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: 2LKKR

Calculation Name: 1ADQ-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ADQ

Chain ID: H

ChEMBL ID:

UniProt ID: P01861

Base Structure: X-ray

Registration Date: 2023-09-26

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2314004.626924
FMO2-HF: Nuclear repulsion 2227134.816495
FMO2-HF: Total energy -86869.810428
FMO2-MP2: Total energy -87121.979984


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:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-86.807-86.02814.044-7.641-7.180.081
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.889 / q_NPA : -0.930
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].
3H3GLN0-0.048-0.0161.798-39.074-38.74314.048-7.529-6.8500.081
4H4LEU0-0.045-0.0294.441-7.054-6.9860.000-0.033-0.0350.000
5H5VAL00.0470.0247.2850.2090.2090.0000.0000.0000.000
6H6GLU-1-0.791-0.8979.89922.40622.4060.0000.0000.0000.000
7H7SER00.012-0.00313.6940.0710.0710.0000.0000.0000.000
8H8GLY0-0.041-0.02216.741-0.627-0.6270.0000.0000.0000.000
9H9GLY0-0.0030.00320.163-0.639-0.6390.0000.0000.0000.000
10H10GLY00.0340.01922.0430.5010.5010.0000.0000.0000.000
11H11LEU0-0.036-0.00724.654-0.227-0.2270.0000.0000.0000.000
12H12VAL0-0.049-0.02728.376-0.109-0.1090.0000.0000.0000.000
13H13GLN00.0650.04130.846-0.166-0.1660.0000.0000.0000.000
14H14PRO0-0.005-0.01833.5780.1650.1650.0000.0000.0000.000
15H15GLY0-0.0170.00234.796-0.195-0.1950.0000.0000.0000.000
16H16ARG10.9140.96629.080-10.477-10.4770.0000.0000.0000.000
17H17SER00.020-0.01329.511-0.056-0.0560.0000.0000.0000.000
18H18LEU0-0.050-0.02824.776-0.015-0.0150.0000.0000.0000.000
19H19ARG10.9360.98220.447-14.493-14.4930.0000.0000.0000.000
20H20LEU00.0330.02119.2550.5230.5230.0000.0000.0000.000
21H21SER0-0.025-0.02317.593-0.695-0.6950.0000.0000.0000.000
22H22CYS0-0.047-0.01112.525-0.229-0.2290.0000.0000.0000.000
23H23VAL00.0160.03110.917-1.371-1.3710.0000.0000.0000.000
24H24THR0-0.026-0.0308.5201.9781.9780.0000.0000.0000.000
25H25SER00.0250.0034.8533.7453.846-0.001-0.007-0.0930.000
26H26GLY00.0690.0204.7692.4732.564-0.001-0.052-0.0370.000
27H27PHE0-0.052-0.0365.318-3.852-3.784-0.001-0.014-0.0520.000
28H28THR00.0400.0018.1350.8140.8140.0000.0000.0000.000
29H29PHE00.0100.00311.939-0.842-0.8420.0000.0000.0000.000
30H30ASP-1-0.853-0.92613.98115.92715.9270.0000.0000.0000.000
31H31ASP-1-0.850-0.89613.48817.02117.0210.0000.0000.0000.000
32H32TYR0-0.046-0.04510.5450.2580.2580.0000.0000.0000.000
33H33ALA0-0.0020.02015.6620.0260.0260.0000.0000.0000.000
34H34MET0-0.0330.01512.2821.2201.2200.0000.0000.0000.000
35H35HIS00.0210.00316.542-1.467-1.4670.0000.0000.0000.000
36H36TRP0-0.0020.00216.5861.2731.2730.0000.0000.0000.000
37H37VAL0-0.003-0.00318.214-0.921-0.9210.0000.0000.0000.000
38H38ARG10.7890.89519.338-11.258-11.2580.0000.0000.0000.000
39H39GLN00.0240.00320.424-0.793-0.7930.0000.0000.0000.000
40H40SER00.0300.02322.4670.0840.0840.0000.0000.0000.000
41H41PRO0-0.001-0.01025.4860.0640.0640.0000.0000.0000.000
42H42GLY00.0270.02525.923-0.482-0.4820.0000.0000.0000.000
43H43LYS10.8510.91427.149-10.695-10.6950.0000.0000.0000.000
44H44GLY00.0560.04124.797-0.256-0.2560.0000.0000.0000.000
45H45LEU0-0.014-0.01619.4330.1090.1090.0000.0000.0000.000
46H46GLU-1-0.774-0.85823.39910.83310.8330.0000.0000.0000.000
47H47TRP00.0080.00321.7110.3730.3730.0000.0000.0000.000
48H48VAL0-0.0020.00022.383-0.411-0.4110.0000.0000.0000.000
49H49SER0-0.025-0.03422.587-0.693-0.6930.0000.0000.0000.000
50H50GLY00.0230.02121.1860.7690.7690.0000.0000.0000.000
51H51ILE0-0.058-0.01820.181-0.711-0.7110.0000.0000.0000.000
52H52SER00.040-0.00320.5940.9510.9510.0000.0000.0000.000
53H52TRP00.0410.01619.0380.1110.1110.0000.0000.0000.000
54H53ASN00.0530.04320.0320.4460.4460.0000.0000.0000.000
55H54THR0-0.011-0.02123.089-0.272-0.2720.0000.0000.0000.000
56H55GLY0-0.023-0.00624.710-0.264-0.2640.0000.0000.0000.000
57H56THR00.0060.00726.015-0.413-0.4130.0000.0000.0000.000
58H57ILE0-0.0030.00025.4350.6150.6150.0000.0000.0000.000
59H58ILE0-0.0270.00124.550-0.484-0.4840.0000.0000.0000.000
60H59TYR00.0370.00925.8210.5630.5630.0000.0000.0000.000
61H60ALA00.0860.05027.006-0.349-0.3490.0000.0000.0000.000
62H61ASP-1-0.785-0.90428.7389.3689.3680.0000.0000.0000.000
63H62SER0-0.064-0.03529.282-0.236-0.2360.0000.0000.0000.000
64H63VAL0-0.044-0.02626.8090.0380.0380.0000.0000.0000.000
65H64LYS10.8290.89930.125-9.694-9.6940.0000.0000.0000.000
66H65GLY00.0020.01131.971-0.248-0.2480.0000.0000.0000.000
67H66ARG10.7200.83930.651-10.204-10.2040.0000.0000.0000.000
68H67PHE0-0.014-0.02025.9000.1640.1640.0000.0000.0000.000
69H68ILE00.0140.01427.038-0.183-0.1830.0000.0000.0000.000
70H69ILE0-0.0060.01020.1320.3760.3760.0000.0000.0000.000
71H70SER0-0.060-0.04322.010-0.724-0.7240.0000.0000.0000.000
72H71ARG10.8120.90017.447-15.784-15.7840.0000.0000.0000.000
73H72ASP-1-0.798-0.88718.59014.21114.2110.0000.0000.0000.000
74H73ASN00.0290.00417.3061.1021.1020.0000.0000.0000.000
75H74ALA00.0160.01816.9690.9010.9010.0000.0000.0000.000
76H75LYS10.8060.89016.809-14.690-14.6900.0000.0000.0000.000
77H76ASN0-0.0070.00912.0841.6101.6100.0000.0000.0000.000
78H77SER00.0070.00812.8341.9601.9600.0000.0000.0000.000
79H78LEU0-0.024-0.01015.343-1.178-1.1780.0000.0000.0000.000
80H79TYR0-0.023-0.03117.0140.1150.1150.0000.0000.0000.000
81H80LEU00.0270.00719.902-0.281-0.2810.0000.0000.0000.000
82H81GLN00.0070.00022.4530.2140.2140.0000.0000.0000.000
83H82MET0-0.0150.01424.429-0.241-0.2410.0000.0000.0000.000
84H82ASN00.0590.02327.120-0.087-0.0870.0000.0000.0000.000
85H82SER00.0120.00430.907-0.106-0.1060.0000.0000.0000.000
86H82LEU00.0000.01827.467-0.040-0.0400.0000.0000.0000.000
87H83ARG10.8810.92031.585-9.427-9.4270.0000.0000.0000.000
88H84VAL00.0370.02831.6070.2770.2770.0000.0000.0000.000
89H85GLU-1-0.808-0.90031.3829.4289.4280.0000.0000.0000.000
90H86ASP-1-0.776-0.83727.90310.82710.8270.0000.0000.0000.000
91H87THR0-0.038-0.01626.7020.5850.5850.0000.0000.0000.000
92H88ALA00.009-0.00123.905-0.190-0.1900.0000.0000.0000.000
93H89LEU0-0.0150.01217.3810.0040.0040.0000.0000.0000.000
94H90TYR0-0.034-0.04919.292-0.259-0.2590.0000.0000.0000.000
95H91TYR00.0070.01014.4050.1260.1260.0000.0000.0000.000
96H93ALA00.016-0.00412.9951.4921.4920.0000.0000.0000.000
97H94LYS10.8160.9198.846-25.281-25.2810.0000.0000.0000.000
98H95THR0-0.043-0.03013.486-0.169-0.1690.0000.0000.0000.000
99H96ARG10.8990.93411.332-17.614-17.6140.0000.0000.0000.000
100H97SER0-0.004-0.00214.242-0.499-0.4990.0000.0000.0000.000
101H98TYR00.0770.03413.2090.5070.5070.0000.0000.0000.000
102H99VAL00.0030.01419.410-0.350-0.3500.0000.0000.0000.000
103H100VAL0-0.001-0.00723.1050.2450.2450.0000.0000.0000.000
104H100ALA00.0010.00525.6050.0280.0280.0000.0000.0000.000
105H100ALA0-0.009-0.00821.715-0.098-0.0980.0000.0000.0000.000
106H100GLU-1-0.905-0.94523.54711.28911.2890.0000.0000.0000.000
107H100TYR0-0.044-0.03319.6890.5070.5070.0000.0000.0000.000
108H100TYR00.0520.03714.3710.1790.1790.0000.0000.0000.000
109H100PHE0-0.018-0.02015.1970.4940.4940.0000.0000.0000.000
110H101HIS00.0260.0238.285-0.075-0.0750.0000.0000.0000.000
111H102TYR00.0310.0104.369-0.1020.018-0.001-0.006-0.1130.000
112H103TRP00.000-0.0159.872-3.027-3.0270.0000.0000.0000.000
113H104GLY00.0570.0529.2283.4853.4850.0000.0000.0000.000
114H105GLN0-0.074-0.05510.4520.7520.7520.0000.0000.0000.000
115H106GLY00.0150.00912.192-1.941-1.9410.0000.0000.0000.000
116H107ILE0-0.046-0.01915.1400.1590.1590.0000.0000.0000.000
117H108LEU0-0.0020.00317.909-0.501-0.5010.0000.0000.0000.000
118H109VAL00.0160.02321.542-0.343-0.3430.0000.0000.0000.000
119H110THR0-0.038-0.04724.376-0.147-0.1470.0000.0000.0000.000
120H111VAL0-0.0030.01327.820-0.127-0.1270.0000.0000.0000.000
121H112SER00.029-0.00931.053-0.142-0.1420.0000.0000.0000.000
122H113SER0-0.014-0.01434.1310.0540.0540.0000.0000.0000.000
123H114GLY0-0.0040.01937.220-0.110-0.1100.0000.0000.0000.000
124H115SER00.022-0.00233.5230.2000.2000.0000.0000.0000.000
125H116ALA00.0230.01634.3810.1580.1580.0000.0000.0000.000
126H117SER0-0.050-0.02636.367-0.276-0.2760.0000.0000.0000.000
127H118ALA00.0380.01238.8120.1280.1280.0000.0000.0000.000
128H119PRO00.0460.02539.588-0.160-0.1600.0000.0000.0000.000
129H120THR0-0.039-0.00641.894-0.242-0.2420.0000.0000.0000.000
130H121LEU0-0.026-0.00544.1960.1370.1370.0000.0000.0000.000
131H122PHE00.0220.00546.310-0.170-0.1700.0000.0000.0000.000
132H123PRO00.0150.01248.0770.1250.1250.0000.0000.0000.000
133H124LEU0-0.025-0.01646.141-0.020-0.0200.0000.0000.0000.000
134H125VAL00.0350.00250.490-0.009-0.0090.0000.0000.0000.000
135H126SER0-0.0300.00252.7890.0210.0210.0000.0000.0000.000
136H127CYS00.005-0.00554.688-0.120-0.1200.0000.0000.0000.000
137H128GLU-1-0.887-0.92557.2145.2595.2590.0000.0000.0000.000
138H129ASN00.016-0.02055.801-0.125-0.1250.0000.0000.0000.000
139H130SER00.020-0.00258.8990.0360.0360.0000.0000.0000.000
140H133ASN00.0060.03259.8250.0360.0360.0000.0000.0000.000
141H134PRO00.0310.02559.607-0.004-0.0040.0000.0000.0000.000
142H135SER00.000-0.00454.7160.1080.1080.0000.0000.0000.000
143H136SER00.0350.01652.659-0.095-0.0950.0000.0000.0000.000
144H137THR0-0.012-0.01754.8330.0240.0240.0000.0000.0000.000
145H138VAL0-0.022-0.01751.3910.1010.1010.0000.0000.0000.000
146H139ALA00.0050.00751.4320.1260.1260.0000.0000.0000.000
147H140VAL00.0190.02151.314-0.033-0.0330.0000.0000.0000.000
148H141GLY00.020-0.00247.6520.1320.1320.0000.0000.0000.000
149H142CYS0-0.087-0.01145.7330.0370.0370.0000.0000.0000.000
150H143LEU00.0190.01842.3650.1980.1980.0000.0000.0000.000
151H144ALA00.0430.02540.615-0.137-0.1370.0000.0000.0000.000
152H145GLN00.037-0.00140.3530.2230.2230.0000.0000.0000.000
153H146ASP-1-0.797-0.87840.0797.5797.5790.0000.0000.0000.000
154H147PHE0-0.057-0.01034.631-0.090-0.0900.0000.0000.0000.000
155H148LEU0-0.0120.00832.1560.1260.1260.0000.0000.0000.000
156H149PRO00.0700.03130.310-0.233-0.2330.0000.0000.0000.000
157H150ASP-1-0.773-0.88729.21810.78110.7810.0000.0000.0000.000
158H151SER0-0.067-0.05230.453-0.288-0.2880.0000.0000.0000.000
159H152ILE0-0.0040.00232.467-0.314-0.3140.0000.0000.0000.000
160H153THR0-0.036-0.02035.2280.1920.1920.0000.0000.0000.000
161H154PHE00.0180.01937.675-0.204-0.2040.0000.0000.0000.000
162H156SER0-0.036-0.03041.0810.1050.1050.0000.0000.0000.000
163H157TRP00.0080.00243.895-0.161-0.1610.0000.0000.0000.000
164H158LYS10.8080.89147.504-6.488-6.4880.0000.0000.0000.000
165H159TYR00.027-0.00350.552-0.033-0.0330.0000.0000.0000.000
166H160LYS10.8030.90154.131-5.281-5.2810.0000.0000.0000.000
167H161ASN00.0130.01256.303-0.128-0.1280.0000.0000.0000.000
168H162ASN00.0310.00353.2880.0430.0430.0000.0000.0000.000
169H163SER00.0200.01848.522-0.078-0.0780.0000.0000.0000.000
170H164ASP-1-0.877-0.92949.8796.1856.1850.0000.0000.0000.000
171H165ILE0-0.010-0.00448.4690.1120.1120.0000.0000.0000.000
172H168SER0-0.004-0.01845.4680.0750.0750.0000.0000.0000.000
173H169SER0-0.030-0.01943.6530.2270.2270.0000.0000.0000.000
174H171THR0-0.0160.00542.385-0.216-0.2160.0000.0000.0000.000
175H172ARG10.8520.92441.596-6.838-6.8380.0000.0000.0000.000
176H173GLY00.0380.00739.072-0.108-0.1080.0000.0000.0000.000
177H174PHE0-0.021-0.00337.1920.0750.0750.0000.0000.0000.000
178H175PRO00.0220.00332.4210.0540.0540.0000.0000.0000.000
179H176SER0-0.005-0.00432.441-0.289-0.2890.0000.0000.0000.000
180H177VAL0-0.032-0.00932.8520.2630.2630.0000.0000.0000.000
181H178LEU00.0290.01430.043-0.133-0.1330.0000.0000.0000.000
182H179ARG10.8860.92833.004-8.134-8.1340.0000.0000.0000.000
183H180GLY00.0390.00235.4620.1680.1680.0000.0000.0000.000
184H183GLY00.0050.01434.802-0.185-0.1850.0000.0000.0000.000
185H184LYS10.8160.89035.799-7.863-7.8630.0000.0000.0000.000
186H185TYR00.0220.02229.0430.1520.1520.0000.0000.0000.000
187H186ALA0-0.037-0.03435.950-0.335-0.3350.0000.0000.0000.000
188H187ALA00.0160.01236.6410.2980.2980.0000.0000.0000.000
189H188THR00.0130.00538.517-0.193-0.1930.0000.0000.0000.000
190H189SER0-0.0110.01240.3770.1380.1380.0000.0000.0000.000
191H190GLN0-0.005-0.01642.879-0.033-0.0330.0000.0000.0000.000
192H191VAL0-0.034-0.01745.6370.1340.1340.0000.0000.0000.000
193H192LEU0-0.0020.01048.271-0.117-0.1170.0000.0000.0000.000
194H193LEU00.0280.01750.2440.0920.0920.0000.0000.0000.000
195H194PRO0-0.018-0.01252.639-0.035-0.0350.0000.0000.0000.000
196H195SER00.0220.00155.103-0.108-0.1080.0000.0000.0000.000
197H196LYS10.8560.91158.021-5.155-5.1550.0000.0000.0000.000
198H197ASP-1-0.816-0.89759.2135.2915.2910.0000.0000.0000.000
199H198VAL0-0.027-0.00460.3940.0700.0700.0000.0000.0000.000
200H199MET0-0.004-0.00860.476-0.127-0.1270.0000.0000.0000.000
201H200GLN0-0.0070.01161.8570.1210.1210.0000.0000.0000.000
202H201GLY0-0.005-0.00960.474-0.043-0.0430.0000.0000.0000.000
203H202THR0-0.087-0.06460.9190.0520.0520.0000.0000.0000.000
204H203ASN00.0230.00857.983-0.048-0.0480.0000.0000.0000.000
205H204GLU-1-0.758-0.85359.7885.2645.2640.0000.0000.0000.000
206H205HIS0-0.102-0.05355.962-0.058-0.0580.0000.0000.0000.000
207H206VAL00.0280.02952.1070.0200.0200.0000.0000.0000.000
208H207VAL0-0.005-0.00450.546-0.029-0.0290.0000.0000.0000.000
209H209LYS10.9070.95144.064-7.425-7.4250.0000.0000.0000.000
210H211VAL0-0.003-0.00141.2570.1900.1900.0000.0000.0000.000
211H212GLN0-0.039-0.02039.449-0.231-0.2310.0000.0000.0000.000
212H213HIS10.8460.90135.032-8.804-8.8040.0000.0000.0000.000
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