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: R85K8

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2577246.758776
FMO2-HF: Nuclear repulsion 2493070.01132
FMO2-HF: Total energy -84176.747456
FMO2-MP2: Total energy -84424.126697


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.
-2.789-0.00400000000000020.509-1.294-1.9980.003
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 : 0.015 / q_NPA : -0.004
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].
3A11GLN0-0.009-0.0233.543-0.9970.6300.002-0.733-0.8950.002
4A12ILE00.0230.0292.686-1.940-0.7820.507-0.561-1.1030.001
5A13MET00.0420.0194.835-0.030-0.0300.0000.0000.0000.000
6A14ARG10.9040.9646.806-0.040-0.0400.0000.0000.0000.000
7A15ASP-1-0.828-0.9338.3301.0551.0550.0000.0000.0000.000
8A16ARG10.7700.8698.039-0.121-0.1210.0000.0000.0000.000
9A17SER00.0490.02310.665-0.049-0.0490.0000.0000.0000.000
10A18GLU-1-0.841-0.88512.5020.1600.1600.0000.0000.0000.000
11A19LEU0-0.0030.00513.700-0.022-0.0220.0000.0000.0000.000
12A20ALA00.0360.01215.146-0.018-0.0180.0000.0000.0000.000
13A21ARG10.8790.92116.651-0.117-0.1170.0000.0000.0000.000
14A22LYS10.8690.92916.215-0.251-0.2510.0000.0000.0000.000
15A23GLY00.007-0.00719.560-0.006-0.0060.0000.0000.0000.000
16A24ILE0-0.046-0.01720.234-0.007-0.0070.0000.0000.0000.000
17A25ALA0-0.0040.00222.623-0.005-0.0050.0000.0000.0000.000
18A26ARG10.8270.92521.067-0.110-0.1100.0000.0000.0000.000
19A27GLY0-0.038-0.01025.918-0.001-0.0010.0000.0000.0000.000
20A28ARG10.9020.93528.056-0.034-0.0340.0000.0000.0000.000
21A29SER00.0260.00430.581-0.001-0.0010.0000.0000.0000.000
22A30VAL0-0.087-0.05331.4570.0000.0000.0000.0000.0000.000
23A31VAL00.0220.02232.405-0.001-0.0010.0000.0000.0000.000
24A32VAL0-0.031-0.02033.4650.0000.0000.0000.0000.0000.000
25A33LEU0-0.0030.00235.722-0.002-0.0020.0000.0000.0000.000
26A34THR0-0.0030.00438.2200.0000.0000.0000.0000.0000.000
27A35PHE0-0.031-0.02240.4540.0010.0010.0000.0000.0000.000
28A36ARG10.8140.88544.1980.0050.0050.0000.0000.0000.000
29A37ASP-1-0.886-0.93847.163-0.007-0.0070.0000.0000.0000.000
30A38GLY0-0.020-0.02143.850-0.001-0.0010.0000.0000.0000.000
31A39VAL0-0.046-0.01137.582-0.001-0.0010.0000.0000.0000.000
32A40LEU00.0230.01640.4540.0010.0010.0000.0000.0000.000
33A41PHE0-0.021-0.02335.106-0.001-0.0010.0000.0000.0000.000
34A42VAL00.0590.02237.4790.0010.0010.0000.0000.0000.000
35A43ALA00.0330.00735.0360.0000.0000.0000.0000.0000.000
36A44GLU-1-0.765-0.86234.1340.0290.0290.0000.0000.0000.000
37A45ASN0-0.062-0.06834.9140.0050.0050.0000.0000.0000.000
38A46PRO00.0460.04136.692-0.001-0.0010.0000.0000.0000.000
39A47SER0-0.035-0.01037.963-0.001-0.0010.0000.0000.0000.000
40A48THR00.0460.01039.822-0.001-0.0010.0000.0000.0000.000
41A49ALA0-0.031-0.01440.633-0.002-0.0020.0000.0000.0000.000
42A50LEU0-0.064-0.02334.437-0.001-0.0010.0000.0000.0000.000
43A51HIS00.0160.01835.6350.0000.0000.0000.0000.0000.000
44A52LYS10.8030.88531.316-0.019-0.0190.0000.0000.0000.000
45A53VAL00.0010.00632.968-0.003-0.0030.0000.0000.0000.000
46A54SER0-0.069-0.03834.9000.0020.0020.0000.0000.0000.000
47A55GLU-1-0.818-0.87436.688-0.012-0.0120.0000.0000.0000.000
48A56LEU0-0.042-0.00732.3090.0000.0000.0000.0000.0000.000
49A57TYR00.024-0.03236.311-0.001-0.0010.0000.0000.0000.000
50A58ASP-1-0.795-0.85439.098-0.015-0.0150.0000.0000.0000.000
51A59ARG10.7730.85740.7210.0170.0170.0000.0000.0000.000
52A60LEU00.0080.01535.132-0.001-0.0010.0000.0000.0000.000
53A61GLY00.0510.01536.2900.0020.0020.0000.0000.0000.000
54A62PHE00.0020.00028.572-0.003-0.0030.0000.0000.0000.000
55A63ALA00.0380.01131.6710.0030.0030.0000.0000.0000.000
56A64ALA0-0.0140.00227.602-0.004-0.0040.0000.0000.0000.000
57A65VAL00.0250.01725.6650.0040.0040.0000.0000.0000.000
58A66GLY00.0620.02524.539-0.002-0.0020.0000.0000.0000.000
59A67LYS10.8760.93922.472-0.064-0.0640.0000.0000.0000.000
60A68TYR00.0270.00325.297-0.004-0.0040.0000.0000.0000.000
61A69ASN00.015-0.00624.4180.0010.0010.0000.0000.0000.000
62A70GLU-1-0.809-0.88421.0310.0510.0510.0000.0000.0000.000
63A71PHE00.0860.03624.444-0.009-0.0090.0000.0000.0000.000
64A72GLU-1-0.766-0.82126.488-0.001-0.0010.0000.0000.0000.000
65A73ASN0-0.032-0.00824.703-0.007-0.0070.0000.0000.0000.000
66A74LEU00.0730.03422.479-0.004-0.0040.0000.0000.0000.000
67A75ARG10.8370.91326.920-0.004-0.0040.0000.0000.0000.000
68A76ARG10.8420.89730.549-0.005-0.0050.0000.0000.0000.000
69A77ALA00.0320.01927.822-0.001-0.0010.0000.0000.0000.000
70A78GLY00.0220.01229.796-0.004-0.0040.0000.0000.0000.000
71A79ILE0-0.002-0.00130.967-0.001-0.0010.0000.0000.0000.000
72A80VAL0-0.030-0.01232.5090.0000.0000.0000.0000.0000.000
73A81HIS0-0.018-0.01029.9020.0000.0000.0000.0000.0000.000
74A82ALA00.0100.00732.559-0.001-0.0010.0000.0000.0000.000
75A83ASP-1-0.787-0.89435.338-0.018-0.0180.0000.0000.0000.000
76A84MET0-0.0310.00632.687-0.001-0.0010.0000.0000.0000.000
77A85ARG10.8600.92432.8800.0400.0400.0000.0000.0000.000
78A86GLY0-0.005-0.00936.430-0.001-0.0010.0000.0000.0000.000
79A87TYR0-0.058-0.03439.9980.0010.0010.0000.0000.0000.000
80A88SER0-0.045-0.03037.9070.0000.0000.0000.0000.0000.000
81A89TYR0-0.076-0.03036.258-0.002-0.0020.0000.0000.0000.000
82A90ASP-1-0.790-0.86741.812-0.020-0.0200.0000.0000.0000.000
83A91ARG10.8170.87141.5060.0170.0170.0000.0000.0000.000
84A92ARG10.8190.89341.2710.0210.0210.0000.0000.0000.000
85A93ASP-1-0.823-0.90539.045-0.032-0.0320.0000.0000.0000.000
86A94VAL0-0.065-0.01035.692-0.004-0.0040.0000.0000.0000.000
87A95THR0-0.003-0.01234.7610.0000.0000.0000.0000.0000.000
88A96GLY00.0330.00833.403-0.002-0.0020.0000.0000.0000.000
89A97ARG10.9771.00130.1820.0520.0520.0000.0000.0000.000
90A98SER0-0.031-0.00129.429-0.005-0.0050.0000.0000.0000.000
91A99LEU0-0.0020.00729.668-0.002-0.0020.0000.0000.0000.000
92A100ALA00.0260.01227.387-0.002-0.0020.0000.0000.0000.000
93A101ASN00.001-0.02024.724-0.010-0.0100.0000.0000.0000.000
94A102ALA00.0200.02723.735-0.008-0.0080.0000.0000.0000.000
95A103TYR0-0.039-0.03523.566-0.002-0.0020.0000.0000.0000.000
96A104ALA00.0350.02521.020-0.002-0.0020.0000.0000.0000.000
97A105GLN00.0230.01817.871-0.009-0.0090.0000.0000.0000.000
98A106THR0-0.035-0.02418.711-0.010-0.0100.0000.0000.0000.000
99A107LEU0-0.024-0.01718.6170.0010.0010.0000.0000.0000.000
100A108GLY00.0770.05215.085-0.003-0.0030.0000.0000.0000.000
101A109THR0-0.049-0.02013.895-0.039-0.0390.0000.0000.0000.000
102A110ILE0-0.039-0.02814.486-0.003-0.0030.0000.0000.0000.000
103A111PHE0-0.029-0.0219.8690.0400.0400.0000.0000.0000.000
104A112THR0-0.033-0.0119.180-0.033-0.0330.0000.0000.0000.000
105A113GLU-1-0.941-0.9719.912-0.180-0.1800.0000.0000.0000.000
106A114GLN0-0.0200.00812.5380.0440.0440.0000.0000.0000.000
107A115PRO00.0150.00512.8410.0160.0160.0000.0000.0000.000
108A116LYS10.7220.83713.302-0.033-0.0330.0000.0000.0000.000
109A117PRO00.0360.04012.584-0.027-0.0270.0000.0000.0000.000
110A118TYR00.006-0.02215.0850.0240.0240.0000.0000.0000.000
111A119GLU-1-0.797-0.88618.5160.1010.1010.0000.0000.0000.000
112A120VAL0-0.054-0.03220.2140.0010.0010.0000.0000.0000.000
113A121GLU-1-0.794-0.89721.240-0.017-0.0170.0000.0000.0000.000
114A122ILE0-0.031-0.02023.8290.0060.0060.0000.0000.0000.000
115A123CYS0-0.017-0.00426.634-0.005-0.0050.0000.0000.0000.000
116A124VAL0-0.037-0.01829.0520.0030.0030.0000.0000.0000.000
117A125ALA00.0220.02131.471-0.002-0.0020.0000.0000.0000.000
118A126GLU-1-0.819-0.93334.935-0.034-0.0340.0000.0000.0000.000
119A127VAL00.0130.01437.2750.0000.0000.0000.0000.0000.000
120A128GLY00.0740.05641.005-0.001-0.0010.0000.0000.0000.000
121A129ARG10.9110.92941.8010.0270.0270.0000.0000.0000.000
122A130VAL00.0110.01345.7650.0000.0000.0000.0000.0000.000
123A131GLY00.0490.02849.0430.0000.0000.0000.0000.0000.000
124A132SER0-0.061-0.02145.986-0.001-0.0010.0000.0000.0000.000
125A133PRO00.0510.02047.3950.0000.0000.0000.0000.0000.000
126A134LYS10.7930.90337.9250.0290.0290.0000.0000.0000.000
127A135ALA00.0750.03741.7340.0010.0010.0000.0000.0000.000
128A136PRO00.0000.00339.206-0.002-0.0020.0000.0000.0000.000
129A137GLN0-0.058-0.04832.9230.0020.0020.0000.0000.0000.000
130A138LEU0-0.0210.00033.0160.0020.0020.0000.0000.0000.000
131A139TYR00.0480.01728.111-0.002-0.0020.0000.0000.0000.000
132A140ARG10.8090.88524.4580.0330.0330.0000.0000.0000.000
133A141ILE0-0.015-0.00921.741-0.008-0.0080.0000.0000.0000.000
134A142THR0-0.001-0.01718.9080.0150.0150.0000.0000.0000.000
135A143TYR00.000-0.02414.535-0.004-0.0040.0000.0000.0000.000
136A144ASP-1-0.800-0.86614.132-0.120-0.1200.0000.0000.0000.000
137A145GLY00.0000.00015.015-0.035-0.0350.0000.0000.0000.000
138A146SER0-0.044-0.03316.876-0.003-0.0030.0000.0000.0000.000
139A147ILE0-0.056-0.03919.0510.0170.0170.0000.0000.0000.000
140A148VAL0-0.0170.00622.814-0.006-0.0060.0000.0000.0000.000
141A149ASP-1-0.908-0.95725.842-0.046-0.0460.0000.0000.0000.000
142A150GLU-1-0.786-0.88428.532-0.031-0.0310.0000.0000.0000.000
143A151GLN00.0170.01232.1160.0030.0030.0000.0000.0000.000
144A152HIS0-0.093-0.04735.5130.0020.0020.0000.0000.0000.000
145A153PHE00.0270.00333.7760.0020.0020.0000.0000.0000.000
146A154VAL00.0270.02530.071-0.003-0.0030.0000.0000.0000.000
147A155VAL0-0.009-0.01130.6800.0030.0030.0000.0000.0000.000
148A156MET0-0.0210.00427.067-0.004-0.0040.0000.0000.0000.000
149A157GLY00.0290.00926.3610.0020.0020.0000.0000.0000.000
150A158GLY00.0520.05826.996-0.003-0.0030.0000.0000.0000.000
151A159THR0-0.020-0.02627.1630.0010.0010.0000.0000.0000.000
152A160THR00.0270.02026.381-0.002-0.0020.0000.0000.0000.000
153A161GLU-1-0.902-0.94626.9040.0200.0200.0000.0000.0000.000
154A162PRO00.0070.01330.191-0.004-0.0040.0000.0000.0000.000
155A163ILE00.0280.03132.245-0.003-0.0030.0000.0000.0000.000
156A164ALA00.000-0.01631.202-0.003-0.0030.0000.0000.0000.000
157A165THR0-0.071-0.05333.011-0.003-0.0030.0000.0000.0000.000
158A166ALA00.0750.04935.264-0.002-0.0020.0000.0000.0000.000
159A167MET0-0.0250.00635.787-0.001-0.0010.0000.0000.0000.000
160A168ARG10.8730.92731.3580.0060.0060.0000.0000.0000.000
161A169GLU-1-0.959-0.96037.5010.0020.0020.0000.0000.0000.000
162A170SER0-0.052-0.03840.8550.0000.0000.0000.0000.0000.000
163A171TYR0-0.027-0.03439.829-0.001-0.0010.0000.0000.0000.000
164A172ARG10.9340.96341.9100.0020.0020.0000.0000.0000.000
165A173ALA00.0330.01344.1540.0000.0000.0000.0000.0000.000
166A174ASP-1-0.858-0.91045.265-0.008-0.0080.0000.0000.0000.000
167A175LEU0-0.0010.01943.6480.0010.0010.0000.0000.0000.000
168A176ASP-1-0.794-0.90747.449-0.004-0.0040.0000.0000.0000.000
169A177LEU00.0190.01146.5980.0000.0000.0000.0000.0000.000
170A178GLU-1-0.894-0.94747.5510.0030.0030.0000.0000.0000.000
171A179ALA0-0.026-0.01148.3810.0010.0010.0000.0000.0000.000
172A180ALA0-0.020-0.01144.0390.0000.0000.0000.0000.0000.000
173A181VAL00.003-0.00843.3990.0000.0000.0000.0000.0000.000
174A182GLY00.0490.02543.9150.0010.0010.0000.0000.0000.000
175A183ILE0-0.051-0.02541.1050.0010.0010.0000.0000.0000.000
176A184ALA00.010-0.00539.4390.0010.0010.0000.0000.0000.000
177A185VAL0-0.0040.00139.5320.0010.0010.0000.0000.0000.000
178A186ASN0-0.009-0.01641.1560.0030.0030.0000.0000.0000.000
179A187ALA00.0060.01237.5710.0010.0010.0000.0000.0000.000
180A188LEU0-0.014-0.01935.1840.0020.0020.0000.0000.0000.000
181A189ARG10.7370.85637.253-0.010-0.0100.0000.0000.0000.000
182A190GLN0-0.0300.00437.1350.0020.0020.0000.0000.0000.000
183A191GLY0-0.019-0.00934.0970.0010.0010.0000.0000.0000.000
184A192GLY0-0.065-0.03033.0640.0040.0040.0000.0000.0000.000
185A201VAL00.002-0.01138.0970.0010.0010.0000.0000.0000.000
186A202ASP-1-0.849-0.93340.1520.0140.0140.0000.0000.0000.000
187A203VAL00.0700.05941.864-0.002-0.0020.0000.0000.0000.000
188A204ALA00.0580.02944.0260.0000.0000.0000.0000.0000.000
189A205SER0-0.122-0.06642.9320.0000.0000.0000.0000.0000.000
190A206LEU0-0.010-0.00439.7640.0020.0020.0000.0000.0000.000
191A207GLU-1-0.725-0.82637.0410.0070.0070.0000.0000.0000.000
192A208VAL00.0490.01839.426-0.001-0.0010.0000.0000.0000.000
193A209ALA0-0.062-0.02540.1630.0000.0000.0000.0000.0000.000
194A210VAL00.0320.02341.5820.0000.0000.0000.0000.0000.000
195A211LEU0-0.063-0.02938.4530.0000.0000.0000.0000.0000.000
196A212ASP-1-0.752-0.84942.403-0.009-0.0090.0000.0000.0000.000
197A213GLN00.007-0.01445.395-0.001-0.0010.0000.0000.0000.000
198A214SER0-0.027-0.03046.7790.0000.0000.0000.0000.0000.000
199A215ARG10.8480.92446.4130.0070.0070.0000.0000.0000.000
200A216PRO00.0190.00149.001-0.001-0.0010.0000.0000.0000.000
201A217ARG10.8860.93445.5690.0120.0120.0000.0000.0000.000
202A218ARG10.8590.91643.3050.0080.0080.0000.0000.0000.000
203A219ALA00.0710.04642.9300.0010.0010.0000.0000.0000.000
204A220PHE0-0.0260.00438.9680.0010.0010.0000.0000.0000.000
205A221ARG10.8550.92043.0210.0050.0050.0000.0000.0000.000
206A222ARG10.8250.88338.776-0.003-0.0030.0000.0000.0000.000
207A223ILE00.0000.00044.351-0.001-0.0010.0000.0000.0000.000
208A224ALA00.0070.00845.9840.0010.0010.0000.0000.0000.000
209A225GLY00.0650.02148.1730.0000.0000.0000.0000.0000.000
210A226THR00.0240.00649.3620.0000.0000.0000.0000.0000.000
211A227ALA0-0.0020.00850.4350.0000.0000.0000.0000.0000.000
212A228LEU0-0.010-0.00944.2620.0000.0000.0000.0000.0000.000
213A229GLU-1-0.903-0.96148.7910.0100.0100.0000.0000.0000.000
214A230GLN0-0.094-0.03551.4090.0000.0000.0000.0000.0000.000
215A231LEU0-0.024-0.01248.172-0.001-0.0010.0000.0000.0000.000
216A232VAL0-0.012-0.00245.5550.0000.0000.0000.0000.0000.000
217A233PRO0-0.0100.01746.6240.0000.0000.0000.0000.0000.000
218A234ALA00.0370.01048.0730.0010.0010.0000.0000.0000.000
219A235GLU-1-0.953-0.97246.5930.0140.0140.0000.0000.0000.000