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: MN29Z

Calculation Name: 1QDL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QDL

Chain ID: B

ChEMBL ID:

UniProt ID: Q06128

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2314592.888126
FMO2-HF: Nuclear repulsion 2239090.192272
FMO2-HF: Total energy -75502.695853
FMO2-MP2: Total energy -75727.990275


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(B:1:MET)


Summations of interaction energy for fragment #1(B: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.
-8.048-2.8133.416-2.659-5.993-0.009
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.023
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].
3B3LEU0-0.0030.0032.6540.3213.9370.417-1.588-2.445-0.001
4B4THR0-0.015-0.0394.3160.4410.571-0.001-0.024-0.1060.000
5B5LEU00.0100.0167.6080.1780.1780.0000.0000.0000.000
6B6ILE0-0.038-0.0389.3890.1390.1390.0000.0000.0000.000
7B7ILE00.004-0.00312.4480.0390.0390.0000.0000.0000.000
8B8ASP-1-0.799-0.92215.385-0.228-0.2280.0000.0000.0000.000
9B9ASN0-0.036-0.01117.5040.0060.0060.0000.0000.0000.000
10B10TYR0-0.071-0.07620.6490.0420.0420.0000.0000.0000.000
11B11ASP-1-0.780-0.91420.295-0.175-0.1750.0000.0000.0000.000
12B12SER0-0.065-0.03520.9500.0150.0150.0000.0000.0000.000
13B13PHE0-0.068-0.02921.0740.0270.0270.0000.0000.0000.000
14B14VAL00.0420.02715.2680.0020.0020.0000.0000.0000.000
15B15TYR00.0420.00413.189-0.031-0.0310.0000.0000.0000.000
16B16ASN0-0.029-0.00415.6470.0590.0590.0000.0000.0000.000
17B17ILE0-0.011-0.01313.9660.0180.0180.0000.0000.0000.000
18B18ALA00.0140.00611.190-0.017-0.0170.0000.0000.0000.000
19B19GLN0-0.018-0.00611.3730.0740.0740.0000.0000.0000.000
20B20ILE00.0230.02813.3410.0660.0660.0000.0000.0000.000
21B21VAL0-0.014-0.0128.7570.0110.0110.0000.0000.0000.000
22B22GLY00.0190.0048.5800.0330.0330.0000.0000.0000.000
23B23GLU-1-0.962-0.9699.6150.3930.3930.0000.0000.0000.000
24B24LEU0-0.132-0.05911.6860.0270.0270.0000.0000.0000.000
25B25GLY0-0.020-0.0068.153-0.145-0.1450.0000.0000.0000.000
26B26SER0-0.0470.0165.7010.4180.4180.0000.0000.0000.000
27B27TYR00.016-0.0032.655-1.951-0.6263.002-1.017-3.310-0.008
28B28PRO0-0.034-0.0144.524-1.230-1.174-0.001-0.024-0.0320.000
29B29ILE00.0090.0054.434-0.0010.107-0.001-0.006-0.1000.000
30B30VAL0-0.030-0.0157.861-0.023-0.0230.0000.0000.0000.000
31B31ILE0-0.0110.00211.5830.0360.0360.0000.0000.0000.000
32B32ARG10.9280.97113.9720.1990.1990.0000.0000.0000.000
33B33ASN0-0.071-0.02717.734-0.020-0.0200.0000.0000.0000.000
34B34ASP-1-0.843-0.89919.694-0.284-0.2840.0000.0000.0000.000
35B35GLU-1-0.853-0.92417.033-0.305-0.3050.0000.0000.0000.000
36B36ILE0-0.023-0.00412.834-0.019-0.0190.0000.0000.0000.000
37B37SER0-0.035-0.00117.037-0.001-0.0010.0000.0000.0000.000
38B38ILE00.1080.03716.750-0.061-0.0610.0000.0000.0000.000
39B39LYS10.9510.97016.9020.4450.4450.0000.0000.0000.000
40B40GLY0-0.044-0.02415.315-0.060-0.0600.0000.0000.0000.000
41B41ILE00.0360.01112.407-0.100-0.1000.0000.0000.0000.000
42B42GLU-1-0.912-0.97511.855-0.909-0.9090.0000.0000.0000.000
43B43ARG10.8580.93112.2790.5320.5320.0000.0000.0000.000
44B44ILE0-0.055-0.0177.0050.0390.0390.0000.0000.0000.000
45B45ASP-1-0.963-0.9757.770-2.770-2.7700.0000.0000.0000.000
46B46PRO0-0.037-0.0106.975-0.589-0.5890.0000.0000.0000.000
47B47ASP-1-0.787-0.8675.375-6.139-6.1390.0000.0000.0000.000
48B48ARG10.7560.8468.1492.5862.5860.0000.0000.0000.000
49B49LEU0-0.004-0.00910.236-0.098-0.0980.0000.0000.0000.000
50B50ILE0-0.018-0.00112.5860.1390.1390.0000.0000.0000.000
51B51ILE0-0.029-0.00114.779-0.001-0.0010.0000.0000.0000.000
52B52SER00.0290.00017.3130.0380.0380.0000.0000.0000.000
53B53PRO0-0.022-0.01718.8330.0030.0030.0000.0000.0000.000
54B54GLY00.0910.04222.012-0.015-0.0150.0000.0000.0000.000
55B55PRO0-0.045-0.01124.6310.0080.0080.0000.0000.0000.000
56B56GLY00.0490.02227.763-0.010-0.0100.0000.0000.0000.000
57B57THR0-0.077-0.05529.770-0.007-0.0070.0000.0000.0000.000
58B58PRO00.0340.00126.992-0.005-0.0050.0000.0000.0000.000
59B59GLU-1-0.944-0.98728.537-0.178-0.1780.0000.0000.0000.000
60B60LYS10.9380.98530.8240.1580.1580.0000.0000.0000.000
61B61ARG10.9640.97023.6370.3130.3130.0000.0000.0000.000
62B62GLU-1-0.954-0.97226.725-0.188-0.1880.0000.0000.0000.000
63B63ASP-1-0.797-0.86626.789-0.191-0.1910.0000.0000.0000.000
64B64ILE0-0.053-0.02823.831-0.014-0.0140.0000.0000.0000.000
65B65GLY00.0390.02722.371-0.038-0.0380.0000.0000.0000.000
66B66VAL0-0.070-0.05617.9960.0100.0100.0000.0000.0000.000
67B67SER00.021-0.01119.782-0.052-0.0520.0000.0000.0000.000
68B68LEU0-0.022-0.01320.842-0.023-0.0230.0000.0000.0000.000
69B69ASP-1-0.891-0.93621.942-0.381-0.3810.0000.0000.0000.000
70B70VAL00.0200.01516.434-0.025-0.0250.0000.0000.0000.000
71B71ILE0-0.019-0.00719.205-0.036-0.0360.0000.0000.0000.000
72B72LYS10.8910.94421.0670.3180.3180.0000.0000.0000.000
73B73TYR0-0.066-0.04320.8730.0160.0160.0000.0000.0000.000
74B74LEU00.0360.01414.9330.0040.0040.0000.0000.0000.000
75B75GLY00.0530.02117.589-0.060-0.0600.0000.0000.0000.000
76B76LYS10.9060.95419.6590.4510.4510.0000.0000.0000.000
77B77ARG10.9100.92916.0320.6630.6630.0000.0000.0000.000
78B78THR00.0820.07512.529-0.035-0.0350.0000.0000.0000.000
79B79PRO0-0.037-0.01913.2450.1480.1480.0000.0000.0000.000
80B80ILE0-0.0130.00914.682-0.075-0.0750.0000.0000.0000.000
81B81LEU0-0.015-0.00216.4670.0790.0790.0000.0000.0000.000
82B82GLY00.005-0.00717.733-0.022-0.0220.0000.0000.0000.000
83B83VAL00.035-0.00119.3330.0320.0320.0000.0000.0000.000
84B84CYS0-0.0240.01021.9400.0070.0070.0000.0000.0000.000
85B85LEU00.0100.02223.811-0.010-0.0100.0000.0000.0000.000
86B86GLY00.0700.02821.436-0.008-0.0080.0000.0000.0000.000
87B87HIS0-0.028-0.00322.418-0.036-0.0360.0000.0000.0000.000
88B88GLN00.0340.00324.6190.0160.0160.0000.0000.0000.000
89B89ALA00.0080.00623.6440.0070.0070.0000.0000.0000.000
90B90ILE00.0140.01220.7880.0020.0020.0000.0000.0000.000
91B91GLY00.0450.00124.8440.0040.0040.0000.0000.0000.000
92B92TYR0-0.022-0.00928.5310.0070.0070.0000.0000.0000.000
93B93ALA0-0.061-0.04525.7680.0080.0080.0000.0000.0000.000
94B94PHE0-0.048-0.03124.668-0.002-0.0020.0000.0000.0000.000
95B95GLY0-0.009-0.00529.8950.0130.0130.0000.0000.0000.000
96B96ALA0-0.0390.00331.7680.0150.0150.0000.0000.0000.000
97B97LYS10.9230.94433.5110.1510.1510.0000.0000.0000.000
98B98ILE0-0.0290.00330.494-0.005-0.0050.0000.0000.0000.000
99B99ARG10.8270.91534.4210.1430.1430.0000.0000.0000.000
100B100ARG10.9800.97835.8440.1040.1040.0000.0000.0000.000
101B101ALA0-0.0170.00335.8470.0000.0000.0000.0000.0000.000
102B102ARG10.8500.91437.8590.1170.1170.0000.0000.0000.000
103B103LYS10.9010.95039.5450.0860.0860.0000.0000.0000.000
104B104VAL00.0390.02336.282-0.007-0.0070.0000.0000.0000.000
105B105PHE0-0.048-0.02233.8950.0090.0090.0000.0000.0000.000
106B106HIS00.0070.00332.714-0.015-0.0150.0000.0000.0000.000
107B107GLY00.0700.02231.0870.0080.0080.0000.0000.0000.000
108B108LYS10.8440.93632.1310.0840.0840.0000.0000.0000.000
109B109ILE00.0180.01331.036-0.009-0.0090.0000.0000.0000.000
110B110SER0-0.099-0.04432.7600.0020.0020.0000.0000.0000.000
111B111ASN00.0380.00333.248-0.001-0.0010.0000.0000.0000.000
112B112ILE0-0.023-0.01129.678-0.003-0.0030.0000.0000.0000.000
113B113ILE00.0380.02032.8480.0060.0060.0000.0000.0000.000
114B114LEU0-0.058-0.02128.670-0.010-0.0100.0000.0000.0000.000
115B115VAL0-0.038-0.03932.6040.0110.0110.0000.0000.0000.000
116B116ASN00.0080.01229.2940.0080.0080.0000.0000.0000.000
117B117ASN00.0110.00232.5630.0130.0130.0000.0000.0000.000
118B118SER00.006-0.00230.5770.0130.0130.0000.0000.0000.000
119B119PRO0-0.013-0.01227.695-0.010-0.0100.0000.0000.0000.000
120B120LEU00.0260.01524.928-0.015-0.0150.0000.0000.0000.000
121B121SER00.0070.00419.9420.0360.0360.0000.0000.0000.000
122B122LEU00.0120.01419.7140.0160.0160.0000.0000.0000.000
123B123TYR00.000-0.00221.7330.0170.0170.0000.0000.0000.000
124B124TYR00.0450.02722.1830.0350.0350.0000.0000.0000.000
125B125GLY0-0.013-0.01723.7790.0070.0070.0000.0000.0000.000
126B126ILE0-0.065-0.01523.5000.0190.0190.0000.0000.0000.000
127B127ALA0-0.001-0.00127.2550.0000.0000.0000.0000.0000.000
128B128LYS10.9720.97730.9580.0800.0800.0000.0000.0000.000
129B129GLU-1-0.858-0.93733.269-0.095-0.0950.0000.0000.0000.000
130B130PHE0-0.081-0.02227.8790.0100.0100.0000.0000.0000.000
131B131LYS10.9510.97831.4700.0570.0570.0000.0000.0000.000
132B132ALA00.0250.00127.754-0.002-0.0020.0000.0000.0000.000
133B133THR0-0.027-0.01127.7000.0060.0060.0000.0000.0000.000
134B134ARG10.7810.85528.5000.1060.1060.0000.0000.0000.000
135B135TYR00.0420.01126.8600.0200.0200.0000.0000.0000.000
136B136HIS00.0250.01429.355-0.006-0.0060.0000.0000.0000.000
137B137SER00.020-0.00131.5450.0070.0070.0000.0000.0000.000
138B138LEU0-0.056-0.02032.0660.0080.0080.0000.0000.0000.000
139B139VAL00.0180.03332.317-0.004-0.0040.0000.0000.0000.000
140B140VAL00.0260.01829.661-0.002-0.0020.0000.0000.0000.000
141B141ASP-1-0.858-0.95032.910-0.137-0.1370.0000.0000.0000.000
142B142GLU-1-0.908-0.94135.900-0.151-0.1510.0000.0000.0000.000
143B143VAL0-0.0020.00332.196-0.009-0.0090.0000.0000.0000.000
144B144HIS10.8400.92634.5660.2150.2150.0000.0000.0000.000
145B145ARG10.9590.98533.2910.1980.1980.0000.0000.0000.000
146B146PRO0-0.003-0.00429.4700.0100.0100.0000.0000.0000.000
147B147LEU0-0.0420.00227.170-0.015-0.0150.0000.0000.0000.000
148B148ILE0-0.025-0.01129.7370.0220.0220.0000.0000.0000.000
149B149VAL00.0010.00230.065-0.013-0.0130.0000.0000.0000.000
150B150ASP-1-0.803-0.89127.477-0.263-0.2630.0000.0000.0000.000
151B151ALA0-0.0070.00229.9600.0120.0120.0000.0000.0000.000
152B152ILE0-0.0090.00131.764-0.005-0.0050.0000.0000.0000.000
153B153SER0-0.053-0.00734.5810.0070.0070.0000.0000.0000.000
154B154ALA00.0550.02035.8550.0020.0020.0000.0000.0000.000
155B155GLU-1-0.820-0.90437.364-0.088-0.0880.0000.0000.0000.000
156B156ASP-1-0.794-0.90037.602-0.106-0.1060.0000.0000.0000.000
157B157ASN00.0350.01938.7020.0030.0030.0000.0000.0000.000
158B158GLU-1-0.806-0.89535.328-0.128-0.1280.0000.0000.0000.000
159B159ILE00.0420.01531.0980.0000.0000.0000.0000.0000.000
160B160MET0-0.042-0.01830.179-0.002-0.0020.0000.0000.0000.000
161B161ALA0-0.009-0.00326.998-0.009-0.0090.0000.0000.0000.000
162B162ILE0-0.0300.00726.5870.0200.0200.0000.0000.0000.000
163B163HIS10.9030.93424.8190.2760.2760.0000.0000.0000.000
164B164HIS00.0340.04224.8160.0190.0190.0000.0000.0000.000
165B165GLU-1-0.882-0.96226.421-0.258-0.2580.0000.0000.0000.000
166B166GLU-1-0.959-0.98525.551-0.349-0.3490.0000.0000.0000.000
167B167TYR0-0.049-0.01721.883-0.033-0.0330.0000.0000.0000.000
168B168PRO00.0210.03717.8390.0470.0470.0000.0000.0000.000
169B169ILE0-0.022-0.01419.075-0.050-0.0500.0000.0000.0000.000
170B170TYR00.008-0.02120.1350.0790.0790.0000.0000.0000.000
171B171GLY00.0230.02721.380-0.029-0.0290.0000.0000.0000.000
172B172VAL0-0.0190.00122.2190.0250.0250.0000.0000.0000.000
173B173GLN00.001-0.02824.729-0.007-0.0070.0000.0000.0000.000
174B174PHE0-0.032-0.02425.1110.0100.0100.0000.0000.0000.000
175B175HIS00.0540.00623.442-0.018-0.0180.0000.0000.0000.000
176B176PRO0-0.0460.00320.3750.0310.0310.0000.0000.0000.000
177B177GLU-1-0.753-0.90018.887-0.165-0.1650.0000.0000.0000.000
178B178SER0-0.0330.02820.7900.0310.0310.0000.0000.0000.000
179B179VAL00.0850.02724.2640.0000.0000.0000.0000.0000.000
180B180GLY0-0.054-0.03225.9960.0060.0060.0000.0000.0000.000
181B181THR0-0.055-0.05825.070-0.001-0.0010.0000.0000.0000.000
182B182SER00.0230.01925.406-0.001-0.0010.0000.0000.0000.000
183B183LEU0-0.022-0.02024.8660.0070.0070.0000.0000.0000.000
184B184GLY00.0250.01322.939-0.021-0.0210.0000.0000.0000.000
185B185TYR00.0690.03115.264-0.062-0.0620.0000.0000.0000.000
186B186LYS10.9500.98018.5610.0750.0750.0000.0000.0000.000
187B187ILE00.0050.00819.610-0.031-0.0310.0000.0000.0000.000
188B188LEU00.0370.01315.844-0.055-0.0550.0000.0000.0000.000
189B189TYR00.0210.00915.098-0.093-0.0930.0000.0000.0000.000
190B190ASN0-0.086-0.05715.431-0.046-0.0460.0000.0000.0000.000
191B191PHE0-0.005-0.01813.548-0.042-0.0420.0000.0000.0000.000
192B192LEU00.004-0.00110.042-0.105-0.1050.0000.0000.0000.000
193B193ASN0-0.020-0.00611.944-0.171-0.1710.0000.0000.0000.000
194B194ARG10.8390.91813.6680.2750.2750.0000.0000.0000.000
195B195VAL0-0.0300.02014.6730.0130.0130.0000.0000.0000.000