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: N9K4Q

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2248336.543776
FMO2-HF: Nuclear repulsion 2169976.495828
FMO2-HF: Total energy -78360.047948
FMO2-MP2: Total energy -78589.438659


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.
-12.627-5.3418.47-6.854-8.902-0.026
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 : -0.060 / 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].
3E15GLN00.0680.0283.897-1.1140.846-0.014-0.975-0.9710.001
4E16THR00.011-0.0066.3510.2760.2760.0000.0000.0000.000
5E17GLY00.0000.0019.103-0.113-0.1130.0000.0000.0000.000
6E18SER0-0.055-0.0169.691-0.111-0.1110.0000.0000.0000.000
7E19SER00.0540.0309.2230.0980.0980.0000.0000.0000.000
8E20ALA0-0.014-0.0096.244-0.098-0.0980.0000.0000.0000.000
9E21GLU-1-0.827-0.8887.9010.2380.2380.0000.0000.0000.000
10E22ILE0-0.022-0.0107.2570.2330.2330.0000.0000.0000.000
11E23THR00.0420.0169.914-0.119-0.1190.0000.0000.0000.000
12E24CYS0-0.0560.00412.8880.0320.0320.0000.0000.0000.000
13E25ASP-1-0.927-0.95914.5660.2020.2020.0000.0000.0000.000
14E26LEU00.015-0.01416.3050.0020.0020.0000.0000.0000.000
15E27ALA00.0170.01019.807-0.009-0.0090.0000.0000.0000.000
16E28GLU-1-0.765-0.88421.4910.2100.2100.0000.0000.0000.000
17E29GLY00.0070.01724.894-0.007-0.0070.0000.0000.0000.000
18E30SER0-0.025-0.02028.3450.0010.0010.0000.0000.0000.000
19E31THR0-0.057-0.02224.6340.0060.0060.0000.0000.0000.000
20E32GLY00.0720.02826.678-0.013-0.0130.0000.0000.0000.000
21E33TYR0-0.042-0.01926.0540.0010.0010.0000.0000.0000.000
22E34ILE00.0070.00619.6650.0030.0030.0000.0000.0000.000
23E35HIS00.0150.00321.0840.0300.0300.0000.0000.0000.000
24E36TRP00.0470.01412.6880.0490.0490.0000.0000.0000.000
25E37TYR0-0.028-0.03516.013-0.058-0.0580.0000.0000.0000.000
26E38LEU00.0310.02811.0030.0890.0890.0000.0000.0000.000
27E39HIS0-0.054-0.02812.634-0.109-0.1090.0000.0000.0000.000
28E40GLN00.0910.01811.8010.1630.1630.0000.0000.0000.000
29E41GLU-1-0.791-0.85812.7780.4400.4400.0000.0000.0000.000
30E42GLY0-0.009-0.01214.631-0.054-0.0540.0000.0000.0000.000
31E43LYS10.8420.91915.017-0.586-0.5860.0000.0000.0000.000
32E44ALA0-0.003-0.00218.2070.0140.0140.0000.0000.0000.000
33E45PRO0-0.039-0.02317.2110.0340.0340.0000.0000.0000.000
34E46GLN00.0130.02217.083-0.038-0.0380.0000.0000.0000.000
35E47ARG10.8120.89317.819-0.234-0.2340.0000.0000.0000.000
36E48LEU00.0030.00014.3390.0010.0010.0000.0000.0000.000
37E49LEU00.0050.00717.142-0.036-0.0360.0000.0000.0000.000
38E50TYR0-0.042-0.03120.7840.0140.0140.0000.0000.0000.000
39E51TYR00.0310.02421.429-0.002-0.0020.0000.0000.0000.000
40E52ASP-1-0.813-0.86523.3800.1600.1600.0000.0000.0000.000
41E53SER0-0.049-0.05124.476-0.006-0.0060.0000.0000.0000.000
42E54TYR0-0.0190.00625.598-0.007-0.0070.0000.0000.0000.000
43E55THR0-0.020-0.04529.061-0.009-0.0090.0000.0000.0000.000
44E56SER0-0.013-0.00825.5920.0000.0000.0000.0000.0000.000
45E57SER00.0110.01325.6060.0130.0130.0000.0000.0000.000
46E58VAL00.0210.00121.2330.0160.0160.0000.0000.0000.000
47E59VAL0-0.0190.00424.341-0.015-0.0150.0000.0000.0000.000
48E60LEU00.021-0.00620.9160.0300.0300.0000.0000.0000.000
49E61GLU-1-0.878-0.92522.5500.2590.2590.0000.0000.0000.000
50E62SER0-0.010-0.01620.7120.0150.0150.0000.0000.0000.000
51E63GLY00.0600.04422.920-0.008-0.0080.0000.0000.0000.000
52E64ILE00.0130.01218.7820.0290.0290.0000.0000.0000.000
53E65SER00.013-0.03118.0930.0280.0280.0000.0000.0000.000
54E66PRO0-0.018-0.01118.9730.0270.0270.0000.0000.0000.000
55E67GLY00.0410.04219.936-0.023-0.0230.0000.0000.0000.000
56E68LYS10.7820.89112.880-0.680-0.6800.0000.0000.0000.000
57E69TYR0-0.041-0.04212.2990.0510.0510.0000.0000.0000.000
58E70ASP-1-0.795-0.84715.6740.2570.2570.0000.0000.0000.000
59E71THR0-0.014-0.02516.2240.0810.0810.0000.0000.0000.000
60E72TYR0-0.0150.00318.445-0.046-0.0460.0000.0000.0000.000
61E73GLY00.0640.00720.0440.0270.0270.0000.0000.0000.000
62E74SER00.0130.01622.634-0.019-0.0190.0000.0000.0000.000
63E75THR00.0300.02525.3070.0060.0060.0000.0000.0000.000
64E76ARG10.9070.94320.410-0.112-0.1120.0000.0000.0000.000
65E77LYS10.8520.92318.611-0.211-0.2110.0000.0000.0000.000
66E78ASN0-0.029-0.02019.504-0.003-0.0030.0000.0000.0000.000
67E79LEU00.0250.02618.4450.0220.0220.0000.0000.0000.000
68E80ARG10.7930.88613.988-0.236-0.2360.0000.0000.0000.000
69E81MET0-0.0090.01012.725-0.008-0.0080.0000.0000.0000.000
70E82ILE0-0.011-0.00611.9040.0800.0800.0000.0000.0000.000
71E83LEU00.0150.0148.699-0.042-0.0420.0000.0000.0000.000
72E84ARG10.8360.87911.643-0.352-0.3520.0000.0000.0000.000
73E85ASN00.0150.00111.854-0.051-0.0510.0000.0000.0000.000
74E86LEU0-0.048-0.0075.8950.1230.1230.0000.0000.0000.000
75E87ILE00.0490.0249.842-0.211-0.2110.0000.0000.0000.000
76E88GLU-1-0.790-0.9098.5250.4540.4540.0000.0000.0000.000
77E89ASN0-0.085-0.0429.0100.1130.1130.0000.0000.0000.000
78E90ASP-1-0.774-0.8628.8490.8480.8480.0000.0000.0000.000
79E91SER0-0.050-0.0226.2870.4820.4820.0000.0000.0000.000
80E92GLY00.0170.0056.939-0.451-0.4510.0000.0000.0000.000
81E93VAL0-0.096-0.0497.3290.4430.4430.0000.0000.0000.000
82E94TYR00.0290.0028.084-0.397-0.3970.0000.0000.0000.000
83E95TYR0-0.007-0.01810.972-0.028-0.0280.0000.0000.0000.000
84E97ALA00.000-0.02316.599-0.022-0.0220.0000.0000.0000.000
85E98THR00.0100.00420.075-0.006-0.0060.0000.0000.0000.000
86E99TRP0-0.015-0.00123.7680.0020.0020.0000.0000.0000.000
87E100ASP-1-0.780-0.90327.1620.1430.1430.0000.0000.0000.000
88E101GLN00.0260.00028.539-0.003-0.0030.0000.0000.0000.000
89E102ASN0-0.065-0.02631.475-0.013-0.0130.0000.0000.0000.000
90E103TYR0-0.017-0.00530.4590.0000.0000.0000.0000.0000.000
91E104TYR00.0320.03132.133-0.001-0.0010.0000.0000.0000.000
92E105LYS10.8980.94827.923-0.144-0.1440.0000.0000.0000.000
93E106LYS10.8530.93523.099-0.271-0.2710.0000.0000.0000.000
94E107LEU0-0.027-0.00122.253-0.008-0.0080.0000.0000.0000.000
95E108PHE00.006-0.00917.5940.0140.0140.0000.0000.0000.000
96E109GLY00.0570.02816.496-0.034-0.0340.0000.0000.0000.000
97E110SER0-0.0220.00013.3330.0460.0460.0000.0000.0000.000
98E111GLY0-0.026-0.00611.729-0.013-0.0130.0000.0000.0000.000
99E112THR00.0190.0005.851-0.259-0.2590.0000.0000.0000.000
100E113SER0-0.021-0.0125.000-0.047-0.0470.0000.0000.0000.000
101E114LEU0-0.0090.0052.804-1.5500.3481.069-1.095-1.8720.009
102E115VAL00.011-0.0082.044-5.697-3.9563.466-1.799-3.408-0.002
103E116VAL00.0370.0232.336-2.754-1.2823.948-2.959-2.462-0.034
104E117THR00.0240.0263.925-0.299-0.0840.001-0.026-0.1890.000
105E137GLN00.0040.00330.9760.0000.0000.0000.0000.0000.000
106E138LYS10.8090.88429.771-0.124-0.1240.0000.0000.0000.000
107E139VAL00.0250.00927.610-0.010-0.0100.0000.0000.0000.000
108E140THR0-0.021-0.01628.7470.0040.0040.0000.0000.0000.000
109E141GLN00.0240.02925.6560.0100.0100.0000.0000.0000.000
110E146VAL00.0700.04126.3540.0020.0020.0000.0000.0000.000
111E147ARG10.8830.92024.539-0.065-0.0650.0000.0000.0000.000
112E148LYS10.9900.98727.382-0.111-0.1110.0000.0000.0000.000
113E149ALA00.0030.00031.6410.0060.0060.0000.0000.0000.000
114E154VAL00.0550.03531.072-0.002-0.0020.0000.0000.0000.000
115E155THR0-0.0100.01433.9050.0000.0000.0000.0000.0000.000
116E156LEU0-0.053-0.01527.8400.0010.0010.0000.0000.0000.000
117E157ASN00.025-0.00930.2460.0040.0040.0000.0000.0000.000
118E158CYS0-0.023-0.00323.8980.0040.0040.0000.0000.0000.000
119E159LEU00.0010.01231.667-0.010-0.0100.0000.0000.0000.000
120E160TYR00.014-0.00931.9440.0110.0110.0000.0000.0000.000
121E161GLU-1-0.804-0.87733.6840.1070.1070.0000.0000.0000.000
122E162THR00.0270.02334.5380.0100.0100.0000.0000.0000.000
123E163SER00.007-0.00735.779-0.004-0.0040.0000.0000.0000.000
124E164TRP00.0110.00831.0460.0040.0040.0000.0000.0000.000
125E165TRP00.0450.02338.778-0.001-0.0010.0000.0000.0000.000
126E166SER0-0.002-0.00739.588-0.002-0.0020.0000.0000.0000.000
127E167TYR0-0.002-0.00134.5770.0040.0040.0000.0000.0000.000
128E168TYR00.0170.01332.647-0.006-0.0060.0000.0000.0000.000
129E169ILE00.0050.00030.9810.0090.0090.0000.0000.0000.000
130E170PHE0-0.020-0.01127.393-0.006-0.0060.0000.0000.0000.000
131E171TRP00.000-0.01026.9900.0100.0100.0000.0000.0000.000
132E172TYR0-0.037-0.03722.130-0.004-0.0040.0000.0000.0000.000
133E173LYS10.8850.94022.343-0.148-0.1480.0000.0000.0000.000
134E174ARG10.9370.98112.757-0.490-0.4900.0000.0000.0000.000
135E175LEU0-0.0050.00318.061-0.022-0.0220.0000.0000.0000.000
136E176PRO00.000-0.02015.8140.0410.0410.0000.0000.0000.000
137E177SER00.000-0.02013.7630.0150.0150.0000.0000.0000.000
138E178LYS10.8280.9079.058-0.464-0.4640.0000.0000.0000.000
139E179GLU-1-0.790-0.85413.5810.2420.2420.0000.0000.0000.000
140E180MET0-0.005-0.00716.504-0.043-0.0430.0000.0000.0000.000
141E181ILE00.0130.02118.685-0.012-0.0120.0000.0000.0000.000
142E182PHE00.034-0.00222.068-0.003-0.0030.0000.0000.0000.000
143E183LEU0-0.101-0.04225.231-0.013-0.0130.0000.0000.0000.000
144E184ILE0-0.017-0.01428.274-0.011-0.0110.0000.0000.0000.000
145E185ARG10.7920.85830.226-0.103-0.1030.0000.0000.0000.000
146E186GLN0-0.025-0.00632.465-0.010-0.0100.0000.0000.0000.000
147E187GLY00.0740.03034.9280.0070.0070.0000.0000.0000.000
148E188SER0-0.057-0.05337.516-0.004-0.0040.0000.0000.0000.000
149E189ASP-1-0.800-0.86739.1270.0860.0860.0000.0000.0000.000
150E190GLU-1-0.775-0.84139.0750.0960.0960.0000.0000.0000.000
151E191GLN00.0390.00841.7780.0010.0010.0000.0000.0000.000
152E192ASN0-0.052-0.02540.0190.0030.0030.0000.0000.0000.000
153E193ALA00.0840.04536.593-0.004-0.0040.0000.0000.0000.000
154E194LYS10.8450.90236.701-0.077-0.0770.0000.0000.0000.000
155E195SER00.0340.02934.476-0.003-0.0030.0000.0000.0000.000
156E196GLY00.0780.04435.1160.0040.0040.0000.0000.0000.000
157E197ARG10.8820.93633.550-0.069-0.0690.0000.0000.0000.000
158E198TYR00.0480.02428.7640.0050.0050.0000.0000.0000.000
159E199SER00.017-0.00834.108-0.006-0.0060.0000.0000.0000.000
160E200VAL0-0.0020.01234.6320.0060.0060.0000.0000.0000.000
161E201ASN00.0170.01936.368-0.005-0.0050.0000.0000.0000.000
162E202PHE0-0.004-0.00138.2320.0040.0040.0000.0000.0000.000
163E203LYS10.8730.94238.566-0.091-0.0910.0000.0000.0000.000
164E204LYS10.8870.93941.124-0.086-0.0860.0000.0000.0000.000
165E205ALA00.0640.03042.0560.0020.0020.0000.0000.0000.000
166E206ALA00.0080.00340.8920.0010.0010.0000.0000.0000.000
167E207LYS10.8730.95437.186-0.089-0.0890.0000.0000.0000.000
168E208SER00.0030.00936.3300.0040.0040.0000.0000.0000.000
169E209VAL00.033-0.00932.798-0.005-0.0050.0000.0000.0000.000
170E210ALA00.0000.00833.4040.0070.0070.0000.0000.0000.000
171E211LEU00.0230.03329.399-0.005-0.0050.0000.0000.0000.000
172E212THR0-0.045-0.04633.139-0.004-0.0040.0000.0000.0000.000
173E213ILE0-0.036-0.02429.4420.0040.0040.0000.0000.0000.000
174E214SER00.0460.03733.977-0.007-0.0070.0000.0000.0000.000
175E223LYS10.8410.90817.978-0.247-0.2470.0000.0000.0000.000
176E224TYR00.0310.00321.0520.0110.0110.0000.0000.0000.000
177E225PHE00.0160.01018.0000.0040.0040.0000.0000.0000.000
178E227ALA00.0480.01524.6440.0150.0150.0000.0000.0000.000
179E228LEU0-0.0120.00326.684-0.016-0.0160.0000.0000.0000.000
180E229GLY00.0330.01528.5600.0160.0160.0000.0000.0000.000
181E230GLU-1-0.878-0.94430.3450.1320.1320.0000.0000.0000.000
182E231SER0-0.002-0.00632.734-0.011-0.0110.0000.0000.0000.000
183E232LEU0-0.0270.00031.9740.0110.0110.0000.0000.0000.000
184E233THR00.004-0.01532.379-0.001-0.0010.0000.0000.0000.000
185E234ARG10.9420.95729.672-0.133-0.1330.0000.0000.0000.000
186E235ALA00.0530.02927.9290.0170.0170.0000.0000.0000.000
187E236ASP-1-0.803-0.86827.7010.1800.1800.0000.0000.0000.000
188E237LYS10.8300.91325.430-0.154-0.1540.0000.0000.0000.000
189E238LEU0-0.046-0.01523.593-0.017-0.0170.0000.0000.0000.000
190E239ILE00.0260.02824.0580.0330.0330.0000.0000.0000.000
191E240PHE00.0330.00021.483-0.014-0.0140.0000.0000.0000.000
192E241GLY00.0530.04424.106-0.005-0.0050.0000.0000.0000.000
193E242LYS10.8890.94220.509-0.211-0.2110.0000.0000.0000.000