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: 39G4L

Calculation Name: 2VXQ-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VXQ

Chain ID: H

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptH
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2161106.497484
FMO2-HF: Nuclear repulsion 2080855.773424
FMO2-HF: Total energy -80250.72406
FMO2-MP2: Total energy -80486.435031


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(H:1:VAL)


Summations of interaction energy for fragment #1(H:1:VAL)
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.
-9.91-3.31811.996-6.071-12.518-0.043
Interaction energy analysis for fragmet #1(H:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.028
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].
3H3LEU0-0.007-0.0063.430-1.2580.9880.043-0.815-1.4740.001
4H4LEU00.0390.0265.2900.1400.145-0.001-0.001-0.0030.000
5H5GLU-1-0.774-0.8939.039-0.407-0.4070.0000.0000.0000.000
6H6SER0-0.053-0.01611.9990.0490.0490.0000.0000.0000.000
7H7GLY00.0450.00314.977-0.003-0.0030.0000.0000.0000.000
8H8PRO0-0.044-0.02618.408-0.001-0.0010.0000.0000.0000.000
9H9GLY00.1090.06521.239-0.009-0.0090.0000.0000.0000.000
10H10LEU0-0.053-0.00722.6180.0020.0020.0000.0000.0000.000
11H11VAL00.0280.01824.0010.0030.0030.0000.0000.0000.000
12H12LYS10.9600.99527.0530.0450.0450.0000.0000.0000.000
13H13PRO00.0780.02330.013-0.003-0.0030.0000.0000.0000.000
14H14ALA0-0.032-0.02331.3800.0040.0040.0000.0000.0000.000
15H15GLN0-0.031-0.00429.0180.0020.0020.0000.0000.0000.000
16H16THR0-0.038-0.03823.741-0.001-0.0010.0000.0000.0000.000
17H17LEU0-0.0370.01019.8040.0040.0040.0000.0000.0000.000
18H18SER0-0.020-0.03220.0370.0010.0010.0000.0000.0000.000
19H19LEU0-0.0190.00015.5340.0020.0020.0000.0000.0000.000
20H20SER00.0020.00113.2090.0060.0060.0000.0000.0000.000
21H21CYS0-0.051-0.0118.091-0.034-0.0340.0000.0000.0000.000
22H22ALA00.0110.0128.2960.0380.0380.0000.0000.0000.000
23H23VAL00.0240.0102.462-0.629-0.3130.604-0.171-0.7490.000
24H24SER0-0.0160.0033.5300.2990.7200.003-0.159-0.2640.000
25H25GLY00.0560.0072.274-4.250-2.5244.697-3.466-2.957-0.032
26H26GLY00.0200.0042.258-1.556-0.6652.840-1.360-2.372-0.004
27H27SER0-0.0300.0153.0350.758-0.2200.0271.124-0.1730.000
28H28ILE00.0400.0046.4030.0430.0430.0000.0000.0000.000
29H29ARG10.9240.9627.946-0.060-0.0600.0000.0000.0000.000
30H30SER0-0.022-0.0127.808-0.001-0.0010.0000.0000.0000.000
31H31GLY0-0.036-0.0069.468-0.016-0.0160.0000.0000.0000.000
32H32GLY00.004-0.0038.4240.0350.0350.0000.0000.0000.000
33H33TYR0-0.001-0.0045.496-0.035-0.0350.0000.0000.0000.000
34H34TYR0-0.042-0.0188.7680.0340.0340.0000.0000.0000.000
35H35TRP00.0160.0043.342-0.439-0.0820.014-0.072-0.3000.000
36H36SER00.031-0.0059.2600.0610.0610.0000.0000.0000.000
37H37TRP00.0030.00310.932-0.058-0.0580.0000.0000.0000.000
38H38ILE00.0170.00412.9810.0360.0360.0000.0000.0000.000
39H39ARG10.8210.91015.4410.1160.1160.0000.0000.0000.000
40H40GLN0-0.011-0.00918.099-0.006-0.0060.0000.0000.0000.000
41H41HIS0-0.047-0.02520.6730.0090.0090.0000.0000.0000.000
42H42PRO00.036-0.00424.186-0.001-0.0010.0000.0000.0000.000
43H43GLY00.0140.02526.036-0.003-0.0030.0000.0000.0000.000
44H44LYS10.8890.95025.1720.0970.0970.0000.0000.0000.000
45H45GLY00.0630.03923.297-0.006-0.0060.0000.0000.0000.000
46H46LEU0-0.0020.00016.6950.0020.0020.0000.0000.0000.000
47H47GLU-1-0.871-0.94119.806-0.115-0.1150.0000.0000.0000.000
48H48TRP00.0320.01313.486-0.014-0.0140.0000.0000.0000.000
49H49ILE0-0.0260.00417.0040.0210.0210.0000.0000.0000.000
50H50GLY00.016-0.01616.6100.0230.0230.0000.0000.0000.000
51H51TYR0-0.009-0.00212.743-0.031-0.0310.0000.0000.0000.000
52H52ILE0-0.0280.00012.3440.0230.0230.0000.0000.0000.000
53H53TYR00.0380.00211.937-0.011-0.0110.0000.0000.0000.000
54H54HIS00.0340.01310.9230.0030.0030.0000.0000.0000.000
55H55SER0-0.032-0.00412.8560.0020.0020.0000.0000.0000.000
56H56GLY00.0280.01115.9200.0050.0050.0000.0000.0000.000
57H57ASN0-0.037-0.01117.340-0.002-0.0020.0000.0000.0000.000
58H58THR00.0050.01216.538-0.010-0.0100.0000.0000.0000.000
59H59TYR0-0.0070.01116.7590.0100.0100.0000.0000.0000.000
60H60TYR00.0720.01818.168-0.016-0.0160.0000.0000.0000.000
61H61ASN00.0410.01420.7010.0160.0160.0000.0000.0000.000
62H62PRO00.0250.00522.4210.0060.0060.0000.0000.0000.000
63H63SER0-0.016-0.01525.7960.0060.0060.0000.0000.0000.000
64H64LEU00.005-0.00522.1310.0030.0030.0000.0000.0000.000
65H65LYS10.9170.94823.8680.0740.0740.0000.0000.0000.000
66H66SER0-0.032-0.01024.9160.0010.0010.0000.0000.0000.000
67H67ARG10.8310.91126.2280.0900.0900.0000.0000.0000.000
68H68ILE0-0.0390.02719.159-0.003-0.0030.0000.0000.0000.000
69H69ALA00.003-0.00221.3120.0070.0070.0000.0000.0000.000
70H70MET0-0.039-0.00113.632-0.006-0.0060.0000.0000.0000.000
71H71SER0-0.003-0.00116.0420.0090.0090.0000.0000.0000.000
72H72VAL00.022-0.00711.341-0.024-0.0240.0000.0000.0000.000
73H73ASP-1-0.795-0.87212.672-0.013-0.0130.0000.0000.0000.000
74H74THR00.020-0.01411.756-0.001-0.0010.0000.0000.0000.000
75H75SER0-0.117-0.06412.2130.0190.0190.0000.0000.0000.000
76H76GLU-1-0.866-0.93312.855-0.012-0.0120.0000.0000.0000.000
77H77ASN0-0.079-0.0345.7760.0550.0550.0000.0000.0000.000
78H78LYS10.9140.9587.895-0.013-0.0130.0000.0000.0000.000
79H79PHE0-0.014-0.0077.0720.0540.0540.0000.0000.0000.000
80H80SER0-0.005-0.01611.516-0.034-0.0340.0000.0000.0000.000
81H81LEU0-0.0190.00714.5060.0070.0070.0000.0000.0000.000
82H82ARG10.9380.96217.3130.0770.0770.0000.0000.0000.000
83H83LEU00.0090.01321.0170.0010.0010.0000.0000.0000.000
84H84ASN00.0300.00423.1780.0040.0040.0000.0000.0000.000
85H85SER00.008-0.00326.830-0.003-0.0030.0000.0000.0000.000
86H86VAL0-0.0190.02025.1290.0000.0000.0000.0000.0000.000
87H87THR00.0470.01828.3710.0070.0070.0000.0000.0000.000
88H88ALA00.0480.00828.567-0.005-0.0050.0000.0000.0000.000
89H89ALA00.0150.00528.787-0.004-0.0040.0000.0000.0000.000
90H90ASP-1-0.748-0.85624.468-0.101-0.1010.0000.0000.0000.000
91H91THR00.0090.03923.804-0.008-0.0080.0000.0000.0000.000
92H92ALA0-0.013-0.00521.1700.0020.0020.0000.0000.0000.000
93H93VAL00.0200.02816.7330.0050.0050.0000.0000.0000.000
94H94TYR0-0.046-0.06516.097-0.002-0.0020.0000.0000.0000.000
95H95TYR00.0600.02511.8970.0000.0000.0000.0000.0000.000
96H97ALA00.0350.0057.332-0.102-0.1020.0000.0000.0000.000
97H98ARG10.8180.9052.530-0.9040.2571.375-0.548-1.988-0.003
98H99LEU00.0000.0066.424-0.047-0.0470.0000.0000.0000.000
99H100ASP-1-0.775-0.8738.585-0.288-0.2880.0000.0000.0000.000
100H101GLY0-0.024-0.0119.7670.0390.0390.0000.0000.0000.000
101H102TYR0-0.077-0.03712.8930.0270.0270.0000.0000.0000.000
102H103THR0-0.073-0.04911.015-0.017-0.0170.0000.0000.0000.000
103H104LEU0-0.018-0.0229.8070.0000.0000.0000.0000.0000.000
104H105ASP-1-0.765-0.8606.353-0.944-0.9440.0000.0000.0000.000
105H106ILE0-0.039-0.0072.345-1.119-0.6722.394-0.603-2.238-0.005
106H107TRP0-0.028-0.0315.6310.3040.3040.0000.0000.0000.000
107H108GLY00.0220.0157.025-0.213-0.2130.0000.0000.0000.000
108H109GLN0-0.048-0.0388.4810.0530.0530.0000.0000.0000.000
109H110GLY00.0110.01411.8100.0590.0590.0000.0000.0000.000
110H111THR0-0.048-0.02714.0100.0330.0330.0000.0000.0000.000
111H112LEU0-0.009-0.00216.6590.0020.0020.0000.0000.0000.000
112H113VAL0-0.0040.00119.6710.0080.0080.0000.0000.0000.000
113H114THR00.006-0.00422.2750.0020.0020.0000.0000.0000.000
114H115VAL0-0.073-0.03926.0310.0050.0050.0000.0000.0000.000
115H116SER0-0.032-0.04728.2510.0110.0110.0000.0000.0000.000
116H117SER0-0.063-0.06330.7840.0020.0020.0000.0000.0000.000
117H118SER00.0290.02432.5870.0020.0020.0000.0000.0000.000
118H119THR0-0.025-0.00429.520-0.001-0.0010.0000.0000.0000.000
119H120LYS10.8540.92732.1690.0330.0330.0000.0000.0000.000
120H121GLY00.0570.03632.410-0.004-0.0040.0000.0000.0000.000
121H122PRO0-0.046-0.01331.7980.0010.0010.0000.0000.0000.000
122H123SER0-0.0090.00034.7140.0030.0030.0000.0000.0000.000
123H124VAL0-0.001-0.00734.471-0.002-0.0020.0000.0000.0000.000
124H125PHE0-0.010-0.01837.4940.0030.0030.0000.0000.0000.000
125H126PRO00.0280.01739.469-0.002-0.0020.0000.0000.0000.000
126H127LEU0-0.045-0.01038.5820.0000.0000.0000.0000.0000.000
127H128ALA00.0370.00541.8620.0000.0000.0000.0000.0000.000
128H129PRO00.000-0.01343.256-0.001-0.0010.0000.0000.0000.000
129H130SER00.0040.01944.3530.0010.0010.0000.0000.0000.000
130H131SER00.0710.03745.2520.0000.0000.0000.0000.0000.000
131H132LYS10.9370.93447.5800.0100.0100.0000.0000.0000.000
132H133SER0-0.091-0.04048.6790.0000.0000.0000.0000.0000.000
133H134THR00.0050.01144.2340.0000.0000.0000.0000.0000.000
134H135SER00.039-0.02544.828-0.001-0.0010.0000.0000.0000.000
135H136GLY00.0140.03346.9210.0010.0010.0000.0000.0000.000
136H137GLY00.0560.08345.905-0.001-0.0010.0000.0000.0000.000
137H138THR0-0.061-0.04441.6830.0010.0010.0000.0000.0000.000
138H139ALA00.0110.00942.5050.0000.0000.0000.0000.0000.000
139H140ALA00.0060.01740.314-0.001-0.0010.0000.0000.0000.000
140H141LEU00.0160.02037.6960.0010.0010.0000.0000.0000.000
141H142GLY00.052-0.00237.052-0.002-0.0020.0000.0000.0000.000
142H143CYS0-0.087-0.00433.0690.0030.0030.0000.0000.0000.000
143H144LEU00.0240.02435.969-0.003-0.0030.0000.0000.0000.000
144H145VAL0-0.014-0.01331.7910.0030.0030.0000.0000.0000.000
145H146LYS10.9000.93334.9310.0260.0260.0000.0000.0000.000
146H147ASP-1-0.813-0.89036.627-0.029-0.0290.0000.0000.0000.000
147H148TYR0-0.011-0.02329.1240.0050.0050.0000.0000.0000.000
148H149PHE00.0480.02331.158-0.004-0.0040.0000.0000.0000.000
149H150PRO00.0100.01626.6160.0050.0050.0000.0000.0000.000
150H151GLU-1-0.767-0.86525.645-0.072-0.0720.0000.0000.0000.000
151H152PRO0-0.015-0.01021.842-0.002-0.0020.0000.0000.0000.000
152H153VAL0-0.006-0.01825.1300.0060.0060.0000.0000.0000.000
153H154THR0-0.012-0.00622.340-0.006-0.0060.0000.0000.0000.000
154H155VAL0-0.014-0.01925.6330.0070.0070.0000.0000.0000.000
155H156SER0-0.0070.00326.392-0.004-0.0040.0000.0000.0000.000
156H157TRP00.0210.01528.3970.0030.0030.0000.0000.0000.000
157H158ASN00.002-0.00830.0610.0010.0010.0000.0000.0000.000
158H159SER00.009-0.00428.4580.0030.0030.0000.0000.0000.000
159H160GLY0-0.014-0.00525.7690.0040.0040.0000.0000.0000.000
160H161ALA0-0.0190.00026.5430.0000.0000.0000.0000.0000.000
161H162LEU0-0.046-0.01328.8430.0000.0000.0000.0000.0000.000
162H163THR00.025-0.00125.303-0.004-0.0040.0000.0000.0000.000
163H164SER00.016-0.00228.521-0.006-0.0060.0000.0000.0000.000
164H165GLY00.0260.00630.7110.0020.0020.0000.0000.0000.000
165H166VAL0-0.035-0.00729.6460.0000.0000.0000.0000.0000.000
166H167HIS0-0.0010.00830.478-0.007-0.0070.0000.0000.0000.000
167H168THR00.0210.00228.3100.0070.0070.0000.0000.0000.000
168H169PHE0-0.041-0.00629.474-0.005-0.0050.0000.0000.0000.000
169H170PRO00.0290.00428.939-0.001-0.0010.0000.0000.0000.000
170H171ALA0-0.0020.01529.4230.0060.0060.0000.0000.0000.000
171H172VAL0-0.009-0.00131.318-0.003-0.0030.0000.0000.0000.000
172H173LEU0-0.050-0.01833.4820.0020.0020.0000.0000.0000.000
173H174GLN0-0.058-0.05535.0450.0040.0040.0000.0000.0000.000
174H175SER00.0310.00638.540-0.001-0.0010.0000.0000.0000.000
175H176SER0-0.007-0.00540.0540.0000.0000.0000.0000.0000.000
176H177GLY00.0190.01437.1410.0010.0010.0000.0000.0000.000
177H178LEU0-0.055-0.01335.116-0.002-0.0020.0000.0000.0000.000
178H179TYR00.0200.01229.9820.0000.0000.0000.0000.0000.000
179H180SER0-0.014-0.01433.9960.0040.0040.0000.0000.0000.000
180H181LEU00.0410.03629.417-0.003-0.0030.0000.0000.0000.000
181H182SER00.0400.01433.9370.0050.0050.0000.0000.0000.000
182H183SER0-0.028-0.01031.121-0.002-0.0020.0000.0000.0000.000
183H184VAL00.025-0.00433.4550.0040.0040.0000.0000.0000.000
184H185VAL00.0180.01533.964-0.002-0.0020.0000.0000.0000.000
185H186THR0-0.021-0.00335.7260.0010.0010.0000.0000.0000.000
186H187VAL0-0.0010.00036.9900.0000.0000.0000.0000.0000.000
187H188PRO00.0520.02238.875-0.001-0.0010.0000.0000.0000.000
188H189SER00.027-0.00342.1230.0010.0010.0000.0000.0000.000
189H190SER0-0.029-0.02044.7780.0000.0000.0000.0000.0000.000
190H191SER0-0.033-0.01941.0630.0010.0010.0000.0000.0000.000
191H192LEU00.002-0.00142.7700.0010.0010.0000.0000.0000.000
192H193GLY0-0.0150.00744.5720.0000.0000.0000.0000.0000.000
193H194THR00.006-0.00243.3380.0000.0000.0000.0000.0000.000
194H195GLN0-0.061-0.02836.7980.0030.0030.0000.0000.0000.000
195H196THR00.0060.01038.357-0.001-0.0010.0000.0000.0000.000
196H197TYR00.0390.00936.2560.0010.0010.0000.0000.0000.000
197H198ILE00.0190.00634.726-0.001-0.0010.0000.0000.0000.000
198H200ASN00.021-0.01729.2010.0020.0020.0000.0000.0000.000
199H201VAL00.0200.01129.482-0.005-0.0050.0000.0000.0000.000
200H202ASN0-0.043-0.02424.7770.0040.0040.0000.0000.0000.000
201H203HIS00.0570.02526.923-0.001-0.0010.0000.0000.0000.000
202H204LYS10.9150.95021.3920.0420.0420.0000.0000.0000.000
203H205PRO00.0090.01924.8300.0040.0040.0000.0000.0000.000
204H206SER0-0.0020.00826.7080.0040.0040.0000.0000.0000.000
205H207ASN0-0.066-0.02927.1350.0060.0060.0000.0000.0000.000
206H208THR00.0460.00828.6960.0060.0060.0000.0000.0000.000
207H209LYS10.9320.94626.2050.0040.0040.0000.0000.0000.000
208H210VAL0-0.0010.00431.0610.0030.0030.0000.0000.0000.000
209H211ASP-1-0.798-0.86532.398-0.003-0.0030.0000.0000.0000.000
210H212LYS10.8840.93434.8050.0120.0120.0000.0000.0000.000
211H213ARG10.9020.95937.5490.0010.0010.0000.0000.0000.000
212H214VAL0-0.025-0.01738.538-0.001-0.0010.0000.0000.0000.000
213H215GLU-1-0.911-0.96741.167-0.001-0.0010.0000.0000.0000.000
214H216PRO00.0020.01044.457-0.001-0.0010.0000.0000.0000.000