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: KGK23

Calculation Name: 1SZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SZI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DBG5

Base Structure: X-ray

Registration Date: 2023-09-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964817.877203
FMO2-HF: Nuclear repulsion 1888815.277745
FMO2-HF: Total energy -76002.599458
FMO2-MP2: Total energy -76223.708522


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:206:ASN)


Summations of interaction energy for fragment #1(A:206:ASN)
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.
-16.974-8.8732.319-4.104-6.316-0.027
Interaction energy analysis for fragmet #1(A:206:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.008
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].
3A208LEU00.0280.0213.8790.7382.226-0.019-0.691-0.7790.000
4A209PRO0-0.044-0.0176.886-0.138-0.1380.0000.0000.0000.000
5A210LEU0-0.002-0.00610.241-0.165-0.1650.0000.0000.0000.000
6A211THR00.005-0.01411.2290.0360.0360.0000.0000.0000.000
7A212GLU-1-0.799-0.88110.862-1.784-1.7840.0000.0000.0000.000
8A213ALA00.0340.02212.295-0.151-0.1510.0000.0000.0000.000
9A214GLU-1-0.840-0.91014.409-0.142-0.1420.0000.0000.0000.000
10A215LEU0-0.040-0.0217.3270.0020.0020.0000.0000.0000.000
11A216ALA00.014-0.00312.025-0.149-0.1490.0000.0000.0000.000
12A217LEU0-0.058-0.01913.5080.0280.0280.0000.0000.0000.000
13A218ILE0-0.040-0.01612.2950.1000.1000.0000.0000.0000.000
14A219ALA0-0.0160.01211.991-0.083-0.0830.0000.0000.0000.000
15A220THR0-0.108-0.07012.5640.3320.3320.0000.0000.0000.000
16A221PRO00.0040.00012.862-0.257-0.2570.0000.0000.0000.000
17A222PRO00.0410.02511.5890.1720.1720.0000.0000.0000.000
18A223GLU-1-0.806-0.88913.823-0.665-0.6650.0000.0000.0000.000
19A224ASP-1-0.925-0.96616.493-1.049-1.0490.0000.0000.0000.000
20A225SER0-0.086-0.04015.7800.0890.0890.0000.0000.0000.000
21A226ASP-1-0.717-0.83916.231-1.091-1.0910.0000.0000.0000.000
22A227MET0-0.006-0.00317.471-0.119-0.1190.0000.0000.0000.000
23A228ALA0-0.034-0.00918.275-0.046-0.0460.0000.0000.0000.000
24A229SER00.025-0.02014.523-0.101-0.1010.0000.0000.0000.000
25A230LEU0-0.070-0.02713.269-0.301-0.3010.0000.0000.0000.000
26A231GLN00.0000.01113.503-0.146-0.1460.0000.0000.0000.000
27A232GLN0-0.060-0.03111.6540.1860.1860.0000.0000.0000.000
28A233GLN00.014-0.0028.603-0.289-0.2890.0000.0000.0000.000
29A234ARG10.8790.9359.0800.8280.8280.0000.0000.0000.000
30A235GLN0-0.051-0.04111.5060.3540.3540.0000.0000.0000.000
31A236GLU-1-0.880-0.9107.274-3.116-3.1160.0000.0000.0000.000
32A237GLN0-0.084-0.0416.592-0.586-0.5860.0000.0000.0000.000
33A238ASN0-0.070-0.0413.579-5.575-5.2430.004-0.131-0.205-0.001
34A239TYR0-0.047-0.0585.7761.4891.4890.0000.0000.0000.000
35A240PHE00.0280.0066.651-1.480-1.4800.0000.0000.0000.000
36A241VAL00.0270.0068.8020.4000.4000.0000.0000.0000.000
37A242ARG10.9310.96611.1720.9420.9420.0000.0000.0000.000
38A243LEU00.0220.01610.5060.0890.0890.0000.0000.0000.000
39A244GLY0-0.007-0.00613.5310.1400.1400.0000.0000.0000.000
40A245SER0-0.035-0.01114.4560.1190.1190.0000.0000.0000.000
41A246LEU00.0190.02910.3800.0010.0010.0000.0000.0000.000
42A247SER00.0310.01114.5280.0640.0640.0000.0000.0000.000
43A248GLU-1-0.922-0.96514.8380.2120.2120.0000.0000.0000.000
44A249ARG10.9800.98513.845-0.661-0.6610.0000.0000.0000.000
45A250LEU00.0210.0139.3050.2130.2130.0000.0000.0000.000
46A251ARG10.9000.94110.2690.1280.1280.0000.0000.0000.000
47A252ASN00.0270.00111.489-0.085-0.0850.0000.0000.0000.000
48A253HIS00.0230.0226.045-0.462-0.4620.0000.0000.0000.000
49A254ALA00.018-0.0016.7460.3740.3740.0000.0000.0000.000
50A255TYR0-0.033-0.0257.815-0.188-0.1880.0000.0000.0000.000
51A256GLU-1-0.895-0.95110.4350.8140.8140.0000.0000.0000.000
52A257HIS0-0.005-0.0032.609-3.261-2.1460.666-0.785-0.996-0.004
53A258SER0-0.022-0.0287.258-0.422-0.4220.0000.0000.0000.000
54A259LEU00.0110.0168.444-0.166-0.1660.0000.0000.0000.000
55A260GLY00.0230.01510.054-0.078-0.0780.0000.0000.0000.000
56A261LYS10.8290.9124.4982.4762.569-0.001-0.009-0.0830.000
57A262LEU00.0370.0199.610-0.082-0.0820.0000.0000.0000.000
58A263GLN00.0450.03212.971-0.044-0.0440.0000.0000.0000.000
59A264ASN0-0.006-0.00511.236-0.043-0.0430.0000.0000.0000.000
60A265ALA0-0.0040.00212.349-0.017-0.0170.0000.0000.0000.000
61A266ARG10.8620.92114.123-0.035-0.0350.0000.0000.0000.000
62A267GLN0-0.044-0.02516.8010.0210.0210.0000.0000.0000.000
63A268LYS10.9120.94613.283-0.151-0.1510.0000.0000.0000.000
64A269ALA00.0250.00918.198-0.014-0.0140.0000.0000.0000.000
65A270GLN0-0.087-0.05719.9990.0280.0280.0000.0000.0000.000
66A271GLU-1-0.877-0.92920.3200.0850.0850.0000.0000.0000.000
67A272THR00.0250.00722.265-0.005-0.0050.0000.0000.0000.000
68A273LEU0-0.0030.00923.9920.0020.0020.0000.0000.0000.000
69A274GLN00.0280.02925.3360.0010.0010.0000.0000.0000.000
70A275GLN0-0.0050.01124.419-0.002-0.0020.0000.0000.0000.000
71A276LEU00.0210.01227.2940.0060.0060.0000.0000.0000.000
72A277THR0-0.016-0.02730.0550.0040.0040.0000.0000.0000.000
73A278SER0-0.036-0.02631.1130.0110.0110.0000.0000.0000.000
74A279VAL00.002-0.00531.8820.0050.0050.0000.0000.0000.000
75A280LEU0-0.0080.00434.0680.0010.0010.0000.0000.0000.000
76A281GLY00.0250.01536.0060.0030.0030.0000.0000.0000.000
77A282LEU0-0.027-0.01135.6500.0040.0040.0000.0000.0000.000
78A283MET0-0.0120.00936.1100.0000.0000.0000.0000.0000.000
79A284GLU-1-0.807-0.87540.057-0.047-0.0470.0000.0000.0000.000
80A285SER0-0.083-0.05341.7240.0040.0040.0000.0000.0000.000
81A286VAL0-0.010-0.00842.8780.0020.0020.0000.0000.0000.000
82A287LYS10.8010.91344.2080.0620.0620.0000.0000.0000.000
83A288GLN0-0.082-0.01945.6010.0020.0020.0000.0000.0000.000
84A321ALA00.0220.00047.9410.0020.0020.0000.0000.0000.000
85A322LYS10.9440.95447.1470.0150.0150.0000.0000.0000.000
86A323PRO00.0450.03746.5340.0010.0010.0000.0000.0000.000
87A324GLU-1-0.850-0.93345.680-0.061-0.0610.0000.0000.0000.000
88A325GLN00.009-0.00443.204-0.002-0.0020.0000.0000.0000.000
89A326VAL0-0.050-0.02041.486-0.003-0.0030.0000.0000.0000.000
90A327GLU-1-0.812-0.89840.642-0.067-0.0670.0000.0000.0000.000
91A328ALA00.0560.02640.082-0.006-0.0060.0000.0000.0000.000
92A329ARG10.9180.98337.0970.0310.0310.0000.0000.0000.000
93A330ALA0-0.008-0.00236.002-0.005-0.0050.0000.0000.0000.000
94A331LEU00.0430.01735.323-0.007-0.0070.0000.0000.0000.000
95A332SER0-0.071-0.05234.498-0.011-0.0110.0000.0000.0000.000
96A333MET00.0320.01731.257-0.008-0.0080.0000.0000.0000.000
97A334PHE00.012-0.00330.546-0.009-0.0090.0000.0000.0000.000
98A335ARG10.8630.94430.4200.1360.1360.0000.0000.0000.000
99A336ASP-1-0.868-0.92227.985-0.208-0.2080.0000.0000.0000.000
100A337ILE0-0.022-0.01726.101-0.022-0.0220.0000.0000.0000.000
101A338THR0-0.027-0.02825.533-0.016-0.0160.0000.0000.0000.000
102A339GLN00.0050.00624.630-0.048-0.0480.0000.0000.0000.000
103A340GLN0-0.0160.00121.524-0.034-0.0340.0000.0000.0000.000
104A341LEU00.0340.01920.828-0.045-0.0450.0000.0000.0000.000
105A342GLN00.0260.00421.574-0.022-0.0220.0000.0000.0000.000
106A343SER0-0.015-0.01518.902-0.064-0.0640.0000.0000.0000.000
107A344MET0-0.023-0.00516.749-0.096-0.0960.0000.0000.0000.000
108A345CYS0-0.023-0.01217.213-0.049-0.0490.0000.0000.0000.000
109A346VAL0-0.030-0.01717.062-0.041-0.0410.0000.0000.0000.000
110A347ALA00.0140.00613.179-0.091-0.0910.0000.0000.0000.000
111A348LEU00.004-0.00113.836-0.134-0.1340.0000.0000.0000.000
112A349GLY00.0080.00515.520-0.026-0.0260.0000.0000.0000.000
113A350ALA00.0160.01213.1180.0070.0070.0000.0000.0000.000
114A351SER0-0.066-0.04211.523-0.051-0.0510.0000.0000.0000.000
115A352ILE00.0210.01512.4650.0810.0810.0000.0000.0000.000
116A353GLN00.0470.02514.232-0.009-0.0090.0000.0000.0000.000
117A354GLY00.000-0.01315.334-0.042-0.0420.0000.0000.0000.000
118A355LEU0-0.0190.00616.1780.0800.0800.0000.0000.0000.000
119A356PRO0-0.003-0.00219.065-0.015-0.0150.0000.0000.0000.000
120A357SER0-0.017-0.02922.8770.0000.0000.0000.0000.0000.000
121A358HIS00.0760.03924.990-0.027-0.0270.0000.0000.0000.000
122A359VAL0-0.0050.01020.5650.0140.0140.0000.0000.0000.000
123A360ARG10.7710.85919.2660.6480.6480.0000.0000.0000.000
124A361GLU-1-0.835-0.91222.609-0.298-0.2980.0000.0000.0000.000
125A362GLN00.000-0.00225.4030.0150.0150.0000.0000.0000.000
126A363ALA00.0270.01021.3010.0090.0090.0000.0000.0000.000
127A364GLN0-0.050-0.03123.1150.0160.0160.0000.0000.0000.000
128A365GLN00.0220.01624.8500.0210.0210.0000.0000.0000.000
129A366ALA00.0480.04124.9800.0130.0130.0000.0000.0000.000
130A367ARG10.9030.95919.0240.6710.6710.0000.0000.0000.000
131A368SER0-0.055-0.03024.998-0.005-0.0050.0000.0000.0000.000
132A369GLN0-0.007-0.01628.5150.0150.0150.0000.0000.0000.000
133A370VAL00.0020.00125.0620.0200.0200.0000.0000.0000.000
134A371ASN00.0080.00325.8950.0060.0060.0000.0000.0000.000
135A372ASP-1-0.791-0.89229.098-0.213-0.2130.0000.0000.0000.000
136A373LEU0-0.0430.01029.8240.0190.0190.0000.0000.0000.000
137A374GLN0-0.030-0.03228.3750.0340.0340.0000.0000.0000.000
138A375ALA00.0060.00431.7190.0100.0100.0000.0000.0000.000
139A376THR0-0.041-0.02734.5290.0150.0150.0000.0000.0000.000
140A377PHE00.0400.00034.2010.0110.0110.0000.0000.0000.000
141A378SER0-0.079-0.03635.4760.0070.0070.0000.0000.0000.000
142A379GLY0-0.006-0.00637.0840.0040.0040.0000.0000.0000.000
143A380ILE0-0.067-0.01538.2460.0090.0090.0000.0000.0000.000
144A381HIS0-0.021-0.02639.700-0.002-0.0020.0000.0000.0000.000
145A382SER0-0.040-0.03042.1750.0070.0070.0000.0000.0000.000
146A383PHE00.050-0.01239.995-0.004-0.0040.0000.0000.0000.000
147A384GLN00.0260.02043.8980.0010.0010.0000.0000.0000.000
148A385ASP-1-0.748-0.85343.354-0.093-0.0930.0000.0000.0000.000
149A386LEU0-0.0260.00639.595-0.005-0.0050.0000.0000.0000.000
150A387SER00.009-0.01043.1990.0070.0070.0000.0000.0000.000
151A388ALA00.0610.01643.633-0.002-0.0020.0000.0000.0000.000
152A389GLY00.0120.01343.379-0.001-0.0010.0000.0000.0000.000
153A390VAL00.0230.01739.226-0.005-0.0050.0000.0000.0000.000
154A391LEU0-0.0010.01038.954-0.006-0.0060.0000.0000.0000.000
155A392ALA00.0040.01138.9210.0020.0020.0000.0000.0000.000
156A393GLN00.013-0.00436.983-0.010-0.0100.0000.0000.0000.000
157A394THR0-0.005-0.01833.821-0.015-0.0150.0000.0000.0000.000
158A395ARG10.7910.85833.5400.0510.0510.0000.0000.0000.000
159A396GLU-1-0.842-0.89533.527-0.129-0.1290.0000.0000.0000.000
160A397ARG10.8390.92531.1280.1700.1700.0000.0000.0000.000
161A398ILE0-0.007-0.00429.151-0.015-0.0150.0000.0000.0000.000
162A399ALA0-0.013-0.00428.7020.0000.0000.0000.0000.0000.000
163A400ARG10.9060.93329.1610.1690.1690.0000.0000.0000.000
164A401ALA0-0.017-0.01225.412-0.017-0.0170.0000.0000.0000.000
165A402ARG10.8610.91824.6270.0290.0290.0000.0000.0000.000
166A403GLU-1-0.931-0.95424.982-0.115-0.1150.0000.0000.0000.000
167A404ALA00.0430.02224.3910.0010.0010.0000.0000.0000.000
168A405LEU0-0.061-0.01919.491-0.027-0.0270.0000.0000.0000.000
169A406ASP-1-0.777-0.88220.679-0.034-0.0340.0000.0000.0000.000
170A407ASN0-0.0020.01322.092-0.011-0.0110.0000.0000.0000.000
171A408THR0-0.031-0.03317.827-0.021-0.0210.0000.0000.0000.000
172A409VAL0-0.056-0.03316.913-0.003-0.0030.0000.0000.0000.000
173A410GLU-1-0.876-0.93118.7670.0040.0040.0000.0000.0000.000
174A411TYR00.0020.00019.5650.0040.0040.0000.0000.0000.000
175A412VAL0-0.016-0.01114.3170.0150.0150.0000.0000.0000.000
176A413ALA0-0.024-0.00716.9660.0480.0480.0000.0000.0000.000
177A414GLN0-0.036-0.00918.2740.0520.0520.0000.0000.0000.000
178A415ASN0-0.066-0.02819.387-0.018-0.0180.0000.0000.0000.000
179A416THR00.0130.01015.3820.0120.0120.0000.0000.0000.000
180A417PRO0-0.005-0.00116.033-0.025-0.0250.0000.0000.0000.000
181A418ALA00.0590.02016.292-0.079-0.0790.0000.0000.0000.000
182A419MET00.0210.00716.658-0.077-0.0770.0000.0000.0000.000
183A420TRP0-0.044-0.02311.658-0.025-0.0250.0000.0000.0000.000
184A421LEU0-0.044-0.02211.9050.0480.0480.0000.0000.0000.000
185A422VAL00.0100.0237.116-0.207-0.2070.0000.0000.0000.000
186A423GLY00.0490.0335.557-0.079-0.0790.0000.0000.0000.000
187A424PRO0-0.043-0.0073.2380.8981.5550.010-0.140-0.5280.000
188A425PHE0-0.056-0.0492.547-7.291-3.9681.534-1.988-2.869-0.023
189A426ALA00.0840.0513.1180.2891.3620.126-0.346-0.8520.001
190A427PRO00.0220.0114.8771.4131.433-0.001-0.014-0.0040.000
191A428GLY0-0.026-0.0327.6550.6830.6830.0000.0000.0000.000
192A429ILE0-0.071-0.0299.3130.2870.2870.0000.0000.0000.000
193A430THR0-0.012-0.00912.723-0.188-0.1880.0000.0000.0000.000
194A431GLU-1-0.930-0.95814.858-0.206-0.2060.0000.0000.0000.000