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

tag_button

FMODB ID: K22L3

Calculation Name: 5T58-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T58

Chain ID: N

ChEMBL ID:

UniProt ID: Q6CLK3

Base Structure: X-ray

Registration Date: 2023-09-27

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1364276.648601
FMO2-HF: Nuclear repulsion 1284554.914133
FMO2-HF: Total energy -79721.734469
FMO2-MP2: Total energy -79955.860561


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(N:5:VAL)


Summations of interaction energy for fragment #1(N:5:VAL)
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.
-1.7511.3880.083-1.624-1.5980
Interaction energy analysis for fragmet #1(N:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.008
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].
3N7LYS10.8170.8833.262-0.7772.3120.084-1.619-1.5540.000
4N8LEU00.0290.0184.9620.3100.360-0.001-0.005-0.0440.000
5N9ASP-1-0.797-0.8728.757-0.994-0.9940.0000.0000.0000.000
6N10ILE00.0620.03110.8790.0630.0630.0000.0000.0000.000
7N11THR00.0010.00014.1150.0390.0390.0000.0000.0000.000
8N12GLN00.1160.04017.571-0.007-0.0070.0000.0000.0000.000
9N13LYS10.9590.97619.9660.2280.2280.0000.0000.0000.000
10N14GLN00.0300.01116.544-0.013-0.0130.0000.0000.0000.000
11N15LEU00.0350.03016.9440.0090.0090.0000.0000.0000.000
12N16ARG10.8190.89219.1230.2110.2110.0000.0000.0000.000
13N17PHE0-0.072-0.02222.5930.0230.0230.0000.0000.0000.000
14N18LEU00.0160.00518.2370.0100.0100.0000.0000.0000.000
15N19HIS00.0520.02722.1240.0310.0310.0000.0000.0000.000
16N20LYS10.7990.86723.3900.1870.1870.0000.0000.0000.000
17N21GLN00.0400.02924.270-0.010-0.0100.0000.0000.0000.000
18N22PHE0-0.036-0.02020.0540.0020.0020.0000.0000.0000.000
19N23LYS10.8780.92025.9990.1580.1580.0000.0000.0000.000
20N24GLU-1-0.927-0.94828.778-0.163-0.1630.0000.0000.0000.000
21N25ILE00.0120.01027.0360.0090.0090.0000.0000.0000.000
22N26ILE0-0.041-0.03026.6390.0110.0110.0000.0000.0000.000
23N27ASP-1-0.874-0.93930.950-0.113-0.1130.0000.0000.0000.000
24N28GLU-1-0.945-0.97733.506-0.134-0.1340.0000.0000.0000.000
25N29LYS10.9090.95733.1340.1240.1240.0000.0000.0000.000
26N30VAL0-0.017-0.00933.8140.0080.0080.0000.0000.0000.000
27N31ARG10.8350.90936.4680.1080.1080.0000.0000.0000.000
28N32THR0-0.102-0.05637.8840.0030.0030.0000.0000.0000.000
29N33ALA0-0.119-0.05938.4840.0050.0050.0000.0000.0000.000
30N34LEU00.0110.00639.1740.0040.0040.0000.0000.0000.000
31N35PRO0-0.034-0.01742.209-0.003-0.0030.0000.0000.0000.000
32N36GLU-1-0.785-0.88241.927-0.089-0.0890.0000.0000.0000.000
33N37SER0-0.094-0.04143.634-0.001-0.0010.0000.0000.0000.000
34N38SER00.0120.00941.853-0.003-0.0030.0000.0000.0000.000
35N39GLU-1-0.950-0.96142.060-0.063-0.0630.0000.0000.0000.000
36N40ASP-1-0.818-0.88742.484-0.057-0.0570.0000.0000.0000.000
37N41ASP-1-0.950-0.95942.514-0.043-0.0430.0000.0000.0000.000
38N42GLN0-0.076-0.04640.346-0.002-0.0020.0000.0000.0000.000
39N43VAL0-0.028-0.01839.686-0.002-0.0020.0000.0000.0000.000
40N44SER00.011-0.00338.803-0.001-0.0010.0000.0000.0000.000
41N45GLN0-0.009-0.04437.163-0.004-0.0040.0000.0000.0000.000
42N46GLU-1-0.873-0.92533.857-0.077-0.0770.0000.0000.0000.000
43N47ILE00.0240.01833.149-0.005-0.0050.0000.0000.0000.000
44N48GLN00.0070.00032.199-0.006-0.0060.0000.0000.0000.000
45N49LEU00.0070.00631.198-0.009-0.0090.0000.0000.0000.000
46N50GLN0-0.069-0.04729.267-0.012-0.0120.0000.0000.0000.000
47N51LEU0-0.021-0.02027.846-0.011-0.0110.0000.0000.0000.000
48N52ASP-1-0.845-0.89926.462-0.151-0.1510.0000.0000.0000.000
49N53GLN0-0.004-0.03625.182-0.010-0.0100.0000.0000.0000.000
50N54PHE00.0180.03222.851-0.013-0.0130.0000.0000.0000.000
51N55LEU0-0.013-0.01522.012-0.025-0.0250.0000.0000.0000.000
52N56MET0-0.094-0.03020.582-0.023-0.0230.0000.0000.0000.000
53N57ASP-1-0.863-0.92019.234-0.160-0.1600.0000.0000.0000.000
54N58VAL0-0.045-0.02417.497-0.036-0.0360.0000.0000.0000.000
55N59LEU0-0.033-0.03016.054-0.058-0.0580.0000.0000.0000.000
56N60GLU-1-0.898-0.93414.990-0.238-0.2380.0000.0000.0000.000
57N61MET00.0240.00813.446-0.029-0.0290.0000.0000.0000.000
58N62ALA0-0.022-0.00311.615-0.088-0.0880.0000.0000.0000.000
59N63GLY0-0.091-0.04610.421-0.162-0.1620.0000.0000.0000.000
60N64GLU-1-0.980-0.9769.110-0.298-0.2980.0000.0000.0000.000
61N65SER0-0.059-0.0414.8150.1240.1240.0000.0000.0000.000
62N66MET0-0.073-0.0296.545-0.281-0.2810.0000.0000.0000.000
63N67ASN0-0.087-0.0437.7310.2380.2380.0000.0000.0000.000
64N68VAL00.006-0.0079.530-0.006-0.0060.0000.0000.0000.000
65N69VAL0-0.064-0.03511.9200.0020.0020.0000.0000.0000.000
66N70ASP-1-0.935-0.96414.282-0.246-0.2460.0000.0000.0000.000
67N71ALA00.0370.02316.9650.0410.0410.0000.0000.0000.000
68N72GLY00.013-0.00214.577-0.035-0.0350.0000.0000.0000.000
69N73LYS10.9130.9506.0060.7430.7430.0000.0000.0000.000
70N74GLY00.0580.03210.903-0.016-0.0160.0000.0000.0000.000
71N75THR0-0.033-0.02112.3330.0510.0510.0000.0000.0000.000
72N76THR0-0.009-0.01715.604-0.017-0.0170.0000.0000.0000.000
73N77VAL00.0490.03414.8220.0140.0140.0000.0000.0000.000
74N78LYS10.9260.93216.0190.2120.2120.0000.0000.0000.000
75N79SER0-0.006-0.00319.9950.0140.0140.0000.0000.0000.000
76N80VAL0-0.023-0.01020.2650.0120.0120.0000.0000.0000.000
77N81ILE0-0.0080.00319.9360.0060.0060.0000.0000.0000.000
78N82GLN00.0340.00822.8510.0180.0180.0000.0000.0000.000
79N83GLU-1-0.849-0.90125.330-0.155-0.1550.0000.0000.0000.000
80N84VAL0-0.021-0.01425.1300.0070.0070.0000.0000.0000.000
81N85GLN00.0290.01826.9360.0020.0020.0000.0000.0000.000
82N86LYS10.7690.87128.6420.0950.0950.0000.0000.0000.000
83N87GLU-1-0.854-0.90029.892-0.147-0.1470.0000.0000.0000.000
84N88TYR0-0.035-0.00228.1090.0020.0020.0000.0000.0000.000
85N89THR00.022-0.01433.6820.0070.0070.0000.0000.0000.000
86N90GLU-1-0.859-0.91233.187-0.080-0.0800.0000.0000.0000.000
87N91PRO0-0.0030.00636.3400.0000.0000.0000.0000.0000.000
88N92PHE00.007-0.01834.5080.0040.0040.0000.0000.0000.000
89N93ASP-1-0.809-0.91140.308-0.042-0.0420.0000.0000.0000.000
90N94VAL0-0.003-0.00743.8130.0030.0030.0000.0000.0000.000
91N95GLU-1-0.885-0.91845.790-0.035-0.0350.0000.0000.0000.000
92N96LEU00.0580.02046.1540.0030.0030.0000.0000.0000.000
93N97ASN00.0200.01342.6550.0040.0040.0000.0000.0000.000
94N98GLU-1-0.805-0.87845.909-0.022-0.0220.0000.0000.0000.000
95N99LYS10.8060.89749.2020.0370.0370.0000.0000.0000.000
96N100VAL00.0150.01445.2850.0020.0020.0000.0000.0000.000
97N101ARG10.8930.93146.7200.0240.0240.0000.0000.0000.000
98N102LYS10.8210.89549.4850.0250.0250.0000.0000.0000.000
99N103LEU00.0520.01651.9540.0010.0010.0000.0000.0000.000
100N104TYR0-0.093-0.03548.1150.0010.0010.0000.0000.0000.000
101N105GLN0-0.040-0.03351.1830.0010.0010.0000.0000.0000.000
102N106GLU-1-0.927-0.95653.463-0.016-0.0160.0000.0000.0000.000
103N107TRP0-0.023-0.00550.6950.0010.0010.0000.0000.0000.000
104N108GLU-1-0.861-0.90450.681-0.008-0.0080.0000.0000.0000.000
105N109ASP-1-0.875-0.93955.013-0.009-0.0090.0000.0000.0000.000
106N110GLU-1-0.819-0.90858.452-0.009-0.0090.0000.0000.0000.000
107N111THR0-0.039-0.02456.0270.0010.0010.0000.0000.0000.000
108N112VAL00.000-0.00557.5890.0010.0010.0000.0000.0000.000
109N113LYS10.7990.88960.0750.0100.0100.0000.0000.0000.000
110N114VAL00.0520.01261.1550.0010.0010.0000.0000.0000.000
111N115SER0-0.100-0.04160.3820.0010.0010.0000.0000.0000.000
112N116LYS10.8320.89162.9170.0040.0040.0000.0000.0000.000
113N117LEU00.0230.01465.5820.0000.0000.0000.0000.0000.000
114N118ARG10.9430.96663.0970.0050.0050.0000.0000.0000.000
115N119ARG10.9250.97361.4900.0010.0010.0000.0000.0000.000
116N120GLU-1-0.847-0.90668.413-0.002-0.0020.0000.0000.0000.000
117N121ALA00.0160.01370.5730.0000.0000.0000.0000.0000.000
118N122PRO0-0.001-0.00370.9410.0000.0000.0000.0000.0000.000
119N123GLN00.0400.00670.1640.0000.0000.0000.0000.0000.000
120N124VAL00.0050.00774.0920.0000.0000.0000.0000.0000.000
121N125ALA00.0150.02576.3860.0000.0000.0000.0000.0000.000
122N126VAL0-0.002-0.00776.7330.0000.0000.0000.0000.0000.000
123N127SER0-0.072-0.01978.0340.0000.0000.0000.0000.0000.000
124N128GLU-1-0.781-0.89379.9410.0000.0000.0000.0000.0000.000
125N129TYR00.0050.00782.0130.0000.0000.0000.0000.0000.000
126N130THR0-0.040-0.04281.6820.0000.0000.0000.0000.0000.000
127N131LYS10.7710.88082.0180.0000.0000.0000.0000.0000.000
128N132GLN0-0.026-0.00585.7000.0000.0000.0000.0000.0000.000
129N133GLU-1-0.915-0.96287.260-0.001-0.0010.0000.0000.0000.000
130N134ASN0-0.063-0.01886.8860.0000.0000.0000.0000.0000.000
131N135GLN0-0.016-0.02589.8720.0000.0000.0000.0000.0000.000
132N136LEU00.0270.02192.1690.0000.0000.0000.0000.0000.000
133N137LEU0-0.040-0.02091.2810.0000.0000.0000.0000.0000.000
134N138GLU-1-0.871-0.91295.0210.0010.0010.0000.0000.0000.000
135N139GLU-1-0.937-0.96497.4710.0010.0010.0000.0000.0000.000
136N140ILE0-0.059-0.04295.9770.0000.0000.0000.0000.0000.000
137N141ASP-1-0.849-0.94294.9370.0030.0030.0000.0000.0000.000
138N142SER0-0.026-0.01798.4300.0000.0000.0000.0000.0000.000
139N143LEU0-0.063-0.044101.5680.0000.0000.0000.0000.0000.000
140N144ILE0-0.029-0.00897.8790.0000.0000.0000.0000.0000.000
141N145ALA00.0130.018100.8650.0000.0000.0000.0000.0000.000
142N146LYS10.8660.924102.468-0.002-0.0020.0000.0000.0000.000
143N147MET0-0.113-0.050103.9630.0000.0000.0000.0000.0000.000
144N148ASP-1-0.903-0.921103.8420.0040.0040.0000.0000.0000.000
145N149SER0-0.078-0.050107.0790.0000.0000.0000.0000.0000.000
146N150SER0-0.026-0.011110.6630.0000.0000.0000.0000.0000.000
147N167LYS10.9030.912143.084-0.001-0.0010.0000.0000.0000.000
148N168THR00.0540.016140.3720.0000.0000.0000.0000.0000.000
149N169GLN00.0330.015140.9950.0000.0000.0000.0000.0000.000
150N170GLU-1-0.811-0.861144.9310.0020.0020.0000.0000.0000.000
151N171TYR00.0440.011145.6090.0000.0000.0000.0000.0000.000
152N172TRP00.0040.011138.8790.0000.0000.0000.0000.0000.000
153N173ASN0-0.006-0.027146.3620.0000.0000.0000.0000.0000.000
154N174GLN0-0.0160.013149.5540.0000.0000.0000.0000.0000.000
155N175VAL00.0320.008146.7060.0000.0000.0000.0000.0000.000
156N176ALA0-0.0110.005148.9910.0000.0000.0000.0000.0000.000
157N177ASN0-0.007-0.018150.6760.0000.0000.0000.0000.0000.000
158N178GLN00.0190.026151.9380.0000.0000.0000.0000.0000.000
159N179TYR00.0160.014151.2330.0000.0000.0000.0000.0000.000
160N180GLY00.0330.009153.3730.0000.0000.0000.0000.0000.000
161N181SER0-0.003-0.011155.9860.0000.0000.0000.0000.0000.000
162N182ILE0-0.010-0.002154.1520.0000.0000.0000.0000.0000.000
163N183LEU0-0.017-0.004154.3600.0000.0000.0000.0000.0000.000
164N184THR0-0.015-0.012158.3860.0000.0000.0000.0000.0000.000
165N185SER0-0.021-0.020161.0210.0000.0000.0000.0000.0000.000
166N186LEU0-0.0280.004158.4680.0000.0000.0000.0000.0000.000
167N187LYS10.8980.931161.904-0.002-0.0020.0000.0000.0000.000
168N188GLU-1-0.840-0.911164.2170.0020.0020.0000.0000.0000.000
169N189ILE0-0.009-0.013164.0070.0000.0000.0000.0000.0000.000
170N190ASN0-0.053-0.036163.2620.0000.0000.0000.0000.0000.000
171N191ASP-1-0.822-0.907166.8830.0020.0020.0000.0000.0000.000
172N192LYS10.7810.886169.748-0.002-0.0020.0000.0000.0000.000
173N193ILE00.0200.025168.0470.0000.0000.0000.0000.0000.000
174N194PRO00.0020.005170.7320.0000.0000.0000.0000.0000.000
175N195THR00.0370.011173.6690.0000.0000.0000.0000.0000.000
176N196HIS0-0.003-0.007174.2280.0000.0000.0000.0000.0000.000
177N197GLU-1-0.791-0.885173.8560.0020.0020.0000.0000.0000.000
178N198SER0-0.073-0.031176.5860.0000.0000.0000.0000.0000.000
179N199LYS10.9140.936179.480-0.002-0.0020.0000.0000.0000.000
180N200GLN00.0540.020175.5540.0000.0000.0000.0000.0000.000
181N201LYS10.9350.988180.392-0.002-0.0020.0000.0000.0000.000
182N202ARG10.8860.937182.418-0.002-0.0020.0000.0000.0000.000
183N203LEU00.0520.030181.1870.0000.0000.0000.0000.0000.000
184N204ARG10.9730.987178.673-0.002-0.0020.0000.0000.0000.000
185N205LEU0-0.029-0.016185.1180.0000.0000.0000.0000.0000.000
186N206LEU0-0.008-0.014187.9850.0000.0000.0000.0000.0000.000
187N207LEU0-0.007-0.005185.2610.0000.0000.0000.0000.0000.000
188N208ASP-1-0.931-0.960188.9930.0020.0020.0000.0000.0000.000
189N209LEU0-0.062-0.036190.6880.0000.0000.0000.0000.0000.000
190N210ILE0-0.041-0.022192.0780.0000.0000.0000.0000.0000.000
191N211GLU-1-0.894-0.936192.2920.0010.0010.0000.0000.0000.000
192N212LYS10.8820.949195.181-0.001-0.0010.0000.0000.0000.000
193N213GLU-1-0.907-0.953197.2610.0010.0010.0000.0000.0000.000
194N214VAL0-0.133-0.050195.8760.0000.0000.0000.0000.0000.000
195N215ALA00.0660.040198.3380.0000.0000.0000.0000.0000.000
196N216THR0-0.089-0.050201.9470.0000.0000.0000.0000.0000.000