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: 6Y6RZ

Calculation Name: 1Q5Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q5Q

Chain ID: A

ChEMBL ID:

UniProt ID: Q53080

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2567995.91629
FMO2-HF: Nuclear repulsion 2483820.62699
FMO2-HF: Total energy -84175.2893
FMO2-MP2: Total energy -84422.710707


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:9:ALA)


Summations of interaction energy for fragment #1(A:9:ALA)
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.
-8.389-4.3731.849-2.424-3.4410.01
Interaction energy analysis for fragmet #1(A:9:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.002
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].
3A11GLN00.032-0.0092.916-3.600-0.7500.261-1.458-1.6530.008
4A12ILE00.0130.0262.478-3.492-2.3261.588-0.966-1.7880.002
5A13MET00.0500.0104.931-0.472-0.4720.0000.0000.0000.000
6A14ARG10.9400.9886.704-0.752-0.7520.0000.0000.0000.000
7A15ASP-1-0.870-0.9448.1371.3851.3850.0000.0000.0000.000
8A16ARG10.7390.8517.981-0.402-0.4020.0000.0000.0000.000
9A17SER00.0290.01610.739-0.118-0.1180.0000.0000.0000.000
10A18GLU-1-0.791-0.86712.6840.2630.2630.0000.0000.0000.000
11A19LEU0-0.049-0.01613.903-0.057-0.0570.0000.0000.0000.000
12A20ALA00.0170.00215.285-0.043-0.0430.0000.0000.0000.000
13A21ARG10.8680.91216.871-0.259-0.2590.0000.0000.0000.000
14A22LYS10.9090.94516.772-0.392-0.3920.0000.0000.0000.000
15A23GLY0-0.008-0.00219.861-0.018-0.0180.0000.0000.0000.000
16A24ILE0-0.019-0.00820.661-0.017-0.0170.0000.0000.0000.000
17A25ALA0-0.021-0.00222.904-0.012-0.0120.0000.0000.0000.000
18A26ARG10.9090.97921.288-0.179-0.1790.0000.0000.0000.000
19A27GLY0-0.040-0.00926.302-0.007-0.0070.0000.0000.0000.000
20A28ARG10.9360.96228.313-0.058-0.0580.0000.0000.0000.000
21A29SER0-0.016-0.02429.9330.0030.0030.0000.0000.0000.000
22A30VAL0-0.050-0.03631.534-0.003-0.0030.0000.0000.0000.000
23A31VAL00.0070.00532.5560.0010.0010.0000.0000.0000.000
24A32VAL0-0.024-0.00733.413-0.002-0.0020.0000.0000.0000.000
25A33LEU00.0090.00535.6110.0000.0000.0000.0000.0000.000
26A34THR00.0160.01038.239-0.001-0.0010.0000.0000.0000.000
27A35PHE0-0.067-0.04640.5840.0010.0010.0000.0000.0000.000
28A36ARG10.8710.94944.324-0.006-0.0060.0000.0000.0000.000
29A37ASP-1-0.886-0.93447.3040.0040.0040.0000.0000.0000.000
30A38GLY0-0.007-0.01544.012-0.001-0.0010.0000.0000.0000.000
31A39VAL0-0.049-0.01237.6640.0000.0000.0000.0000.0000.000
32A40LEU00.0100.01140.2840.0000.0000.0000.0000.0000.000
33A41PHE0-0.045-0.02934.8760.0000.0000.0000.0000.0000.000
34A42VAL00.0810.03837.5030.0000.0000.0000.0000.0000.000
35A43ALA00.0190.00334.8950.0020.0020.0000.0000.0000.000
36A44GLU-1-0.834-0.91034.7430.0510.0510.0000.0000.0000.000
37A45ASN0-0.095-0.08934.9720.0070.0070.0000.0000.0000.000
38A46PRO00.0110.01836.384-0.002-0.0020.0000.0000.0000.000
39A47SER0-0.0080.00937.852-0.003-0.0030.0000.0000.0000.000
40A48THR00.0640.02439.787-0.001-0.0010.0000.0000.0000.000
41A49ALA0-0.047-0.01840.404-0.002-0.0020.0000.0000.0000.000
42A50LEU0-0.067-0.03434.916-0.001-0.0010.0000.0000.0000.000
43A51HIS0-0.0120.00236.2650.0020.0020.0000.0000.0000.000
44A52LYS10.9080.95030.436-0.049-0.0490.0000.0000.0000.000
45A53VAL0-0.0010.01033.012-0.002-0.0020.0000.0000.0000.000
46A54SER0-0.051-0.04135.1170.0000.0000.0000.0000.0000.000
47A55GLU-1-0.864-0.90036.565-0.001-0.0010.0000.0000.0000.000
48A56LEU0-0.044-0.01432.4060.0000.0000.0000.0000.0000.000
49A57TYR00.0580.00736.472-0.002-0.0020.0000.0000.0000.000
50A58ASP-1-0.782-0.85939.239-0.007-0.0070.0000.0000.0000.000
51A59ARG10.7740.86640.8620.0070.0070.0000.0000.0000.000
52A60LEU00.0200.02935.0970.0000.0000.0000.0000.0000.000
53A61GLY00.0380.01436.4190.0010.0010.0000.0000.0000.000
54A62PHE0-0.011-0.00928.674-0.002-0.0020.0000.0000.0000.000
55A63ALA00.0750.03331.6630.0020.0020.0000.0000.0000.000
56A64ALA0-0.0120.00627.382-0.003-0.0030.0000.0000.0000.000
57A65VAL00.0000.00325.6780.0030.0030.0000.0000.0000.000
58A66GLY00.0610.02224.5150.0000.0000.0000.0000.0000.000
59A67LYS10.9000.94122.378-0.099-0.0990.0000.0000.0000.000
60A68TYR00.0490.01425.315-0.006-0.0060.0000.0000.0000.000
61A69ASN00.008-0.00524.6240.0000.0000.0000.0000.0000.000
62A70GLU-1-0.795-0.88420.9690.0850.0850.0000.0000.0000.000
63A71PHE00.0890.04024.832-0.010-0.0100.0000.0000.0000.000
64A72GLU-1-0.755-0.83526.6280.0120.0120.0000.0000.0000.000
65A73ASN0-0.077-0.03425.916-0.010-0.0100.0000.0000.0000.000
66A74LEU00.0700.02522.556-0.006-0.0060.0000.0000.0000.000
67A75ARG10.8120.89926.934-0.019-0.0190.0000.0000.0000.000
68A76ARG10.8580.92130.519-0.016-0.0160.0000.0000.0000.000
69A77ALA00.0300.02427.880-0.003-0.0030.0000.0000.0000.000
70A78GLY00.0390.02129.809-0.005-0.0050.0000.0000.0000.000
71A79ILE0-0.005-0.00531.000-0.002-0.0020.0000.0000.0000.000
72A80VAL0-0.0170.00332.297-0.001-0.0010.0000.0000.0000.000
73A81HIS0-0.011-0.01030.366-0.002-0.0020.0000.0000.0000.000
74A82ALA0-0.007-0.01432.784-0.002-0.0020.0000.0000.0000.000
75A83ASP-1-0.889-0.96035.534-0.011-0.0110.0000.0000.0000.000
76A84MET0-0.034-0.00732.623-0.002-0.0020.0000.0000.0000.000
77A85ARG10.9210.95333.0450.0360.0360.0000.0000.0000.000
78A86GLY00.005-0.00337.2260.0000.0000.0000.0000.0000.000
79A87TYR0-0.079-0.03040.4220.0010.0010.0000.0000.0000.000
80A88SER0-0.031-0.01538.886-0.001-0.0010.0000.0000.0000.000
81A89TYR0-0.087-0.02736.743-0.002-0.0020.0000.0000.0000.000
82A90ASP-1-0.755-0.87342.161-0.015-0.0150.0000.0000.0000.000
83A91ARG10.8480.88742.0960.0100.0100.0000.0000.0000.000
84A92ARG10.8170.89941.7790.0160.0160.0000.0000.0000.000
85A93ASP-1-0.878-0.93439.472-0.026-0.0260.0000.0000.0000.000
86A94VAL0-0.083-0.02836.353-0.003-0.0030.0000.0000.0000.000
87A95THR0-0.009-0.00634.7140.0010.0010.0000.0000.0000.000
88A96GLY00.0700.01834.026-0.001-0.0010.0000.0000.0000.000
89A97ARG10.9600.98630.1200.0400.0400.0000.0000.0000.000
90A98SER0-0.059-0.02229.726-0.006-0.0060.0000.0000.0000.000
91A99LEU00.0380.00929.328-0.004-0.0040.0000.0000.0000.000
92A100ALA00.0040.01727.726-0.001-0.0010.0000.0000.0000.000
93A101ASN00.019-0.00525.206-0.007-0.0070.0000.0000.0000.000
94A102ALA00.0070.02024.252-0.008-0.0080.0000.0000.0000.000
95A103TYR0-0.028-0.04023.889-0.003-0.0030.0000.0000.0000.000
96A104ALA00.0200.01521.3810.0010.0010.0000.0000.0000.000
97A105GLN00.0080.00419.217-0.003-0.0030.0000.0000.0000.000
98A106THR0-0.028-0.02719.129-0.012-0.0120.0000.0000.0000.000
99A107LEU0-0.035-0.02718.742-0.001-0.0010.0000.0000.0000.000
100A108GLY00.0670.04215.6860.0060.0060.0000.0000.0000.000
101A109THR0-0.026-0.00514.260-0.032-0.0320.0000.0000.0000.000
102A110ILE0-0.052-0.01914.440-0.006-0.0060.0000.0000.0000.000
103A111PHE0-0.023-0.02210.2380.0470.0470.0000.0000.0000.000
104A112THR0-0.0020.0209.458-0.009-0.0090.0000.0000.0000.000
105A113GLU-1-0.935-0.9659.843-0.235-0.2350.0000.0000.0000.000
106A114GLN0-0.0330.00612.4260.0180.0180.0000.0000.0000.000
107A115PRO00.015-0.00112.5500.0240.0240.0000.0000.0000.000
108A116LYS10.7260.84313.066-0.073-0.0730.0000.0000.0000.000
109A117PRO0-0.0020.02912.577-0.041-0.0410.0000.0000.0000.000
110A118TYR00.0520.01014.9820.0120.0120.0000.0000.0000.000
111A119GLU-1-0.870-0.92618.5580.1650.1650.0000.0000.0000.000
112A120VAL0-0.060-0.03820.101-0.006-0.0060.0000.0000.0000.000
113A121GLU-1-0.859-0.93821.3830.0530.0530.0000.0000.0000.000
114A122ILE0-0.033-0.02623.8960.0010.0010.0000.0000.0000.000
115A123CYS00.0000.01426.485-0.004-0.0040.0000.0000.0000.000
116A124VAL0-0.036-0.01529.2810.0000.0000.0000.0000.0000.000
117A125ALA00.0090.00831.657-0.001-0.0010.0000.0000.0000.000
118A126GLU-1-0.877-0.96435.145-0.018-0.0180.0000.0000.0000.000
119A127VAL00.0150.02937.6660.0010.0010.0000.0000.0000.000
120A128GLY00.0300.02141.326-0.002-0.0020.0000.0000.0000.000
121A129ARG10.9370.94343.1080.0170.0170.0000.0000.0000.000
122A130VAL00.0260.01846.3640.0000.0000.0000.0000.0000.000
123A131GLY00.0060.01549.7230.0010.0010.0000.0000.0000.000
124A132SER0-0.047-0.03245.3810.0000.0000.0000.0000.0000.000
125A133PRO00.0930.05947.6810.0010.0010.0000.0000.0000.000
126A134LYS10.8620.93538.6280.0140.0140.0000.0000.0000.000
127A135ALA00.0500.02541.5170.0010.0010.0000.0000.0000.000
128A136PRO0-0.004-0.00939.725-0.002-0.0020.0000.0000.0000.000
129A137GLN0-0.032-0.01733.9880.0000.0000.0000.0000.0000.000
130A138LEU00.0050.01233.0580.0010.0010.0000.0000.0000.000
131A139TYR00.0500.02528.540-0.005-0.0050.0000.0000.0000.000
132A140ARG10.9480.98223.799-0.014-0.0140.0000.0000.0000.000
133A141ILE0-0.028-0.01021.852-0.007-0.0070.0000.0000.0000.000
134A142THR00.021-0.00618.5710.0090.0090.0000.0000.0000.000
135A143TYR00.001-0.02314.443-0.019-0.0190.0000.0000.0000.000
136A144ASP-1-0.866-0.92013.837-0.035-0.0350.0000.0000.0000.000
137A145GLY0-0.0090.00415.435-0.039-0.0390.0000.0000.0000.000
138A146SER0-0.049-0.01717.484-0.018-0.0180.0000.0000.0000.000
139A147ILE0-0.041-0.04319.6000.0130.0130.0000.0000.0000.000
140A148VAL0-0.027-0.00123.280-0.005-0.0050.0000.0000.0000.000
141A149ASP-1-0.973-0.98826.110-0.021-0.0210.0000.0000.0000.000
142A150GLU-1-0.859-0.92429.7280.0040.0040.0000.0000.0000.000
143A151GLN0-0.026-0.02232.330-0.002-0.0020.0000.0000.0000.000
144A152HIS0-0.074-0.03635.6080.0000.0000.0000.0000.0000.000
145A153PHE00.032-0.00533.5840.0010.0010.0000.0000.0000.000
146A154VAL00.0140.01329.556-0.001-0.0010.0000.0000.0000.000
147A155VAL00.0120.00730.5170.0010.0010.0000.0000.0000.000
148A156MET0-0.031-0.00326.9950.0000.0000.0000.0000.0000.000
149A157GLY00.0150.00626.706-0.002-0.0020.0000.0000.0000.000
150A158GLY00.0600.06527.201-0.004-0.0040.0000.0000.0000.000
151A159THR0-0.038-0.04026.9030.0060.0060.0000.0000.0000.000
152A160THR00.0650.02726.618-0.005-0.0050.0000.0000.0000.000
153A161GLU-1-0.932-0.95326.6240.0750.0750.0000.0000.0000.000
154A162PRO0-0.0020.01130.056-0.006-0.0060.0000.0000.0000.000
155A163ILE00.0660.03232.526-0.005-0.0050.0000.0000.0000.000
156A164ALA0-0.036-0.02631.049-0.005-0.0050.0000.0000.0000.000
157A165THR0-0.007-0.03333.084-0.006-0.0060.0000.0000.0000.000
158A166ALA00.0690.05635.250-0.003-0.0030.0000.0000.0000.000
159A167MET0-0.0010.01135.939-0.003-0.0030.0000.0000.0000.000
160A168ARG10.8210.90532.008-0.032-0.0320.0000.0000.0000.000
161A169GLU-1-0.961-0.95737.4170.0230.0230.0000.0000.0000.000
162A170SER0-0.075-0.03540.766-0.002-0.0020.0000.0000.0000.000
163A171TYR0-0.010-0.01039.847-0.002-0.0020.0000.0000.0000.000
164A172ARG10.9330.96041.930-0.016-0.0160.0000.0000.0000.000
165A173ALA00.0100.00944.4220.0000.0000.0000.0000.0000.000
166A174ASP-1-0.884-0.95545.2800.0040.0040.0000.0000.0000.000
167A175LEU0-0.0060.01144.1010.0010.0010.0000.0000.0000.000
168A176ASP-1-0.793-0.91147.6470.0090.0090.0000.0000.0000.000
169A177LEU00.0090.00346.5360.0010.0010.0000.0000.0000.000
170A178GLU-1-0.908-0.97147.4040.0150.0150.0000.0000.0000.000
171A179ALA0-0.023-0.00748.4850.0010.0010.0000.0000.0000.000
172A180ALA0-0.020-0.01543.7250.0010.0010.0000.0000.0000.000
173A181VAL00.022-0.00143.3670.0020.0020.0000.0000.0000.000
174A182GLY00.0390.02743.8390.0020.0020.0000.0000.0000.000
175A183ILE0-0.075-0.03941.1020.0020.0020.0000.0000.0000.000
176A184ALA00.013-0.00639.4680.0020.0020.0000.0000.0000.000
177A185VAL00.005-0.00339.7850.0030.0030.0000.0000.0000.000
178A186ASN0-0.008-0.01341.4940.0030.0030.0000.0000.0000.000
179A187ALA0-0.015-0.00637.5360.0020.0020.0000.0000.0000.000
180A188LEU0-0.022-0.02435.4270.0030.0030.0000.0000.0000.000
181A189ARG10.8370.93937.407-0.028-0.0280.0000.0000.0000.000
182A190GLN0-0.068-0.01037.0940.0020.0020.0000.0000.0000.000
183A191GLY00.0140.00334.3880.0030.0030.0000.0000.0000.000
184A192GLY0-0.050-0.01932.884-0.001-0.0010.0000.0000.0000.000
185A201VAL0-0.003-0.00938.4090.0010.0010.0000.0000.0000.000
186A202ASP-1-0.867-0.94740.3630.0360.0360.0000.0000.0000.000
187A203VAL00.0630.04741.782-0.002-0.0020.0000.0000.0000.000
188A204ALA00.0350.01544.1080.0000.0000.0000.0000.0000.000
189A205SER0-0.110-0.06742.7750.0000.0000.0000.0000.0000.000
190A206LEU00.018-0.00239.8350.0030.0030.0000.0000.0000.000
191A207GLU-1-0.748-0.86836.9210.0240.0240.0000.0000.0000.000
192A208VAL00.0610.02839.2960.0000.0000.0000.0000.0000.000
193A209ALA0-0.061-0.03440.338-0.001-0.0010.0000.0000.0000.000
194A210VAL00.0270.01741.4850.0000.0000.0000.0000.0000.000
195A211LEU0-0.045-0.01938.628-0.001-0.0010.0000.0000.0000.000
196A212ASP-1-0.803-0.90442.6020.0020.0020.0000.0000.0000.000
197A213GLN00.024-0.00845.6880.0000.0000.0000.0000.0000.000
198A214SER0-0.026-0.00346.905-0.001-0.0010.0000.0000.0000.000
199A215ARG10.9040.96947.467-0.004-0.0040.0000.0000.0000.000
200A216PRO00.0300.00649.248-0.001-0.0010.0000.0000.0000.000
201A217ARG10.9110.95445.6870.0050.0050.0000.0000.0000.000
202A218ARG10.8700.93143.627-0.001-0.0010.0000.0000.0000.000
203A219ALA00.0560.02043.4860.0010.0010.0000.0000.0000.000
204A220PHE0-0.0050.02838.8020.0010.0010.0000.0000.0000.000
205A221ARG10.8400.90643.139-0.007-0.0070.0000.0000.0000.000
206A222ARG10.8860.94338.424-0.016-0.0160.0000.0000.0000.000
207A223ILE0-0.006-0.00644.631-0.001-0.0010.0000.0000.0000.000
208A224ALA0-0.0060.00046.1330.0010.0010.0000.0000.0000.000
209A225GLY00.0980.03648.3290.0000.0000.0000.0000.0000.000
210A226THR00.0380.01649.7310.0000.0000.0000.0000.0000.000
211A227ALA0-0.012-0.01150.6690.0000.0000.0000.0000.0000.000
212A228LEU0-0.007-0.01144.5000.0000.0000.0000.0000.0000.000
213A229GLU-1-0.956-0.97949.0680.0210.0210.0000.0000.0000.000
214A230GLN0-0.078-0.03151.5370.0000.0000.0000.0000.0000.000
215A231LEU0-0.0090.00848.273-0.001-0.0010.0000.0000.0000.000
216A232VAL0-0.0270.00245.8450.0000.0000.0000.0000.0000.000
217A233PRO00.0030.01846.7150.0000.0000.0000.0000.0000.000
218A234ALA00.0210.00248.2090.0020.0020.0000.0000.0000.000
219A235GLU-1-0.977-0.98746.3730.0340.0340.0000.0000.0000.000