.0580.02133.2150.0000.0000.0000.0000.0000.000
164A335PRO0-0.0240.00533.6110.0010.0010.0000.0000.0000.000
165A336ILE00.0170.00031.698-0.001-0.0010.0000.0000.0000.000
166A337ILE00.0260.00934.9540.0020.0020.0000.0000.0000.000
167A338ASN0-0.061-0.02336.4430.0050.0050.0000.0000.0000.000
168A339PRO0-0.0060.00336.036-0.001-0.0010.0000.0000.0000.000
169A340PRO0-0.011-0.00238.9630.0030.0030.0000.0000.0000.000
170A341GLN00.0480.05141.171-0.004-0.0040.0000.0000.0000.000
171A342SER00.0640.00642.4280.0000.0000.0000.0000.0000.000
172A343ALA0-0.030-0.02842.303-0.002-0.0020.0000.0000.0000.000
173A344ILE0-0.079-0.02436.3050.0020.0020.0000.0000.0000.000
174A345LEU00.0250.02140.671-0.002-0.0020.0000.0000.0000.000
175A346GLY0-0.018-0.02237.8000.0020.0020.0000.0000.0000.000
176A347MET0-0.037-0.01438.253-0.002-0.0020.0000.0000.0000.000
177A348HIS0-0.014-0.01335.088-0.001-0.0010.0000.0000.0000.000
178A349ALA0-0.005-0.01735.1730.0010.0010.0000.0000.0000.000
179A350ILE0-0.019-0.00537.198-0.001-0.0010.0000.0000.0000.000
180A351LYS10.8980.94335.7590.0350.0350.0000.0000.0000.000
181A352ASP-1-0.887-0.93641.126-0.021-0.0210.0000.0000.0000.000
182A353ARG10.7850.85543.1130.0210.0210.0000.0000.0000.000
183A354PRO00.002-0.00145.3520.0020.0020.0000.0000.0000.000
184A355MET0-0.030-0.01148.3730.0000.0000.0000.0000.0000.000
185A356ALA00.0120.01150.8940.0000.0000.0000.0000.0000.000
186A357VAL00.0120.00354.2680.0010.0010.0000.0000.0000.000
187A358ASN0-0.023-0.01856.9150.0000.0000.0000.0000.0000.000
188A359GLY00.0060.01359.5360.0000.0000.0000.0000.0000.000
189A360GLN0-0.0200.00258.702-0.001-0.0010.0000.0000.0000.000
190A361VAL0-0.014-0.01352.4060.0000.0000.0000.0000.0000.000
191A362GLU-1-0.901-0.95153.128-0.015-0.0150.0000.0000.0000.000
192A363ILE0-0.045-0.03047.228-0.001-0.0010.0000.0000.0000.000
193A364LEU00.0130.01548.4660.0010.0010.0000.0000.0000.000
194A365PRO00.0220.00244.938-0.001-0.0010.0000.0000.0000.000
195A366MET0-0.0160.03044.2900.0020.0020.0000.0000.0000.000
196A367MET0-0.034-0.00940.441-0.001-0.0010.0000.0000.0000.000
197A368TYR00.0120.00439.5900.0000.0000.0000.0000.0000.000
198A369LEU0-0.031-0.00640.8280.0010.0010.0000.0000.0000.000
199A370ALA00.0160.00538.753-0.002-0.0020.0000.0000.0000.000
200A371LEU00.0180.01740.8350.0020.0020.0000.0000.0000.000
201A372SER0-0.011-0.02237.280-0.003-0.0030.0000.0000.0000.000
202A373TYR0-0.002-0.01340.4590.0020.0020.0000.0000.0000.000
203A374ASP-1-0.678-0.84142.7360.0080.0080.0000.0000.0000.000
204A375HIS00.0140.00843.9320.0000.0000.0000.0000.0000.000
205A376ARG10.8220.89744.346-0.014-0.0140.0000.0000.0000.000
206A377LEU0-0.0100.01147.7060.0010.0010.0000.0000.0000.000
207A378ILE0-0.0250.00346.346-0.001-0.0010.0000.0000.0000.000
208A379ASP-1-0.731-0.87648.562-0.003-0.0030.0000.0000.0000.000
209A380GLY00.0080.02149.1490.0000.0000.0000.0000.0000.000
210A381ARG10.8330.89350.1890.0000.0000.0000.0000.0000.000
211A382GLU-1-0.822-0.90351.9130.0010.0010.0000.0000.0000.000
212A383SER0-0.030-0.02746.8890.0000.0000.0000.0000.0000.000
213A384VAL0-0.017-0.01648.5800.0000.0000.0000.0000.0000.000
214A385GLY00.0290.01850.0210.0000.0000.0000.0000.0000.000
215A386PHE00.0300.02446.1740.0000.0000.0000.0000.0000.000
216A387LEU0-0.046-0.02444.3780.0000.0000.0000.0000.0000.000
217A388VAL0-0.001-0.00448.322-0.001-0.0010.0000.0000.0000.000
218A389THR0-0.008-0.01051.2820.0000.0000.0000.0000.0000.000
219A390ILE0-0.013-0.01446.2990.0000.0000.0000.0000.0000.000
220A391LYS10.8040.88548.9720.0110.0110.0000.0000.0000.000
221A392GLU-1-0.802-0.88249.976-0.004-0.0040.0000.0000.0000.000
222A393LEU0-0.036-0.01452.3320.0000.0000.0000.0000.0000.000
223A394LEU0-0.080-0.04246.8890.0010.0010.0000.0000.0000.000
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