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: LZR69

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2160749.39841
FMO2-HF: Nuclear repulsion 2080491.251476
FMO2-HF: Total energy -80258.146934
FMO2-MP2: Total energy -80493.805135


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.
-9.913-2.68310.372-6-11.602-0.044
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 : -0.051 / 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].
3H3LEU0-0.0010.0043.409-1.1781.0150.014-0.834-1.3720.001
4H4LEU00.0330.0165.2880.1280.137-0.001-0.001-0.0060.000
5H5GLU-1-0.769-0.8849.024-0.357-0.3570.0000.0000.0000.000
6H6SER0-0.043-0.01411.9730.0450.0450.0000.0000.0000.000
7H7GLY00.0420.00415.030-0.006-0.0060.0000.0000.0000.000
8H8PRO0-0.041-0.02518.4620.0010.0010.0000.0000.0000.000
9H9GLY00.1020.06121.208-0.009-0.0090.0000.0000.0000.000
10H10LEU0-0.065-0.03022.6180.0010.0010.0000.0000.0000.000
11H11VAL00.0420.02623.8720.0020.0020.0000.0000.0000.000
12H12LYS10.9430.99927.0130.0360.0360.0000.0000.0000.000
13H13PRO00.0710.02329.962-0.003-0.0030.0000.0000.0000.000
14H14ALA0-0.033-0.01931.3400.0030.0030.0000.0000.0000.000
15H15GLN0-0.045-0.01428.9670.0020.0020.0000.0000.0000.000
16H16THR0-0.036-0.03623.731-0.001-0.0010.0000.0000.0000.000
17H17LEU0-0.0330.01119.7830.0040.0040.0000.0000.0000.000
18H18SER0-0.014-0.02820.1210.0000.0000.0000.0000.0000.000
19H19LEU00.0010.01715.4500.0040.0040.0000.0000.0000.000
20H20SER00.004-0.00213.6850.0030.0030.0000.0000.0000.000
21H21CYS0-0.074-0.0188.040-0.029-0.0290.0000.0000.0000.000
22H22ALA00.0140.0168.4340.0250.0250.0000.0000.0000.000
23H23VAL00.0180.0072.559-0.598-0.2830.592-0.162-0.7450.000
24H24SER0-0.0080.0073.6560.1570.5350.002-0.141-0.2390.000
25H25GLY00.0470.0052.288-3.689-2.1204.520-3.249-2.839-0.030
26H26GLY00.0200.0072.302-1.939-0.9332.532-1.268-2.271-0.006
27H27SER0-0.0170.0133.0940.605-0.0640.0310.810-0.1730.000
28H28ILE00.0450.0176.5030.0230.0230.0000.0000.0000.000
29H29ARG10.9450.9747.832-0.006-0.0060.0000.0000.0000.000
30H30SER0-0.055-0.0387.6380.0070.0070.0000.0000.0000.000
31H31GLY0-0.039-0.0049.602-0.005-0.0050.0000.0000.0000.000
32H32GLY00.004-0.0108.4650.0080.0080.0000.0000.0000.000
33H33TYR0-0.002-0.0095.351-0.025-0.0250.0000.0000.0000.000
34H34TYR0-0.045-0.0198.6700.0430.0430.0000.0000.0000.000
35H35TRP00.0110.0023.463-0.444-0.0890.012-0.072-0.2960.000
36H36SER00.026-0.0049.3010.0600.0600.0000.0000.0000.000
37H37TRP00.0140.00410.925-0.046-0.0460.0000.0000.0000.000
38H38ILE00.0090.00213.2940.0300.0300.0000.0000.0000.000
39H39ARG10.8050.87715.5290.1070.1070.0000.0000.0000.000
40H40GLN0-0.0030.00218.197-0.008-0.0080.0000.0000.0000.000
41H41HIS0-0.022-0.00320.8110.0090.0090.0000.0000.0000.000
42H42PRO00.0470.00424.310-0.001-0.0010.0000.0000.0000.000
43H43GLY00.0120.02326.213-0.002-0.0020.0000.0000.0000.000
44H44LYS10.8680.93825.3910.0840.0840.0000.0000.0000.000
45H45GLY00.0630.03423.489-0.004-0.0040.0000.0000.0000.000
46H46LEU00.0010.00016.6710.0030.0030.0000.0000.0000.000
47H47GLU-1-0.846-0.90819.927-0.107-0.1070.0000.0000.0000.000
48H48TRP00.0390.01413.435-0.012-0.0120.0000.0000.0000.000
49H49ILE0-0.0260.00016.8230.0190.0190.0000.0000.0000.000
50H50GLY00.027-0.01116.6360.0200.0200.0000.0000.0000.000
51H51TYR0-0.012-0.00712.792-0.027-0.0270.0000.0000.0000.000
52H52ILE0-0.0230.00112.2910.0230.0230.0000.0000.0000.000
53H53TYR00.0360.00711.818-0.018-0.0180.0000.0000.0000.000
54H54HIS00.0150.00910.8040.0100.0100.0000.0000.0000.000
55H55SER0-0.024-0.00312.7780.0050.0050.0000.0000.0000.000
56H56GLY00.0220.00915.8710.0080.0080.0000.0000.0000.000
57H57ASN0-0.032-0.00917.2420.0020.0020.0000.0000.0000.000
58H58THR00.0150.01416.510-0.011-0.0110.0000.0000.0000.000
59H59TYR0-0.0190.00316.6620.0100.0100.0000.0000.0000.000
60H60TYR00.0710.02218.215-0.014-0.0140.0000.0000.0000.000
61H61ASN00.0410.01620.7600.0120.0120.0000.0000.0000.000
62H62PRO00.0190.00022.5040.0070.0070.0000.0000.0000.000
63H63SER0-0.005-0.00726.0900.0040.0040.0000.0000.0000.000
64H64LEU0-0.001-0.00722.1400.0040.0040.0000.0000.0000.000
65H65LYS10.9180.96123.9460.0730.0730.0000.0000.0000.000
66H66SER0-0.0070.00124.9920.0000.0000.0000.0000.0000.000
67H67ARG10.7900.87426.2540.0810.0810.0000.0000.0000.000
68H68ILE0-0.0440.01118.738-0.002-0.0020.0000.0000.0000.000
69H69ALA00.0130.00721.3830.0050.0050.0000.0000.0000.000
70H70MET0-0.0450.00413.919-0.004-0.0040.0000.0000.0000.000
71H71SER0-0.008-0.00716.1050.0070.0070.0000.0000.0000.000
72H72VAL00.021-0.00111.537-0.022-0.0220.0000.0000.0000.000
73H73ASP-1-0.800-0.88512.591-0.026-0.0260.0000.0000.0000.000
74H74THR00.024-0.01611.548-0.004-0.0040.0000.0000.0000.000
75H75SER0-0.066-0.03512.0290.0120.0120.0000.0000.0000.000
76H76GLU-1-0.846-0.91612.736-0.013-0.0130.0000.0000.0000.000
77H77ASN0-0.078-0.0295.5570.0390.0390.0000.0000.0000.000
78H78LYS10.8540.9217.838-0.007-0.0070.0000.0000.0000.000
79H79PHE0-0.010-0.0056.9520.0410.0410.0000.0000.0000.000
80H80SER00.016-0.01611.542-0.020-0.0200.0000.0000.0000.000
81H81LEU0-0.0330.00114.6000.0030.0030.0000.0000.0000.000
82H82ARG10.9210.95217.2200.0740.0740.0000.0000.0000.000
83H83LEU00.0240.01420.9600.0000.0000.0000.0000.0000.000
84H84ASN00.015-0.00223.1010.0060.0060.0000.0000.0000.000
85H85SER00.0260.00526.740-0.003-0.0030.0000.0000.0000.000
86H86VAL0-0.0290.01125.1290.0000.0000.0000.0000.0000.000
87H87THR00.0300.01028.3380.0060.0060.0000.0000.0000.000
88H88ALA00.0550.01328.583-0.005-0.0050.0000.0000.0000.000
89H89ALA00.0130.00628.845-0.003-0.0030.0000.0000.0000.000
90H90ASP-1-0.743-0.83124.514-0.090-0.0900.0000.0000.0000.000
91H91THR00.0070.02323.841-0.007-0.0070.0000.0000.0000.000
92H92ALA0-0.021-0.01521.2830.0010.0010.0000.0000.0000.000
93H93VAL00.0130.02516.8650.0050.0050.0000.0000.0000.000
94H94TYR0-0.029-0.04816.090-0.005-0.0050.0000.0000.0000.000
95H95TYR00.0550.01812.1090.0020.0020.0000.0000.0000.000
96H97ALA00.0310.0027.443-0.085-0.0850.0000.0000.0000.000
97H98ARG10.7910.8762.664-0.6300.7590.880-0.497-1.772-0.004
98H99LEU00.0020.0026.508-0.044-0.0440.0000.0000.0000.000
99H100ASP-1-0.788-0.8728.536-0.343-0.3430.0000.0000.0000.000
100H101GLY0-0.010-0.0069.7060.0380.0380.0000.0000.0000.000
101H102TYR0-0.079-0.04112.8590.0350.0350.0000.0000.0000.000
102H103THR0-0.077-0.05910.947-0.001-0.0010.0000.0000.0000.000
103H104LEU0-0.012-0.0109.906-0.011-0.0110.0000.0000.0000.000
104H105ASP-1-0.747-0.8325.919-1.121-1.1210.0000.0000.0000.000
105H106ILE0-0.033-0.0032.391-1.212-0.5271.790-0.586-1.889-0.005
106H107TRP0-0.022-0.0335.9080.2780.2780.0000.0000.0000.000
107H108GLY00.0110.0097.246-0.176-0.1760.0000.0000.0000.000
108H109GLN0-0.065-0.0448.4360.1340.1340.0000.0000.0000.000
109H110GLY00.0040.01211.9730.0480.0480.0000.0000.0000.000
110H111THR0-0.050-0.02814.1320.0320.0320.0000.0000.0000.000
111H112LEU0-0.0090.00016.728-0.001-0.0010.0000.0000.0000.000
112H113VAL0-0.010-0.00419.6740.0070.0070.0000.0000.0000.000
113H114THR00.010-0.00122.3070.0010.0010.0000.0000.0000.000
114H115VAL0-0.023-0.03226.0700.0040.0040.0000.0000.0000.000
115H116SER0-0.081-0.06028.2620.0050.0050.0000.0000.0000.000
116H117SER0-0.024-0.04730.7870.0020.0020.0000.0000.0000.000
117H118SER00.0260.03032.5360.0010.0010.0000.0000.0000.000
118H119THR0-0.0180.00129.764-0.001-0.0010.0000.0000.0000.000
119H120LYS10.8440.91532.1690.0210.0210.0000.0000.0000.000
120H121GLY00.0750.05032.446-0.003-0.0030.0000.0000.0000.000
121H122PRO0-0.046-0.01031.8550.0010.0010.0000.0000.0000.000
122H123SER0-0.019-0.00234.7850.0020.0020.0000.0000.0000.000
123H124VAL00.001-0.00534.559-0.002-0.0020.0000.0000.0000.000
124H125PHE0-0.014-0.02037.5990.0020.0020.0000.0000.0000.000
125H126PRO00.0330.02139.607-0.001-0.0010.0000.0000.0000.000
126H127LEU0-0.047-0.01338.844-0.001-0.0010.0000.0000.0000.000
127H128ALA00.0360.00642.0380.0010.0010.0000.0000.0000.000
128H129PRO0-0.002-0.01243.313-0.001-0.0010.0000.0000.0000.000
129H130SER0-0.0110.01944.4520.0010.0010.0000.0000.0000.000
130H131SER00.0580.01245.3490.0000.0000.0000.0000.0000.000
131H132LYS10.9670.96047.6750.0030.0030.0000.0000.0000.000
132H133SER0-0.090-0.04248.856-0.001-0.0010.0000.0000.0000.000
133H134THR00.0140.01644.5250.0000.0000.0000.0000.0000.000
134H135SER00.035-0.01444.963-0.001-0.0010.0000.0000.0000.000
135H136GLY00.0310.04547.0110.0010.0010.0000.0000.0000.000
136H137GLY00.0380.05745.998-0.001-0.0010.0000.0000.0000.000
137H138THR0-0.093-0.05441.6800.0010.0010.0000.0000.0000.000
138H139ALA00.0210.01442.6030.0000.0000.0000.0000.0000.000
139H140ALA00.0100.02240.4090.0000.0000.0000.0000.0000.000
140H141LEU00.0170.01837.8430.0010.0010.0000.0000.0000.000
141H142GLY00.0590.00337.236-0.002-0.0020.0000.0000.0000.000
142H143CYS0-0.087-0.00633.1220.0030.0030.0000.0000.0000.000
143H144LEU00.0260.02636.128-0.003-0.0030.0000.0000.0000.000
144H145VAL0-0.014-0.01331.9090.0030.0030.0000.0000.0000.000
145H146LYS10.8630.90035.0540.0160.0160.0000.0000.0000.000
146H147ASP-1-0.790-0.87136.702-0.019-0.0190.0000.0000.0000.000
147H148TYR0-0.014-0.03029.3230.0040.0040.0000.0000.0000.000
148H149PHE00.0410.02631.226-0.004-0.0040.0000.0000.0000.000
149H150PRO00.0050.01426.6190.0040.0040.0000.0000.0000.000
150H151GLU-1-0.762-0.86225.742-0.051-0.0510.0000.0000.0000.000
151H152PRO0-0.016-0.01021.899-0.003-0.0030.0000.0000.0000.000
152H153VAL0-0.009-0.01725.2280.0060.0060.0000.0000.0000.000
153H154THR0-0.027-0.01122.425-0.005-0.0050.0000.0000.0000.000
154H155VAL0-0.017-0.02325.7610.0050.0050.0000.0000.0000.000
155H156SER0-0.019-0.00726.454-0.002-0.0020.0000.0000.0000.000
156H157TRP00.0250.01528.4940.0010.0010.0000.0000.0000.000
157H158ASN0-0.008-0.01530.1700.0020.0020.0000.0000.0000.000
158H159SER00.005-0.00928.4830.0020.0020.0000.0000.0000.000
159H160GLY0-0.0030.00325.8790.0060.0060.0000.0000.0000.000
160H161ALA0-0.021-0.00126.6520.0010.0010.0000.0000.0000.000
161H162LEU0-0.048-0.01328.953-0.001-0.0010.0000.0000.0000.000
162H163THR00.0280.00125.385-0.004-0.0040.0000.0000.0000.000
163H164SER00.015-0.00228.623-0.006-0.0060.0000.0000.0000.000
164H165GLY00.0320.00830.8080.0010.0010.0000.0000.0000.000
165H166VAL0-0.041-0.01229.741-0.001-0.0010.0000.0000.0000.000
166H167HIS0-0.0040.00730.569-0.006-0.0060.0000.0000.0000.000
167H168THR00.0220.00928.5050.0050.0050.0000.0000.0000.000
168H169PHE0-0.039-0.00529.683-0.004-0.0040.0000.0000.0000.000
169H170PRO00.0340.00529.1300.0000.0000.0000.0000.0000.000
170H171ALA0-0.0020.01329.5840.0040.0040.0000.0000.0000.000
171H172VAL0-0.011-0.00331.472-0.003-0.0030.0000.0000.0000.000
172H173LEU0-0.049-0.01933.4630.0020.0020.0000.0000.0000.000
173H174GLN0-0.032-0.03935.1650.0030.0030.0000.0000.0000.000
174H175SER00.0350.00738.640-0.001-0.0010.0000.0000.0000.000
175H176SER0-0.008-0.00540.200-0.001-0.0010.0000.0000.0000.000
176H177GLY00.0140.01137.2160.0010.0010.0000.0000.0000.000
177H178LEU0-0.057-0.01535.181-0.002-0.0020.0000.0000.0000.000
178H179TYR00.0170.01129.8880.0000.0000.0000.0000.0000.000
179H180SER0-0.022-0.01434.1020.0040.0040.0000.0000.0000.000
180H181LEU00.0450.04029.580-0.003-0.0030.0000.0000.0000.000
181H182SER00.0280.01034.0920.0040.0040.0000.0000.0000.000
182H183SER0-0.025-0.01331.256-0.002-0.0020.0000.0000.0000.000
183H184VAL00.023-0.00833.6390.0030.0030.0000.0000.0000.000
184H185VAL00.0190.01534.043-0.001-0.0010.0000.0000.0000.000
185H186THR0-0.0160.00235.8230.0000.0000.0000.0000.0000.000
186H187VAL0-0.0010.00037.0880.0010.0010.0000.0000.0000.000
187H188PRO00.0580.02238.981-0.001-0.0010.0000.0000.0000.000
188H189SER00.029-0.00142.2220.0010.0010.0000.0000.0000.000
189H190SER0-0.026-0.01944.8920.0000.0000.0000.0000.0000.000
190H191SER0-0.034-0.01841.1650.0010.0010.0000.0000.0000.000
191H192LEU0-0.004-0.00342.8510.0010.0010.0000.0000.0000.000
192H193GLY0-0.0120.00844.6790.0000.0000.0000.0000.0000.000
193H194THR0-0.002-0.00543.5590.0000.0000.0000.0000.0000.000
194H195GLN0-0.053-0.01736.9210.0020.0020.0000.0000.0000.000
195H196THR00.0250.01938.147-0.002-0.0020.0000.0000.0000.000
196H197TYR00.0300.00236.4150.0020.0020.0000.0000.0000.000
197H198ILE00.0380.01434.599-0.002-0.0020.0000.0000.0000.000
198H200ASN00.032-0.00229.1960.0010.0010.0000.0000.0000.000
199H201VAL00.0140.00829.605-0.004-0.0040.0000.0000.0000.000
200H202ASN0-0.053-0.03425.0800.0050.0050.0000.0000.0000.000
201H203HIS00.049-0.00227.008-0.001-0.0010.0000.0000.0000.000
202H204LYS10.9320.95421.1270.0130.0130.0000.0000.0000.000
203H205PRO00.0070.01524.8980.0030.0030.0000.0000.0000.000
204H206SER00.021-0.01226.7090.0010.0010.0000.0000.0000.000
205H207ASN0-0.029-0.00527.8260.0060.0060.0000.0000.0000.000
206H208THR00.0150.03628.7660.0030.0030.0000.0000.0000.000
207H209LYS10.9320.95926.646-0.013-0.0130.0000.0000.0000.000
208H210VAL0-0.008-0.00131.1090.0010.0010.0000.0000.0000.000
209H211ASP-1-0.810-0.87432.4630.0140.0140.0000.0000.0000.000
210H212LYS10.8710.92834.8200.0010.0010.0000.0000.0000.000
211H213ARG10.8590.92137.557-0.010-0.0100.0000.0000.0000.000
212H214VAL0-0.039-0.02438.643-0.002-0.0020.0000.0000.0000.000
213H215GLU-1-0.852-0.91641.2540.0090.0090.0000.0000.0000.000
214H216PRO00.0110.00744.565-0.001-0.0010.0000.0000.0000.000