Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6N4MZ

Calculation Name: 5X3X-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X3X

Chain ID: M

ChEMBL ID:

UniProt ID: D5AUZ9

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1992252.266615
FMO2-HF: Nuclear repulsion 1919682.874468
FMO2-HF: Total energy -72569.392146
FMO2-MP2: Total energy -72782.099835


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:MET)


Summations of interaction energy for fragment #1(M:1:MET)
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.
-11.229-17.0728.077-9.656-12.5770.022
Interaction energy analysis for fragmet #1(M:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.045
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].
3M3ILE0-0.022-0.0133.722-2.183-0.076-0.010-1.184-0.9130.006
4M4MET00.0620.0516.3580.5670.5670.0000.0000.0000.000
5M5GLU-1-0.662-0.8297.644-0.847-0.8470.0000.0000.0000.000
6M6GLY0-0.043-0.01711.3180.0600.0600.0000.0000.0000.000
7M7TYR0-0.0050.0079.9050.0660.0660.0000.0000.0000.000
8M8LEU0-0.0050.00311.3130.0450.0450.0000.0000.0000.000
9M9PRO00.0320.03513.9890.0440.0440.0000.0000.0000.000
10M10VAL00.0610.00217.764-0.043-0.0430.0000.0000.0000.000
11M11THR00.0180.01019.984-0.022-0.0220.0000.0000.0000.000
12M12HIS00.0400.01216.176-0.007-0.0070.0000.0000.0000.000
13M13ALA0-0.0180.01215.789-0.057-0.0570.0000.0000.0000.000
14M14ILE00.0340.00916.834-0.031-0.0310.0000.0000.0000.000
15M15GLY00.0210.01819.6970.0120.0120.0000.0000.0000.000
16M16TRP00.0170.00214.605-0.014-0.0140.0000.0000.0000.000
17M17SER0-0.009-0.00516.678-0.034-0.0340.0000.0000.0000.000
18M18LEU0-0.045-0.02617.7420.0320.0320.0000.0000.0000.000
19M19ALA0-0.0130.00117.4560.0350.0350.0000.0000.0000.000
20M20ALA00.010-0.00315.2370.0100.0100.0000.0000.0000.000
21M21ALA00.0250.01017.0910.0270.0270.0000.0000.0000.000
22M22PRO00.0140.01120.2130.0310.0310.0000.0000.0000.000
23M23PHE00.0070.00317.5910.0330.0330.0000.0000.0000.000
24M24VAL00.0140.00216.5190.0230.0230.0000.0000.0000.000
25M25VAL00.0090.00019.0850.0360.0360.0000.0000.0000.000
26M26ALA00.0030.00821.7600.0370.0370.0000.0000.0000.000
27M27GLY0-0.008-0.01020.2620.0340.0340.0000.0000.0000.000
28M28ALA0-0.0080.00421.3470.0250.0250.0000.0000.0000.000
29M29LEU0-0.012-0.01922.9170.0350.0350.0000.0000.0000.000
30M30LYS10.9010.95822.3590.3200.3200.0000.0000.0000.000
31M31ILE00.0500.02620.1720.0260.0260.0000.0000.0000.000
32M32ARG10.9530.97324.7040.2860.2860.0000.0000.0000.000
33M33LYS10.9400.98027.8670.2230.2230.0000.0000.0000.000
34M34ILE00.0420.01625.0230.0110.0110.0000.0000.0000.000
35M35VAL0-0.036-0.01326.4720.0130.0130.0000.0000.0000.000
36M36ALA0-0.037-0.01529.2290.0120.0120.0000.0000.0000.000
37M37GLU-1-0.960-0.97231.828-0.160-0.1600.0000.0000.0000.000
38M38ARG10.8610.92430.1700.1420.1420.0000.0000.0000.000
39M39PRO00.0490.02630.142-0.013-0.0130.0000.0000.0000.000
40M40GLU-1-0.779-0.90929.679-0.148-0.1480.0000.0000.0000.000
41M41ALA0-0.019-0.02126.109-0.004-0.0040.0000.0000.0000.000
42M42ARG10.9080.96125.0060.1650.1650.0000.0000.0000.000
43M43MET00.0190.01724.381-0.021-0.0210.0000.0000.0000.000
44M44THR00.0040.00223.685-0.015-0.0150.0000.0000.0000.000
45M45LEU00.0190.00920.625-0.015-0.0150.0000.0000.0000.000
46M46ALA0-0.0080.00219.430-0.039-0.0390.0000.0000.0000.000
47M47ALA00.0060.00019.383-0.012-0.0120.0000.0000.0000.000
48M48ALA0-0.0040.00317.6320.0010.0010.0000.0000.0000.000
49M49GLY00.0230.00614.885-0.039-0.0390.0000.0000.0000.000
50M50ALA00.0050.00114.179-0.056-0.0560.0000.0000.0000.000
51M51PHE0-0.003-0.00315.0440.0170.0170.0000.0000.0000.000
52M52ALA0-0.002-0.00211.1690.0300.0300.0000.0000.0000.000
53M53PHE00.0210.01410.102-0.067-0.0670.0000.0000.0000.000
54M54VAL00.0310.02410.6470.0360.0360.0000.0000.0000.000
55M55LEU00.0060.0049.1330.1090.1090.0000.0000.0000.000
56M56SER0-0.078-0.0416.3870.0990.0990.0000.0000.0000.000
57M57ALA00.0220.0036.7150.0870.0870.0000.0000.0000.000
58M58LEU0-0.069-0.0129.1180.1460.1460.0000.0000.0000.000
59M59LYS10.9330.9689.176-0.288-0.2880.0000.0000.0000.000
60M60ILE00.0480.0129.160-0.202-0.2020.0000.0000.0000.000
61M61PRO00.0050.01110.3350.3250.3250.0000.0000.0000.000
62M62SER0-0.013-0.0159.4420.0840.0840.0000.0000.0000.000
63M63VAL00.0250.01511.215-0.246-0.2460.0000.0000.0000.000
64M64THR00.0160.00411.481-0.101-0.1010.0000.0000.0000.000
65M65GLY00.0320.01913.622-0.007-0.0070.0000.0000.0000.000
66M66SER0-0.021-0.0088.147-0.106-0.1060.0000.0000.0000.000
67M67CYS0-0.049-0.0328.929-0.399-0.3990.0000.0000.0000.000
68M68SER0-0.0090.0165.6600.3860.462-0.001-0.013-0.0610.000
69M69HIS10.8660.9164.737-2.330-2.224-0.001-0.009-0.0950.000
70M70PRO00.0270.0254.7590.8130.994-0.001-0.009-0.1710.000
71M71THR0-0.006-0.0112.461-2.791-2.6252.850-0.889-2.127-0.010
72M72GLY00.0690.0304.664-0.259-0.177-0.001-0.014-0.0670.000
73M73THR0-0.0460.0085.5780.0050.0050.0000.0000.0000.000
74M74GLY00.032-0.0108.1850.1560.1560.0000.0000.0000.000
75M75LEU00.0230.01410.5740.0410.0410.0000.0000.0000.000
76M76GLY00.0310.01911.5460.0440.0440.0000.0000.0000.000
77M77ALA0-0.0070.00812.4960.0490.0490.0000.0000.0000.000
78M78VAL0-0.014-0.02214.2820.0460.0460.0000.0000.0000.000
79M79VAL0-0.067-0.01915.9370.0400.0400.0000.0000.0000.000
80M80PHE0-0.062-0.04115.2680.0230.0230.0000.0000.0000.000
81M81GLY00.0390.02716.759-0.050-0.0500.0000.0000.0000.000
82M82PRO00.030-0.01015.892-0.006-0.0060.0000.0000.0000.000
83M83SER0-0.022-0.01016.727-0.033-0.0330.0000.0000.0000.000
84M84VAL0-0.010-0.00518.015-0.029-0.0290.0000.0000.0000.000
85M85MET00.0510.04311.5170.0150.0150.0000.0000.0000.000
86M86ALA00.0250.02414.017-0.089-0.0890.0000.0000.0000.000
87M87VAL0-0.008-0.02315.087-0.050-0.0500.0000.0000.0000.000
88M88LEU0-0.015-0.00214.966-0.011-0.0110.0000.0000.0000.000
89M89GLY00.0200.01211.365-0.037-0.0370.0000.0000.0000.000
90M90VAL00.0430.01711.357-0.139-0.1390.0000.0000.0000.000
91M91ILE0-0.036-0.01213.263-0.024-0.0240.0000.0000.0000.000
92M92VAL0-0.008-0.0068.9630.0270.0270.0000.0000.0000.000
93M93LEU00.0060.0086.766-0.022-0.0220.0000.0000.0000.000
94M94LEU00.0120.0089.7750.0100.0100.0000.0000.0000.000
95M95PHE00.0110.00512.8220.0480.0480.0000.0000.0000.000
96M96GLN00.0580.0266.429-0.234-0.2340.0000.0000.0000.000
97M97ALA0-0.037-0.0039.028-0.002-0.0020.0000.0000.0000.000
98M98LEU0-0.049-0.03410.5470.1070.1070.0000.0000.0000.000
99M99LEU0-0.067-0.02812.5400.0900.0900.0000.0000.0000.000
100M100LEU0-0.049-0.0238.7400.0780.0780.0000.0000.0000.000
101M101ALA0-0.0180.0149.9680.0830.0830.0000.0000.0000.000
102M102HIS0-0.047-0.0372.148-0.0620.3651.379-0.430-1.375-0.001
103M103GLY0-0.035-0.0275.855-0.520-0.5200.0000.0000.0000.000
104M104GLY00.0400.0207.503-0.245-0.2450.0000.0000.0000.000
105M105LEU0-0.054-0.05110.430-0.046-0.0460.0000.0000.0000.000
106M106THR0-0.073-0.05513.8280.0160.0160.0000.0000.0000.000
107M107THR0-0.002-0.0239.3000.1190.1190.0000.0000.0000.000
108M108LEU0-0.0290.00710.792-0.220-0.2200.0000.0000.0000.000
109M109GLY00.0400.00811.5190.1830.1830.0000.0000.0000.000
110M110ALA00.009-0.00210.8050.0590.0590.0000.0000.0000.000
111M111ASN00.0440.0216.794-0.646-0.6460.0000.0000.0000.000
112M112ALA0-0.010-0.0068.619-0.025-0.0250.0000.0000.0000.000
113M113PHE0-0.003-0.00411.1470.0900.0900.0000.0000.0000.000
114M114SER00.0320.0287.1830.0910.0910.0000.0000.0000.000
115M115MET00.0510.0152.637-0.4620.4150.392-0.211-1.0590.000
116M116ALA00.0230.0227.2740.3530.3530.0000.0000.0000.000
117M117ILE0-0.079-0.03010.5730.1540.1540.0000.0000.0000.000
118M118VAL0-0.027-0.00210.6540.1390.1390.0000.0000.0000.000
119M119GLY00.0660.0178.6280.1280.1280.0000.0000.0000.000
120M120PRO0-0.048-0.0469.4550.2220.2220.0000.0000.0000.000
121M121TRP0-0.051-0.00912.1760.1180.1180.0000.0000.0000.000
122M122VAL00.0170.01011.8480.0850.0850.0000.0000.0000.000
123M123ALA00.0310.03011.0430.0930.0930.0000.0000.0000.000
124M124PHE00.0320.00013.0490.0870.0870.0000.0000.0000.000
125M125GLY0-0.029-0.01016.4180.0500.0500.0000.0000.0000.000
126M126VAL00.012-0.00614.9820.0380.0380.0000.0000.0000.000
127M127TYR00.000-0.00316.6950.0320.0320.0000.0000.0000.000
128M128LYS10.9290.95918.2230.2250.2250.0000.0000.0000.000
129M129LEU0-0.074-0.03220.2930.0170.0170.0000.0000.0000.000
130M130ALA00.0540.03019.9910.0160.0160.0000.0000.0000.000
131M131GLY00.0340.02021.9820.0140.0140.0000.0000.0000.000
132M132LYS10.9040.96223.9660.0750.0750.0000.0000.0000.000
133M133ALA0-0.057-0.02825.0670.0020.0020.0000.0000.0000.000
134M134GLY00.0240.01426.9910.0120.0120.0000.0000.0000.000
135M135ALA0-0.042-0.00722.4380.0130.0130.0000.0000.0000.000
136M136SER00.0340.01324.304-0.012-0.0120.0000.0000.0000.000
137M137MET00.0430.02721.366-0.005-0.0050.0000.0000.0000.000
138M138ALA00.0820.03119.956-0.007-0.0070.0000.0000.0000.000
139M139VAL00.0060.00418.7030.0230.0230.0000.0000.0000.000
140M140ALA00.0170.00718.2400.0040.0040.0000.0000.0000.000
141M141VAL00.005-0.00815.278-0.029-0.0290.0000.0000.0000.000
142M142PHE0-0.0060.01313.987-0.026-0.0260.0000.0000.0000.000
143M143LEU0-0.011-0.01013.4900.0340.0340.0000.0000.0000.000
144M144ALA0-0.024-0.01213.468-0.036-0.0360.0000.0000.0000.000
145M145ALA00.007-0.0099.891-0.118-0.1180.0000.0000.0000.000
146M146PHE00.0200.0288.533-0.086-0.0860.0000.0000.0000.000
147M147LEU0-0.021-0.0269.4990.0320.0320.0000.0000.0000.000
148M148GLY00.0010.0009.444-0.083-0.0830.0000.0000.0000.000
149M149ASP-1-0.829-0.9234.432-1.116-0.992-0.001-0.017-0.1060.000
150M150LEU0-0.017-0.0015.892-0.227-0.2270.0000.0000.0000.000
151M151ALA00.0330.0248.088-0.031-0.0310.0000.0000.0000.000
152M152THR0-0.052-0.0104.595-0.541-0.439-0.001-0.008-0.0930.000
153M153TYR00.010-0.0025.408-0.361-0.3610.0000.0000.0000.000
154M154VAL0-0.0030.0136.3470.0280.0280.0000.0000.0000.000
155M155THR0-0.043-0.0489.0710.0000.0000.0000.0000.0000.000
156M156THR00.002-0.0154.926-0.011-0.0110.0000.0000.0000.000
157M157SER0-0.026-0.0297.9090.0670.0670.0000.0000.0000.000
158M158LEU0-0.013-0.0029.3910.1570.1570.0000.0000.0000.000
159M159GLN0-0.056-0.0239.946-0.139-0.1390.0000.0000.0000.000
160M160LEU00.0110.0056.9280.0920.0920.0000.0000.0000.000
161M161ALA00.0110.01611.4710.1220.1220.0000.0000.0000.000
162M162LEU0-0.062-0.03714.3190.0650.0650.0000.0000.0000.000
163M163ALA0-0.039-0.02613.9600.0530.0530.0000.0000.0000.000
164M164TYR0-0.083-0.04512.7810.0880.0880.0000.0000.0000.000
165M165PRO00.0170.01216.3980.0370.0370.0000.0000.0000.000
166M166ASP-1-0.839-0.92518.418-0.077-0.0770.0000.0000.0000.000
167M167PRO00.010-0.00419.8140.0020.0020.0000.0000.0000.000
168M168ALA0-0.036-0.01023.2470.0060.0060.0000.0000.0000.000
169M169SER00.023-0.00921.7510.0110.0110.0000.0000.0000.000
170M170GLY00.0360.05422.2580.0030.0030.0000.0000.0000.000
171M171PHE00.004-0.00518.7170.0080.0080.0000.0000.0000.000
172M172LEU00.0250.01017.827-0.014-0.0140.0000.0000.0000.000
173M173GLY00.0610.02818.7450.0290.0290.0000.0000.0000.000
174M174ALA0-0.018-0.01315.1620.0370.0370.0000.0000.0000.000
175M175ALA0-0.002-0.00713.966-0.010-0.0100.0000.0000.0000.000
176M176LEU0-0.0050.00513.6990.0490.0490.0000.0000.0000.000
177M177LYS10.8630.94914.4130.1310.1310.0000.0000.0000.000
178M178PHE00.0180.0009.4480.0680.0680.0000.0000.0000.000
179M179GLY00.0420.0249.3560.1310.1310.0000.0000.0000.000
180M180SER0-0.027-0.02010.8850.2510.2510.0000.0000.0000.000
181M181VAL00.0050.0009.0730.1850.1850.0000.0000.0000.000
182M182PHE00.0120.0034.9590.0550.0550.0000.0000.0000.000
183M183ALA00.0030.0077.3560.9850.9850.0000.0000.0000.000
184M184LEU0-0.033-0.0139.9820.2470.2470.0000.0000.0000.000
185M185THR0-0.016-0.0155.6630.2740.2740.0000.0000.0000.000
186M186GLN0-0.011-0.0292.128-3.795-11.97118.304-5.914-4.2140.030
187M187ILE00.0290.0276.227-0.638-0.609-0.001-0.003-0.0240.000
188M188PRO0-0.009-0.0109.124-0.284-0.2840.0000.0000.0000.000
189M189LEU00.0170.0132.8860.837-1.1055.169-0.955-2.272-0.003
190M190ALA00.0210.0076.638-0.710-0.7100.0000.0000.0000.000
191M191ILE0-0.027-0.0137.320-0.411-0.4110.0000.0000.0000.000
192M192ALA0-0.0020.0069.585-0.239-0.2390.0000.0000.0000.000
193M193GLU-1-0.808-0.8986.6860.1420.1420.0000.0000.0000.000
194M194GLY00.0370.0108.848-0.290-0.2900.0000.0000.0000.000
195M195PHE0-0.033-0.03011.537-0.103-0.1030.0000.0000.0000.000
196M196LEU0-0.011-0.00810.319-0.105-0.1050.0000.0000.0000.000
197M197THR0-0.028-0.03710.474-0.128-0.1280.0000.0000.0000.000
198M198VAL00.0010.00713.316-0.072-0.0720.0000.0000.0000.000
199M199ILE00.0360.02616.534-0.038-0.0380.0000.0000.0000.000
200M200VAL0-0.055-0.02414.686-0.036-0.0360.0000.0000.0000.000
201M201VAL00.014-0.00616.546-0.034-0.0340.0000.0000.0000.000
202M202ASP-1-0.908-0.93819.0600.1290.1290.0000.0000.0000.000
203M203ALA0-0.018-0.00820.900-0.016-0.0160.0000.0000.0000.000
204M204LEU0-0.064-0.04318.752-0.018-0.0180.0000.0000.0000.000
205M205ALA0-0.0240.01922.519-0.014-0.0140.0000.0000.0000.000
206M206GLY0-0.025-0.00224.968-0.003-0.0030.0000.0000.0000.000
207M207LYS10.8730.92422.399-0.016-0.0160.0000.0000.0000.000