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: 85RLY

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 OptHSide
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 -2247765.309923
FMO2-HF: Nuclear repulsion 2169406.447276
FMO2-HF: Total energy -78358.862647
FMO2-MP2: Total energy -78588.355848


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.
-13.56-4.5966.062-6.408-8.619-0.026
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 : -0.073 / q_NPA : -0.041
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].
3E15GLN00.0960.0553.833-1.5580.845-0.029-1.268-1.1060.001
4E16THR00.010-0.0106.5270.3490.3490.0000.0000.0000.000
5E17GLY00.0070.0109.381-0.096-0.0960.0000.0000.0000.000
6E18SER0-0.052-0.0169.435-0.059-0.0590.0000.0000.0000.000
7E19SER00.0470.0249.4880.1600.1600.0000.0000.0000.000
8E20ALA0-0.012-0.0196.1860.0200.0200.0000.0000.0000.000
9E21GLU-1-0.820-0.8788.1240.4190.4190.0000.0000.0000.000
10E22ILE0-0.028-0.0186.6700.1610.1610.0000.0000.0000.000
11E23THR00.014-0.0069.657-0.168-0.1680.0000.0000.0000.000
12E24CYS0-0.0330.01412.4100.0210.0210.0000.0000.0000.000
13E25ASP-1-0.931-0.96714.4100.1850.1850.0000.0000.0000.000
14E26LEU00.0410.00016.195-0.017-0.0170.0000.0000.0000.000
15E27ALA0-0.0030.00119.853-0.005-0.0050.0000.0000.0000.000
16E28GLU-1-0.764-0.87421.5460.2100.2100.0000.0000.0000.000
17E29GLY0-0.0090.00324.685-0.006-0.0060.0000.0000.0000.000
18E30SER0-0.025-0.02328.2220.0000.0000.0000.0000.0000.000
19E31THR0-0.042-0.01524.6680.0030.0030.0000.0000.0000.000
20E32GLY00.0490.01726.950-0.012-0.0120.0000.0000.0000.000
21E33TYR0-0.0070.01325.7530.0050.0050.0000.0000.0000.000
22E34ILE00.0010.00119.3910.0000.0000.0000.0000.0000.000
23E35HIS0-0.028-0.01920.7250.0310.0310.0000.0000.0000.000
24E36TRP00.0710.02412.1780.0360.0360.0000.0000.0000.000
25E37TYR0-0.046-0.03816.032-0.042-0.0420.0000.0000.0000.000
26E38LEU00.0440.03911.0220.0590.0590.0000.0000.0000.000
27E39HIS00.000-0.00412.283-0.113-0.1130.0000.0000.0000.000
28E40GLN00.0580.01811.6310.1440.1440.0000.0000.0000.000
29E41GLU-1-0.770-0.84412.8960.3160.3160.0000.0000.0000.000
30E42GLY0-0.017-0.02914.758-0.037-0.0370.0000.0000.0000.000
31E43LYS10.8380.91614.774-0.491-0.4910.0000.0000.0000.000
32E44ALA0-0.0090.00017.8800.0160.0160.0000.0000.0000.000
33E45PRO0-0.024-0.01616.8810.0300.0300.0000.0000.0000.000
34E46GLN00.0200.01716.863-0.029-0.0290.0000.0000.0000.000
35E47ARG10.8200.90817.433-0.211-0.2110.0000.0000.0000.000
36E48LEU0-0.0200.00214.070-0.024-0.0240.0000.0000.0000.000
37E49LEU00.0160.01117.157-0.037-0.0370.0000.0000.0000.000
38E50TYR0-0.050-0.04320.3710.0130.0130.0000.0000.0000.000
39E51TYR00.0600.04521.378-0.002-0.0020.0000.0000.0000.000
40E52ASP-1-0.829-0.89023.3040.1670.1670.0000.0000.0000.000
41E53SER0-0.011-0.01824.395-0.005-0.0050.0000.0000.0000.000
42E54TYR0-0.023-0.00225.384-0.004-0.0040.0000.0000.0000.000
43E55THR0-0.029-0.03028.931-0.011-0.0110.0000.0000.0000.000
44E56SER0-0.034-0.03025.445-0.002-0.0020.0000.0000.0000.000
45E57SER00.000-0.00625.1890.0190.0190.0000.0000.0000.000
46E58VAL00.0310.00621.3210.0170.0170.0000.0000.0000.000
47E59VAL0-0.035-0.01024.507-0.015-0.0150.0000.0000.0000.000
48E60LEU00.010-0.00620.8430.0250.0250.0000.0000.0000.000
49E61GLU-1-0.838-0.90922.1850.2370.2370.0000.0000.0000.000
50E62SER0-0.042-0.02820.9320.0170.0170.0000.0000.0000.000
51E63GLY00.0590.04723.272-0.011-0.0110.0000.0000.0000.000
52E64ILE00.0100.01218.4880.0270.0270.0000.0000.0000.000
53E65SER00.025-0.03717.9760.0360.0360.0000.0000.0000.000
54E66PRO0-0.049-0.02819.0070.0310.0310.0000.0000.0000.000
55E67GLY00.0630.05119.991-0.030-0.0300.0000.0000.0000.000
56E68LYS10.7730.89313.094-0.675-0.6750.0000.0000.0000.000
57E69TYR0-0.031-0.02912.5310.0620.0620.0000.0000.0000.000
58E70ASP-1-0.801-0.86715.4380.3260.3260.0000.0000.0000.000
59E71THR00.0210.00616.0180.0750.0750.0000.0000.0000.000
60E72TYR0-0.022-0.00918.314-0.041-0.0410.0000.0000.0000.000
61E73GLY00.033-0.00519.8310.0160.0160.0000.0000.0000.000
62E74SER00.0090.02322.744-0.017-0.0170.0000.0000.0000.000
63E75THR00.0260.02325.4150.0050.0050.0000.0000.0000.000
64E76ARG10.9010.93920.492-0.148-0.1480.0000.0000.0000.000
65E77LYS10.8560.92418.754-0.207-0.2070.0000.0000.0000.000
66E78ASN0-0.029-0.02619.503-0.004-0.0040.0000.0000.0000.000
67E79LEU00.0460.03218.6590.0260.0260.0000.0000.0000.000
68E80ARG10.7620.86914.013-0.324-0.3240.0000.0000.0000.000
69E81MET00.004-0.00212.687-0.019-0.0190.0000.0000.0000.000
70E82ILE0-0.0070.00611.6840.1370.1370.0000.0000.0000.000
71E83LEU00.0090.0198.690-0.113-0.1130.0000.0000.0000.000
72E84ARG10.8630.89911.345-0.422-0.4220.0000.0000.0000.000
73E85ASN00.0180.01812.041-0.054-0.0540.0000.0000.0000.000
74E86LEU0-0.044-0.0146.0540.0960.0960.0000.0000.0000.000
75E87ILE00.0500.0199.973-0.200-0.2000.0000.0000.0000.000
76E88GLU-1-0.785-0.9058.4130.4150.4150.0000.0000.0000.000
77E89ASN0-0.069-0.0408.8860.1070.1070.0000.0000.0000.000
78E90ASP-1-0.831-0.8929.0670.8100.8100.0000.0000.0000.000
79E91SER0-0.053-0.0176.3820.4150.4150.0000.0000.0000.000
80E92GLY00.0240.0006.839-0.353-0.3530.0000.0000.0000.000
81E93VAL0-0.108-0.0537.2670.3840.3840.0000.0000.0000.000
82E94TYR0-0.013-0.0337.903-0.243-0.2430.0000.0000.0000.000
83E95TYR0-0.026-0.01410.700-0.053-0.0530.0000.0000.0000.000
84E97ALA00.013-0.02516.342-0.034-0.0340.0000.0000.0000.000
85E98THR00.0320.02619.9440.0010.0010.0000.0000.0000.000
86E99TRP0-0.033-0.01223.580-0.005-0.0050.0000.0000.0000.000
87E100ASP-1-0.798-0.91526.9140.1260.1260.0000.0000.0000.000
88E101GLN00.0470.01828.390-0.002-0.0020.0000.0000.0000.000
89E102ASN0-0.058-0.02231.253-0.011-0.0110.0000.0000.0000.000
90E103TYR0-0.017-0.00530.2890.0010.0010.0000.0000.0000.000
91E104TYR00.0030.02131.753-0.003-0.0030.0000.0000.0000.000
92E105LYS10.9130.96027.429-0.124-0.1240.0000.0000.0000.000
93E106LYS10.8280.91622.985-0.242-0.2420.0000.0000.0000.000
94E107LEU0-0.014-0.00122.269-0.008-0.0080.0000.0000.0000.000
95E108PHE0-0.013-0.01417.6950.0160.0160.0000.0000.0000.000
96E109GLY00.0450.02516.727-0.027-0.0270.0000.0000.0000.000
97E110SER0-0.0120.01212.4630.0180.0180.0000.0000.0000.000
98E111GLY00.0040.00611.492-0.043-0.0430.0000.0000.0000.000
99E112THR00.0190.0095.884-0.200-0.2000.0000.0000.0000.000
100E113SER0-0.006-0.0094.9210.1240.1240.0000.0000.0000.000
101E114LEU0-0.0080.0152.961-2.953-0.4990.597-1.188-1.8640.006
102E115VAL00.015-0.0232.115-4.768-3.0733.178-1.649-3.224-0.004
103E116VAL00.0420.0312.532-3.664-1.4482.315-2.282-2.249-0.029
104E117THR00.0020.0183.964-0.307-0.1110.001-0.021-0.1760.000
105E137GLN0-0.002-0.00231.133-0.002-0.0020.0000.0000.0000.000
106E138LYS10.8140.89029.545-0.104-0.1040.0000.0000.0000.000
107E139VAL00.008-0.00727.293-0.006-0.0060.0000.0000.0000.000
108E140THR0-0.023-0.01628.4300.0030.0030.0000.0000.0000.000
109E141GLN00.0500.04325.5660.0050.0050.0000.0000.0000.000
110E146VAL00.0490.02726.1560.0010.0010.0000.0000.0000.000
111E147ARG10.9210.93724.182-0.024-0.0240.0000.0000.0000.000
112E148LYS10.9700.97527.191-0.071-0.0710.0000.0000.0000.000
113E149ALA00.0040.00031.3950.0050.0050.0000.0000.0000.000
114E154VAL00.0490.04231.017-0.001-0.0010.0000.0000.0000.000
115E155THR0-0.013-0.00934.2480.0000.0000.0000.0000.0000.000
116E156LEU0-0.059-0.00627.7890.0000.0000.0000.0000.0000.000
117E157ASN00.0480.01230.5120.0040.0040.0000.0000.0000.000
118E158CYS0-0.038-0.01423.9020.0060.0060.0000.0000.0000.000
119E159LEU0-0.0110.01231.568-0.005-0.0050.0000.0000.0000.000
120E160TYR00.0340.00631.8980.0080.0080.0000.0000.0000.000
121E161GLU-1-0.837-0.90033.4420.0920.0920.0000.0000.0000.000
122E162THR00.0250.00434.3170.0090.0090.0000.0000.0000.000
123E163SER00.0290.01335.981-0.003-0.0030.0000.0000.0000.000
124E164TRP00.0050.02130.8910.0020.0020.0000.0000.0000.000
125E165TRP00.0560.03138.636-0.003-0.0030.0000.0000.0000.000
126E166SER00.0160.01138.706-0.001-0.0010.0000.0000.0000.000
127E167TYR00.006-0.01934.8120.0040.0040.0000.0000.0000.000
128E168TYR00.0430.02732.425-0.004-0.0040.0000.0000.0000.000
129E169ILE00.0150.00930.7250.0080.0080.0000.0000.0000.000
130E170PHE0-0.046-0.02627.318-0.006-0.0060.0000.0000.0000.000
131E171TRP00.0180.00826.9150.0060.0060.0000.0000.0000.000
132E172TYR0-0.019-0.02322.135-0.004-0.0040.0000.0000.0000.000
133E173LYS10.8870.94522.356-0.100-0.1000.0000.0000.0000.000
134E174ARG10.9770.97812.862-0.319-0.3190.0000.0000.0000.000
135E175LEU00.0150.01018.311-0.018-0.0180.0000.0000.0000.000
136E176PRO00.010-0.00415.8160.0320.0320.0000.0000.0000.000
137E177SER00.029-0.00213.615-0.017-0.0170.0000.0000.0000.000
138E178LYS10.7680.8568.773-0.296-0.2960.0000.0000.0000.000
139E179GLU-1-0.808-0.85713.7410.1930.1930.0000.0000.0000.000
140E180MET0-0.065-0.02816.302-0.041-0.0410.0000.0000.0000.000
141E181ILE00.0520.03818.715-0.004-0.0040.0000.0000.0000.000
142E182PHE00.007-0.00822.223-0.004-0.0040.0000.0000.0000.000
143E183LEU0-0.088-0.03925.345-0.011-0.0110.0000.0000.0000.000
144E184ILE0-0.011-0.00928.248-0.007-0.0070.0000.0000.0000.000
145E185ARG10.7890.85230.571-0.089-0.0890.0000.0000.0000.000
146E186GLN0-0.033-0.00532.510-0.008-0.0080.0000.0000.0000.000
147E187GLY00.0650.02035.0220.0060.0060.0000.0000.0000.000
148E188SER0-0.050-0.02937.384-0.003-0.0030.0000.0000.0000.000
149E189ASP-1-0.823-0.90238.8340.0730.0730.0000.0000.0000.000
150E190GLU-1-0.792-0.84438.8930.0820.0820.0000.0000.0000.000
151E191GLN00.0480.01741.6430.0000.0000.0000.0000.0000.000
152E192ASN0-0.064-0.02940.0000.0010.0010.0000.0000.0000.000
153E193ALA00.0750.04436.909-0.004-0.0040.0000.0000.0000.000
154E194LYS10.8480.90737.046-0.060-0.0600.0000.0000.0000.000
155E195SER00.0360.02934.863-0.002-0.0020.0000.0000.0000.000
156E196GLY00.0590.03835.0440.0020.0020.0000.0000.0000.000
157E197ARG10.9040.94033.675-0.048-0.0480.0000.0000.0000.000
158E198TYR00.0080.00028.8780.0010.0010.0000.0000.0000.000
159E199SER00.0400.00434.179-0.002-0.0020.0000.0000.0000.000
160E200VAL00.002-0.01234.8380.0050.0050.0000.0000.0000.000
161E201ASN00.0170.02236.773-0.003-0.0030.0000.0000.0000.000
162E202PHE00.007-0.00238.3010.0030.0030.0000.0000.0000.000
163E203LYS10.9060.97938.527-0.069-0.0690.0000.0000.0000.000
164E204LYS10.9140.94540.795-0.072-0.0720.0000.0000.0000.000
165E205ALA00.0720.02141.9520.0020.0020.0000.0000.0000.000
166E206ALA0-0.019-0.00140.3670.0000.0000.0000.0000.0000.000
167E207LYS10.9150.98437.381-0.073-0.0730.0000.0000.0000.000
168E208SER0-0.027-0.02736.3960.0020.0020.0000.0000.0000.000
169E209VAL00.005-0.00532.680-0.004-0.0040.0000.0000.0000.000
170E210ALA0-0.017-0.00333.4220.0050.0050.0000.0000.0000.000
171E211LEU00.0120.02429.728-0.005-0.0050.0000.0000.0000.000
172E212THR0-0.018-0.02433.413-0.004-0.0040.0000.0000.0000.000
173E213ILE0-0.043-0.01229.0990.0010.0010.0000.0000.0000.000
174E214SER00.0630.04633.549-0.005-0.0050.0000.0000.0000.000
175E223LYS10.8240.89618.361-0.170-0.1700.0000.0000.0000.000
176E224TYR00.022-0.00821.3870.0070.0070.0000.0000.0000.000
177E225PHE00.0260.02718.1600.0010.0010.0000.0000.0000.000
178E227ALA00.0420.00524.6060.0070.0070.0000.0000.0000.000
179E228LEU0-0.0020.00826.665-0.013-0.0130.0000.0000.0000.000
180E229GLY00.0140.01228.4990.0150.0150.0000.0000.0000.000
181E230GLU-1-0.888-0.94730.1530.1210.1210.0000.0000.0000.000
182E231SER00.003-0.00532.563-0.011-0.0110.0000.0000.0000.000
183E232LEU0-0.034-0.00331.7950.0110.0110.0000.0000.0000.000
184E233THR00.0220.00332.133-0.002-0.0020.0000.0000.0000.000
185E234ARG10.9630.96829.233-0.135-0.1350.0000.0000.0000.000
186E235ALA00.0300.01627.7520.0170.0170.0000.0000.0000.000
187E236ASP-1-0.791-0.86627.8390.1660.1660.0000.0000.0000.000
188E237LYS10.8210.91625.339-0.144-0.1440.0000.0000.0000.000
189E238LEU0-0.033-0.02223.337-0.015-0.0150.0000.0000.0000.000
190E239ILE00.0300.01024.0910.0270.0270.0000.0000.0000.000
191E240PHE00.016-0.01521.360-0.010-0.0100.0000.0000.0000.000
192E241GLY00.0640.04923.918-0.003-0.0030.0000.0000.0000.000
193E242LYS10.8990.93620.146-0.153-0.1530.0000.0000.0000.000