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: ZVV4N

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2793435.779348
FMO2-HF: Nuclear repulsion 2701038.646709
FMO2-HF: Total energy -92397.132639
FMO2-MP2: Total energy -92662.521531


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.
-2.543-1.3-0.006-0.675-0.5630.003
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 : 0.013 / 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].
3A174SER00.0590.0303.834-1.1460.097-0.006-0.675-0.5630.003
4A175GLU-1-0.924-0.9536.1910.1650.1650.0000.0000.0000.000
5A176LYS10.9290.9656.912-0.697-0.6970.0000.0000.0000.000
6A177ARG10.9910.9968.635-0.364-0.3640.0000.0000.0000.000
7A178VAL00.001-0.00511.9150.0980.0980.0000.0000.0000.000
8A179PRO00.0140.00814.368-0.069-0.0690.0000.0000.0000.000
9A180MET00.0010.01318.067-0.001-0.0010.0000.0000.0000.000
10A181THR00.0330.00720.667-0.009-0.0090.0000.0000.0000.000
11A182ARG11.0561.00023.151-0.160-0.1600.0000.0000.0000.000
12A183LEU0-0.0090.00726.682-0.010-0.0100.0000.0000.0000.000
13A184ARG11.0110.98821.013-0.124-0.1240.0000.0000.0000.000
14A185LYS10.8260.90924.232-0.110-0.1100.0000.0000.0000.000
15A186ARG11.0251.02826.301-0.099-0.0990.0000.0000.0000.000
16A187VAL0-0.025-0.00327.641-0.005-0.0050.0000.0000.0000.000
17A188ALA00.0230.00325.453-0.007-0.0070.0000.0000.0000.000
18A189GLU-1-0.842-0.91527.5630.0780.0780.0000.0000.0000.000
19A190ARG10.9330.94930.081-0.062-0.0620.0000.0000.0000.000
20A191LEU00.0120.03428.492-0.003-0.0030.0000.0000.0000.000
21A192LEU0-0.013-0.00429.210-0.005-0.0050.0000.0000.0000.000
22A193GLU-1-0.901-0.95232.2480.0300.0300.0000.0000.0000.000
23A194ALA00.020-0.00535.431-0.003-0.0030.0000.0000.0000.000
24A195LYS10.9030.95333.319-0.008-0.0080.0000.0000.0000.000
25A196ASN0-0.040-0.02733.703-0.008-0.0080.0000.0000.0000.000
26A197SER00.0050.01737.493-0.001-0.0010.0000.0000.0000.000
27A198THR0-0.071-0.02539.436-0.001-0.0010.0000.0000.0000.000
28A199ALA0-0.017-0.00840.602-0.001-0.0010.0000.0000.0000.000
29A200MET0-0.058-0.00535.4850.0000.0000.0000.0000.0000.000
30A201LEU0-0.0120.01740.410-0.003-0.0030.0000.0000.0000.000
31A202THR0-0.029-0.03938.8710.0010.0010.0000.0000.0000.000
32A203THR0-0.0140.01941.432-0.003-0.0030.0000.0000.0000.000
33A204PHE00.008-0.02438.5390.0010.0010.0000.0000.0000.000
34A205ASN00.0450.01843.9020.0000.0000.0000.0000.0000.000
35A206GLU-1-0.800-0.87244.338-0.022-0.0220.0000.0000.0000.000
36A207VAL0-0.0070.00345.3990.0010.0010.0000.0000.0000.000
37A208ASN00.1000.02346.608-0.002-0.0020.0000.0000.0000.000
38A209MET00.011-0.00144.6390.0020.0020.0000.0000.0000.000
39A210LYS10.8620.92247.9510.0130.0130.0000.0000.0000.000
40A211PRO00.0350.02750.4150.0010.0010.0000.0000.0000.000
41A212ILE00.0460.02548.2420.0010.0010.0000.0000.0000.000
42A213MET0-0.076-0.04745.3550.0010.0010.0000.0000.0000.000
43A214ASP-1-0.775-0.87049.268-0.010-0.0100.0000.0000.0000.000
44A215LEU00.0520.03952.8440.0010.0010.0000.0000.0000.000
45A216ARG10.7970.89944.9710.0040.0040.0000.0000.0000.000
46A217LYS10.8240.90749.1690.0110.0110.0000.0000.0000.000
47A218GLN0-0.0170.00352.1440.0000.0000.0000.0000.0000.000
48A219TYR00.0140.00054.7920.0010.0010.0000.0000.0000.000
49A220GLY00.0060.01251.6160.0010.0010.0000.0000.0000.000
50A221GLU-1-0.835-0.90952.3990.0020.0020.0000.0000.0000.000
51A222ALA00.0570.01553.9960.0010.0010.0000.0000.0000.000
52A223PHE0-0.014-0.00651.4010.0010.0010.0000.0000.0000.000
53A224GLU-1-0.938-0.97848.4000.0070.0070.0000.0000.0000.000
54A225LYS10.8010.89452.690-0.001-0.0010.0000.0000.0000.000
55A226ARG10.9180.98255.821-0.005-0.0050.0000.0000.0000.000
56A227HIS0-0.011-0.01553.5160.0010.0010.0000.0000.0000.000
57A228GLY00.0410.03152.4580.0010.0010.0000.0000.0000.000
58A229ILE0-0.091-0.05345.9180.0020.0020.0000.0000.0000.000
59A230ARG11.0081.00942.808-0.003-0.0030.0000.0000.0000.000
60A231LEU00.0210.02847.7430.0010.0010.0000.0000.0000.000
61A232GLY0-0.0090.00345.023-0.002-0.0020.0000.0000.0000.000
62A233PHE00.0560.00042.587-0.001-0.0010.0000.0000.0000.000
63A234MET00.0450.01739.641-0.001-0.0010.0000.0000.0000.000
64A235SER0-0.025-0.01744.4130.0000.0000.0000.0000.0000.000
65A236PHE00.0210.00347.9590.0000.0000.0000.0000.0000.000
66A237TYR00.021-0.01041.7810.0000.0000.0000.0000.0000.000
67A238VAL00.0120.00745.3940.0000.0000.0000.0000.0000.000
68A239LYS10.8820.94447.711-0.008-0.0080.0000.0000.0000.000
69A240ALA00.0300.02249.2630.0000.0000.0000.0000.0000.000
70A241VAL0-0.006-0.01445.6660.0000.0000.0000.0000.0000.000
71A242VAL0-0.025-0.01249.1020.0000.0000.0000.0000.0000.000
72A243GLU-1-0.819-0.90351.7140.0040.0040.0000.0000.0000.000
73A244ALA00.0060.00350.7110.0000.0000.0000.0000.0000.000
74A245LEU0-0.041-0.04048.1530.0000.0000.0000.0000.0000.000
75A246LYS10.8070.90552.204-0.008-0.0080.0000.0000.0000.000
76A247ARG10.8200.89755.712-0.001-0.0010.0000.0000.0000.000
77A248TYR0-0.035-0.00452.857-0.001-0.0010.0000.0000.0000.000
78A249PRO00.0390.01453.0200.0010.0010.0000.0000.0000.000
79A250GLU-1-0.780-0.86952.6980.0080.0080.0000.0000.0000.000
80A251VAL0-0.058-0.04047.6330.0010.0010.0000.0000.0000.000
81A252ASN0-0.051-0.01448.4400.0020.0020.0000.0000.0000.000
82A253ALA00.0280.03750.4190.0020.0020.0000.0000.0000.000
83A254SER0-0.0210.00146.0780.0000.0000.0000.0000.0000.000
84A255ILE0-0.0150.00047.147-0.001-0.0010.0000.0000.0000.000
85A256ASP-1-1.005-0.99947.0140.0260.0260.0000.0000.0000.000
86A257GLY00.0150.01248.0420.0000.0000.0000.0000.0000.000
87A258ASP-1-0.985-0.99349.7470.0150.0150.0000.0000.0000.000
88A259ASP-1-0.920-0.95152.2790.0150.0150.0000.0000.0000.000
89A260VAL0-0.022-0.01251.7700.0010.0010.0000.0000.0000.000
90A261VAL0-0.026-0.02051.0590.0000.0000.0000.0000.0000.000
91A262TYR0-0.025-0.04251.9790.0000.0000.0000.0000.0000.000
92A263HIS10.8030.89848.536-0.017-0.0170.0000.0000.0000.000
93A264ASN0-0.007-0.00653.629-0.001-0.0010.0000.0000.0000.000
94A265TYR00.0450.02349.2590.0000.0000.0000.0000.0000.000
95A266PHE00.012-0.01351.0370.0000.0000.0000.0000.0000.000
96A267ASP-1-0.777-0.86646.6260.0230.0230.0000.0000.0000.000
97A268VAL0-0.025-0.01943.792-0.001-0.0010.0000.0000.0000.000
98A269SER00.0320.01439.7170.0010.0010.0000.0000.0000.000
99A270MET00.002-0.00838.150-0.004-0.0040.0000.0000.0000.000
100A271ALA0-0.027-0.00934.1870.0030.0030.0000.0000.0000.000
101A272VAL0-0.006-0.00834.199-0.003-0.0030.0000.0000.0000.000
102A273SER0-0.035-0.01629.1090.0030.0030.0000.0000.0000.000
103A274THR0-0.017-0.01928.5930.0030.0030.0000.0000.0000.000
104A275PRO00.008-0.00725.8570.0020.0020.0000.0000.0000.000
105A276ARG10.8960.95024.346-0.116-0.1160.0000.0000.0000.000
106A277GLY0-0.0050.00525.6940.0050.0050.0000.0000.0000.000
107A278LEU0-0.0010.00626.442-0.005-0.0050.0000.0000.0000.000
108A279VAL0-0.011-0.00529.7400.0040.0040.0000.0000.0000.000
109A280THR00.019-0.00832.983-0.004-0.0040.0000.0000.0000.000
110A281PRO00.0050.01936.1770.0010.0010.0000.0000.0000.000
111A282VAL0-0.0160.00039.212-0.003-0.0030.0000.0000.0000.000
112A283LEU0-0.056-0.01642.7600.0010.0010.0000.0000.0000.000
113A284ARG10.8470.88844.347-0.030-0.0300.0000.0000.0000.000
114A285ASP-1-0.826-0.89948.6890.0180.0180.0000.0000.0000.000
115A286VAL00.0050.00247.613-0.001-0.0010.0000.0000.0000.000
116A287ASP-1-0.893-0.94550.9140.0100.0100.0000.0000.0000.000
117A288THR0-0.041-0.01754.235-0.001-0.0010.0000.0000.0000.000
118A289LEU0-0.038-0.00350.1060.0000.0000.0000.0000.0000.000
119A290GLY00.0560.03653.937-0.001-0.0010.0000.0000.0000.000
120A291MET00.031-0.01451.2010.0010.0010.0000.0000.0000.000
121A292ALA0-0.006-0.00150.5030.0000.0000.0000.0000.0000.000
122A293ASP-1-0.858-0.94150.2710.0140.0140.0000.0000.0000.000
123A294ILE00.0060.01247.0470.0010.0010.0000.0000.0000.000
124A295GLU-1-0.825-0.90245.2970.0090.0090.0000.0000.0000.000
125A296LYS10.8490.92945.290-0.012-0.0120.0000.0000.0000.000
126A297LYS10.9080.93845.368-0.025-0.0250.0000.0000.0000.000
127A298ILE00.0350.02341.0510.0020.0020.0000.0000.0000.000
128A299LYS10.9330.97140.939-0.016-0.0160.0000.0000.0000.000
129A300GLU-1-0.848-0.90840.7430.0310.0310.0000.0000.0000.000
130A301LEU00.0400.00439.9040.0030.0030.0000.0000.0000.000
131A302ALA0-0.006-0.00236.9710.0030.0030.0000.0000.0000.000
132A303VAL0-0.022-0.01335.9140.0030.0030.0000.0000.0000.000
133A304LYS10.8840.95636.170-0.034-0.0340.0000.0000.0000.000
134A305GLY0-0.008-0.00234.3610.0050.0050.0000.0000.0000.000
135A306ARG10.9170.97032.024-0.028-0.0280.0000.0000.0000.000
136A307ASP-1-0.924-0.96131.5280.0530.0530.0000.0000.0000.000
137A308GLY0-0.064-0.03032.0210.0050.0050.0000.0000.0000.000
138A309LYS10.9000.94132.845-0.055-0.0550.0000.0000.0000.000
139A310LEU0-0.026-0.00234.852-0.003-0.0030.0000.0000.0000.000
140A311THR0-0.002-0.01636.6120.0040.0040.0000.0000.0000.000
141A312VAL00.033-0.00838.514-0.001-0.0010.0000.0000.0000.000
142A313GLU-1-0.901-0.93739.3770.0350.0350.0000.0000.0000.000
143A314ASP-1-0.777-0.87739.9190.0380.0380.0000.0000.0000.000
144A315LEU0-0.053-0.03335.766-0.002-0.0020.0000.0000.0000.000
145A316THR0-0.037-0.00139.218-0.001-0.0010.0000.0000.0000.000
146A317GLY00.0410.03141.525-0.001-0.0010.0000.0000.0000.000
147A318GLY0-0.006-0.00442.5220.0010.0010.0000.0000.0000.000
148A319ASN0-0.038-0.02744.5490.0020.0020.0000.0000.0000.000
149A320PHE00.0470.02444.059-0.002-0.0020.0000.0000.0000.000
150A321THR0-0.007-0.02137.7750.0030.0030.0000.0000.0000.000
151A322ILE00.0250.03040.587-0.003-0.0030.0000.0000.0000.000
152A323THR0-0.019-0.02134.1590.0030.0030.0000.0000.0000.000
153A324ASN00.0410.00835.992-0.005-0.0050.0000.0000.0000.000
154A325GLY00.0540.03232.7760.0020.0020.0000.0000.0000.000
155A326GLY00.0330.00132.830-0.004-0.0040.0000.0000.0000.000
156A327VAL0-0.080-0.02732.155-0.003-0.0030.0000.0000.0000.000
157A328PHE0-0.033-0.02928.6170.0000.0000.0000.0000.0000.000
158A329GLY00.0090.01929.889-0.006-0.0060.0000.0000.0000.000
159A330SER0-0.044-0.01131.894-0.005-0.0050.0000.0000.0000.000
160A331LEU00.0340.02032.9450.0020.0020.0000.0000.0000.000
161A332MET00.027-0.00634.8300.0030.0030.0000.0000.0000.000
162A333SER0-0.074-0.03132.850-0.002-0.0020.0000.0000.0000.000
163A334THR00.0650.02233.6330.0000.0000.0000.0000.0000.000
164A335PRO0-0.0330.00533.9950.0010.0010.0000.0000.0000.000
165A336ILE00.0290.00632.071-0.001-0.0010.0000.0000.0000.000
166A337ILE00.0410.01435.1630.0020.0020.0000.0000.0000.000
167A338ASN0-0.068-0.02436.6790.0050.0050.0000.0000.0000.000
168A339PRO0-0.0140.01636.233-0.001-0.0010.0000.0000.0000.000
169A340PRO0-0.017-0.01539.1750.0030.0030.0000.0000.0000.000
170A341GLN00.0390.02641.526-0.004-0.0040.0000.0000.0000.000
171A342SER00.0680.00842.6340.0000.0000.0000.0000.0000.000
172A343ALA0-0.014-0.01742.738-0.002-0.0020.0000.0000.0000.000
173A344ILE0-0.086-0.02436.7170.0020.0020.0000.0000.0000.000
174A345LEU00.0200.01541.103-0.002-0.0020.0000.0000.0000.000
175A346GLY0-0.018-0.01938.0140.0020.0020.0000.0000.0000.000
176A347MET0-0.051-0.02538.345-0.002-0.0020.0000.0000.0000.000
177A348HIS0-0.021-0.02235.190-0.001-0.0010.0000.0000.0000.000
178A349ALA0-0.001-0.01035.4850.0020.0020.0000.0000.0000.000
179A350ILE0-0.036-0.00837.540-0.001-0.0010.0000.0000.0000.000
180A351LYS10.9110.94136.0410.0370.0370.0000.0000.0000.000
181A352ASP-1-0.893-0.93441.143-0.022-0.0220.0000.0000.0000.000
182A353ARG10.7950.86143.2300.0210.0210.0000.0000.0000.000
183A354PRO0-0.011-0.00645.4040.0020.0020.0000.0000.0000.000
184A355MET0-0.026-0.00748.2540.0000.0000.0000.0000.0000.000
185A356ALA00.0060.00751.0210.0000.0000.0000.0000.0000.000
186A357VAL00.021-0.00154.3230.0010.0010.0000.0000.0000.000
187A358ASN0-0.010-0.00956.9500.0000.0000.0000.0000.0000.000
188A359GLY00.0080.00759.5830.0000.0000.0000.0000.0000.000
189A360GLN0-0.0210.00158.453-0.001-0.0010.0000.0000.0000.000
190A361VAL0-0.020-0.00252.1130.0000.0000.0000.0000.0000.000
191A362GLU-1-0.901-0.96053.329-0.016-0.0160.0000.0000.0000.000
192A363ILE0-0.041-0.01947.128-0.001-0.0010.0000.0000.0000.000
193A364LEU00.0050.01848.5530.0010.0010.0000.0000.0000.000
194A365PRO00.0320.01145.240-0.002-0.0020.0000.0000.0000.000
195A366MET0-0.0350.00544.4670.0020.0020.0000.0000.0000.000
196A367MET0-0.025-0.00340.745-0.001-0.0010.0000.0000.0000.000
197A368TYR00.0210.01039.7750.0000.0000.0000.0000.0000.000
198A369LEU0-0.033-0.01040.9170.0010.0010.0000.0000.0000.000
199A370ALA00.0140.00038.860-0.002-0.0020.0000.0000.0000.000
200A371LEU00.0120.02140.9490.0020.0020.0000.0000.0000.000
201A372SER0-0.012-0.03037.810-0.003-0.0030.0000.0000.0000.000
202A373TYR0-0.001-0.01340.9830.0020.0020.0000.0000.0000.000
203A374ASP-1-0.687-0.84643.2470.0080.0080.0000.0000.0000.000
204A375HIS00.009-0.00744.2960.0000.0000.0000.0000.0000.000
205A376ARG10.8140.90244.683-0.013-0.0130.0000.0000.0000.000
206A377LEU0-0.0090.00547.9970.0000.0000.0000.0000.0000.000
207A378ILE0-0.0170.00646.7870.0000.0000.0000.0000.0000.000
208A379ASP-1-0.734-0.87949.031-0.003-0.0030.0000.0000.0000.000
209A380GLY00.0010.00149.7580.0000.0000.0000.0000.0000.000
210A381ARG10.9370.96150.8170.0010.0010.0000.0000.0000.000
211A382GLU-1-0.883-0.95252.5970.0020.0020.0000.0000.0000.000
212A383SER0-0.031-0.00847.3200.0000.0000.0000.0000.0000.000
213A384VAL0-0.026-0.02448.9780.0000.0000.0000.0000.0000.000
214A385GLY00.0290.01850.4780.0000.0000.0000.0000.0000.000
215A386PHE00.0240.01646.6390.0000.0000.0000.0000.0000.000
216A387LEU0-0.031-0.02644.9540.0000.0000.0000.0000.0000.000
217A388VAL0-0.006-0.00648.831-0.001-0.0010.0000.0000.0000.000
218A389THR0-0.0040.00251.8430.0000.0000.0000.0000.0000.000
219A390ILE0-0.002-0.00646.8080.0000.0000.0000.0000.0000.000
220A391LYS10.7990.88049.3270.0110.0110.0000.0000.0000.000
221A392GLU-1-0.834-0.90150.418-0.005-0.0050.0000.0000.0000.000
222A393LEU0-0.027-0.01052.6860.0000.0000.0000.0000.0000.000
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