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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: 3QL2L

Calculation Name: 3M7M-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M7M

Chain ID: X

ChEMBL ID:

UniProt ID: P0A6Y5

Base Structure: X-ray

Registration Date: 2023-06-19

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2867306.429548
FMO2-HF: Nuclear repulsion 2776724.465695
FMO2-HF: Total energy -90581.963853
FMO2-MP2: Total energy -90846.624011


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(X:2:ILE)


Summations of interaction energy for fragment #1(X:2:ILE)
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.
-4.576-0.839-0.045-1.998-1.695-0.007
Interaction energy analysis for fragmet #1(X:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.046
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].
3X4PRO00.0080.0123.821-1.9321.805-0.045-1.998-1.695-0.007
4X5GLN00.010-0.0196.694-0.008-0.0080.0000.0000.0000.000
5X6HIS00.0230.0349.547-0.020-0.0200.0000.0000.0000.000
6X7ASP-1-0.756-0.82512.574-0.261-0.2610.0000.0000.0000.000
7X8GLN0-0.015-0.0258.658-0.105-0.1050.0000.0000.0000.000
8X9LEU0-0.034-0.00914.4670.0200.0200.0000.0000.0000.000
9X10HIS00.003-0.01510.7980.0500.0500.0000.0000.0000.000
10X11ARG10.8450.92815.5170.3680.3680.0000.0000.0000.000
11X12TYR00.0350.01416.430-0.053-0.0530.0000.0000.0000.000
12X13LEU0-0.020-0.01018.3130.0390.0390.0000.0000.0000.000
13X14PHE00.020-0.00620.607-0.024-0.0240.0000.0000.0000.000
14X15GLU-1-0.747-0.84621.368-0.241-0.2410.0000.0000.0000.000
15X16ASN0-0.107-0.05723.9890.0120.0120.0000.0000.0000.000
16X17PHE0-0.048-0.03625.8470.0090.0090.0000.0000.0000.000
17X18ALA0-0.060-0.00727.2990.0100.0100.0000.0000.0000.000
18X19VAL00.0590.02225.6650.0110.0110.0000.0000.0000.000
19X20ARG10.8270.91722.9350.2130.2130.0000.0000.0000.000
20X21GLY00.032-0.00421.8070.0240.0240.0000.0000.0000.000
21X22GLU-1-0.855-0.94319.145-0.285-0.2850.0000.0000.0000.000
22X23LEU00.0320.03215.3320.0310.0310.0000.0000.0000.000
23X24VAL0-0.021-0.01817.302-0.040-0.0400.0000.0000.0000.000
24X25THR0-0.0210.01315.7710.0210.0210.0000.0000.0000.000
25X26VAL00.010-0.01717.641-0.010-0.0100.0000.0000.0000.000
26X27SER00.0460.02618.6590.0280.0280.0000.0000.0000.000
27X28GLU-1-0.925-0.96915.3690.0220.0220.0000.0000.0000.000
28X29THR0-0.043-0.05219.2510.0280.0280.0000.0000.0000.000
29X30LEU0-0.017-0.02821.2460.0150.0150.0000.0000.0000.000
30X31GLN0-0.0220.01219.2820.0190.0190.0000.0000.0000.000
31X32GLN0-0.030-0.03119.7770.0130.0130.0000.0000.0000.000
32X33ILE0-0.056-0.01924.8230.0050.0050.0000.0000.0000.000
33X34LEU0-0.033-0.02727.1810.0030.0030.0000.0000.0000.000
34X35GLU-1-0.921-0.94625.6930.0400.0400.0000.0000.0000.000
35X36ASN0-0.088-0.04329.3020.0020.0020.0000.0000.0000.000
36X37HIS0-0.087-0.03731.875-0.001-0.0010.0000.0000.0000.000
37X38ASP-1-0.920-0.94234.0550.0080.0080.0000.0000.0000.000
38X39TYR0-0.007-0.01632.470-0.004-0.0040.0000.0000.0000.000
39X40PRO00.0710.02535.3190.0020.0020.0000.0000.0000.000
40X41GLN00.0210.00631.224-0.003-0.0030.0000.0000.0000.000
41X42PRO00.1300.06434.407-0.003-0.0030.0000.0000.0000.000
42X43VAL00.001-0.01234.905-0.005-0.0050.0000.0000.0000.000
43X44LYS10.8540.93130.6550.0100.0100.0000.0000.0000.000
44X45ASN00.0020.00230.547-0.001-0.0010.0000.0000.0000.000
45X46VAL00.0840.04831.116-0.008-0.0080.0000.0000.0000.000
46X47LEU0-0.0190.00630.221-0.007-0.0070.0000.0000.0000.000
47X48ALA00.0280.02026.955-0.009-0.0090.0000.0000.0000.000
48X49GLU-1-0.885-0.96727.361-0.101-0.1010.0000.0000.0000.000
49X50LEU0-0.019-0.00928.917-0.009-0.0090.0000.0000.0000.000
50X51LEU0-0.037-0.00223.745-0.008-0.0080.0000.0000.0000.000
51X52VAL0-0.0010.00623.314-0.012-0.0120.0000.0000.0000.000
52X53ALA00.0710.02425.155-0.014-0.0140.0000.0000.0000.000
53X54THR0-0.052-0.03927.449-0.003-0.0030.0000.0000.0000.000
54X55SER00.0150.00621.935-0.011-0.0110.0000.0000.0000.000
55X56LEU00.0100.01522.243-0.016-0.0160.0000.0000.0000.000
56X57LEU00.0620.02124.619-0.002-0.0020.0000.0000.0000.000
57X58THR0-0.080-0.03424.8230.0060.0060.0000.0000.0000.000
58X59ALA0-0.083-0.01321.6250.0000.0000.0000.0000.0000.000
59X60THR0-0.059-0.04323.451-0.012-0.0120.0000.0000.0000.000
60X61LEU00.0100.01226.0350.0100.0100.0000.0000.0000.000
61X62LYS10.9250.96526.7240.1620.1620.0000.0000.0000.000
62X63PHE0-0.051-0.04627.7990.0120.0120.0000.0000.0000.000
63X64ASP-1-0.865-0.92326.711-0.138-0.1380.0000.0000.0000.000
64X65GLY0-0.043-0.00528.4440.0120.0120.0000.0000.0000.000
65X66ASP-1-0.930-0.96728.929-0.086-0.0860.0000.0000.0000.000
66X67ILE00.0070.00228.8370.0020.0020.0000.0000.0000.000
67X68THR0-0.078-0.03231.1290.0010.0010.0000.0000.0000.000
68X69VAL00.0680.04631.1600.0000.0000.0000.0000.0000.000
69X70GLN0-0.010-0.02433.7150.0010.0010.0000.0000.0000.000
70X71LEU00.0340.03835.786-0.002-0.0020.0000.0000.0000.000
71X72GLN0-0.018-0.02338.4790.0030.0030.0000.0000.0000.000
72X73GLY00.0660.00742.110-0.001-0.0010.0000.0000.0000.000
73X74ASP-1-0.904-0.87445.291-0.033-0.0330.0000.0000.0000.000
74X75GLY00.0580.06544.9360.0020.0020.0000.0000.0000.000
75X76PRO0-0.033-0.01743.7050.0010.0010.0000.0000.0000.000
76X77MET0-0.0160.01138.1110.0030.0030.0000.0000.0000.000
77X78ASN00.0090.01742.360-0.002-0.0020.0000.0000.0000.000
78X79LEU0-0.067-0.05238.864-0.002-0.0020.0000.0000.0000.000
79X80ALA00.0300.01735.4110.0030.0030.0000.0000.0000.000
80X81VAL0-0.022-0.00234.330-0.003-0.0030.0000.0000.0000.000
81X82ILE00.0380.03427.7690.0060.0060.0000.0000.0000.000
82X83ASN0-0.061-0.04330.1450.0060.0060.0000.0000.0000.000
83X84GLY00.1020.03227.0020.0020.0020.0000.0000.0000.000
84X85ASN00.0020.00524.755-0.006-0.0060.0000.0000.0000.000
85X86ASN00.0100.00224.940-0.001-0.0010.0000.0000.0000.000
86X87ASN0-0.102-0.06021.588-0.032-0.0320.0000.0000.0000.000
87X88GLN00.0490.01319.8140.0040.0040.0000.0000.0000.000
88X89GLN0-0.028-0.01021.3100.0100.0100.0000.0000.0000.000
89X90MET0-0.024-0.00823.1620.0140.0140.0000.0000.0000.000
90X91ARG10.8540.92225.0560.0550.0550.0000.0000.0000.000
91X92GLY00.0550.02427.869-0.007-0.0070.0000.0000.0000.000
92X93VAL0-0.065-0.01630.9800.0070.0070.0000.0000.0000.000
93X94ALA00.0780.04133.954-0.005-0.0050.0000.0000.0000.000
94X95ARG10.8280.91536.4820.0280.0280.0000.0000.0000.000
95X96VAL00.0310.02139.434-0.002-0.0020.0000.0000.0000.000
96X97GLN0-0.082-0.04642.0640.0040.0040.0000.0000.0000.000
97X98GLY0-0.020-0.02345.2160.0010.0010.0000.0000.0000.000
98X99GLU-1-0.944-0.96745.634-0.011-0.0110.0000.0000.0000.000
99X100ILE0-0.024-0.02640.608-0.003-0.0030.0000.0000.0000.000
100X101PRO0-0.018-0.01243.1930.0010.0010.0000.0000.0000.000
101X102GLU-1-0.871-0.93741.582-0.017-0.0170.0000.0000.0000.000
102X103ASN0-0.114-0.05039.214-0.003-0.0030.0000.0000.0000.000
103X104ALA0-0.019-0.00540.469-0.002-0.0020.0000.0000.0000.000
104X105ASP-1-0.739-0.85339.231-0.049-0.0490.0000.0000.0000.000
105X106LEU00.0580.03236.8700.0030.0030.0000.0000.0000.000
106X107LYS10.8770.92139.9340.0570.0570.0000.0000.0000.000
107X108THR0-0.094-0.05643.3140.0040.0040.0000.0000.0000.000
108X109LEU0-0.104-0.06437.7900.0030.0030.0000.0000.0000.000
109X110VAL0-0.049-0.02639.7030.0020.0020.0000.0000.0000.000
110X111GLY0-0.060-0.05542.9120.0010.0010.0000.0000.0000.000
111X112ASN0-0.034-0.06945.489-0.002-0.0020.0000.0000.0000.000
112X113GLY0-0.051-0.03844.446-0.001-0.0010.0000.0000.0000.000
113X114TYR00.0000.01142.3600.0010.0010.0000.0000.0000.000
114X115VAL00.0340.01935.5380.0010.0010.0000.0000.0000.000
115X116VAL0-0.109-0.04738.3150.0000.0000.0000.0000.0000.000
116X117ILE00.0300.01333.315-0.002-0.0020.0000.0000.0000.000
117X118THR0-0.041-0.01135.5870.0020.0020.0000.0000.0000.000
118X119ILE00.0510.02232.103-0.002-0.0020.0000.0000.0000.000
119X120THR0-0.069-0.05434.0430.0070.0070.0000.0000.0000.000
120X121PRO00.0250.00832.7430.0010.0010.0000.0000.0000.000
121X122SER00.033-0.02431.8090.0050.0050.0000.0000.0000.000
122X123GLU-1-1.030-0.98234.013-0.059-0.0590.0000.0000.0000.000
123X124GLY00.0590.02636.806-0.002-0.0020.0000.0000.0000.000
124X125GLU-1-0.956-0.93838.762-0.069-0.0690.0000.0000.0000.000
125X126ARG10.8640.92637.9620.0580.0580.0000.0000.0000.000
126X127TYR0-0.025-0.04335.541-0.001-0.0010.0000.0000.0000.000
127X128GLN0-0.001-0.00137.580-0.003-0.0030.0000.0000.0000.000
128X129GLY00.0700.04438.0050.0000.0000.0000.0000.0000.000
129X130VAL0-0.089-0.04539.0000.0010.0010.0000.0000.0000.000
130X131VAL00.0670.03637.2110.0010.0010.0000.0000.0000.000
131X132GLY00.0180.00740.6940.0020.0020.0000.0000.0000.000
132X133LEU00.0240.01339.493-0.004-0.0040.0000.0000.0000.000
133X134GLU-1-0.917-0.96542.237-0.052-0.0520.0000.0000.0000.000
134X135GLY00.0030.01740.1700.0020.0020.0000.0000.0000.000
135X136ASP-1-0.937-0.97438.665-0.069-0.0690.0000.0000.0000.000
136X137THR0-0.029-0.01533.5780.0000.0000.0000.0000.0000.000
137X138LEU00.0540.06032.104-0.002-0.0020.0000.0000.0000.000
138X139ALA00.002-0.01531.030-0.003-0.0030.0000.0000.0000.000
139X140ALA00.0340.01832.572-0.004-0.0040.0000.0000.0000.000
140X141ASP-1-0.860-0.94435.652-0.074-0.0740.0000.0000.0000.000
141X142LEU0-0.009-0.00431.5100.0000.0000.0000.0000.0000.000
142X143GLU-1-0.770-0.84831.941-0.125-0.1250.0000.0000.0000.000
143X144ASP-1-0.831-0.90334.442-0.076-0.0760.0000.0000.0000.000
144X145TYR0-0.092-0.08236.1140.0050.0050.0000.0000.0000.000
145X146PHE0-0.010-0.04432.4120.0010.0010.0000.0000.0000.000
146X147MET0-0.0180.00736.183-0.001-0.0010.0000.0000.0000.000
147X148ARG10.7430.85238.2980.0750.0750.0000.0000.0000.000
148X149SER0-0.024-0.01640.1330.0020.0020.0000.0000.0000.000
149X150GLU-1-0.919-0.93435.881-0.097-0.0970.0000.0000.0000.000
150X151GLU-1-1.003-0.97538.080-0.082-0.0820.0000.0000.0000.000
151X152LEU0-0.058-0.02131.090-0.003-0.0030.0000.0000.0000.000
152X153PRO0-0.001-0.00733.430-0.001-0.0010.0000.0000.0000.000
153X154THR00.023-0.00529.223-0.014-0.0140.0000.0000.0000.000
154X155ARG10.7720.85529.0170.1350.1350.0000.0000.0000.000
155X156LEU0-0.028-0.01527.555-0.016-0.0160.0000.0000.0000.000
156X157PHE00.002-0.01525.1300.0120.0120.0000.0000.0000.000
157X158ILE00.0110.01325.117-0.018-0.0180.0000.0000.0000.000
158X159ARG10.8200.92923.5810.1630.1630.0000.0000.0000.000
159X160THR00.019-0.00624.645-0.006-0.0060.0000.0000.0000.000
160X161GLY0-0.020-0.01125.4810.0050.0050.0000.0000.0000.000
161X162ASP-1-0.908-0.95724.845-0.028-0.0280.0000.0000.0000.000
162X163VAL00.0300.02118.433-0.001-0.0010.0000.0000.0000.000
163X164ASP-1-0.908-0.95218.6420.0980.0980.0000.0000.0000.000
164X165GLY0-0.077-0.03222.2100.0140.0140.0000.0000.0000.000
165X166LYS10.8500.92519.720-0.086-0.0860.0000.0000.0000.000
166X167PRO00.0610.03023.814-0.008-0.0080.0000.0000.0000.000
167X168ALA0-0.052-0.02621.0170.0010.0010.0000.0000.0000.000
168X169ALA00.022-0.01621.7510.0050.0050.0000.0000.0000.000
169X170GLY00.0630.02620.586-0.019-0.0190.0000.0000.0000.000
170X171GLY0-0.032-0.04020.8490.0280.0280.0000.0000.0000.000
171X172MET0-0.0200.00119.999-0.041-0.0410.0000.0000.0000.000
172X173LEU0-0.0280.01922.5420.0270.0270.0000.0000.0000.000
173X174LEU00.0160.02423.557-0.021-0.0210.0000.0000.0000.000
174X175GLN00.019-0.00826.0990.0060.0060.0000.0000.0000.000
175X176VAL00.0150.02628.157-0.010-0.0100.0000.0000.0000.000
176X177MET0-0.0210.00026.717-0.004-0.0040.0000.0000.0000.000
177X178PRO00.0540.02029.6150.0090.0090.0000.0000.0000.000
178X179ALA0-0.065-0.05032.858-0.001-0.0010.0000.0000.0000.000
179X180GLN00.0040.00328.718-0.001-0.0010.0000.0000.0000.000
180X181ASN0-0.083-0.04233.7230.0010.0010.0000.0000.0000.000
181X182ALA00.0640.05131.5150.0040.0040.0000.0000.0000.000
182X183GLN0-0.058-0.03533.3740.0100.0100.0000.0000.0000.000
183X184GLN0-0.031-0.01733.735-0.005-0.0050.0000.0000.0000.000
184X185ASP-1-0.914-0.96633.990-0.110-0.1100.0000.0000.0000.000
185X186ASP-1-0.855-0.94129.995-0.145-0.1450.0000.0000.0000.000
186X187PHE0-0.0150.00229.371-0.010-0.0100.0000.0000.0000.000
187X188ASP-1-0.804-0.87230.152-0.122-0.1220.0000.0000.0000.000
188X189HIS0-0.0370.00130.264-0.003-0.0030.0000.0000.0000.000
189X190LEU00.0540.02024.344-0.007-0.0070.0000.0000.0000.000
190X191ALA0-0.013-0.01526.767-0.010-0.0100.0000.0000.0000.000
191X192THR0-0.058-0.05228.7240.0030.0030.0000.0000.0000.000
192X193LEU0-0.041-0.00923.7890.0030.0030.0000.0000.0000.000
193X194THR00.013-0.00423.760-0.013-0.0130.0000.0000.0000.000
194X195GLU-1-0.883-0.90825.211-0.129-0.1290.0000.0000.0000.000
195X196THR0-0.154-0.09525.4250.0050.0050.0000.0000.0000.000
196X197ILE0-0.046-0.00219.7450.0030.0030.0000.0000.0000.000
197X198LYS10.8880.92222.5260.1940.1940.0000.0000.0000.000
198X199THR00.009-0.00521.880-0.013-0.0130.0000.0000.0000.000
199X200GLU-1-0.866-0.92519.862-0.118-0.1180.0000.0000.0000.000
200X201GLU-1-0.777-0.89818.378-0.219-0.2190.0000.0000.0000.000
201X202LEU0-0.007-0.00517.177-0.029-0.0290.0000.0000.0000.000
202X203LEU0-0.060-0.01317.408-0.028-0.0280.0000.0000.0000.000
203X204THR0-0.054-0.02915.970-0.005-0.0050.0000.0000.0000.000
204X205LEU0-0.044-0.00913.480-0.003-0.0030.0000.0000.0000.000
205X206PRO00.0170.0158.874-0.041-0.0410.0000.0000.0000.000
206X207ALA00.0870.05410.827-0.006-0.0060.0000.0000.0000.000
207X208ASN00.0500.0097.954-0.012-0.0120.0000.0000.0000.000
208X209GLU-1-0.847-0.90910.934-0.349-0.3490.0000.0000.0000.000
209X210VAL0-0.0020.00512.4110.0950.0950.0000.0000.0000.000
210X211LEU00.005-0.00713.5920.0520.0520.0000.0000.0000.000
211X212TRP0-0.0050.01113.5330.0650.0650.0000.0000.0000.000
212X213ARG10.7320.82315.5460.3420.3420.0000.0000.0000.000
213X214LEU0-0.0500.00017.9800.0410.0410.0000.0000.0000.000
214X215TYR00.047-0.01318.2460.0290.0290.0000.0000.0000.000
215X216HIS10.7770.89217.7400.2660.2660.0000.0000.0000.000
216X217GLU-1-0.958-0.95818.683-0.206-0.2060.0000.0000.0000.000
217X218GLU-1-0.900-0.95920.591-0.200-0.2000.0000.0000.0000.000
218X219GLU-1-0.996-0.98019.892-0.316-0.3160.0000.0000.0000.000
219X220VAL0-0.022-0.02816.4470.0070.0070.0000.0000.0000.000
220X221THR0-0.050-0.04016.907-0.037-0.0370.0000.0000.0000.000
221X222VAL0-0.052-0.03811.8820.0160.0160.0000.0000.0000.000
222X223TYR0-0.033-0.01313.653-0.017-0.0170.0000.0000.0000.000
223X224ASP-1-0.939-0.97411.975-0.717-0.7170.0000.0000.0000.000
224X225PRO0-0.056-0.0179.6280.0720.0720.0000.0000.0000.000
225X226GLN00.0540.03012.9980.0520.0520.0000.0000.0000.000
226X227ASP-1-0.899-0.93812.891-0.446-0.4460.0000.0000.0000.000
227X228VAL0-0.019-0.00815.4030.0300.0300.0000.0000.0000.000
228X229GLU-1-0.856-0.91317.491-0.097-0.0970.0000.0000.0000.000
229X230PHE00.0400.03019.7730.0010.0010.0000.0000.0000.000
230X231LYS10.9330.98122.7960.0660.0660.0000.0000.0000.000
231X232CYS0-0.032-0.01925.4780.0050.0050.0000.0000.0000.000