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: 1741Z

Calculation Name: 3QSQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QSQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9IFX1

Base Structure: X-ray

Registration Date: 2023-06-21

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2667424.123735
FMO2-HF: Nuclear repulsion 2581756.061992
FMO2-HF: Total energy -85668.061742
FMO2-MP2: Total energy -85919.511973


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(A:430:GLU)


Summations of interaction energy for fragment #1(A:430: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.
-29.696-25.06814.624-8.441-10.8090.052
Interaction energy analysis for fragmet #1(A:430:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.898 / q_NPA : -0.972
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].
3A432PHE00.0110.0112.059-4.949-3.6326.516-3.233-4.6000.032
4A433ARG10.8180.9115.674-28.751-28.7510.0000.0000.0000.000
5A434VAL0-0.018-0.0089.4820.9150.9150.0000.0000.0000.000
6A435LEU0-0.003-0.00312.040-1.264-1.2640.0000.0000.0000.000
7A436LEU0-0.036-0.01514.1090.1040.1040.0000.0000.0000.000
8A437THR00.0420.02617.447-0.759-0.7590.0000.0000.0000.000
9A438VAL00.0130.00520.9430.1530.1530.0000.0000.0000.000
10A439GLY00.0220.01523.171-0.335-0.3350.0000.0000.0000.000
11A440PRO0-0.017-0.02325.508-0.223-0.2230.0000.0000.0000.000
12A441PRO0-0.015-0.00228.1970.2560.2560.0000.0000.0000.000
13A442MET0-0.0200.01526.7720.0320.0320.0000.0000.0000.000
14A443ALA00.0470.03330.077-0.104-0.1040.0000.0000.0000.000
15A444PRO0-0.018-0.02231.9760.2270.2270.0000.0000.0000.000
16A445ASN00.0020.01529.249-0.541-0.5410.0000.0000.0000.000
17A446THR00.015-0.00732.9240.0430.0430.0000.0000.0000.000
18A447ALA00.018-0.00733.1550.0900.0900.0000.0000.0000.000
19A448ASN0-0.024-0.00434.2100.1570.1570.0000.0000.0000.000
20A449SER0-0.0040.01934.536-0.179-0.1790.0000.0000.0000.000
21A450GLN00.0250.00534.4640.1810.1810.0000.0000.0000.000
22A451ASN0-0.038-0.03027.7110.1550.1550.0000.0000.0000.000
23A452TRP0-0.026-0.02631.184-0.126-0.1260.0000.0000.0000.000
24A453VAL00.0250.01327.0580.3580.3580.0000.0000.0000.000
25A454ASN0-0.064-0.06327.105-0.782-0.7820.0000.0000.0000.000
26A455LYS10.8470.92228.246-8.540-8.5400.0000.0000.0000.000
27A456THR00.006-0.00729.9260.1660.1660.0000.0000.0000.000
28A457ILE00.0360.01327.0110.2920.2920.0000.0000.0000.000
29A458VAL0-0.027-0.00729.3480.1420.1420.0000.0000.0000.000
30A459PRO0-0.0230.00531.366-0.061-0.0610.0000.0000.0000.000
31A460PRO00.002-0.01133.293-0.207-0.2070.0000.0000.0000.000
32A461GLU-1-0.844-0.92436.4097.7417.7410.0000.0000.0000.000
33A462ASN0-0.075-0.03937.8250.0560.0560.0000.0000.0000.000
34A463GLN0-0.0090.01934.3380.3230.3230.0000.0000.0000.000
35A464TYR00.006-0.01229.7840.1430.1430.0000.0000.0000.000
36A465THR00.0260.01427.0250.0620.0620.0000.0000.0000.000
37A466VAL00.0010.00022.1260.0890.0890.0000.0000.0000.000
38A467LYS10.8880.95222.634-10.977-10.9770.0000.0000.0000.000
39A468ILE00.0130.00616.1360.2250.2250.0000.0000.0000.000
40A469GLY00.0440.00216.517-0.217-0.2170.0000.0000.0000.000
41A470ILE0-0.0020.00313.5280.4520.4520.0000.0000.0000.000
42A471ASP-1-0.845-0.90316.68113.96313.9630.0000.0000.0000.000
43A472LEU0-0.006-0.01620.3060.0010.0010.0000.0000.0000.000
44A473GLU-1-0.918-0.95222.50611.35611.3560.0000.0000.0000.000
45A474HIS10.7880.89517.721-13.842-13.8420.0000.0000.0000.000
46A475TYR00.0310.01118.4350.5420.5420.0000.0000.0000.000
47A476THR0-0.020-0.00718.351-0.528-0.5280.0000.0000.0000.000
48A477THR0-0.047-0.05220.8670.1930.1930.0000.0000.0000.000
49A478MET0-0.0030.01422.1070.2030.2030.0000.0000.0000.000
50A479GLN00.0360.04323.037-0.407-0.4070.0000.0000.0000.000
51A480GLY00.0490.02223.514-0.408-0.4080.0000.0000.0000.000
52A481PHE0-0.004-0.02322.6440.5330.5330.0000.0000.0000.000
53A482THR00.000-0.00121.506-0.634-0.6340.0000.0000.0000.000
54A483PRO0-0.004-0.00321.6290.7880.7880.0000.0000.0000.000
55A484VAL0-0.0160.00317.586-0.152-0.1520.0000.0000.0000.000
56A485GLU-1-0.936-0.97520.94812.54412.5440.0000.0000.0000.000
57A486SER0-0.047-0.02618.8750.2370.2370.0000.0000.0000.000
58A487VAL00.0130.00312.751-0.322-0.3220.0000.0000.0000.000
59A488SER0-0.0270.00614.791-0.152-0.1520.0000.0000.0000.000
60A489TRP00.0720.0148.7791.0601.0600.0000.0000.0000.000
61A490TYR0-0.006-0.0039.883-1.786-1.7860.0000.0000.0000.000
62A491THR00.0700.0356.0532.3482.3480.0000.0000.0000.000
63A492ALA00.0300.0104.631-4.244-4.231-0.001-0.004-0.0080.000
64A493ASP-1-0.946-0.9666.35528.83428.8340.0000.0000.0000.000
65A494PHE0-0.044-0.0399.163-1.854-1.8540.0000.0000.0000.000
66A495GLN00.1110.06310.781-1.352-1.3520.0000.0000.0000.000
67A496PRO0-0.086-0.04410.7252.3852.3850.0000.0000.0000.000
68A497SER00.0020.0057.8832.0532.0530.0000.0000.0000.000
69A498ASP-1-0.889-0.9259.34921.34121.3410.0000.0000.0000.000
70A499GLU-1-0.993-1.0178.69826.12626.1260.0000.0000.0000.000
71A500PRO0-0.0160.0135.3960.8410.8410.0000.0000.0000.000
72A501SER0-0.004-0.0277.183-5.838-5.8380.0000.0000.0000.000
73A502PRO0-0.028-0.0107.7953.1123.1120.0000.0000.0000.000
74A503ILE0-0.013-0.0097.1201.2321.2320.0000.0000.0000.000
75A504PRO00.012-0.0029.181-3.188-3.1880.0000.0000.0000.000
76A505GLY0-0.018-0.00911.793-0.060-0.0600.0000.0000.0000.000
77A506LEU0-0.032-0.00310.874-1.558-1.5580.0000.0000.0000.000
78A507TYR0-0.009-0.01813.9740.0440.0440.0000.0000.0000.000
79A508ALA00.0230.02516.962-0.450-0.4500.0000.0000.0000.000
80A509ARG10.8710.92718.300-15.162-15.1620.0000.0000.0000.000
81A510VAL00.0480.02722.743-0.194-0.1940.0000.0000.0000.000
82A511ASN00.007-0.00326.430-0.068-0.0680.0000.0000.0000.000
83A512ASN0-0.002-0.00324.7430.2180.2180.0000.0000.0000.000
84A513THR0-0.0160.00625.3030.1810.1810.0000.0000.0000.000
85A514LYS10.9140.95519.921-14.381-14.3810.0000.0000.0000.000
86A515LYS10.9380.97321.887-11.899-11.8990.0000.0000.0000.000
87A516ALA00.0200.01418.849-0.197-0.1970.0000.0000.0000.000
88A517ASP-1-0.825-0.89914.21218.93918.9390.0000.0000.0000.000
89A518VAL0-0.029-0.03011.352-0.586-0.5860.0000.0000.0000.000
90A519TYR00.0340.0099.7180.2850.2850.0000.0000.0000.000
91A520GLY00.0360.0318.1334.1324.1320.0000.0000.0000.000
92A521VAL0-0.056-0.0168.070-3.323-3.3230.0000.0000.0000.000
93A522GLN00.0480.0349.0970.9610.9610.0000.0000.0000.000
94A523GLN0-0.029-0.03311.473-1.190-1.1900.0000.0000.0000.000
95A524PHE00.0050.01314.2200.2180.2180.0000.0000.0000.000
96A525LYS10.8950.94416.045-16.207-16.2070.0000.0000.0000.000
97A526SER0-0.0080.00319.5530.0000.0000.0000.0000.0000.000
98A527SER0-0.006-0.00623.011-0.009-0.0090.0000.0000.0000.000
99A528HIS0-0.051-0.03125.933-0.111-0.1110.0000.0000.0000.000
100A529THR00.0210.00529.148-0.261-0.2610.0000.0000.0000.000
101A530ASN00.028-0.00629.1450.5070.5070.0000.0000.0000.000
102A531ASN0-0.012-0.00829.2970.3360.3360.0000.0000.0000.000
103A532ARG10.9611.00128.726-9.314-9.3140.0000.0000.0000.000
104A533HIS10.7940.90623.481-10.855-10.8550.0000.0000.0000.000
105A534GLN00.0620.02023.506-0.574-0.5740.0000.0000.0000.000
106A535ILE0-0.022-0.02418.1540.3550.3550.0000.0000.0000.000
107A536THR0-0.006-0.01218.796-0.520-0.5200.0000.0000.0000.000
108A537SER0-0.0350.00015.5850.9310.9310.0000.0000.0000.000
109A538VAL0-0.025-0.01413.717-0.913-0.9130.0000.0000.0000.000
110A539PHE00.014-0.00613.3881.2151.2150.0000.0000.0000.000
111A540LEU00.0410.04011.545-1.376-1.3760.0000.0000.0000.000
112A541VAL0-0.023-0.01513.5071.2531.2530.0000.0000.0000.000
113A542ARG10.9610.98115.903-18.386-18.3860.0000.0000.0000.000
114A543VAL0-0.029-0.01017.4450.0730.0730.0000.0000.0000.000
115A544THR00.0310.01218.920-0.341-0.3410.0000.0000.0000.000
116A545THR0-0.049-0.02921.601-0.595-0.5950.0000.0000.0000.000
117A546SER00.0240.01025.2990.2840.2840.0000.0000.0000.000
118A547PHE0-0.051-0.02024.107-0.253-0.2530.0000.0000.0000.000
119A548GLN00.000-0.00229.210-0.047-0.0470.0000.0000.0000.000
120A549VAL0-0.032-0.00128.440-0.020-0.0200.0000.0000.0000.000
121A550ILE00.0400.03531.283-0.040-0.0400.0000.0000.0000.000
122A551ASN0-0.061-0.05029.2370.3610.3610.0000.0000.0000.000
123A552TYR00.0600.03132.927-0.214-0.2140.0000.0000.0000.000
124A553THR0-0.014-0.00631.4390.1790.1790.0000.0000.0000.000
125A554SER0-0.010-0.03432.421-0.383-0.3830.0000.0000.0000.000
126A555TYR00.0480.03532.1140.1500.1500.0000.0000.0000.000
127A556PHE00.0130.00427.532-0.260-0.2600.0000.0000.0000.000
128A557ILE0-0.0060.00233.015-0.153-0.1530.0000.0000.0000.000
129A558ARG10.9670.96633.810-8.418-8.4180.0000.0000.0000.000
130A559GLY00.0150.03937.758-0.091-0.0910.0000.0000.0000.000
131A560ALA00.0110.00840.9880.1260.1260.0000.0000.0000.000
132A561GLU-1-0.919-0.96242.2986.9596.9590.0000.0000.0000.000
133A562SER0-0.020-0.01544.848-0.078-0.0780.0000.0000.0000.000
134A563GLY00.003-0.00646.5980.0610.0610.0000.0000.0000.000
135A564SER0-0.005-0.00743.8160.0580.0580.0000.0000.0000.000
136A565ASN0-0.0080.01042.9400.1230.1230.0000.0000.0000.000
137A566VAL00.0070.00437.4120.1100.1100.0000.0000.0000.000
138A567SER00.0160.00638.769-0.033-0.0330.0000.0000.0000.000
139A568ASN0-0.043-0.03835.4650.3580.3580.0000.0000.0000.000
140A569LEU0-0.0070.00430.098-0.162-0.1620.0000.0000.0000.000
141A570LYS10.9470.97733.186-7.722-7.7220.0000.0000.0000.000
142A571ILE00.0050.01630.8210.0670.0670.0000.0000.0000.000
143A572ARG10.8840.94433.640-8.172-8.1720.0000.0000.0000.000
144A573ASP-1-0.863-0.92436.2607.8177.8170.0000.0000.0000.000
145A574GLN00.0450.01437.9590.2610.2610.0000.0000.0000.000
146A575THR0-0.038-0.01435.2950.1850.1850.0000.0000.0000.000
147A576TYR0-0.055-0.02736.648-0.223-0.2230.0000.0000.0000.000
148A577HIS00.0030.00836.3000.2550.2550.0000.0000.0000.000
149A578THR00.0030.00134.407-0.173-0.1730.0000.0000.0000.000
150A579PRO00.0260.01234.3490.2270.2270.0000.0000.0000.000
151A580LEU0-0.0250.00028.5570.0470.0470.0000.0000.0000.000
152A581GLN00.0800.02530.2970.0620.0620.0000.0000.0000.000
153A582PHE0-0.0030.00324.0410.2780.2780.0000.0000.0000.000
154A583THR0-0.044-0.04325.430-0.415-0.4150.0000.0000.0000.000
155A584GLN00.021-0.00423.6760.2210.2210.0000.0000.0000.000
156A585GLY00.0080.00120.878-0.352-0.3520.0000.0000.0000.000
157A586LYS10.9320.98120.842-11.756-11.7560.0000.0000.0000.000
158A587TRP00.0280.02012.6700.2950.2950.0000.0000.0000.000
159A588TYR00.021-0.00618.435-1.066-1.0660.0000.0000.0000.000
160A589LEU00.0140.02115.6491.0161.0160.0000.0000.0000.000
161A590LEU0-0.045-0.03117.803-1.061-1.0610.0000.0000.0000.000
162A591THR00.0290.01617.9270.6660.6660.0000.0000.0000.000
163A592SER0-0.009-0.01619.585-0.732-0.7320.0000.0000.0000.000
164A593THR00.011-0.02120.3070.4820.4820.0000.0000.0000.000
165A594VAL0-0.049-0.01621.675-0.490-0.4900.0000.0000.0000.000
166A595MET0-0.065-0.02824.0080.1750.1750.0000.0000.0000.000
167A596HIS0-0.029-0.02522.9470.2320.2320.0000.0000.0000.000
168A597ASP-1-0.836-0.93125.9929.1359.1350.0000.0000.0000.000
169A598GLY00.0030.01927.2010.3090.3090.0000.0000.0000.000
170A599PRO00.0500.02025.8620.0060.0060.0000.0000.0000.000
171A600THR0-0.008-0.01721.2860.0090.0090.0000.0000.0000.000
172A601SER00.0290.03119.6870.2810.2810.0000.0000.0000.000
173A602SER0-0.018-0.01817.4860.4670.4670.0000.0000.0000.000
174A603GLY00.0380.02513.341-0.090-0.0900.0000.0000.0000.000
175A604TRP00.0210.01511.146-0.270-0.2700.0000.0000.0000.000
176A605VAL0-0.021-0.01113.567-0.668-0.6680.0000.0000.0000.000
177A606TRP00.0080.01313.648-0.040-0.0400.0000.0000.0000.000
178A607MET00.0200.00418.538-0.473-0.4730.0000.0000.0000.000
179A608ASN00.0490.05121.8570.5110.5110.0000.0000.0000.000
180A609GLN0-0.003-0.00124.171-0.306-0.3060.0000.0000.0000.000
181A610GLU-1-0.920-0.94426.3339.2199.2190.0000.0000.0000.000
182A611LEU00.0160.00926.721-0.016-0.0160.0000.0000.0000.000
183A612THR0-0.020-0.01529.664-0.310-0.3100.0000.0000.0000.000
184A613ASN00.1020.03432.5960.2270.2270.0000.0000.0000.000
185A614ASN0-0.052-0.03336.011-0.050-0.0500.0000.0000.0000.000
186A615ILE00.0280.03330.745-0.099-0.0990.0000.0000.0000.000
187A616ALA0-0.057-0.02633.1450.0360.0360.0000.0000.0000.000
188A617TYR00.0540.02427.2540.0920.0920.0000.0000.0000.000
189A618ARG10.9050.95126.774-10.341-10.3410.0000.0000.0000.000
190A619VAL00.0650.03125.6710.1770.1770.0000.0000.0000.000
191A620ASP-1-0.751-0.83621.21813.30413.3040.0000.0000.0000.000
192A621PRO00.046-0.01018.458-0.138-0.1380.0000.0000.0000.000
193A622GLY00.0130.01118.7690.5510.5510.0000.0000.0000.000
194A623MET0-0.061-0.01719.478-0.096-0.0960.0000.0000.0000.000
195A624MET0-0.017-0.02022.923-0.364-0.3640.0000.0000.0000.000
196A625TYR0-0.0160.00819.298-0.261-0.2610.0000.0000.0000.000
197A626LEU0-0.0020.00023.114-0.064-0.0640.0000.0000.0000.000
198A627ILE0-0.0200.00026.725-0.376-0.3760.0000.0000.0000.000
199A628THR0-0.003-0.01529.809-0.349-0.3490.0000.0000.0000.000
200A629PRO0-0.037-0.01228.3070.4000.4000.0000.0000.0000.000
201A630PRO00.0100.02724.333-0.240-0.2400.0000.0000.0000.000
202A631PRO00.0180.01127.364-0.070-0.0700.0000.0000.0000.000
203A632ALA00.0270.01827.0580.4380.4380.0000.0000.0000.000
204A633ALA0-0.026-0.02425.476-0.280-0.2800.0000.0000.0000.000
205A634SER0-0.054-0.02225.0320.2710.2710.0000.0000.0000.000
206A635GLN00.020-0.00919.8540.1540.1540.0000.0000.0000.000
207A636LEU0-0.044-0.01618.411-0.375-0.3750.0000.0000.0000.000
208A637TYR0-0.031-0.03612.7501.0811.0810.0000.0000.0000.000
209A638PHE0-0.033-0.02212.743-0.780-0.7800.0000.0000.0000.000
210A639GLU-1-0.829-0.8739.52022.89922.8990.0000.0000.0000.000
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212A641HIS00.001-0.0014.7595.4015.401-0.001-0.0200.0220.000
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