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

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FMODB ID: MVLLZ

Calculation Name: 5DMX-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DMX

Chain ID: E

ChEMBL ID:

UniProt ID: B2I1J3

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2157742.893949
FMO2-HF: Nuclear repulsion 2081673.310579
FMO2-HF: Total energy -76069.58337
FMO2-MP2: Total energy -76292.973962


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:4:ALA)


Summations of interaction energy for fragment #1(E:4:ALA)
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.
-11.216-5.6032.87-3.209-5.275-0.011
Interaction energy analysis for fragmet #1(E:4:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015
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].
3E6LYS10.7970.8922.367-4.310-2.3261.160-1.326-1.8180.002
4E7PHE00.0280.0082.366-1.061-0.0970.655-0.421-1.1980.001
5E8GLY00.0390.0365.5140.0480.0480.0000.0000.0000.000
6E9LYS10.8310.8996.9340.0980.0980.0000.0000.0000.000
7E10VAL0-0.0010.0006.7370.1570.1570.0000.0000.0000.000
8E11ALA00.0220.0209.654-0.056-0.0560.0000.0000.0000.000
9E12VAL0-0.007-0.01211.4750.0290.0290.0000.0000.0000.000
10E13LEU0-0.030-0.01613.8290.0260.0260.0000.0000.0000.000
11E14LEU0-0.017-0.01317.4460.0050.0050.0000.0000.0000.000
12E15GLY00.0400.01319.6760.0080.0080.0000.0000.0000.000
13E16GLY0-0.015-0.01123.3370.0140.0140.0000.0000.0000.000
14E17LYS10.9160.93425.2550.0980.0980.0000.0000.0000.000
15E18SER0-0.120-0.05227.4710.0070.0070.0000.0000.0000.000
16E19ALA00.0280.00330.022-0.004-0.0040.0000.0000.0000.000
17E20GLU-1-0.884-0.95327.498-0.110-0.1100.0000.0000.0000.000
18E21ARG10.8250.90025.3140.1600.1600.0000.0000.0000.000
19E22ALA00.0270.00125.324-0.015-0.0150.0000.0000.0000.000
20E23VAL00.0320.01224.523-0.011-0.0110.0000.0000.0000.000
21E24SER00.0050.00321.402-0.017-0.0170.0000.0000.0000.000
22E25LEU00.0040.00220.738-0.025-0.0250.0000.0000.0000.000
23E26ASP-1-0.901-0.93620.511-0.245-0.2450.0000.0000.0000.000
24E27SER0-0.090-0.07719.189-0.027-0.0270.0000.0000.0000.000
25E28GLY00.031-0.00116.663-0.031-0.0310.0000.0000.0000.000
26E29GLN0-0.038-0.02215.479-0.057-0.0570.0000.0000.0000.000
27E30ALA0-0.0060.01315.587-0.052-0.0520.0000.0000.0000.000
28E31VAL0-0.001-0.00711.863-0.060-0.0600.0000.0000.0000.000
29E32LEU0-0.001-0.00211.168-0.125-0.1250.0000.0000.0000.000
30E33ASP-1-0.876-0.93910.831-0.689-0.6890.0000.0000.0000.000
31E34ALA0-0.037-0.02210.911-0.112-0.1120.0000.0000.0000.000
32E35LEU0-0.022-0.0086.574-0.174-0.1740.0000.0000.0000.000
33E36LEU0-0.0040.0026.137-0.538-0.5380.0000.0000.0000.000
34E37ARG10.8190.9027.2800.4710.4710.0000.0000.0000.000
35E38SER0-0.065-0.0244.7630.1110.154-0.001-0.004-0.0390.000
36E39GLY0-0.038-0.0133.208-2.418-1.2450.151-0.539-0.785-0.004
37E40VAL0-0.025-0.0112.811-3.442-2.0660.883-0.978-1.281-0.010
38E41GLN0-0.012-0.0093.5740.9100.9830.0220.059-0.1540.000
39E42ALA00.0020.0016.8190.3310.3310.0000.0000.0000.000
40E43GLU-1-0.786-0.8549.000-0.484-0.4840.0000.0000.0000.000
41E44ALA00.0030.01612.7980.0330.0330.0000.0000.0000.000
42E45PHE00.002-0.01315.8320.0230.0230.0000.0000.0000.000
43E46ASP-1-0.679-0.82018.189-0.188-0.1880.0000.0000.0000.000
44E47PRO0-0.031-0.02721.1100.0160.0160.0000.0000.0000.000
45E48GLN0-0.169-0.07523.6870.0220.0220.0000.0000.0000.000
46E49ASP-1-0.884-0.93724.615-0.166-0.1660.0000.0000.0000.000
47E50ARG10.8290.91017.5480.2730.2730.0000.0000.0000.000
48E51SER00.0280.02324.2940.0050.0050.0000.0000.0000.000
49E52VAL00.0600.00322.723-0.009-0.0090.0000.0000.0000.000
50E53THR0-0.033-0.02222.571-0.002-0.0020.0000.0000.0000.000
51E54GLU-1-0.859-0.91621.061-0.178-0.1780.0000.0000.0000.000
52E55LEU00.004-0.00617.617-0.021-0.0210.0000.0000.0000.000
53E56VAL00.0130.00617.643-0.010-0.0100.0000.0000.0000.000
54E57ASN0-0.125-0.06117.3740.0250.0250.0000.0000.0000.000
55E58TYR0-0.087-0.05012.484-0.012-0.0120.0000.0000.0000.000
56E59ASP-1-0.811-0.89310.510-0.170-0.1700.0000.0000.0000.000
57E60ARG10.8090.8907.8020.0920.0920.0000.0000.0000.000
58E61ALA0-0.0060.00112.221-0.075-0.0750.0000.0000.0000.000
59E62PHE00.0170.00610.4510.0400.0400.0000.0000.0000.000
60E63ILE0-0.027-0.01513.203-0.017-0.0170.0000.0000.0000.000
61E64VAL00.015-0.00916.3540.0090.0090.0000.0000.0000.000
62E65LEU0-0.0150.03918.4100.0020.0020.0000.0000.0000.000
63E66HIS00.0430.02721.243-0.002-0.0020.0000.0000.0000.000
64E67GLY00.1070.07324.7730.0010.0010.0000.0000.0000.000
65E68ARG10.9230.95027.4800.0870.0870.0000.0000.0000.000
66E69GLY0-0.083-0.05527.070-0.009-0.0090.0000.0000.0000.000
67E70GLY00.0290.01223.566-0.002-0.0020.0000.0000.0000.000
68E71GLU-1-0.755-0.87823.693-0.106-0.1060.0000.0000.0000.000
69E72ASP-1-0.789-0.90125.779-0.072-0.0720.0000.0000.0000.000
70E73GLY00.0310.01526.1770.0090.0090.0000.0000.0000.000
71E74GLN0-0.069-0.03026.4810.0000.0000.0000.0000.0000.000
72E75ILE00.0030.00621.1060.0040.0040.0000.0000.0000.000
73E76GLN00.0390.01221.5330.0000.0000.0000.0000.0000.000
74E77GLY00.0240.01722.9420.0100.0100.0000.0000.0000.000
75E78VAL0-0.064-0.04022.3880.0070.0070.0000.0000.0000.000
76E79LEU00.0070.00017.586-0.001-0.0010.0000.0000.0000.000
77E80GLU-1-0.835-0.88220.8430.0120.0120.0000.0000.0000.000
78E81TRP0-0.064-0.03822.9220.0120.0120.0000.0000.0000.000
79E82LEU0-0.064-0.03120.7450.0040.0040.0000.0000.0000.000
80E83ASN0-0.085-0.02820.3250.0130.0130.0000.0000.0000.000
81E84ILE0-0.0020.02515.0950.0120.0120.0000.0000.0000.000
82E85PRO00.0270.01913.275-0.013-0.0130.0000.0000.0000.000
83E86TYR0-0.078-0.10114.478-0.055-0.0550.0000.0000.0000.000
84E87THR00.0130.02512.8770.0100.0100.0000.0000.0000.000
85E88GLY0-0.020-0.00915.422-0.006-0.0060.0000.0000.0000.000
86E89THR0-0.0120.01318.5830.0230.0230.0000.0000.0000.000
87E90GLY00.1500.08122.111-0.009-0.0090.0000.0000.0000.000
88E91VAL00.002-0.01323.504-0.008-0.0080.0000.0000.0000.000
89E92GLN0-0.002-0.00526.532-0.002-0.0020.0000.0000.0000.000
90E93GLY00.0840.03127.235-0.003-0.0030.0000.0000.0000.000
91E94SER0-0.052-0.03424.627-0.008-0.0080.0000.0000.0000.000
92E95ALA0-0.0070.00627.071-0.004-0.0040.0000.0000.0000.000
93E96ILE0-0.089-0.02730.4390.0000.0000.0000.0000.0000.000
94E97GLY00.045-0.00229.419-0.001-0.0010.0000.0000.0000.000
95E98MET0-0.0350.01029.538-0.005-0.0050.0000.0000.0000.000
96E99ASP-1-0.808-0.89831.373-0.037-0.0370.0000.0000.0000.000
97E100LYS10.8610.91034.8710.0620.0620.0000.0000.0000.000
98E101VAL0-0.030-0.01036.8420.0030.0030.0000.0000.0000.000
99E102LYS10.8870.93736.1210.0330.0330.0000.0000.0000.000
100E103THR00.0110.00632.7130.0030.0030.0000.0000.0000.000
101E104LYS10.9060.95935.6730.0350.0350.0000.0000.0000.000
102E105GLN0-0.027-0.01739.0680.0020.0020.0000.0000.0000.000
103E106ILE0-0.0020.00833.9100.0030.0030.0000.0000.0000.000
104E107TRP0-0.027-0.00132.3180.0020.0020.0000.0000.0000.000
105E108GLN0-0.008-0.01438.0770.0030.0030.0000.0000.0000.000
106E109GLY0-0.012-0.00941.0930.0020.0020.0000.0000.0000.000
107E110SER0-0.041-0.01637.2280.0040.0040.0000.0000.0000.000
108E111ASP-1-0.978-0.98439.3610.0040.0040.0000.0000.0000.000
109E112LEU0-0.027-0.00535.2610.0000.0000.0000.0000.0000.000
110E113PRO0-0.033-0.00338.994-0.002-0.0020.0000.0000.0000.000
111E114THR00.028-0.01139.698-0.004-0.0040.0000.0000.0000.000
112E115ALA0-0.025-0.00341.6670.0020.0020.0000.0000.0000.000
113E116PRO00.0250.00144.093-0.001-0.0010.0000.0000.0000.000
114E117TYR0-0.0090.00643.578-0.002-0.0020.0000.0000.0000.000
115E184PHE0-0.038-0.03933.553-0.001-0.0010.0000.0000.0000.000
116E185THR0-0.028-0.00328.246-0.003-0.0030.0000.0000.0000.000
117E186ILE00.0310.02727.438-0.003-0.0030.0000.0000.0000.000
118E187SER00.0110.00023.142-0.005-0.0050.0000.0000.0000.000
119E188PHE0-0.036-0.03122.6450.0090.0090.0000.0000.0000.000
120E189LEU00.0550.02215.021-0.021-0.0210.0000.0000.0000.000
121E190ASN00.0260.01216.3600.0180.0180.0000.0000.0000.000
122E191GLY00.0370.03418.2990.0190.0190.0000.0000.0000.000
123E192GLN0-0.045-0.02521.025-0.001-0.0010.0000.0000.0000.000
124E193PRO0-0.066-0.02322.691-0.013-0.0130.0000.0000.0000.000
125E194LEU00.0030.00421.0500.0030.0030.0000.0000.0000.000
126E195PRO0-0.004-0.00424.1380.0010.0010.0000.0000.0000.000
127E196VAL0-0.028-0.00527.124-0.009-0.0090.0000.0000.0000.000
128E197ILE0-0.026-0.01026.224-0.002-0.0020.0000.0000.0000.000
129E198ARG10.8820.94630.5620.0550.0550.0000.0000.0000.000
130E199LEU00.0320.00131.246-0.006-0.0060.0000.0000.0000.000
131E200GLN00.0080.01734.8050.0010.0010.0000.0000.0000.000
132E221TYR00.1160.03827.439-0.005-0.0050.0000.0000.0000.000
133E222GLY0-0.106-0.04431.0070.0040.0040.0000.0000.0000.000
134E223ILE00.0430.03327.0730.0050.0050.0000.0000.0000.000
135E224PRO00.035-0.00531.276-0.004-0.0040.0000.0000.0000.000
136E225CYS00.0230.04533.0010.0000.0000.0000.0000.0000.000
137E226GLY00.1220.11734.6910.0020.0020.0000.0000.0000.000
138E227LEU0-0.184-0.16836.3800.0030.0030.0000.0000.0000.000
139E228SER0-0.034-0.03537.269-0.002-0.0020.0000.0000.0000.000
140E229GLU-1-0.771-0.87633.116-0.001-0.0010.0000.0000.0000.000
141E230THR00.045-0.01134.7660.0000.0000.0000.0000.0000.000
142E231GLU-1-0.869-0.89837.164-0.008-0.0080.0000.0000.0000.000
143E232GLU-1-0.797-0.89230.402-0.036-0.0360.0000.0000.0000.000
144E233LYS10.8650.90430.656-0.003-0.0030.0000.0000.0000.000
145E234LYS10.8320.91233.4970.0070.0070.0000.0000.0000.000
146E235LEU00.0080.00233.7330.0010.0010.0000.0000.0000.000
147E236GLN00.0140.00327.802-0.002-0.0020.0000.0000.0000.000
148E237ALA00.0150.01230.6520.0010.0010.0000.0000.0000.000
149E238LEU0-0.010-0.00132.5230.0020.0020.0000.0000.0000.000
150E239CYS0-0.015-0.01230.437-0.001-0.0010.0000.0000.0000.000
151E240LEU00.0180.01226.546-0.003-0.0030.0000.0000.0000.000
152E241ARG10.9300.97329.574-0.004-0.0040.0000.0000.0000.000
153E242ALA00.0120.00032.2990.0010.0010.0000.0000.0000.000
154E243PHE0-0.0090.04323.159-0.004-0.0040.0000.0000.0000.000
155E244GLN00.0420.00526.960-0.001-0.0010.0000.0000.0000.000
156E245ALA0-0.047-0.01429.2310.0020.0020.0000.0000.0000.000
157E246VAL0-0.040-0.02529.6200.0010.0010.0000.0000.0000.000
158E247GLY00.0150.01028.243-0.002-0.0020.0000.0000.0000.000
159E248ALA0-0.067-0.04225.022-0.003-0.0030.0000.0000.0000.000
160E249GLU-1-0.818-0.87620.3360.0440.0440.0000.0000.0000.000
161E250GLY0-0.059-0.09120.139-0.016-0.0160.0000.0000.0000.000
162E251TRP0-0.046-0.04417.0950.0020.0020.0000.0000.0000.000
163E252GLY00.0620.02519.399-0.010-0.0100.0000.0000.0000.000
164E253ARG10.8190.88822.8960.0900.0900.0000.0000.0000.000
165E254ILE00.0110.02726.1290.0000.0000.0000.0000.0000.000
166E268GLU-1-0.825-0.89732.697-0.059-0.0590.0000.0000.0000.000
167E269VAL0-0.025-0.01727.6990.0010.0010.0000.0000.0000.000
168E270ASN0-0.061-0.03125.8020.0000.0000.0000.0000.0000.000
169E271THR00.020-0.00124.092-0.002-0.0020.0000.0000.0000.000
170E272VAL00.0040.02719.595-0.002-0.0020.0000.0000.0000.000
171E273PRO0-0.033-0.00720.2770.0010.0010.0000.0000.0000.000
172E274GLY0-0.0020.00320.819-0.017-0.0170.0000.0000.0000.000
173E275MET0-0.028-0.02315.0760.0170.0170.0000.0000.0000.000
174E276THR00.0430.03618.949-0.024-0.0240.0000.0000.0000.000
175E277SER00.0520.00121.698-0.001-0.0010.0000.0000.0000.000
176E278HIS0-0.035-0.00522.7760.0000.0000.0000.0000.0000.000
177E279SER0-0.0100.00022.2450.0190.0190.0000.0000.0000.000
178E280LEU0-0.032-0.03823.818-0.003-0.0030.0000.0000.0000.000
179E281VAL00.0690.03519.6470.0070.0070.0000.0000.0000.000
180E282PRO00.0630.02918.6580.0080.0080.0000.0000.0000.000
181E283LYS10.8600.95520.0050.1130.1130.0000.0000.0000.000
182E284ALA00.030-0.00323.1000.0040.0040.0000.0000.0000.000
183E285ALA00.0380.02817.8460.0120.0120.0000.0000.0000.000
184E286LYS10.9930.99919.3480.1920.1920.0000.0000.0000.000
185E287ALA0-0.100-0.04720.2760.0080.0080.0000.0000.0000.000
186E288VAL0-0.026-0.01620.6270.0140.0140.0000.0000.0000.000
187E289GLY0-0.019-0.00819.1770.0130.0130.0000.0000.0000.000
188E290TYR00.0040.01713.2010.0000.0000.0000.0000.0000.000
189E291SER0-0.075-0.05913.179-0.029-0.0290.0000.0000.0000.000
190E292PHE0-0.007-0.02013.8060.0150.0150.0000.0000.0000.000
191E293ASP-1-0.740-0.8789.545-0.711-0.7110.0000.0000.0000.000
192E294GLU-1-0.814-0.8669.348-0.334-0.3340.0000.0000.0000.000
193E295LEU0-0.046-0.03010.5280.0590.0590.0000.0000.0000.000
194E296CYS0-0.033-0.01810.2950.0540.0540.0000.0000.0000.000
195E297VAL00.0520.0245.6340.0000.0000.0000.0000.0000.000
196E298ALA0-0.002-0.0068.0790.1390.1390.0000.0000.0000.000
197E299ILE0-0.048-0.02811.0040.0700.0700.0000.0000.0000.000
198E300LEU00.0140.0115.8350.0290.0290.0000.0000.0000.000
199E301GLU-1-0.884-0.9257.5350.6330.6330.0000.0000.0000.000
200E302GLN00.0170.0189.9970.0560.0560.0000.0000.0000.000
201E303THR0-0.056-0.01810.1510.0240.0240.0000.0000.0000.000
202E304LEU0-0.057-0.0297.3310.0780.0780.0000.0000.0000.000
203E305GLU-1-0.946-0.95811.7620.1860.1860.0000.0000.0000.000