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: 1N64Z

Calculation Name: 5V89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V89

Chain ID: A

ChEMBL ID:

UniProt ID: Q13616

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2202470.698429
FMO2-HF: Nuclear repulsion 2122795.894911
FMO2-HF: Total energy -79674.803518
FMO2-MP2: Total energy -79904.296879


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:101:SER)


Summations of interaction energy for fragment #1(A:101:SER)
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.
-0.5111.132-0.016-0.812-0.814-0.001
Interaction energy analysis for fragmet #1(A:101:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.012
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].
3A103SER00.0700.0323.869-0.3911.252-0.016-0.812-0.814-0.001
4A104LYS10.7910.8865.9790.6560.6560.0000.0000.0000.000
5A105ARG10.8870.9287.505-0.533-0.5330.0000.0000.0000.000
6A106CYS0-0.013-0.0077.7800.0950.0950.0000.0000.0000.000
7A107LEU0-0.0020.0069.6480.0480.0480.0000.0000.0000.000
8A108GLU-1-0.810-0.89612.009-0.027-0.0270.0000.0000.0000.000
9A109TRP00.002-0.00411.5010.0260.0260.0000.0000.0000.000
10A110PHE0-0.0140.00213.7830.0160.0160.0000.0000.0000.000
11A111TYR0-0.027-0.05115.6130.0090.0090.0000.0000.0000.000
12A112GLU-1-0.939-0.95417.3100.0350.0350.0000.0000.0000.000
13A113TYR0-0.096-0.07316.8910.0200.0200.0000.0000.0000.000
14A114ALA00.0140.00819.9350.0040.0040.0000.0000.0000.000
15A115GLY00.0130.02221.6940.0040.0040.0000.0000.0000.000
16A116THR0-0.075-0.04723.8600.0070.0070.0000.0000.0000.000
17A117ASP-1-0.910-0.95823.547-0.162-0.1620.0000.0000.0000.000
18A118ASP-1-0.861-0.91619.376-0.321-0.3210.0000.0000.0000.000
19A119VAL0-0.040-0.04220.547-0.028-0.0280.0000.0000.0000.000
20A120VAL00.0110.03019.3320.0170.0170.0000.0000.0000.000
21A121GLY00.0630.02122.263-0.005-0.0050.0000.0000.0000.000
22A122PRO0-0.002-0.01425.6630.0060.0060.0000.0000.0000.000
23A123GLU-1-0.889-0.93127.419-0.043-0.0430.0000.0000.0000.000
24A124GLY00.0230.01724.1470.0090.0090.0000.0000.0000.000
25A125MET0-0.038-0.02521.8960.0080.0080.0000.0000.0000.000
26A126GLU-1-0.916-0.95524.215-0.020-0.0200.0000.0000.0000.000
27A127LYS10.8510.92620.7030.0110.0110.0000.0000.0000.000
28A128PHE0-0.009-0.01516.7420.0130.0130.0000.0000.0000.000
29A129CYS0-0.077-0.04221.5180.0140.0140.0000.0000.0000.000
30A130GLU-1-0.906-0.94823.9670.0360.0360.0000.0000.0000.000
31A131ASP-1-0.789-0.86020.1740.0490.0490.0000.0000.0000.000
32A132ILE0-0.085-0.04918.5460.0330.0330.0000.0000.0000.000
33A133GLY0-0.067-0.02821.1860.0150.0150.0000.0000.0000.000
34A134VAL0-0.100-0.05924.0930.0020.0020.0000.0000.0000.000
35A135GLU-1-0.866-0.92826.4770.0070.0070.0000.0000.0000.000
36A136PRO00.036-0.01726.839-0.001-0.0010.0000.0000.0000.000
37A137GLU-1-0.888-0.91627.865-0.034-0.0340.0000.0000.0000.000
38A138ASN00.019-0.00226.8770.0080.0080.0000.0000.0000.000
39A139VAL00.0380.01326.952-0.007-0.0070.0000.0000.0000.000
40A140VAL0-0.028-0.01521.602-0.008-0.0080.0000.0000.0000.000
41A141MET00.0380.02921.989-0.004-0.0040.0000.0000.0000.000
42A142LEU00.0060.01222.978-0.019-0.0190.0000.0000.0000.000
43A143VAL0-0.031-0.01620.900-0.017-0.0170.0000.0000.0000.000
44A144LEU00.007-0.00116.458-0.014-0.0140.0000.0000.0000.000
45A145ALA00.0340.01518.721-0.030-0.0300.0000.0000.0000.000
46A146TRP0-0.029-0.00620.549-0.026-0.0260.0000.0000.0000.000
47A147LYS10.8940.95015.8590.1020.1020.0000.0000.0000.000
48A148LEU0-0.045-0.01715.197-0.049-0.0490.0000.0000.0000.000
49A149ASP-1-0.930-0.94617.196-0.313-0.3130.0000.0000.0000.000
50A150ALA00.0040.02320.113-0.009-0.0090.0000.0000.0000.000
51A151GLN0-0.056-0.04221.6990.0330.0330.0000.0000.0000.000
52A152ASN0-0.055-0.02224.9750.0200.0200.0000.0000.0000.000
53A153MET00.0180.00425.871-0.001-0.0010.0000.0000.0000.000
54A154GLY0-0.002-0.00126.3130.0050.0050.0000.0000.0000.000
55A155TYR0-0.046-0.02824.3330.0050.0050.0000.0000.0000.000
56A156PHE0-0.018-0.01118.694-0.004-0.0040.0000.0000.0000.000
57A157THR00.001-0.02819.877-0.015-0.0150.0000.0000.0000.000
58A158LEU00.0050.00214.883-0.029-0.0290.0000.0000.0000.000
59A159GLN0-0.016-0.02014.753-0.123-0.1230.0000.0000.0000.000
60A160GLU-1-0.772-0.84414.987-0.299-0.2990.0000.0000.0000.000
61A161TRP00.0470.02212.3460.0000.0000.0000.0000.0000.000
62A162LEU0-0.0070.0028.757-0.034-0.0340.0000.0000.0000.000
63A163LYS10.8560.93010.1680.2600.2600.0000.0000.0000.000
64A164GLY00.0440.02911.599-0.014-0.0140.0000.0000.0000.000
65A165MET0-0.0160.00910.6040.0870.0870.0000.0000.0000.000
66A166THR0-0.035-0.0315.659-0.013-0.0130.0000.0000.0000.000
67A167SER0-0.122-0.0657.9800.1980.1980.0000.0000.0000.000
68A168LEU0-0.014-0.00810.6880.1020.1020.0000.0000.0000.000
69A169GLN0-0.032-0.0066.8340.3920.3920.0000.0000.0000.000
70A170CYS0-0.046-0.0117.6420.3470.3470.0000.0000.0000.000
71A171ASP-1-0.748-0.8686.8530.4970.4970.0000.0000.0000.000
72A172THR0-0.006-0.0238.9460.0010.0010.0000.0000.0000.000
73A173THR00.0940.05112.2850.0020.0020.0000.0000.0000.000
74A174GLU-1-0.847-0.91413.6910.5190.5190.0000.0000.0000.000
75A175LYS10.8340.9196.917-1.349-1.3490.0000.0000.0000.000
76A176LEU00.0470.02513.442-0.017-0.0170.0000.0000.0000.000
77A177ARG10.8630.93115.101-0.134-0.1340.0000.0000.0000.000
78A178ASN0-0.062-0.03215.999-0.038-0.0380.0000.0000.0000.000
79A179THR0-0.029-0.01814.1370.0170.0170.0000.0000.0000.000
80A180LEU00.0010.00716.790-0.040-0.0400.0000.0000.0000.000
81A181ASP-1-0.823-0.90620.0860.0770.0770.0000.0000.0000.000
82A182TYR00.0040.00815.699-0.022-0.0220.0000.0000.0000.000
83A183LEU00.0140.01517.227-0.026-0.0260.0000.0000.0000.000
84A184ARG10.8970.92020.360-0.083-0.0830.0000.0000.0000.000
85A185SER0-0.075-0.04521.603-0.012-0.0120.0000.0000.0000.000
86A186PHE00.0200.00018.689-0.012-0.0120.0000.0000.0000.000
87A187LEU0-0.033-0.00924.325-0.011-0.0110.0000.0000.0000.000
88A188ASN0-0.037-0.01926.941-0.001-0.0010.0000.0000.0000.000
89A189ASP-1-0.769-0.84627.153-0.047-0.0470.0000.0000.0000.000
90A190SER00.0230.00529.148-0.007-0.0070.0000.0000.0000.000
91A191THR0-0.022-0.02028.423-0.005-0.0050.0000.0000.0000.000
92A192ASN0-0.015-0.04623.801-0.018-0.0180.0000.0000.0000.000
93A193PHE00.0290.03426.812-0.009-0.0090.0000.0000.0000.000
94A194LYS10.8250.89929.0450.0540.0540.0000.0000.0000.000
95A195LEU0-0.053-0.02325.468-0.005-0.0050.0000.0000.0000.000
96A196ILE00.0340.02024.015-0.005-0.0050.0000.0000.0000.000
97A197TYR00.011-0.01827.125-0.002-0.0020.0000.0000.0000.000
98A198ARG10.8520.90130.8090.0690.0690.0000.0000.0000.000
99A199TYR0-0.029-0.02523.7060.0050.0050.0000.0000.0000.000
100A200ALA00.0210.00628.468-0.004-0.0040.0000.0000.0000.000
101A201PHE0-0.017-0.00129.3450.0000.0000.0000.0000.0000.000
102A202ASP-1-0.815-0.91929.650-0.106-0.1060.0000.0000.0000.000
103A203PHE00.0250.02824.310-0.001-0.0010.0000.0000.0000.000
104A204ALA00.0420.01228.490-0.001-0.0010.0000.0000.0000.000
105A205ARG10.7680.91531.4180.1120.1120.0000.0000.0000.000
106A206GLU-1-0.820-0.90832.805-0.081-0.0810.0000.0000.0000.000
107A207LYS10.8660.90433.2520.1070.1070.0000.0000.0000.000
108A208ASP-1-0.864-0.91634.740-0.095-0.0950.0000.0000.0000.000
109A209GLN0-0.0090.00937.5720.0050.0050.0000.0000.0000.000
110A210ARG10.8690.91237.6460.0830.0830.0000.0000.0000.000
111A211SER0-0.018-0.01739.2270.0020.0020.0000.0000.0000.000
112A212LEU00.0180.04434.407-0.003-0.0030.0000.0000.0000.000
113A213ASP-1-0.713-0.85138.260-0.041-0.0410.0000.0000.0000.000
114A214ILE0-0.001-0.00739.8770.0000.0000.0000.0000.0000.000
115A215ASN0-0.026-0.03040.5770.0050.0050.0000.0000.0000.000
116A216THR00.0420.00734.5170.0010.0010.0000.0000.0000.000
117A217ALA0-0.032-0.01836.2430.0000.0000.0000.0000.0000.000
118A218LYS10.8120.90337.7430.0270.0270.0000.0000.0000.000
119A219CYS0-0.036-0.01835.0230.0040.0040.0000.0000.0000.000
120A220MET00.0170.00530.3180.0020.0020.0000.0000.0000.000
121A221LEU0-0.005-0.00533.7970.0010.0010.0000.0000.0000.000
122A222GLY00.0260.01436.4620.0030.0030.0000.0000.0000.000
123A223LEU0-0.069-0.03230.2240.0040.0040.0000.0000.0000.000
124A224LEU0-0.052-0.01629.5100.0030.0030.0000.0000.0000.000
125A225LEU00.014-0.01332.7790.0030.0030.0000.0000.0000.000
126A226GLY00.0240.01736.2330.0030.0030.0000.0000.0000.000
127A227LYS10.8550.92133.879-0.007-0.0070.0000.0000.0000.000
128A228ILE0-0.018-0.00433.3150.0040.0040.0000.0000.0000.000
129A229TRP00.0460.03636.948-0.001-0.0010.0000.0000.0000.000
130A230PRO00.000-0.01140.108-0.001-0.0010.0000.0000.0000.000
131A231LEU00.0490.03843.3440.0010.0010.0000.0000.0000.000
132A232PHE0-0.0030.02339.827-0.001-0.0010.0000.0000.0000.000
133A233PRO00.003-0.00442.589-0.001-0.0010.0000.0000.0000.000
134A234VAL00.0430.02344.626-0.001-0.0010.0000.0000.0000.000
135A235PHE00.0160.01742.014-0.002-0.0020.0000.0000.0000.000
136A236HIS0-0.048-0.03842.605-0.001-0.0010.0000.0000.0000.000
137A237GLN00.007-0.00444.504-0.001-0.0010.0000.0000.0000.000
138A238PHE00.0000.00647.680-0.001-0.0010.0000.0000.0000.000
139A239LEU00.001-0.00243.116-0.001-0.0010.0000.0000.0000.000
140A240GLU-1-0.827-0.88444.318-0.022-0.0220.0000.0000.0000.000
141A241GLN0-0.064-0.01747.7230.0010.0010.0000.0000.0000.000
142A242SER0-0.057-0.01648.321-0.001-0.0010.0000.0000.0000.000
143A243LYS10.8600.89550.8410.0290.0290.0000.0000.0000.000
144A244TYR0-0.048-0.04646.632-0.002-0.0020.0000.0000.0000.000
145A245LYS10.8730.91646.3000.0310.0310.0000.0000.0000.000
146A246VAL0-0.0120.00742.837-0.001-0.0010.0000.0000.0000.000
147A247ILE00.0060.01340.1860.0020.0020.0000.0000.0000.000
148A248ASN00.0390.01140.141-0.005-0.0050.0000.0000.0000.000
149A249LYS10.8720.91932.8340.0970.0970.0000.0000.0000.000
150A250ASP-1-0.850-0.92638.724-0.054-0.0540.0000.0000.0000.000
151A251GLN00.0520.03141.3530.0000.0000.0000.0000.0000.000
152A252TRP0-0.005-0.00133.1920.0030.0030.0000.0000.0000.000
153A253CYS0-0.090-0.04636.8800.0000.0000.0000.0000.0000.000
154A254ASN00.002-0.01738.3760.0030.0030.0000.0000.0000.000
155A255VAL00.0330.02839.4580.0030.0030.0000.0000.0000.000
156A256LEU0-0.0270.00934.3790.0030.0030.0000.0000.0000.000
157A257GLU-1-0.739-0.84437.470-0.050-0.0500.0000.0000.0000.000
158A258PHE00.0700.05640.6050.0030.0030.0000.0000.0000.000
159A259SER0-0.081-0.06539.1090.0030.0030.0000.0000.0000.000
160A260ARG10.8060.90332.8160.0410.0410.0000.0000.0000.000
161A261THR0-0.074-0.05340.8090.0010.0010.0000.0000.0000.000
162A262ILE0-0.0270.02044.3900.0010.0010.0000.0000.0000.000
163A263ASN0-0.036-0.02546.1820.0010.0010.0000.0000.0000.000
164A264LEU0-0.003-0.02844.3100.0000.0000.0000.0000.0000.000
165A265ASP-1-0.812-0.87648.320-0.009-0.0090.0000.0000.0000.000
166A266LEU0-0.027-0.01749.3940.0000.0000.0000.0000.0000.000
167A267SER0-0.072-0.05351.900-0.001-0.0010.0000.0000.0000.000
168A268ASN0-0.049-0.03148.5500.0010.0010.0000.0000.0000.000
169A269TYR0-0.061-0.06548.913-0.002-0.0020.0000.0000.0000.000
170A270ASP-1-0.893-0.95352.406-0.025-0.0250.0000.0000.0000.000
171A271GLU-1-0.891-0.94753.424-0.020-0.0200.0000.0000.0000.000
172A272ASP-1-0.956-0.95655.880-0.024-0.0240.0000.0000.0000.000
173A273GLY0-0.0130.01052.427-0.001-0.0010.0000.0000.0000.000
174A274ALA0-0.080-0.05149.4230.0000.0000.0000.0000.0000.000
175A275TRP00.0030.00644.377-0.004-0.0040.0000.0000.0000.000
176A276PRO0-0.023-0.01445.0370.0000.0000.0000.0000.0000.000
177A277VAL00.0630.02948.3590.0010.0010.0000.0000.0000.000
178A278LEU0-0.077-0.02445.3010.0020.0020.0000.0000.0000.000
179A279LEU0-0.029-0.02444.5050.0020.0020.0000.0000.0000.000
180A280ASP-1-0.732-0.83948.746-0.028-0.0280.0000.0000.0000.000
181A281GLU-1-0.748-0.84751.858-0.028-0.0280.0000.0000.0000.000
182A282PHE0-0.034-0.01147.2160.0020.0020.0000.0000.0000.000
183A283VAL00.0350.01150.6120.0020.0020.0000.0000.0000.000
184A284GLU-1-0.941-0.96552.839-0.019-0.0190.0000.0000.0000.000
185A285TRP0-0.041-0.03751.2650.0020.0020.0000.0000.0000.000
186A286TYR0-0.030-0.02651.4040.0020.0020.0000.0000.0000.000
187A287LYS10.8790.92354.0560.0180.0180.0000.0000.0000.000
188A288ASP-1-0.857-0.91157.226-0.011-0.0110.0000.0000.0000.000
189A289LYS10.7910.89255.3200.0150.0150.0000.0000.0000.000
190A290GLN0-0.139-0.04754.5900.0030.0030.0000.0000.0000.000