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: 94Q22

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2155075.20771
FMO2-HF: Nuclear repulsion 2074816.542308
FMO2-HF: Total energy -80258.665402
FMO2-MP2: Total energy -80494.201896


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.
-10.364-3.94211.905-6.325-12.005-0.049
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 : -0.054 / q_NPA : -0.033
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].
3H3LEU00.0090.0123.474-1.0200.916-0.007-0.809-1.1200.002
4H4LEU00.0300.0205.6270.1500.1500.0000.0000.0000.000
5H5GLU-1-0.746-0.8689.472-0.368-0.3680.0000.0000.0000.000
6H6SER0-0.051-0.02312.3910.0510.0510.0000.0000.0000.000
7H7GLY00.0570.01615.499-0.010-0.0100.0000.0000.0000.000
8H8PRO0-0.034-0.02019.0320.0030.0030.0000.0000.0000.000
9H9GLY00.0970.05322.081-0.009-0.0090.0000.0000.0000.000
10H10LEU0-0.058-0.02622.8940.0010.0010.0000.0000.0000.000
11H11VAL00.0190.01324.3160.0020.0020.0000.0000.0000.000
12H12LYS10.9520.99127.4750.0360.0360.0000.0000.0000.000
13H13PRO00.0490.00830.285-0.004-0.0040.0000.0000.0000.000
14H14ALA0-0.011-0.00632.0360.0030.0030.0000.0000.0000.000
15H15GLN0-0.041-0.00829.2800.0020.0020.0000.0000.0000.000
16H16THR0-0.031-0.03624.058-0.002-0.0020.0000.0000.0000.000
17H17LEU0-0.0100.02720.2920.0040.0040.0000.0000.0000.000
18H18SER0-0.031-0.03420.851-0.003-0.0030.0000.0000.0000.000
19H19LEU0-0.031-0.00116.0970.0070.0070.0000.0000.0000.000
20H20SER00.000-0.01414.221-0.001-0.0010.0000.0000.0000.000
21H21CYS0-0.073-0.0258.602-0.018-0.0180.0000.0000.0000.000
22H22ALA00.0400.0318.9530.0100.0100.0000.0000.0000.000
23H23VAL00.0080.0013.118-0.512-0.1980.051-0.068-0.2970.000
24H24SER0-0.0140.0013.7660.2790.6240.000-0.131-0.2140.000
25H25GLY00.0500.0082.252-3.870-2.5426.160-4.239-3.250-0.031
26H26GLY00.0190.0102.465-2.191-1.5602.091-0.357-2.365-0.008
27H27SER0-0.0060.0103.1900.342-0.0980.0080.581-0.1500.000
28H28ILE00.0580.0366.4920.0050.0050.0000.0000.0000.000
29H29ARG10.9380.9688.0940.0180.0180.0000.0000.0000.000
30H30SER0-0.049-0.0437.4870.0320.0320.0000.0000.0000.000
31H31GLY0-0.037-0.0029.8250.0010.0010.0000.0000.0000.000
32H32GLY0-0.006-0.0188.508-0.015-0.0150.0000.0000.0000.000
33H33TYR00.010-0.0025.229-0.048-0.0480.0000.0000.0000.000
34H34TYR0-0.045-0.0198.5820.0510.0510.0000.0000.0000.000
35H35TRP00.009-0.0013.615-0.442-0.1200.007-0.065-0.2640.000
36H36SER00.020-0.0049.3470.0820.0820.0000.0000.0000.000
37H37TRP00.0130.00211.147-0.045-0.0450.0000.0000.0000.000
38H38ILE00.0150.00813.2550.0300.0300.0000.0000.0000.000
39H39ARG10.7730.85215.8650.1220.1220.0000.0000.0000.000
40H40GLN00.0160.00618.480-0.013-0.0130.0000.0000.0000.000
41H41HIS0-0.0100.00321.1960.0110.0110.0000.0000.0000.000
42H42PRO00.016-0.00824.733-0.002-0.0020.0000.0000.0000.000
43H43GLY00.0260.03126.356-0.001-0.0010.0000.0000.0000.000
44H44LYS10.8650.93325.4220.0930.0930.0000.0000.0000.000
45H45GLY00.0710.03923.313-0.003-0.0030.0000.0000.0000.000
46H46LEU00.0050.00116.4520.0040.0040.0000.0000.0000.000
47H47GLU-1-0.848-0.90119.986-0.117-0.1170.0000.0000.0000.000
48H48TRP00.0410.01413.342-0.012-0.0120.0000.0000.0000.000
49H49ILE0-0.035-0.01317.3090.0220.0220.0000.0000.0000.000
50H50GLY00.026-0.00916.9070.0230.0230.0000.0000.0000.000
51H51TYR0-0.016-0.00112.832-0.030-0.0300.0000.0000.0000.000
52H52ILE0-0.030-0.00412.5270.0300.0300.0000.0000.0000.000
53H53TYR00.0470.02211.677-0.032-0.0320.0000.0000.0000.000
54H54HIS00.0130.00411.3130.0200.0200.0000.0000.0000.000
55H55SER0-0.023-0.01213.2440.0090.0090.0000.0000.0000.000
56H56GLY00.0170.00916.2740.0120.0120.0000.0000.0000.000
57H57ASN0-0.028-0.00317.2510.0030.0030.0000.0000.0000.000
58H58THR00.0300.01716.723-0.017-0.0170.0000.0000.0000.000
59H59TYR0-0.0010.01716.8010.0100.0100.0000.0000.0000.000
60H60TYR00.0560.00818.387-0.015-0.0150.0000.0000.0000.000
61H61ASN00.0360.02120.9450.0130.0130.0000.0000.0000.000
62H62PRO00.0340.00422.7590.0080.0080.0000.0000.0000.000
63H63SER0-0.0040.00226.3160.0060.0060.0000.0000.0000.000
64H64LEU0-0.007-0.00422.3310.0050.0050.0000.0000.0000.000
65H65LYS10.8930.93724.5620.0860.0860.0000.0000.0000.000
66H66SER0-0.0030.01125.5400.0010.0010.0000.0000.0000.000
67H67ARG10.7970.86626.8040.0880.0880.0000.0000.0000.000
68H68ILE0-0.0490.00319.2060.0010.0010.0000.0000.0000.000
69H69ALA00.0150.01321.7200.0040.0040.0000.0000.0000.000
70H70MET0-0.042-0.00914.004-0.005-0.0050.0000.0000.0000.000
71H71SER0-0.011-0.00616.2390.0090.0090.0000.0000.0000.000
72H72VAL00.0340.00111.688-0.027-0.0270.0000.0000.0000.000
73H73ASP-1-0.815-0.88012.770-0.021-0.0210.0000.0000.0000.000
74H74THR00.020-0.01211.915-0.008-0.0080.0000.0000.0000.000
75H75SER0-0.060-0.04412.5200.0160.0160.0000.0000.0000.000
76H76GLU-1-0.850-0.91513.2180.0120.0120.0000.0000.0000.000
77H77ASN0-0.068-0.0245.830-0.003-0.0030.0000.0000.0000.000
78H78LYS10.8570.9248.245-0.013-0.0130.0000.0000.0000.000
79H79PHE00.0200.0087.2130.0380.0380.0000.0000.0000.000
80H80SER0-0.058-0.03511.7000.0050.0050.0000.0000.0000.000
81H81LEU00.0080.02014.828-0.002-0.0020.0000.0000.0000.000
82H82ARG10.9230.94617.6440.0830.0830.0000.0000.0000.000
83H83LEU00.0260.02321.4740.0010.0010.0000.0000.0000.000
84H84ASN00.000-0.01323.4260.0100.0100.0000.0000.0000.000
85H85SER00.0280.01127.044-0.003-0.0030.0000.0000.0000.000
86H86VAL0-0.0380.01125.659-0.001-0.0010.0000.0000.0000.000
87H87THR00.005-0.01328.7800.0070.0070.0000.0000.0000.000
88H88ALA00.0530.01129.299-0.004-0.0040.0000.0000.0000.000
89H89ALA00.0310.01529.449-0.003-0.0030.0000.0000.0000.000
90H90ASP-1-0.732-0.81425.246-0.095-0.0950.0000.0000.0000.000
91H91THR00.0080.02224.476-0.006-0.0060.0000.0000.0000.000
92H92ALA0-0.018-0.01521.8270.0000.0000.0000.0000.0000.000
93H93VAL00.0180.02417.4000.0060.0060.0000.0000.0000.000
94H94TYR0-0.017-0.03916.644-0.007-0.0070.0000.0000.0000.000
95H95TYR00.0440.01112.4970.0040.0040.0000.0000.0000.000
96H97ALA00.0260.0067.450-0.083-0.0830.0000.0000.0000.000
97H98ARG10.7980.8782.470-0.6270.6981.646-0.664-2.307-0.007
98H99LEU00.000-0.0026.606-0.012-0.0120.0000.0000.0000.000
99H100ASP-1-0.777-0.8638.673-0.396-0.3960.0000.0000.0000.000
100H101GLY0-0.0060.0019.7700.0460.0460.0000.0000.0000.000
101H102TYR0-0.085-0.03913.0290.0420.0420.0000.0000.0000.000
102H103THR0-0.080-0.06711.0340.0000.0000.0000.0000.0000.000
103H104LEU0-0.018-0.01810.051-0.015-0.0150.0000.0000.0000.000
104H105ASP-1-0.750-0.8365.644-1.267-1.2670.0000.0000.0000.000
105H106ILE0-0.030-0.0032.427-1.228-0.5671.949-0.573-2.038-0.005
106H107TRP0-0.022-0.0345.6800.2870.2870.0000.0000.0000.000
107H108GLY00.0000.0086.833-0.204-0.2040.0000.0000.0000.000
108H109GLN0-0.075-0.0588.5540.1230.1230.0000.0000.0000.000
109H110GLY0-0.0120.00312.0410.0440.0440.0000.0000.0000.000
110H111THR0-0.053-0.03114.3800.0360.0360.0000.0000.0000.000
111H112LEU0-0.0100.00517.312-0.005-0.0050.0000.0000.0000.000
112H113VAL0-0.027-0.01020.1030.0080.0080.0000.0000.0000.000
113H114THR00.003-0.00322.7870.0000.0000.0000.0000.0000.000
114H115VAL0-0.019-0.01526.5980.0040.0040.0000.0000.0000.000
115H116SER0-0.054-0.03228.9650.0040.0040.0000.0000.0000.000
116H117SER0-0.020-0.04631.5290.0020.0020.0000.0000.0000.000
117H118SER00.0260.03233.0880.0020.0020.0000.0000.0000.000
118H119THR00.009-0.00530.405-0.004-0.0040.0000.0000.0000.000
119H120LYS10.8190.91132.9140.0180.0180.0000.0000.0000.000
120H121GLY00.0770.05532.462-0.003-0.0030.0000.0000.0000.000
121H122PRO0-0.055-0.01931.8990.0010.0010.0000.0000.0000.000
122H123SER00.0060.00734.8030.0030.0030.0000.0000.0000.000
123H124VAL0-0.003-0.00134.692-0.002-0.0020.0000.0000.0000.000
124H125PHE0-0.007-0.01337.8890.0030.0030.0000.0000.0000.000
125H126PRO00.0340.02139.866-0.001-0.0010.0000.0000.0000.000
126H127LEU0-0.050-0.01939.101-0.001-0.0010.0000.0000.0000.000
127H128ALA00.0580.02142.1420.0010.0010.0000.0000.0000.000
128H129PRO0-0.012-0.01243.677-0.001-0.0010.0000.0000.0000.000
129H130SER00.0150.03544.7130.0010.0010.0000.0000.0000.000
130H131SER00.0500.00345.4240.0000.0000.0000.0000.0000.000
131H132LYS10.9610.99247.7200.0020.0020.0000.0000.0000.000
132H133SER0-0.062-0.04449.311-0.001-0.0010.0000.0000.0000.000
133H134THR00.0090.01044.8150.0000.0000.0000.0000.0000.000
134H135SER00.0500.01444.925-0.001-0.0010.0000.0000.0000.000
135H136GLY00.0120.02247.0340.0010.0010.0000.0000.0000.000
136H137GLY00.0020.00746.746-0.001-0.0010.0000.0000.0000.000
137H138THR0-0.084-0.03941.8970.0010.0010.0000.0000.0000.000
138H139ALA00.0260.01242.878-0.001-0.0010.0000.0000.0000.000
139H140ALA0-0.015-0.00540.6220.0000.0000.0000.0000.0000.000
140H141LEU00.0030.02338.1440.0000.0000.0000.0000.0000.000
141H142GLY00.031-0.01437.403-0.001-0.0010.0000.0000.0000.000
142H143CYS0-0.0590.00933.2300.0040.0040.0000.0000.0000.000
143H144LEU00.0350.04336.113-0.003-0.0030.0000.0000.0000.000
144H145VAL0-0.020-0.01932.0380.0030.0030.0000.0000.0000.000
145H146LYS10.8700.90235.0340.0140.0140.0000.0000.0000.000
146H147ASP-1-0.780-0.86836.990-0.017-0.0170.0000.0000.0000.000
147H148TYR0-0.036-0.03529.7520.0040.0040.0000.0000.0000.000
148H149PHE00.0360.02230.965-0.004-0.0040.0000.0000.0000.000
149H150PRO00.0210.01526.9700.0050.0050.0000.0000.0000.000
150H151GLU-1-0.764-0.86726.149-0.047-0.0470.0000.0000.0000.000
151H152PRO0-0.014-0.00122.001-0.003-0.0030.0000.0000.0000.000
152H153VAL0-0.039-0.02725.3320.0070.0070.0000.0000.0000.000
153H154THR0-0.064-0.03522.702-0.003-0.0030.0000.0000.0000.000
154H155VAL00.010-0.01526.0010.0050.0050.0000.0000.0000.000
155H156SER0-0.0150.00526.551-0.002-0.0020.0000.0000.0000.000
156H157TRP00.0280.00828.5330.0000.0000.0000.0000.0000.000
157H158ASN00.006-0.00630.1690.0020.0020.0000.0000.0000.000
158H159SER0-0.013-0.01529.0410.0030.0030.0000.0000.0000.000
159H160GLY00.0070.01026.0590.0070.0070.0000.0000.0000.000
160H161ALA0-0.039-0.01026.8180.0000.0000.0000.0000.0000.000
161H162LEU0-0.036-0.01029.169-0.002-0.0020.0000.0000.0000.000
162H163THR00.0280.00125.487-0.003-0.0030.0000.0000.0000.000
163H164SER00.0360.00928.776-0.006-0.0060.0000.0000.0000.000
164H165GLY00.0310.01430.9260.0020.0020.0000.0000.0000.000
165H166VAL0-0.045-0.01130.035-0.001-0.0010.0000.0000.0000.000
166H167HIS0-0.0060.00730.985-0.007-0.0070.0000.0000.0000.000
167H168THR00.0160.00028.7830.0060.0060.0000.0000.0000.000
168H169PHE0-0.0230.00629.858-0.005-0.0050.0000.0000.0000.000
169H170PRO00.0350.00229.1810.0000.0000.0000.0000.0000.000
170H171ALA0-0.0120.01229.6430.0040.0040.0000.0000.0000.000
171H172VAL0-0.003-0.00631.481-0.003-0.0030.0000.0000.0000.000
172H173LEU0-0.042-0.01833.7500.0030.0030.0000.0000.0000.000
173H174GLN0-0.028-0.02735.3920.0020.0020.0000.0000.0000.000
174H175SER00.0320.00539.081-0.001-0.0010.0000.0000.0000.000
175H176SER0-0.016-0.00540.6410.0000.0000.0000.0000.0000.000
176H177GLY00.0180.01337.9700.0010.0010.0000.0000.0000.000
177H178LEU0-0.051-0.01735.661-0.001-0.0010.0000.0000.0000.000
178H179TYR00.0220.01029.9420.0000.0000.0000.0000.0000.000
179H180SER0-0.018-0.00934.2940.0040.0040.0000.0000.0000.000
180H181LEU00.0490.04229.637-0.003-0.0030.0000.0000.0000.000
181H182SER0-0.003-0.02334.1220.0050.0050.0000.0000.0000.000
182H183SER0-0.0090.00631.378-0.002-0.0020.0000.0000.0000.000
183H184VAL00.017-0.01133.6510.0030.0030.0000.0000.0000.000
184H185VAL00.0200.01134.307-0.001-0.0010.0000.0000.0000.000
185H186THR0-0.025-0.00236.0190.0000.0000.0000.0000.0000.000
186H187VAL00.0100.00437.2800.0010.0010.0000.0000.0000.000
187H188PRO00.0780.02539.162-0.001-0.0010.0000.0000.0000.000
188H189SER00.0290.01242.4000.0010.0010.0000.0000.0000.000
189H190SER0-0.014-0.00545.2600.0000.0000.0000.0000.0000.000
190H191SER0-0.012-0.00541.2960.0010.0010.0000.0000.0000.000
191H192LEU00.0080.00042.8700.0010.0010.0000.0000.0000.000
192H193GLY0-0.0100.01144.8660.0000.0000.0000.0000.0000.000
193H194THR0-0.041-0.02644.0280.0010.0010.0000.0000.0000.000
194H195GLN0-0.051-0.02237.1560.0030.0030.0000.0000.0000.000
195H196THR00.0210.02038.630-0.002-0.0020.0000.0000.0000.000
196H197TYR00.029-0.00236.5640.0020.0020.0000.0000.0000.000
197H198ILE00.028-0.00534.693-0.001-0.0010.0000.0000.0000.000
198H200ASN00.0450.00529.4390.0010.0010.0000.0000.0000.000
199H201VAL00.0120.01629.674-0.003-0.0030.0000.0000.0000.000
200H202ASN0-0.015-0.02825.3620.0050.0050.0000.0000.0000.000
201H203HIS00.015-0.00827.081-0.001-0.0010.0000.0000.0000.000
202H204LYS10.9370.95821.3480.0040.0040.0000.0000.0000.000
203H205PRO00.0180.01325.2990.0040.0040.0000.0000.0000.000
204H206SER00.0330.00427.1190.0000.0000.0000.0000.0000.000
205H207ASN0-0.006-0.00327.5820.0060.0060.0000.0000.0000.000
206H208THR00.0560.05328.7710.0050.0050.0000.0000.0000.000
207H209LYS10.8680.93527.715-0.021-0.0210.0000.0000.0000.000
208H210VAL0-0.020-0.01631.5820.0000.0000.0000.0000.0000.000
209H211ASP-1-0.833-0.88832.7100.0220.0220.0000.0000.0000.000
210H212LYS10.8390.90734.869-0.004-0.0040.0000.0000.0000.000
211H213ARG10.8560.91537.663-0.015-0.0150.0000.0000.0000.000
212H214VAL0-0.038-0.01838.898-0.002-0.0020.0000.0000.0000.000
213H215GLU-1-0.835-0.90441.5720.0130.0130.0000.0000.0000.000
214H216PRO00.0040.00444.884-0.002-0.0020.0000.0000.0000.000