FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VKQQ1

Calculation Name: 1W26-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W26

Chain ID: A

ChEMBL ID:

UniProt ID: P0A850

Base Structure: X-ray

Registration Date: 2023-09-27

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 432
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6070720.045999
FMO2-HF: Nuclear repulsion 5901973.971615
FMO2-HF: Total energy -168746.074384
FMO2-MP2: Total energy -169239.967134


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-26.07-24.03626.115-11.569-16.5820.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.053
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].
3A3VAL0-0.008-0.0212.338-1.7590.5671.890-1.435-2.781-0.001
4A4SER00.0290.0275.3160.6240.723-0.001-0.010-0.0880.000
5A5VAL0-0.0090.0018.6820.0010.0010.0000.0000.0000.000
6A6GLU-1-0.847-0.90910.511-0.926-0.9260.0000.0000.0000.000
7A7THR0-0.007-0.00214.1700.0500.0500.0000.0000.0000.000
8A8THR0-0.034-0.02316.9300.0220.0220.0000.0000.0000.000
9A9GLN00.001-0.00919.4030.0390.0390.0000.0000.0000.000
10A10GLY00.0860.06322.3620.0140.0140.0000.0000.0000.000
11A11LEU00.0680.03820.067-0.037-0.0370.0000.0000.0000.000
12A12GLY0-0.0280.00518.211-0.031-0.0310.0000.0000.0000.000
13A13ARG10.8580.90613.3570.4930.4930.0000.0000.0000.000
14A14ARG10.7880.86712.6870.8300.8300.0000.0000.0000.000
15A15VAL0-0.0330.0006.580-0.132-0.1320.0000.0000.0000.000
16A16THR00.0190.0008.6450.2550.2550.0000.0000.0000.000
17A17ILE0-0.013-0.0042.957-1.766-0.9560.109-0.175-0.745-0.001
18A18THR00.0200.0174.0331.2061.400-0.001-0.025-0.1680.000
19A19ILE0-0.051-0.0162.782-3.026-1.2700.407-1.050-1.114-0.012
20A20ALA00.0700.0344.575-0.591-0.556-0.001-0.007-0.0260.000
21A21ALA00.0450.0206.3210.4210.4210.0000.0000.0000.000
22A22ASP-1-0.897-0.9678.2051.1801.1800.0000.0000.0000.000
23A23SER00.0110.0066.2600.6510.6510.0000.0000.0000.000
24A24ILE0-0.0060.0098.5370.0150.0150.0000.0000.0000.000
25A25GLU-1-0.850-0.92410.6860.4430.4430.0000.0000.0000.000
26A26THR0-0.073-0.04711.277-0.145-0.1450.0000.0000.0000.000
27A27ALA00.0540.03010.685-0.079-0.0790.0000.0000.0000.000
28A28VAL00.0110.01712.744-0.140-0.1400.0000.0000.0000.000
29A29LYS10.7800.87615.810-0.713-0.7130.0000.0000.0000.000
30A30SER0-0.058-0.02714.905-0.043-0.0430.0000.0000.0000.000
31A31GLU-1-0.783-0.89116.5260.5010.5010.0000.0000.0000.000
32A32LEU0-0.055-0.01918.163-0.073-0.0730.0000.0000.0000.000
33A33VAL0-0.051-0.03820.016-0.051-0.0510.0000.0000.0000.000
34A34ASN00.0000.00017.939-0.045-0.0450.0000.0000.0000.000
35A35VAL0-0.0050.00421.832-0.049-0.0490.0000.0000.0000.000
36A36ALA00.008-0.00224.049-0.034-0.0340.0000.0000.0000.000
37A37LYS10.9530.98722.817-0.521-0.5210.0000.0000.0000.000
38A38LYS10.9090.96523.628-0.354-0.3540.0000.0000.0000.000
39A39VAL0-0.023-0.01827.402-0.022-0.0220.0000.0000.0000.000
40A40ARG10.8990.97029.658-0.284-0.2840.0000.0000.0000.000
41A41ILE00.016-0.01229.980-0.016-0.0160.0000.0000.0000.000
42A42ASP-1-0.889-0.95127.3220.3160.3160.0000.0000.0000.000
43A43GLY00.0070.00228.9570.0010.0010.0000.0000.0000.000
44A44PHE0-0.034-0.00932.212-0.013-0.0130.0000.0000.0000.000
45A45ARG10.8590.93826.133-0.325-0.3250.0000.0000.0000.000
46A46LYS10.9890.97330.859-0.168-0.1680.0000.0000.0000.000
47A47GLY0-0.0110.00128.882-0.002-0.0020.0000.0000.0000.000
48A48LYS10.9540.98629.738-0.142-0.1420.0000.0000.0000.000
49A49VAL00.0150.01626.668-0.012-0.0120.0000.0000.0000.000
50A50PRO00.0760.04223.5570.0190.0190.0000.0000.0000.000
51A51MET00.0580.00821.326-0.030-0.0300.0000.0000.0000.000
52A52ASN00.0610.01818.9360.0130.0130.0000.0000.0000.000
53A53ILE0-0.0080.00420.255-0.022-0.0220.0000.0000.0000.000
54A54VAL0-0.013-0.00923.103-0.022-0.0220.0000.0000.0000.000
55A55ALA00.0490.03918.669-0.024-0.0240.0000.0000.0000.000
56A56GLN00.009-0.00320.512-0.032-0.0320.0000.0000.0000.000
57A57ARG10.8970.94221.359-0.190-0.1900.0000.0000.0000.000
58A58TYR0-0.050-0.03323.589-0.022-0.0220.0000.0000.0000.000
59A59GLY00.0630.03520.0870.0120.0120.0000.0000.0000.000
60A60ALA0-0.0180.00220.2710.0120.0120.0000.0000.0000.000
61A61SER0-0.004-0.00721.526-0.009-0.0090.0000.0000.0000.000
62A62VAL0-0.028-0.01317.7400.0050.0050.0000.0000.0000.000
63A63ARG10.9410.96914.678-0.236-0.2360.0000.0000.0000.000
64A64GLN00.0000.01815.8230.0090.0090.0000.0000.0000.000
65A65ASP-1-0.811-0.90516.1200.2270.2270.0000.0000.0000.000
66A66VAL0-0.005-0.00412.5490.0560.0560.0000.0000.0000.000
67A67LEU0-0.031-0.03011.5500.1090.1090.0000.0000.0000.000
68A68GLY00.0190.01511.493-0.068-0.0680.0000.0000.0000.000
69A69ASP-1-0.831-0.89511.9721.0841.0840.0000.0000.0000.000
70A70LEU0-0.042-0.0357.3390.1630.1630.0000.0000.0000.000
71A71MET0-0.0010.0176.9990.0290.0290.0000.0000.0000.000
72A72SER00.0010.0267.384-0.341-0.3410.0000.0000.0000.000
73A73ARG10.8610.9017.351-2.034-2.0340.0000.0000.0000.000
74A74ASN0-0.005-0.0212.844-2.920-1.3431.090-0.769-1.898-0.003
75A75PHE00.0310.0122.623-4.703-3.3850.912-0.994-1.236-0.014
76A76ILE00.0320.0085.172-0.254-0.212-0.001-0.004-0.0370.000
77A77ASP-1-0.831-0.9052.2146.8407.4341.904-0.707-1.791-0.005
78A78ALA00.007-0.0032.106-0.422-0.0023.095-1.255-2.260-0.016
79A79ILE00.0040.0153.1640.9290.5290.1790.526-0.306-0.001
80A80ILE00.0070.0115.8150.2570.2570.0000.0000.0000.000
81A81LYS10.6850.8052.206-16.563-23.30016.533-5.664-4.1320.067
82A82GLU-1-0.922-0.9595.751-1.361-1.3610.0000.0000.0000.000
83A83LYS10.7720.8838.376-0.400-0.4000.0000.0000.0000.000
84A84ILE00.0050.0198.381-0.010-0.0100.0000.0000.0000.000
85A85ASN00.0390.00710.9810.0730.0730.0000.0000.0000.000
86A86PRO0-0.036-0.01411.507-0.007-0.0070.0000.0000.0000.000
87A87ALA00.0410.02814.3350.0670.0670.0000.0000.0000.000
88A88GLY00.0080.00017.979-0.024-0.0240.0000.0000.0000.000
89A89ALA0-0.045-0.02616.359-0.012-0.0120.0000.0000.0000.000
90A90PRO00.0130.00712.033-0.030-0.0300.0000.0000.0000.000
91A91THR00.0070.00814.4140.0780.0780.0000.0000.0000.000
92A92TYR0-0.041-0.0149.106-0.050-0.0500.0000.0000.0000.000
93A93VAL00.0240.00112.8240.0910.0910.0000.0000.0000.000
94A94PRO0-0.024-0.00713.078-0.126-0.1260.0000.0000.0000.000
95A95GLY00.0570.05113.1390.0240.0240.0000.0000.0000.000
96A96GLU-1-0.895-0.94814.724-0.279-0.2790.0000.0000.0000.000
97A97TYR00.016-0.01112.1790.0170.0170.0000.0000.0000.000
98A98LYS10.9100.96514.5900.4030.4030.0000.0000.0000.000
99A99LEU0-0.035-0.03315.0970.0310.0310.0000.0000.0000.000
100A100GLY0-0.064-0.03515.484-0.011-0.0110.0000.0000.0000.000
101A101GLU-1-0.918-0.95613.099-0.294-0.2940.0000.0000.0000.000
102A102ASP-1-0.868-0.9417.921-0.387-0.3870.0000.0000.0000.000
103A103PHE0-0.050-0.0397.9320.0610.0610.0000.0000.0000.000
104A104THR00.0190.0067.370-0.066-0.0660.0000.0000.0000.000
105A105TYR0-0.083-0.0505.6170.1250.1250.0000.0000.0000.000
106A106SER00.0340.0019.381-0.335-0.3350.0000.0000.0000.000
107A107VAL0-0.029-0.0148.7440.1990.1990.0000.0000.0000.000
108A108GLU-1-0.844-0.89911.394-0.713-0.7130.0000.0000.0000.000
109A109PHE00.001-0.02310.6400.0610.0610.0000.0000.0000.000
110A110GLU-1-0.786-0.89715.596-0.306-0.3060.0000.0000.0000.000
111A111VAL0-0.066-0.02514.4320.0060.0060.0000.0000.0000.000
112A112TYR00.0320.00617.0520.0220.0220.0000.0000.0000.000
113A113PRO0-0.034-0.00419.657-0.028-0.0280.0000.0000.0000.000
114A114GLU-1-0.923-0.96221.064-0.132-0.1320.0000.0000.0000.000
115A115VAL0-0.045-0.03423.378-0.001-0.0010.0000.0000.0000.000
116A116GLU-1-0.921-0.94626.810-0.103-0.1030.0000.0000.0000.000
117A117LEU0-0.037-0.02729.6710.0010.0010.0000.0000.0000.000
118A118GLN0-0.008-0.01832.3360.0000.0000.0000.0000.0000.000
119A119GLY00.003-0.01335.5880.0070.0070.0000.0000.0000.000
120A120LEU00.0160.02234.9640.0040.0040.0000.0000.0000.000
121A121GLU-1-0.848-0.92839.092-0.029-0.0290.0000.0000.0000.000
122A122ALA0-0.124-0.06741.9560.0010.0010.0000.0000.0000.000
123A123ILE0-0.0090.01838.8190.0000.0000.0000.0000.0000.000
124A124GLU-1-0.874-0.92643.467-0.028-0.0280.0000.0000.0000.000
125A125VAL0-0.047-0.03344.2350.0000.0000.0000.0000.0000.000
126A126GLU-1-0.793-0.87947.447-0.013-0.0130.0000.0000.0000.000
127A127LYS10.8750.93649.763-0.004-0.0040.0000.0000.0000.000
128A128PRO0-0.011-0.00751.3710.0000.0000.0000.0000.0000.000
129A129ILE0-0.036-0.01054.4080.0020.0020.0000.0000.0000.000
130A130VAL0-0.025-0.02456.039-0.001-0.0010.0000.0000.0000.000
131A131GLU-1-0.921-0.97058.4630.0080.0080.0000.0000.0000.000
132A132VAL0-0.0250.00059.320-0.001-0.0010.0000.0000.0000.000
133A133THR0-0.017-0.03261.9410.0010.0010.0000.0000.0000.000
134A134ASP-1-0.860-0.94965.6670.0090.0090.0000.0000.0000.000
135A135ALA00.0130.01168.3530.0000.0000.0000.0000.0000.000
136A136ASP-1-0.840-0.90063.9110.0020.0020.0000.0000.0000.000
137A137VAL00.010-0.00664.9160.0000.0000.0000.0000.0000.000
138A138ASP-1-0.865-0.91366.6360.0060.0060.0000.0000.0000.000
139A139GLY00.0410.02367.9740.0000.0000.0000.0000.0000.000
140A140MET00.0190.00762.813-0.001-0.0010.0000.0000.0000.000
141A141LEU00.001-0.00766.0650.0000.0000.0000.0000.0000.000
142A142ASP-1-0.863-0.91568.8070.0010.0010.0000.0000.0000.000
143A143THR0-0.034-0.02764.843-0.001-0.0010.0000.0000.0000.000
144A144LEU0-0.0080.00764.0590.0000.0000.0000.0000.0000.000
145A145ARG10.8770.93067.665-0.006-0.0060.0000.0000.0000.000
146A146LYS10.8700.91669.9650.0000.0000.0000.0000.0000.000
147A147GLN0-0.080-0.02762.6650.0000.0000.0000.0000.0000.000
148A148GLN0-0.066-0.02767.706-0.001-0.0010.0000.0000.0000.000
149A149ALA00.0380.00270.2770.0010.0010.0000.0000.0000.000
150A150THR0-0.026-0.01973.6940.0000.0000.0000.0000.0000.000
151A151TRP0-0.043-0.01773.7250.0000.0000.0000.0000.0000.000
152A152LYS10.8020.91278.518-0.001-0.0010.0000.0000.0000.000
153A153GLU-1-0.822-0.92982.146-0.002-0.0020.0000.0000.0000.000
154A154LYS10.7070.85482.2430.0030.0030.0000.0000.0000.000
155A155ASP-1-0.872-0.96487.335-0.003-0.0030.0000.0000.0000.000
156A156GLY0-0.067-0.02988.7160.0000.0000.0000.0000.0000.000
157A157ALA0-0.023-0.02986.3950.0000.0000.0000.0000.0000.000
158A158VAL00.0280.02581.5870.0000.0000.0000.0000.0000.000
159A159GLU-1-0.869-0.91680.616-0.004-0.0040.0000.0000.0000.000
160A160ALA0-0.067-0.05576.8070.0000.0000.0000.0000.0000.000
161A161GLU-1-0.913-0.95674.616-0.004-0.0040.0000.0000.0000.000
162A162ASP-1-0.768-0.86175.893-0.003-0.0030.0000.0000.0000.000
163A163ARG10.7590.84275.0910.0020.0020.0000.0000.0000.000
164A164VAL00.0160.00277.8280.0000.0000.0000.0000.0000.000
165A165THR0-0.005-0.01779.1510.0000.0000.0000.0000.0000.000
166A166ILE0-0.031-0.01880.3390.0000.0000.0000.0000.0000.000
167A167ASP-1-0.763-0.85081.540-0.008-0.0080.0000.0000.0000.000
168A168PHE00.004-0.02376.7240.0000.0000.0000.0000.0000.000
169A169THR0-0.028-0.01382.2150.0000.0000.0000.0000.0000.000
170A170GLY00.0300.01680.9790.0000.0000.0000.0000.0000.000
171A171SER0-0.032-0.02182.0430.0000.0000.0000.0000.0000.000
172A172VAL0-0.029-0.01780.0520.0000.0000.0000.0000.0000.000
173A173ASP-1-0.897-0.96682.578-0.019-0.0190.0000.0000.0000.000
174A174GLY0-0.039-0.01486.0520.0000.0000.0000.0000.0000.000
175A175GLU-1-1.003-0.99482.073-0.020-0.0200.0000.0000.0000.000
176A176GLU-1-0.887-0.92683.180-0.014-0.0140.0000.0000.0000.000
177A177PHE00.0300.00877.961-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.906-0.95272.681-0.022-0.0220.0000.0000.0000.000
179A179GLY00.0060.01075.7520.0000.0000.0000.0000.0000.000
180A180GLY0-0.014-0.01676.5040.0000.0000.0000.0000.0000.000
181A181LYS10.9110.95577.5050.0170.0170.0000.0000.0000.000
182A182ALA0-0.0190.00178.5340.0000.0000.0000.0000.0000.000
183A183SER0-0.039-0.02380.0410.0000.0000.0000.0000.0000.000
184A184ASP-1-0.858-0.90980.682-0.006-0.0060.0000.0000.0000.000
185A185PHE0-0.035-0.01473.1280.0000.0000.0000.0000.0000.000
186A186VAL00.0120.01574.9460.0010.0010.0000.0000.0000.000
187A187LEU0-0.052-0.04573.457-0.001-0.0010.0000.0000.0000.000
188A188ALA0-0.007-0.00672.1600.0010.0010.0000.0000.0000.000
189A189MET00.0070.01572.518-0.001-0.0010.0000.0000.0000.000
190A190GLY00.0410.02372.6220.0010.0010.0000.0000.0000.000
191A191GLN0-0.080-0.05067.8940.0000.0000.0000.0000.0000.000
192A192GLY00.0130.02067.850-0.001-0.0010.0000.0000.0000.000
193A193ARG10.9140.96968.3740.0080.0080.0000.0000.0000.000
194A194MET0-0.065-0.01369.654-0.001-0.0010.0000.0000.0000.000
195A195ILE0-0.0010.00371.119-0.001-0.0010.0000.0000.0000.000
196A196PRO00.0340.01470.4760.0010.0010.0000.0000.0000.000
197A197GLY00.0350.01373.080-0.001-0.0010.0000.0000.0000.000
198A198PHE0-0.005-0.01475.9450.0010.0010.0000.0000.0000.000
199A199GLU-1-0.804-0.93074.019-0.010-0.0100.0000.0000.0000.000
200A200ASP-1-0.886-0.95476.238-0.010-0.0100.0000.0000.0000.000
201A201GLY0-0.026-0.00979.2230.0000.0000.0000.0000.0000.000
202A202ILE0-0.024-0.01280.0660.0000.0000.0000.0000.0000.000
203A203LYS10.8380.94377.4030.0090.0090.0000.0000.0000.000
204A204GLY0-0.021-0.02082.7860.0000.0000.0000.0000.0000.000
205A205HIS0-0.069-0.02785.8880.0000.0000.0000.0000.0000.000
206A206LYS10.9430.96887.6520.0050.0050.0000.0000.0000.000
207A207ALA00.013-0.00287.7570.0000.0000.0000.0000.0000.000
208A208GLY0-0.028-0.00888.7590.0000.0000.0000.0000.0000.000
209A209GLU-1-0.932-0.94790.718-0.007-0.0070.0000.0000.0000.000
210A210GLU-1-0.916-0.95389.748-0.008-0.0080.0000.0000.0000.000
211A211PHE0-0.058-0.03988.7980.0000.0000.0000.0000.0000.000
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