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: JL1R9

Calculation Name: 5CHL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CHL

Chain ID: B

ChEMBL ID:

UniProt ID: P0C0S5

Base Structure: X-ray

Registration Date: 2023-09-20

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1760476.356237
FMO2-HF: Nuclear repulsion 1693758.888666
FMO2-HF: Total energy -66717.467571
FMO2-MP2: Total energy -66915.981333


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(B:4:GLU)


Summations of interaction energy for fragment #1(B:4:GLU)
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.
-193.539-187.2111.901-3.605-4.623-0.017
Interaction energy analysis for fragmet #1(B:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.902 / q_NPA : -0.946
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].
3B6TYR00.013-0.0252.850-7.861-5.4640.187-1.145-1.437-0.001
4B7SER00.0700.0226.194-2.278-2.2780.0000.0000.0000.000
5B8ILE0-0.0010.0039.257-2.054-2.0540.0000.0000.0000.000
6B9TYR0-0.019-0.0246.785-0.779-0.7790.0000.0000.0000.000
7B10VAL00.0550.0299.719-1.343-1.3430.0000.0000.0000.000
8B11TYR00.0010.00112.354-1.403-1.4030.0000.0000.0000.000
9B12LYS10.8710.93013.358-17.688-17.6880.0000.0000.0000.000
10B13VAL00.0380.02314.460-0.732-0.7320.0000.0000.0000.000
11B14LEU0-0.019-0.00716.656-0.665-0.6650.0000.0000.0000.000
12B15LYS10.7400.85418.632-14.088-14.0880.0000.0000.0000.000
13B16GLN0-0.008-0.00118.628-0.139-0.1390.0000.0000.0000.000
14B17VAL00.0280.02320.332-0.436-0.4360.0000.0000.0000.000
15B18HIS0-0.055-0.02422.567-0.643-0.6430.0000.0000.0000.000
16B19PRO00.0470.02923.6490.4010.4010.0000.0000.0000.000
17B20ASP-1-0.897-0.92524.71410.89110.8910.0000.0000.0000.000
18B21THR0-0.052-0.01622.549-0.250-0.2500.0000.0000.0000.000
19B22GLY0-0.0050.00821.1290.4720.4720.0000.0000.0000.000
20B23ILE00.003-0.01014.885-0.125-0.1250.0000.0000.0000.000
21B24SER0-0.018-0.00417.9230.2310.2310.0000.0000.0000.000
22B25SER00.0790.01314.6420.4430.4430.0000.0000.0000.000
23B26LYS10.9981.00013.146-16.664-16.6640.0000.0000.0000.000
24B27ALA00.0000.00013.2840.9790.9790.0000.0000.0000.000
25B28MET00.0310.03010.5421.0171.0170.0000.0000.0000.000
26B29GLY00.0120.0098.8171.9321.9320.0000.0000.0000.000
27B30ILE00.0080.0058.4662.6442.6440.0000.0000.0000.000
28B31MET00.0250.01810.0250.7030.7030.0000.0000.0000.000
29B32ASN00.0050.0103.225-3.145-2.7960.007-0.150-0.2060.001
30B33SER0-0.001-0.0045.5634.7684.7680.0000.0000.0000.000
31B34PHE00.0780.0426.5610.1800.1800.0000.0000.0000.000
32B35VAL00.005-0.0066.807-0.526-0.5260.0000.0000.0000.000
33B36ASN0-0.080-0.0722.575-3.220-0.1091.695-2.190-2.617-0.018
34B37ASP-1-0.852-0.9135.66133.32933.3290.0000.0000.0000.000
35B38ILE0-0.008-0.0058.087-2.140-2.1400.0000.0000.0000.000
36B39PHE0-0.052-0.0365.515-2.108-2.1080.0000.0000.0000.000
37B40GLU-1-0.737-0.8405.88834.99334.9930.0000.0000.0000.000
38B41ARG10.8640.9398.939-21.072-21.0720.0000.0000.0000.000
39B42ILE00.0190.01012.269-1.477-1.4770.0000.0000.0000.000
40B43ALA0-0.031-0.01710.633-1.352-1.3520.0000.0000.0000.000
41B44GLY00.0380.02012.597-0.921-0.9210.0000.0000.0000.000
42B45GLU-1-0.738-0.83414.23613.21113.2110.0000.0000.0000.000
43B46ALA0-0.029-0.02515.782-1.023-1.0230.0000.0000.0000.000
44B47SER0-0.078-0.04115.862-0.942-0.9420.0000.0000.0000.000
45B48ARG10.8430.89217.845-14.076-14.0760.0000.0000.0000.000
46B49LEU00.017-0.00520.499-0.809-0.8090.0000.0000.0000.000
47B50ALA0-0.0060.00320.568-0.627-0.6270.0000.0000.0000.000
48B51HIS10.8130.90020.961-14.023-14.0230.0000.0000.0000.000
49B52TYR00.0330.03524.969-0.286-0.2860.0000.0000.0000.000
50B53ASN0-0.074-0.03223.700-0.611-0.6110.0000.0000.0000.000
51B54LYS11.0060.98427.897-8.623-8.6230.0000.0000.0000.000
52B55ARG10.9490.97225.763-10.618-10.6180.0000.0000.0000.000
53B56SER00.0290.03623.9860.3410.3410.0000.0000.0000.000
54B57THR0-0.067-0.02721.5920.3130.3130.0000.0000.0000.000
55B58ILE00.0740.04016.290-0.190-0.1900.0000.0000.0000.000
56B59THR0-0.126-0.10318.888-0.060-0.0600.0000.0000.0000.000
57B60SER00.0630.01219.4450.3420.3420.0000.0000.0000.000
58B61ARG10.8620.93420.451-11.336-11.3360.0000.0000.0000.000
59B62GLU-1-0.706-0.83119.99212.28712.2870.0000.0000.0000.000
60B63ILE00.0070.00815.0230.1720.1720.0000.0000.0000.000
61B64GLN00.0540.04718.3240.3090.3090.0000.0000.0000.000
62B65THR0-0.045-0.02621.228-0.335-0.3350.0000.0000.0000.000
63B66ALA00.0360.01417.498-0.120-0.1200.0000.0000.0000.000
64B67VAL0-0.007-0.00817.0320.1960.1960.0000.0000.0000.000
65B68ARG10.9350.96119.174-11.198-11.1980.0000.0000.0000.000
66B69LEU0-0.043-0.00621.186-0.335-0.3350.0000.0000.0000.000
67B70LEU0-0.039-0.00915.6040.1550.1550.0000.0000.0000.000
68B71LEU0-0.034-0.00616.6330.4160.4160.0000.0000.0000.000
69B72PRO00.0300.02520.431-0.483-0.4830.0000.0000.0000.000
70B73GLY00.0450.00723.7610.0820.0820.0000.0000.0000.000
71B74GLU-1-0.774-0.88326.07510.01810.0180.0000.0000.0000.000
72B75LEU00.0190.02419.9510.2110.2110.0000.0000.0000.000
73B76ALA0-0.0170.00121.8090.3130.3130.0000.0000.0000.000
74B77LYS10.7690.85422.857-9.846-9.8460.0000.0000.0000.000
75B78HIS0-0.011-0.00423.619-0.344-0.3440.0000.0000.0000.000
76B79ALA00.0270.01619.0950.1290.1290.0000.0000.0000.000
77B80VAL0-0.029-0.01820.8660.1500.1500.0000.0000.0000.000
78B81SER0-0.0030.01922.970-0.214-0.2140.0000.0000.0000.000
79B82GLU-1-0.762-0.86820.32711.77111.7710.0000.0000.0000.000
80B83GLY00.003-0.00319.6240.1680.1680.0000.0000.0000.000
81B84THR0-0.038-0.03520.512-0.115-0.1150.0000.0000.0000.000
82B85LYS10.8270.91023.511-11.590-11.5900.0000.0000.0000.000
83B86ALA00.0040.01119.302-0.197-0.1970.0000.0000.0000.000
84B87VAL0-0.031-0.03320.105-0.067-0.0670.0000.0000.0000.000
85B88THR00.0160.00722.181-0.299-0.2990.0000.0000.0000.000
86B89LYS10.9531.00223.669-10.955-10.9550.0000.0000.0000.000
87B90TYR0-0.015-0.00120.867-0.170-0.1700.0000.0000.0000.000
88B91THR0-0.077-0.06323.261-0.262-0.2620.0000.0000.0000.000
89B92SER0-0.007-0.00725.840-0.253-0.2530.0000.0000.0000.000
90B93SER0-0.006-0.00926.913-0.212-0.2120.0000.0000.0000.000
91B94LYS10.8930.95023.751-10.412-10.4120.0000.0000.0000.000
92B95GLN00.0470.03823.2400.4990.4990.0000.0000.0000.000
93B96ARG10.9620.95116.060-14.084-14.0840.0000.0000.0000.000
94B97ALA0-0.018-0.00918.1850.5830.5830.0000.0000.0000.000
95B98GLY00.0100.01319.0880.1750.1750.0000.0000.0000.000
96B99LEU0-0.0300.00314.9330.0680.0680.0000.0000.0000.000
97B100GLN00.0330.02014.6100.6460.6460.0000.0000.0000.000
98B101PHE00.0270.0158.2081.2871.2870.0000.0000.0000.000
99B102PRO0-0.0290.0007.123-1.214-1.2140.0000.0000.0000.000
100B103VAL00.0670.0149.0330.9930.9930.0000.0000.0000.000
101B104GLY0-0.012-0.00211.2660.0580.0580.0000.0000.0000.000
102B105ARG10.8870.9293.299-36.079-35.7460.013-0.109-0.2370.001
103B106ILE00.0810.0577.0931.0271.0270.0000.0000.0000.000
104B107HIS00.001-0.0158.1760.4260.4260.0000.0000.0000.000
105B108ARG10.8930.9348.429-22.681-22.6810.0000.0000.0000.000
106B109HIS00.0120.0034.545-1.251-1.113-0.001-0.011-0.1260.000
107B110LEU00.0480.0277.810-0.165-0.1650.0000.0000.0000.000
108B111LYS10.8150.90511.117-18.883-18.8830.0000.0000.0000.000
109B112SER0-0.054-0.0188.8540.0050.0050.0000.0000.0000.000
110B113ARG10.8760.9056.382-35.102-35.1020.0000.0000.0000.000
111B114THR0-0.054-0.00612.432-1.131-1.1310.0000.0000.0000.000
112B115THR00.0760.04715.911-0.303-0.3030.0000.0000.0000.000
113B116SER0-0.046-0.02518.854-1.020-1.0200.0000.0000.0000.000
114B117HIS00.0710.03220.2180.7730.7730.0000.0000.0000.000
115B118GLY0-0.0010.02722.194-0.365-0.3650.0000.0000.0000.000
116B119ARG10.9210.95219.808-10.966-10.9660.0000.0000.0000.000
117B120VAL00.0850.04114.289-0.181-0.1810.0000.0000.0000.000
118B121GLY0-0.022-0.00517.549-0.168-0.1680.0000.0000.0000.000
119B122ALA00.031-0.00316.8980.5950.5950.0000.0000.0000.000
120B123THR00.025-0.00117.0400.5800.5800.0000.0000.0000.000
121B124ALA00.0660.05115.9550.0300.0300.0000.0000.0000.000
122B125ALA00.0030.00612.6530.6940.6940.0000.0000.0000.000
123B126VAL0-0.045-0.02013.4340.5530.5530.0000.0000.0000.000
124B127TYR00.038-0.00216.0390.2460.2460.0000.0000.0000.000
125B128SER00.017-0.00911.8350.1560.1560.0000.0000.0000.000
126B129ALA0-0.043-0.02311.6950.6970.6970.0000.0000.0000.000
127B130ALA00.0170.00812.6660.1700.1700.0000.0000.0000.000
128B131ILE00.0060.01314.507-0.165-0.1650.0000.0000.0000.000
129B132LEU00.0090.0058.3650.1380.1380.0000.0000.0000.000
130B133GLU-1-0.844-0.91612.44416.07616.0760.0000.0000.0000.000
131B134TYR0-0.050-0.05614.616-0.050-0.0500.0000.0000.0000.000
132B135LEU00.0630.02714.112-0.227-0.2270.0000.0000.0000.000
133B136THR0-0.062-0.04412.5270.5570.5570.0000.0000.0000.000
134B137ALA0-0.005-0.01414.753-0.276-0.2760.0000.0000.0000.000
135B138GLU-1-0.797-0.85818.31212.29212.2920.0000.0000.0000.000
136B139VAL0-0.018-0.00316.038-0.305-0.3050.0000.0000.0000.000
137B140LEU0-0.058-0.04915.528-0.350-0.3500.0000.0000.0000.000
138B141GLU-1-0.911-0.95119.23911.27011.2700.0000.0000.0000.000
139B142LEU00.0860.04722.342-0.522-0.5220.0000.0000.0000.000
140B143ALA0-0.021-0.01320.212-0.301-0.3010.0000.0000.0000.000
141B144GLY0-0.041-0.03222.232-0.300-0.3000.0000.0000.0000.000
142B145ASN0-0.031-0.02024.103-0.695-0.6950.0000.0000.0000.000
143B146ALA0-0.0050.01725.083-0.367-0.3670.0000.0000.0000.000
144B147SER0-0.118-0.10127.0130.0570.0570.0000.0000.0000.000
145B148LYS10.9560.97130.340-8.561-8.5610.0000.0000.0000.000
146B149ASP-1-0.896-0.93433.7878.0668.0660.0000.0000.0000.000
147B150LEU00.0240.03332.9960.0970.0970.0000.0000.0000.000
148B151LYS10.9881.01127.637-10.434-10.4340.0000.0000.0000.000
149B152VAL0-0.019-0.00624.5790.0430.0430.0000.0000.0000.000
150B153LYS10.9910.98526.945-9.561-9.5610.0000.0000.0000.000
151B154ARG10.9380.96521.469-12.748-12.7480.0000.0000.0000.000
152B155ILE00.0580.04918.507-0.206-0.2060.0000.0000.0000.000
153B156THR0-0.034-0.04719.4140.7090.7090.0000.0000.0000.000
154B157PRO00.031-0.01316.777-0.016-0.0160.0000.0000.0000.000
155B158ARG10.9741.00518.620-11.503-11.5030.0000.0000.0000.000
156B159HIS00.0450.03021.3290.2090.2090.0000.0000.0000.000
157B160LEU00.0350.01914.956-0.145-0.1450.0000.0000.0000.000
158B161GLN00.0170.02019.048-0.503-0.5030.0000.0000.0000.000
159B162LEU0-0.026-0.01820.860-0.265-0.2650.0000.0000.0000.000
160B163ALA00.0160.01820.455-0.320-0.3200.0000.0000.0000.000
161B164ILE00.0010.00116.285-0.065-0.0650.0000.0000.0000.000
162B165ARG10.8880.93020.731-12.317-12.3170.0000.0000.0000.000
163B166GLY0-0.050-0.02023.444-0.421-0.4210.0000.0000.0000.000
164B167ASP-1-0.821-0.89823.27311.90311.9030.0000.0000.0000.000
165B168GLU-1-0.925-0.95924.18910.61510.6150.0000.0000.0000.000
166B169GLU-1-0.751-0.87823.50911.85711.8570.0000.0000.0000.000
167B170LEU0-0.007-0.01818.5270.8550.8550.0000.0000.0000.000
168B171ASP-1-0.834-0.89219.54113.91013.9100.0000.0000.0000.000
169B172SER0-0.026-0.01920.9240.4680.4680.0000.0000.0000.000
170B173LEU00.0160.01116.3260.3980.3980.0000.0000.0000.000
171B174ILE0-0.027-0.00814.6311.0681.0680.0000.0000.0000.000
172B175LYS10.8130.89116.359-12.272-12.2720.0000.0000.0000.000
173B176ALA00.0230.01918.4190.2230.2230.0000.0000.0000.000
174B177THR0-0.093-0.05611.9700.5240.5240.0000.0000.0000.000
175B178ILE0-0.033-0.01212.7371.1931.1930.0000.0000.0000.000
176B179ALA0-0.0360.00514.8530.3330.3330.0000.0000.0000.000