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: G6N31

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2669161.182512
FMO2-HF: Nuclear repulsion 2583492.353303
FMO2-HF: Total energy -85668.829209
FMO2-MP2: Total energy -85920.253024


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.
-52.233-53.03225.324-13.105-11.4210.072
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 : -0.880 / 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].
3A432PHE00.0210.0172.414-4.840-0.6071.735-2.219-3.7490.015
4A433ARG10.7880.8985.583-27.656-27.6560.0000.0000.0000.000
5A434VAL0-0.019-0.0109.3950.7010.7010.0000.0000.0000.000
6A435LEU0-0.0030.00211.965-1.151-1.1510.0000.0000.0000.000
7A436LEU0-0.034-0.01413.9700.0590.0590.0000.0000.0000.000
8A437THR00.0390.02417.391-0.632-0.6320.0000.0000.0000.000
9A438VAL00.0200.01320.8850.1900.1900.0000.0000.0000.000
10A439GLY00.0140.01223.126-0.357-0.3570.0000.0000.0000.000
11A440PRO0-0.017-0.02325.473-0.216-0.2160.0000.0000.0000.000
12A441PRO0-0.0110.00128.1750.2680.2680.0000.0000.0000.000
13A442MET0-0.0090.01726.9280.0150.0150.0000.0000.0000.000
14A443ALA00.0390.03030.072-0.101-0.1010.0000.0000.0000.000
15A444PRO0-0.015-0.01932.1060.2540.2540.0000.0000.0000.000
16A445ASN0-0.0310.00129.855-0.336-0.3360.0000.0000.0000.000
17A446THR00.016-0.00932.9160.0360.0360.0000.0000.0000.000
18A447ALA00.019-0.00433.1190.0940.0940.0000.0000.0000.000
19A448ASN0-0.0160.00234.1760.1760.1760.0000.0000.0000.000
20A449SER0-0.0120.01434.478-0.185-0.1850.0000.0000.0000.000
21A450GLN00.0350.00534.4400.1800.1800.0000.0000.0000.000
22A451ASN0-0.030-0.02527.8810.2490.2490.0000.0000.0000.000
23A452TRP0-0.026-0.01931.256-0.125-0.1250.0000.0000.0000.000
24A453VAL00.0110.00427.1470.3690.3690.0000.0000.0000.000
25A454ASN0-0.057-0.05927.131-0.813-0.8130.0000.0000.0000.000
26A455LYS10.8150.91828.337-8.743-8.7430.0000.0000.0000.000
27A456THR00.006-0.00230.0380.1720.1720.0000.0000.0000.000
28A457ILE00.0360.00927.1080.3120.3120.0000.0000.0000.000
29A458VAL0-0.024-0.01229.4500.1590.1590.0000.0000.0000.000
30A459PRO0-0.0130.00931.323-0.076-0.0760.0000.0000.0000.000
31A460PRO00.002-0.00933.359-0.218-0.2180.0000.0000.0000.000
32A461GLU-1-0.855-0.93336.4587.9377.9370.0000.0000.0000.000
33A462ASN0-0.080-0.04037.8280.0110.0110.0000.0000.0000.000
34A463GLN00.0000.02134.3740.3370.3370.0000.0000.0000.000
35A464TYR00.014-0.00929.8010.1660.1660.0000.0000.0000.000
36A465THR00.0200.01227.0710.0820.0820.0000.0000.0000.000
37A466VAL00.0000.00122.1680.1000.1000.0000.0000.0000.000
38A467LYS10.8690.94422.688-11.406-11.4060.0000.0000.0000.000
39A468ILE00.0210.00716.2530.2390.2390.0000.0000.0000.000
40A469GLY00.0520.01016.596-0.228-0.2280.0000.0000.0000.000
41A470ILE00.0040.01613.5320.4920.4920.0000.0000.0000.000
42A471ASP-1-0.814-0.87316.73614.75714.7570.0000.0000.0000.000
43A472LEU0-0.010-0.01420.3670.0030.0030.0000.0000.0000.000
44A473GLU-1-0.924-0.95622.56311.83511.8350.0000.0000.0000.000
45A474HIS10.7660.86817.899-14.418-14.4180.0000.0000.0000.000
46A475TYR00.0240.01318.5330.6010.6010.0000.0000.0000.000
47A476THR0-0.013-0.01018.506-0.567-0.5670.0000.0000.0000.000
48A477THR0-0.031-0.02920.9790.1780.1780.0000.0000.0000.000
49A478MET0-0.0060.02622.1780.1940.1940.0000.0000.0000.000
50A479GLN00.0310.03223.107-0.474-0.4740.0000.0000.0000.000
51A480GLY00.0590.02923.615-0.434-0.4340.0000.0000.0000.000
52A481PHE0-0.006-0.02322.6970.5430.5430.0000.0000.0000.000
53A482THR0-0.010-0.00721.577-0.534-0.5340.0000.0000.0000.000
54A483PRO00.0210.00921.6200.8100.8100.0000.0000.0000.000
55A484VAL0-0.0160.00417.547-0.171-0.1710.0000.0000.0000.000
56A485GLU-1-0.837-0.91720.92112.69712.6970.0000.0000.0000.000
57A486SER0-0.052-0.02219.358-0.013-0.0130.0000.0000.0000.000
58A487VAL00.0230.00312.887-0.319-0.3190.0000.0000.0000.000
59A488SER0-0.0280.00614.975-0.244-0.2440.0000.0000.0000.000
60A489TRP00.0700.0159.0421.0861.0860.0000.0000.0000.000
61A490TYR0-0.006-0.0069.779-1.749-1.7490.0000.0000.0000.000
62A491THR00.0420.0046.1082.3072.3070.0000.0000.0000.000
63A492ALA00.0420.0174.610-3.548-3.537-0.001-0.005-0.0050.000
64A493ASP-1-0.934-0.9426.37327.13627.1360.0000.0000.0000.000
65A494PHE0-0.017-0.0329.175-1.755-1.7550.0000.0000.0000.000
66A495GLN00.0460.04310.782-1.707-1.7070.0000.0000.0000.000
67A496PRO0-0.026-0.02110.7802.1672.1670.0000.0000.0000.000
68A497SER0-0.0080.0018.3111.8311.8310.0000.0000.0000.000
69A498ASP-1-0.887-0.9309.62421.02721.0270.0000.0000.0000.000
70A499GLU-1-0.873-0.9539.30825.31525.3150.0000.0000.0000.000
71A500PRO0-0.0150.0095.9520.3720.3720.0000.0000.0000.000
72A501SER0-0.003-0.0237.372-4.497-4.4970.0000.0000.0000.000
73A502PRO0-0.020-0.0047.5193.5683.5680.0000.0000.0000.000
74A503ILE0-0.011-0.0066.9871.4201.4200.0000.0000.0000.000
75A504PRO00.009-0.0058.448-3.753-3.7530.0000.0000.0000.000
76A505GLY0-0.023-0.01011.5030.0530.0530.0000.0000.0000.000
77A506LEU0-0.032-0.00610.839-1.759-1.7590.0000.0000.0000.000
78A507TYR00.007-0.00913.9770.0050.0050.0000.0000.0000.000
79A508ALA00.0220.02316.949-0.488-0.4880.0000.0000.0000.000
80A509ARG10.8470.90618.162-15.912-15.9120.0000.0000.0000.000
81A510VAL00.0390.02122.744-0.210-0.2100.0000.0000.0000.000
82A511ASN00.010-0.00226.433-0.095-0.0950.0000.0000.0000.000
83A512ASN0-0.015-0.01224.5930.3330.3330.0000.0000.0000.000
84A513THR0-0.0020.01825.2930.1760.1760.0000.0000.0000.000
85A514LYS10.9200.95919.043-15.323-15.3230.0000.0000.0000.000
86A515LYS10.9290.97021.509-12.283-12.2830.0000.0000.0000.000
87A516ALA00.0150.01318.497-0.247-0.2470.0000.0000.0000.000
88A517ASP-1-0.826-0.90213.78119.69619.6960.0000.0000.0000.000
89A518VAL0-0.029-0.03111.520-0.713-0.7130.0000.0000.0000.000
90A519TYR00.003-0.0149.4160.8970.8970.0000.0000.0000.000
91A520GLY00.0360.0317.9204.4564.4560.0000.0000.0000.000
92A521VAL0-0.058-0.0188.227-3.730-3.7300.0000.0000.0000.000
93A522GLN00.0390.0189.2081.1011.1010.0000.0000.0000.000
94A523GLN0-0.009-0.01511.614-1.418-1.4180.0000.0000.0000.000
95A524PHE00.0010.01414.3960.2040.2040.0000.0000.0000.000
96A525LYS10.8900.93716.052-16.624-16.6240.0000.0000.0000.000
97A526SER0-0.0150.00019.761-0.231-0.2310.0000.0000.0000.000
98A527SER00.0240.01223.2220.0010.0010.0000.0000.0000.000
99A528HIS0-0.046-0.02526.155-0.134-0.1340.0000.0000.0000.000
100A529THR00.0200.00629.362-0.264-0.2640.0000.0000.0000.000
101A530ASN00.029-0.00229.3740.4980.4980.0000.0000.0000.000
102A531ASN0-0.045-0.02229.5340.2480.2480.0000.0000.0000.000
103A532ARG10.9110.95429.008-9.605-9.6050.0000.0000.0000.000
104A533HIS10.8180.90023.834-11.087-11.0870.0000.0000.0000.000
105A534GLN00.0370.02123.719-0.568-0.5680.0000.0000.0000.000
106A535ILE0-0.023-0.02718.2890.3610.3610.0000.0000.0000.000
107A536THR0-0.008-0.01019.015-0.501-0.5010.0000.0000.0000.000
108A537SER0-0.0300.00115.6900.9910.9910.0000.0000.0000.000
109A538VAL0-0.030-0.01913.849-0.991-0.9910.0000.0000.0000.000
110A539PHE00.008-0.01013.4361.3541.3540.0000.0000.0000.000
111A540LEU00.0420.04111.440-1.521-1.5210.0000.0000.0000.000
112A541VAL0-0.019-0.01913.2771.4051.4050.0000.0000.0000.000
113A542ARG10.9050.96915.741-19.443-19.4430.0000.0000.0000.000
114A543VAL0-0.032-0.01317.3190.1320.1320.0000.0000.0000.000
115A544THR00.0300.01418.542-0.379-0.3790.0000.0000.0000.000
116A545THR0-0.062-0.03721.310-0.639-0.6390.0000.0000.0000.000
117A546SER00.0380.01724.9590.3090.3090.0000.0000.0000.000
118A547PHE0-0.056-0.02423.680-0.247-0.2470.0000.0000.0000.000
119A548GLN00.002-0.00428.826-0.031-0.0310.0000.0000.0000.000
120A549VAL0-0.0270.00028.400-0.017-0.0170.0000.0000.0000.000
121A550ILE00.0370.03431.288-0.049-0.0490.0000.0000.0000.000
122A551ASN0-0.075-0.06129.2810.4020.4020.0000.0000.0000.000
123A552TYR00.0650.03832.974-0.276-0.2760.0000.0000.0000.000
124A553THR0-0.011-0.00931.4360.1990.1990.0000.0000.0000.000
125A554SER00.000-0.02732.497-0.407-0.4070.0000.0000.0000.000
126A555TYR00.0500.04132.2100.1560.1560.0000.0000.0000.000
127A556PHE00.0220.00627.605-0.267-0.2670.0000.0000.0000.000
128A557ILE0-0.0030.00333.128-0.166-0.1660.0000.0000.0000.000
129A558ARG10.9610.96534.451-8.491-8.4910.0000.0000.0000.000
130A559GLY00.0100.03637.892-0.099-0.0990.0000.0000.0000.000
131A560ALA00.0040.00341.1320.1290.1290.0000.0000.0000.000
132A561GLU-1-0.910-0.95942.5476.9666.9660.0000.0000.0000.000
133A562SER0-0.012-0.00745.005-0.078-0.0780.0000.0000.0000.000
134A563GLY0-0.003-0.01046.7220.0650.0650.0000.0000.0000.000
135A564SER00.0160.00043.8920.0460.0460.0000.0000.0000.000
136A565ASN0-0.038-0.00242.9400.1150.1150.0000.0000.0000.000
137A566VAL00.0110.00537.6050.1110.1110.0000.0000.0000.000
138A567SER00.0160.00738.949-0.017-0.0170.0000.0000.0000.000
139A568ASN0-0.040-0.04035.6990.3960.3960.0000.0000.0000.000
140A569LEU0-0.0050.00730.234-0.166-0.1660.0000.0000.0000.000
141A570LYS10.8940.94533.343-7.758-7.7580.0000.0000.0000.000
142A571ILE00.0000.01531.0950.0570.0570.0000.0000.0000.000
143A572ARG10.8520.91933.770-8.348-8.3480.0000.0000.0000.000
144A573ASP-1-0.835-0.90536.3757.9817.9810.0000.0000.0000.000
145A574GLN00.0570.02638.0740.2460.2460.0000.0000.0000.000
146A575THR0-0.030-0.00435.7080.2070.2070.0000.0000.0000.000
147A576TYR0-0.034-0.02136.721-0.326-0.3260.0000.0000.0000.000
148A577HIS00.0020.00936.3560.2720.2720.0000.0000.0000.000
149A578THR00.0060.00334.341-0.136-0.1360.0000.0000.0000.000
150A579PRO00.0230.01334.3590.2330.2330.0000.0000.0000.000
151A580LEU0-0.032-0.00428.6510.0370.0370.0000.0000.0000.000
152A581GLN00.0580.02130.0820.0200.0200.0000.0000.0000.000
153A582PHE00.0090.00323.9080.2820.2820.0000.0000.0000.000
154A583THR0-0.016-0.02525.298-0.467-0.4670.0000.0000.0000.000
155A584GLN00.006-0.01123.5460.2850.2850.0000.0000.0000.000
156A585GLY00.008-0.00120.946-0.385-0.3850.0000.0000.0000.000
157A586LYS10.8320.91021.027-12.320-12.3200.0000.0000.0000.000
158A587TRP00.0080.01012.9280.3790.3790.0000.0000.0000.000
159A588TYR00.004-0.01318.402-1.127-1.1270.0000.0000.0000.000
160A589LEU00.0100.02515.7971.0831.0830.0000.0000.0000.000
161A590LEU0-0.038-0.02517.833-1.103-1.1030.0000.0000.0000.000
162A591THR00.0180.00517.9920.7120.7120.0000.0000.0000.000
163A592SER0-0.011-0.02919.695-0.689-0.6890.0000.0000.0000.000
164A593THR0-0.003-0.01820.4470.4980.4980.0000.0000.0000.000
165A594VAL0-0.029-0.00521.652-0.532-0.5320.0000.0000.0000.000
166A595MET0-0.0080.01824.1910.1140.1140.0000.0000.0000.000
167A596HIS00.0080.00322.6880.3600.3600.0000.0000.0000.000
168A597ASP-1-0.823-0.92226.1999.3499.3490.0000.0000.0000.000
169A598GLY00.0010.01127.4240.3230.3230.0000.0000.0000.000
170A599PRO00.0430.01926.0910.0010.0010.0000.0000.0000.000
171A600THR0-0.017-0.01821.3450.0540.0540.0000.0000.0000.000
172A601SER00.0290.02019.8450.2990.2990.0000.0000.0000.000
173A602SER0-0.029-0.02117.5970.4720.4720.0000.0000.0000.000
174A603GLY00.0480.03113.579-0.084-0.0840.0000.0000.0000.000
175A604TRP00.0200.01211.169-0.301-0.3010.0000.0000.0000.000
176A605VAL0-0.023-0.01413.776-0.704-0.7040.0000.0000.0000.000
177A606TRP00.0180.01513.718-0.072-0.0720.0000.0000.0000.000
178A607MET00.0110.00018.703-0.530-0.5300.0000.0000.0000.000
179A608ASN00.0480.03922.0060.5200.5200.0000.0000.0000.000
180A609GLN0-0.002-0.00224.310-0.315-0.3150.0000.0000.0000.000
181A610GLU-1-0.852-0.92626.4679.4289.4280.0000.0000.0000.000
182A611LEU00.0120.01026.831-0.010-0.0100.0000.0000.0000.000
183A612THR0-0.020-0.00929.800-0.319-0.3190.0000.0000.0000.000
184A613ASN00.031-0.01532.7480.2390.2390.0000.0000.0000.000
185A614ASN00.004-0.00236.161-0.072-0.0720.0000.0000.0000.000
186A615ILE00.0270.04031.088-0.096-0.0960.0000.0000.0000.000
187A616ALA0-0.040-0.01433.3210.0460.0460.0000.0000.0000.000
188A617TYR00.0410.01527.2310.0970.0970.0000.0000.0000.000
189A618ARG10.8710.93026.886-10.654-10.6540.0000.0000.0000.000
190A619VAL00.0660.03325.7380.2080.2080.0000.0000.0000.000
191A620ASP-1-0.758-0.83721.13713.61113.6110.0000.0000.0000.000
192A621PRO00.059-0.00118.430-0.161-0.1610.0000.0000.0000.000
193A622GLY00.0230.01918.8830.5250.5250.0000.0000.0000.000
194A623MET0-0.057-0.02119.600-0.087-0.0870.0000.0000.0000.000
195A624MET0-0.021-0.02022.881-0.404-0.4040.0000.0000.0000.000
196A625TYR0-0.029-0.01519.495-0.192-0.1920.0000.0000.0000.000
197A626LEU00.0000.00323.024-0.050-0.0500.0000.0000.0000.000
198A627ILE0-0.0190.00226.710-0.373-0.3730.0000.0000.0000.000
199A628THR00.0280.00129.868-0.397-0.3970.0000.0000.0000.000
200A629PRO0-0.046-0.01628.2780.3800.3800.0000.0000.0000.000
201A630PRO0-0.0080.01324.279-0.254-0.2540.0000.0000.0000.000
202A631PRO00.0130.01327.322-0.061-0.0610.0000.0000.0000.000
203A632ALA00.0340.01627.0040.4320.4320.0000.0000.0000.000
204A633ALA0-0.031-0.02625.379-0.290-0.2900.0000.0000.0000.000
205A634SER0-0.051-0.01924.9640.2610.2610.0000.0000.0000.000
206A635GLN00.011-0.02019.7060.3040.3040.0000.0000.0000.000
207A636LEU0-0.046-0.01418.530-0.369-0.3690.0000.0000.0000.000
208A637TYR0-0.032-0.03012.9460.9600.9600.0000.0000.0000.000
209A638PHE0-0.028-0.01912.809-0.674-0.6740.0000.0000.0000.000
210A639GLU-1-0.789-0.8579.55023.19623.1960.0000.0000.0000.000
211A640LEU0-0.042-0.0228.005-1.628-1.6280.0000.0000.0000.000
212A641HIS0-0.016-0.0174.8775.4755.4750.0000.0000.0000.000
213A642THR00.029-0.0191.618-37.943-43.76523.510-10.709-6.9790.057
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