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: YVNY2

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 OptH
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 -2199221.256819
FMO2-HF: Nuclear repulsion 2119547.596916
FMO2-HF: Total energy -79673.659902
FMO2-MP2: Total energy -79903.124131


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.
-2.358-0.41-0.022-0.961-0.965-0.002
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 : 0.017 / q_NPA : -0.014
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].
3A103SER00.0860.0373.811-1.5700.378-0.022-0.961-0.965-0.002
4A104LYS10.8620.9296.2991.3671.3670.0000.0000.0000.000
5A105ARG10.9250.9796.6811.3831.3830.0000.0000.0000.000
6A106CYS00.0290.0127.9360.2730.2730.0000.0000.0000.000
7A107LEU00.004-0.0039.6380.1940.1940.0000.0000.0000.000
8A108GLU-1-0.879-0.93211.869-0.582-0.5820.0000.0000.0000.000
9A109TRP00.0220.01911.8460.0230.0230.0000.0000.0000.000
10A110PHE0-0.0130.00313.9700.0860.0860.0000.0000.0000.000
11A111TYR0-0.044-0.04915.9200.0440.0440.0000.0000.0000.000
12A112GLU-1-0.997-0.98316.563-0.489-0.4890.0000.0000.0000.000
13A113TYR0-0.114-0.10017.4280.0360.0360.0000.0000.0000.000
14A114ALA0-0.028-0.01319.8240.0350.0350.0000.0000.0000.000
15A115GLY00.0320.03421.7960.0290.0290.0000.0000.0000.000
16A116THR0-0.049-0.04223.385-0.009-0.0090.0000.0000.0000.000
17A117ASP-1-0.930-0.95724.193-0.338-0.3380.0000.0000.0000.000
18A118ASP-1-0.872-0.92920.197-0.559-0.5590.0000.0000.0000.000
19A119VAL0-0.068-0.06220.857-0.036-0.0360.0000.0000.0000.000
20A120VAL00.0220.03919.6270.0140.0140.0000.0000.0000.000
21A121GLY00.0430.01622.5730.0050.0050.0000.0000.0000.000
22A122PRO00.034-0.00125.902-0.012-0.0120.0000.0000.0000.000
23A123GLU-1-0.907-0.94528.194-0.239-0.2390.0000.0000.0000.000
24A124GLY00.0250.01424.5250.0000.0000.0000.0000.0000.000
25A125MET0-0.034-0.02622.479-0.030-0.0300.0000.0000.0000.000
26A126GLU-1-0.920-0.95624.664-0.245-0.2450.0000.0000.0000.000
27A127LYS10.9390.99122.3950.3560.3560.0000.0000.0000.000
28A128PHE00.002-0.00417.256-0.018-0.0180.0000.0000.0000.000
29A129CYS0-0.073-0.04621.820-0.015-0.0150.0000.0000.0000.000
30A130GLU-1-0.905-0.94224.117-0.238-0.2380.0000.0000.0000.000
31A131ASP-1-0.841-0.89120.518-0.377-0.3770.0000.0000.0000.000
32A132ILE0-0.113-0.06818.595-0.007-0.0070.0000.0000.0000.000
33A133GLY0-0.060-0.02421.4020.0100.0100.0000.0000.0000.000
34A134VAL0-0.117-0.06024.3030.0190.0190.0000.0000.0000.000
35A135GLU-1-0.879-0.94326.616-0.202-0.2020.0000.0000.0000.000
36A136PRO00.042-0.00627.213-0.013-0.0130.0000.0000.0000.000
37A137GLU-1-0.923-0.95128.278-0.206-0.2060.0000.0000.0000.000
38A138ASN00.0380.00827.3320.0050.0050.0000.0000.0000.000
39A139VAL00.0440.01927.574-0.019-0.0190.0000.0000.0000.000
40A140VAL0-0.031-0.02022.112-0.013-0.0130.0000.0000.0000.000
41A141MET00.0340.02222.367-0.050-0.0500.0000.0000.0000.000
42A142LEU0-0.0030.00923.540-0.020-0.0200.0000.0000.0000.000
43A143VAL0-0.050-0.02121.097-0.015-0.0150.0000.0000.0000.000
44A144LEU00.0060.00016.797-0.034-0.0340.0000.0000.0000.000
45A145ALA00.0300.01719.163-0.050-0.0500.0000.0000.0000.000
46A146TRP0-0.008-0.00220.845-0.028-0.0280.0000.0000.0000.000
47A147LYS10.9030.94716.0310.5790.5790.0000.0000.0000.000
48A148LEU0-0.074-0.03315.264-0.086-0.0860.0000.0000.0000.000
49A149ASP-1-0.987-0.98217.455-0.435-0.4350.0000.0000.0000.000
50A150ALA0-0.0090.01520.3590.0150.0150.0000.0000.0000.000
51A151GLN0-0.054-0.03421.9280.0700.0700.0000.0000.0000.000
52A152ASN0-0.039-0.01525.1110.0470.0470.0000.0000.0000.000
53A153MET00.0220.00425.978-0.023-0.0230.0000.0000.0000.000
54A154GLY0-0.005-0.00426.4970.0180.0180.0000.0000.0000.000
55A155TYR0-0.057-0.03424.6480.0040.0040.0000.0000.0000.000
56A156PHE00.0130.01218.887-0.021-0.0210.0000.0000.0000.000
57A157THR00.0150.01119.765-0.021-0.0210.0000.0000.0000.000
58A158LEU00.0680.03414.673-0.074-0.0740.0000.0000.0000.000
59A159GLN0-0.030-0.03514.722-0.185-0.1850.0000.0000.0000.000
60A160GLU-1-0.829-0.90314.944-0.581-0.5810.0000.0000.0000.000
61A161TRP00.0690.03512.683-0.042-0.0420.0000.0000.0000.000
62A162LEU0-0.0020.0088.783-0.190-0.1900.0000.0000.0000.000
63A163LYS10.9720.99410.0850.3940.3940.0000.0000.0000.000
64A164GLY00.0530.02111.413-0.084-0.0840.0000.0000.0000.000
65A165MET00.0020.02910.864-0.020-0.0200.0000.0000.0000.000
66A166THR0-0.073-0.0545.768-0.438-0.4380.0000.0000.0000.000
67A167SER0-0.141-0.0807.863-0.097-0.0970.0000.0000.0000.000
68A168LEU0-0.014-0.01710.4200.1040.1040.0000.0000.0000.000
69A169GLN0-0.061-0.0145.4200.3940.3940.0000.0000.0000.000
70A170CYS0-0.068-0.0207.9860.1910.1910.0000.0000.0000.000
71A171ASP-1-0.849-0.9516.490-2.145-2.1450.0000.0000.0000.000
72A172THR00.0290.0019.4040.1450.1450.0000.0000.0000.000
73A173THR00.1070.05312.424-0.037-0.0370.0000.0000.0000.000
74A174GLU-1-0.966-0.97014.077-0.397-0.3970.0000.0000.0000.000
75A175LYS10.9470.9677.4531.3801.3800.0000.0000.0000.000
76A176LEU00.0520.03313.3820.0160.0160.0000.0000.0000.000
77A177ARG10.9020.94715.4340.3880.3880.0000.0000.0000.000
78A178ASN0-0.053-0.02415.4270.0740.0740.0000.0000.0000.000
79A179THR0-0.013-0.01414.1630.0010.0010.0000.0000.0000.000
80A180LEU0-0.0020.00416.5180.0250.0250.0000.0000.0000.000
81A181ASP-1-0.837-0.91820.071-0.241-0.2410.0000.0000.0000.000
82A182TYR0-0.022-0.00716.0320.0040.0040.0000.0000.0000.000
83A183LEU00.0170.01417.4260.0180.0180.0000.0000.0000.000
84A184ARG10.9350.94820.4480.3100.3100.0000.0000.0000.000
85A185SER0-0.079-0.03921.4590.0280.0280.0000.0000.0000.000
86A186PHE0-0.002-0.00618.5560.0190.0190.0000.0000.0000.000
87A187LEU0-0.036-0.02124.1050.0180.0180.0000.0000.0000.000
88A188ASN0-0.030-0.01427.0240.0190.0190.0000.0000.0000.000
89A189ASP-1-0.846-0.90326.734-0.174-0.1740.0000.0000.0000.000
90A190SER00.0050.00228.623-0.010-0.0100.0000.0000.0000.000
91A191THR00.0250.00528.0340.0020.0020.0000.0000.0000.000
92A192ASN00.042-0.00623.657-0.014-0.0140.0000.0000.0000.000
93A193PHE00.0070.02726.847-0.013-0.0130.0000.0000.0000.000
94A194LYS10.9090.95729.2180.1430.1430.0000.0000.0000.000
95A195LEU0-0.057-0.02925.2800.0020.0020.0000.0000.0000.000
96A196ILE00.0340.03124.271-0.007-0.0070.0000.0000.0000.000
97A197TYR0-0.007-0.02027.342-0.002-0.0020.0000.0000.0000.000
98A198ARG10.8980.93530.8340.1710.1710.0000.0000.0000.000
99A199TYR00.013-0.00323.7560.0100.0100.0000.0000.0000.000
100A200ALA00.0250.00928.491-0.004-0.0040.0000.0000.0000.000
101A201PHE0-0.046-0.01629.8150.0050.0050.0000.0000.0000.000
102A202ASP-1-0.914-0.97629.366-0.215-0.2150.0000.0000.0000.000
103A203PHE00.0160.01524.9010.0020.0020.0000.0000.0000.000
104A204ALA00.0250.01328.734-0.004-0.0040.0000.0000.0000.000
105A205ARG10.8270.92931.5720.2140.2140.0000.0000.0000.000
106A206GLU-1-0.854-0.91132.713-0.186-0.1860.0000.0000.0000.000
107A207LYS10.9720.96533.2500.2040.2040.0000.0000.0000.000
108A208ASP-1-0.972-0.99534.898-0.158-0.1580.0000.0000.0000.000
109A209GLN00.0080.03137.3910.0150.0150.0000.0000.0000.000
110A210ARG10.8830.91837.8510.1450.1450.0000.0000.0000.000
111A211SER0-0.051-0.03739.5200.0030.0030.0000.0000.0000.000
112A212LEU00.0590.06034.848-0.004-0.0040.0000.0000.0000.000
113A213ASP-1-0.757-0.85838.710-0.152-0.1520.0000.0000.0000.000
114A214ILE00.025-0.00940.098-0.006-0.0060.0000.0000.0000.000
115A215ASN00.009-0.00140.8850.0030.0030.0000.0000.0000.000
116A216THR00.032-0.00335.003-0.005-0.0050.0000.0000.0000.000
117A217ALA0-0.021-0.01136.547-0.007-0.0070.0000.0000.0000.000
118A218LYS10.8210.90237.9970.1220.1220.0000.0000.0000.000
119A219CYS0-0.0170.00835.323-0.002-0.0020.0000.0000.0000.000
120A220MET00.0170.00331.064-0.004-0.0040.0000.0000.0000.000
121A221LEU0-0.019-0.00934.027-0.004-0.0040.0000.0000.0000.000
122A222GLY00.0260.01636.5010.0030.0030.0000.0000.0000.000
123A223LEU0-0.053-0.02130.375-0.001-0.0010.0000.0000.0000.000
124A224LEU0-0.061-0.02729.872-0.004-0.0040.0000.0000.0000.000
125A225LEU0-0.005-0.02432.9770.0030.0030.0000.0000.0000.000
126A226GLY00.0060.02036.0560.0090.0090.0000.0000.0000.000
127A227LYS10.8740.92833.8920.1500.1500.0000.0000.0000.000
128A228ILE00.0200.00833.4990.0080.0080.0000.0000.0000.000
129A229TRP00.0450.03836.7430.0050.0050.0000.0000.0000.000
130A230PRO00.007-0.00439.9170.0000.0000.0000.0000.0000.000
131A231LEU00.0320.01743.0960.0020.0020.0000.0000.0000.000
132A232PHE00.0040.03039.9120.0000.0000.0000.0000.0000.000
133A233PRO00.005-0.00442.4730.0000.0000.0000.0000.0000.000
134A234VAL00.0500.02744.7020.0010.0010.0000.0000.0000.000
135A235PHE00.0160.00642.4310.0010.0010.0000.0000.0000.000
136A236HIS0-0.007-0.00641.4330.0030.0030.0000.0000.0000.000
137A237GLN00.0330.01244.6740.0000.0000.0000.0000.0000.000
138A238PHE0-0.011-0.00447.7980.0020.0020.0000.0000.0000.000
139A239LEU00.007-0.00643.0680.0010.0010.0000.0000.0000.000
140A240GLU-1-0.889-0.93145.248-0.115-0.1150.0000.0000.0000.000
141A241GLN0-0.095-0.03047.9560.0050.0050.0000.0000.0000.000
142A242SER0-0.047-0.00348.8020.0040.0040.0000.0000.0000.000
143A243LYS10.9410.95751.1440.0820.0820.0000.0000.0000.000
144A244TYR0-0.095-0.08746.822-0.002-0.0020.0000.0000.0000.000
145A245LYS10.9490.96946.7900.0970.0970.0000.0000.0000.000
146A246VAL0-0.023-0.00342.810-0.005-0.0050.0000.0000.0000.000
147A247ILE00.0250.02540.2090.0060.0060.0000.0000.0000.000
148A248ASN00.0370.01640.395-0.010-0.0100.0000.0000.0000.000
149A249LYS10.9400.96433.5080.1870.1870.0000.0000.0000.000
150A250ASP-1-0.884-0.94638.996-0.116-0.1160.0000.0000.0000.000
151A251GLN00.0760.03441.644-0.003-0.0030.0000.0000.0000.000
152A252TRP0-0.005-0.00333.5070.0060.0060.0000.0000.0000.000
153A253CYS0-0.100-0.05736.830-0.006-0.0060.0000.0000.0000.000
154A254ASN00.0340.00038.4050.0050.0050.0000.0000.0000.000
155A255VAL00.0290.03639.9050.0050.0050.0000.0000.0000.000
156A256LEU0-0.0280.00134.5100.0010.0010.0000.0000.0000.000
157A257GLU-1-0.874-0.94337.812-0.128-0.1280.0000.0000.0000.000
158A258PHE00.0410.02840.7720.0050.0050.0000.0000.0000.000
159A259SER0-0.103-0.07239.3710.0020.0020.0000.0000.0000.000
160A260ARG10.8550.92132.9650.1480.1480.0000.0000.0000.000
161A261THR0-0.071-0.02940.7780.0050.0050.0000.0000.0000.000
162A262ILE0-0.0200.01844.1390.0060.0060.0000.0000.0000.000
163A263ASN0-0.036-0.02346.103-0.005-0.0050.0000.0000.0000.000
164A264LEU00.022-0.01344.093-0.001-0.0010.0000.0000.0000.000
165A265ASP-1-0.843-0.90348.106-0.066-0.0660.0000.0000.0000.000
166A266LEU0-0.046-0.03849.3990.0020.0020.0000.0000.0000.000
167A267SER0-0.066-0.04051.8400.0010.0010.0000.0000.0000.000
168A268ASN0-0.027-0.01348.4520.0010.0010.0000.0000.0000.000
169A269TYR0-0.074-0.08349.140-0.003-0.0030.0000.0000.0000.000
170A270ASP-1-0.885-0.93752.302-0.061-0.0610.0000.0000.0000.000
171A271GLU-1-0.974-1.00153.648-0.064-0.0640.0000.0000.0000.000
172A272ASP-1-0.966-0.96055.981-0.058-0.0580.0000.0000.0000.000
173A273GLY0-0.037-0.01452.3290.0000.0000.0000.0000.0000.000
174A274ALA0-0.069-0.05049.2950.0000.0000.0000.0000.0000.000
175A275TRP00.0020.00844.154-0.008-0.0080.0000.0000.0000.000
176A276PRO0-0.015-0.00945.2310.0010.0010.0000.0000.0000.000
177A277VAL00.1010.04848.5080.0000.0000.0000.0000.0000.000
178A278LEU0-0.061-0.01045.6100.0000.0000.0000.0000.0000.000
179A279LEU0-0.044-0.03544.600-0.001-0.0010.0000.0000.0000.000
180A280ASP-1-0.749-0.83148.935-0.077-0.0770.0000.0000.0000.000
181A281GLU-1-0.852-0.91752.066-0.082-0.0820.0000.0000.0000.000
182A282PHE0-0.072-0.02547.8190.0010.0010.0000.0000.0000.000
183A283VAL00.0310.00850.7870.0020.0020.0000.0000.0000.000
184A284GLU-1-0.928-0.95952.906-0.065-0.0650.0000.0000.0000.000
185A285TRP0-0.036-0.01950.9070.0020.0020.0000.0000.0000.000
186A286TYR00.009-0.01151.2560.0020.0020.0000.0000.0000.000
187A287LYS10.9680.96454.2360.0660.0660.0000.0000.0000.000
188A288ASP-1-0.906-0.93957.326-0.060-0.0600.0000.0000.0000.000
189A289LYS10.7830.90555.3590.0710.0710.0000.0000.0000.000
190A290GLN0-0.109-0.02554.6820.0030.0030.0000.0000.0000.000