Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52RQZ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2116283.757594
FMO2-HF: Nuclear repulsion 2038678.574435
FMO2-HF: Total energy -77605.183159
FMO2-MP2: Total energy -77830.339006


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.
48.85449.6967.128-2.894-5.077-0.029
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 : 0.950 / q_NPA : 0.967
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].
3A138ARG10.9600.9882.89836.19638.7620.120-1.144-1.5420.002
4A139VAL00.0080.0105.4893.4333.4330.0000.0000.0000.000
5A140ALA00.0080.0179.0950.0450.0450.0000.0000.0000.000
6A141LEU00.004-0.00911.4420.4050.4050.0000.0000.0000.000
7A142SER00.0230.01515.2970.5270.5270.0000.0000.0000.000
8A143ASN00.007-0.01418.0090.2130.2130.0000.0000.0000.000
9A144HIS00.0300.02916.8140.9260.9260.0000.0000.0000.000
10A145LEU00.0810.04020.3440.2230.2230.0000.0000.0000.000
11A146LEU00.011-0.00123.5310.4140.4140.0000.0000.0000.000
12A147TRP00.0190.00221.2150.4360.4360.0000.0000.0000.000
13A148SER0-0.021-0.01022.6510.1660.1660.0000.0000.0000.000
14A149LYS10.8210.90125.0899.8529.8520.0000.0000.0000.000
15A150PHE0-0.027-0.02127.6280.3950.3950.0000.0000.0000.000
16A151ASN00.0310.01424.6630.4050.4050.0000.0000.0000.000
17A152GLN0-0.011-0.01027.5940.4230.4230.0000.0000.0000.000
18A153HIS10.8050.91229.8129.4699.4690.0000.0000.0000.000
19A154GLN00.0060.00630.8210.4520.4520.0000.0000.0000.000
20A155THR00.0450.01927.4130.3240.3240.0000.0000.0000.000
21A156GLU-1-0.681-0.81230.516-8.568-8.5680.0000.0000.0000.000
22A157MET0-0.055-0.01627.2950.0790.0790.0000.0000.0000.000
23A158ILE00.0220.02232.4800.0890.0890.0000.0000.0000.000
24A159ILE0-0.0050.00333.464-0.193-0.1930.0000.0000.0000.000
25A160THR0-0.026-0.04035.9930.2880.2880.0000.0000.0000.000
26A161LYS11.0441.03937.5676.9716.9710.0000.0000.0000.000
27A162GLN00.0040.00638.633-0.252-0.2520.0000.0000.0000.000
28A163GLY00.0340.01234.911-0.140-0.1400.0000.0000.0000.000
29A164ARG10.8890.94934.1138.2078.2070.0000.0000.0000.000
30A165ARG10.9030.95229.6919.3649.3640.0000.0000.0000.000
31A166MET00.0070.01324.0040.0810.0810.0000.0000.0000.000
32A167PHE0-0.009-0.00428.5000.0490.0490.0000.0000.0000.000
33A168PRO00.0790.04125.1940.3470.3470.0000.0000.0000.000
34A169PHE00.005-0.00123.991-0.119-0.1190.0000.0000.0000.000
35A170LEU00.0430.02518.336-0.109-0.1090.0000.0000.0000.000
36A171SER0-0.012-0.02119.0580.4840.4840.0000.0000.0000.000
37A172PHE0-0.038-0.01313.0200.2320.2320.0000.0000.0000.000
38A173THR00.0580.03611.5190.7790.7790.0000.0000.0000.000
39A174VAL00.0160.0097.763-0.883-0.8830.0000.0000.0000.000
40A175ALA00.0470.0256.0841.3381.3380.0000.0000.0000.000
41A176GLY0-0.027-0.0132.357-0.219-1.1443.978-1.840-1.2130.003
42A177LEU0-0.0010.0202.369-11.883-12.7263.0310.095-2.284-0.034
43A178GLU-1-0.804-0.8765.019-26.046-26.002-0.001-0.005-0.0380.000
44A179PRO00.001-0.0168.0551.1971.1970.0000.0000.0000.000
45A180THR00.0470.01011.1240.8050.8050.0000.0000.0000.000
46A181SER00.0200.02410.2661.6921.6920.0000.0000.0000.000
47A182HIS0-0.007-0.01712.4200.6910.6910.0000.0000.0000.000
48A183TYR0-0.017-0.0108.031-1.417-1.4170.0000.0000.0000.000
49A184ARG10.9160.95413.20316.12116.1210.0000.0000.0000.000
50A185MET0-0.0180.02010.493-0.836-0.8360.0000.0000.0000.000
51A186PHE00.0320.00115.4031.3831.3830.0000.0000.0000.000
52A187VAL0-0.0020.01917.223-0.998-0.9980.0000.0000.0000.000
53A188ASP-1-0.764-0.84219.553-14.952-14.9520.0000.0000.0000.000
54A189VAL0-0.006-0.01421.242-0.346-0.3460.0000.0000.0000.000
55A190VAL00.0150.02321.6090.4730.4730.0000.0000.0000.000
56A191LEU0-0.032-0.01424.3490.0550.0550.0000.0000.0000.000
57A192VAL0-0.044-0.02424.411-0.167-0.1670.0000.0000.0000.000
58A193ASP-1-0.849-0.94526.627-10.370-10.3700.0000.0000.0000.000
59A194GLN0-0.018-0.02028.8500.2410.2410.0000.0000.0000.000
60A195HIS0-0.0150.00632.7890.4780.4780.0000.0000.0000.000
61A196HIS00.0080.01635.190-0.214-0.2140.0000.0000.0000.000
62A197TRP00.009-0.00732.808-0.132-0.1320.0000.0000.0000.000
63A198ARG10.9070.92837.8767.3107.3100.0000.0000.0000.000
64A199TYR00.0460.02939.099-0.044-0.0440.0000.0000.0000.000
65A200GLN00.0510.02041.5090.2080.2080.0000.0000.0000.000
66A201SER00.0120.00243.534-0.102-0.1020.0000.0000.0000.000
67A202GLY00.0600.04542.597-0.004-0.0040.0000.0000.0000.000
68A203LYS10.9150.96437.2588.0618.0610.0000.0000.0000.000
69A204TRP0-0.027-0.01836.1310.0940.0940.0000.0000.0000.000
70A205VAL0-0.041-0.02537.571-0.146-0.1460.0000.0000.0000.000
71A206GLN00.0410.02934.3380.1310.1310.0000.0000.0000.000
72A207CYS0-0.049-0.03638.3580.3370.3370.0000.0000.0000.000
73A208GLY00.0070.00640.315-0.146-0.1460.0000.0000.0000.000
74A209LYS10.9750.97839.4987.6667.6660.0000.0000.0000.000
75A210ALA0-0.0020.00135.759-0.048-0.0480.0000.0000.0000.000
76A211GLU-1-0.801-0.88936.635-8.456-8.4560.0000.0000.0000.000
77A212GLY0-0.0150.00033.883-0.007-0.0070.0000.0000.0000.000
78A213SER0-0.085-0.05434.594-0.073-0.0730.0000.0000.0000.000
79A214MET00.0110.00627.7770.0850.0850.0000.0000.0000.000
80A215PRO00.0900.03726.8220.1220.1220.0000.0000.0000.000
81A216GLY0-0.066-0.02827.525-0.287-0.2870.0000.0000.0000.000
82A217ASN00.049-0.00222.876-0.245-0.2450.0000.0000.0000.000
83A218ARG10.8970.94526.29410.55410.5540.0000.0000.0000.000
84A219LEU00.0490.03421.756-0.205-0.2050.0000.0000.0000.000
85A220TYR0-0.027-0.00822.7980.5720.5720.0000.0000.0000.000
86A221VAL00.0190.00520.431-0.755-0.7550.0000.0000.0000.000
87A222HIS0-0.024-0.00618.9710.3840.3840.0000.0000.0000.000
88A223PRO0-0.033-0.03920.915-0.024-0.0240.0000.0000.0000.000
89A224ASP-1-0.854-0.90220.079-12.036-12.0360.0000.0000.0000.000
90A225SER0-0.020-0.00218.135-0.827-0.8270.0000.0000.0000.000
91A226PRO0-0.021-0.02817.2990.5460.5460.0000.0000.0000.000
92A227ASN00.013-0.00316.0340.6270.6270.0000.0000.0000.000
93A228THR00.0660.02514.297-1.002-1.0020.0000.0000.0000.000
94A229GLY00.037-0.00310.472-0.118-0.1180.0000.0000.0000.000
95A230ALA0-0.018-0.01511.170-0.133-0.1330.0000.0000.0000.000
96A231HIS00.0160.00913.2790.4750.4750.0000.0000.0000.000
97A232TRP0-0.006-0.01511.4160.8140.8140.0000.0000.0000.000
98A233MET0-0.063-0.0288.210-0.623-0.6230.0000.0000.0000.000
99A234ARG10.8080.91811.84714.29914.2990.0000.0000.0000.000
100A235GLN0-0.019-0.01415.3760.5520.5520.0000.0000.0000.000
101A236GLU-1-0.896-0.93415.862-13.302-13.3020.0000.0000.0000.000
102A237VAL00.0220.03813.6750.2100.2100.0000.0000.0000.000
103A238SER0-0.031-0.03816.9740.0420.0420.0000.0000.0000.000
104A239PHE00.0610.01717.3220.3640.3640.0000.0000.0000.000
105A240GLY00.0420.02322.5380.3970.3970.0000.0000.0000.000
106A241LYS10.9020.93325.81210.77110.7710.0000.0000.0000.000
107A242LEU00.0040.03223.6610.2990.2990.0000.0000.0000.000
108A243LYS10.8450.92227.1368.9708.9700.0000.0000.0000.000
109A244LEU00.0520.02928.053-0.220-0.2200.0000.0000.0000.000
110A245THR00.015-0.01131.8110.3960.3960.0000.0000.0000.000
111A246ASN00.0290.01534.776-0.185-0.1850.0000.0000.0000.000
112A247ASN0-0.029-0.02937.2580.3430.3430.0000.0000.0000.000
113A248LYS11.0020.99535.0988.7218.7210.0000.0000.0000.000
114A249GLY00.0300.02637.028-0.139-0.1390.0000.0000.0000.000
115A250ALA0-0.005-0.00735.7210.2210.2210.0000.0000.0000.000
116A251SER00.0290.00737.511-0.049-0.0490.0000.0000.0000.000
117A252ASN0-0.023-0.00838.943-0.122-0.1220.0000.0000.0000.000
118A253ASN00.0010.00833.626-0.355-0.3550.0000.0000.0000.000
119A254VAL00.0380.02634.9440.0370.0370.0000.0000.0000.000
120A255THR0-0.023-0.02433.801-0.013-0.0130.0000.0000.0000.000
121A256GLN0-0.029-0.01125.007-0.027-0.0270.0000.0000.0000.000
122A257MET00.0010.00029.181-0.183-0.1830.0000.0000.0000.000
123A258ILE00.0200.00925.2490.1140.1140.0000.0000.0000.000
124A259VAL0-0.063-0.02529.7830.2360.2360.0000.0000.0000.000
125A260LEU00.002-0.00228.787-0.286-0.2860.0000.0000.0000.000
126A261GLN00.0140.02032.7660.2970.2970.0000.0000.0000.000
127A262SER00.014-0.01834.657-0.213-0.2130.0000.0000.0000.000
128A263LEU0-0.0040.01037.0710.0340.0340.0000.0000.0000.000
129A264HIS10.7970.88232.8638.9998.9990.0000.0000.0000.000
130A265LYS10.9310.98729.09210.62210.6220.0000.0000.0000.000
131A266TYR00.0010.01026.9650.1160.1160.0000.0000.0000.000
132A267GLN00.0640.01820.332-0.228-0.2280.0000.0000.0000.000
133A268PRO0-0.050-0.01320.721-0.147-0.1470.0000.0000.0000.000
134A269ARG10.8490.89716.82615.59215.5920.0000.0000.0000.000
135A270LEU0-0.0170.00413.1120.9120.9120.0000.0000.0000.000
136A271HIS10.7930.89013.06016.78716.7870.0000.0000.0000.000
137A272ILE00.0070.0017.2461.3991.3990.0000.0000.0000.000
138A273VAL00.0260.02310.296-1.909-1.9090.0000.0000.0000.000
139A274GLU-1-0.807-0.9086.767-37.073-37.0730.0000.0000.0000.000
140A275VAL0-0.073-0.03311.2070.5550.5550.0000.0000.0000.000
141A276ASN00.007-0.01612.960-0.258-0.2580.0000.0000.0000.000
142A277ASP-1-0.890-0.92415.020-15.693-15.6930.0000.0000.0000.000
143A278GLY00.0460.00017.970-0.163-0.1630.0000.0000.0000.000
144A279GLU-1-1.000-0.98818.729-14.359-14.3590.0000.0000.0000.000
145A280PRO0-0.0040.01920.0310.6810.6810.0000.0000.0000.000
146A281GLU-1-0.907-0.95621.556-12.653-12.6530.0000.0000.0000.000
147A282ALA0-0.065-0.04919.8320.1050.1050.0000.0000.0000.000
148A283ALA0-0.034-0.02215.414-1.026-1.0260.0000.0000.0000.000
149A284CYS0-0.0330.01115.3950.6010.6010.0000.0000.0000.000
150A285SER0-0.023-0.01314.3160.6110.6110.0000.0000.0000.000
151A286ALA0-0.034-0.02311.198-1.839-1.8390.0000.0000.0000.000
152A287SER00.0580.02911.4641.6121.6120.0000.0000.0000.000
153A288ASN0-0.065-0.0478.056-2.115-2.1150.0000.0000.0000.000
154A289THR0-0.008-0.01510.1651.9541.9540.0000.0000.0000.000
155A290HIS00.0120.0315.4512.0812.0810.0000.0000.0000.000
156A291VAL0-0.046-0.04910.0532.9582.9580.0000.0000.0000.000
157A292PHE00.0170.0206.775-0.926-0.9260.0000.0000.0000.000
158A293THR0-0.021-0.02312.8921.5731.5730.0000.0000.0000.000
159A294PHE00.0450.03113.103-0.515-0.5150.0000.0000.0000.000
160A295GLN00.0370.04017.9910.6070.6070.0000.0000.0000.000
161A296GLU-1-0.883-0.95618.150-15.607-15.6070.0000.0000.0000.000
162A297THR0-0.058-0.06620.1810.5120.5120.0000.0000.0000.000
163A298GLN0-0.010-0.00622.8870.2760.2760.0000.0000.0000.000
164A299PHE0-0.046-0.02625.2770.3370.3370.0000.0000.0000.000
165A300ILE00.0160.01328.798-0.099-0.0990.0000.0000.0000.000
166A301ALA0-0.0040.01232.1730.0910.0910.0000.0000.0000.000
167A302VAL00.012-0.00133.5360.2200.2200.0000.0000.0000.000
168A303THR00.0240.00337.147-0.074-0.0740.0000.0000.0000.000
169A304ALA00.0020.00140.0550.1020.1020.0000.0000.0000.000
170A305TYR0-0.011-0.00334.753-0.194-0.1940.0000.0000.0000.000
171A306GLN0-0.079-0.03839.0420.3030.3030.0000.0000.0000.000
172A307ASN00.019-0.00336.3950.3870.3870.0000.0000.0000.000
173A308ALA00.0520.01838.733-0.110-0.1100.0000.0000.0000.000
174A309GLU-1-0.799-0.89035.885-8.534-8.5340.0000.0000.0000.000
175A310ILE0-0.0010.01232.320-0.149-0.1490.0000.0000.0000.000
176A311THR0-0.042-0.03135.571-0.084-0.0840.0000.0000.0000.000
177A312GLN00.0400.03138.079-0.029-0.0290.0000.0000.0000.000
178A313LEU00.0370.02232.526-0.028-0.0280.0000.0000.0000.000
179A314LYS10.7830.89231.6219.3329.3320.0000.0000.0000.000
180A315ILE00.0080.02034.537-0.084-0.0840.0000.0000.0000.000
181A316ASP-1-0.802-0.90033.602-8.773-8.7730.0000.0000.0000.000
182A317ASN0-0.036-0.01630.256-0.292-0.2920.0000.0000.0000.000
183A318ASN0-0.016-0.00431.492-0.040-0.0400.0000.0000.0000.000
184A319PRO00.0250.00831.6750.2600.2600.0000.0000.0000.000
185A320PHE0-0.003-0.00732.2070.1530.1530.0000.0000.0000.000
186A321ALA0-0.0190.00436.7240.2080.2080.0000.0000.0000.000
187A322LYS10.8240.88135.0458.4328.4320.0000.0000.0000.000
188A323GLY00.0060.01639.8910.1110.1110.0000.0000.0000.000
189A324PHE0-0.026-0.00641.9430.1250.1250.0000.0000.0000.000
190A325ARG10.8650.91838.6157.5767.5760.0000.0000.0000.000
191A326GLU-1-0.891-0.94042.703-6.316-6.3160.0000.0000.0000.000
192A327ASN0-0.046-0.01145.2200.1630.1630.0000.0000.0000.000