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: JQM59

Calculation Name: 4IV1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IV1

Chain ID: B

ChEMBL ID:

UniProt ID: Q6PN23

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2368008.516876
FMO2-HF: Nuclear repulsion 2286797.385755
FMO2-HF: Total energy -81211.13112
FMO2-MP2: Total energy -81450.3703


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:12:ASP)


Summations of interaction energy for fragment #1(B:12:ASP)
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.
-69.867-63.2964.186-4.889-5.8680.053
Interaction energy analysis for fragmet #1(B:12:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.897 / q_NPA : -0.964
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].
3B14ILE0-0.038-0.0142.246-31.146-25.4964.041-4.577-5.1140.053
4B15LEU00.0470.0413.4168.1559.0760.145-0.312-0.7540.000
5B16THR0-0.021-0.0316.070-4.325-4.3250.0000.0000.0000.000
6B17THR0-0.024-0.0069.0870.7230.7230.0000.0000.0000.000
7B18ARG10.8940.93011.901-19.037-19.0370.0000.0000.0000.000
8B19ASN0-0.017-0.00314.806-0.497-0.4970.0000.0000.0000.000
9B20GLY00.0840.05118.316-0.571-0.5710.0000.0000.0000.000
10B21HIS0-0.028-0.02319.4861.2111.2110.0000.0000.0000.000
11B22THR0-0.046-0.02819.357-0.331-0.3310.0000.0000.0000.000
12B23THR00.0530.01414.1010.1240.1240.0000.0000.0000.000
13B24SER0-0.104-0.06413.741-1.149-1.1490.0000.0000.0000.000
14B25THR00.0570.0338.4321.6111.6110.0000.0000.0000.000
15B26THR0-0.027-0.0108.418-1.763-1.7630.0000.0000.0000.000
16B27GLN00.0650.0216.5975.5635.5630.0000.0000.0000.000
17B28SER0-0.0040.0097.4860.6620.6620.0000.0000.0000.000
18B29SER0-0.022-0.0046.446-4.820-4.8200.0000.0000.0000.000
19B30VAL00.022-0.0047.1433.3363.3360.0000.0000.0000.000
20B31GLY00.0500.0417.184-1.464-1.4640.0000.0000.0000.000
21B32VAL0-0.023-0.0028.022-1.613-1.6130.0000.0000.0000.000
22B33THR0-0.0070.00810.9220.2210.2210.0000.0000.0000.000
23B34TYR00.0080.00211.9720.0930.0930.0000.0000.0000.000
24B35GLY00.013-0.00716.591-0.338-0.3380.0000.0000.0000.000
25B36TYR0-0.014-0.02820.139-0.215-0.2150.0000.0000.0000.000
26B37SER00.0380.02221.193-0.377-0.3770.0000.0000.0000.000
27B38THR0-0.018-0.00816.9980.3100.3100.0000.0000.0000.000
28B39GLN0-0.039-0.01919.2030.3720.3720.0000.0000.0000.000
29B40GLU-1-0.797-0.89521.97912.26812.2680.0000.0000.0000.000
30B41ASP-1-0.814-0.88725.24010.01510.0150.0000.0000.0000.000
31B42HIS00.0300.00928.8380.3450.3450.0000.0000.0000.000
32B43VAL00.0180.01028.959-0.158-0.1580.0000.0000.0000.000
33B44SER0-0.019-0.02231.850-0.087-0.0870.0000.0000.0000.000
34B45GLY0-0.010-0.00835.307-0.040-0.0400.0000.0000.0000.000
35B46PRO00.011-0.01737.645-0.060-0.0600.0000.0000.0000.000
36B47ASN0-0.044-0.02137.712-0.067-0.0670.0000.0000.0000.000
37B48THR0-0.005-0.02437.696-0.074-0.0740.0000.0000.0000.000
38B49SER0-0.057-0.02440.702-0.100-0.1000.0000.0000.0000.000
39B50GLY00.0090.01039.354-0.133-0.1330.0000.0000.0000.000
40B51LEU0-0.020-0.00240.1020.0090.0090.0000.0000.0000.000
41B52GLU-1-0.822-0.85635.0628.6188.6180.0000.0000.0000.000
42B53THR0-0.010-0.00434.4540.0950.0950.0000.0000.0000.000
43B54ARG10.8380.88523.011-12.488-12.4880.0000.0000.0000.000
44B55VAL00.0080.00529.943-0.124-0.1240.0000.0000.0000.000
45B56VAL00.0420.00725.4160.2890.2890.0000.0000.0000.000
46B57GLN0-0.007-0.00425.7620.5190.5190.0000.0000.0000.000
47B58ALA0-0.009-0.01027.6040.0410.0410.0000.0000.0000.000
48B59GLU-1-0.797-0.85022.72013.21313.2130.0000.0000.0000.000
49B60ARG10.9190.95321.349-12.510-12.5100.0000.0000.0000.000
50B61PHE00.003-0.01215.550-0.470-0.4700.0000.0000.0000.000
51B62PHE0-0.058-0.02321.560-0.578-0.5780.0000.0000.0000.000
52B63LYS10.8980.93219.820-15.113-15.1130.0000.0000.0000.000
53B64LYS10.9290.97224.064-11.403-11.4030.0000.0000.0000.000
54B65HIS0-0.0230.00224.7130.3630.3630.0000.0000.0000.000
55B66LEU0-0.065-0.03123.595-0.292-0.2920.0000.0000.0000.000
56B67PHE00.0900.02825.311-0.375-0.3750.0000.0000.0000.000
57B68ASP-1-0.798-0.87926.74711.57011.5700.0000.0000.0000.000
58B69TRP00.0120.00721.329-0.213-0.2130.0000.0000.0000.000
59B70THR0-0.041-0.07327.4220.2930.2930.0000.0000.0000.000
60B71PRO00.014-0.00729.6520.0110.0110.0000.0000.0000.000
61B72ASP-1-0.854-0.87630.8959.5029.5020.0000.0000.0000.000
62B73LYS10.8590.94630.191-10.333-10.3330.0000.0000.0000.000
63B74ALA00.0420.01230.7200.2640.2640.0000.0000.0000.000
64B75PHE00.000-0.00528.2890.1770.1770.0000.0000.0000.000
65B76GLY00.0070.00229.348-0.348-0.3480.0000.0000.0000.000
66B77HIS0-0.073-0.04129.670-0.350-0.3500.0000.0000.0000.000
67B78LEU0-0.038-0.02929.1710.4050.4050.0000.0000.0000.000
68B79GLU-1-0.823-0.88028.3639.9529.9520.0000.0000.0000.000
69B80LYS10.8520.91828.395-8.981-8.9810.0000.0000.0000.000
70B81LEU0-0.025-0.01926.289-0.223-0.2230.0000.0000.0000.000
71B82GLU-1-0.865-0.91828.4749.5219.5210.0000.0000.0000.000
72B83LEU0-0.078-0.01325.0110.0690.0690.0000.0000.0000.000
73B84PRO00.0400.01129.499-0.138-0.1380.0000.0000.0000.000
74B85THR00.0400.01328.976-0.317-0.3170.0000.0000.0000.000
75B86ASP-1-0.860-0.91331.6829.0349.0340.0000.0000.0000.000
76B87HIS00.0120.00627.186-0.013-0.0130.0000.0000.0000.000
77B88LYS10.8740.91131.849-9.169-9.1690.0000.0000.0000.000
78B89GLY00.0300.02230.717-0.053-0.0530.0000.0000.0000.000
79B90VAL00.010-0.00729.837-0.203-0.2030.0000.0000.0000.000
80B91TYR00.003-0.03128.698-0.289-0.2890.0000.0000.0000.000
81B92GLY00.0220.01130.835-0.206-0.2060.0000.0000.0000.000
82B93HIS00.0230.01733.673-0.188-0.1880.0000.0000.0000.000
83B94LEU0-0.016-0.00531.464-0.230-0.2300.0000.0000.0000.000
84B95VAL00.021-0.00233.833-0.228-0.2280.0000.0000.0000.000
85B96ASP-1-0.845-0.91636.4797.5907.5900.0000.0000.0000.000
86B97SER0-0.0310.00738.643-0.255-0.2550.0000.0000.0000.000
87B98PHE00.0130.01437.185-0.086-0.0860.0000.0000.0000.000
88B99ALA0-0.030-0.00339.4880.0630.0630.0000.0000.0000.000
89B100TYR0-0.043-0.03038.071-0.018-0.0180.0000.0000.0000.000
90B101MET0-0.018-0.00631.9900.0590.0590.0000.0000.0000.000
91B102ARG10.8070.90428.047-10.646-10.6460.0000.0000.0000.000
92B103ASN0-0.0130.01026.046-0.420-0.4200.0000.0000.0000.000
93B104GLY00.0820.06123.743-0.256-0.2560.0000.0000.0000.000
94B105TRP0-0.025-0.01522.175-0.185-0.1850.0000.0000.0000.000
95B106ASP-1-0.740-0.83315.94620.52720.5270.0000.0000.0000.000
96B107VAL0-0.009-0.02517.914-0.407-0.4070.0000.0000.0000.000
97B108GLU-1-0.767-0.85412.85024.75424.7540.0000.0000.0000.000
98B109VAL0-0.004-0.00816.678-1.151-1.1510.0000.0000.0000.000
99B110SER0-0.034-0.02216.2350.9140.9140.0000.0000.0000.000
100B111ALA00.025-0.00317.454-1.157-1.1570.0000.0000.0000.000
101B112VAL0-0.011-0.01416.7230.5890.5890.0000.0000.0000.000
102B113GLY00.0590.03019.044-0.942-0.9420.0000.0000.0000.000
103B114ASN0-0.030-0.02618.7630.4150.4150.0000.0000.0000.000
104B115GLN00.0530.01316.478-0.396-0.3960.0000.0000.0000.000
105B116PHE0-0.034-0.01818.366-0.129-0.1290.0000.0000.0000.000
106B117ASN0-0.035-0.01221.315-0.347-0.3470.0000.0000.0000.000
107B118GLY00.0320.01821.3330.6350.6350.0000.0000.0000.000
108B119GLY00.0560.02922.469-0.313-0.3130.0000.0000.0000.000
109B120CYS0-0.120-0.06819.1630.8340.8340.0000.0000.0000.000
110B121LEU00.0400.03520.369-0.718-0.7180.0000.0000.0000.000
111B122LEU00.0150.00919.9740.8100.8100.0000.0000.0000.000
112B123VAL0-0.010-0.01118.824-0.473-0.4730.0000.0000.0000.000
113B124ALA00.0450.00520.0910.5080.5080.0000.0000.0000.000
114B125MET0-0.0230.01621.144-0.249-0.2490.0000.0000.0000.000
115B126VAL0-0.002-0.02123.654-0.029-0.0290.0000.0000.0000.000
116B127PRO0-0.0040.00726.914-0.071-0.0710.0000.0000.0000.000
117B128GLU-1-0.835-0.91129.3308.9858.9850.0000.0000.0000.000
118B129TRP0-0.031-0.01930.1630.1080.1080.0000.0000.0000.000
119B130LYS10.8650.90732.996-8.892-8.8920.0000.0000.0000.000
120B131GLU-1-0.856-0.93134.6039.1649.1640.0000.0000.0000.000
121B132PHE0-0.0230.00530.804-0.189-0.1890.0000.0000.0000.000
122B133THR0-0.008-0.04034.985-0.062-0.0620.0000.0000.0000.000
123B134PRO00.030-0.01435.0670.2400.2400.0000.0000.0000.000
124B135ARG10.9770.98034.279-7.673-7.6730.0000.0000.0000.000
125B136GLU-1-0.732-0.82733.3148.7948.7940.0000.0000.0000.000
126B137LYS10.8970.95430.474-9.187-9.1870.0000.0000.0000.000
127B138TYR0-0.042-0.02028.8890.2930.2930.0000.0000.0000.000
128B139GLN0-0.027-0.01728.1080.1970.1970.0000.0000.0000.000
129B140LEU00.0290.01626.2850.0870.0870.0000.0000.0000.000
130B141THR0-0.012-0.00321.9710.1370.1370.0000.0000.0000.000
131B142LEU0-0.0120.00423.0660.3240.3240.0000.0000.0000.000
132B143PHE0-0.032-0.00124.447-0.038-0.0380.0000.0000.0000.000
133B144PRO00.0140.01320.0350.5370.5370.0000.0000.0000.000
134B145HIS0-0.041-0.02918.9200.0740.0740.0000.0000.0000.000
135B146GLN00.005-0.00711.6540.9810.9810.0000.0000.0000.000
136B147PHE00.0420.01615.502-0.986-0.9860.0000.0000.0000.000
137B148ILE0-0.0100.01015.2421.3121.3120.0000.0000.0000.000
138B149SER0-0.007-0.01715.820-1.253-1.2530.0000.0000.0000.000
139B150PRO00.0310.02815.8851.2481.2480.0000.0000.0000.000
140B151ARG10.9500.99016.217-16.111-16.1110.0000.0000.0000.000
141B152THR0-0.059-0.03511.0790.6220.6220.0000.0000.0000.000
142B153ASN0-0.011-0.02511.2631.8331.8330.0000.0000.0000.000
143B154MET00.0310.03712.663-2.084-2.0840.0000.0000.0000.000
144B155THR0-0.016-0.00911.823-0.583-0.5830.0000.0000.0000.000
145B156ALA00.0210.03812.9721.0981.0980.0000.0000.0000.000
146B157HIS10.7850.85411.919-23.918-23.9180.0000.0000.0000.000
147B158ILE0-0.0190.00313.8670.4670.4670.0000.0000.0000.000
148B159VAL0-0.0070.00814.924-0.257-0.2570.0000.0000.0000.000
149B160VAL0-0.025-0.01017.533-0.144-0.1440.0000.0000.0000.000
150B161PRO00.0390.03721.0720.0390.0390.0000.0000.0000.000
151B162TYR0-0.005-0.02023.711-0.160-0.1600.0000.0000.0000.000
152B163LEU0-0.044-0.02127.1470.0060.0060.0000.0000.0000.000
153B164GLY00.0620.01729.710-0.068-0.0680.0000.0000.0000.000
154B165VAL0-0.035-0.01733.281-0.021-0.0210.0000.0000.0000.000
155B166ASN0-0.0080.01536.271-0.297-0.2970.0000.0000.0000.000
156B167ARG10.9360.98533.806-8.708-8.7080.0000.0000.0000.000
157B168TYR0-0.015-0.02633.7990.3030.3030.0000.0000.0000.000
158B169ASP-1-0.755-0.85934.5588.6828.6820.0000.0000.0000.000
159B170GLN00.0320.01936.420-0.147-0.1470.0000.0000.0000.000
160B171TYR00.045-0.01130.143-0.177-0.1770.0000.0000.0000.000
161B172LYS10.7770.87736.184-7.980-7.9800.0000.0000.0000.000
162B173LYS10.8590.91939.184-7.535-7.5350.0000.0000.0000.000
163B174HIS10.7420.83534.309-9.070-9.0700.0000.0000.0000.000
164B175LYS10.8980.95132.588-9.217-9.2170.0000.0000.0000.000
165B176PRO00.0280.02830.2430.0270.0270.0000.0000.0000.000
166B177TRP00.0120.00024.5250.1960.1960.0000.0000.0000.000
167B178THR0-0.018-0.00727.949-0.278-0.2780.0000.0000.0000.000
168B179LEU0-0.0040.00521.9310.2990.2990.0000.0000.0000.000
169B180VAL0-0.008-0.00924.776-0.483-0.4830.0000.0000.0000.000
170B181VAL0-0.011-0.01022.9630.6950.6950.0000.0000.0000.000
171B182MET0-0.0190.00724.513-0.698-0.6980.0000.0000.0000.000
172B183VAL0-0.0040.01024.7250.6010.6010.0000.0000.0000.000
173B184VAL0-0.029-0.00822.720-0.420-0.4200.0000.0000.0000.000
174B185SER00.005-0.01524.273-0.535-0.5350.0000.0000.0000.000
175B186PRO00.0470.01525.3890.4620.4620.0000.0000.0000.000
176B187LEU0-0.0190.01224.1640.2680.2680.0000.0000.0000.000
177B188THR00.006-0.00125.675-0.318-0.3180.0000.0000.0000.000
178B189THR00.0180.00026.0990.4180.4180.0000.0000.0000.000
179B190ASN0-0.080-0.04326.633-0.057-0.0570.0000.0000.0000.000
180B191THR00.0380.01228.8140.0860.0860.0000.0000.0000.000
181B192VAL00.0370.01925.302-0.051-0.0510.0000.0000.0000.000
182B193SER0-0.0300.01224.2510.3910.3910.0000.0000.0000.000
183B194ALA00.0180.02623.773-0.377-0.3770.0000.0000.0000.000
184B195GLY00.0350.01025.621-0.139-0.1390.0000.0000.0000.000
185B196GLN0-0.001-0.00827.228-0.144-0.1440.0000.0000.0000.000
186B197ILE0-0.0270.00321.2910.3260.3260.0000.0000.0000.000
187B198LYS10.8310.91624.158-11.489-11.4890.0000.0000.0000.000
188B199VAL0-0.0110.00021.6100.7580.7580.0000.0000.0000.000
189B200TYR00.007-0.00121.033-0.786-0.7860.0000.0000.0000.000
190B201ALA00.0340.01920.5260.7600.7600.0000.0000.0000.000
191B202ASN0-0.037-0.01716.339-1.637-1.6370.0000.0000.0000.000
192B203ILE00.0340.00319.0990.6870.6870.0000.0000.0000.000
193B204ALA00.0160.02019.743-0.422-0.4220.0000.0000.0000.000
194B205PRO0-0.0330.01521.7290.1670.1670.0000.0000.0000.000
195B206THR00.014-0.01619.8660.0980.0980.0000.0000.0000.000
196B207HIS0-0.048-0.03721.222-0.227-0.2270.0000.0000.0000.000
197B208VAL0-0.0130.00725.457-0.377-0.3770.0000.0000.0000.000
198B209HIS0-0.018-0.01927.847-0.101-0.1010.0000.0000.0000.000
199B210VAL0-0.023-0.00631.7020.0010.0010.0000.0000.0000.000
200B211ALA00.0640.01735.129-0.039-0.0390.0000.0000.0000.000
201B212GLY00.0240.01238.678-0.009-0.0090.0000.0000.0000.000
202B213GLU-1-0.915-0.94841.7187.7007.7000.0000.0000.0000.000
203B214LEU0-0.052-0.02642.190-0.206-0.2060.0000.0000.0000.000
204B215PRO0-0.0120.00244.8020.0170.0170.0000.0000.0000.000
205B216SER00.0130.00146.3820.1200.1200.0000.0000.0000.000
206B217LYS10.8270.88243.297-7.575-7.5750.0000.0000.0000.000
207B218GLU-1-0.961-0.95648.6806.4466.4460.0000.0000.0000.000