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: NNN8Q

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2458273.084825
FMO2-HF: Nuclear repulsion 2374785.923672
FMO2-HF: Total energy -83487.161153
FMO2-MP2: Total energy -83727.606962


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.
4.2328.050.183-2.179-1.822-0.008
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 : 0.981 / q_NPA : 0.988
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].
3M3SER00.004-0.0032.957-9.339-5.5210.183-2.179-1.822-0.008
4M4PRO0-0.030-0.0085.4652.4192.4190.0000.0000.0000.000
5M5TYR0-0.057-0.0438.5361.8451.8450.0000.0000.0000.000
6M6VAL00.0350.0239.559-2.156-2.1560.0000.0000.0000.000
7M7PHE0-0.0100.00012.3171.0551.0550.0000.0000.0000.000
8M8ASN00.008-0.02415.684-0.209-0.2090.0000.0000.0000.000
9M9GLY00.0180.03718.6550.6670.6670.0000.0000.0000.000
10M10GLY00.0530.02921.3850.2570.2570.0000.0000.0000.000
11M11THR0-0.055-0.02624.640-0.461-0.4610.0000.0000.0000.000
12M12ILE00.000-0.01026.3990.2710.2710.0000.0000.0000.000
13M13LEU0-0.0120.00129.654-0.069-0.0690.0000.0000.0000.000
14M14ALA0-0.0090.00932.9830.1180.1180.0000.0000.0000.000
15M15ILE00.007-0.01335.247-0.020-0.0200.0000.0000.0000.000
16M16ALA0-0.030-0.00138.8370.0320.0320.0000.0000.0000.000
17M17GLY00.0350.01941.6050.0350.0350.0000.0000.0000.000
18M18GLU-1-0.902-0.96745.430-6.489-6.4890.0000.0000.0000.000
19M19ASP-1-0.904-0.95448.261-6.379-6.3790.0000.0000.0000.000
20M20PHE00.0160.01943.339-0.039-0.0390.0000.0000.0000.000
21M21ALA00.0220.00139.706-0.083-0.0830.0000.0000.0000.000
22M22ILE0-0.053-0.01737.7300.0710.0710.0000.0000.0000.000
23M23VAL00.0000.00433.022-0.156-0.1560.0000.0000.0000.000
24M24ALA00.0210.00934.1670.1330.1330.0000.0000.0000.000
25M25SER00.002-0.00929.257-0.251-0.2510.0000.0000.0000.000
26M26ASP-1-0.717-0.84327.530-10.805-10.8050.0000.0000.0000.000
27M27THR0-0.034-0.02529.4620.0090.0090.0000.0000.0000.000
28M28ARG10.8030.91725.54010.57710.5770.0000.0000.0000.000
29M29LEU00.0070.01521.324-0.339-0.3390.0000.0000.0000.000
30M30SER0-0.052-0.04521.4340.1520.1520.0000.0000.0000.000
31M31GLU-1-0.789-0.89915.232-18.234-18.2340.0000.0000.0000.000
32M32GLY00.0270.02316.1370.0750.0750.0000.0000.0000.000
33M33PHE0-0.014-0.00816.7510.3830.3830.0000.0000.0000.000
34M34SER00.0010.01619.2250.8040.8040.0000.0000.0000.000
35M35ILE0-0.016-0.02421.103-0.190-0.1900.0000.0000.0000.000
36M36HIS0-0.026-0.01017.7150.8610.8610.0000.0000.0000.000
37M37THR0-0.009-0.01923.1860.5210.5210.0000.0000.0000.000
38M38ARG10.8570.89626.7519.8559.8550.0000.0000.0000.000
39M39ASP-1-0.827-0.88229.674-8.821-8.8210.0000.0000.0000.000
40M40SER0-0.009-0.00525.913-0.125-0.1250.0000.0000.0000.000
41M41PRO0-0.036-0.01027.429-0.278-0.2780.0000.0000.0000.000
42M42LYS10.7650.88024.51911.50611.5060.0000.0000.0000.000
43M43CYS0-0.0240.00327.778-0.071-0.0710.0000.0000.0000.000
44M44TYR00.0260.00225.4220.0830.0830.0000.0000.0000.000
45M45LYS10.8790.92131.7447.9807.9800.0000.0000.0000.000
46M46LEU0-0.047-0.02131.321-0.109-0.1090.0000.0000.0000.000
47M47THR0-0.009-0.01835.4510.0930.0930.0000.0000.0000.000
48M48ASP-1-0.863-0.92839.237-7.259-7.2590.0000.0000.0000.000
49M49LYS10.8290.91041.3647.1777.1770.0000.0000.0000.000
50M50THR0-0.075-0.04335.428-0.101-0.1010.0000.0000.0000.000
51M51VAL00.0420.02833.615-0.011-0.0110.0000.0000.0000.000
52M52ILE00.0020.00028.095-0.002-0.0020.0000.0000.0000.000
53M53GLY00.0400.02329.2070.0720.0720.0000.0000.0000.000
54M54CYS0-0.044-0.02324.130-0.066-0.0660.0000.0000.0000.000
55M55SER00.010-0.00622.882-0.210-0.2100.0000.0000.0000.000
56M56GLY00.0400.00919.015-0.122-0.1220.0000.0000.0000.000
57M57PHE00.0380.02813.917-0.086-0.0860.0000.0000.0000.000
58M58HIS00.0750.01816.7400.3400.3400.0000.0000.0000.000
59M59GLY00.0080.01516.8410.5810.5810.0000.0000.0000.000
60M60ASP-1-0.761-0.86215.788-17.074-17.0740.0000.0000.0000.000
61M61CYS0-0.049-0.01518.4980.7560.7560.0000.0000.0000.000
62M62LEU00.0010.01521.3800.6990.6990.0000.0000.0000.000
63M63THR0-0.040-0.03619.6340.5460.5460.0000.0000.0000.000
64M64LEU00.000-0.00422.0950.4550.4550.0000.0000.0000.000
65M65THR00.000-0.00823.7110.6020.6020.0000.0000.0000.000
66M66LYS10.9710.98125.90211.16411.1640.0000.0000.0000.000
67M67ILE0-0.0120.00623.0080.3830.3830.0000.0000.0000.000
68M68ILE00.0120.00627.2800.3890.3890.0000.0000.0000.000
69M69GLU-1-0.855-0.91729.803-9.056-9.0560.0000.0000.0000.000
70M70ALA0-0.044-0.01530.0770.3570.3570.0000.0000.0000.000
71M71ARG10.9470.95328.86410.31710.3170.0000.0000.0000.000
72M72LEU00.0270.01532.8760.2780.2780.0000.0000.0000.000
73M73LYS10.8460.92233.6969.1469.1460.0000.0000.0000.000
74M74MET0-0.016-0.00332.4520.1280.1280.0000.0000.0000.000
75M75TYR00.0140.01136.7240.2360.2360.0000.0000.0000.000
76M76LYS10.9080.95338.4897.2577.2570.0000.0000.0000.000
77M77HIS0-0.006-0.02339.6390.3360.3360.0000.0000.0000.000
78M78SER0-0.025-0.00239.7330.1020.1020.0000.0000.0000.000
79M79ASN0-0.069-0.03440.4020.1470.1470.0000.0000.0000.000
80M80ASN0-0.019-0.00444.0200.1140.1140.0000.0000.0000.000
81M81LYS10.9621.00443.5847.1897.1890.0000.0000.0000.000
82M82ALA00.0560.02141.685-0.168-0.1680.0000.0000.0000.000
83M83MET0-0.036-0.02035.0230.0220.0220.0000.0000.0000.000
84M84THR00.0520.03439.996-0.041-0.0410.0000.0000.0000.000
85M85THR00.0380.00537.134-0.135-0.1350.0000.0000.0000.000
86M86GLY00.0290.01836.519-0.239-0.2390.0000.0000.0000.000
87M87ALA0-0.011-0.00336.366-0.201-0.2010.0000.0000.0000.000
88M88ILE00.009-0.00332.949-0.246-0.2460.0000.0000.0000.000
89M89ALA00.0120.00732.279-0.343-0.3430.0000.0000.0000.000
90M90ALA00.0340.01631.460-0.324-0.3240.0000.0000.0000.000
91M91MET0-0.053-0.01830.833-0.242-0.2420.0000.0000.0000.000
92M92LEU00.0260.02326.061-0.358-0.3580.0000.0000.0000.000
93M93SER0-0.016-0.00726.902-0.475-0.4750.0000.0000.0000.000
94M94THR0-0.052-0.04526.449-0.369-0.3690.0000.0000.0000.000
95M95ILE0-0.018-0.00824.261-0.296-0.2960.0000.0000.0000.000
96M96LEU0-0.0060.02022.051-0.532-0.5320.0000.0000.0000.000
97M97TYR00.0530.02421.434-0.807-0.8070.0000.0000.0000.000
98M98SER0-0.115-0.06922.168-0.455-0.4550.0000.0000.0000.000
99M99ARG10.8340.90315.82316.48516.4850.0000.0000.0000.000
100M100ARG10.9290.97017.49414.40314.4030.0000.0000.0000.000
101M101PHE0-0.028-0.02215.249-0.249-0.2490.0000.0000.0000.000
102M102PHE0-0.030-0.00811.200-1.488-1.4880.0000.0000.0000.000
103M103PRO00.0490.03913.7200.6200.6200.0000.0000.0000.000
104M104TYR00.0570.04615.533-0.837-0.8370.0000.0000.0000.000
105M105TYR0-0.019-0.00613.7630.3240.3240.0000.0000.0000.000
106M106VAL0-0.031-0.03216.6020.1100.1100.0000.0000.0000.000
107M107TYR00.0000.00919.0910.1460.1460.0000.0000.0000.000
108M108ASN00.008-0.01123.1970.3480.3480.0000.0000.0000.000
109M109ILE00.010-0.00626.2910.1150.1150.0000.0000.0000.000
110M110ILE0-0.0160.00729.9880.0770.0770.0000.0000.0000.000
111M111GLY00.0460.00132.7800.0690.0690.0000.0000.0000.000
112M112GLY00.008-0.00536.284-0.048-0.0480.0000.0000.0000.000
113M113LEU0-0.0200.01739.4890.0880.0880.0000.0000.0000.000
114M114ASP-1-0.755-0.86542.549-7.098-7.0980.0000.0000.0000.000
115M115GLU-1-0.862-0.95443.674-6.999-6.9990.0000.0000.0000.000
116M116GLU-1-0.881-0.91246.853-6.257-6.2570.0000.0000.0000.000
117M117GLY0-0.033-0.00746.9730.1140.1140.0000.0000.0000.000
118M118LYS10.8960.94646.0146.3786.3780.0000.0000.0000.000
119M119GLY00.0230.01942.973-0.147-0.1470.0000.0000.0000.000
120M120ALA0-0.076-0.04140.078-0.029-0.0290.0000.0000.0000.000
121M121VAL00.0120.00934.838-0.131-0.1310.0000.0000.0000.000
122M122TYR00.006-0.01133.2820.1490.1490.0000.0000.0000.000
123M123SER0-0.044-0.02429.653-0.257-0.2570.0000.0000.0000.000
124M124PHE00.008-0.00225.9440.1440.1440.0000.0000.0000.000
125M125ASP-1-0.809-0.89922.548-13.168-13.1680.0000.0000.0000.000
126M126PRO00.004-0.02318.3920.1820.1820.0000.0000.0000.000
127M127VAL0-0.075-0.03618.771-0.464-0.4640.0000.0000.0000.000
128M128GLY00.0220.01721.4000.2600.2600.0000.0000.0000.000
129M129SER0-0.0290.00824.8700.7360.7360.0000.0000.0000.000
130M130TYR0-0.003-0.01626.858-0.120-0.1200.0000.0000.0000.000
131M131GLN00.0060.01429.779-0.021-0.0210.0000.0000.0000.000
132M132ARG10.8140.87833.2947.4707.4700.0000.0000.0000.000
133M133ASP-1-0.790-0.87433.648-9.270-9.2700.0000.0000.0000.000
134M134SER00.0330.01337.1180.1160.1160.0000.0000.0000.000
135M135PHE0-0.013-0.02236.4990.1070.1070.0000.0000.0000.000
136M136LYS10.7790.90030.4339.5339.5330.0000.0000.0000.000
137M137ALA00.0520.03930.9260.0390.0390.0000.0000.0000.000
138M138GLY00.0010.00027.010-0.212-0.2120.0000.0000.0000.000
139M139GLY00.010-0.00123.5080.2150.2150.0000.0000.0000.000
140M140SER0-0.041-0.05722.6940.0140.0140.0000.0000.0000.000
141M141ALA00.0450.01624.145-0.013-0.0130.0000.0000.0000.000
142M142SER0-0.080-0.03226.7760.4370.4370.0000.0000.0000.000
143M143ALA00.041-0.00427.7340.3670.3670.0000.0000.0000.000
144M144MET0-0.050-0.01627.9880.3420.3420.0000.0000.0000.000
145M145LEU00.002-0.00131.3630.3400.3400.0000.0000.0000.000
146M146GLN00.0150.00031.7470.2050.2050.0000.0000.0000.000
147M147PRO00.0270.01933.2890.2910.2910.0000.0000.0000.000
148M148LEU00.0320.02236.4820.2440.2440.0000.0000.0000.000
149M149LEU00.0190.01635.4090.2490.2490.0000.0000.0000.000
150M150ASP-1-0.804-0.90536.035-8.395-8.3950.0000.0000.0000.000
151M151ASN0-0.041-0.02139.2990.2090.2090.0000.0000.0000.000
152M152GLN0-0.015-0.01042.1160.2890.2890.0000.0000.0000.000
153M153VAL0-0.017-0.01641.4410.1880.1880.0000.0000.0000.000
154M154GLY0-0.009-0.00242.1770.0740.0740.0000.0000.0000.000
155M155PHE00.0040.00843.0760.0590.0590.0000.0000.0000.000
156M156LYS10.8660.93138.5648.1418.1410.0000.0000.0000.000
157M157ASN0-0.038-0.03741.6230.0120.0120.0000.0000.0000.000
158M158MET0-0.0250.02445.5700.0530.0530.0000.0000.0000.000
159M159GLN00.0390.02148.7510.0120.0120.0000.0000.0000.000
160M160ASN0-0.067-0.04852.0920.0400.0400.0000.0000.0000.000
161M161VAL00.0400.04349.7990.0730.0730.0000.0000.0000.000
162M162GLU-1-0.883-0.94453.042-5.921-5.9210.0000.0000.0000.000
163M163HIS0-0.053-0.02249.479-0.170-0.1700.0000.0000.0000.000
164M164VAL0-0.023-0.01251.1140.0220.0220.0000.0000.0000.000
165M165PRO00.0180.00749.429-0.143-0.1430.0000.0000.0000.000
166M166LEU0-0.018-0.01743.3940.0670.0670.0000.0000.0000.000
167M167SER00.0660.02847.706-0.068-0.0680.0000.0000.0000.000
168M168LEU00.0550.02644.599-0.121-0.1210.0000.0000.0000.000
169M169ASP-1-0.796-0.86646.016-6.429-6.4290.0000.0000.0000.000
170M170ARG10.8870.93546.4666.6526.6520.0000.0000.0000.000
171M171ALA00.0120.00642.678-0.137-0.1370.0000.0000.0000.000
172M172MET0-0.022-0.00942.155-0.254-0.2540.0000.0000.0000.000
173M173ARG10.7780.86342.5326.3876.3870.0000.0000.0000.000
174M174LEU00.0720.04141.374-0.156-0.1560.0000.0000.0000.000
175M175VAL0-0.004-0.00936.914-0.223-0.2230.0000.0000.0000.000
176M176LYS10.8680.92537.5106.9856.9850.0000.0000.0000.000
177M177ASP-1-0.864-0.92938.616-7.431-7.4310.0000.0000.0000.000
178M178VAL0-0.017-0.00135.584-0.150-0.1500.0000.0000.0000.000
179M179PHE0-0.012-0.01130.658-0.299-0.2990.0000.0000.0000.000
180M180ILE0-0.006-0.00134.236-0.220-0.2200.0000.0000.0000.000
181M181SER0-0.038-0.03435.909-0.057-0.0570.0000.0000.0000.000
182M182ALA0-0.013-0.00930.877-0.163-0.1630.0000.0000.0000.000
183M183ALA0-0.003-0.00231.300-0.293-0.2930.0000.0000.0000.000
184M184GLU-1-0.903-0.92532.525-8.576-8.5760.0000.0000.0000.000
185M185ARG10.8690.92431.3229.0149.0140.0000.0000.0000.000
186M186ASP-1-0.743-0.81825.439-12.308-12.3080.0000.0000.0000.000
187M187VAL00.0280.01423.6550.2110.2110.0000.0000.0000.000
188M188TYR0-0.086-0.04719.326-0.011-0.0110.0000.0000.0000.000
189M189THR0-0.039-0.03124.8630.0690.0690.0000.0000.0000.000
190M190GLY00.0480.00828.3470.1980.1980.0000.0000.0000.000
191M191ASP-1-0.800-0.86530.241-9.967-9.9670.0000.0000.0000.000
192M192ALA0-0.035-0.02832.3550.4090.4090.0000.0000.0000.000
193M193LEU00.0190.03332.590-0.296-0.2960.0000.0000.0000.000
194M194ARG10.8290.88933.6739.0349.0340.0000.0000.0000.000
195M195ILE0-0.002-0.01334.849-0.198-0.1980.0000.0000.0000.000
196M196CYS00.0070.01335.6620.1650.1650.0000.0000.0000.000
197M197ILE0-0.024-0.03038.354-0.035-0.0350.0000.0000.0000.000
198M198VAL0-0.040-0.00139.6430.0910.0910.0000.0000.0000.000
199M199THR00.005-0.03542.591-0.022-0.0220.0000.0000.0000.000
200M200LYS10.8170.89646.3226.3956.3950.0000.0000.0000.000
201M201GLU-1-0.861-0.91048.998-6.211-6.2110.0000.0000.0000.000
202M202GLY00.0090.02145.4890.0180.0180.0000.0000.0000.000
203M203ILE0-0.053-0.03439.271-0.092-0.0920.0000.0000.0000.000
204M204ARG10.8630.92842.8476.9036.9030.0000.0000.0000.000
205M205GLU-1-0.829-0.91737.089-8.373-8.3730.0000.0000.0000.000
206M206GLU-1-0.789-0.86839.825-6.869-6.8690.0000.0000.0000.000
207M207THR0-0.037-0.03136.887-0.322-0.3220.0000.0000.0000.000
208M208VAL00.0080.01438.0480.2360.2360.0000.0000.0000.000
209M209SER00.0080.00837.314-0.322-0.3220.0000.0000.0000.000
210M210LEU00.0190.01733.1070.0900.0900.0000.0000.0000.000
211M211ARG10.8130.86233.4818.8928.8920.0000.0000.0000.000
212M212LYS10.8460.92032.6128.3138.3130.0000.0000.0000.000
213M213ASP-1-0.786-0.84929.044-9.500-9.5000.0000.0000.0000.000