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: 49QKN

Calculation Name: 5T1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JKD8

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 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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115667.473225
FMO2-HF: Nuclear repulsion 2038063.951367
FMO2-HF: Total energy -77603.521857
FMO2-MP2: Total energy -77828.891681


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:136:LYS)


Summations of interaction energy for fragment #1(A:136:LYS)
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.
45.7149.4482.791-2.376-4.153-0.012
Interaction energy analysis for fragmet #1(A:136:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.964
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].
3A138ARG10.9640.9943.16333.27236.1960.026-1.303-1.6470.002
4A139VAL00.0380.0205.8122.3662.487-0.001-0.007-0.1130.000
5A140ALA0-0.0020.0209.3480.4570.4570.0000.0000.0000.000
6A141LEU00.0390.00111.8840.3710.3710.0000.0000.0000.000
7A142SER00.0450.02415.6660.5260.5260.0000.0000.0000.000
8A143ASN00.010-0.01818.2990.2150.2150.0000.0000.0000.000
9A144HIS00.0340.03317.0400.7340.7340.0000.0000.0000.000
10A145LEU00.0700.02320.2240.2270.2270.0000.0000.0000.000
11A146LEU0-0.008-0.01823.4250.3300.3300.0000.0000.0000.000
12A147TRP00.0370.01721.5780.4830.4830.0000.0000.0000.000
13A148SER00.0240.01422.6160.1210.1210.0000.0000.0000.000
14A149LYS10.8670.94125.04710.05810.0580.0000.0000.0000.000
15A150PHE0-0.020-0.02527.7020.3490.3490.0000.0000.0000.000
16A151ASN0-0.0150.01124.9750.3260.3260.0000.0000.0000.000
17A152GLN00.013-0.00527.7810.4040.4040.0000.0000.0000.000
18A153HIS10.8080.91230.0269.3419.3410.0000.0000.0000.000
19A154GLN00.000-0.00330.9560.4440.4440.0000.0000.0000.000
20A155THR00.0630.03727.5250.3130.3130.0000.0000.0000.000
21A156GLU-1-0.752-0.88930.691-8.486-8.4860.0000.0000.0000.000
22A157MET0-0.0470.00427.1670.1440.1440.0000.0000.0000.000
23A158ILE00.0140.02032.3630.0930.0930.0000.0000.0000.000
24A159ILE0-0.0020.00333.267-0.141-0.1410.0000.0000.0000.000
25A160THR0-0.056-0.05535.8040.3080.3080.0000.0000.0000.000
26A161LYS11.0261.02537.6707.0247.0240.0000.0000.0000.000
27A162GLN00.0110.01338.810-0.162-0.1620.0000.0000.0000.000
28A163GLY00.0390.01135.438-0.168-0.1680.0000.0000.0000.000
29A164ARG10.8800.93833.9358.2918.2910.0000.0000.0000.000
30A165ARG10.9711.00429.4009.2269.2260.0000.0000.0000.000
31A166MET0-0.0070.00224.0440.1300.1300.0000.0000.0000.000
32A167PHE0-0.0300.00128.3230.0100.0100.0000.0000.0000.000
33A168PRO00.0540.03125.3920.3020.3020.0000.0000.0000.000
34A169PHE00.009-0.00824.031-0.310-0.3100.0000.0000.0000.000
35A170LEU00.0490.02618.446-0.077-0.0770.0000.0000.0000.000
36A171SER0-0.026-0.03419.0750.2600.2600.0000.0000.0000.000
37A172PHE0-0.065-0.02513.2400.2820.2820.0000.0000.0000.000
38A173THR00.0630.04411.5920.6890.6890.0000.0000.0000.000
39A174VAL00.0340.0168.067-0.944-0.9440.0000.0000.0000.000
40A175ALA00.0370.0136.1771.3891.3890.0000.0000.0000.000
41A176GLY0-0.065-0.0412.432-2.137-2.4712.577-1.427-0.8160.004
42A177LEU0-0.0250.0092.838-8.963-7.9360.1890.361-1.577-0.018
43A178GLU-1-0.814-0.9025.562-28.001-28.0010.0000.0000.0000.000
44A179PRO00.005-0.0128.2880.9810.9810.0000.0000.0000.000
45A180THR00.0470.00711.6660.7820.7820.0000.0000.0000.000
46A181SER00.0060.0299.9201.4541.4540.0000.0000.0000.000
47A182HIS00.010-0.00712.1740.8910.8910.0000.0000.0000.000
48A183TYR0-0.0120.0027.651-0.955-0.9550.0000.0000.0000.000
49A184ARG10.9650.96612.98016.66116.6610.0000.0000.0000.000
50A185MET0-0.0100.01911.199-0.843-0.8430.0000.0000.0000.000
51A186PHE00.0250.00415.8661.3911.3910.0000.0000.0000.000
52A187VAL0-0.035-0.01617.266-0.946-0.9460.0000.0000.0000.000
53A188ASP-1-0.800-0.87819.432-14.963-14.9630.0000.0000.0000.000
54A189VAL0-0.013-0.00120.969-0.420-0.4200.0000.0000.0000.000
55A190VAL00.0290.02421.0300.4500.4500.0000.0000.0000.000
56A191LEU0-0.030-0.02123.8480.1200.1200.0000.0000.0000.000
57A192VAL0-0.056-0.02524.571-0.089-0.0890.0000.0000.0000.000
58A193ASP-1-0.841-0.92626.505-10.477-10.4770.0000.0000.0000.000
59A194GLN0-0.019-0.03729.0020.2830.2830.0000.0000.0000.000
60A195HIS0-0.0400.00732.6820.4370.4370.0000.0000.0000.000
61A196HIS00.0290.02334.828-0.212-0.2120.0000.0000.0000.000
62A197TRP0-0.006-0.02132.834-0.151-0.1510.0000.0000.0000.000
63A198ARG10.9360.94238.0217.3397.3390.0000.0000.0000.000
64A199TYR00.0480.02838.781-0.024-0.0240.0000.0000.0000.000
65A200GLN00.0450.02441.7740.0730.0730.0000.0000.0000.000
66A201SER00.003-0.01143.155-0.141-0.1410.0000.0000.0000.000
67A202GLY00.0490.04142.208-0.023-0.0230.0000.0000.0000.000
68A203LYS10.9370.96537.9477.9537.9530.0000.0000.0000.000
69A204TRP0-0.024-0.00236.0300.0550.0550.0000.0000.0000.000
70A205VAL0-0.042-0.02337.634-0.140-0.1400.0000.0000.0000.000
71A206GLN00.0510.03234.0070.1580.1580.0000.0000.0000.000
72A207CYS0-0.043-0.02138.4020.3620.3620.0000.0000.0000.000
73A208GLY0-0.0020.00840.095-0.160-0.1600.0000.0000.0000.000
74A209LYS10.9840.97339.3857.6677.6670.0000.0000.0000.000
75A210ALA00.0000.00435.5740.0240.0240.0000.0000.0000.000
76A211GLU-1-0.815-0.89036.293-8.504-8.5040.0000.0000.0000.000
77A212GLY00.0080.00333.814-0.073-0.0730.0000.0000.0000.000
78A213SER0-0.119-0.06434.622-0.056-0.0560.0000.0000.0000.000
79A214MET0-0.008-0.02028.090-0.007-0.0070.0000.0000.0000.000
80A215PRO00.0460.02226.1840.1830.1830.0000.0000.0000.000
81A216GLY0-0.035-0.00927.028-0.268-0.2680.0000.0000.0000.000
82A217ASN00.1080.04222.592-0.214-0.2140.0000.0000.0000.000
83A218ARG10.8820.93725.96410.64810.6480.0000.0000.0000.000
84A219LEU00.0410.02521.805-0.123-0.1230.0000.0000.0000.000
85A220TYR0-0.025-0.00922.5940.5840.5840.0000.0000.0000.000
86A221VAL00.0180.00720.178-0.748-0.7480.0000.0000.0000.000
87A222HIS0-0.0180.00318.9920.5880.5880.0000.0000.0000.000
88A223PRO0-0.043-0.03921.0600.0480.0480.0000.0000.0000.000
89A224ASP-1-0.867-0.91720.725-11.841-11.8410.0000.0000.0000.000
90A225SER0-0.0360.00618.358-1.109-1.1090.0000.0000.0000.000
91A226PRO0-0.036-0.03717.4540.5220.5220.0000.0000.0000.000
92A227ASN00.0290.00916.5580.6130.6130.0000.0000.0000.000
93A228THR00.0230.00814.632-1.006-1.0060.0000.0000.0000.000
94A229GLY00.0700.00210.888-0.111-0.1110.0000.0000.0000.000
95A230ALA0-0.016-0.00311.498-0.232-0.2320.0000.0000.0000.000
96A231HIS00.0170.00713.1060.4170.4170.0000.0000.0000.000
97A232TRP0-0.014-0.01911.4630.8040.8040.0000.0000.0000.000
98A233MET0-0.047-0.0348.268-0.320-0.3200.0000.0000.0000.000
99A234ARG10.7840.91811.80614.50114.5010.0000.0000.0000.000
100A235GLN0-0.012-0.00615.5600.4620.4620.0000.0000.0000.000
101A236GLU-1-0.899-0.95315.938-12.777-12.7770.0000.0000.0000.000
102A237VAL00.0260.05114.0660.1490.1490.0000.0000.0000.000
103A238SER0-0.025-0.02317.348-0.001-0.0010.0000.0000.0000.000
104A239PHE00.0410.00117.1530.1940.1940.0000.0000.0000.000
105A240GLY00.011-0.00122.4190.3420.3420.0000.0000.0000.000
106A241LYS10.8950.93025.66610.54110.5410.0000.0000.0000.000
107A242LEU00.0070.03923.6510.3750.3750.0000.0000.0000.000
108A243LYS10.9360.96127.1629.1439.1430.0000.0000.0000.000
109A244LEU00.002-0.00128.055-0.199-0.1990.0000.0000.0000.000
110A245THR00.016-0.00431.8880.3740.3740.0000.0000.0000.000
111A246ASN00.0500.02434.714-0.166-0.1660.0000.0000.0000.000
112A247ASN0-0.021-0.01437.2430.2900.2900.0000.0000.0000.000
113A248LYS11.0060.99934.9818.6778.6770.0000.0000.0000.000
114A249GLY00.0320.02537.035-0.071-0.0710.0000.0000.0000.000
115A250ALA0-0.044-0.02535.7770.1910.1910.0000.0000.0000.000
116A251SER00.0150.00037.497-0.021-0.0210.0000.0000.0000.000
117A252ASN0-0.006-0.01138.614-0.120-0.1200.0000.0000.0000.000
118A253ASN0-0.034-0.01233.529-0.203-0.2030.0000.0000.0000.000
119A254VAL00.0930.05434.8100.0990.0990.0000.0000.0000.000
120A255THR0-0.033-0.01733.644-0.004-0.0040.0000.0000.0000.000
121A256GLN0-0.0010.01525.312-0.033-0.0330.0000.0000.0000.000
122A257MET0-0.026-0.02029.039-0.223-0.2230.0000.0000.0000.000
123A258ILE00.0130.00824.9480.1670.1670.0000.0000.0000.000
124A259VAL0-0.030-0.01229.4190.3020.3020.0000.0000.0000.000
125A260LEU0-0.045-0.03328.614-0.214-0.2140.0000.0000.0000.000
126A261GLN00.0390.03132.6520.3740.3740.0000.0000.0000.000
127A262SER0-0.007-0.02334.653-0.209-0.2090.0000.0000.0000.000
128A263LEU0-0.0070.00136.6310.0110.0110.0000.0000.0000.000
129A264HIS10.8260.89132.5659.0299.0290.0000.0000.0000.000
130A265LYS10.9330.98828.83510.48110.4810.0000.0000.0000.000
131A266TYR00.0030.01727.0300.0430.0430.0000.0000.0000.000
132A267GLN00.0500.00120.759-0.169-0.1690.0000.0000.0000.000
133A268PRO0-0.049-0.00420.959-0.174-0.1740.0000.0000.0000.000
134A269ARG10.8660.90416.72015.82315.8230.0000.0000.0000.000
135A270LEU0-0.0120.00013.1140.8340.8340.0000.0000.0000.000
136A271HIS10.8190.91112.88016.74116.7410.0000.0000.0000.000
137A272ILE00.0110.0057.4641.5181.5180.0000.0000.0000.000
138A273VAL00.0100.02710.331-1.846-1.8460.0000.0000.0000.000
139A274GLU-1-0.849-0.9336.984-36.295-36.2950.0000.0000.0000.000
140A275VAL0-0.063-0.03211.7630.1160.1160.0000.0000.0000.000
141A276ASN0-0.0050.00113.0270.1220.1220.0000.0000.0000.000
142A277ASP-1-0.860-0.91814.744-15.634-15.6340.0000.0000.0000.000
143A278GLY00.020-0.00217.233-0.475-0.4750.0000.0000.0000.000
144A279GLU-1-0.984-1.00018.685-14.552-14.5520.0000.0000.0000.000
145A280PRO0-0.049-0.00519.5020.4750.4750.0000.0000.0000.000
146A281GLU-1-0.884-0.94022.473-12.255-12.2550.0000.0000.0000.000
147A282ALA0-0.043-0.03319.7410.1240.1240.0000.0000.0000.000
148A283ALA0-0.061-0.03715.530-1.145-1.1450.0000.0000.0000.000
149A284CYS0-0.0270.02615.4630.6870.6870.0000.0000.0000.000
150A285SER0-0.002-0.01613.9070.5840.5840.0000.0000.0000.000
151A286ALA0-0.003-0.03110.961-1.782-1.7820.0000.0000.0000.000
152A287SER00.0170.02611.6221.4111.4110.0000.0000.0000.000
153A288ASN0-0.056-0.0337.657-1.448-1.4480.0000.0000.0000.000
154A289THR00.0010.0019.3862.3132.3130.0000.0000.0000.000
155A290HIS00.0430.0255.1801.2491.2490.0000.0000.0000.000
156A291VAL0-0.050-0.04810.2422.9832.9830.0000.0000.0000.000
157A292PHE00.0200.0156.795-0.902-0.9020.0000.0000.0000.000
158A293THR0-0.024-0.01812.7601.6311.6310.0000.0000.0000.000
159A294PHE00.0250.00813.476-0.433-0.4330.0000.0000.0000.000
160A295GLN00.0550.04618.0940.3910.3910.0000.0000.0000.000
161A296GLU-1-0.911-0.95918.429-15.224-15.2240.0000.0000.0000.000
162A297THR0-0.044-0.05720.3520.2900.2900.0000.0000.0000.000
163A298GLN0-0.013-0.00523.199-0.076-0.0760.0000.0000.0000.000
164A299PHE0-0.039-0.03025.6030.2890.2890.0000.0000.0000.000
165A300ILE00.0440.02729.081-0.081-0.0810.0000.0000.0000.000
166A301ALA0-0.0340.00932.3330.0410.0410.0000.0000.0000.000
167A302VAL00.0350.01633.8050.2370.2370.0000.0000.0000.000
168A303THR00.016-0.00737.216-0.147-0.1470.0000.0000.0000.000
169A304ALA00.0180.00139.9920.1140.1140.0000.0000.0000.000
170A305TYR0-0.044-0.01435.120-0.156-0.1560.0000.0000.0000.000
171A306GLN0-0.047-0.02739.0310.2920.2920.0000.0000.0000.000
172A307ASN00.0090.00136.8610.3760.3760.0000.0000.0000.000
173A308ALA00.0440.01639.434-0.070-0.0700.0000.0000.0000.000
174A309GLU-1-0.798-0.88235.918-8.411-8.4110.0000.0000.0000.000
175A310ILE00.0080.02532.524-0.129-0.1290.0000.0000.0000.000
176A311THR0-0.007-0.01335.854-0.094-0.0940.0000.0000.0000.000
177A312GLN00.0330.02738.2640.0320.0320.0000.0000.0000.000
178A313LEU00.0360.01832.387-0.068-0.0680.0000.0000.0000.000
179A314LYS10.7720.88831.2919.3589.3580.0000.0000.0000.000
180A315ILE00.0250.02734.545-0.106-0.1060.0000.0000.0000.000
181A316ASP-1-0.832-0.91134.534-8.562-8.5620.0000.0000.0000.000
182A317ASN0-0.037-0.03030.719-0.322-0.3220.0000.0000.0000.000
183A318ASN0-0.021-0.00331.796-0.132-0.1320.0000.0000.0000.000
184A319PRO00.0370.01331.8590.2740.2740.0000.0000.0000.000
185A320PHE0-0.041-0.01632.2080.1010.1010.0000.0000.0000.000
186A321ALA0-0.040-0.02737.0660.1940.1940.0000.0000.0000.000
187A322LYS10.8250.89135.5198.2598.2590.0000.0000.0000.000
188A323GLY00.0180.02340.4660.1220.1220.0000.0000.0000.000
189A324PHE0-0.037-0.01642.3480.1130.1130.0000.0000.0000.000
190A325ARG10.9140.92739.0377.4717.4710.0000.0000.0000.000
191A326GLU-1-0.929-0.94343.252-6.316-6.3160.0000.0000.0000.000
192A327ASN0-0.028-0.00345.5490.2170.2170.0000.0000.0000.000