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: 94RR2

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2156184.177874
FMO2-HF: Nuclear repulsion 2080116.496646
FMO2-HF: Total energy -76067.681228
FMO2-MP2: Total energy -76291.15039


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.
-12.23-6.6362.639-3.131-5.102-0.011
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 : 0.002 / q_NPA : -0.014
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].
3E6LYS10.8980.9642.408-4.887-2.8701.144-1.337-1.8240.002
4E7PHE00.0240.0082.435-1.135-0.1820.534-0.351-1.1360.001
5E8GLY00.0500.0405.4990.0180.0180.0000.0000.0000.000
6E9LYS10.8960.9616.9050.0590.0590.0000.0000.0000.000
7E10VAL00.0050.0056.6650.1500.1500.0000.0000.0000.000
8E11ALA00.0190.0179.606-0.058-0.0580.0000.0000.0000.000
9E12VAL00.002-0.01011.5080.0290.0290.0000.0000.0000.000
10E13LEU0-0.018-0.00913.8010.0250.0250.0000.0000.0000.000
11E14LEU0-0.029-0.01417.2700.0060.0060.0000.0000.0000.000
12E15GLY00.0470.02019.6560.0090.0090.0000.0000.0000.000
13E16GLY0-0.001-0.00623.3260.0150.0150.0000.0000.0000.000
14E17LYS10.9270.95425.2240.0980.0980.0000.0000.0000.000
15E18SER0-0.123-0.06727.5860.0080.0080.0000.0000.0000.000
16E19ALA00.0370.00329.978-0.004-0.0040.0000.0000.0000.000
17E20GLU-1-0.933-0.96627.177-0.118-0.1180.0000.0000.0000.000
18E21ARG10.8610.92625.7300.1630.1630.0000.0000.0000.000
19E22ALA00.018-0.00425.319-0.015-0.0150.0000.0000.0000.000
20E23VAL00.0370.01824.374-0.012-0.0120.0000.0000.0000.000
21E24SER0-0.009-0.00921.432-0.017-0.0170.0000.0000.0000.000
22E25LEU0-0.0010.00120.732-0.025-0.0250.0000.0000.0000.000
23E26ASP-1-0.901-0.93920.537-0.255-0.2550.0000.0000.0000.000
24E27SER0-0.074-0.05619.135-0.028-0.0280.0000.0000.0000.000
25E28GLY00.029-0.00516.651-0.033-0.0330.0000.0000.0000.000
26E29GLN0-0.020-0.01315.499-0.064-0.0640.0000.0000.0000.000
27E30ALA0-0.0180.00815.644-0.053-0.0530.0000.0000.0000.000
28E31VAL0-0.001-0.00911.824-0.062-0.0620.0000.0000.0000.000
29E32LEU0-0.007-0.00211.192-0.126-0.1260.0000.0000.0000.000
30E33ASP-1-0.885-0.94610.906-0.725-0.7250.0000.0000.0000.000
31E34ALA0-0.041-0.02410.972-0.119-0.1190.0000.0000.0000.000
32E35LEU0-0.030-0.0166.514-0.186-0.1860.0000.0000.0000.000
33E36LEU0-0.0010.0036.179-0.574-0.5740.0000.0000.0000.000
34E37ARG10.8530.9307.2820.4850.4850.0000.0000.0000.000
35E38SER0-0.069-0.0264.8370.1620.1620.0000.0000.0000.000
36E39GLY0-0.038-0.0123.143-2.642-1.4010.148-0.577-0.812-0.005
37E40VAL0-0.027-0.0092.661-3.305-2.0220.796-0.900-1.179-0.009
38E41GLN0-0.024-0.0193.6700.9341.0340.0170.034-0.1510.000
39E42ALA0-0.0010.0036.9010.3360.3360.0000.0000.0000.000
40E43GLU-1-0.833-0.9129.043-0.488-0.4880.0000.0000.0000.000
41E44ALA00.0000.01012.8430.0330.0330.0000.0000.0000.000
42E45PHE0-0.018-0.01115.8610.0250.0250.0000.0000.0000.000
43E46ASP-1-0.695-0.84518.187-0.193-0.1930.0000.0000.0000.000
44E47PRO0-0.033-0.02621.1930.0160.0160.0000.0000.0000.000
45E48GLN0-0.159-0.06523.6590.0240.0240.0000.0000.0000.000
46E49ASP-1-0.892-0.93924.570-0.169-0.1690.0000.0000.0000.000
47E50ARG10.8350.90817.6810.2720.2720.0000.0000.0000.000
48E51SER00.020-0.00324.2730.0060.0060.0000.0000.0000.000
49E52VAL00.0570.00522.673-0.010-0.0100.0000.0000.0000.000
50E53THR00.0130.01722.512-0.002-0.0020.0000.0000.0000.000
51E54GLU-1-0.900-0.94121.046-0.171-0.1710.0000.0000.0000.000
52E55LEU0-0.005-0.01217.257-0.021-0.0210.0000.0000.0000.000
53E56VAL00.0060.00617.580-0.010-0.0100.0000.0000.0000.000
54E57ASN0-0.110-0.04617.2650.0260.0260.0000.0000.0000.000
55E58TYR0-0.095-0.04912.384-0.012-0.0120.0000.0000.0000.000
56E59ASP-1-0.817-0.91010.446-0.116-0.1160.0000.0000.0000.000
57E60ARG10.8050.8857.7530.0650.0650.0000.0000.0000.000
58E61ALA00.0010.00012.103-0.078-0.0780.0000.0000.0000.000
59E62PHE00.008-0.00110.1410.0460.0460.0000.0000.0000.000
60E63ILE0-0.038-0.01313.111-0.018-0.0180.0000.0000.0000.000
61E64VAL00.005-0.00416.4150.0090.0090.0000.0000.0000.000
62E65LEU0-0.0130.03518.3480.0020.0020.0000.0000.0000.000
63E66HIS00.0400.02321.278-0.003-0.0030.0000.0000.0000.000
64E67GLY00.0960.06324.7100.0010.0010.0000.0000.0000.000
65E68ARG10.9310.94827.3970.0870.0870.0000.0000.0000.000
66E69GLY0-0.080-0.04026.999-0.009-0.0090.0000.0000.0000.000
67E70GLY00.0220.00723.477-0.002-0.0020.0000.0000.0000.000
68E71GLU-1-0.791-0.91123.590-0.106-0.1060.0000.0000.0000.000
69E72ASP-1-0.828-0.94025.678-0.070-0.0700.0000.0000.0000.000
70E73GLY00.0370.01726.0520.0090.0090.0000.0000.0000.000
71E74GLN0-0.039-0.01826.356-0.002-0.0020.0000.0000.0000.000
72E75ILE00.0050.00321.0390.0040.0040.0000.0000.0000.000
73E76GLN00.0330.01721.4730.0000.0000.0000.0000.0000.000
74E77GLY00.0240.01722.8150.0110.0110.0000.0000.0000.000
75E78VAL0-0.055-0.03222.4460.0070.0070.0000.0000.0000.000
76E79LEU0-0.008-0.00917.666-0.001-0.0010.0000.0000.0000.000
77E80GLU-1-0.845-0.91420.7120.0170.0170.0000.0000.0000.000
78E81TRP0-0.073-0.03522.7800.0110.0110.0000.0000.0000.000
79E82LEU0-0.069-0.03920.7330.0040.0040.0000.0000.0000.000
80E83ASN0-0.067-0.01920.2270.0130.0130.0000.0000.0000.000
81E84ILE0-0.0050.02115.0340.0120.0120.0000.0000.0000.000
82E85PRO00.0360.02313.173-0.012-0.0120.0000.0000.0000.000
83E86TYR0-0.056-0.07114.319-0.057-0.0570.0000.0000.0000.000
84E87THR00.0120.02112.6930.0100.0100.0000.0000.0000.000
85E88GLY0-0.027-0.01515.277-0.007-0.0070.0000.0000.0000.000
86E89THR00.0100.02118.4350.0230.0230.0000.0000.0000.000
87E90GLY00.1620.08921.958-0.009-0.0090.0000.0000.0000.000
88E91VAL00.0070.01123.347-0.009-0.0090.0000.0000.0000.000
89E92GLN0-0.008-0.00726.384-0.002-0.0020.0000.0000.0000.000
90E93GLY00.0810.02727.079-0.003-0.0030.0000.0000.0000.000
91E94SER0-0.048-0.05624.704-0.008-0.0080.0000.0000.0000.000
92E95ALA0-0.0180.00226.936-0.004-0.0040.0000.0000.0000.000
93E96ILE0-0.107-0.03330.307-0.001-0.0010.0000.0000.0000.000
94E97GLY00.0540.00429.290-0.001-0.0010.0000.0000.0000.000
95E98MET0-0.0240.01629.504-0.006-0.0060.0000.0000.0000.000
96E99ASP-1-0.869-0.94931.260-0.038-0.0380.0000.0000.0000.000
97E100LYS11.0170.99534.9570.0590.0590.0000.0000.0000.000
98E101VAL0-0.083-0.01536.7250.0040.0040.0000.0000.0000.000
99E102LYS10.9520.99236.1650.0290.0290.0000.0000.0000.000
100E103THR0-0.0090.00132.6370.0020.0020.0000.0000.0000.000
101E104LYS10.9460.96535.5360.0370.0370.0000.0000.0000.000
102E105GLN0-0.018-0.01438.9310.0030.0030.0000.0000.0000.000
103E106ILE00.0140.01333.9170.0030.0030.0000.0000.0000.000
104E107TRP0-0.028-0.00432.3220.0020.0020.0000.0000.0000.000
105E108GLN0-0.019-0.02037.9250.0030.0030.0000.0000.0000.000
106E109GLY0-0.015-0.01240.9300.0020.0020.0000.0000.0000.000
107E110SER0-0.039-0.01637.0980.0040.0040.0000.0000.0000.000
108E111ASP-1-0.974-0.98139.1950.0060.0060.0000.0000.0000.000
109E112LEU0-0.060-0.02835.2120.0000.0000.0000.0000.0000.000
110E113PRO0-0.0310.00138.695-0.002-0.0020.0000.0000.0000.000
111E114THR00.025-0.01539.514-0.004-0.0040.0000.0000.0000.000
112E115ALA0-0.021-0.00741.5360.0020.0020.0000.0000.0000.000
113E116PRO00.003-0.00443.969-0.001-0.0010.0000.0000.0000.000
114E117TYR0-0.0050.01343.762-0.002-0.0020.0000.0000.0000.000
115E184PHE0-0.031-0.03633.379-0.001-0.0010.0000.0000.0000.000
116E185THR0-0.058-0.00828.654-0.004-0.0040.0000.0000.0000.000
117E186ILE00.0520.02927.356-0.003-0.0030.0000.0000.0000.000
118E187SER0-0.023-0.01422.928-0.005-0.0050.0000.0000.0000.000
119E188PHE0-0.008-0.02122.5280.0090.0090.0000.0000.0000.000
120E189LEU00.0660.02014.754-0.021-0.0210.0000.0000.0000.000
121E190ASN00.0100.00415.5070.0240.0240.0000.0000.0000.000
122E191GLY00.0370.02418.1520.0190.0190.0000.0000.0000.000
123E192GLN0-0.054-0.02120.219-0.001-0.0010.0000.0000.0000.000
124E193PRO0-0.056-0.02022.563-0.014-0.0140.0000.0000.0000.000
125E194LEU0-0.028-0.01421.1040.0030.0030.0000.0000.0000.000
126E195PRO00.0320.02223.8640.0010.0010.0000.0000.0000.000
127E196VAL0-0.0080.01227.037-0.009-0.0090.0000.0000.0000.000
128E197ILE0-0.054-0.01626.062-0.003-0.0030.0000.0000.0000.000
129E198ARG10.9300.96530.4940.0560.0560.0000.0000.0000.000
130E199LEU0-0.004-0.01531.114-0.006-0.0060.0000.0000.0000.000
131E200GLN00.0090.01534.7480.0000.0000.0000.0000.0000.000
132E221TYR00.0940.02727.284-0.002-0.0020.0000.0000.0000.000
133E222GLY0-0.085-0.03930.9580.0040.0040.0000.0000.0000.000
134E223ILE00.0410.02827.4250.0050.0050.0000.0000.0000.000
135E224PRO00.039-0.00131.228-0.004-0.0040.0000.0000.0000.000
136E225CYS00.0660.06332.3150.0000.0000.0000.0000.0000.000
137E226GLY00.0460.06334.6260.0020.0020.0000.0000.0000.000
138E227LEU0-0.155-0.13936.2740.0030.0030.0000.0000.0000.000
139E228SER0-0.053-0.05637.187-0.003-0.0030.0000.0000.0000.000
140E229GLU-1-0.880-0.93833.3850.0000.0000.0000.0000.0000.000
141E230THR0-0.011-0.04534.6630.0000.0000.0000.0000.0000.000
142E231GLU-1-0.881-0.88936.995-0.010-0.0100.0000.0000.0000.000
143E232GLU-1-0.826-0.90730.040-0.036-0.0360.0000.0000.0000.000
144E233LYS10.9630.95929.877-0.012-0.0120.0000.0000.0000.000
145E234LYS10.9530.97833.3800.0050.0050.0000.0000.0000.000
146E235LEU00.0020.00633.4250.0010.0010.0000.0000.0000.000
147E236GLN00.002-0.00828.437-0.008-0.0080.0000.0000.0000.000
148E237ALA00.0120.00730.5220.0010.0010.0000.0000.0000.000
149E238LEU0-0.0090.00032.3880.0020.0020.0000.0000.0000.000
150E239CYS0-0.007-0.00330.236-0.001-0.0010.0000.0000.0000.000
151E240LEU00.0100.01126.432-0.003-0.0030.0000.0000.0000.000
152E241ARG10.9530.98929.434-0.006-0.0060.0000.0000.0000.000
153E242ALA00.0160.00532.1370.0010.0010.0000.0000.0000.000
154E243PHE0-0.0010.05222.854-0.004-0.0040.0000.0000.0000.000
155E244GLN00.039-0.00226.939-0.003-0.0030.0000.0000.0000.000
156E245ALA0-0.049-0.01229.0630.0020.0020.0000.0000.0000.000
157E246VAL0-0.040-0.02729.3380.0010.0010.0000.0000.0000.000
158E247GLY00.0160.01228.071-0.003-0.0030.0000.0000.0000.000
159E248ALA0-0.068-0.03824.776-0.003-0.0030.0000.0000.0000.000
160E249GLU-1-0.913-0.95120.0550.0480.0480.0000.0000.0000.000
161E250GLY00.079-0.00519.987-0.009-0.0090.0000.0000.0000.000
162E251TRP0-0.061-0.03116.5390.0010.0010.0000.0000.0000.000
163E252GLY00.0340.00919.3240.0020.0020.0000.0000.0000.000
164E253ARG10.9020.94122.7770.0950.0950.0000.0000.0000.000
165E254ILE00.0070.02626.0200.0000.0000.0000.0000.0000.000
166E268GLU-1-0.947-0.98432.193-0.062-0.0620.0000.0000.0000.000
167E269VAL0-0.053-0.02627.7210.0020.0020.0000.0000.0000.000
168E270ASN0-0.022-0.00125.7220.0030.0030.0000.0000.0000.000
169E271THR00.006-0.00523.3690.0000.0000.0000.0000.0000.000
170E272VAL00.0130.01819.057-0.001-0.0010.0000.0000.0000.000
171E273PRO0-0.037-0.00720.1740.0010.0010.0000.0000.0000.000
172E274GLY0-0.0070.00720.753-0.017-0.0170.0000.0000.0000.000
173E275MET0-0.025-0.02715.1630.0160.0160.0000.0000.0000.000
174E276THR00.0530.06018.946-0.025-0.0250.0000.0000.0000.000
175E277SER00.0640.00321.6960.0010.0010.0000.0000.0000.000
176E278HIS0-0.059-0.02622.7950.0010.0010.0000.0000.0000.000
177E279SER0-0.008-0.00522.2150.0190.0190.0000.0000.0000.000
178E280LEU0-0.027-0.03823.789-0.004-0.0040.0000.0000.0000.000
179E281VAL00.0600.03519.4350.0070.0070.0000.0000.0000.000
180E282PRO00.0700.03118.5260.0080.0080.0000.0000.0000.000
181E283LYS10.8540.95019.9620.1190.1190.0000.0000.0000.000
182E284ALA00.0430.01023.0560.0040.0040.0000.0000.0000.000
183E285ALA00.0380.01917.7610.0130.0130.0000.0000.0000.000
184E286LYS10.9800.99319.3020.1910.1910.0000.0000.0000.000
185E287ALA0-0.099-0.04520.2370.0090.0090.0000.0000.0000.000
186E288VAL0-0.028-0.01520.1830.0150.0150.0000.0000.0000.000
187E289GLY0-0.020-0.01019.1300.0130.0130.0000.0000.0000.000
188E290TYR00.0100.02013.2550.0000.0000.0000.0000.0000.000
189E291SER0-0.038-0.01812.632-0.026-0.0260.0000.0000.0000.000
190E292PHE00.019-0.01913.6750.0150.0150.0000.0000.0000.000
191E293ASP-1-0.769-0.8949.494-0.749-0.7490.0000.0000.0000.000
192E294GLU-1-0.881-0.9309.324-0.352-0.3520.0000.0000.0000.000
193E295LEU0-0.017-0.01110.4520.0610.0610.0000.0000.0000.000
194E296CYS0-0.039-0.01310.1730.0560.0560.0000.0000.0000.000
195E297VAL00.0410.0205.289-0.012-0.0120.0000.0000.0000.000
196E298ALA00.0030.0057.9870.1460.1460.0000.0000.0000.000
197E299ILE0-0.053-0.03410.8790.0750.0750.0000.0000.0000.000
198E300LEU00.0140.0105.6170.0300.0300.0000.0000.0000.000
199E301GLU-1-0.959-0.9837.7490.4320.4320.0000.0000.0000.000
200E302GLN00.0190.0169.8150.0610.0610.0000.0000.0000.000
201E303THR0-0.056-0.00710.0350.0240.0240.0000.0000.0000.000
202E304LEU0-0.063-0.0317.1210.0900.0900.0000.0000.0000.000
203E305GLU-1-0.946-0.95211.7640.1990.1990.0000.0000.0000.000