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: 3964L

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1776206.954601
FMO2-HF: Nuclear repulsion 1709489.316256
FMO2-HF: Total energy -66717.638345
FMO2-MP2: Total energy -66916.281647


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.
-200.162-193.6974.668-4.851-6.282-0.027
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 : -0.905 / q_NPA : -0.952
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].
3B6TYR00.004-0.0152.367-8.371-5.9062.009-1.692-2.783-0.006
4B7SER00.0760.0155.767-2.580-2.5800.0000.0000.0000.000
5B8ILE00.0140.0119.003-2.148-2.1480.0000.0000.0000.000
6B9TYR0-0.019-0.0236.266-0.717-0.7170.0000.0000.0000.000
7B10VAL00.0470.0309.342-1.341-1.3410.0000.0000.0000.000
8B11TYR00.0150.00611.969-1.440-1.4400.0000.0000.0000.000
9B12LYS10.8080.90012.837-18.244-18.2440.0000.0000.0000.000
10B13VAL00.0420.02813.921-0.762-0.7620.0000.0000.0000.000
11B14LEU0-0.036-0.01516.180-0.662-0.6620.0000.0000.0000.000
12B15LYS10.7550.86318.244-14.461-14.4610.0000.0000.0000.000
13B16GLN0-0.022-0.00317.910-0.163-0.1630.0000.0000.0000.000
14B17VAL00.0120.01419.827-0.435-0.4350.0000.0000.0000.000
15B18HIS0-0.046-0.02222.057-0.660-0.6600.0000.0000.0000.000
16B19PRO00.0270.02423.2010.3940.3940.0000.0000.0000.000
17B20ASP-1-0.859-0.91923.93311.03611.0360.0000.0000.0000.000
18B21THR0-0.075-0.02122.034-0.196-0.1960.0000.0000.0000.000
19B22GLY00.0090.00820.9140.4940.4940.0000.0000.0000.000
20B23ILE00.003-0.00314.722-0.049-0.0490.0000.0000.0000.000
21B24SER00.002-0.02116.951-0.278-0.2780.0000.0000.0000.000
22B25SER00.0460.01013.7340.4170.4170.0000.0000.0000.000
23B26LYS11.0071.00712.344-16.854-16.8540.0000.0000.0000.000
24B27ALA00.0120.01212.8570.8670.8670.0000.0000.0000.000
25B28MET00.0190.02710.0050.9730.9730.0000.0000.0000.000
26B29GLY00.0200.0128.3301.9591.9590.0000.0000.0000.000
27B30ILE00.0010.0088.2452.4912.4910.0000.0000.0000.000
28B31MET00.0130.01010.0130.6010.6010.0000.0000.0000.000
29B32ASN00.002-0.0053.130-3.470-2.9270.016-0.267-0.2920.002
30B33SER0-0.011-0.0065.6674.2264.2260.0000.0000.0000.000
31B34PHE00.0850.0426.6470.3790.3790.0000.0000.0000.000
32B35VAL00.0160.0056.778-0.746-0.7460.0000.0000.0000.000
33B36ASN0-0.078-0.0682.417-2.1780.4922.587-2.622-2.635-0.024
34B37ASP-1-0.863-0.9255.54232.02632.0260.0000.0000.0000.000
35B38ILE0-0.002-0.0038.218-1.990-1.9900.0000.0000.0000.000
36B39PHE0-0.046-0.0255.564-1.987-1.9870.0000.0000.0000.000
37B40GLU-1-0.730-0.8326.07635.49735.4970.0000.0000.0000.000
38B41ARG10.8580.9439.196-21.033-21.0330.0000.0000.0000.000
39B42ILE00.0080.00512.184-1.546-1.5460.0000.0000.0000.000
40B43ALA0-0.038-0.02510.622-1.299-1.2990.0000.0000.0000.000
41B44GLY00.0480.02712.588-0.941-0.9410.0000.0000.0000.000
42B45GLU-1-0.716-0.80514.46513.08313.0830.0000.0000.0000.000
43B46ALA0-0.032-0.02315.579-1.015-1.0150.0000.0000.0000.000
44B47SER0-0.094-0.05715.590-0.976-0.9760.0000.0000.0000.000
45B48ARG10.8430.88817.595-13.929-13.9290.0000.0000.0000.000
46B49LEU00.010-0.01420.173-0.830-0.8300.0000.0000.0000.000
47B50ALA0-0.017-0.00919.962-0.635-0.6350.0000.0000.0000.000
48B51HIS10.7990.89121.011-13.961-13.9610.0000.0000.0000.000
49B52TYR00.0370.03924.844-0.296-0.2960.0000.0000.0000.000
50B53ASN0-0.037-0.01223.377-0.593-0.5930.0000.0000.0000.000
51B54LYS11.0140.98227.523-8.476-8.4760.0000.0000.0000.000
52B55ARG10.9320.97326.206-10.587-10.5870.0000.0000.0000.000
53B56SER00.0120.02023.8770.3740.3740.0000.0000.0000.000
54B57THR0-0.062-0.03221.5370.4140.4140.0000.0000.0000.000
55B58ILE00.0780.04816.200-0.073-0.0730.0000.0000.0000.000
56B59THR0-0.105-0.08318.995-0.081-0.0810.0000.0000.0000.000
57B60SER00.0600.01319.0780.3370.3370.0000.0000.0000.000
58B61ARG10.8530.93120.070-11.454-11.4540.0000.0000.0000.000
59B62GLU-1-0.697-0.80819.73512.30712.3070.0000.0000.0000.000
60B63ILE00.0080.00814.4750.1870.1870.0000.0000.0000.000
61B64GLN00.0540.04417.9500.2830.2830.0000.0000.0000.000
62B65THR0-0.068-0.04620.858-0.367-0.3670.0000.0000.0000.000
63B66ALA00.0480.01517.385-0.147-0.1470.0000.0000.0000.000
64B67VAL0-0.011-0.01016.6190.1370.1370.0000.0000.0000.000
65B68ARG10.9340.95818.872-11.272-11.2720.0000.0000.0000.000
66B69LEU0-0.041-0.00621.184-0.503-0.5030.0000.0000.0000.000
67B70LEU0-0.046-0.01615.5380.2300.2300.0000.0000.0000.000
68B71LEU0-0.038-0.00216.4940.5990.5990.0000.0000.0000.000
69B72PRO00.0130.02320.191-0.453-0.4530.0000.0000.0000.000
70B73GLY00.0740.02823.5360.1150.1150.0000.0000.0000.000
71B74GLU-1-0.766-0.88125.97610.02010.0200.0000.0000.0000.000
72B75LEU00.0140.01219.4260.2200.2200.0000.0000.0000.000
73B76ALA0-0.028-0.01621.3310.3710.3710.0000.0000.0000.000
74B77LYS10.7760.86422.554-9.875-9.8750.0000.0000.0000.000
75B78HIS0-0.015-0.01123.143-0.350-0.3500.0000.0000.0000.000
76B79ALA00.0240.01218.8650.1800.1800.0000.0000.0000.000
77B80VAL0-0.039-0.02220.4380.0960.0960.0000.0000.0000.000
78B81SER0-0.0080.00722.794-0.317-0.3170.0000.0000.0000.000
79B82GLU-1-0.754-0.85519.74311.68311.6830.0000.0000.0000.000
80B83GLY00.0200.00218.8140.1760.1760.0000.0000.0000.000
81B84THR0-0.029-0.03019.695-0.108-0.1080.0000.0000.0000.000
82B85LYS10.8240.91122.995-11.495-11.4950.0000.0000.0000.000
83B86ALA00.0080.01218.665-0.210-0.2100.0000.0000.0000.000
84B87VAL0-0.032-0.02919.588-0.102-0.1020.0000.0000.0000.000
85B88THR00.0150.01721.685-0.355-0.3550.0000.0000.0000.000
86B89LYS10.9430.99523.133-10.876-10.8760.0000.0000.0000.000
87B90TYR0-0.0010.01220.540-0.150-0.1500.0000.0000.0000.000
88B91THR0-0.052-0.05822.657-0.303-0.3030.0000.0000.0000.000
89B92SER0-0.009-0.01525.234-0.227-0.2270.0000.0000.0000.000
90B93SER00.006-0.00626.259-0.203-0.2030.0000.0000.0000.000
91B94LYS10.8510.92423.492-10.365-10.3650.0000.0000.0000.000
92B95GLN00.0260.01822.3980.6270.6270.0000.0000.0000.000
93B96ARG10.9840.97015.802-14.404-14.4040.0000.0000.0000.000
94B97ALA0-0.035-0.01817.7900.5860.5860.0000.0000.0000.000
95B98GLY00.0300.03018.9160.0630.0630.0000.0000.0000.000
96B99LEU0-0.0310.00114.4700.0810.0810.0000.0000.0000.000
97B100GLN00.0290.02314.1750.6230.6230.0000.0000.0000.000
98B101PHE00.0840.0317.7631.2881.2880.0000.0000.0000.000
99B102PRO0-0.0170.0126.586-1.267-1.2670.0000.0000.0000.000
100B103VAL00.0490.0118.7151.1091.1090.0000.0000.0000.000
101B104GLY0-0.004-0.00211.0310.0400.0400.0000.0000.0000.000
102B105ARG10.8410.9103.067-38.441-37.8530.056-0.233-0.4110.001
103B106ILE00.0540.0347.1400.6810.6810.0000.0000.0000.000
104B107HIS00.0340.0038.0800.3670.3670.0000.0000.0000.000
105B108ARG10.8740.9348.548-23.397-23.3970.0000.0000.0000.000
106B109HIS00.0130.0053.900-1.284-1.0850.000-0.037-0.1610.000
107B110LEU00.0450.0267.570-0.416-0.4160.0000.0000.0000.000
108B111LYS10.8220.90410.995-18.799-18.7990.0000.0000.0000.000
109B112SER0-0.075-0.0368.5440.1920.1920.0000.0000.0000.000
110B113ARG10.8610.8886.236-35.191-35.1910.0000.0000.0000.000
111B114THR0-0.037-0.00312.251-1.171-1.1710.0000.0000.0000.000
112B115THR00.0650.04315.766-0.141-0.1410.0000.0000.0000.000
113B116SER0-0.044-0.02618.785-0.956-0.9560.0000.0000.0000.000
114B117HIS00.0700.03420.0230.8230.8230.0000.0000.0000.000
115B118GLY0-0.0110.02022.293-0.269-0.2690.0000.0000.0000.000
116B119ARG10.9260.95519.461-11.069-11.0690.0000.0000.0000.000
117B120VAL00.0920.04514.247-0.333-0.3330.0000.0000.0000.000
118B121GLY0-0.015-0.00617.533-0.193-0.1930.0000.0000.0000.000
119B122ALA00.017-0.00616.4480.6090.6090.0000.0000.0000.000
120B123THR00.0280.00316.6100.5920.5920.0000.0000.0000.000
121B124ALA00.0680.04815.6650.0370.0370.0000.0000.0000.000
122B125ALA00.0080.01112.1960.6420.6420.0000.0000.0000.000
123B126VAL0-0.039-0.02113.0050.5560.5560.0000.0000.0000.000
124B127TYR00.031-0.00215.6060.2410.2410.0000.0000.0000.000
125B128SER00.014-0.01711.3730.2140.2140.0000.0000.0000.000
126B129ALA0-0.043-0.02211.1090.6630.6630.0000.0000.0000.000
127B130ALA00.0320.01612.1020.2480.2480.0000.0000.0000.000
128B131ILE00.0030.01414.269-0.218-0.2180.0000.0000.0000.000
129B132LEU00.0040.0097.9600.1610.1610.0000.0000.0000.000
130B133GLU-1-0.827-0.90412.01316.58216.5820.0000.0000.0000.000
131B134TYR0-0.046-0.05913.818-0.036-0.0360.0000.0000.0000.000
132B135LEU00.0440.01613.969-0.225-0.2250.0000.0000.0000.000
133B136THR0-0.067-0.05212.0690.7050.7050.0000.0000.0000.000
134B137ALA00.001-0.01014.310-0.249-0.2490.0000.0000.0000.000
135B138GLU-1-0.790-0.85417.88812.47312.4730.0000.0000.0000.000
136B139VAL00.0010.00115.964-0.336-0.3360.0000.0000.0000.000
137B140LEU0-0.039-0.03514.930-0.284-0.2840.0000.0000.0000.000
138B141GLU-1-0.895-0.95018.70511.44111.4410.0000.0000.0000.000
139B142LEU00.0640.04221.901-0.526-0.5260.0000.0000.0000.000
140B143ALA0-0.006-0.00719.821-0.328-0.3280.0000.0000.0000.000
141B144GLY0-0.034-0.03821.809-0.282-0.2820.0000.0000.0000.000
142B145ASN0-0.006-0.01123.730-0.724-0.7240.0000.0000.0000.000
143B146ALA00.0070.02824.494-0.367-0.3670.0000.0000.0000.000
144B147SER0-0.102-0.09826.4400.0450.0450.0000.0000.0000.000
145B148LYS10.9560.96529.882-8.599-8.5990.0000.0000.0000.000
146B149ASP-1-0.855-0.92133.3708.1138.1130.0000.0000.0000.000
147B150LEU0-0.0040.02332.7470.1730.1730.0000.0000.0000.000
148B151LYS10.9270.98426.431-10.769-10.7690.0000.0000.0000.000
149B152VAL0-0.028-0.00823.8400.0210.0210.0000.0000.0000.000
150B153LYS11.0191.01226.270-9.597-9.5970.0000.0000.0000.000
151B154ARG10.9100.95820.952-12.947-12.9470.0000.0000.0000.000
152B155ILE00.0570.04217.849-0.187-0.1870.0000.0000.0000.000
153B156THR0-0.024-0.04118.7420.5950.5950.0000.0000.0000.000
154B157PRO00.038-0.00716.372-0.061-0.0610.0000.0000.0000.000
155B158ARG10.9200.98918.336-11.558-11.5580.0000.0000.0000.000
156B159HIS00.0300.03420.8200.2500.2500.0000.0000.0000.000
157B160LEU00.0380.02114.642-0.152-0.1520.0000.0000.0000.000
158B161GLN00.0140.01718.744-0.543-0.5430.0000.0000.0000.000
159B162LEU0-0.022-0.02220.574-0.308-0.3080.0000.0000.0000.000
160B163ALA00.0150.01920.261-0.367-0.3670.0000.0000.0000.000
161B164ILE0-0.018-0.01516.037-0.116-0.1160.0000.0000.0000.000
162B165ARG10.8730.92620.483-12.232-12.2320.0000.0000.0000.000
163B166GLY0-0.013-0.00423.344-0.503-0.5030.0000.0000.0000.000
164B167ASP-1-0.814-0.90823.46711.87211.8720.0000.0000.0000.000
165B168GLU-1-0.929-0.95224.23310.65410.6540.0000.0000.0000.000
166B169GLU-1-0.771-0.87623.09412.00612.0060.0000.0000.0000.000
167B170LEU00.007-0.01418.1120.8270.8270.0000.0000.0000.000
168B171ASP-1-0.826-0.88719.48813.72313.7230.0000.0000.0000.000
169B172SER0-0.025-0.02120.9070.4380.4380.0000.0000.0000.000
170B173LEU00.0230.01716.1660.4590.4590.0000.0000.0000.000
171B174ILE0-0.026-0.00614.6321.0081.0080.0000.0000.0000.000
172B175LYS10.8050.88816.134-12.258-12.2580.0000.0000.0000.000
173B176ALA00.0320.02318.2290.2980.2980.0000.0000.0000.000
174B177THR0-0.082-0.05512.0030.5140.5140.0000.0000.0000.000
175B178ILE0-0.033-0.02212.4671.1081.1080.0000.0000.0000.000
176B179ALA0-0.0390.00014.7020.1560.1560.0000.0000.0000.000