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: QVKNY

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963091.37008
FMO2-HF: Nuclear repulsion 1887089.590996
FMO2-HF: Total energy -76001.779084
FMO2-MP2: Total energy -76223.088325


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.
-16.74-8.7252.004-4.063-5.955-0.023
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 : -0.001 / q_NPA : -0.009
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].
3A208LEU00.0190.0083.8150.5142.166-0.025-0.747-0.8790.000
4A209PRO0-0.044-0.0176.756-0.327-0.3270.0000.0000.0000.000
5A210LEU0-0.010-0.01210.006-0.209-0.2090.0000.0000.0000.000
6A211THR00.017-0.01111.1450.0540.0540.0000.0000.0000.000
7A212GLU-1-0.849-0.91411.262-1.617-1.6170.0000.0000.0000.000
8A213ALA00.0270.02212.464-0.147-0.1470.0000.0000.0000.000
9A214GLU-1-0.821-0.90714.204-0.011-0.0110.0000.0000.0000.000
10A215LEU0-0.065-0.0347.485-0.010-0.0100.0000.0000.0000.000
11A216ALA00.0190.00511.990-0.132-0.1320.0000.0000.0000.000
12A217LEU0-0.062-0.01913.7100.0180.0180.0000.0000.0000.000
13A218ILE0-0.045-0.01912.3310.1020.1020.0000.0000.0000.000
14A219ALA0-0.0310.00011.897-0.087-0.0870.0000.0000.0000.000
15A220THR0-0.118-0.06912.7360.2900.2900.0000.0000.0000.000
16A221PRO00.0100.00113.069-0.248-0.2480.0000.0000.0000.000
17A222PRO00.0370.01512.0560.1590.1590.0000.0000.0000.000
18A223GLU-1-0.762-0.87014.360-0.669-0.6690.0000.0000.0000.000
19A224ASP-1-0.992-0.98317.224-0.997-0.9970.0000.0000.0000.000
20A225SER0-0.065-0.04215.9890.0060.0060.0000.0000.0000.000
21A226ASP-1-0.759-0.87617.070-1.011-1.0110.0000.0000.0000.000
22A227MET0-0.021-0.02618.139-0.103-0.1030.0000.0000.0000.000
23A228ALA0-0.032-0.00418.261-0.064-0.0640.0000.0000.0000.000
24A229SER00.0310.00114.598-0.092-0.0920.0000.0000.0000.000
25A230LEU0-0.067-0.02313.723-0.252-0.2520.0000.0000.0000.000
26A231GLN00.0370.01913.537-0.144-0.1440.0000.0000.0000.000
27A232GLN0-0.055-0.02211.7740.2000.2000.0000.0000.0000.000
28A233GLN00.0380.0108.818-0.237-0.2370.0000.0000.0000.000
29A234ARG10.8650.9309.3350.7960.7960.0000.0000.0000.000
30A235GLN0-0.044-0.03011.8450.2400.2400.0000.0000.0000.000
31A236GLU-1-0.906-0.9247.559-3.114-3.1140.0000.0000.0000.000
32A237GLN0-0.040-0.0156.598-0.732-0.7320.0000.0000.0000.000
33A238ASN0-0.071-0.0393.768-5.226-5.0180.000-0.082-0.1270.000
34A239TYR0-0.035-0.0466.0071.1881.1880.0000.0000.0000.000
35A240PHE00.0380.0096.863-1.150-1.1500.0000.0000.0000.000
36A241VAL00.0440.0208.8760.4330.4330.0000.0000.0000.000
37A242ARG10.9400.98211.2320.8260.8260.0000.0000.0000.000
38A243LEU00.0320.02910.5480.1240.1240.0000.0000.0000.000
39A244GLY0-0.011-0.03613.5040.1150.1150.0000.0000.0000.000
40A245SER0-0.056-0.02914.5160.0860.0860.0000.0000.0000.000
41A246LEU00.0000.0289.8850.0290.0290.0000.0000.0000.000
42A247SER00.0180.00314.2920.0450.0450.0000.0000.0000.000
43A248GLU-1-0.911-0.96514.8180.3020.3020.0000.0000.0000.000
44A249ARG11.0021.00313.816-0.762-0.7620.0000.0000.0000.000
45A250LEU00.0480.0259.1360.1930.1930.0000.0000.0000.000
46A251ARG10.9000.96610.3310.0880.0880.0000.0000.0000.000
47A252ASN00.023-0.01111.536-0.103-0.1030.0000.0000.0000.000
48A253HIS00.0070.0185.982-0.637-0.6370.0000.0000.0000.000
49A254ALA00.008-0.0186.7240.2840.2840.0000.0000.0000.000
50A255TYR0-0.028-0.0207.781-0.150-0.1500.0000.0000.0000.000
51A256GLU-1-0.896-0.95010.3270.8070.8070.0000.0000.0000.000
52A257HIS0-0.030-0.0142.839-2.636-1.6910.232-0.463-0.714-0.002
53A258SER0-0.034-0.0387.340-0.506-0.5060.0000.0000.0000.000
54A259LEU0-0.0030.0048.513-0.175-0.1750.0000.0000.0000.000
55A260GLY00.0660.03810.137-0.069-0.0690.0000.0000.0000.000
56A261LYS10.8630.9454.7942.9493.023-0.001-0.008-0.0650.000
57A262LEU00.0390.0169.754-0.069-0.0690.0000.0000.0000.000
58A263GLN00.0370.03312.989-0.053-0.0530.0000.0000.0000.000
59A264ASN0-0.047-0.03411.261-0.002-0.0020.0000.0000.0000.000
60A265ALA0-0.030-0.00312.703-0.024-0.0240.0000.0000.0000.000
61A266ARG10.9090.94114.4250.0330.0330.0000.0000.0000.000
62A267GLN0-0.057-0.03817.0610.0220.0220.0000.0000.0000.000
63A268LYS10.9440.96712.6850.2230.2230.0000.0000.0000.000
64A269ALA00.0270.00518.295-0.034-0.0340.0000.0000.0000.000
65A270GLN0-0.071-0.04220.1370.0270.0270.0000.0000.0000.000
66A271GLU-1-0.857-0.90920.703-0.001-0.0010.0000.0000.0000.000
67A272THR00.0300.01122.384-0.006-0.0060.0000.0000.0000.000
68A273LEU00.0000.00923.9520.0100.0100.0000.0000.0000.000
69A274GLN00.0430.02325.7860.0050.0050.0000.0000.0000.000
70A275GLN0-0.0040.00824.9440.0010.0010.0000.0000.0000.000
71A276LEU00.0170.01427.7140.0100.0100.0000.0000.0000.000
72A277THR0-0.023-0.02930.3360.0080.0080.0000.0000.0000.000
73A278SER0-0.043-0.02331.4760.0140.0140.0000.0000.0000.000
74A279VAL00.008-0.00432.1630.0060.0060.0000.0000.0000.000
75A280LEU0-0.0060.00834.4990.0040.0040.0000.0000.0000.000
76A281GLY00.0390.02136.2960.0050.0050.0000.0000.0000.000
77A282LEU0-0.038-0.01536.2840.0070.0070.0000.0000.0000.000
78A283MET0-0.019-0.00836.5980.0020.0020.0000.0000.0000.000
79A284GLU-1-0.814-0.86640.521-0.069-0.0690.0000.0000.0000.000
80A285SER0-0.047-0.03442.1990.0050.0050.0000.0000.0000.000
81A286VAL0-0.019-0.01743.1810.0030.0030.0000.0000.0000.000
82A287LYS10.8530.94344.6370.0790.0790.0000.0000.0000.000
83A288GLN0-0.099-0.02946.3840.0040.0040.0000.0000.0000.000
84A321ALA00.008-0.00247.6740.0020.0020.0000.0000.0000.000
85A322LYS10.9590.96447.1720.0360.0360.0000.0000.0000.000
86A323PRO00.0120.01347.3130.0000.0000.0000.0000.0000.000
87A324GLU-1-0.845-0.93746.240-0.084-0.0840.0000.0000.0000.000
88A325GLN00.009-0.00143.514-0.001-0.0010.0000.0000.0000.000
89A326VAL0-0.038-0.01241.797-0.006-0.0060.0000.0000.0000.000
90A327GLU-1-0.792-0.88340.950-0.093-0.0930.0000.0000.0000.000
91A328ALA00.0680.03040.270-0.007-0.0070.0000.0000.0000.000
92A329ARG10.9200.98537.3980.0630.0630.0000.0000.0000.000
93A330ALA00.0050.00636.366-0.007-0.0070.0000.0000.0000.000
94A331LEU00.0490.02235.467-0.011-0.0110.0000.0000.0000.000
95A332SER0-0.084-0.06034.921-0.014-0.0140.0000.0000.0000.000
96A333MET00.0340.02231.564-0.009-0.0090.0000.0000.0000.000
97A334PHE0-0.025-0.02331.013-0.011-0.0110.0000.0000.0000.000
98A335ARG10.8750.92330.7680.1680.1680.0000.0000.0000.000
99A336ASP-1-0.867-0.92628.236-0.258-0.2580.0000.0000.0000.000
100A337ILE0-0.020-0.00626.410-0.025-0.0250.0000.0000.0000.000
101A338THR0-0.022-0.01425.657-0.024-0.0240.0000.0000.0000.000
102A339GLN00.0100.00125.124-0.047-0.0470.0000.0000.0000.000
103A340GLN0-0.0030.00322.070-0.032-0.0320.0000.0000.0000.000
104A341LEU00.0170.00221.197-0.056-0.0560.0000.0000.0000.000
105A342GLN00.0240.00221.781-0.023-0.0230.0000.0000.0000.000
106A343SER0-0.0170.00018.988-0.062-0.0620.0000.0000.0000.000
107A344MET0-0.034-0.00717.303-0.099-0.0990.0000.0000.0000.000
108A345CYS0-0.051-0.01917.479-0.042-0.0420.0000.0000.0000.000
109A346VAL0-0.011-0.00717.278-0.043-0.0430.0000.0000.0000.000
110A347ALA00.0050.00913.601-0.103-0.1030.0000.0000.0000.000
111A348LEU00.0370.00514.637-0.095-0.0950.0000.0000.0000.000
112A349GLY0-0.035-0.01915.9820.0030.0030.0000.0000.0000.000
113A350ALA00.002-0.00313.7390.0140.0140.0000.0000.0000.000
114A351SER0-0.076-0.02511.700-0.127-0.1270.0000.0000.0000.000
115A352ILE00.0220.01512.9820.1000.1000.0000.0000.0000.000
116A353GLN00.0630.03414.7390.0310.0310.0000.0000.0000.000
117A354GLY00.0250.00515.546-0.059-0.0590.0000.0000.0000.000
118A355LEU0-0.050-0.01316.3400.0940.0940.0000.0000.0000.000
119A356PRO00.0160.00519.361-0.016-0.0160.0000.0000.0000.000
120A357SER00.015-0.00423.118-0.012-0.0120.0000.0000.0000.000
121A358HIS00.0480.03025.285-0.018-0.0180.0000.0000.0000.000
122A359VAL0-0.022-0.01121.0170.0120.0120.0000.0000.0000.000
123A360ARG10.7690.84219.4690.6470.6470.0000.0000.0000.000
124A361GLU-1-0.865-0.92623.080-0.309-0.3090.0000.0000.0000.000
125A362GLN00.0230.00825.9350.0080.0080.0000.0000.0000.000
126A363ALA00.0280.01721.7330.0070.0070.0000.0000.0000.000
127A364GLN0-0.038-0.02423.3190.0170.0170.0000.0000.0000.000
128A365GLN00.0310.01225.2330.0150.0150.0000.0000.0000.000
129A366ALA00.0640.04925.5210.0120.0120.0000.0000.0000.000
130A367ARG10.9550.98220.0640.6750.6750.0000.0000.0000.000
131A368SER0-0.037-0.02825.256-0.008-0.0080.0000.0000.0000.000
132A369GLN0-0.009-0.00928.5680.0220.0220.0000.0000.0000.000
133A370VAL0-0.014-0.00625.7870.0190.0190.0000.0000.0000.000
134A371ASN00.0140.00826.3880.0030.0030.0000.0000.0000.000
135A372ASP-1-0.834-0.90629.527-0.243-0.2430.0000.0000.0000.000
136A373LEU0-0.0470.00030.4040.0200.0200.0000.0000.0000.000
137A374GLN0-0.045-0.02928.6890.0360.0360.0000.0000.0000.000
138A375ALA00.0140.00532.0810.0110.0110.0000.0000.0000.000
139A376THR0-0.024-0.00734.7810.0160.0160.0000.0000.0000.000
140A377PHE00.0490.00534.6990.0120.0120.0000.0000.0000.000
141A378SER0-0.090-0.03635.7180.0060.0060.0000.0000.0000.000
142A379GLY0-0.010-0.01337.3720.0030.0030.0000.0000.0000.000
143A380ILE0-0.078-0.01838.6740.0100.0100.0000.0000.0000.000
144A381HIS0-0.011-0.02640.255-0.004-0.0040.0000.0000.0000.000
145A382SER00.0090.01042.6940.0070.0070.0000.0000.0000.000
146A383PHE00.019-0.01340.543-0.003-0.0030.0000.0000.0000.000
147A384GLN00.0080.00444.3880.0040.0040.0000.0000.0000.000
148A385ASP-1-0.802-0.90143.506-0.115-0.1150.0000.0000.0000.000
149A386LEU0-0.041-0.00139.745-0.005-0.0050.0000.0000.0000.000
150A387SER0-0.001-0.01443.3200.0080.0080.0000.0000.0000.000
151A388ALA00.0650.01743.989-0.002-0.0020.0000.0000.0000.000
152A389GLY00.0160.00843.787-0.001-0.0010.0000.0000.0000.000
153A390VAL00.0170.01339.628-0.005-0.0050.0000.0000.0000.000
154A391LEU00.0090.02539.280-0.009-0.0090.0000.0000.0000.000
155A392ALA00.0020.00238.894-0.001-0.0010.0000.0000.0000.000
156A393GLN00.0180.00537.314-0.009-0.0090.0000.0000.0000.000
157A394THR0-0.020-0.03034.263-0.015-0.0150.0000.0000.0000.000
158A395ARG10.8160.87533.9960.0720.0720.0000.0000.0000.000
159A396GLU-1-0.834-0.89233.812-0.148-0.1480.0000.0000.0000.000
160A397ARG10.8910.94731.7150.1920.1920.0000.0000.0000.000
161A398ILE0-0.028-0.01129.353-0.015-0.0150.0000.0000.0000.000
162A399ALA0-0.014-0.00729.071-0.004-0.0040.0000.0000.0000.000
163A400ARG10.8770.91529.4650.1810.1810.0000.0000.0000.000
164A401ALA0-0.020-0.01225.610-0.016-0.0160.0000.0000.0000.000
165A402ARG10.8650.91825.0690.0760.0760.0000.0000.0000.000
166A403GLU-1-0.919-0.95125.283-0.134-0.1340.0000.0000.0000.000
167A404ALA00.0420.02824.6680.0020.0020.0000.0000.0000.000
168A405LEU0-0.064-0.02419.533-0.020-0.0200.0000.0000.0000.000
169A406ASP-1-0.802-0.90621.308-0.085-0.0850.0000.0000.0000.000
170A407ASN00.0140.01722.860-0.005-0.0050.0000.0000.0000.000
171A408THR0-0.032-0.03318.319-0.014-0.0140.0000.0000.0000.000
172A409VAL0-0.050-0.03817.0540.0020.0020.0000.0000.0000.000
173A410GLU-1-0.912-0.95318.9390.0070.0070.0000.0000.0000.000
174A411TYR0-0.0020.00519.9110.0100.0100.0000.0000.0000.000
175A412VAL0-0.037-0.01914.5900.0240.0240.0000.0000.0000.000
176A413ALA0-0.023-0.00917.3410.0490.0490.0000.0000.0000.000
177A414GLN0-0.039-0.00518.3020.0560.0560.0000.0000.0000.000
178A415ASN0-0.067-0.03419.300-0.007-0.0070.0000.0000.0000.000
179A416THR00.0010.00415.3240.0240.0240.0000.0000.0000.000
180A417PRO00.002-0.00616.038-0.019-0.0190.0000.0000.0000.000
181A418ALA00.0780.04216.210-0.063-0.0630.0000.0000.0000.000
182A419MET00.0200.01316.676-0.065-0.0650.0000.0000.0000.000
183A420TRP0-0.032-0.02011.961-0.015-0.0150.0000.0000.0000.000
184A421LEU0-0.041-0.01811.8560.0460.0460.0000.0000.0000.000
185A422VAL00.0070.0137.151-0.144-0.1440.0000.0000.0000.000
186A423GLY00.0230.0335.346-0.078-0.0780.0000.0000.0000.000
187A424PRO0-0.056-0.0313.3530.7701.3030.004-0.107-0.4300.000
188A425PHE0-0.037-0.0342.478-7.644-4.5331.731-2.049-2.792-0.022
189A426ALA00.0590.0283.450-0.2701.1890.064-0.596-0.9270.001
190A427PRO00.0350.0335.1421.4901.523-0.001-0.011-0.0210.000
191A428GLY0-0.034-0.0547.7150.6330.6330.0000.0000.0000.000
192A429ILE0-0.042-0.0198.7780.2430.2430.0000.0000.0000.000
193A430THR0-0.0120.00512.504-0.207-0.2070.0000.0000.0000.000
194A431GLU-1-0.932-0.96414.449-0.073-0.0730.0000.0000.0000.000