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: 8997Y

Calculation Name: 4R3O-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: M

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2450278.973566
FMO2-HF: Nuclear repulsion 2366792.030662
FMO2-HF: Total energy -83486.942904
FMO2-MP2: Total energy -83727.284223


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(M:1:ARG)


Summations of interaction energy for fragment #1(M:1:ARG)
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.
8.37411.669-0.001-1.698-1.5960
Interaction energy analysis for fragmet #1(M:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.983 / q_NPA : 0.986
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].
3M3SER0-0.0100.0033.451-5.226-1.9820.000-1.696-1.5490.000
4M4PRO0-0.016-0.0045.3352.3612.412-0.001-0.002-0.0470.000
5M5TYR0-0.054-0.0458.4571.9101.9100.0000.0000.0000.000
6M6VAL00.0360.0119.855-1.818-1.8180.0000.0000.0000.000
7M7PHE0-0.024-0.00212.6091.0891.0890.0000.0000.0000.000
8M8ASN00.012-0.01315.813-0.167-0.1670.0000.0000.0000.000
9M9GLY00.0120.02318.8530.6830.6830.0000.0000.0000.000
10M10GLY00.003-0.00821.5620.0470.0470.0000.0000.0000.000
11M11THR0-0.043-0.02824.903-0.377-0.3770.0000.0000.0000.000
12M12ILE00.003-0.00826.6620.2400.2400.0000.0000.0000.000
13M13LEU0-0.0160.00229.675-0.050-0.0500.0000.0000.0000.000
14M14ALA0-0.0120.00033.0090.1030.1030.0000.0000.0000.000
15M15ILE0-0.001-0.00635.388-0.007-0.0070.0000.0000.0000.000
16M16ALA0-0.017-0.00438.9270.0500.0500.0000.0000.0000.000
17M17GLY00.0050.00641.2970.0580.0580.0000.0000.0000.000
18M18GLU-1-0.915-0.97345.038-6.457-6.4570.0000.0000.0000.000
19M19ASP-1-0.921-0.96547.992-6.345-6.3450.0000.0000.0000.000
20M20PHE00.0070.00643.401-0.018-0.0180.0000.0000.0000.000
21M21ALA00.0160.01039.530-0.083-0.0830.0000.0000.0000.000
22M22ILE0-0.047-0.01938.1540.0330.0330.0000.0000.0000.000
23M23VAL00.0100.00833.250-0.169-0.1690.0000.0000.0000.000
24M24ALA00.0140.00134.6170.1030.1030.0000.0000.0000.000
25M25SER00.0330.01529.607-0.285-0.2850.0000.0000.0000.000
26M26ASP-1-0.743-0.84627.985-10.690-10.6900.0000.0000.0000.000
27M27THR0-0.066-0.05629.688-0.082-0.0820.0000.0000.0000.000
28M28ARG10.8120.91625.53810.59510.5950.0000.0000.0000.000
29M29LEU00.0130.01921.147-0.315-0.3150.0000.0000.0000.000
30M30SER00.0060.00721.3310.2880.2880.0000.0000.0000.000
31M31GLU-1-0.813-0.91214.892-18.286-18.2860.0000.0000.0000.000
32M32GLY00.0030.01116.0960.1570.1570.0000.0000.0000.000
33M33PHE0-0.015-0.01716.6880.3330.3330.0000.0000.0000.000
34M34SER0-0.0010.00919.5750.7850.7850.0000.0000.0000.000
35M35ILE0-0.021-0.02221.375-0.180-0.1800.0000.0000.0000.000
36M36HIS0-0.040-0.02717.8160.7360.7360.0000.0000.0000.000
37M37THR0-0.006-0.02123.1680.5460.5460.0000.0000.0000.000
38M38ARG10.8620.90626.7099.7499.7490.0000.0000.0000.000
39M39ASP-1-0.883-0.91429.625-8.833-8.8330.0000.0000.0000.000
40M40SER0-0.008-0.00926.212-0.155-0.1550.0000.0000.0000.000
41M41PRO0-0.032-0.01027.892-0.232-0.2320.0000.0000.0000.000
42M42LYS10.8110.91325.18311.21011.2100.0000.0000.0000.000
43M43CYS0-0.029-0.00228.248-0.032-0.0320.0000.0000.0000.000
44M44TYR00.0270.00425.6680.0250.0250.0000.0000.0000.000
45M45LYS10.8790.92832.0537.9527.9520.0000.0000.0000.000
46M46LEU0-0.033-0.00131.289-0.064-0.0640.0000.0000.0000.000
47M47THR0-0.007-0.01835.3510.1160.1160.0000.0000.0000.000
48M48ASP-1-0.881-0.93839.024-7.236-7.2360.0000.0000.0000.000
49M49LYS10.8390.90441.0877.1197.1190.0000.0000.0000.000
50M50THR0-0.063-0.02935.380-0.071-0.0710.0000.0000.0000.000
51M51VAL00.0500.03134.046-0.042-0.0420.0000.0000.0000.000
52M52ILE0-0.005-0.00628.388-0.015-0.0150.0000.0000.0000.000
53M53GLY00.0320.02029.4290.0140.0140.0000.0000.0000.000
54M54CYS0-0.058-0.03424.232-0.099-0.0990.0000.0000.0000.000
55M55SER00.001-0.01623.397-0.178-0.1780.0000.0000.0000.000
56M56GLY00.0430.01719.433-0.202-0.2020.0000.0000.0000.000
57M57PHE00.0350.01913.912-0.140-0.1400.0000.0000.0000.000
58M58HIS00.1010.03517.0830.3250.3250.0000.0000.0000.000
59M59GLY0-0.0010.01117.0620.5980.5980.0000.0000.0000.000
60M60ASP-1-0.766-0.88115.802-16.762-16.7620.0000.0000.0000.000
61M61CYS0-0.050-0.01518.5310.7320.7320.0000.0000.0000.000
62M62LEU00.0170.01321.3520.6120.6120.0000.0000.0000.000
63M63THR0-0.060-0.04219.6680.5490.5490.0000.0000.0000.000
64M64LEU00.0150.00722.0720.4820.4820.0000.0000.0000.000
65M65THR00.0320.01823.6660.4480.4480.0000.0000.0000.000
66M66LYS10.9520.97425.57611.26911.2690.0000.0000.0000.000
67M67ILE0-0.027-0.00422.8750.4250.4250.0000.0000.0000.000
68M68ILE00.0190.00427.1150.4020.4020.0000.0000.0000.000
69M69GLU-1-0.839-0.91129.556-8.916-8.9160.0000.0000.0000.000
70M70ALA0-0.068-0.03130.0930.3630.3630.0000.0000.0000.000
71M71ARG10.9800.95928.99810.20810.2080.0000.0000.0000.000
72M72LEU00.0130.01332.6510.2480.2480.0000.0000.0000.000
73M73LYS10.8560.91933.7589.0599.0590.0000.0000.0000.000
74M74MET0-0.0200.00632.3650.1240.1240.0000.0000.0000.000
75M75TYR00.0300.01936.7560.2140.2140.0000.0000.0000.000
76M76LYS10.9280.97438.4227.2647.2640.0000.0000.0000.000
77M77HIS0-0.007-0.02339.4120.3170.3170.0000.0000.0000.000
78M78SER0-0.0070.01239.9430.0970.0970.0000.0000.0000.000
79M79ASN0-0.067-0.03840.4530.1770.1770.0000.0000.0000.000
80M80ASN0-0.060-0.02144.0220.1350.1350.0000.0000.0000.000
81M81LYS10.9771.00443.5537.0927.0920.0000.0000.0000.000
82M82ALA00.0440.01741.507-0.158-0.1580.0000.0000.0000.000
83M83MET0-0.048-0.02334.7000.0240.0240.0000.0000.0000.000
84M84THR00.0540.03239.661-0.066-0.0660.0000.0000.0000.000
85M85THR00.0610.01237.072-0.140-0.1400.0000.0000.0000.000
86M86GLY00.0180.01036.474-0.240-0.2400.0000.0000.0000.000
87M87ALA0-0.017-0.00636.266-0.216-0.2160.0000.0000.0000.000
88M88ILE00.011-0.00232.692-0.246-0.2460.0000.0000.0000.000
89M89ALA00.0130.00732.253-0.343-0.3430.0000.0000.0000.000
90M90ALA00.0500.02431.363-0.346-0.3460.0000.0000.0000.000
91M91MET0-0.045-0.01530.723-0.257-0.2570.0000.0000.0000.000
92M92LEU00.0170.01725.983-0.363-0.3630.0000.0000.0000.000
93M93SER0-0.009-0.01126.910-0.465-0.4650.0000.0000.0000.000
94M94THR0-0.052-0.04426.539-0.380-0.3800.0000.0000.0000.000
95M95ILE0-0.037-0.02424.307-0.347-0.3470.0000.0000.0000.000
96M96LEU0-0.0140.01022.033-0.529-0.5290.0000.0000.0000.000
97M97TYR00.0350.01921.650-0.821-0.8210.0000.0000.0000.000
98M98SER0-0.107-0.05622.262-0.457-0.4570.0000.0000.0000.000
99M99ARG10.8420.90715.63216.29816.2980.0000.0000.0000.000
100M100ARG10.9360.98117.11414.59814.5980.0000.0000.0000.000
101M101PHE0-0.033-0.02915.216-0.392-0.3920.0000.0000.0000.000
102M102PHE0-0.032-0.00610.904-1.484-1.4840.0000.0000.0000.000
103M103PRO00.0520.04613.7380.7180.7180.0000.0000.0000.000
104M104TYR00.0430.03715.170-0.939-0.9390.0000.0000.0000.000
105M105TYR0-0.029-0.01013.9560.2350.2350.0000.0000.0000.000
106M106VAL0-0.018-0.02816.7430.1880.1880.0000.0000.0000.000
107M107TYR0-0.0090.00619.5560.1530.1530.0000.0000.0000.000
108M108ASN00.0340.00423.3890.3720.3720.0000.0000.0000.000
109M109ILE00.011-0.00126.5320.0870.0870.0000.0000.0000.000
110M110ILE0-0.0210.00330.1490.0960.0960.0000.0000.0000.000
111M111GLY00.0570.01932.9330.0830.0830.0000.0000.0000.000
112M112GLY0-0.011-0.02036.355-0.027-0.0270.0000.0000.0000.000
113M113LEU0-0.0110.01439.5540.1050.1050.0000.0000.0000.000
114M114ASP-1-0.784-0.88942.242-7.107-7.1070.0000.0000.0000.000
115M115GLU-1-0.870-0.96043.674-6.950-6.9500.0000.0000.0000.000
116M116GLU-1-0.895-0.91846.675-6.231-6.2310.0000.0000.0000.000
117M117GLY0-0.034-0.01147.3760.1200.1200.0000.0000.0000.000
118M118LYS10.9450.97046.3846.3116.3110.0000.0000.0000.000
119M119GLY00.0090.02843.120-0.134-0.1340.0000.0000.0000.000
120M120ALA0-0.056-0.03739.762-0.009-0.0090.0000.0000.0000.000
121M121VAL00.0140.00734.632-0.109-0.1090.0000.0000.0000.000
122M122TYR0-0.002-0.01033.2390.1110.1110.0000.0000.0000.000
123M123SER0-0.017-0.01830.034-0.277-0.2770.0000.0000.0000.000
124M124PHE0-0.003-0.00526.1990.1260.1260.0000.0000.0000.000
125M125ASP-1-0.833-0.90923.257-12.956-12.9560.0000.0000.0000.000
126M126PRO0-0.004-0.02019.0420.1740.1740.0000.0000.0000.000
127M127VAL0-0.053-0.02519.159-0.357-0.3570.0000.0000.0000.000
128M128GLY00.0080.00721.7260.3030.3030.0000.0000.0000.000
129M129SER0-0.0240.01625.1650.7300.7300.0000.0000.0000.000
130M130TYR00.000-0.01427.187-0.084-0.0840.0000.0000.0000.000
131M131GLN00.0110.01330.1200.0660.0660.0000.0000.0000.000
132M132ARG10.8110.88833.4317.4677.4670.0000.0000.0000.000
133M133ASP-1-0.810-0.87533.795-9.186-9.1860.0000.0000.0000.000
134M134SER00.0210.00937.2540.0990.0990.0000.0000.0000.000
135M135PHE0-0.001-0.01836.8690.1100.1100.0000.0000.0000.000
136M136LYS10.8210.91430.6719.4139.4130.0000.0000.0000.000
137M137ALA00.0370.03331.1240.0320.0320.0000.0000.0000.000
138M138GLY00.0070.00627.266-0.187-0.1870.0000.0000.0000.000
139M139GLY0-0.005-0.00923.8870.2070.2070.0000.0000.0000.000
140M140SER0-0.027-0.03823.065-0.036-0.0360.0000.0000.0000.000
141M141ALA00.0250.01024.3970.0160.0160.0000.0000.0000.000
142M142SER0-0.066-0.02826.9900.4380.4380.0000.0000.0000.000
143M143ALA00.0420.00227.7950.3490.3490.0000.0000.0000.000
144M144MET0-0.045-0.01628.5200.3550.3550.0000.0000.0000.000
145M145LEU0-0.004-0.00531.5070.3360.3360.0000.0000.0000.000
146M146GLN00.0350.00431.9080.2350.2350.0000.0000.0000.000
147M147PRO00.0250.02233.3420.2600.2600.0000.0000.0000.000
148M148LEU00.0370.02336.4970.2440.2440.0000.0000.0000.000
149M149LEU00.0040.01035.5060.2620.2620.0000.0000.0000.000
150M150ASP-1-0.806-0.89936.633-8.302-8.3020.0000.0000.0000.000
151M151ASN0-0.045-0.01939.8590.2250.2250.0000.0000.0000.000
152M152GLN0-0.009-0.02242.4120.2880.2880.0000.0000.0000.000
153M153VAL0-0.018-0.01041.5230.1790.1790.0000.0000.0000.000
154M154GLY00.0020.00842.8850.0880.0880.0000.0000.0000.000
155M155PHE0-0.0080.00643.8390.0810.0810.0000.0000.0000.000
156M156LYS10.8790.92839.0248.0858.0850.0000.0000.0000.000
157M157ASN0-0.060-0.04541.7700.0140.0140.0000.0000.0000.000
158M158MET0-0.0320.01045.9630.0570.0570.0000.0000.0000.000
159M159GLN00.0340.02648.968-0.056-0.0560.0000.0000.0000.000
160M160ASN0-0.079-0.05952.4240.0630.0630.0000.0000.0000.000
161M161VAL00.0470.03650.4850.0420.0420.0000.0000.0000.000
162M162GLU-1-0.905-0.94653.332-5.888-5.8880.0000.0000.0000.000
163M163HIS0-0.046-0.02850.399-0.157-0.1570.0000.0000.0000.000
164M164VAL0-0.0210.00051.5920.0350.0350.0000.0000.0000.000
165M165PRO00.0370.01449.445-0.135-0.1350.0000.0000.0000.000
166M166LEU0-0.012-0.00743.5950.0570.0570.0000.0000.0000.000
167M167SER00.0500.02247.809-0.034-0.0340.0000.0000.0000.000
168M168LEU00.0630.02044.960-0.119-0.1190.0000.0000.0000.000
169M169ASP-1-0.812-0.88346.247-6.398-6.3980.0000.0000.0000.000
170M170ARG10.9080.94646.6476.6186.6180.0000.0000.0000.000
171M171ALA00.0230.01342.980-0.135-0.1350.0000.0000.0000.000
172M172MET0-0.027-0.00342.370-0.263-0.2630.0000.0000.0000.000
173M173ARG10.8290.88142.4256.2826.2820.0000.0000.0000.000
174M174LEU00.0600.04141.523-0.093-0.0930.0000.0000.0000.000
175M175VAL0-0.009-0.00637.124-0.213-0.2130.0000.0000.0000.000
176M176LYS10.8600.91038.0276.9076.9070.0000.0000.0000.000
177M177ASP-1-0.867-0.92239.253-7.375-7.3750.0000.0000.0000.000
178M178VAL0-0.035-0.02236.000-0.164-0.1640.0000.0000.0000.000
179M179PHE0-0.012-0.02131.110-0.307-0.3070.0000.0000.0000.000
180M180ILE0-0.0060.00434.857-0.204-0.2040.0000.0000.0000.000
181M181SER0-0.026-0.01136.555-0.014-0.0140.0000.0000.0000.000
182M182ALA0-0.017-0.01531.380-0.175-0.1750.0000.0000.0000.000
183M183ALA0-0.022-0.01231.455-0.297-0.2970.0000.0000.0000.000
184M184GLU-1-0.891-0.91332.364-8.465-8.4650.0000.0000.0000.000
185M185ARG10.8860.93631.6138.8698.8690.0000.0000.0000.000
186M186ASP-1-0.760-0.85025.867-12.156-12.1560.0000.0000.0000.000
187M187VAL00.0260.01423.7290.2030.2030.0000.0000.0000.000
188M188TYR0-0.059-0.03919.052-0.184-0.1840.0000.0000.0000.000
189M189THR0-0.053-0.02425.1450.1140.1140.0000.0000.0000.000
190M190GLY00.0720.02028.6700.1930.1930.0000.0000.0000.000
191M191ASP-1-0.792-0.85929.752-9.976-9.9760.0000.0000.0000.000
192M192ALA0-0.036-0.02932.5120.3950.3950.0000.0000.0000.000
193M193LEU00.0260.03033.033-0.276-0.2760.0000.0000.0000.000
194M194ARG10.8600.93134.2078.9648.9640.0000.0000.0000.000
195M195ILE0-0.002-0.01135.266-0.177-0.1770.0000.0000.0000.000
196M196CYS00.0180.01635.7870.1420.1420.0000.0000.0000.000
197M197ILE0-0.027-0.02438.683-0.032-0.0320.0000.0000.0000.000
198M198VAL0-0.0150.00739.4560.0510.0510.0000.0000.0000.000
199M199THR00.009-0.03342.672-0.020-0.0200.0000.0000.0000.000
200M200LYS10.8090.90046.1926.3916.3910.0000.0000.0000.000
201M201GLU-1-0.875-0.91448.735-6.194-6.1940.0000.0000.0000.000
202M202GLY00.0240.02645.4080.0180.0180.0000.0000.0000.000
203M203ILE0-0.039-0.03139.208-0.088-0.0880.0000.0000.0000.000
204M204ARG10.8550.93442.9046.8526.8520.0000.0000.0000.000
205M205GLU-1-0.827-0.92137.631-8.276-8.2760.0000.0000.0000.000
206M206GLU-1-0.826-0.88840.353-6.829-6.8290.0000.0000.0000.000
207M207THR0-0.010-0.01737.383-0.306-0.3060.0000.0000.0000.000
208M208VAL00.0050.01038.6040.2190.2190.0000.0000.0000.000
209M209SER0-0.004-0.00537.816-0.310-0.3100.0000.0000.0000.000
210M210LEU00.0290.02633.3860.0940.0940.0000.0000.0000.000
211M211ARG10.8090.85633.6408.8238.8230.0000.0000.0000.000
212M212LYS10.8300.90432.4008.2678.2670.0000.0000.0000.000
213M213ASP-1-0.790-0.84528.572-9.416-9.4160.0000.0000.0000.000