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: 72KKK

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166834.972329
FMO2-HF: Nuclear repulsion 2090764.134453
FMO2-HF: Total energy -76070.837876
FMO2-MP2: Total energy -76294.146254


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.
-11.327-5.2493.956-3.824-6.212-0.024
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 : 0.037 / 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].
3E6LYS10.8120.8952.974-4.380-2.1240.102-1.017-1.3410.002
4E7PHE00.0160.0082.828-0.9130.2260.252-0.437-0.956-0.002
5E8GLY00.0430.0445.8810.1530.1530.0000.0000.0000.000
6E9LYS10.7910.8847.0670.0290.0290.0000.0000.0000.000
7E10VAL0-0.015-0.0147.1060.1020.1020.0000.0000.0000.000
8E11ALA00.0120.0179.955-0.040-0.0400.0000.0000.0000.000
9E12VAL0-0.005-0.01511.5910.0100.0100.0000.0000.0000.000
10E13LEU0-0.013-0.01113.9820.0340.0340.0000.0000.0000.000
11E14LEU0-0.011-0.00517.4040.0090.0090.0000.0000.0000.000
12E15GLY00.0360.01519.5430.0120.0120.0000.0000.0000.000
13E16GLY00.0030.00323.2190.0140.0140.0000.0000.0000.000
14E17LYS10.9240.95025.1110.1040.1040.0000.0000.0000.000
15E18SER0-0.045-0.01527.0880.0110.0110.0000.0000.0000.000
16E19ALA0-0.005-0.00929.743-0.002-0.0020.0000.0000.0000.000
17E20GLU-1-0.874-0.95827.464-0.113-0.1130.0000.0000.0000.000
18E21ARG10.8140.90425.2350.1570.1570.0000.0000.0000.000
19E22ALA00.027-0.00125.091-0.015-0.0150.0000.0000.0000.000
20E23VAL00.0350.01224.320-0.012-0.0120.0000.0000.0000.000
21E24SER0-0.015-0.01721.338-0.017-0.0170.0000.0000.0000.000
22E25LEU00.0180.00520.502-0.025-0.0250.0000.0000.0000.000
23E26ASP-1-0.923-0.94920.168-0.240-0.2400.0000.0000.0000.000
24E27SER0-0.063-0.05819.154-0.025-0.0250.0000.0000.0000.000
25E28GLY00.0280.01416.649-0.034-0.0340.0000.0000.0000.000
26E29GLN0-0.031-0.02615.398-0.046-0.0460.0000.0000.0000.000
27E30ALA0-0.0090.01315.016-0.055-0.0550.0000.0000.0000.000
28E31VAL00.007-0.00911.887-0.059-0.0590.0000.0000.0000.000
29E32LEU00.0030.00910.853-0.127-0.1270.0000.0000.0000.000
30E33ASP-1-0.853-0.93710.394-0.664-0.6640.0000.0000.0000.000
31E34ALA0-0.038-0.01710.620-0.095-0.0950.0000.0000.0000.000
32E35LEU0-0.023-0.0016.774-0.192-0.1920.0000.0000.0000.000
33E36LEU0-0.012-0.0025.616-0.532-0.5320.0000.0000.0000.000
34E37ARG10.8020.8997.0400.4710.4710.0000.0000.0000.000
35E38SER0-0.058-0.0294.6410.0860.141-0.001-0.006-0.0470.000
36E39GLY0-0.035-0.0142.780-3.281-1.6340.704-0.975-1.377-0.010
37E40VAL0-0.022-0.0132.251-2.875-1.7552.851-1.675-2.296-0.014
38E41GLN00.002-0.0023.2491.1200.9810.0480.286-0.1950.000
39E42ALA00.0120.0076.7100.2900.2900.0000.0000.0000.000
40E43GLU-1-0.791-0.8638.812-0.421-0.4210.0000.0000.0000.000
41E44ALA00.0170.01712.6070.0270.0270.0000.0000.0000.000
42E45PHE00.005-0.00715.7800.0270.0270.0000.0000.0000.000
43E46ASP-1-0.713-0.83118.159-0.190-0.1900.0000.0000.0000.000
44E47PRO0-0.030-0.03121.2200.0150.0150.0000.0000.0000.000
45E48GLN0-0.183-0.08524.0600.0200.0200.0000.0000.0000.000
46E49ASP-1-0.844-0.90824.386-0.159-0.1590.0000.0000.0000.000
47E50ARG10.8050.89317.1910.2680.2680.0000.0000.0000.000
48E51SER00.0220.02824.1830.0070.0070.0000.0000.0000.000
49E52VAL00.043-0.00322.759-0.007-0.0070.0000.0000.0000.000
50E53THR0-0.035-0.02222.8490.0000.0000.0000.0000.0000.000
51E54GLU-1-0.825-0.91021.009-0.173-0.1730.0000.0000.0000.000
52E55LEU00.0030.00117.960-0.020-0.0200.0000.0000.0000.000
53E56VAL00.0110.00417.734-0.013-0.0130.0000.0000.0000.000
54E57ASN0-0.117-0.05417.1990.0250.0250.0000.0000.0000.000
55E58TYR0-0.064-0.05512.417-0.020-0.0200.0000.0000.0000.000
56E59ASP-1-0.836-0.90210.823-0.155-0.1550.0000.0000.0000.000
57E60ARG10.8140.8868.3840.1960.1960.0000.0000.0000.000
58E61ALA0-0.002-0.00212.616-0.071-0.0710.0000.0000.0000.000
59E62PHE00.0270.01210.7570.0370.0370.0000.0000.0000.000
60E63ILE0-0.034-0.00813.502-0.003-0.0030.0000.0000.0000.000
61E64VAL00.019-0.01216.4610.0030.0030.0000.0000.0000.000
62E65LEU0-0.0170.03518.5190.0100.0100.0000.0000.0000.000
63E66HIS00.0310.01321.0430.0030.0030.0000.0000.0000.000
64E67GLY00.0710.03624.6910.0020.0020.0000.0000.0000.000
65E68ARG10.8450.90827.3630.0920.0920.0000.0000.0000.000
66E69GLY0-0.021-0.02727.028-0.004-0.0040.0000.0000.0000.000
67E70GLY00.0180.01323.830-0.005-0.0050.0000.0000.0000.000
68E71GLU-1-0.732-0.85024.136-0.118-0.1180.0000.0000.0000.000
69E72ASP-1-0.800-0.90426.180-0.082-0.0820.0000.0000.0000.000
70E73GLY00.0320.01326.0500.0090.0090.0000.0000.0000.000
71E74GLN0-0.092-0.04426.6190.0020.0020.0000.0000.0000.000
72E75ILE00.0080.00521.0390.0040.0040.0000.0000.0000.000
73E76GLN00.0360.01621.702-0.002-0.0020.0000.0000.0000.000
74E77GLY00.0080.01223.1360.0090.0090.0000.0000.0000.000
75E78VAL0-0.038-0.02922.9010.0080.0080.0000.0000.0000.000
76E79LEU0-0.0090.00317.9530.0000.0000.0000.0000.0000.000
77E80GLU-1-0.816-0.88121.220-0.016-0.0160.0000.0000.0000.000
78E81TRP0-0.046-0.01623.3060.0120.0120.0000.0000.0000.000
79E82LEU0-0.077-0.04621.1940.0080.0080.0000.0000.0000.000
80E83ASN0-0.084-0.02920.9990.0140.0140.0000.0000.0000.000
81E84ILE0-0.0130.01415.5830.0100.0100.0000.0000.0000.000
82E85PRO00.0200.01813.647-0.013-0.0130.0000.0000.0000.000
83E86TYR0-0.054-0.09014.754-0.056-0.0560.0000.0000.0000.000
84E87THR00.0150.02312.9430.0090.0090.0000.0000.0000.000
85E88GLY0-0.014-0.00915.875-0.004-0.0040.0000.0000.0000.000
86E89THR0-0.042-0.00219.1170.0220.0220.0000.0000.0000.000
87E90GLY00.1380.07722.746-0.010-0.0100.0000.0000.0000.000
88E91VAL0-0.005-0.01023.868-0.002-0.0020.0000.0000.0000.000
89E92GLN00.0010.00126.939-0.001-0.0010.0000.0000.0000.000
90E93GLY00.0880.04027.986-0.001-0.0010.0000.0000.0000.000
91E94SER0-0.044-0.03425.411-0.007-0.0070.0000.0000.0000.000
92E95ALA0-0.032-0.00927.817-0.002-0.0020.0000.0000.0000.000
93E96ILE0-0.072-0.03131.1190.0010.0010.0000.0000.0000.000
94E97GLY00.0500.02429.8610.0010.0010.0000.0000.0000.000
95E98MET0-0.057-0.01129.979-0.004-0.0040.0000.0000.0000.000
96E99ASP-1-0.788-0.87231.660-0.042-0.0420.0000.0000.0000.000
97E100LYS10.8500.89934.7560.0690.0690.0000.0000.0000.000
98E101VAL0-0.059-0.02537.2410.0030.0030.0000.0000.0000.000
99E102LYS10.8770.92836.3670.0400.0400.0000.0000.0000.000
100E103THR00.0170.00033.4290.0040.0040.0000.0000.0000.000
101E104LYS10.8520.93336.1830.0390.0390.0000.0000.0000.000
102E105GLN00.000-0.00339.6230.0020.0020.0000.0000.0000.000
103E106ILE00.0250.01134.3060.0030.0030.0000.0000.0000.000
104E107TRP0-0.051-0.01132.7400.0010.0010.0000.0000.0000.000
105E108GLN0-0.014-0.01838.4830.0030.0030.0000.0000.0000.000
106E109GLY0-0.035-0.01541.3700.0020.0020.0000.0000.0000.000
107E110SER0-0.033-0.02237.3570.0030.0030.0000.0000.0000.000
108E111ASP-1-0.962-0.96239.285-0.003-0.0030.0000.0000.0000.000
109E112LEU00.0180.01835.6350.0000.0000.0000.0000.0000.000
110E113PRO0-0.0350.00239.779-0.001-0.0010.0000.0000.0000.000
111E114THR00.027-0.00539.624-0.003-0.0030.0000.0000.0000.000
112E115ALA00.0070.01341.9290.0020.0020.0000.0000.0000.000
113E116PRO00.0480.01344.265-0.001-0.0010.0000.0000.0000.000
114E117TYR0-0.0020.00943.946-0.002-0.0020.0000.0000.0000.000
115E184PHE0-0.024-0.02834.111-0.001-0.0010.0000.0000.0000.000
116E185THR0-0.040-0.01528.870-0.001-0.0010.0000.0000.0000.000
117E186ILE00.0340.02228.039-0.003-0.0030.0000.0000.0000.000
118E187SER00.0160.00823.408-0.007-0.0070.0000.0000.0000.000
119E188PHE0-0.004-0.01222.9750.0120.0120.0000.0000.0000.000
120E189LEU00.0270.00515.679-0.024-0.0240.0000.0000.0000.000
121E190ASN00.0240.02316.4720.0190.0190.0000.0000.0000.000
122E191GLY00.0480.03318.1500.0210.0210.0000.0000.0000.000
123E192GLN0-0.072-0.03121.0850.0030.0030.0000.0000.0000.000
124E193PRO0-0.026-0.00723.200-0.014-0.0140.0000.0000.0000.000
125E194LEU00.0010.00021.0210.0010.0010.0000.0000.0000.000
126E195PRO0-0.014-0.00824.7190.0000.0000.0000.0000.0000.000
127E196VAL0-0.043-0.01727.585-0.009-0.0090.0000.0000.0000.000
128E197ILE0-0.007-0.00326.2300.0000.0000.0000.0000.0000.000
129E198ARG10.8470.91630.7140.0560.0560.0000.0000.0000.000
130E199LEU00.0410.02031.432-0.005-0.0050.0000.0000.0000.000
131E200GLN00.0260.01834.8480.0050.0050.0000.0000.0000.000
132E221TYR00.1070.04927.319-0.003-0.0030.0000.0000.0000.000
133E222GLY0-0.016-0.02631.872-0.006-0.0060.0000.0000.0000.000
134E223ILE00.0110.02727.3160.0030.0030.0000.0000.0000.000
135E224PRO00.025-0.01031.703-0.004-0.0040.0000.0000.0000.000
136E225CYS0-0.058-0.02332.8340.0000.0000.0000.0000.0000.000
137E226GLY00.0400.03935.4510.0010.0010.0000.0000.0000.000
138E227LEU0-0.046-0.01136.5550.0000.0000.0000.0000.0000.000
139E228SER00.015-0.02437.480-0.002-0.0020.0000.0000.0000.000
140E229GLU-1-0.742-0.84933.349-0.008-0.0080.0000.0000.0000.000
141E230THR00.0630.00435.3620.0000.0000.0000.0000.0000.000
142E231GLU-1-0.859-0.88337.819-0.012-0.0120.0000.0000.0000.000
143E232GLU-1-0.796-0.88930.881-0.043-0.0430.0000.0000.0000.000
144E233LYS10.8510.90831.1880.0040.0040.0000.0000.0000.000
145E234LYS10.8160.89334.0650.0110.0110.0000.0000.0000.000
146E235LEU00.0140.00434.2350.0000.0000.0000.0000.0000.000
147E236GLN00.005-0.01828.183-0.001-0.0010.0000.0000.0000.000
148E237ALA00.0150.01531.0000.0000.0000.0000.0000.0000.000
149E238LEU0-0.023-0.00532.8380.0020.0020.0000.0000.0000.000
150E239CYS0-0.023-0.01730.774-0.002-0.0020.0000.0000.0000.000
151E240LEU00.0180.01826.794-0.003-0.0030.0000.0000.0000.000
152E241ARG10.8750.92029.9050.0050.0050.0000.0000.0000.000
153E242ALA00.0080.00032.5490.0010.0010.0000.0000.0000.000
154E243PHE00.0140.00823.359-0.002-0.0020.0000.0000.0000.000
155E244GLN00.0350.00327.236-0.001-0.0010.0000.0000.0000.000
156E245ALA0-0.0260.00129.4250.0020.0020.0000.0000.0000.000
157E246VAL0-0.063-0.03229.4800.0000.0000.0000.0000.0000.000
158E247GLY00.0150.01228.307-0.002-0.0020.0000.0000.0000.000
159E248ALA0-0.053-0.03225.841-0.005-0.0050.0000.0000.0000.000
160E249GLU-1-0.874-0.94620.6290.0080.0080.0000.0000.0000.000
161E250GLY0-0.0210.00319.979-0.017-0.0170.0000.0000.0000.000
162E251TRP0-0.038-0.05217.917-0.005-0.0050.0000.0000.0000.000
163E252GLY00.0550.02220.011-0.006-0.0060.0000.0000.0000.000
164E253ARG10.7860.88323.2760.0980.0980.0000.0000.0000.000
165E254ILE00.0280.03526.4380.0010.0010.0000.0000.0000.000
166E268GLU-1-0.825-0.89833.065-0.065-0.0650.0000.0000.0000.000
167E269VAL0-0.024-0.02827.8060.0010.0010.0000.0000.0000.000
168E270ASN0-0.067-0.02525.7280.0020.0020.0000.0000.0000.000
169E271THR00.012-0.00824.624-0.002-0.0020.0000.0000.0000.000
170E272VAL00.0090.02019.772-0.004-0.0040.0000.0000.0000.000
171E273PRO0-0.0210.01120.5820.0000.0000.0000.0000.0000.000
172E274GLY0-0.015-0.00120.776-0.018-0.0180.0000.0000.0000.000
173E275MET0-0.020-0.02415.0580.0170.0170.0000.0000.0000.000
174E276THR00.0460.02418.799-0.023-0.0230.0000.0000.0000.000
175E277SER00.032-0.00221.463-0.002-0.0020.0000.0000.0000.000
176E278HIS0-0.0100.01822.4230.0010.0010.0000.0000.0000.000
177E279SER0-0.032-0.01421.9070.0180.0180.0000.0000.0000.000
178E280LEU0-0.022-0.03323.513-0.003-0.0030.0000.0000.0000.000
179E281VAL00.0770.04519.7180.0070.0070.0000.0000.0000.000
180E282PRO00.0530.01918.5770.0070.0070.0000.0000.0000.000
181E283LYS10.8040.92120.0770.1140.1140.0000.0000.0000.000
182E284ALA00.0200.00023.3510.0070.0070.0000.0000.0000.000
183E285ALA00.0470.02018.1340.0110.0110.0000.0000.0000.000
184E286LYS10.9780.99419.7460.2010.2010.0000.0000.0000.000
185E287ALA0-0.080-0.03620.6370.0090.0090.0000.0000.0000.000
186E288VAL0-0.042-0.02521.0050.0160.0160.0000.0000.0000.000
187E289GLY0-0.016-0.00619.5910.0100.0100.0000.0000.0000.000
188E290TYR00.0010.01513.608-0.005-0.0050.0000.0000.0000.000
189E291SER0-0.054-0.05513.168-0.030-0.0300.0000.0000.0000.000
190E292PHE0-0.020-0.03213.6140.0110.0110.0000.0000.0000.000
191E293ASP-1-0.739-0.8729.076-0.716-0.7160.0000.0000.0000.000
192E294GLU-1-0.820-0.8739.427-0.337-0.3370.0000.0000.0000.000
193E295LEU0-0.026-0.01010.4570.0600.0600.0000.0000.0000.000
194E296CYS0-0.034-0.01510.2570.0540.0540.0000.0000.0000.000
195E297VAL00.0250.0095.807-0.030-0.0300.0000.0000.0000.000
196E298ALA00.0120.0018.4050.1140.1140.0000.0000.0000.000
197E299ILE0-0.064-0.03011.3820.0680.0680.0000.0000.0000.000
198E300LEU00.0300.0136.2060.0360.0360.0000.0000.0000.000
199E301GLU-1-0.877-0.9277.1740.4620.4620.0000.0000.0000.000
200E302GLN00.0090.0159.7080.0740.0740.0000.0000.0000.000
201E303THR0-0.047-0.01410.3770.0270.0270.0000.0000.0000.000
202E304LEU0-0.026-0.0087.5180.0490.0490.0000.0000.0000.000
203E305GLU-1-0.987-0.98111.9560.2040.2040.0000.0000.0000.000