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: Z692N

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 OptH
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 -1730775.496142
FMO2-HF: Nuclear repulsion 1660196.594392
FMO2-HF: Total energy -70578.901751
FMO2-MP2: Total energy -70784.522946


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.
0.3982.3178.673617379884E-19-0.751-1.1670.003
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 : 0.017 / q_NPA : -0.002
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].
3H3LYS10.9480.9893.8651.0602.366-0.013-0.544-0.7490.002
4H4LEU00.012-0.0265.7800.2640.2640.0000.0000.0000.000
5H5GLN00.0110.0139.608-0.042-0.0420.0000.0000.0000.000
6H6GLU-1-0.751-0.87812.220-0.287-0.2870.0000.0000.0000.000
7H7SER0-0.055-0.02115.995-0.004-0.0040.0000.0000.0000.000
8H8GLY00.039-0.00118.3990.0200.0200.0000.0000.0000.000
9H9PRO0-0.033-0.01422.070-0.007-0.0070.0000.0000.0000.000
10H10GLY00.0410.04424.8900.0030.0030.0000.0000.0000.000
11H11ILE0-0.017-0.01425.9390.0060.0060.0000.0000.0000.000
12H12LEU0-0.030-0.00829.336-0.001-0.0010.0000.0000.0000.000
13H13LYS10.9710.99031.5400.0680.0680.0000.0000.0000.000
14H14PRO00.0620.01034.717-0.001-0.0010.0000.0000.0000.000
15H15SER0-0.017-0.01336.9010.0020.0020.0000.0000.0000.000
16H16GLN0-0.0380.00033.589-0.001-0.0010.0000.0000.0000.000
17H17THR00.008-0.01030.0720.0050.0050.0000.0000.0000.000
18H18LEU0-0.015-0.00125.474-0.005-0.0050.0000.0000.0000.000
19H19SER0-0.065-0.03925.1700.0080.0080.0000.0000.0000.000
20H20LEU00.0120.01621.150-0.011-0.0110.0000.0000.0000.000
21H21THR0-0.022-0.01416.8610.0190.0190.0000.0000.0000.000
22H22CYS0-0.0410.00114.463-0.021-0.0210.0000.0000.0000.000
23H23SER00.0330.01712.4940.0550.0550.0000.0000.0000.000
24H24PHE0-0.0110.0069.184-0.095-0.0950.0000.0000.0000.000
25H25SER00.027-0.0043.982-0.0460.066-0.001-0.018-0.0920.000
26H26GLY00.0250.0093.442-1.221-0.9370.015-0.165-0.1340.001
27H27PHE0-0.015-0.0074.2361.1011.318-0.001-0.024-0.1920.000
28H28SER00.0590.0267.852-0.282-0.2820.0000.0000.0000.000
29H29LEU00.0150.01011.2740.0220.0220.0000.0000.0000.000
30H30THR00.0220.01814.4300.0000.0000.0000.0000.0000.000
31H31THR0-0.034-0.02513.3500.0210.0210.0000.0000.0000.000
32H32TYR00.0380.00415.871-0.024-0.0240.0000.0000.0000.000
33H33GLY00.0350.03718.0570.0270.0270.0000.0000.0000.000
34H34MET0-0.050-0.01511.963-0.017-0.0170.0000.0000.0000.000
35H35GLY00.0520.00615.402-0.025-0.0250.0000.0000.0000.000
36H35VAL0-0.055-0.01713.9630.0020.0020.0000.0000.0000.000
37H35GLY00.0450.03216.4920.0130.0130.0000.0000.0000.000
38H36TRP0-0.029-0.01518.152-0.035-0.0350.0000.0000.0000.000
39H37ILE00.001-0.00318.4300.0210.0210.0000.0000.0000.000
40H38ARG10.9080.96721.1790.0440.0440.0000.0000.0000.000
41H39GLN00.0400.00922.4010.0170.0170.0000.0000.0000.000
42H40SER00.0320.01925.177-0.008-0.0080.0000.0000.0000.000
43H41SER00.025-0.01127.684-0.001-0.0010.0000.0000.0000.000
44H42GLY00.0020.00928.2610.0060.0060.0000.0000.0000.000
45H43LYS10.9160.96728.5280.0560.0560.0000.0000.0000.000
46H44GLY00.0440.02927.256-0.003-0.0030.0000.0000.0000.000
47H45LEU0-0.0020.00021.521-0.005-0.0050.0000.0000.0000.000
48H46GLU-1-0.884-0.94325.102-0.038-0.0380.0000.0000.0000.000
49H47TRP00.0290.02122.247-0.008-0.0080.0000.0000.0000.000
50H48LEU0-0.048-0.02723.6670.0040.0040.0000.0000.0000.000
51H49ALA00.0320.00023.7680.0080.0080.0000.0000.0000.000
52H50HIS00.0160.00818.031-0.027-0.0270.0000.0000.0000.000
53H51ILE0-0.074-0.02419.2920.0030.0030.0000.0000.0000.000
54H52TRP00.0390.01319.0520.0130.0130.0000.0000.0000.000
55H53TRP00.024-0.00918.077-0.008-0.0080.0000.0000.0000.000
56H54ASP-1-0.913-0.95919.3790.0740.0740.0000.0000.0000.000
57H55ASP-1-0.946-0.98222.341-0.002-0.0020.0000.0000.0000.000
58H56ASP-1-0.854-0.88523.9190.0290.0290.0000.0000.0000.000
59H57LYS10.7810.86824.146-0.008-0.0080.0000.0000.0000.000
60H58TYR0-0.0100.00925.1230.0030.0030.0000.0000.0000.000
61H59TYR00.0180.01725.913-0.010-0.0100.0000.0000.0000.000
62H60ASN00.0130.01628.2380.0110.0110.0000.0000.0000.000
63H61PRO0-0.007-0.02429.736-0.003-0.0030.0000.0000.0000.000
64H62SER00.0250.01232.9830.0000.0000.0000.0000.0000.000
65H63LEU0-0.020-0.01230.102-0.002-0.0020.0000.0000.0000.000
66H64LYS10.9761.00231.4460.0010.0010.0000.0000.0000.000
67H65SER0-0.009-0.01132.447-0.003-0.0030.0000.0000.0000.000
68H66ARG10.8320.92632.4860.0490.0490.0000.0000.0000.000
69H67LEU0-0.018-0.00427.489-0.007-0.0070.0000.0000.0000.000
70H68THR0-0.014-0.01727.7210.0070.0070.0000.0000.0000.000
71H69ILE0-0.017-0.01020.837-0.012-0.0120.0000.0000.0000.000
72H70SER0-0.004-0.00622.8100.0090.0090.0000.0000.0000.000
73H71LYS10.9580.97718.343-0.058-0.0580.0000.0000.0000.000
74H72ASP-1-0.751-0.84118.088-0.048-0.0480.0000.0000.0000.000
75H73THR00.048-0.00315.172-0.033-0.0330.0000.0000.0000.000
76H74SER0-0.086-0.03115.1070.0010.0010.0000.0000.0000.000
77H75ARG10.8560.89715.5450.1000.1000.0000.0000.0000.000
78H76ASN0-0.0450.00010.0420.0150.0150.0000.0000.0000.000
79H77GLN0-0.007-0.02112.813-0.048-0.0480.0000.0000.0000.000
80H78VAL0-0.0010.01415.4520.0470.0470.0000.0000.0000.000
81H79PHE0-0.045-0.03217.771-0.028-0.0280.0000.0000.0000.000
82H80LEU00.0230.00921.0040.0190.0190.0000.0000.0000.000
83H81LYS10.9250.95123.8250.0750.0750.0000.0000.0000.000
84H82ILE00.0280.02226.3110.0070.0070.0000.0000.0000.000
85H82THR00.0470.03129.711-0.004-0.0040.0000.0000.0000.000
86H82SER00.0420.00833.3090.0010.0010.0000.0000.0000.000
87H82VAL0-0.0520.00031.0050.0010.0010.0000.0000.0000.000
88H83ALA00.0610.03033.8500.0030.0030.0000.0000.0000.000
89H84THR00.0600.00933.731-0.003-0.0030.0000.0000.0000.000
90H85ALA0-0.010-0.00233.574-0.004-0.0040.0000.0000.0000.000
91H86ASP-1-0.895-0.95530.211-0.060-0.0600.0000.0000.0000.000
92H87THR00.0000.03028.974-0.008-0.0080.0000.0000.0000.000
93H88ALA0-0.065-0.03026.0640.0050.0050.0000.0000.0000.000
94H89THR00.0000.01220.267-0.010-0.0100.0000.0000.0000.000
95H90TYR0-0.064-0.04121.0730.0140.0140.0000.0000.0000.000
96H91TYR00.0260.01215.997-0.013-0.0130.0000.0000.0000.000
97H93ALA00.0420.01413.495-0.049-0.0490.0000.0000.0000.000
98H94ARG10.8210.9057.840-0.408-0.4080.0000.0000.0000.000
99H95ARG10.8300.93613.632-0.165-0.1650.0000.0000.0000.000
100H96ALA00.0230.00713.0080.0450.0450.0000.0000.0000.000
101H97PRO0-0.038-0.01010.688-0.016-0.0160.0000.0000.0000.000
102H98PHE0-0.013-0.01512.6440.0350.0350.0000.0000.0000.000
103H99TYR00.0970.02716.903-0.034-0.0340.0000.0000.0000.000
104H100GLY0-0.031-0.00920.553-0.002-0.0020.0000.0000.0000.000
105H100ASN0-0.0080.00817.485-0.036-0.0360.0000.0000.0000.000
106H100HIS00.0490.00818.8720.0170.0170.0000.0000.0000.000
107H100ALA00.0060.02117.633-0.023-0.0230.0000.0000.0000.000
108H100MET0-0.013-0.01715.5500.0170.0170.0000.0000.0000.000
109H101ASP-1-0.718-0.84810.8160.1790.1790.0000.0000.0000.000
110H102TYR0-0.057-0.0195.865-0.032-0.0320.0000.0000.0000.000
111H103TRP0-0.002-0.02610.4440.0180.0180.0000.0000.0000.000
112H104GLY00.0300.02910.584-0.097-0.0970.0000.0000.0000.000
113H105GLN0-0.069-0.04312.1120.0050.0050.0000.0000.0000.000
114H106GLY00.0310.01613.9570.0460.0460.0000.0000.0000.000
115H107THR0-0.079-0.03917.019-0.003-0.0030.0000.0000.0000.000
116H108THR00.0190.00019.8220.0160.0160.0000.0000.0000.000
117H109VAL0-0.065-0.02623.400-0.002-0.0020.0000.0000.0000.000
118H110THR00.031-0.00326.2200.0080.0080.0000.0000.0000.000
119H111VAL0-0.029-0.01929.745-0.001-0.0010.0000.0000.0000.000
120H112SER00.012-0.00832.5720.0040.0040.0000.0000.0000.000
121H113SER0-0.015-0.00735.672-0.002-0.0020.0000.0000.0000.000
122H114ALA00.0470.02937.1750.0030.0030.0000.0000.0000.000
123H115LYS10.9420.95437.4910.0550.0550.0000.0000.0000.000
124H116THR00.0060.00534.5880.0010.0010.0000.0000.0000.000
125H117THR0-0.0140.01736.8720.0030.0030.0000.0000.0000.000
126H118PRO00.0110.00538.458-0.001-0.0010.0000.0000.0000.000
127H142CYS0-0.075-0.05340.2990.0010.0010.0000.0000.0000.000
128H143LEU0-0.019-0.01442.5810.0000.0000.0000.0000.0000.000
129H144VAL0-0.057-0.02438.0410.0000.0000.0000.0000.0000.000
130H145LYS10.9900.98940.4420.0450.0450.0000.0000.0000.000
131H146GLY00.023-0.01141.549-0.002-0.0020.0000.0000.0000.000
132H147TYR00.0170.01433.1990.0010.0010.0000.0000.0000.000
133H148PHE00.0330.06333.409-0.001-0.0010.0000.0000.0000.000
134H149PRO0-0.051-0.05031.0520.0020.0020.0000.0000.0000.000
135H150GLU-1-0.849-0.89229.518-0.086-0.0860.0000.0000.0000.000
136H151PRO00.0650.02727.375-0.002-0.0020.0000.0000.0000.000
137H152VAL0-0.074-0.10230.0560.0030.0030.0000.0000.0000.000
138H153THR0-0.042-0.01930.180-0.006-0.0060.0000.0000.0000.000
139H154VAL00.0060.00932.4940.0020.0020.0000.0000.0000.000
140H156THR0-0.0210.00033.2970.0000.0000.0000.0000.0000.000
141H157TRP00.067-0.00235.8550.0050.0050.0000.0000.0000.000
142H161ASN0-0.0060.00738.881-0.001-0.0010.0000.0000.0000.000
143H162SER00.016-0.00536.8560.0000.0000.0000.0000.0000.000
144H163GLY0-0.0040.02035.291-0.004-0.0040.0000.0000.0000.000
145H164SER0-0.096-0.04836.0040.0020.0020.0000.0000.0000.000
146H165LEU00.0800.02938.9230.0010.0010.0000.0000.0000.000
147H166SER0-0.0220.01034.251-0.001-0.0010.0000.0000.0000.000
148H167SER00.006-0.01835.897-0.001-0.0010.0000.0000.0000.000
149H168GLY00.0380.00537.6180.0010.0010.0000.0000.0000.000
150H171VAL0-0.0170.00336.2010.0010.0010.0000.0000.0000.000
151H172HIS0-0.055-0.03336.423-0.001-0.0010.0000.0000.0000.000
152H173THR0-0.0010.00233.7800.0030.0030.0000.0000.0000.000
153H174PHE0-0.006-0.01534.371-0.002-0.0020.0000.0000.0000.000
154H175PRO0-0.0170.00432.775-0.004-0.0040.0000.0000.0000.000
155H176ALA00.0210.00133.5880.0050.0050.0000.0000.0000.000
156H177VAL0-0.0070.00235.0480.0000.0000.0000.0000.0000.000
157H178LEU0-0.024-0.02735.796-0.001-0.0010.0000.0000.0000.000
158H179GLN0-0.0010.01538.7220.0020.0020.0000.0000.0000.000
159H180SER00.005-0.00841.7220.0000.0000.0000.0000.0000.000
160H183ASP-1-0.959-0.97939.279-0.054-0.0540.0000.0000.0000.000
161H184LEU0-0.0420.01138.819-0.003-0.0030.0000.0000.0000.000
162H185TYR00.0160.00732.4680.0000.0000.0000.0000.0000.000
163H186THR0-0.007-0.02937.5320.0020.0020.0000.0000.0000.000
164H187LEU00.0130.03734.4430.0010.0010.0000.0000.0000.000
165H188SER0-0.007-0.02638.3920.0030.0030.0000.0000.0000.000
166H189SER00.0020.00637.185-0.002-0.0020.0000.0000.0000.000
167H190SER00.0410.03239.4200.0000.0000.0000.0000.0000.000
168H191VAL00.0550.03540.388-0.002-0.0020.0000.0000.0000.000
169H192THR0-0.0170.00142.3580.0020.0020.0000.0000.0000.000
170H209ASN00.0330.02936.9510.0020.0020.0000.0000.0000.000
171H210VAL00.0070.01936.806-0.004-0.0040.0000.0000.0000.000
172H211ALA0-0.0010.00033.2080.0010.0010.0000.0000.0000.000
173H212HIS10.8420.89133.3980.0850.0850.0000.0000.0000.000
174H213PRO00.0460.00529.1890.0030.0030.0000.0000.0000.000
175H214ALA00.0120.03731.350-0.001-0.0010.0000.0000.0000.000
176H215SER00.0090.00632.2590.0000.0000.0000.0000.0000.000
177H216SER0-0.019-0.01334.1280.0030.0030.0000.0000.0000.000
178H217THR0-0.0010.01735.2380.0030.0030.0000.0000.0000.000
179H218LYS10.9750.97335.7780.0780.0780.0000.0000.0000.000
180H219VAL00.0160.01238.3290.0030.0030.0000.0000.0000.000
181H220ASP-1-0.861-0.92839.587-0.069-0.0690.0000.0000.0000.000
182H221LYS10.9400.97941.7600.0520.0520.0000.0000.0000.000