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: R9418

Calculation Name: 1JRH-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JRH

Chain ID: H

ChEMBL ID:

UniProt ID: P01869

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1730780.612207
FMO2-HF: Nuclear repulsion 1660200.663987
FMO2-HF: Total energy -70579.94822
FMO2-MP2: Total energy -70785.472197


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:1:ALA)


Summations of interaction energy for fragment #1(H:1:ALA)
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.
0.1932.123-8.673617379884E-19-0.761-1.1690.003
Interaction energy analysis for fragmet #1(H:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.004
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].
3H3LYS10.9450.9913.8650.7592.070-0.012-0.551-0.7480.002
4H4LEU00.010-0.0225.8430.2650.2650.0000.0000.0000.000
5H5GLN00.0000.0069.670-0.051-0.0510.0000.0000.0000.000
6H6GLU-1-0.742-0.86412.259-0.255-0.2550.0000.0000.0000.000
7H7SER0-0.074-0.03316.035-0.011-0.0110.0000.0000.0000.000
8H8GLY00.0580.00818.4400.0190.0190.0000.0000.0000.000
9H9PRO0-0.033-0.01522.110-0.007-0.0070.0000.0000.0000.000
10H10GLY00.0330.04124.9350.0020.0020.0000.0000.0000.000
11H11ILE0-0.019-0.01725.9700.0050.0050.0000.0000.0000.000
12H12LEU0-0.048-0.01329.260-0.001-0.0010.0000.0000.0000.000
13H13LYS10.9800.99131.5770.0610.0610.0000.0000.0000.000
14H14PRO00.0660.01434.758-0.001-0.0010.0000.0000.0000.000
15H15SER0-0.030-0.01736.9600.0000.0000.0000.0000.0000.000
16H16GLN0-0.0090.01633.712-0.001-0.0010.0000.0000.0000.000
17H17THR00.003-0.01630.1640.0040.0040.0000.0000.0000.000
18H18LEU0-0.015-0.00225.543-0.005-0.0050.0000.0000.0000.000
19H19SER0-0.036-0.01925.0590.0080.0080.0000.0000.0000.000
20H20LEU00.0090.01621.269-0.011-0.0110.0000.0000.0000.000
21H21THR0-0.016-0.01416.8970.0180.0180.0000.0000.0000.000
22H22CYS0-0.040-0.00114.636-0.018-0.0180.0000.0000.0000.000
23H23SER00.0470.02512.5700.0550.0550.0000.0000.0000.000
24H24PHE0-0.0210.0019.150-0.098-0.0980.0000.0000.0000.000
25H25SER00.0290.0014.4020.0880.204-0.001-0.013-0.1010.000
26H26GLY00.0300.0103.529-1.137-0.8460.014-0.172-0.1330.001
27H27PHE0-0.006-0.0134.3240.9601.172-0.001-0.025-0.1870.000
28H28SER00.0620.0327.942-0.280-0.2800.0000.0000.0000.000
29H29LEU00.0130.01311.3620.0150.0150.0000.0000.0000.000
30H30THR00.0410.01214.518-0.002-0.0020.0000.0000.0000.000
31H31THR0-0.059-0.03113.3650.0190.0190.0000.0000.0000.000
32H32TYR00.0330.00515.948-0.022-0.0220.0000.0000.0000.000
33H33GLY00.0290.03418.0350.0260.0260.0000.0000.0000.000
34H34MET0-0.041-0.00511.771-0.012-0.0120.0000.0000.0000.000
35H35GLY00.0520.01015.396-0.027-0.0270.0000.0000.0000.000
36H35VAL0-0.055-0.02113.7720.0060.0060.0000.0000.0000.000
37H35GLY00.0480.03716.4920.0090.0090.0000.0000.0000.000
38H36TRP0-0.031-0.01818.205-0.032-0.0320.0000.0000.0000.000
39H37ILE0-0.019-0.01218.2890.0190.0190.0000.0000.0000.000
40H38ARG10.8420.92421.2270.0340.0340.0000.0000.0000.000
41H39GLN00.0520.02221.9220.0160.0160.0000.0000.0000.000
42H40SER00.0100.00025.217-0.007-0.0070.0000.0000.0000.000
43H41SER00.011-0.01827.718-0.001-0.0010.0000.0000.0000.000
44H42GLY00.0060.00928.2890.0050.0050.0000.0000.0000.000
45H43LYS10.9210.97228.5590.0490.0490.0000.0000.0000.000
46H44GLY00.0390.02627.283-0.003-0.0030.0000.0000.0000.000
47H45LEU0-0.005-0.00121.322-0.005-0.0050.0000.0000.0000.000
48H46GLU-1-0.854-0.91525.124-0.030-0.0300.0000.0000.0000.000
49H47TRP00.0220.01322.483-0.006-0.0060.0000.0000.0000.000
50H48LEU0-0.021-0.01223.9800.0020.0020.0000.0000.0000.000
51H49ALA00.028-0.00423.8020.0070.0070.0000.0000.0000.000
52H50HIS0-0.004-0.00318.186-0.025-0.0250.0000.0000.0000.000
53H51ILE0-0.076-0.02019.2700.0010.0010.0000.0000.0000.000
54H52TRP00.0730.02918.9180.0160.0160.0000.0000.0000.000
55H53TRP00.0700.01318.199-0.008-0.0080.0000.0000.0000.000
56H54ASP-1-0.892-0.95319.4680.0920.0920.0000.0000.0000.000
57H55ASP-1-0.870-0.92122.4640.0160.0160.0000.0000.0000.000
58H56ASP-1-0.832-0.87824.0040.0390.0390.0000.0000.0000.000
59H57LYS10.7560.84024.146-0.020-0.0200.0000.0000.0000.000
60H58TYR0-0.0170.00624.9140.0020.0020.0000.0000.0000.000
61H59TYR00.0250.00325.913-0.008-0.0080.0000.0000.0000.000
62H60ASN00.0170.01628.2850.0090.0090.0000.0000.0000.000
63H61PRO0-0.014-0.02929.736-0.003-0.0030.0000.0000.0000.000
64H62SER00.0120.00633.0970.0000.0000.0000.0000.0000.000
65H63LEU00.0070.00530.418-0.002-0.0020.0000.0000.0000.000
66H64LYS10.9710.99631.444-0.007-0.0070.0000.0000.0000.000
67H65SER0-0.013-0.01032.447-0.002-0.0020.0000.0000.0000.000
68H66ARG10.7720.88032.5310.0390.0390.0000.0000.0000.000
69H67LEU0-0.020-0.00627.338-0.006-0.0060.0000.0000.0000.000
70H68THR0-0.011-0.01027.6860.0070.0070.0000.0000.0000.000
71H69ILE0-0.014-0.00520.882-0.011-0.0110.0000.0000.0000.000
72H70SER0-0.003-0.00422.8940.0080.0080.0000.0000.0000.000
73H71LYS10.8360.91618.145-0.080-0.0800.0000.0000.0000.000
74H72ASP-1-0.754-0.82618.149-0.025-0.0250.0000.0000.0000.000
75H73THR00.045-0.00215.057-0.025-0.0250.0000.0000.0000.000
76H74SER0-0.092-0.04515.1750.0050.0050.0000.0000.0000.000
77H75ARG10.8600.90115.5810.0720.0720.0000.0000.0000.000
78H76ASN0-0.050-0.00610.8130.0050.0050.0000.0000.0000.000
79H77GLN0-0.008-0.02112.871-0.044-0.0440.0000.0000.0000.000
80H78VAL00.0010.01315.5110.0430.0430.0000.0000.0000.000
81H79PHE0-0.036-0.03117.836-0.029-0.0290.0000.0000.0000.000
82H80LEU00.0130.00421.0630.0180.0180.0000.0000.0000.000
83H81LYS10.9040.93923.8520.0600.0600.0000.0000.0000.000
84H82ILE00.0230.01626.1790.0070.0070.0000.0000.0000.000
85H82THR00.0470.03529.773-0.004-0.0040.0000.0000.0000.000
86H82SER00.0450.01033.3590.0000.0000.0000.0000.0000.000
87H82VAL0-0.063-0.01431.1850.0010.0010.0000.0000.0000.000
88H83ALA00.0590.02433.9090.0020.0020.0000.0000.0000.000
89H84THR00.0550.00933.786-0.003-0.0030.0000.0000.0000.000
90H85ALA00.0070.00433.624-0.004-0.0040.0000.0000.0000.000
91H86ASP-1-0.791-0.87330.192-0.048-0.0480.0000.0000.0000.000
92H87THR00.0000.02729.026-0.008-0.0080.0000.0000.0000.000
93H88ALA0-0.050-0.01926.1310.0050.0050.0000.0000.0000.000
94H89THR00.0040.01120.277-0.009-0.0090.0000.0000.0000.000
95H90TYR0-0.089-0.06021.1240.0130.0130.0000.0000.0000.000
96H91TYR00.0280.01716.250-0.014-0.0140.0000.0000.0000.000
97H93ALA00.0320.01213.542-0.045-0.0450.0000.0000.0000.000
98H94ARG10.8120.8857.834-0.452-0.4520.0000.0000.0000.000
99H95ARG10.8260.92913.637-0.184-0.1840.0000.0000.0000.000
100H96ALA00.0210.00613.0070.0470.0470.0000.0000.0000.000
101H97PRO0-0.032-0.00510.582-0.015-0.0150.0000.0000.0000.000
102H98PHE0-0.014-0.01512.3840.0290.0290.0000.0000.0000.000
103H99TYR00.0780.02116.893-0.032-0.0320.0000.0000.0000.000
104H100GLY0-0.022-0.00620.542-0.003-0.0030.0000.0000.0000.000
105H100ASN0-0.0140.00117.649-0.033-0.0330.0000.0000.0000.000
106H100HIS00.0530.00818.8680.0180.0180.0000.0000.0000.000
107H100ALA00.0060.02517.675-0.021-0.0210.0000.0000.0000.000
108H100MET0-0.008-0.01315.5520.0160.0160.0000.0000.0000.000
109H101ASP-1-0.712-0.83310.7190.2170.2170.0000.0000.0000.000
110H102TYR0-0.051-0.0175.6350.0440.0440.0000.0000.0000.000
111H103TRP00.002-0.02710.4730.0170.0170.0000.0000.0000.000
112H104GLY00.0380.03010.624-0.089-0.0890.0000.0000.0000.000
113H105GLN0-0.075-0.04712.1610.0040.0040.0000.0000.0000.000
114H106GLY00.0280.01313.9970.0420.0420.0000.0000.0000.000
115H107THR0-0.082-0.03917.066-0.004-0.0040.0000.0000.0000.000
116H108THR00.009-0.00119.8730.0140.0140.0000.0000.0000.000
117H109VAL0-0.047-0.02423.448-0.002-0.0020.0000.0000.0000.000
118H110THR00.010-0.00226.2730.0080.0080.0000.0000.0000.000
119H111VAL0-0.020-0.01929.795-0.001-0.0010.0000.0000.0000.000
120H112SER0-0.018-0.03032.6260.0030.0030.0000.0000.0000.000
121H113SER0-0.036-0.01735.725-0.002-0.0020.0000.0000.0000.000
122H114ALA00.0510.02837.2280.0030.0030.0000.0000.0000.000
123H115LYS10.9370.95437.5090.0490.0490.0000.0000.0000.000
124H116THR0-0.005-0.00534.4030.0010.0010.0000.0000.0000.000
125H117THR0-0.0060.02536.8920.0020.0020.0000.0000.0000.000
126H118PRO00.0140.00738.517-0.001-0.0010.0000.0000.0000.000
127H142CYS0-0.089-0.05040.2800.0010.0010.0000.0000.0000.000
128H143LEU0-0.010-0.00942.6120.0000.0000.0000.0000.0000.000
129H144VAL0-0.031-0.01438.2210.0000.0000.0000.0000.0000.000
130H145LYS10.9740.98140.4720.0420.0420.0000.0000.0000.000
131H146GLY0-0.0030.00542.169-0.001-0.0010.0000.0000.0000.000
132H147TYR0-0.020-0.03233.7630.0020.0020.0000.0000.0000.000
133H148PHE00.0280.04234.006-0.001-0.0010.0000.0000.0000.000
134H149PRO0-0.034-0.02631.0760.0010.0010.0000.0000.0000.000
135H150GLU-1-0.757-0.85129.555-0.080-0.0800.0000.0000.0000.000
136H151PRO0-0.040-0.01927.003-0.003-0.0030.0000.0000.0000.000
137H152VAL00.029-0.01230.0890.0030.0030.0000.0000.0000.000
138H153THR0-0.043-0.02230.196-0.005-0.0050.0000.0000.0000.000
139H154VAL00.0090.00932.5150.0020.0020.0000.0000.0000.000
140H156THR0-0.0080.00733.1460.0000.0000.0000.0000.0000.000
141H157TRP00.0740.00835.8650.0040.0040.0000.0000.0000.000
142H161ASN00.0080.01438.884-0.002-0.0020.0000.0000.0000.000
143H162SER00.007-0.01636.8650.0000.0000.0000.0000.0000.000
144H163GLY00.0030.02435.289-0.004-0.0040.0000.0000.0000.000
145H164SER0-0.068-0.04236.0040.0020.0020.0000.0000.0000.000
146H165LEU00.0330.00938.3910.0020.0020.0000.0000.0000.000
147H166SER0-0.0200.00734.057-0.001-0.0010.0000.0000.0000.000
148H167SER0-0.019-0.01935.8920.0000.0000.0000.0000.0000.000
149H168GLY00.0620.01437.6110.0010.0010.0000.0000.0000.000
150H171VAL0-0.0070.00436.2600.0020.0020.0000.0000.0000.000
151H172HIS0-0.065-0.03836.426-0.001-0.0010.0000.0000.0000.000
152H173THR0-0.032-0.02033.8470.0010.0010.0000.0000.0000.000
153H174PHE0-0.001-0.01734.385-0.002-0.0020.0000.0000.0000.000
154H175PRO0-0.0120.00032.599-0.003-0.0030.0000.0000.0000.000
155H176ALA00.007-0.00133.6180.0040.0040.0000.0000.0000.000
156H177VAL0-0.011-0.00235.0790.0000.0000.0000.0000.0000.000
157H178LEU0-0.026-0.02435.759-0.001-0.0010.0000.0000.0000.000
158H179GLN00.0120.02538.7600.0030.0030.0000.0000.0000.000
159H180SER00.007-0.01441.7650.0000.0000.0000.0000.0000.000
160H183ASP-1-0.913-0.95538.769-0.051-0.0510.0000.0000.0000.000
161H184LEU0-0.0400.00438.869-0.003-0.0030.0000.0000.0000.000
162H185TYR00.014-0.00331.9780.0010.0010.0000.0000.0000.000
163H186THR0-0.017-0.02337.5690.0020.0020.0000.0000.0000.000
164H187LEU00.0320.03834.4370.0010.0010.0000.0000.0000.000
165H188SER0-0.009-0.02438.3970.0030.0030.0000.0000.0000.000
166H189SER00.0520.03537.926-0.004-0.0040.0000.0000.0000.000
167H190SER00.0190.02139.4350.0010.0010.0000.0000.0000.000
168H191VAL00.0180.01940.395-0.002-0.0020.0000.0000.0000.000
169H192THR0-0.0060.01042.3630.0020.0020.0000.0000.0000.000
170H209ASN00.0130.00737.1310.0020.0020.0000.0000.0000.000
171H210VAL00.0150.02336.822-0.003-0.0030.0000.0000.0000.000
172H211ALA0-0.003-0.00133.2710.0010.0010.0000.0000.0000.000
173H212HIS10.8200.86233.3980.0810.0810.0000.0000.0000.000
174H213PRO00.0540.00729.1550.0030.0030.0000.0000.0000.000
175H214ALA00.0020.03231.3550.0000.0000.0000.0000.0000.000
176H215SER00.0190.01132.2720.0000.0000.0000.0000.0000.000
177H216SER0-0.012-0.01034.1740.0030.0030.0000.0000.0000.000
178H217THR0-0.0170.01335.2440.0030.0030.0000.0000.0000.000
179H218LYS10.9010.92236.2270.0680.0680.0000.0000.0000.000
180H219VAL00.0240.02038.3540.0030.0030.0000.0000.0000.000
181H220ASP-1-0.779-0.86039.489-0.067-0.0670.0000.0000.0000.000
182H221LYS10.9350.97241.7780.0500.0500.0000.0000.0000.000