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: Q1RNY

Calculation Name: 4IYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IYP

Chain ID: A

ChEMBL ID:

UniProt ID: P78318

Base Structure: X-ray

Registration Date: 2023-06-20

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2478573.42127
FMO2-HF: Nuclear repulsion 2393358.571701
FMO2-HF: Total energy -85214.849569
FMO2-MP2: Total energy -85462.169172


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-7.781-4.2940.083-1.521-2.0480.001
Interaction energy analysis for fragmet #1(A:0: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 : -0.020
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].
3A2ALA00.0110.0213.391-1.4011.1820.018-1.246-1.3550.001
4A3ALA00.011-0.0073.088-1.044-0.4790.066-0.152-0.4780.000
5A4GLU-1-0.966-0.9933.972-5.315-4.976-0.001-0.123-0.2150.000
6A5ASP-1-0.944-0.9545.903-0.169-0.1690.0000.0000.0000.000
7A6GLU-1-0.949-0.9817.9250.5740.5740.0000.0000.0000.000
8A7LEU0-0.118-0.0317.0710.1710.1710.0000.0000.0000.000
9A8GLN00.000-0.00410.124-0.070-0.0700.0000.0000.0000.000
10A9LEU0-0.011-0.01112.0530.0650.0650.0000.0000.0000.000
11A10PRO0-0.014-0.00215.465-0.008-0.0080.0000.0000.0000.000
12A11ARG10.9380.97416.9300.1780.1780.0000.0000.0000.000
13A12LEU00.0580.02720.8200.0200.0200.0000.0000.0000.000
14A13PRO00.0080.00123.8010.0110.0110.0000.0000.0000.000
15A14GLU-1-0.853-0.92921.774-0.054-0.0540.0000.0000.0000.000
16A15LEU0-0.040-0.00919.7190.0150.0150.0000.0000.0000.000
17A16PHE00.0320.00923.8320.0100.0100.0000.0000.0000.000
18A17GLU-1-0.818-0.88627.440-0.025-0.0250.0000.0000.0000.000
19A18THR0-0.010-0.02225.0210.0120.0120.0000.0000.0000.000
20A19GLY0-0.003-0.00727.0390.0070.0070.0000.0000.0000.000
21A20ARG10.8050.87827.9690.0350.0350.0000.0000.0000.000
22A21GLN0-0.059-0.03330.4590.0080.0080.0000.0000.0000.000
23A22LEU0-0.0070.00126.6700.0050.0050.0000.0000.0000.000
24A23LEU0-0.038-0.00831.0770.0030.0030.0000.0000.0000.000
25A24ASP-1-0.928-0.97233.574-0.016-0.0160.0000.0000.0000.000
26A25GLU-1-0.904-0.95432.1540.0140.0140.0000.0000.0000.000
27A26VAL0-0.057-0.03632.8280.0030.0030.0000.0000.0000.000
28A27GLU-1-0.890-0.92135.920-0.013-0.0130.0000.0000.0000.000
29A28VAL0-0.050-0.02538.8720.0000.0000.0000.0000.0000.000
30A29ALA0-0.0290.00837.6070.0030.0030.0000.0000.0000.000
31A30THR0-0.045-0.02239.5080.0000.0000.0000.0000.0000.000
32A31GLU-1-0.855-0.93136.6570.0180.0180.0000.0000.0000.000
33A32PRO00.0090.00240.112-0.002-0.0020.0000.0000.0000.000
34A33ALA00.0800.03238.3290.0020.0020.0000.0000.0000.000
35A34GLY00.0100.00336.856-0.001-0.0010.0000.0000.0000.000
36A35SER0-0.074-0.03636.5770.0040.0040.0000.0000.0000.000
37A36ARG10.8600.90128.847-0.059-0.0590.0000.0000.0000.000
38A37ILE00.0300.01731.6590.0000.0000.0000.0000.0000.000
39A38VAL00.0400.03832.655-0.002-0.0020.0000.0000.0000.000
40A39GLN0-0.008-0.02931.514-0.005-0.0050.0000.0000.0000.000
41A40GLU-1-0.839-0.91227.5960.0480.0480.0000.0000.0000.000
42A41LYS10.8420.93127.348-0.019-0.0190.0000.0000.0000.000
43A42VAL00.0270.00928.705-0.006-0.0060.0000.0000.0000.000
44A43PHE0-0.038-0.01421.870-0.007-0.0070.0000.0000.0000.000
45A44LYS10.9700.98421.502-0.008-0.0080.0000.0000.0000.000
46A45GLY00.0540.02024.512-0.009-0.0090.0000.0000.0000.000
47A46LEU0-0.022-0.01826.358-0.010-0.0100.0000.0000.0000.000
48A47ASP-1-0.845-0.89919.658-0.069-0.0690.0000.0000.0000.000
49A48LEU0-0.032-0.02021.039-0.017-0.0170.0000.0000.0000.000
50A49LEU00.0230.00422.870-0.016-0.0160.0000.0000.0000.000
51A50GLU-1-0.966-0.97721.495-0.111-0.1110.0000.0000.0000.000
52A51LYS10.8150.89517.0180.0850.0850.0000.0000.0000.000
53A52ALA0-0.012-0.00520.881-0.018-0.0180.0000.0000.0000.000
54A53ALA00.0040.00123.841-0.005-0.0050.0000.0000.0000.000
55A54GLU-1-0.824-0.90719.600-0.234-0.2340.0000.0000.0000.000
56A55MET0-0.065-0.03720.194-0.022-0.0220.0000.0000.0000.000
57A56LEU0-0.020-0.01622.0590.0010.0010.0000.0000.0000.000
58A57SER0-0.049-0.01023.6410.0040.0040.0000.0000.0000.000
59A58GLN0-0.086-0.06719.573-0.009-0.0090.0000.0000.0000.000
60A59LEU0-0.084-0.04622.924-0.010-0.0100.0000.0000.0000.000
61A60ASP-1-0.952-0.96625.628-0.119-0.1190.0000.0000.0000.000
62A61LEU0-0.051-0.01928.1270.0080.0080.0000.0000.0000.000
63A62PHE0-0.036-0.02030.6810.0090.0090.0000.0000.0000.000
64A63SER00.0600.01533.151-0.001-0.0010.0000.0000.0000.000
65A64ARG10.9400.95934.8130.0730.0730.0000.0000.0000.000
66A65ASN0-0.120-0.07537.8480.0040.0040.0000.0000.0000.000
67A66GLU-1-0.767-0.82736.606-0.087-0.0870.0000.0000.0000.000
68A67ASP-1-0.858-0.92040.840-0.048-0.0480.0000.0000.0000.000
69A68LEU00.006-0.00940.294-0.003-0.0030.0000.0000.0000.000
70A69GLU-1-0.903-0.96441.192-0.046-0.0460.0000.0000.0000.000
71A70GLU-1-0.957-0.96639.482-0.062-0.0620.0000.0000.0000.000
72A71ILE0-0.0530.00035.631-0.004-0.0040.0000.0000.0000.000
73A72ALA00.0660.03334.9990.0060.0060.0000.0000.0000.000
74A73SER00.011-0.02836.675-0.002-0.0020.0000.0000.0000.000
75A74THR0-0.063-0.04633.4140.0040.0040.0000.0000.0000.000
76A75ASP-1-0.861-0.92332.201-0.085-0.0850.0000.0000.0000.000
77A76LEU00.0310.02433.633-0.002-0.0020.0000.0000.0000.000
78A77LYS10.8640.93731.2400.0640.0640.0000.0000.0000.000
79A78TYR0-0.016-0.01629.1780.0040.0040.0000.0000.0000.000
80A79LEU00.0550.04231.458-0.004-0.0040.0000.0000.0000.000
81A80LEU0-0.048-0.02834.1150.0010.0010.0000.0000.0000.000
82A81VAL0-0.0080.01727.5790.0050.0050.0000.0000.0000.000
83A82PRO00.0600.02730.9200.0040.0040.0000.0000.0000.000
84A83ALA00.0130.01132.1960.0050.0050.0000.0000.0000.000
85A84PHE00.008-0.00831.2910.0060.0060.0000.0000.0000.000
86A85GLN00.0420.02326.7460.0040.0040.0000.0000.0000.000
87A86GLY00.0260.02331.0650.0040.0040.0000.0000.0000.000
88A87ALA0-0.001-0.00234.4300.0040.0040.0000.0000.0000.000
89A88LEU00.0040.00229.5700.0050.0050.0000.0000.0000.000
90A89THR0-0.040-0.03331.7670.0040.0040.0000.0000.0000.000
91A90MET0-0.063-0.02233.0570.0040.0040.0000.0000.0000.000
92A91LYS10.7970.89834.7700.0170.0170.0000.0000.0000.000
93A92GLN00.0160.02429.5030.0010.0010.0000.0000.0000.000
94A93VAL0-0.039-0.01734.072-0.001-0.0010.0000.0000.0000.000
95A94ASN00.025-0.00232.6180.0030.0030.0000.0000.0000.000
96A95PRO00.0490.01835.610-0.003-0.0030.0000.0000.0000.000
97A96SER0-0.053-0.01935.753-0.003-0.0030.0000.0000.0000.000
98A97LYS10.9110.95231.0340.0000.0000.0000.0000.0000.000
99A98ARG10.8300.89535.5420.0110.0110.0000.0000.0000.000
100A99LEU00.0410.01337.830-0.002-0.0020.0000.0000.0000.000
101A100ASP-1-0.853-0.89932.145-0.038-0.0380.0000.0000.0000.000
102A101HIS0-0.013-0.02231.5800.0010.0010.0000.0000.0000.000
103A102LEU0-0.0020.01134.649-0.003-0.0030.0000.0000.0000.000
104A103GLN00.0070.00036.406-0.002-0.0020.0000.0000.0000.000
105A104ARG10.9450.95027.8390.0520.0520.0000.0000.0000.000
106A105ALA00.0270.01933.653-0.004-0.0040.0000.0000.0000.000
107A106ARG10.7260.83035.5110.0360.0360.0000.0000.0000.000
108A107GLU-1-0.927-0.95732.201-0.070-0.0700.0000.0000.0000.000
109A108HIS00.0090.01628.784-0.005-0.0050.0000.0000.0000.000
110A109PHE00.013-0.00933.905-0.002-0.0020.0000.0000.0000.000
111A110ILE0-0.015-0.00437.4660.0000.0000.0000.0000.0000.000
112A111ASN0-0.025-0.00633.308-0.004-0.0040.0000.0000.0000.000
113A112TYR0-0.010-0.00135.628-0.002-0.0020.0000.0000.0000.000
114A113LEU0-0.0010.00336.6240.0000.0000.0000.0000.0000.000
115A114THR0-0.009-0.03338.0610.0010.0010.0000.0000.0000.000
116A115GLN00.0130.00634.3030.0050.0050.0000.0000.0000.000
117A116CYS0-0.023-0.01638.1390.0010.0010.0000.0000.0000.000
118A117HIS0-0.069-0.02840.6670.0000.0000.0000.0000.0000.000
119A118CYS0-0.072-0.03439.9770.0010.0010.0000.0000.0000.000
120A119TYR0-0.014-0.01536.5680.0010.0010.0000.0000.0000.000
121A120HIS0-0.096-0.05441.9810.0040.0040.0000.0000.0000.000
122A121VAL00.0050.00940.9140.0020.0020.0000.0000.0000.000
123A122ALA0-0.034-0.02744.3850.0030.0030.0000.0000.0000.000
124A123GLU-1-0.947-0.95847.450-0.033-0.0330.0000.0000.0000.000
125A124PHE0-0.063-0.04243.2930.0020.0020.0000.0000.0000.000
126A125GLU-1-0.949-0.97148.976-0.031-0.0310.0000.0000.0000.000
127A126LEU00.0040.00841.9240.0010.0010.0000.0000.0000.000
128A127PRO0-0.017-0.00843.9940.0010.0010.0000.0000.0000.000
129A142SER00.0150.00644.456-0.002-0.0020.0000.0000.0000.000
130A143MET00.0750.02740.0870.0000.0000.0000.0000.0000.000
131A144ALA0-0.0010.00540.125-0.001-0.0010.0000.0000.0000.000
132A145TYR00.0110.02642.0130.0020.0020.0000.0000.0000.000
133A146PRO0-0.072-0.02944.181-0.001-0.0010.0000.0000.0000.000
134A147SER00.0800.01446.227-0.002-0.0020.0000.0000.0000.000
135A148LEU0-0.097-0.03947.9980.0020.0020.0000.0000.0000.000
136A149VAL00.0670.03351.7260.0000.0000.0000.0000.0000.000
137A150ALA00.0350.00853.7770.0010.0010.0000.0000.0000.000
138A151MET0-0.078-0.05357.3990.0000.0000.0000.0000.0000.000
139A152ALA00.0410.02456.5180.0000.0000.0000.0000.0000.000
140A153SER00.0280.01457.149-0.001-0.0010.0000.0000.0000.000
141A154GLN0-0.0090.02157.4530.0010.0010.0000.0000.0000.000
142A155ARG10.9980.97356.5470.0110.0110.0000.0000.0000.000
143A156GLN00.002-0.00357.5640.0000.0000.0000.0000.0000.000
144A157ALA00.0890.04954.2300.0000.0000.0000.0000.0000.000
145A158LYS10.8790.92350.2780.0180.0180.0000.0000.0000.000
146A159ILE0-0.049-0.02254.2130.0010.0010.0000.0000.0000.000
147A160GLN0-0.042-0.02555.3000.0000.0000.0000.0000.0000.000
148A161ARG10.8460.89648.3890.0240.0240.0000.0000.0000.000
149A162TYR0-0.0080.00351.3350.0000.0000.0000.0000.0000.000
150A163LYS10.9190.94752.7250.0140.0140.0000.0000.0000.000
151A164GLN00.0280.02850.3800.0010.0010.0000.0000.0000.000
152A165LYS10.9530.96946.4120.0200.0200.0000.0000.0000.000
153A166LYS10.8270.91049.0870.0130.0130.0000.0000.0000.000
154A167GLU-1-0.790-0.87251.711-0.016-0.0160.0000.0000.0000.000
155A168LEU0-0.017-0.00447.0660.0000.0000.0000.0000.0000.000
156A169GLU-1-0.792-0.88245.908-0.016-0.0160.0000.0000.0000.000
157A170HIS0-0.048-0.00248.0620.0010.0010.0000.0000.0000.000
158A171ARG10.8680.91849.5860.0210.0210.0000.0000.0000.000
159A172LEU00.0240.01043.4220.0000.0000.0000.0000.0000.000
160A173SER0-0.105-0.05945.8570.0010.0010.0000.0000.0000.000
161A174ALA0-0.038-0.01747.5950.0010.0010.0000.0000.0000.000
162A175MET0-0.038-0.00745.8530.0000.0000.0000.0000.0000.000
163A176LYS10.9240.97138.5170.0160.0160.0000.0000.0000.000
164A177SER0-0.014-0.01942.343-0.001-0.0010.0000.0000.0000.000
165A178ALA00.0220.02043.4500.0000.0000.0000.0000.0000.000
166A179VAL00.0300.01239.901-0.001-0.0010.0000.0000.0000.000
167A180GLU-1-0.812-0.89237.982-0.024-0.0240.0000.0000.0000.000
168A181SER0-0.068-0.04238.7940.0000.0000.0000.0000.0000.000
169A182GLY00.0110.00440.7950.0010.0010.0000.0000.0000.000
170A183GLN0-0.101-0.02741.3560.0010.0010.0000.0000.0000.000
171A184ALA0-0.007-0.00643.7950.0010.0010.0000.0000.0000.000
172A185ASP-1-0.846-0.91444.198-0.026-0.0260.0000.0000.0000.000
173A186ASP-1-0.802-0.90741.467-0.043-0.0430.0000.0000.0000.000
174A187GLU-1-0.929-0.94244.085-0.029-0.0290.0000.0000.0000.000
175A188ARG10.8670.89546.3110.0210.0210.0000.0000.0000.000
176A189VAL0-0.034-0.01139.7610.0000.0000.0000.0000.0000.000
177A190ARG10.7910.87340.1900.0490.0490.0000.0000.0000.000
178A191GLU-1-0.827-0.89043.076-0.025-0.0250.0000.0000.0000.000
179A192TYR0-0.045-0.03939.4310.0010.0010.0000.0000.0000.000
180A193TYR00.024-0.00836.5610.0000.0000.0000.0000.0000.000
181A194LEU00.0380.03240.922-0.001-0.0010.0000.0000.0000.000
182A195LEU0-0.021-0.01543.6080.0010.0010.0000.0000.0000.000
183A196HIS0-0.016-0.01439.8120.0000.0000.0000.0000.0000.000
184A197LEU00.0230.01837.5590.0010.0010.0000.0000.0000.000
185A198GLN00.0240.00741.2070.0000.0000.0000.0000.0000.000
186A199ARG10.8810.93441.0120.0230.0230.0000.0000.0000.000
187A200TRP00.032-0.00937.9990.0020.0020.0000.0000.0000.000
188A201ILE00.0110.03441.375-0.001-0.0010.0000.0000.0000.000
189A202ASP-1-0.883-0.95843.214-0.026-0.0260.0000.0000.0000.000
190A203ILE0-0.073-0.05141.1250.0020.0020.0000.0000.0000.000
191A204SER00.019-0.00239.8850.0000.0000.0000.0000.0000.000
192A205LEU0-0.022-0.00641.7320.0000.0000.0000.0000.0000.000
193A206GLU-1-0.845-0.89245.141-0.018-0.0180.0000.0000.0000.000
194A207GLU-1-0.814-0.93340.920-0.020-0.0200.0000.0000.0000.000
195A208ILE00.0050.01240.7910.0000.0000.0000.0000.0000.000
196A209GLU-1-0.831-0.87643.502-0.022-0.0220.0000.0000.0000.000
197A210SER0-0.065-0.02044.2290.0020.0020.0000.0000.0000.000
198A211ILE00.0430.00439.2850.0020.0020.0000.0000.0000.000
199A212ASP-1-0.714-0.83943.216-0.030-0.0300.0000.0000.0000.000
200A213GLN0-0.064-0.03645.5930.0010.0010.0000.0000.0000.000
201A214GLU-1-0.774-0.85342.462-0.012-0.0120.0000.0000.0000.000
202A215ILE0-0.007-0.01140.6030.0010.0010.0000.0000.0000.000
203A216LYS10.7670.87144.2840.0170.0170.0000.0000.0000.000
204A217ILE00.0110.01047.8670.0010.0010.0000.0000.0000.000
205A218LEU0-0.019-0.01441.5150.0010.0010.0000.0000.0000.000
206A219ARG10.8410.93541.1400.0290.0290.0000.0000.0000.000
207A220GLU-1-0.851-0.88446.193-0.016-0.0160.0000.0000.0000.000
208A221ARG10.8460.91842.7880.0110.0110.0000.0000.0000.000