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: 52G2Z

Calculation Name: 1OSP-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OSP

Chain ID: H

ChEMBL ID:

UniProt ID: P01867

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2209547.993779
FMO2-HF: Nuclear repulsion 2126918.663645
FMO2-HF: Total energy -82629.330134
FMO2-MP2: Total energy -82869.516856


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:GLU)


Summations of interaction energy for fragment #1(H:1: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.
-6.960.0609999999999851.48-3.588-4.9130.016
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.939 / q_NPA : -0.974
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].
3H3GLN00.0020.0142.9823.2966.7300.172-1.678-1.9280.001
4H4LEU0-0.005-0.0195.826-3.150-3.1500.0000.0000.0000.000
5H5GLN0-0.021-0.0258.8720.3660.3660.0000.0000.0000.000
6H6GLU-1-0.744-0.84812.27820.21620.2160.0000.0000.0000.000
7H7SER00.0080.00515.574-0.543-0.5430.0000.0000.0000.000
8H8GLY00.0300.00418.828-0.180-0.1800.0000.0000.0000.000
9H9PRO0-0.016-0.00822.4030.0820.0820.0000.0000.0000.000
10H10SER00.0710.03925.3560.0250.0250.0000.0000.0000.000
11H11LEU0-0.058-0.02326.352-0.129-0.1290.0000.0000.0000.000
12H12VAL0-0.0010.00928.688-0.133-0.1330.0000.0000.0000.000
13H13LYS10.9670.98431.085-8.204-8.2040.0000.0000.0000.000
14H14PRO00.0610.02634.2800.0710.0710.0000.0000.0000.000
15H15SER0-0.059-0.02135.567-0.256-0.2560.0000.0000.0000.000
16H16GLN0-0.035-0.02233.4230.0120.0120.0000.0000.0000.000
17H17THR00.017-0.01028.9950.0100.0100.0000.0000.0000.000
18H18LEU0-0.044-0.00224.595-0.058-0.0580.0000.0000.0000.000
19H19SER00.000-0.00924.6950.0510.0510.0000.0000.0000.000
20H20LEU0-0.0210.00019.696-0.062-0.0620.0000.0000.0000.000
21H21THR0-0.021-0.02117.393-0.321-0.3210.0000.0000.0000.000
22H22CYS00.0130.03612.4090.6990.6990.0000.0000.0000.000
23H23SER0-0.033-0.02713.506-0.509-0.5090.0000.0000.0000.000
24H24VAL00.004-0.0067.9581.1011.1010.0000.0000.0000.000
25H25THR0-0.031-0.0157.331-1.051-1.0510.0000.0000.0000.000
26H26GLY00.0440.0183.4012.1912.3200.008-0.082-0.0550.000
27H27GLU-1-0.775-0.8593.48436.48937.2530.012-0.313-0.463-0.002
28H28PRO0-0.0200.0136.198-1.166-1.1660.0000.0000.0000.000
29H29ILE00.026-0.00610.0170.4610.4610.0000.0000.0000.000
30H30THR0-0.083-0.04912.042-0.653-0.6530.0000.0000.0000.000
31H31SER00.0070.00211.220-1.634-1.6340.0000.0000.0000.000
32H32GLY00.0400.03011.6141.2901.2900.0000.0000.0000.000
33H33PHE0-0.073-0.03612.437-1.961-1.9610.0000.0000.0000.000
34H34TRP00.0460.0307.7641.8441.8440.0000.0000.0000.000
35H35ASP-1-0.768-0.92213.52718.11618.1160.0000.0000.0000.000
36H36TRP00.0220.02614.8780.8260.8260.0000.0000.0000.000
37H37ILE0-0.016-0.00714.780-0.861-0.8610.0000.0000.0000.000
38H38ARG10.8190.89418.277-11.707-11.7070.0000.0000.0000.000
39H39LYS10.9220.94719.171-15.432-15.4320.0000.0000.0000.000
40H40PHE00.013-0.00521.875-0.230-0.2300.0000.0000.0000.000
41H41PRO00.0590.01225.3360.2380.2380.0000.0000.0000.000
42H42GLY0-0.0310.00327.463-0.061-0.0610.0000.0000.0000.000
43H43ASN0-0.016-0.00922.6460.5070.5070.0000.0000.0000.000
44H44LYS10.8680.95423.968-11.167-11.1670.0000.0000.0000.000
45H45LEU00.0070.00218.2590.0190.0190.0000.0000.0000.000
46H46GLU-1-0.809-0.91221.60111.20711.2070.0000.0000.0000.000
47H47PHE0-0.0040.02918.1850.2000.2000.0000.0000.0000.000
48H48MET0-0.0090.00620.271-0.708-0.7080.0000.0000.0000.000
49H49GLY00.0520.00320.069-0.790-0.7900.0000.0000.0000.000
50H50TYR0-0.0080.00616.9750.5500.5500.0000.0000.0000.000
51H51ILE0-0.040-0.01116.953-0.978-0.9780.0000.0000.0000.000
52H52ARG10.9710.97916.505-13.764-13.7640.0000.0000.0000.000
53H53TYR00.0220.01217.171-0.613-0.6130.0000.0000.0000.000
54H54GLY0-0.009-0.01218.343-0.576-0.5760.0000.0000.0000.000
55H55GLY0-0.058-0.02519.681-0.553-0.5530.0000.0000.0000.000
56H56GLY00.0210.02921.152-0.426-0.4260.0000.0000.0000.000
57H57THR0-0.023-0.02321.0170.6700.6700.0000.0000.0000.000
58H58TYR0-0.0070.00721.890-0.365-0.3650.0000.0000.0000.000
59H59TYR00.0350.00522.6400.5940.5940.0000.0000.0000.000
60H60ASN00.0130.00224.215-0.720-0.7200.0000.0000.0000.000
61H61PRO00.009-0.00225.865-0.209-0.2090.0000.0000.0000.000
62H62SER0-0.036-0.02228.835-0.440-0.4400.0000.0000.0000.000
63H63LEU0-0.077-0.01525.001-0.050-0.0500.0000.0000.0000.000
64H64LYS10.9470.98329.241-9.247-9.2470.0000.0000.0000.000
65H65SER00.0160.00730.550-0.396-0.3960.0000.0000.0000.000
66H66PRO00.0070.00929.4400.3740.3740.0000.0000.0000.000
67H67ILE0-0.005-0.01023.1750.0010.0010.0000.0000.0000.000
68H68SER0-0.053-0.02025.766-0.186-0.1860.0000.0000.0000.000
69H69ILE00.0160.01019.2430.2740.2740.0000.0000.0000.000
70H70THR00.0040.00721.531-0.142-0.1420.0000.0000.0000.000
71H71ARG10.9780.97817.127-13.975-13.9750.0000.0000.0000.000
72H72ASP-1-0.801-0.87918.20712.62012.6200.0000.0000.0000.000
73H73THR00.012-0.01615.9930.4480.4480.0000.0000.0000.000
74H74SER0-0.058-0.00715.6640.5640.5640.0000.0000.0000.000
75H75LYS10.9050.93716.279-12.749-12.7490.0000.0000.0000.000
76H76ASN0-0.040-0.0099.6040.0480.0480.0000.0000.0000.000
77H77HIS00.0000.01213.0470.4560.4560.0000.0000.0000.000
78H78TYR0-0.029-0.03912.285-0.335-0.3350.0000.0000.0000.000
79H79TYR0-0.023-0.02417.2480.2460.2460.0000.0000.0000.000
80H80LEU00.0230.02519.865-0.030-0.0300.0000.0000.0000.000
81H81GLN0-0.024-0.02221.668-0.441-0.4410.0000.0000.0000.000
82H82LEU00.0170.01725.431-0.041-0.0410.0000.0000.0000.000
83H83ASN00.0360.02927.843-0.084-0.0840.0000.0000.0000.000
84H84SER0-0.042-0.01731.514-0.024-0.0240.0000.0000.0000.000
85H85VAL00.0000.02029.108-0.059-0.0590.0000.0000.0000.000
86H86VAL0-0.011-0.02932.154-0.432-0.4320.0000.0000.0000.000
87H87THR00.028-0.01832.1670.2020.2020.0000.0000.0000.000
88H88GLU-1-0.938-0.95631.9749.3549.3540.0000.0000.0000.000
89H89ASP-1-0.806-0.87928.12610.65910.6590.0000.0000.0000.000
90H90THR0-0.0130.01127.0830.4270.4270.0000.0000.0000.000
91H91ALA0-0.012-0.01223.572-0.030-0.0300.0000.0000.0000.000
92H92THR0-0.0160.01518.737-0.099-0.0990.0000.0000.0000.000
93H93TYR0-0.029-0.04019.3380.1020.1020.0000.0000.0000.000
94H94TYR00.0150.00113.986-0.452-0.4520.0000.0000.0000.000
95H95CYS0-0.103-0.04912.504-0.561-0.5610.0000.0000.0000.000
96H96ALA00.036-0.00910.1401.3751.3750.0000.0000.0000.000
97H97ARG10.8270.9325.935-37.003-37.0030.0000.0000.0000.000
98H98SER0-0.024-0.0329.7911.0101.0100.0000.0000.0000.000
99H99ARG10.8000.8589.275-23.535-23.5350.0000.0000.0000.000
100H100ASP-1-0.827-0.8879.49525.67725.6770.0000.0000.0000.000
101H101TYR0-0.043-0.0597.129-0.712-0.7120.0000.0000.0000.000
102H102TYR0-0.044-0.02513.095-1.202-1.2020.0000.0000.0000.000
103H103GLY0-0.006-0.00116.3730.5210.5210.0000.0000.0000.000
104H104SER00.0040.00117.6950.3730.3730.0000.0000.0000.000
105H105SER00.0000.01413.9760.5780.5780.0000.0000.0000.000
106H106GLY00.0340.01914.553-0.563-0.5630.0000.0000.0000.000
107H107PHE0-0.0010.00011.9590.5650.5650.0000.0000.0000.000
108H108ALA00.0000.0117.591-0.554-0.5540.0000.0000.0000.000
109H109PHE00.0060.0182.696-6.189-3.4951.288-1.515-2.4670.017
110H110TRP0-0.038-0.0326.734-5.843-5.8430.0000.0000.0000.000
111H111GLY00.0760.0468.4802.5242.5240.0000.0000.0000.000
112H112GLU-1-0.935-0.96310.68519.80419.8040.0000.0000.0000.000
113H113GLY0-0.016-0.01113.189-0.945-0.9450.0000.0000.0000.000
114H114THR0-0.016-0.01516.027-0.718-0.7180.0000.0000.0000.000
115H115LEU0-0.021-0.00319.360-0.193-0.1930.0000.0000.0000.000
116H116VAL0-0.005-0.00422.706-0.297-0.2970.0000.0000.0000.000
117H117THR0-0.024-0.02125.235-0.148-0.1480.0000.0000.0000.000
118H118VAL00.0090.00528.844-0.142-0.1420.0000.0000.0000.000
119H119SER00.024-0.01031.338-0.305-0.3050.0000.0000.0000.000
120H120ALA00.002-0.01134.7750.0370.0370.0000.0000.0000.000
121H121ALA0-0.044-0.00536.985-0.199-0.1990.0000.0000.0000.000
122H122LYS10.9800.98636.916-7.223-7.2230.0000.0000.0000.000
123H123THR00.0290.00533.8680.0530.0530.0000.0000.0000.000
124H124THR0-0.053-0.02336.166-0.285-0.2850.0000.0000.0000.000
125H125PRO00.0460.03235.7920.2320.2320.0000.0000.0000.000
126H126PRO00.0080.01334.166-0.198-0.1980.0000.0000.0000.000
127H127SER0-0.0230.00537.276-0.168-0.1680.0000.0000.0000.000
128H128VAL0-0.007-0.01136.6570.0360.0360.0000.0000.0000.000
129H129TYR0-0.013-0.02338.991-0.181-0.1810.0000.0000.0000.000
130H130PRO00.0350.01940.0880.1950.1950.0000.0000.0000.000
131H131LEU0-0.062-0.02738.877-0.162-0.1620.0000.0000.0000.000
132H132ALA00.0350.01241.4810.1760.1760.0000.0000.0000.000
133H133PRO0-0.020-0.06543.526-0.099-0.0990.0000.0000.0000.000
134H134GLY00.0680.11146.398-0.073-0.0730.0000.0000.0000.000
135H135CYS0-0.091-0.06749.2710.0640.0640.0000.0000.0000.000
136H136GLY00.0030.00751.697-0.035-0.0350.0000.0000.0000.000
137H137ASP-1-0.918-0.94551.7345.8845.8840.0000.0000.0000.000
138H138THR0-0.014-0.00850.6060.0750.0750.0000.0000.0000.000
139H139THR0-0.008-0.02745.173-0.031-0.0310.0000.0000.0000.000
140H140GLY00.0480.04046.609-0.086-0.0860.0000.0000.0000.000
141H141SER0-0.0070.00343.177-0.016-0.0160.0000.0000.0000.000
142H142SER00.0380.02039.1970.0220.0220.0000.0000.0000.000
143H143VAL0-0.043-0.00840.601-0.158-0.1580.0000.0000.0000.000
144H144THR0-0.024-0.02237.4340.1760.1760.0000.0000.0000.000
145H145LEU00.0000.01438.231-0.225-0.2250.0000.0000.0000.000
146H146GLY00.047-0.00536.6590.2760.2760.0000.0000.0000.000
147H147CYS0-0.093-0.01633.754-0.001-0.0010.0000.0000.0000.000
148H148LEU00.0000.01736.0380.2150.2150.0000.0000.0000.000
149H149VAL00.0140.00433.400-0.153-0.1530.0000.0000.0000.000
150H150LYS10.9720.95936.235-7.273-7.2730.0000.0000.0000.000
151H151GLY00.0100.01038.718-0.086-0.0860.0000.0000.0000.000
152H152TYR00.0150.00830.836-0.238-0.2380.0000.0000.0000.000
153H153PHE0-0.016-0.03534.0760.0270.0270.0000.0000.0000.000
154H154PRO0-0.0260.01030.7070.1040.1040.0000.0000.0000.000
155H155GLU-1-0.744-0.87227.94410.81810.8180.0000.0000.0000.000
156H156SER0-0.053-0.02525.2890.4510.4510.0000.0000.0000.000
157H157VAL00.0000.00027.289-0.207-0.2070.0000.0000.0000.000
158H158THR0-0.046-0.02724.6820.4680.4680.0000.0000.0000.000
159H159VAL00.0020.00227.343-0.327-0.3270.0000.0000.0000.000
160H160THR0-0.0150.00427.4620.5020.5020.0000.0000.0000.000
161H161TRP00.007-0.00729.118-0.514-0.5140.0000.0000.0000.000
162H162ASN0-0.021-0.00330.6770.1270.1270.0000.0000.0000.000
163H163SER00.0300.02033.291-0.232-0.2320.0000.0000.0000.000
164H164GLY00.0450.03035.1380.1160.1160.0000.0000.0000.000
165H165SER0-0.061-0.04035.2090.0840.0840.0000.0000.0000.000
166H166LEU00.0320.01831.5340.1870.1870.0000.0000.0000.000
167H167SER0-0.046-0.01630.7090.3210.3210.0000.0000.0000.000
168H168SER00.0200.01530.898-0.273-0.2730.0000.0000.0000.000
169H169SER00.0160.01730.4690.3670.3670.0000.0000.0000.000
170H170VAL0-0.014-0.01728.258-0.351-0.3510.0000.0000.0000.000
171H171HIS00.0030.01728.9040.4240.4240.0000.0000.0000.000
172H172THR00.0140.00726.811-0.462-0.4620.0000.0000.0000.000
173H173PHE0-0.014-0.01428.8510.2260.2260.0000.0000.0000.000
174H174PRO00.014-0.01028.0960.0000.0000.0000.0000.0000.000
175H175ALA00.0070.03029.641-0.400-0.4000.0000.0000.0000.000
176H176LEU0-0.016-0.01231.4480.1060.1060.0000.0000.0000.000
177H177LEU0-0.036-0.00234.241-0.196-0.1960.0000.0000.0000.000
178H178GLN0-0.002-0.00936.302-0.210-0.2100.0000.0000.0000.000
179H179SER0-0.027-0.02840.128-0.007-0.0070.0000.0000.0000.000
180H180GLY00.0090.01239.174-0.090-0.0900.0000.0000.0000.000
181H181LEU0-0.043-0.01337.7930.1180.1180.0000.0000.0000.000
182H182TYR00.0350.01331.127-0.078-0.0780.0000.0000.0000.000
183H183THR0-0.041-0.02735.524-0.267-0.2670.0000.0000.0000.000
184H184MET00.0120.02829.5320.0180.0180.0000.0000.0000.000
185H185SER00.0200.00533.371-0.296-0.2960.0000.0000.0000.000
186H186SER00.0040.01030.8360.3280.3280.0000.0000.0000.000
187H187SER00.0190.00432.820-0.361-0.3610.0000.0000.0000.000
188H188VAL00.0170.00132.2960.3580.3580.0000.0000.0000.000
189H189THR00.0060.01734.358-0.389-0.3890.0000.0000.0000.000
190H190VAL00.0210.00035.1740.3130.3130.0000.0000.0000.000
191H191PRO00.0350.02136.971-0.212-0.2120.0000.0000.0000.000
192H192SER00.0860.01340.1730.0340.0340.0000.0000.0000.000
193H193SER0-0.055-0.02443.195-0.040-0.0400.0000.0000.0000.000
194H194THR0-0.071-0.06339.2860.0640.0640.0000.0000.0000.000
195H195TRP00.0620.03340.8830.1010.1010.0000.0000.0000.000
196H196PRO00.0000.01342.245-0.005-0.0050.0000.0000.0000.000
197H197SER0-0.069-0.03244.556-0.039-0.0390.0000.0000.0000.000
198H198GLN0-0.001-0.00940.0020.1300.1300.0000.0000.0000.000
199H199THR00.008-0.00239.5090.0380.0380.0000.0000.0000.000
200H200VAL00.0150.00136.1940.2200.2200.0000.0000.0000.000
201H201THR0-0.040-0.02835.984-0.328-0.3280.0000.0000.0000.000
202H203SER00.015-0.01631.162-0.170-0.1700.0000.0000.0000.000
203H204VAL0-0.021-0.02631.1250.3330.3330.0000.0000.0000.000
204H205ALA00.0320.03528.311-0.258-0.2580.0000.0000.0000.000
205H206HIS00.0100.00429.4830.0280.0280.0000.0000.0000.000
206H207PRO00.0630.01725.713-0.308-0.3080.0000.0000.0000.000
207H208ALA0-0.0040.00828.508-0.164-0.1640.0000.0000.0000.000
208H209SER0-0.045-0.04030.163-0.280-0.2800.0000.0000.0000.000
209H210SER0-0.042-0.01731.302-0.207-0.2070.0000.0000.0000.000
210H211THR0-0.008-0.00632.315-0.253-0.2530.0000.0000.0000.000
211H212THR00.017-0.02531.4870.4730.4730.0000.0000.0000.000
212H213VAL0-0.060-0.01833.597-0.302-0.3020.0000.0000.0000.000
213H214ASP-1-0.799-0.87134.4989.2779.2770.0000.0000.0000.000
214H215LYS10.8330.91536.842-8.016-8.0160.0000.0000.0000.000
215H216LYS10.9540.98438.561-6.925-6.9250.0000.0000.0000.000
216H217LEU0-0.039-0.02638.556-0.151-0.1510.0000.0000.0000.000
217H218GLU-1-0.933-0.96241.9876.6056.6050.0000.0000.0000.000