FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: N9L4Q

Calculation Name: 5XQ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XQ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q8CIB5

Base Structure: X-ray

Registration Date: 2023-06-22

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 432
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7935906.693134
FMO2-HF: Nuclear repulsion 7757855.818203
FMO2-HF: Total energy -178050.874931
FMO2-MP2: Total energy -178566.839088


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:18:TRP)


Summations of interaction energy for fragment #1(A:18:TRP)
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.
-24.472-13.77519.177-6.38-23.493-0.039
Interaction energy analysis for fragmet #1(A:18:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.029
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].
3A20LEU00.0120.0122.421-4.855-1.6662.057-2.124-3.122-0.015
4A21SER0-0.008-0.0064.2981.1941.319-0.001-0.021-0.1030.000
5A22VAL00.0140.0047.8010.0000.0000.0000.0000.0000.000
6A23HIS0-0.003-0.00710.7230.1900.1900.0000.0000.0000.000
7A24VAL00.012-0.00314.306-0.006-0.0060.0000.0000.0000.000
8A25THR00.0290.01516.9360.0880.0880.0000.0000.0000.000
9A26ASP-1-0.788-0.88219.573-0.462-0.4620.0000.0000.0000.000
10A27LEU0-0.035-0.02319.9340.0400.0400.0000.0000.0000.000
11A28ASN0-0.024-0.00620.3230.0000.0000.0000.0000.0000.000
12A29ARG10.9520.97917.4950.4340.4340.0000.0000.0000.000
13A30ASP-1-0.814-0.87513.149-0.923-0.9230.0000.0000.0000.000
14A31VAL0-0.005-0.00311.5850.0900.0900.0000.0000.0000.000
15A32THR00.0040.0057.212-0.252-0.2520.0000.0000.0000.000
16A33LEU0-0.019-0.0076.9580.4140.4140.0000.0000.0000.000
17A34ARG10.8920.9212.507-3.839-2.8430.941-0.677-1.260-0.001
18A35VAL0-0.058-0.0352.921-0.9181.0551.252-0.821-2.4040.005
19A36THR00.026-0.0032.513-4.063-2.7162.153-1.451-2.049-0.015
20A37GLY00.0680.0482.530-0.3150.6964.579-2.674-2.9160.008
21A38GLU-1-0.838-0.9153.0201.576-2.6530.3134.727-0.8120.002
22A39VAL0-0.054-0.0395.9640.1710.1710.0000.0000.0000.000
23A40HIS0-0.024-0.0227.507-0.280-0.2800.0000.0000.0000.000
24A41ILE00.0210.0138.205-0.114-0.1140.0000.0000.0000.000
25A42GLY00.0390.01110.375-0.022-0.0220.0000.0000.0000.000
26A43GLY0-0.016-0.00811.7640.0740.0740.0000.0000.0000.000
27A44VAL0-0.031-0.0167.233-0.019-0.0190.0000.0000.0000.000
28A45MET0-0.010-0.01110.0410.0370.0370.0000.0000.0000.000
29A46LEU00.0150.01313.5340.0600.0600.0000.0000.0000.000
30A47LYS10.9320.9677.9331.0021.0020.0000.0000.0000.000
31A48LEU0-0.027-0.00712.2490.0150.0150.0000.0000.0000.000
32A49VAL0-0.001-0.00113.7740.0720.0720.0000.0000.0000.000
33A50GLU-1-0.950-0.97414.028-0.447-0.4470.0000.0000.0000.000
34A51LYS10.8430.91611.2700.9480.9480.0000.0000.0000.000
35A52LEU0-0.037-0.02415.9230.0260.0260.0000.0000.0000.000
36A53ASP-1-0.860-0.91418.660-0.231-0.2310.0000.0000.0000.000
37A54VAL0-0.0080.00621.0540.0400.0400.0000.0000.0000.000
38A55LYS10.8150.89923.6010.2470.2470.0000.0000.0000.000
39A56LYS10.8210.91221.7140.4630.4630.0000.0000.0000.000
40A57ASP-1-0.802-0.87124.652-0.364-0.3640.0000.0000.0000.000
41A58TRP0-0.001-0.02218.984-0.051-0.0510.0000.0000.0000.000
42A59SER0-0.007-0.02221.587-0.034-0.0340.0000.0000.0000.000
43A60ASP-1-0.749-0.87423.748-0.400-0.4000.0000.0000.0000.000
44A61HIS0-0.099-0.04018.421-0.001-0.0010.0000.0000.0000.000
45A62ALA00.0040.01116.846-0.011-0.0110.0000.0000.0000.000
46A63LEU0-0.018-0.01210.256-0.024-0.0240.0000.0000.0000.000
47A64TRP00.003-0.00813.3670.0150.0150.0000.0000.0000.000
48A65TRP00.007-0.0067.699-0.295-0.2950.0000.0000.0000.000
49A66GLU-1-0.775-0.87012.265-0.504-0.5040.0000.0000.0000.000
50A67LYS10.8920.9409.6320.8240.8240.0000.0000.0000.000
51A68LYS10.9260.96010.4441.0531.0530.0000.0000.0000.000
52A69ARG10.7710.88214.1150.4250.4250.0000.0000.0000.000
53A70THR00.014-0.00114.1540.0170.0170.0000.0000.0000.000
54A71TRP00.0580.03414.428-0.146-0.1460.0000.0000.0000.000
55A72LEU0-0.058-0.0389.596-0.010-0.0100.0000.0000.0000.000
56A73LEU00.0770.03613.468-0.029-0.0290.0000.0000.0000.000
57A74LYS10.8690.95512.4211.0121.0120.0000.0000.0000.000
58A75THR00.0690.00713.526-0.096-0.0960.0000.0000.0000.000
59A76HIS00.0790.03713.271-0.097-0.0970.0000.0000.0000.000
60A77TRP0-0.026-0.01910.8160.0680.0680.0000.0000.0000.000
61A78THR0-0.002-0.0077.036-0.119-0.1190.0000.0000.0000.000
62A79LEU00.0140.0033.053-1.588-0.1300.236-0.475-1.2200.002
63A80ASP-1-0.816-0.9072.588-8.655-5.8720.703-1.536-1.951-0.023
64A81LYS10.8790.9614.8651.1011.132-0.001-0.003-0.0270.000
65A82CYS0-0.080-0.0367.0880.3600.3600.0000.0000.0000.000
66A83GLY0-0.0100.0016.4880.1410.1410.0000.0000.0000.000
67A84ILE0-0.076-0.0483.5410.3550.7200.001-0.067-0.2990.000
68A85GLN00.0100.0132.569-4.528-3.0200.906-0.797-1.617-0.010
69A86ALA00.0590.0232.339-5.991-3.6215.958-3.700-4.6260.007
70A87ASP-1-0.904-0.9533.1341.340-1.0600.0813.246-0.9270.001
71A88ALA0-0.076-0.0334.6710.4420.612-0.001-0.007-0.1600.000
72A89LYS10.8530.9036.3580.6730.6730.0000.0000.0000.000
73A90LEU0-0.0270.0006.6500.1640.1640.0000.0000.0000.000
74A91GLN00.009-0.00310.0090.1740.1740.0000.0000.0000.000
75A92PHE00.001-0.00413.385-0.087-0.0870.0000.0000.0000.000
76A93THR00.005-0.01915.2650.0890.0890.0000.0000.0000.000
77A94PRO0-0.0080.01918.848-0.023-0.0230.0000.0000.0000.000
78A95GLN0-0.007-0.02920.565-0.009-0.0090.0000.0000.0000.000
79A96HIS0-0.075-0.04422.5400.0380.0380.0000.0000.0000.000
80A97LYS10.8320.91221.7510.4670.4670.0000.0000.0000.000
81A98LEU0-0.002-0.01726.9850.0190.0190.0000.0000.0000.000
82A99LEU0-0.012-0.00329.491-0.015-0.0150.0000.0000.0000.000
83A100ARG10.8680.93731.8760.2150.2150.0000.0000.0000.000
84A101LEU0-0.013-0.01934.501-0.005-0.0050.0000.0000.0000.000
85A102GLN00.0620.04637.4020.0060.0060.0000.0000.0000.000
86A103LEU0-0.006-0.00640.644-0.004-0.0040.0000.0000.0000.000
87A104PRO00.019-0.00642.9060.0030.0030.0000.0000.0000.000
88A105ASN0-0.056-0.01945.4920.0000.0000.0000.0000.0000.000
89A106MET0-0.0050.00945.2820.0010.0010.0000.0000.0000.000
90A107LYS10.9360.98645.2860.1160.1160.0000.0000.0000.000
91A108TYR0-0.004-0.01338.948-0.009-0.0090.0000.0000.0000.000
92A109VAL0-0.0290.00139.2110.0060.0060.0000.0000.0000.000
93A110LYN0-0.0130.00436.035-0.010-0.0100.0000.0000.0000.000
94A111VAL0-0.007-0.00833.6140.0060.0060.0000.0000.0000.000
95A112LYS10.8460.93426.8950.3300.3300.0000.0000.0000.000
96A113VAL00.0190.00829.2880.0080.0080.0000.0000.0000.000
97A114ASN00.0550.03724.421-0.047-0.0470.0000.0000.0000.000
98A115PHE00.022-0.00923.4320.0070.0070.0000.0000.0000.000
99A116SER0-0.068-0.06120.914-0.028-0.0280.0000.0000.0000.000
100A117ASP-1-0.798-0.88322.623-0.340-0.3400.0000.0000.0000.000
101A118ARG10.8800.93924.8630.3120.3120.0000.0000.0000.000
102A119VAL00.0300.00927.1210.0140.0140.0000.0000.0000.000
103A120PHE00.0000.00729.8520.0150.0150.0000.0000.0000.000
104A121LYS10.8470.92329.2140.2970.2970.0000.0000.0000.000
105A122ALA00.0140.00229.4560.0090.0090.0000.0000.0000.000
106A123VAL00.0190.01231.5300.0110.0110.0000.0000.0000.000
107A124SER00.0610.03134.7680.0160.0160.0000.0000.0000.000
108A125ASP-1-0.827-0.90032.394-0.229-0.2290.0000.0000.0000.000
109A126ILE0-0.0010.01633.2400.0080.0080.0000.0000.0000.000
110A127CYS0-0.041-0.02036.6650.0120.0120.0000.0000.0000.000
111A128LYS10.8100.88935.8090.2090.2090.0000.0000.0000.000
112A129THR0-0.042-0.02937.3030.0060.0060.0000.0000.0000.000
113A130PHE0-0.023-0.02038.8200.0050.0050.0000.0000.0000.000
114A131ASN0-0.037-0.01442.5550.0070.0070.0000.0000.0000.000
115A132ILE0-0.035-0.01242.7060.0080.0080.0000.0000.0000.000
116A133ARG10.7840.84643.0880.1060.1060.0000.0000.0000.000
117A134HIS10.7920.88043.2710.1250.1250.0000.0000.0000.000
118A135PRO00.0960.04738.2690.0020.0020.0000.0000.0000.000
119A136GLU-1-0.706-0.82238.700-0.146-0.1460.0000.0000.0000.000
120A137GLU-1-0.757-0.85139.757-0.119-0.1190.0000.0000.0000.000
121A138LEU0-0.048-0.01340.0720.0040.0040.0000.0000.0000.000
122A139SER0-0.013-0.01034.980-0.009-0.0090.0000.0000.0000.000
123A140LEU00.0040.00331.9820.0050.0050.0000.0000.0000.000
124A141LEU00.0080.02134.848-0.004-0.0040.0000.0000.0000.000
125A142LYS10.8660.91427.8120.2670.2670.0000.0000.0000.000
126A143LYS10.8850.92734.6760.1650.1650.0000.0000.0000.000
127A144PRO0-0.0140.01136.417-0.003-0.0030.0000.0000.0000.000
128A160GLU-1-0.969-0.97640.290-0.119-0.1190.0000.0000.0000.000
129A161ASP-1-0.852-0.94442.164-0.129-0.1290.0000.0000.0000.000
130A162GLU-1-0.876-0.92836.452-0.180-0.1800.0000.0000.0000.000
131A163ALA0-0.008-0.00838.747-0.009-0.0090.0000.0000.0000.000
132A164LEU0-0.014-0.00740.2810.0090.0090.0000.0000.0000.000
133A165GLU-1-0.851-0.92338.837-0.183-0.1830.0000.0000.0000.000
134A166LEU0-0.012-0.01839.1110.0050.0050.0000.0000.0000.000
135A167GLU-1-0.891-0.94441.697-0.119-0.1190.0000.0000.0000.000
136A218PRO0-0.013-0.02045.510-0.001-0.0010.0000.0000.0000.000
137A219GLY00.010-0.00447.2500.0020.0020.0000.0000.0000.000
138A220ILE0-0.0110.00244.5340.0040.0040.0000.0000.0000.000
139A221LEU00.0010.02143.0100.0010.0010.0000.0000.0000.000
140A222ALA00.0150.00147.0780.0020.0020.0000.0000.0000.000
141A223VAL0-0.0160.00650.7740.0040.0040.0000.0000.0000.000
142A224SER0-0.068-0.06251.749-0.002-0.0020.0000.0000.0000.000
143A225GLN00.0090.00554.0990.0000.0000.0000.0000.0000.000
144A226PRO00.0060.00855.248-0.002-0.0020.0000.0000.0000.000
145A227VAL00.0300.01553.888-0.001-0.0010.0000.0000.0000.000
146A228THR0-0.005-0.01156.0710.0030.0030.0000.0000.0000.000
147A229SER00.007-0.00157.7350.0020.0020.0000.0000.0000.000
148A230PRO00.0510.00957.601-0.003-0.0030.0000.0000.0000.000
149A231GLU-1-0.861-0.91155.711-0.078-0.0780.0000.0000.0000.000
150A232ILE0-0.008-0.00551.964-0.002-0.0020.0000.0000.0000.000
151A233LEU00.0270.01552.449-0.003-0.0030.0000.0000.0000.000
152A234ALA0-0.004-0.00553.163-0.001-0.0010.0000.0000.0000.000
153A235LYS10.8240.90250.4960.0840.0840.0000.0000.0000.000
154A236MET00.0080.00847.448-0.002-0.0020.0000.0000.0000.000
155A237PHE0-0.0220.00548.781-0.004-0.0040.0000.0000.0000.000
156A238LYS10.8280.90944.6730.1060.1060.0000.0000.0000.000
157A239PRO0-0.030-0.01346.6450.0030.0030.0000.0000.0000.000
158A240GLN00.0490.03047.773-0.006-0.0060.0000.0000.0000.000
159A241ALA00.0220.02049.7350.0020.0020.0000.0000.0000.000
160A242LEU00.0340.00248.406-0.005-0.0050.0000.0000.0000.000
161A243LEU0-0.004-0.00545.599-0.004-0.0040.0000.0000.0000.000
162A244ASP-1-0.843-0.91944.317-0.098-0.0980.0000.0000.0000.000
163A245LYS10.8090.90243.7760.0810.0810.0000.0000.0000.000
164A246ALA0-0.022-0.01042.806-0.007-0.0070.0000.0000.0000.000
165A247LYS10.9430.96539.6990.1080.1080.0000.0000.0000.000
166A248THR0-0.028-0.01938.984-0.009-0.0090.0000.0000.0000.000
167A249ASN00.000-0.00938.741-0.013-0.0130.0000.0000.0000.000
168A250GLN0-0.071-0.05135.581-0.007-0.0070.0000.0000.0000.000
169A251GLY00.0010.00834.118-0.011-0.0110.0000.0000.0000.000
170A252TRP0-0.043-0.03534.236-0.012-0.0120.0000.0000.0000.000
171A253LEU0-0.032-0.01529.431-0.008-0.0080.0000.0000.0000.000
172A254ASP-1-0.737-0.83527.480-0.263-0.2630.0000.0000.0000.000
173A255SER00.006-0.04928.889-0.017-0.0170.0000.0000.0000.000
174A256SER0-0.069-0.04727.836-0.007-0.0070.0000.0000.0000.000
175A257ARG10.7890.89022.8140.3290.3290.0000.0000.0000.000
176A258SER0-0.007-0.02321.9620.0130.0130.0000.0000.0000.000
177A259LEU00.0280.00924.6030.0030.0030.0000.0000.0000.000
178A260MET00.0050.02219.4300.0150.0150.0000.0000.0000.000
179A261GLU-1-0.821-0.87619.786-0.465-0.4650.0000.0000.0000.000
180A262GLN0-0.053-0.01621.5210.0370.0370.0000.0000.0000.000
181A263ASP-1-0.813-0.87723.053-0.344-0.3440.0000.0000.0000.000
182A264VAL00.0250.03024.7960.0320.0320.0000.0000.0000.000
183A265LYS10.8010.88221.0160.3990.3990.0000.0000.0000.000
184A266GLU-1-0.817-0.91225.090-0.361-0.3610.0000.0000.0000.000
185A267ASN0-0.054-0.03426.8770.0210.0210.0000.0000.0000.000
186A268GLU-1-0.803-0.88027.972-0.277-0.2770.0000.0000.0000.000
187A269ALA00.011-0.00231.1420.0030.0030.0000.0000.0000.000
188A270LEU0-0.060-0.02030.738-0.003-0.0030.0000.0000.0000.000
189A271LEU0-0.0010.00535.0630.0070.0070.0000.0000.0000.000
190A272LEU0-0.0050.00437.537-0.005-0.0050.0000.0000.0000.000
191A273ARG10.8330.90239.1110.1500.1500.0000.0000.0000.000
192A274PHE00.004-0.01240.811-0.007-0.0070.0000.0000.0000.000
193A275LYS10.8450.94534.7430.1910.1910.0000.0000.0000.000
194A276TYR0-0.043-0.03337.5060.0020.0020.0000.0000.0000.000
195A277TYR00.0230.01343.4950.0020.0020.0000.0000.0000.000
196A278SER0-0.063-0.05046.5840.0070.0070.0000.0000.0000.000
197A279PHE00.0020.00746.473-0.002-0.0020.0000.0000.0000.000
198A280PHE00.0120.01747.7930.0050.0050.0000.0000.0000.000
199A281ASP-1-0.815-0.90149.554-0.102-0.1020.0000.0000.0000.000
200A282LEU00.0350.01750.490-0.002-0.0020.0000.0000.0000.000
201A283ASN00.000-0.01052.7220.0060.0060.0000.0000.0000.000
202A284PRO00.0670.01754.125-0.003-0.0030.0000.0000.0000.000
203A285LYS10.9130.97255.9950.0800.0800.0000.0000.0000.000
204A286TYR0-0.017-0.01351.0300.0000.0000.0000.0000.0000.000
205A287ASP-1-0.761-0.83049.531-0.114-0.1140.0000.0000.0000.000
206A288ALA00.0260.02051.2530.0000.0000.0000.0000.0000.000
207A289ILE00.0240.01546.3790.0020.0020.0000.0000.0000.000
208A290ARG10.7670.85346.9560.1150.1150.0000.0000.0000.000
209A291ILE00.016-0.00148.3980.0000.0000.0000.0000.0000.000
210A292ASN0-0.020-0.00250.1830.0060.0060.0000.0000.0000.000
211A293GLN00.045-0.01145.9450.0010.0010.0000.0000.0000.000
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