Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: JQ4Q9

Calculation Name: 1OI4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OI4

Chain ID: A

ChEMBL ID:

UniProt ID: P45470

Base Structure: X-ray

Registration Date: 2023-09-22

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166160.841194
FMO2-HF: Nuclear repulsion 2093272.388379
FMO2-HF: Total energy -72888.452815
FMO2-MP2: Total energy -73106.950273


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-24.206-21.57410.984-6.93-6.686-0.072
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.011
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].
3A4TYR0-0.074-0.0672.580-6.920-3.1250.396-2.288-1.904-0.012
4A5HIS0-0.0030.0005.1691.0631.157-0.001-0.004-0.0880.000
5A6HIS0-0.045-0.0317.6190.0410.0410.0000.0000.0000.000
6A7HIS00.0190.0139.5750.1360.1360.0000.0000.0000.000
7A8HIS0-0.050-0.02611.1420.0670.0670.0000.0000.0000.000
8A9HIS0-0.004-0.01814.715-0.054-0.0540.0000.0000.0000.000
9A10HIS10.7380.83716.5290.6700.6700.0000.0000.0000.000
10A11LEU0-0.018-0.01118.851-0.023-0.0230.0000.0000.0000.000
11A12GLU-1-0.747-0.85816.536-0.503-0.5030.0000.0000.0000.000
12A13SER0-0.015-0.02220.4360.0270.0270.0000.0000.0000.000
13A14THR00.0010.00221.3950.0170.0170.0000.0000.0000.000
14A15SER0-0.0150.00323.1020.0360.0360.0000.0000.0000.000
15A16LEU00.0360.00024.8890.0020.0020.0000.0000.0000.000
16A17TYR00.0020.00625.9180.0160.0160.0000.0000.0000.000
17A18LYS10.8450.92722.7690.3980.3980.0000.0000.0000.000
18A19LYS10.9230.96027.5590.1570.1570.0000.0000.0000.000
19A20ALA0-0.0040.00131.0010.0080.0080.0000.0000.0000.000
20A21GLY00.0050.00829.8390.0050.0050.0000.0000.0000.000
21A22LEU0-0.035-0.02230.875-0.003-0.0030.0000.0000.0000.000
22A23SER0-0.035-0.01825.8980.0120.0120.0000.0000.0000.000
23A24LYS10.8790.94825.9710.2280.2280.0000.0000.0000.000
24A25LYS10.7880.87925.0620.2780.2780.0000.0000.0000.000
25A26ILE0-0.010-0.00520.5570.0190.0190.0000.0000.0000.000
26A27ALA00.0150.01722.212-0.040-0.0400.0000.0000.0000.000
27A28VAL00.008-0.01217.211-0.027-0.0270.0000.0000.0000.000
28A29LEU0-0.0030.01820.6610.0020.0020.0000.0000.0000.000
29A30ILE0-0.048-0.02614.911-0.025-0.0250.0000.0000.0000.000
30A31THR0-0.021-0.03418.2790.0530.0530.0000.0000.0000.000
31A32ASP-1-0.781-0.89616.167-0.940-0.9400.0000.0000.0000.000
32A33GLU-1-0.812-0.89913.617-0.659-0.6590.0000.0000.0000.000
33A34PHE00.0130.01210.2950.0460.0460.0000.0000.0000.000
34A35GLU-1-0.820-0.8878.229-2.374-2.3740.0000.0000.0000.000
35A36ASP-1-0.755-0.8846.333-3.069-3.0690.0000.0000.0000.000
36A37SER00.001-0.0196.0430.0820.0820.0000.0000.0000.000
37A38GLU-1-0.749-0.9157.455-0.565-0.5650.0000.0000.0000.000
38A39PHE0-0.0210.00510.7970.2300.2300.0000.0000.0000.000
39A40THR0-0.025-0.0377.6300.1070.1070.0000.0000.0000.000
40A41SER00.0170.0299.0180.2920.2920.0000.0000.0000.000
41A42PRO00.0230.00210.5760.1670.1670.0000.0000.0000.000
42A43ALA00.0210.01813.3670.1160.1160.0000.0000.0000.000
43A44ASP-1-0.734-0.82110.243-1.320-1.3200.0000.0000.0000.000
44A45GLU-1-0.888-0.92013.672-0.348-0.3480.0000.0000.0000.000
45A46PHE0-0.018-0.02416.1110.0790.0790.0000.0000.0000.000
46A47ARG10.8140.90113.2750.8890.8890.0000.0000.0000.000
47A48LYS10.7670.85513.5540.5920.5920.0000.0000.0000.000
48A49ALA0-0.039-0.00518.4260.0560.0560.0000.0000.0000.000
49A50GLY0-0.0180.00221.2620.0340.0340.0000.0000.0000.000
50A51HIS00.0210.01021.7430.0220.0220.0000.0000.0000.000
51A52GLU-1-0.812-0.89521.485-0.466-0.4660.0000.0000.0000.000
52A53VAL00.0090.01017.6160.0170.0170.0000.0000.0000.000
53A54ILE0-0.034-0.02120.6540.0020.0020.0000.0000.0000.000
54A55THR0-0.020-0.02517.4730.0310.0310.0000.0000.0000.000
55A56ILE0-0.023-0.00220.6180.0440.0440.0000.0000.0000.000
56A57GLU-1-0.721-0.84321.402-0.614-0.6140.0000.0000.0000.000
57A58LYS10.8550.92423.0880.5290.5290.0000.0000.0000.000
58A59GLN0-0.0010.00025.2330.0130.0130.0000.0000.0000.000
59A60ALA00.0330.03324.513-0.042-0.0420.0000.0000.0000.000
60A61GLY0-0.027-0.01623.5430.0240.0240.0000.0000.0000.000
61A62LYS10.7960.89620.3630.6150.6150.0000.0000.0000.000
62A63THR0-0.032-0.02016.101-0.044-0.0440.0000.0000.0000.000
63A64VAL0-0.033-0.00415.7530.0610.0610.0000.0000.0000.000
64A65LYS10.8870.92112.5861.1261.1260.0000.0000.0000.000
65A66GLY00.0280.0259.9690.2070.2070.0000.0000.0000.000
66A67LYS10.8410.90510.7140.7980.7980.0000.0000.0000.000
67A68LYS10.8240.9104.8122.9632.9630.0000.0000.0000.000
68A69GLY0-0.0270.0007.7170.1180.1180.0000.0000.0000.000
69A70GLU-1-0.927-0.9521.901-18.537-19.79410.589-4.638-4.694-0.060
70A71ALA00.0530.0275.908-0.415-0.4150.0000.0000.0000.000
71A72SER0-0.070-0.0518.2940.6960.6960.0000.0000.0000.000
72A73VAL00.0380.03712.021-0.036-0.0360.0000.0000.0000.000
73A74THR00.0010.00514.6100.0750.0750.0000.0000.0000.000
74A75ILE0-0.0070.02218.434-0.025-0.0250.0000.0000.0000.000
75A76ASP-1-0.775-0.86020.964-0.577-0.5770.0000.0000.0000.000
76A77LYS10.8100.89323.4740.3820.3820.0000.0000.0000.000
77A78SER0-0.025-0.03825.305-0.042-0.0420.0000.0000.0000.000
78A79ILE00.017-0.01627.1640.0110.0110.0000.0000.0000.000
79A80ASP-1-0.869-0.90028.718-0.285-0.2850.0000.0000.0000.000
80A81GLU-1-0.820-0.87629.430-0.317-0.3170.0000.0000.0000.000
81A82VAL0-0.025-0.00927.752-0.006-0.0060.0000.0000.0000.000
82A83THR00.0080.00130.9870.0110.0110.0000.0000.0000.000
83A84PRO00.0630.02530.243-0.009-0.0090.0000.0000.0000.000
84A85ALA00.0060.01131.3230.0030.0030.0000.0000.0000.000
85A86GLU-1-0.859-0.91929.708-0.296-0.2960.0000.0000.0000.000
86A87PHE00.0370.01226.239-0.011-0.0110.0000.0000.0000.000
87A88ASP-1-0.808-0.89627.029-0.252-0.2520.0000.0000.0000.000
88A89ALA0-0.007-0.01124.3470.0150.0150.0000.0000.0000.000
89A90LEU0-0.0200.00422.924-0.018-0.0180.0000.0000.0000.000
90A91LEU0-0.0120.00015.6430.0190.0190.0000.0000.0000.000
91A92LEU0-0.011-0.01819.578-0.013-0.0130.0000.0000.0000.000
92A93PRO00.0250.01514.0940.0330.0330.0000.0000.0000.000
93A94GLY00.0330.00914.7330.0710.0710.0000.0000.0000.000
94A95GLY0-0.025-0.01114.234-0.108-0.1080.0000.0000.0000.000
95A96HIS0-0.004-0.01714.7610.1110.1110.0000.0000.0000.000
96A97SER00.0310.03916.7030.0640.0640.0000.0000.0000.000
97A98PRO00.0210.00617.6890.0560.0560.0000.0000.0000.000
98A99ASP-1-0.830-0.91420.917-0.330-0.3300.0000.0000.0000.000
99A100TYR0-0.099-0.08018.5350.0660.0660.0000.0000.0000.000
100A101LEU0-0.020-0.02021.4570.0090.0090.0000.0000.0000.000
101A102ARG10.7820.90724.7010.3410.3410.0000.0000.0000.000
102A103GLY00.0340.01626.7230.0280.0280.0000.0000.0000.000
103A104ASP-1-0.812-0.87627.922-0.311-0.3110.0000.0000.0000.000
104A105ASN00.041-0.00529.648-0.016-0.0160.0000.0000.0000.000
105A106ARG10.8020.88429.8100.3200.3200.0000.0000.0000.000
106A107PHE00.0400.01624.567-0.001-0.0010.0000.0000.0000.000
107A108VAL0-0.0070.01528.019-0.003-0.0030.0000.0000.0000.000
108A109THR0-0.036-0.03029.8270.0130.0130.0000.0000.0000.000
109A110PHE00.0280.01226.7250.0070.0070.0000.0000.0000.000
110A111THR00.000-0.02026.639-0.007-0.0070.0000.0000.0000.000
111A112ARG10.8570.93028.4570.2240.2240.0000.0000.0000.000
112A113ASP-1-0.851-0.94331.953-0.203-0.2030.0000.0000.0000.000
113A114PHE0-0.044-0.00628.0410.0060.0060.0000.0000.0000.000
114A115VAL0-0.0190.01129.0020.0100.0100.0000.0000.0000.000
115A116ASN0-0.014-0.01131.3020.0150.0150.0000.0000.0000.000
116A117SER0-0.094-0.05232.3540.0110.0110.0000.0000.0000.000
117A118GLY00.0010.00133.9800.0060.0060.0000.0000.0000.000
118A119LYS10.7850.89529.7530.2500.2500.0000.0000.0000.000
119A120PRO00.000-0.00326.374-0.005-0.0050.0000.0000.0000.000
120A121VAL0-0.022-0.01124.125-0.018-0.0180.0000.0000.0000.000
121A122PHE00.0200.00919.9950.0200.0200.0000.0000.0000.000
122A123ALA0-0.001-0.00519.953-0.051-0.0510.0000.0000.0000.000
123A124ILE0-0.026-0.00514.2390.0540.0540.0000.0000.0000.000
124A125CYS0-0.0040.00014.392-0.027-0.0270.0000.0000.0000.000
125A126HIS00.0360.00716.7550.0870.0870.0000.0000.0000.000
126A127GLY00.0360.03218.4830.0310.0310.0000.0000.0000.000
127A128PRO0-0.016-0.03320.0950.0320.0320.0000.0000.0000.000
128A129GLN00.006-0.00921.9910.0020.0020.0000.0000.0000.000
129A130LEU00.0000.00922.4620.0280.0280.0000.0000.0000.000
130A131LEU00.0110.00024.8150.0260.0260.0000.0000.0000.000
131A132ILE0-0.029-0.01026.3820.0240.0240.0000.0000.0000.000
132A133SER0-0.018-0.00728.5190.0170.0170.0000.0000.0000.000
133A134ALA0-0.021-0.01129.7700.0140.0140.0000.0000.0000.000
134A135ASP-1-0.871-0.90831.532-0.161-0.1610.0000.0000.0000.000
135A136VAL0-0.0040.01230.4380.0110.0110.0000.0000.0000.000
136A137ILE0-0.004-0.02428.420-0.001-0.0010.0000.0000.0000.000
137A138ARG10.8440.91931.8960.1670.1670.0000.0000.0000.000
138A139GLY0-0.0120.00035.1650.0040.0040.0000.0000.0000.000
139A140ARG10.7310.84431.6130.1960.1960.0000.0000.0000.000
140A141LYS10.8270.90630.7450.1100.1100.0000.0000.0000.000
141A142LEU00.0140.00025.969-0.011-0.0110.0000.0000.0000.000
142A143THR0-0.020-0.03321.7420.0140.0140.0000.0000.0000.000
143A144ALA00.0260.01121.241-0.025-0.0250.0000.0000.0000.000
144A145VAL00.0250.02417.0590.0410.0410.0000.0000.0000.000
145A146LYS10.8910.91519.9100.1480.1480.0000.0000.0000.000
146A147PRO0-0.020-0.00820.2700.0200.0200.0000.0000.0000.000
147A148ILE00.0170.02122.0680.0100.0100.0000.0000.0000.000
148A149ILE0-0.0090.01024.0940.0100.0100.0000.0000.0000.000
149A150ILE0-0.025-0.01426.5950.0110.0110.0000.0000.0000.000
150A151ASP-1-0.804-0.89927.147-0.243-0.2430.0000.0000.0000.000
151A152VAL00.010-0.00425.7580.0050.0050.0000.0000.0000.000
152A153LYS10.9340.97028.8820.1360.1360.0000.0000.0000.000
153A154ASN00.0000.00632.1240.0180.0180.0000.0000.0000.000
154A155ALA0-0.015-0.00531.1750.0070.0070.0000.0000.0000.000
155A156GLY00.003-0.00333.1900.0020.0020.0000.0000.0000.000
156A157ALA0-0.0040.01630.4550.0050.0050.0000.0000.0000.000
157A158GLU-1-0.817-0.87932.242-0.103-0.1030.0000.0000.0000.000
158A159PHE0-0.005-0.01824.528-0.001-0.0010.0000.0000.0000.000
159A160TYR0-0.040-0.03527.4780.0200.0200.0000.0000.0000.000
160A161ASP-1-0.861-0.90723.193-0.142-0.1420.0000.0000.0000.000
161A162GLN0-0.031-0.03023.7450.0340.0340.0000.0000.0000.000
162A163GLU-1-0.787-0.87919.580-0.126-0.1260.0000.0000.0000.000
163A164VAL0-0.0070.00919.692-0.047-0.0470.0000.0000.0000.000
164A165VAL0-0.068-0.01122.2770.0330.0330.0000.0000.0000.000
165A166VAL00.0510.02124.875-0.027-0.0270.0000.0000.0000.000
166A167ASP-1-0.745-0.84027.160-0.143-0.1430.0000.0000.0000.000
167A168LYS10.8080.89230.2130.1400.1400.0000.0000.0000.000
168A169ASP-1-0.808-0.88329.506-0.153-0.1530.0000.0000.0000.000
169A170GLN0-0.0210.00929.3050.0060.0060.0000.0000.0000.000
170A171LEU0-0.020-0.01326.426-0.023-0.0230.0000.0000.0000.000
171A172VAL00.0230.02421.1530.0190.0190.0000.0000.0000.000
172A173THR0-0.022-0.01221.397-0.026-0.0260.0000.0000.0000.000
173A174SER00.035-0.02217.5560.0280.0280.0000.0000.0000.000
174A175ARG10.7550.84118.3960.1170.1170.0000.0000.0000.000
175A176THR0-0.037-0.05813.746-0.024-0.0240.0000.0000.0000.000
176A177PRO00.0550.0189.1160.0670.0670.0000.0000.0000.000
177A178ASP-1-0.860-0.89911.267-0.111-0.1110.0000.0000.0000.000
178A179ASP-1-0.726-0.83212.908-0.154-0.1540.0000.0000.0000.000
179A180LEU0-0.030-0.0049.8150.0030.0030.0000.0000.0000.000
180A181PRO0-0.003-0.00712.678-0.004-0.0040.0000.0000.0000.000
181A182ALA0-0.0120.00815.3510.0150.0150.0000.0000.0000.000
182A183PHE00.001-0.01015.602-0.004-0.0040.0000.0000.0000.000
183A184ASN00.024-0.00612.880-0.016-0.0160.0000.0000.0000.000
184A185ARG10.7720.88417.3310.1540.1540.0000.0000.0000.000
185A186GLU-1-0.792-0.89920.335-0.156-0.1560.0000.0000.0000.000
186A187ALA00.0160.00819.4750.0080.0080.0000.0000.0000.000
187A188LEU0-0.033-0.02418.7270.0090.0090.0000.0000.0000.000
188A189ARG10.7600.87122.1890.1790.1790.0000.0000.0000.000
189A190LEU0-0.036-0.01925.0640.0120.0120.0000.0000.0000.000
190A191LEU0-0.0320.00321.8620.0030.0030.0000.0000.0000.000
191A192GLY0-0.0230.00725.8960.0050.0050.0000.0000.0000.000