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: G6J11

Calculation Name: 3OMZ-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OMZ

Chain ID: E

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2247889.194778
FMO2-HF: Nuclear repulsion 2169530.970521
FMO2-HF: Total energy -78358.224257
FMO2-MP2: Total energy -78587.715999


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(E:13:ILE)


Summations of interaction energy for fragment #1(E:13:ILE)
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.
-13.942-5.1885.904-6.253-8.405-0.02
Interaction energy analysis for fragmet #1(E:13:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.039
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].
3E15GLN00.1050.0633.833-1.4570.913-0.029-1.247-1.0940.001
4E16THR0-0.011-0.0196.6100.3580.3580.0000.0000.0000.000
5E17GLY00.0160.0179.425-0.107-0.1070.0000.0000.0000.000
6E18SER0-0.057-0.0179.007-0.057-0.0570.0000.0000.0000.000
7E19SER00.0510.0199.5130.1650.1650.0000.0000.0000.000
8E20ALA0-0.019-0.0296.114-0.009-0.0090.0000.0000.0000.000
9E21GLU-1-0.835-0.8838.0280.4300.4300.0000.0000.0000.000
10E22ILE0-0.025-0.0196.5070.1580.1580.0000.0000.0000.000
11E23THR00.006-0.0079.611-0.181-0.1810.0000.0000.0000.000
12E24CYS0-0.0290.01212.4470.0300.0300.0000.0000.0000.000
13E25ASP-1-0.907-0.95314.3620.2070.2070.0000.0000.0000.000
14E26LEU00.040-0.00216.217-0.016-0.0160.0000.0000.0000.000
15E27ALA00.0010.00519.881-0.008-0.0080.0000.0000.0000.000
16E28GLU-1-0.771-0.87821.7350.2240.2240.0000.0000.0000.000
17E29GLY0-0.0080.00324.788-0.007-0.0070.0000.0000.0000.000
18E30SER0-0.020-0.02128.289-0.001-0.0010.0000.0000.0000.000
19E31THR0-0.043-0.01624.8660.0040.0040.0000.0000.0000.000
20E32GLY00.0460.01126.968-0.013-0.0130.0000.0000.0000.000
21E33TYR0-0.0250.00425.8500.0080.0080.0000.0000.0000.000
22E34ILE0-0.015-0.00719.4500.0010.0010.0000.0000.0000.000
23E35HIS0-0.030-0.02120.8090.0350.0350.0000.0000.0000.000
24E36TRP00.0830.03112.4160.0430.0430.0000.0000.0000.000
25E37TYR0-0.036-0.02816.104-0.050-0.0500.0000.0000.0000.000
26E38LEU00.0290.03810.6560.0570.0570.0000.0000.0000.000
27E39HIS00.0080.00512.384-0.130-0.1300.0000.0000.0000.000
28E40GLN00.0540.02411.6350.1560.1560.0000.0000.0000.000
29E41GLU-1-0.767-0.84612.9910.3800.3800.0000.0000.0000.000
30E42GLY0-0.021-0.03414.882-0.044-0.0440.0000.0000.0000.000
31E43LYS10.8410.92514.890-0.554-0.5540.0000.0000.0000.000
32E44ALA0-0.017-0.00617.8900.0200.0200.0000.0000.0000.000
33E45PRO0-0.022-0.02116.9840.0320.0320.0000.0000.0000.000
34E46GLN00.0300.01817.021-0.048-0.0480.0000.0000.0000.000
35E47ARG10.8420.92817.537-0.230-0.2300.0000.0000.0000.000
36E48LEU0-0.027-0.00414.258-0.022-0.0220.0000.0000.0000.000
37E49LEU00.0240.02117.332-0.043-0.0430.0000.0000.0000.000
38E50TYR0-0.032-0.04320.4670.0160.0160.0000.0000.0000.000
39E51TYR00.0350.03721.327-0.006-0.0060.0000.0000.0000.000
40E52ASP-1-0.836-0.89323.3450.1790.1790.0000.0000.0000.000
41E53SER0-0.022-0.02224.481-0.006-0.0060.0000.0000.0000.000
42E54TYR0-0.026-0.00425.399-0.006-0.0060.0000.0000.0000.000
43E55THR0-0.045-0.03628.944-0.012-0.0120.0000.0000.0000.000
44E56SER0-0.014-0.02025.423-0.002-0.0020.0000.0000.0000.000
45E57SER0-0.002-0.00725.1890.0200.0200.0000.0000.0000.000
46E58VAL00.0370.00921.2770.0190.0190.0000.0000.0000.000
47E59VAL0-0.040-0.00824.517-0.016-0.0160.0000.0000.0000.000
48E60LEU00.001-0.01420.7490.0280.0280.0000.0000.0000.000
49E61GLU-1-0.876-0.93721.9990.2630.2630.0000.0000.0000.000
50E62SER0-0.034-0.02520.7200.0190.0190.0000.0000.0000.000
51E63GLY00.0640.04723.079-0.008-0.0080.0000.0000.0000.000
52E64ILE00.0140.01318.2230.0310.0310.0000.0000.0000.000
53E65SER00.018-0.04917.9460.0390.0390.0000.0000.0000.000
54E66PRO0-0.044-0.03818.9910.0250.0250.0000.0000.0000.000
55E67GLY00.0760.06620.019-0.033-0.0330.0000.0000.0000.000
56E68LYS10.7560.90513.154-0.726-0.7260.0000.0000.0000.000
57E69TYR0-0.031-0.03512.8140.0710.0710.0000.0000.0000.000
58E70ASP-1-0.813-0.89715.4360.3150.3150.0000.0000.0000.000
59E71THR00.0120.00216.0180.0790.0790.0000.0000.0000.000
60E72TYR0-0.020-0.00818.314-0.045-0.0450.0000.0000.0000.000
61E73GLY00.040-0.00319.7400.0170.0170.0000.0000.0000.000
62E74SER00.0110.02422.779-0.019-0.0190.0000.0000.0000.000
63E75THR00.0260.02325.3310.0060.0060.0000.0000.0000.000
64E76ARG10.9050.93920.298-0.145-0.1450.0000.0000.0000.000
65E77LYS10.8420.92018.750-0.222-0.2220.0000.0000.0000.000
66E78ASN0-0.034-0.03219.396-0.004-0.0040.0000.0000.0000.000
67E79LEU00.0450.03418.6080.0260.0260.0000.0000.0000.000
68E80ARG10.7680.86713.773-0.313-0.3130.0000.0000.0000.000
69E81MET00.0060.00012.637-0.022-0.0220.0000.0000.0000.000
70E82ILE0-0.0120.00811.6820.1350.1350.0000.0000.0000.000
71E83LEU00.0100.0148.777-0.112-0.1120.0000.0000.0000.000
72E84ARG10.8890.93611.345-0.443-0.4430.0000.0000.0000.000
73E85ASN00.0270.02012.068-0.063-0.0630.0000.0000.0000.000
74E86LEU0-0.045-0.0146.2040.1130.1130.0000.0000.0000.000
75E87ILE00.0490.0169.983-0.212-0.2120.0000.0000.0000.000
76E88GLU-1-0.794-0.9078.4760.4550.4550.0000.0000.0000.000
77E89ASN0-0.041-0.0278.8860.1710.1710.0000.0000.0000.000
78E90ASP-1-0.835-0.8959.1660.8620.8620.0000.0000.0000.000
79E91SER0-0.078-0.0126.4130.4680.4680.0000.0000.0000.000
80E92GLY00.026-0.0016.855-0.409-0.4090.0000.0000.0000.000
81E93VAL0-0.112-0.0557.3660.4600.4600.0000.0000.0000.000
82E94TYR0-0.014-0.0497.796-0.344-0.3440.0000.0000.0000.000
83E95TYR0-0.031-0.02710.788-0.054-0.0540.0000.0000.0000.000
84E97ALA00.013-0.02416.414-0.035-0.0350.0000.0000.0000.000
85E98THR00.0280.02020.014-0.002-0.0020.0000.0000.0000.000
86E99TRP0-0.044-0.01123.647-0.003-0.0030.0000.0000.0000.000
87E100ASP-1-0.783-0.89626.9820.1460.1460.0000.0000.0000.000
88E101GLN00.0420.01728.446-0.004-0.0040.0000.0000.0000.000
89E102ASN0-0.049-0.01731.304-0.012-0.0120.0000.0000.0000.000
90E103TYR0-0.019-0.00631.0390.0010.0010.0000.0000.0000.000
91E104TYR0-0.0240.00731.878-0.005-0.0050.0000.0000.0000.000
92E105LYS10.9330.95727.184-0.143-0.1430.0000.0000.0000.000
93E106LYS10.8700.94023.179-0.273-0.2730.0000.0000.0000.000
94E107LEU0-0.015-0.01922.314-0.008-0.0080.0000.0000.0000.000
95E108PHE0-0.028-0.02217.7610.0160.0160.0000.0000.0000.000
96E109GLY00.0400.02316.768-0.030-0.0300.0000.0000.0000.000
97E110SER0-0.0380.00312.3900.0330.0330.0000.0000.0000.000
98E111GLY00.0110.00811.537-0.043-0.0430.0000.0000.0000.000
99E112THR00.004-0.0015.987-0.185-0.1850.0000.0000.0000.000
100E113SER0-0.012-0.0134.9840.0530.0530.0000.0000.0000.000
101E114LEU0-0.0040.0152.787-2.794-0.5090.990-1.208-2.0670.010
102E115VAL00.014-0.0242.141-4.986-3.2572.692-1.498-2.924-0.003
103E116VAL00.0480.0412.519-3.753-1.5502.251-2.286-2.167-0.028
104E117THR0-0.0040.0114.149-0.354-0.1870.000-0.014-0.1530.000
105E137GLN00.0050.00231.193-0.001-0.0010.0000.0000.0000.000
106E138LYS10.8190.90029.564-0.118-0.1180.0000.0000.0000.000
107E139VAL00.001-0.01527.409-0.007-0.0070.0000.0000.0000.000
108E140THR0-0.016-0.00928.4430.0040.0040.0000.0000.0000.000
109E141GLN00.0420.04325.6400.0060.0060.0000.0000.0000.000
110E146VAL00.016-0.00126.1450.0000.0000.0000.0000.0000.000
111E147ARG10.9530.96324.111-0.039-0.0390.0000.0000.0000.000
112E148LYS10.9820.98227.090-0.089-0.0890.0000.0000.0000.000
113E149ALA00.0170.00231.4710.0060.0060.0000.0000.0000.000
114E154VAL00.0330.03231.110-0.001-0.0010.0000.0000.0000.000
115E155THR00.0070.00334.2500.0010.0010.0000.0000.0000.000
116E156LEU0-0.0570.00027.8290.0000.0000.0000.0000.0000.000
117E157ASN00.0460.00730.7590.0030.0030.0000.0000.0000.000
118E158CYS0-0.035-0.02723.9730.0060.0060.0000.0000.0000.000
119E159LEU0-0.0050.02131.647-0.007-0.0070.0000.0000.0000.000
120E160TYR00.0490.02131.9880.0080.0080.0000.0000.0000.000
121E161GLU-1-0.849-0.90233.5350.1040.1040.0000.0000.0000.000
122E162THR00.032-0.00234.4010.0100.0100.0000.0000.0000.000
123E163SER00.0330.01536.082-0.004-0.0040.0000.0000.0000.000
124E164TRP00.0090.02731.1800.0020.0020.0000.0000.0000.000
125E165TRP00.0530.02838.737-0.003-0.0030.0000.0000.0000.000
126E166SER00.0030.00338.718-0.001-0.0010.0000.0000.0000.000
127E167TYR00.008-0.03134.9680.0040.0040.0000.0000.0000.000
128E168TYR00.0320.03132.513-0.008-0.0080.0000.0000.0000.000
129E169ILE00.0140.00930.9420.0090.0090.0000.0000.0000.000
130E170PHE0-0.039-0.02227.408-0.007-0.0070.0000.0000.0000.000
131E171TRP00.0200.00426.9660.0080.0080.0000.0000.0000.000
132E172TYR00.004-0.00222.241-0.005-0.0050.0000.0000.0000.000
133E173LYS10.9010.95722.235-0.120-0.1200.0000.0000.0000.000
134E174ARG10.9650.97213.006-0.391-0.3910.0000.0000.0000.000
135E175LEU00.0270.01018.429-0.020-0.0200.0000.0000.0000.000
136E176PRO00.011-0.00115.8110.0390.0390.0000.0000.0000.000
137E177SER00.0310.00013.587-0.016-0.0160.0000.0000.0000.000
138E178LYS10.7810.8758.630-0.365-0.3650.0000.0000.0000.000
139E179GLU-1-0.798-0.85513.7750.2260.2260.0000.0000.0000.000
140E180MET0-0.067-0.03216.333-0.045-0.0450.0000.0000.0000.000
141E181ILE00.0500.04018.764-0.006-0.0060.0000.0000.0000.000
142E182PHE0-0.003-0.02222.265-0.004-0.0040.0000.0000.0000.000
143E183LEU0-0.100-0.03825.397-0.012-0.0120.0000.0000.0000.000
144E184ILE00.000-0.00628.297-0.009-0.0090.0000.0000.0000.000
145E185ARG10.7940.85230.634-0.099-0.0990.0000.0000.0000.000
146E186GLN0-0.038-0.00832.577-0.009-0.0090.0000.0000.0000.000
147E187GLY00.0710.01535.1000.0070.0070.0000.0000.0000.000
148E188SER0-0.0100.02037.461-0.004-0.0040.0000.0000.0000.000
149E189ASP-1-0.878-0.94238.9180.0810.0810.0000.0000.0000.000
150E190GLU-1-0.800-0.84438.9340.0910.0910.0000.0000.0000.000
151E191GLN00.0390.01041.7180.0000.0000.0000.0000.0000.000
152E192ASN0-0.063-0.02940.0670.0020.0020.0000.0000.0000.000
153E193ALA00.0800.04636.964-0.004-0.0040.0000.0000.0000.000
154E194LYS10.8420.90637.117-0.069-0.0690.0000.0000.0000.000
155E195SER00.0300.02334.971-0.002-0.0020.0000.0000.0000.000
156E196GLY00.0660.04335.0740.0020.0020.0000.0000.0000.000
157E197ARG10.9010.94433.609-0.059-0.0590.0000.0000.0000.000
158E198TYR0-0.011-0.01129.1130.0010.0010.0000.0000.0000.000
159E199SER00.0540.01334.223-0.003-0.0030.0000.0000.0000.000
160E200VAL0-0.011-0.02234.8950.0060.0060.0000.0000.0000.000
161E201ASN00.0290.03036.835-0.003-0.0030.0000.0000.0000.000
162E202PHE0-0.010-0.00738.3600.0040.0040.0000.0000.0000.000
163E203LYS10.9120.98238.630-0.080-0.0800.0000.0000.0000.000
164E204LYS10.9410.95240.878-0.081-0.0810.0000.0000.0000.000
165E205ALA00.0700.01942.0410.0020.0020.0000.0000.0000.000
166E206ALA0-0.0070.00140.393-0.001-0.0010.0000.0000.0000.000
167E207LYS10.9190.98737.963-0.083-0.0830.0000.0000.0000.000
168E208SER0-0.047-0.04036.4790.0020.0020.0000.0000.0000.000
169E209VAL0-0.007-0.00532.653-0.005-0.0050.0000.0000.0000.000
170E210ALA0-0.0070.00033.4960.0060.0060.0000.0000.0000.000
171E211LEU00.0070.02029.810-0.006-0.0060.0000.0000.0000.000
172E212THR0-0.017-0.01533.475-0.004-0.0040.0000.0000.0000.000
173E213ILE0-0.032-0.01229.1520.0010.0010.0000.0000.0000.000
174E214SER00.0560.04133.590-0.006-0.0060.0000.0000.0000.000
175E223LYS10.8640.93018.525-0.202-0.2020.0000.0000.0000.000
176E224TYR0-0.003-0.02021.4390.0100.0100.0000.0000.0000.000
177E225PHE00.0180.01618.6670.0030.0030.0000.0000.0000.000
178E227ALA00.0270.01024.6640.0080.0080.0000.0000.0000.000
179E228LEU0-0.0050.00526.751-0.015-0.0150.0000.0000.0000.000
180E229GLY00.0050.01228.5940.0160.0160.0000.0000.0000.000
181E230GLU-1-0.896-0.94730.2440.1340.1340.0000.0000.0000.000
182E231SER00.008-0.00432.679-0.012-0.0120.0000.0000.0000.000
183E232LEU0-0.033-0.00231.9000.0110.0110.0000.0000.0000.000
184E233THR00.0300.02332.339-0.003-0.0030.0000.0000.0000.000
185E234ARG11.0171.00429.231-0.142-0.1420.0000.0000.0000.000
186E235ALA00.0460.01927.8350.0180.0180.0000.0000.0000.000
187E236ASP-1-0.789-0.89127.9330.1850.1850.0000.0000.0000.000
188E237LYS10.8000.89325.200-0.161-0.1610.0000.0000.0000.000
189E238LEU0-0.039-0.00422.852-0.015-0.0150.0000.0000.0000.000
190E239ILE00.0300.00024.1870.0290.0290.0000.0000.0000.000
191E240PHE00.008-0.01821.524-0.011-0.0110.0000.0000.0000.000
192E241GLY00.0660.04924.012-0.003-0.0030.0000.0000.0000.000
193E242LYS10.8890.92020.123-0.182-0.1820.0000.0000.0000.000