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: QYNVY

Calculation Name: 3K66-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K66

Chain ID: A

ChEMBL ID:

UniProt ID: Q10651

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2436194.265323
FMO2-HF: Nuclear repulsion 2344741.913299
FMO2-HF: Total energy -91452.352024
FMO2-MP2: Total energy -91719.089633


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:234:SER)


Summations of interaction energy for fragment #1(A:234: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.
-3.5840.7690.423-2.706-2.07-0.01
Interaction energy analysis for fragmet #1(A:234:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.021
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].
3A236ASP-1-0.783-0.8912.551-10.948-6.5950.423-2.706-2.070-0.010
4A237PRO00.000-0.0044.9730.3960.3960.0000.0000.0000.000
5A238TYR0-0.047-0.0756.7640.4690.4690.0000.0000.0000.000
6A239PHE00.026-0.0067.9960.2340.2340.0000.0000.0000.000
7A240LYS10.8350.9244.9553.0813.0810.0000.0000.0000.000
8A241ILE0-0.0070.01310.2040.1490.1490.0000.0000.0000.000
9A242ALA00.0450.00712.9330.0210.0210.0000.0000.0000.000
10A243ASN00.0680.09716.2080.0500.0500.0000.0000.0000.000
11A244TRP00.0200.00815.4770.0330.0330.0000.0000.0000.000
12A245THR00.017-0.04919.2190.0090.0090.0000.0000.0000.000
13A246ASN0-0.032-0.01619.6960.0330.0330.0000.0000.0000.000
14A247GLU-1-0.657-0.77217.173-0.710-0.7100.0000.0000.0000.000
15A248HIS0-0.074-0.03718.424-0.066-0.0660.0000.0000.0000.000
16A249ASP-1-0.774-0.88118.712-0.430-0.4300.0000.0000.0000.000
17A250ASP-1-0.872-0.96814.161-0.604-0.6040.0000.0000.0000.000
18A251PHE00.0010.00814.275-0.111-0.1110.0000.0000.0000.000
19A252LYS10.9200.96715.7100.3590.3590.0000.0000.0000.000
20A253LYS10.8290.91513.9670.5450.5450.0000.0000.0000.000
21A254ALA0-0.006-0.01211.411-0.054-0.0540.0000.0000.0000.000
22A255GLU-1-0.835-0.90512.503-0.638-0.6380.0000.0000.0000.000
23A256MET0-0.0120.00815.2130.0310.0310.0000.0000.0000.000
24A257ARG10.8940.9358.8771.4851.4850.0000.0000.0000.000
25A258MET0-0.053-0.01011.858-0.060-0.0600.0000.0000.0000.000
26A259ASP-1-0.910-0.97312.664-0.441-0.4410.0000.0000.0000.000
27A260GLU-1-0.924-0.99514.423-0.384-0.3840.0000.0000.0000.000
28A261LYS10.9140.9658.0471.7481.7480.0000.0000.0000.000
29A262HIS00.004-0.00913.4260.0310.0310.0000.0000.0000.000
30A263ARG11.0031.01116.1070.4730.4730.0000.0000.0000.000
31A264LYS10.8870.97114.2250.4180.4180.0000.0000.0000.000
32A265LYS10.8640.92911.9110.7300.7300.0000.0000.0000.000
33A266VAL00.0330.01717.7150.0450.0450.0000.0000.0000.000
34A267ASP-1-0.872-0.92821.095-0.198-0.1980.0000.0000.0000.000
35A268LYS10.8790.94117.3080.1750.1750.0000.0000.0000.000
36A269VAL0-0.017-0.00520.5050.0260.0260.0000.0000.0000.000
37A270MET00.0170.00322.9710.0280.0280.0000.0000.0000.000
38A271LYS10.8620.93024.7660.0790.0790.0000.0000.0000.000
39A272GLU-1-0.842-0.93622.089-0.114-0.1140.0000.0000.0000.000
40A273TRP0-0.040-0.02126.3260.0120.0120.0000.0000.0000.000
41A274GLY00.0630.03628.8920.0090.0090.0000.0000.0000.000
42A275ASP-1-0.843-0.90128.374-0.047-0.0470.0000.0000.0000.000
43A276LEU0-0.079-0.05128.0180.0090.0090.0000.0000.0000.000
44A277GLU-1-0.909-0.95731.787-0.066-0.0660.0000.0000.0000.000
45A278THR0-0.043-0.02534.2680.0050.0050.0000.0000.0000.000
46A279ARG10.8430.91534.8050.0250.0250.0000.0000.0000.000
47A280TYR0-0.079-0.10136.5190.0040.0040.0000.0000.0000.000
48A281ASN00.003-0.02138.3220.0030.0030.0000.0000.0000.000
49A282GLU-1-0.897-0.93138.686-0.019-0.0190.0000.0000.0000.000
50A283GLN0-0.015-0.02139.5390.0020.0020.0000.0000.0000.000
51A284LYS10.9461.00142.1800.0470.0470.0000.0000.0000.000
52A285ALA00.0290.01043.8690.0010.0010.0000.0000.0000.000
53A286LYS10.9400.97642.9540.0120.0120.0000.0000.0000.000
54A287ASP-1-0.843-0.91943.012-0.013-0.0130.0000.0000.0000.000
55A288PRO00.0390.03744.076-0.002-0.0020.0000.0000.0000.000
56A289LYS10.9580.97844.5630.0150.0150.0000.0000.0000.000
57A290GLY00.011-0.00541.969-0.002-0.0020.0000.0000.0000.000
58A291ALA0-0.047-0.04040.118-0.003-0.0030.0000.0000.0000.000
59A292GLU-1-0.801-0.85839.404-0.052-0.0520.0000.0000.0000.000
60A293LYS10.8890.96139.1160.0190.0190.0000.0000.0000.000
61A294PHE00.0070.00632.991-0.005-0.0050.0000.0000.0000.000
62A295LYS11.0071.01134.9420.0580.0580.0000.0000.0000.000
63A296SER00.0080.00835.079-0.008-0.0080.0000.0000.0000.000
64A297GLN0-0.055-0.03633.128-0.004-0.0040.0000.0000.0000.000
65A298MET00.013-0.00529.666-0.009-0.0090.0000.0000.0000.000
66A299ASN00.0130.03130.196-0.016-0.0160.0000.0000.0000.000
67A300ALA00.0460.03630.215-0.012-0.0120.0000.0000.0000.000
68A301ARG10.8430.92423.4430.1010.1010.0000.0000.0000.000
69A302PHE00.0290.01026.057-0.018-0.0180.0000.0000.0000.000
70A303GLN00.024-0.00326.322-0.011-0.0110.0000.0000.0000.000
71A304LYS10.9690.97424.9790.0890.0890.0000.0000.0000.000
72A305THR0-0.045-0.02420.906-0.019-0.0190.0000.0000.0000.000
73A306VAL0-0.0010.00721.680-0.035-0.0350.0000.0000.0000.000
74A307SER00.0490.02122.333-0.025-0.0250.0000.0000.0000.000
75A308SER0-0.0180.00519.118-0.041-0.0410.0000.0000.0000.000
76A309LEU00.003-0.01316.811-0.052-0.0520.0000.0000.0000.000
77A310GLU-1-0.970-0.98418.647-0.338-0.3380.0000.0000.0000.000
78A311GLU-1-0.949-0.97819.493-0.340-0.3400.0000.0000.0000.000
79A312GLU-1-0.852-0.91813.059-0.844-0.8440.0000.0000.0000.000
80A313HIS0-0.003-0.00115.906-0.050-0.0500.0000.0000.0000.000
81A314LYS10.9750.98817.2810.3380.3380.0000.0000.0000.000
82A315ARG10.9200.95610.6231.1621.1620.0000.0000.0000.000
83A316MET0-0.075-0.06610.256-0.108-0.1080.0000.0000.0000.000
84A317ARG10.8160.91014.6480.4680.4680.0000.0000.0000.000
85A318LYS11.0081.00017.0710.4110.4110.0000.0000.0000.000
86A319GLU-1-0.973-0.96611.801-1.402-1.4020.0000.0000.0000.000
87A320ILE0-0.002-0.01812.448-0.005-0.0050.0000.0000.0000.000
88A321GLU-1-0.895-0.94914.964-0.452-0.4520.0000.0000.0000.000
89A322ALA0-0.0210.00118.4010.0540.0540.0000.0000.0000.000
90A323VAL00.0190.01214.0900.0290.0290.0000.0000.0000.000
91A324HIS10.8920.97117.2930.5980.5980.0000.0000.0000.000
92A325GLU-1-0.912-0.98118.615-0.332-0.3320.0000.0000.0000.000
93A326GLU-1-0.956-0.96918.829-0.425-0.4250.0000.0000.0000.000
94A327ARG10.8850.94312.7740.8670.8670.0000.0000.0000.000
95A328VAL0-0.035-0.01120.8270.0470.0470.0000.0000.0000.000
96A329GLN00.0360.00123.4580.0380.0380.0000.0000.0000.000
97A330ALA0-0.0010.01722.9640.0330.0330.0000.0000.0000.000
98A331MET00.002-0.00822.5670.0170.0170.0000.0000.0000.000
99A332LEU0-0.066-0.04125.4390.0270.0270.0000.0000.0000.000
100A333ASN0-0.010-0.02128.2760.0320.0320.0000.0000.0000.000
101A334GLU-1-0.936-0.94726.189-0.203-0.2030.0000.0000.0000.000
102A335LYS10.9670.99529.3510.1900.1900.0000.0000.0000.000
103A336LYS10.8100.89931.4970.1930.1930.0000.0000.0000.000
104A337ARG10.9310.98529.2280.1600.1600.0000.0000.0000.000
105A338ASP-1-0.851-0.94631.111-0.140-0.1400.0000.0000.0000.000
106A339ALA0-0.034-0.01734.4160.0080.0080.0000.0000.0000.000
107A340THR0-0.056-0.04536.7300.0100.0100.0000.0000.0000.000
108A341HIS0-0.034-0.00337.2890.0060.0060.0000.0000.0000.000
109A342ASP-1-0.840-0.92037.396-0.100-0.1000.0000.0000.0000.000
110A343TYR0-0.053-0.03940.2890.0080.0080.0000.0000.0000.000
111A344ARG10.9720.95142.4570.0840.0840.0000.0000.0000.000
112A345GLN00.0140.01841.6530.0070.0070.0000.0000.0000.000
113A346ALA0-0.039-0.03244.3650.0050.0050.0000.0000.0000.000
114A347LEU00.0650.01646.2200.0040.0040.0000.0000.0000.000
115A348ALA00.0240.02347.6770.0040.0040.0000.0000.0000.000
116A349THR0-0.091-0.06847.4160.0040.0040.0000.0000.0000.000
117A350HIS0-0.050-0.02849.9560.0020.0020.0000.0000.0000.000
118A351VAL00.0000.02152.3320.0020.0020.0000.0000.0000.000
119A352ASN0-0.075-0.01152.3860.0030.0030.0000.0000.0000.000
120A353LYS10.9740.97851.2530.0500.0500.0000.0000.0000.000
121A354PRO00.032-0.01253.391-0.003-0.0030.0000.0000.0000.000
122A355ASN00.0000.04946.7640.0010.0010.0000.0000.0000.000
123A356LYS10.9350.95549.7940.0490.0490.0000.0000.0000.000
124A357HIS00.0230.00945.560-0.003-0.0030.0000.0000.0000.000
125A358SER00.0010.00645.398-0.005-0.0050.0000.0000.0000.000
126A359VAL00.0670.03345.262-0.005-0.0050.0000.0000.0000.000
127A360LEU00.0230.01445.701-0.005-0.0050.0000.0000.0000.000
128A361GLN0-0.034-0.01941.705-0.009-0.0090.0000.0000.0000.000
129A362SER00.0070.02841.437-0.008-0.0080.0000.0000.0000.000
130A363LEU00.0270.01441.109-0.006-0.0060.0000.0000.0000.000
131A364LYS10.9120.95541.7730.0860.0860.0000.0000.0000.000
132A365ALA0-0.0130.00037.463-0.008-0.0080.0000.0000.0000.000
133A366TYR0-0.001-0.02637.242-0.008-0.0080.0000.0000.0000.000
134A367ILE00.0130.00038.012-0.007-0.0070.0000.0000.0000.000
135A368ARG10.9000.96035.9440.1210.1210.0000.0000.0000.000
136A369ALA0-0.085-0.04633.781-0.011-0.0110.0000.0000.0000.000
137A370GLU-1-0.699-0.84233.848-0.161-0.1610.0000.0000.0000.000
138A371GLU-1-0.714-0.84135.496-0.143-0.1430.0000.0000.0000.000
139A372LYS10.8880.96227.1460.2430.2430.0000.0000.0000.000
140A373ASP-1-0.816-0.90131.322-0.221-0.2210.0000.0000.0000.000
141A374ARG10.9370.99332.3020.1350.1350.0000.0000.0000.000
142A375MET0-0.0060.01730.458-0.006-0.0060.0000.0000.0000.000
143A376HIS0-0.009-0.01625.7740.0020.0020.0000.0000.0000.000
144A377THR0-0.036-0.02229.753-0.013-0.0130.0000.0000.0000.000
145A378LEU00.005-0.00331.496-0.004-0.0040.0000.0000.0000.000
146A379ASN00.0330.00629.5910.0090.0090.0000.0000.0000.000
147A380ARG10.8860.96024.2380.3320.3320.0000.0000.0000.000
148A381TYR0-0.015-0.01928.952-0.001-0.0010.0000.0000.0000.000
149A382ARG10.8860.93531.7430.1790.1790.0000.0000.0000.000
150A383HIS00.0370.00726.2180.0110.0110.0000.0000.0000.000
151A384LEU0-0.001-0.00926.7860.0010.0010.0000.0000.0000.000
152A385LEU0-0.022-0.01229.5850.0070.0070.0000.0000.0000.000
153A386LYS10.7870.88530.8990.1910.1910.0000.0000.0000.000
154A387ALA0-0.0310.00126.8800.0020.0020.0000.0000.0000.000
155A388ASP-1-0.853-0.92127.442-0.275-0.2750.0000.0000.0000.000
156A389SER00.0190.00130.3610.0050.0050.0000.0000.0000.000
157A390LYS10.8640.92629.9160.2390.2390.0000.0000.0000.000
158A391GLU-1-0.880-0.95126.540-0.315-0.3150.0000.0000.0000.000
159A392ALA00.0210.01730.9580.0020.0020.0000.0000.0000.000
160A393ALA00.0310.00032.9410.0080.0080.0000.0000.0000.000
161A394ALA0-0.071-0.02032.5010.0100.0100.0000.0000.0000.000
162A395TYR00.0200.00229.547-0.009-0.0090.0000.0000.0000.000
163A396LYS10.9961.00333.4590.1430.1430.0000.0000.0000.000
164A397PRO00.0010.01336.4070.0050.0050.0000.0000.0000.000
165A398THR00.0440.00032.2560.0090.0090.0000.0000.0000.000
166A399VAL0-0.0140.00433.5370.0010.0010.0000.0000.0000.000
167A400ILE0-0.009-0.01235.7130.0050.0050.0000.0000.0000.000
168A401HIS0-0.024-0.00437.3350.0020.0020.0000.0000.0000.000
169A402ARG10.9330.96028.8540.2380.2380.0000.0000.0000.000
170A403LEU00.004-0.00536.5790.0040.0040.0000.0000.0000.000
171A404ARG10.9851.00638.7760.1190.1190.0000.0000.0000.000
172A405TYR00.012-0.01038.8220.0050.0050.0000.0000.0000.000
173A406ILE0-0.0440.00835.1240.0030.0030.0000.0000.0000.000
174A407ASP-1-0.825-0.89939.321-0.115-0.1150.0000.0000.0000.000
175A408LEU0-0.059-0.02742.8710.0050.0050.0000.0000.0000.000
176A409ARG10.8900.95236.5080.1510.1510.0000.0000.0000.000
177A410ILE00.0400.05139.8550.0050.0050.0000.0000.0000.000
178A411ASN00.023-0.00843.1550.0070.0070.0000.0000.0000.000
179A412GLY0-0.023-0.00945.8570.0050.0050.0000.0000.0000.000
180A413THR0-0.027-0.05742.6730.0040.0040.0000.0000.0000.000
181A414LEU0-0.019-0.01245.2810.0040.0040.0000.0000.0000.000
182A415ALA0-0.023-0.01248.2440.0050.0050.0000.0000.0000.000
183A416MET0-0.059-0.01644.1720.0030.0030.0000.0000.0000.000
184A417LEU0-0.022-0.01348.7300.0020.0020.0000.0000.0000.000
185A418ARG10.9390.97952.0200.0700.0700.0000.0000.0000.000
186A419ASP-1-0.879-0.92754.108-0.055-0.0550.0000.0000.0000.000
187A420PHE0-0.040-0.01452.3640.0020.0020.0000.0000.0000.000
188A421PRO00.0550.05156.064-0.001-0.0010.0000.0000.0000.000
189A422ASP-1-0.880-0.96457.110-0.053-0.0530.0000.0000.0000.000
190A423LEU00.012-0.01051.500-0.001-0.0010.0000.0000.0000.000
191A424GLU-1-0.981-1.00054.226-0.066-0.0660.0000.0000.0000.000
192A425LYS10.9140.96455.3340.0470.0470.0000.0000.0000.000
193A426TYR0-0.005-0.01956.2310.0000.0000.0000.0000.0000.000
194A427VAL00.0050.00349.699-0.002-0.0020.0000.0000.0000.000
195A428ARG11.0291.01751.0940.0690.0690.0000.0000.0000.000
196A429PRO0-0.0110.00451.135-0.004-0.0040.0000.0000.0000.000
197A430ILE00.0130.00849.066-0.002-0.0020.0000.0000.0000.000
198A431ALA0-0.001-0.00546.721-0.004-0.0040.0000.0000.0000.000
199A432VAL0-0.002-0.00746.702-0.004-0.0040.0000.0000.0000.000
200A433THR00.0190.01647.916-0.003-0.0030.0000.0000.0000.000
201A434TYR00.0270.03539.852-0.004-0.0040.0000.0000.0000.000
202A435TRP0-0.073-0.04241.829-0.002-0.0020.0000.0000.0000.000
203A436LYS10.8390.90543.6140.0890.0890.0000.0000.0000.000
204A437ASP-1-0.862-0.95044.880-0.095-0.0950.0000.0000.0000.000
205A438TYR0-0.022-0.03135.102-0.007-0.0070.0000.0000.0000.000
206A439ARG10.7770.84840.0520.1190.1190.0000.0000.0000.000
207A440ASP-1-0.825-0.88740.507-0.110-0.1100.0000.0000.0000.000
208A441GLU-1-0.994-0.98939.487-0.124-0.1240.0000.0000.0000.000
209A442VAL0-0.046-0.02734.598-0.009-0.0090.0000.0000.0000.000
210A443SER0-0.131-0.07535.779-0.011-0.0110.0000.0000.0000.000
211A444PRO00.0350.01237.6850.0040.0040.0000.0000.0000.000
212A445ASP-1-0.940-0.95540.894-0.114-0.1140.0000.0000.0000.000
213A446ILE0-0.045-0.01838.752-0.006-0.0060.0000.0000.0000.000
214A447SER00.0350.00642.0820.0020.0020.0000.0000.0000.000
215A448VAL0-0.056-0.02240.0060.0020.0020.0000.0000.0000.000
216A449GLU-1-0.780-0.85437.952-0.160-0.1600.0000.0000.0000.000
217A450ASP-1-0.956-0.96741.088-0.132-0.1320.0000.0000.0000.000