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: 6NR9Z

Calculation Name: 5IFH-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFH

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 -1662731.264028
FMO2-HF: Nuclear repulsion 1594552.947362
FMO2-HF: Total energy -68178.316666
FMO2-MP2: Total energy -68375.303025


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(H:2:VAL)


Summations of interaction energy for fragment #1(H:2: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.
-11.708-4.64910.83-6.163-11.725-0.034
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.031
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].
3H4LEU0-0.006-0.0063.879-0.4231.576-0.024-1.029-0.9460.001
4H5VAL00.0250.0096.656-0.098-0.0980.0000.0000.0000.000
5H6GLU-1-0.768-0.87510.323-0.135-0.1350.0000.0000.0000.000
6H7SER0-0.044-0.03013.3780.0340.0340.0000.0000.0000.000
7H8GLY00.0410.00816.949-0.011-0.0110.0000.0000.0000.000
8H9GLY00.0140.01919.729-0.010-0.0100.0000.0000.0000.000
9H10GLY0-0.009-0.01521.3720.0140.0140.0000.0000.0000.000
10H11LEU0-0.056-0.02524.994-0.011-0.0110.0000.0000.0000.000
11H12VAL0-0.015-0.00627.4650.0070.0070.0000.0000.0000.000
12H13LYS10.8490.91830.266-0.014-0.0140.0000.0000.0000.000
13H14PRO00.016-0.00532.9580.0020.0020.0000.0000.0000.000
14H15GLY0-0.0150.00133.5960.0020.0020.0000.0000.0000.000
15H16GLY0-0.0080.00432.2130.0030.0030.0000.0000.0000.000
16H17SER0-0.018-0.03728.440-0.006-0.0060.0000.0000.0000.000
17H18LEU0-0.039-0.01223.4040.0020.0020.0000.0000.0000.000
18H19ARG10.8570.93420.520-0.098-0.0980.0000.0000.0000.000
19H20LEU00.0190.03117.7280.0110.0110.0000.0000.0000.000
20H21SER0-0.005-0.01716.0670.0160.0160.0000.0000.0000.000
21H22CYS0-0.082-0.02910.3280.0230.0230.0000.0000.0000.000
22H23ALA00.0190.02610.2680.0290.0290.0000.0000.0000.000
23H24ALA00.0190.0016.403-0.125-0.1250.0000.0000.0000.000
24H25SER0-0.034-0.0174.6000.2730.429-0.001-0.051-0.1040.000
25H26GLY00.0830.0282.428-1.997-0.2444.408-3.432-2.729-0.014
26H27PHE0-0.014-0.0062.378-5.757-3.9843.471-0.716-4.528-0.015
27H28THR00.0110.0014.157-0.0500.0450.001-0.038-0.0580.000
28H29PHE00.0640.0337.287-0.168-0.1680.0000.0000.0000.000
29H30ARG10.9840.9818.113-0.343-0.3430.0000.0000.0000.000
30H31SER0-0.043-0.0259.297-0.037-0.0370.0000.0000.0000.000
31H32TYR00.0190.0215.9740.0100.0100.0000.0000.0000.000
32H33SER00.010-0.0039.4200.0630.0630.0000.0000.0000.000
33H34MET0-0.054-0.0108.108-0.011-0.0110.0000.0000.0000.000
34H35ASN0-0.013-0.00110.9390.0460.0460.0000.0000.0000.000
35H36TRP00.0130.00612.580-0.016-0.0160.0000.0000.0000.000
36H37VAL0-0.012-0.00614.4530.0060.0060.0000.0000.0000.000
37H38ARG10.7860.86716.4460.0680.0680.0000.0000.0000.000
38H39GLN00.0220.01919.029-0.025-0.0250.0000.0000.0000.000
39H40ALA00.0460.03420.9680.0090.0090.0000.0000.0000.000
40H41PRO00.018-0.01324.471-0.011-0.0110.0000.0000.0000.000
41H42GLY00.0240.02624.9680.0050.0050.0000.0000.0000.000
42H43LYS10.8600.93624.6830.0960.0960.0000.0000.0000.000
43H44GLY00.0620.03122.734-0.013-0.0130.0000.0000.0000.000
44H45LEU0-0.009-0.00316.2660.0090.0090.0000.0000.0000.000
45H46GLU-1-0.787-0.85020.266-0.074-0.0740.0000.0000.0000.000
46H47TRP0-0.008-0.01816.8480.0020.0020.0000.0000.0000.000
47H48VAL0-0.0090.00218.5190.0160.0160.0000.0000.0000.000
48H49SER0-0.010-0.03818.3070.0220.0220.0000.0000.0000.000
49H50SER00.002-0.00915.511-0.017-0.0170.0000.0000.0000.000
50H51ILE0-0.044-0.01714.6340.0170.0170.0000.0000.0000.000
51H52ILE00.0280.01814.422-0.004-0.0040.0000.0000.0000.000
52H53SER00.0230.01712.2980.0250.0250.0000.0000.0000.000
53H54SER0-0.036-0.03614.336-0.017-0.0170.0000.0000.0000.000
54H55SER0-0.0040.00917.2520.0100.0100.0000.0000.0000.000
55H56SER0-0.058-0.02217.8930.0070.0070.0000.0000.0000.000
56H57TYR00.0360.02118.8900.0010.0010.0000.0000.0000.000
57H58ILE00.0070.00119.250-0.003-0.0030.0000.0000.0000.000
58H59TYR00.0020.00619.624-0.003-0.0030.0000.0000.0000.000
59H60TYR00.0260.01521.1000.0020.0020.0000.0000.0000.000
60H61ALA00.0710.04722.9800.0000.0000.0000.0000.0000.000
61H62ASP-1-0.839-0.92524.621-0.041-0.0410.0000.0000.0000.000
62H63SER0-0.022-0.00825.5920.0060.0060.0000.0000.0000.000
63H64VAL0-0.017-0.01823.1810.0050.0050.0000.0000.0000.000
64H65LYS10.8430.91326.6470.0520.0520.0000.0000.0000.000
65H66GLY00.0020.00627.8290.0010.0010.0000.0000.0000.000
66H67ARG10.7010.82728.0770.0260.0260.0000.0000.0000.000
67H68PHE00.011-0.00922.5710.0070.0070.0000.0000.0000.000
68H69THR0-0.048-0.03223.5290.0010.0010.0000.0000.0000.000
69H70ILE00.0090.02415.7870.0120.0120.0000.0000.0000.000
70H71SER0-0.006-0.01418.3240.0110.0110.0000.0000.0000.000
71H72ARG10.8130.90610.743-0.128-0.1280.0000.0000.0000.000
72H73ASP-1-0.796-0.87515.0160.2760.2760.0000.0000.0000.000
73H74ASN00.004-0.02313.3310.0580.0580.0000.0000.0000.000
74H75ALA0-0.0030.01213.9500.0400.0400.0000.0000.0000.000
75H76LYS10.8430.90914.168-0.252-0.2520.0000.0000.0000.000
76H77ASN0-0.0130.0068.877-0.063-0.0630.0000.0000.0000.000
77H78SER00.0580.02510.1490.0360.0360.0000.0000.0000.000
78H79LEU0-0.0100.00011.722-0.033-0.0330.0000.0000.0000.000
79H80TYR0-0.014-0.03313.839-0.001-0.0010.0000.0000.0000.000
80H81LEU00.0180.00717.214-0.018-0.0180.0000.0000.0000.000
81H82GLN00.0060.01719.5270.0130.0130.0000.0000.0000.000
82H83MET0-0.019-0.00122.539-0.015-0.0150.0000.0000.0000.000
83H84ASN00.0610.02525.2050.0120.0120.0000.0000.0000.000
84H85SER00.0300.02029.034-0.004-0.0040.0000.0000.0000.000
85H86LEU0-0.0170.01526.094-0.006-0.0060.0000.0000.0000.000
86H87ARG10.9200.94829.9010.0300.0300.0000.0000.0000.000
87H88ALA00.0620.03530.048-0.002-0.0020.0000.0000.0000.000
88H89GLU-1-0.835-0.93029.863-0.036-0.0360.0000.0000.0000.000
89H90ASP-1-0.765-0.83325.868-0.038-0.0380.0000.0000.0000.000
90H91THR0-0.0160.00524.9970.0010.0010.0000.0000.0000.000
91H92ALA0-0.012-0.01421.902-0.008-0.0080.0000.0000.0000.000
92H93LEU0-0.0210.01717.1780.0200.0200.0000.0000.0000.000
93H94TYR0-0.025-0.04617.422-0.016-0.0160.0000.0000.0000.000
94H95TYR00.0240.00012.4400.0140.0140.0000.0000.0000.000
95H97ALA00.0500.0128.226-0.102-0.1020.0000.0000.0000.000
96H98ARG10.7790.8482.978-0.3070.7521.036-0.468-1.626-0.005
97H99ASP-1-0.845-0.9147.687-0.439-0.4390.0000.0000.0000.000
98H100GLN00.0160.0149.5660.0530.0530.0000.0000.0000.000
99H101ASN0-0.026-0.01312.810-0.023-0.0230.0000.0000.0000.000
100H102ALA00.010-0.01012.4240.0120.0120.0000.0000.0000.000
101H103MET0-0.0370.0039.847-0.023-0.0230.0000.0000.0000.000
102H104ASP-1-0.731-0.8284.656-1.521-1.412-0.001-0.007-0.1010.000
103H105VAL0-0.036-0.0122.289-0.731-0.6701.941-0.422-1.580-0.001
104H106TRP0-0.006-0.0285.2710.3450.399-0.0010.000-0.0530.000
105H107GLY00.0210.0226.864-0.256-0.2560.0000.0000.0000.000
106H108GLN0-0.053-0.0369.031-0.028-0.0280.0000.0000.0000.000
107H109GLY00.0020.00512.4310.0240.0240.0000.0000.0000.000
108H110THR0-0.048-0.02814.5350.0360.0360.0000.0000.0000.000
109H111THR00.0370.00917.607-0.014-0.0140.0000.0000.0000.000
110H112VAL0-0.0050.00721.1700.0190.0190.0000.0000.0000.000
111H113THR0-0.017-0.01323.732-0.011-0.0110.0000.0000.0000.000
112H114VAL0-0.004-0.00227.3860.0080.0080.0000.0000.0000.000
113H115SER00.016-0.02930.009-0.004-0.0040.0000.0000.0000.000
114H116SER00.0360.00133.4650.0040.0040.0000.0000.0000.000
115H117ASP-1-0.850-0.86634.893-0.007-0.0070.0000.0000.0000.000
116H118SER0-0.010-0.01735.3680.0020.0020.0000.0000.0000.000
117H119ALA00.0130.01332.019-0.003-0.0030.0000.0000.0000.000
118H120SER0-0.036-0.03633.3150.0010.0010.0000.0000.0000.000
119H121ALA00.0080.01432.808-0.002-0.0020.0000.0000.0000.000
120H122PRO0-0.0020.00831.599-0.003-0.0030.0000.0000.0000.000
121H123THR00.0000.00834.7020.0050.0050.0000.0000.0000.000
122H124LEU00.014-0.00333.804-0.003-0.0030.0000.0000.0000.000
123H125PHE0-0.010-0.00638.0830.0030.0030.0000.0000.0000.000
124H126PRO00.0170.01839.451-0.002-0.0020.0000.0000.0000.000
125H127LEU0-0.019-0.00338.790-0.001-0.0010.0000.0000.0000.000
126H128VAL00.018-0.00741.4850.0010.0010.0000.0000.0000.000
127H129SER00.0220.02743.834-0.001-0.0010.0000.0000.0000.000
128H142VAL0-0.015-0.01437.9670.0000.0000.0000.0000.0000.000
129H143GLY00.0410.01036.833-0.003-0.0030.0000.0000.0000.000
130H144CYS0-0.064-0.00633.1710.0040.0040.0000.0000.0000.000
131H145LEU00.0230.03635.454-0.003-0.0030.0000.0000.0000.000
132H146ALA00.0180.00133.6880.0050.0050.0000.0000.0000.000
133H147GLN0-0.001-0.01035.696-0.007-0.0070.0000.0000.0000.000
134H148ASP-1-0.758-0.87636.743-0.001-0.0010.0000.0000.0000.000
135H149PHE0-0.0160.03530.2700.0050.0050.0000.0000.0000.000
136H150LEU0-0.008-0.00331.645-0.005-0.0050.0000.0000.0000.000
137H151PRO00.0780.02727.1540.0060.0060.0000.0000.0000.000
138H152ASP-1-0.813-0.88827.832-0.034-0.0340.0000.0000.0000.000
139H153SER0-0.064-0.04224.531-0.005-0.0050.0000.0000.0000.000
140H154ILE00.0200.02125.7390.0120.0120.0000.0000.0000.000
141H155THR0-0.048-0.01522.896-0.010-0.0100.0000.0000.0000.000
142H156PHE00.0390.00425.9530.0080.0080.0000.0000.0000.000
143H157SER0-0.018-0.00726.0650.0020.0020.0000.0000.0000.000
144H158TRP00.0550.02227.9350.0040.0040.0000.0000.0000.000
145H171GLY00.0130.00328.5720.0040.0040.0000.0000.0000.000
146H172PHE0-0.0260.00529.408-0.007-0.0070.0000.0000.0000.000
147H173PRO0-0.009-0.00128.7180.0030.0030.0000.0000.0000.000
148H174SER0-0.041-0.05529.2770.0060.0060.0000.0000.0000.000
149H175VAL0-0.031-0.01031.406-0.005-0.0050.0000.0000.0000.000
150H176LEU0-0.030-0.00234.0950.0050.0050.0000.0000.0000.000
151H177ARG10.8430.87935.6090.0120.0120.0000.0000.0000.000
152H178GLY00.0170.01139.2260.0020.0020.0000.0000.0000.000
153H179GLY00.0460.03037.4100.0020.0020.0000.0000.0000.000
154H180LYS10.7990.89535.370-0.001-0.0010.0000.0000.0000.000
155H181TYR00.0480.01530.739-0.002-0.0020.0000.0000.0000.000
156H182ALA0-0.033-0.00834.3390.0050.0050.0000.0000.0000.000
157H183ALA00.0580.03431.490-0.005-0.0050.0000.0000.0000.000
158H184THR0-0.015-0.02733.0700.0050.0050.0000.0000.0000.000
159H185SER0-0.0030.00330.702-0.003-0.0030.0000.0000.0000.000
160H186GLN00.026-0.01132.7980.0010.0010.0000.0000.0000.000
161H187VAL0-0.0100.02132.078-0.003-0.0030.0000.0000.0000.000
162H203VAL0-0.013-0.01833.9450.0000.0000.0000.0000.0000.000
163H205LYS10.8820.91929.597-0.049-0.0490.0000.0000.0000.000
164H206VAL00.0140.02128.740-0.005-0.0050.0000.0000.0000.000
165H207GLN0-0.021-0.02823.9530.0020.0020.0000.0000.0000.000
166H208HIS00.0610.01226.808-0.005-0.0050.0000.0000.0000.000
167H209PRO00.0080.01925.0490.0090.0090.0000.0000.0000.000
168H210ASN0-0.022-0.01526.8310.0020.0020.0000.0000.0000.000
169H211GLY00.004-0.00329.7010.0010.0010.0000.0000.0000.000
170H212ASN0-0.047-0.02926.439-0.002-0.0020.0000.0000.0000.000
171H213LYS10.9280.97830.380-0.033-0.0330.0000.0000.0000.000
172H214GLU-1-0.843-0.90932.3260.0470.0470.0000.0000.0000.000
173H215LYS10.8700.92534.822-0.016-0.0160.0000.0000.0000.000
174H216ASN00.0020.00637.1950.0000.0000.0000.0000.0000.000
175H217VAL00.0110.00537.532-0.002-0.0020.0000.0000.0000.000
176H218PRO0-0.0040.01540.1780.0010.0010.0000.0000.0000.000