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: N965Q

Calculation Name: 3U9P-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U9P

Chain ID: H

ChEMBL ID:

UniProt ID: P11672

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1844838.953252
FMO2-HF: Nuclear repulsion 1772309.837
FMO2-HF: Total energy -72529.116251
FMO2-MP2: Total energy -72739.111494


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.
-85.906-84.146-0.017-0.867-0.8760.004
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 : -0.934 / q_NPA : -0.968
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].
3H3LYS10.8620.9163.843-30.466-28.793-0.015-0.827-0.8310.004
4H4LEU00.0230.0146.465-1.958-1.9580.0000.0000.0000.000
5H5GLN0-0.012-0.00110.2390.3610.3610.0000.0000.0000.000
6H6GLU-1-0.745-0.88512.38218.60718.6070.0000.0000.0000.000
7H7SER0-0.031-0.01516.163-0.118-0.1180.0000.0000.0000.000
8H8GLY00.0260.00418.638-0.376-0.3760.0000.0000.0000.000
9H9PRO0-0.022-0.02222.281-0.021-0.0210.0000.0000.0000.000
10H10SER00.0380.01323.839-0.070-0.0700.0000.0000.0000.000
11H11LEU0-0.048-0.00925.908-0.157-0.1570.0000.0000.0000.000
12H12VAL0-0.034-0.01128.984-0.078-0.0780.0000.0000.0000.000
13H13GLN00.0280.01531.810-0.206-0.2060.0000.0000.0000.000
14H14PRO00.034-0.00235.3470.1060.1060.0000.0000.0000.000
15H15SER0-0.025-0.00536.993-0.210-0.2100.0000.0000.0000.000
16H16GLN0-0.0060.02633.883-0.048-0.0480.0000.0000.0000.000
17H17THR0-0.037-0.05030.325-0.006-0.0060.0000.0000.0000.000
18H18LEU00.0190.03125.6770.0820.0820.0000.0000.0000.000
19H19SER0-0.009-0.02625.834-0.081-0.0810.0000.0000.0000.000
20H20LEU00.0180.04020.8750.1480.1480.0000.0000.0000.000
21H21THR0-0.040-0.04717.667-0.338-0.3380.0000.0000.0000.000
22H22CYS0-0.066-0.00414.3840.4500.4500.0000.0000.0000.000
23H23THR00.0270.03111.735-0.806-0.8060.0000.0000.0000.000
24H24VAL0-0.014-0.01310.0120.9880.9880.0000.0000.0000.000
25H25SER00.0180.0125.355-0.970-0.9700.0000.0000.0000.000
26H26GLY00.0830.0324.5921.8951.871-0.001-0.0310.0560.000
27H27PHE0-0.037-0.0235.214-0.394-0.283-0.001-0.009-0.1010.000
28H28SER00.0660.0428.482-1.195-1.1950.0000.0000.0000.000
29H29LEU00.0550.02012.127-0.348-0.3480.0000.0000.0000.000
30H30THR00.019-0.00115.065-0.550-0.5500.0000.0000.0000.000
31H31SER0-0.054-0.02213.458-0.354-0.3540.0000.0000.0000.000
32H32ASN0-0.023-0.01011.5541.5031.5030.0000.0000.0000.000
33H33SER0-0.0190.00014.932-0.863-0.8630.0000.0000.0000.000
34H34VAL00.0260.01113.7271.0511.0510.0000.0000.0000.000
35H35HIS00.0070.00716.353-1.462-1.4620.0000.0000.0000.000
36H36TRP00.005-0.00317.8180.9140.9140.0000.0000.0000.000
37H37VAL0-0.016-0.00319.363-0.659-0.6590.0000.0000.0000.000
38H38ARG10.7880.86620.638-10.240-10.2400.0000.0000.0000.000
39H39GLN00.002-0.01122.3990.3720.3720.0000.0000.0000.000
40H40PRO00.0250.01524.6780.1020.1020.0000.0000.0000.000
41H41PRO00.0110.01327.5610.1650.1650.0000.0000.0000.000
42H42GLY0-0.012-0.00928.211-0.378-0.3780.0000.0000.0000.000
43H43GLN0-0.020-0.00329.292-0.107-0.1070.0000.0000.0000.000
44H44GLY00.0350.01726.3000.3430.3430.0000.0000.0000.000
45H45LEU0-0.023-0.01620.7420.0480.0480.0000.0000.0000.000
46H46GLU-1-0.785-0.87324.55810.22610.2260.0000.0000.0000.000
47H47TRP0-0.012-0.00721.6700.1010.1010.0000.0000.0000.000
48H48MET0-0.019-0.00222.977-0.691-0.6910.0000.0000.0000.000
49H49GLY00.0410.00423.594-0.588-0.5880.0000.0000.0000.000
50H50GLY00.0180.01021.2280.6800.6800.0000.0000.0000.000
51H51ILE0-0.047-0.00119.183-0.592-0.5920.0000.0000.0000.000
52H52TRP00.024-0.01819.5061.1421.1420.0000.0000.0000.000
53H53GLY00.0440.03318.335-0.156-0.1560.0000.0000.0000.000
54H54ASP-1-0.791-0.88919.21912.16912.1690.0000.0000.0000.000
55H55GLY0-0.039-0.02122.052-0.442-0.4420.0000.0000.0000.000
56H56ARG10.8870.94323.479-11.865-11.8650.0000.0000.0000.000
57H57THR0-0.001-0.00823.9280.4580.4580.0000.0000.0000.000
58H58ASP-1-0.868-0.93025.3469.9559.9550.0000.0000.0000.000
59H59TYR00.017-0.00325.9560.4330.4330.0000.0000.0000.000
60H60ASN00.0120.00827.980-0.506-0.5060.0000.0000.0000.000
61H61SER0-0.008-0.02729.624-0.099-0.0990.0000.0000.0000.000
62H62ALA00.0120.01532.625-0.233-0.2330.0000.0000.0000.000
63H63LEU0-0.027-0.02528.345-0.178-0.1780.0000.0000.0000.000
64H64LYS10.8670.94430.800-9.738-9.7380.0000.0000.0000.000
65H65SER0-0.018-0.00832.7280.0840.0840.0000.0000.0000.000
66H66ARG10.8850.94932.219-9.345-9.3450.0000.0000.0000.000
67H67LEU0-0.027-0.00825.7850.1330.1330.0000.0000.0000.000
68H68SER0-0.039-0.01028.344-0.044-0.0440.0000.0000.0000.000
69H69ILE00.0090.01322.0460.3160.3160.0000.0000.0000.000
70H70SER00.0030.00923.471-0.164-0.1640.0000.0000.0000.000
71H71ARG10.8790.92319.012-13.624-13.6240.0000.0000.0000.000
72H72ASP-1-0.772-0.85719.31612.67112.6710.0000.0000.0000.000
73H73THR00.003-0.01517.1960.6280.6280.0000.0000.0000.000
74H74SER0-0.043-0.00916.4470.5840.5840.0000.0000.0000.000
75H75LYS10.8500.89716.251-12.125-12.1250.0000.0000.0000.000
76H76SER0-0.0250.00811.6040.5310.5310.0000.0000.0000.000
77H77GLN0-0.037-0.03413.8160.2650.2650.0000.0000.0000.000
78H78VAL0-0.003-0.00716.396-0.594-0.5940.0000.0000.0000.000
79H79PHE00.0110.00718.5320.2440.2440.0000.0000.0000.000
80H80LEU00.0110.00621.612-0.076-0.0760.0000.0000.0000.000
81H81LYS10.9450.96224.050-10.071-10.0710.0000.0000.0000.000
82H82MET00.0430.03027.290-0.110-0.1100.0000.0000.0000.000
83H83ASN0-0.042-0.00829.896-0.089-0.0890.0000.0000.0000.000
84H84SER00.0430.02733.480-0.236-0.2360.0000.0000.0000.000
85H85LEU0-0.058-0.01933.7390.0440.0440.0000.0000.0000.000
86H86GLN00.007-0.03235.175-0.236-0.2360.0000.0000.0000.000
87H87THR00.0320.01134.880-0.057-0.0570.0000.0000.0000.000
88H88ASH0-0.009-0.00733.9910.1290.1290.0000.0000.0000.000
89H89ASP-1-0.773-0.85730.2519.7639.7630.0000.0000.0000.000
90H90THR0-0.0170.01729.0370.4080.4080.0000.0000.0000.000
91H91ALA0-0.011-0.01325.716-0.099-0.0990.0000.0000.0000.000
92H92ILE00.0060.01920.3480.0900.0900.0000.0000.0000.000
93H93TYR0-0.023-0.04921.223-0.100-0.1000.0000.0000.0000.000
94H94PHE00.0370.02516.2490.4810.4810.0000.0000.0000.000
95H96THR00.001-0.00913.5040.9360.9360.0000.0000.0000.000
96H97ARG10.8420.8798.518-28.317-28.3170.0000.0000.0000.000
97H98CYS0-0.0260.02613.6180.4540.4540.0000.0000.0000.000
98H99ARG10.8770.94011.327-24.838-24.8380.0000.0000.0000.000
99H100ARG10.8920.92514.225-19.071-19.0710.0000.0000.0000.000
100H101ASP-1-0.834-0.91314.40818.92118.9210.0000.0000.0000.000
101H102SER0-0.038-0.01514.8860.3570.3570.0000.0000.0000.000
102H103SER0-0.009-0.01317.046-0.491-0.4910.0000.0000.0000.000
103H104TYR0-0.061-0.03717.933-0.411-0.4110.0000.0000.0000.000
104H105VAL00.0560.04215.776-0.385-0.3850.0000.0000.0000.000
105H106VAL00.016-0.01715.1360.8200.8200.0000.0000.0000.000
106H107ASP-1-0.781-0.85211.22926.24426.2440.0000.0000.0000.000
107H108ALA0-0.0020.0038.8942.3952.3950.0000.0000.0000.000
108H109TRP00.021-0.01310.383-2.468-2.4680.0000.0000.0000.000
109H110GLY0-0.0140.00710.9211.8221.8220.0000.0000.0000.000
110H111GLN0-0.021-0.00312.0851.4211.4210.0000.0000.0000.000
111H112GLY00.0280.01014.146-0.723-0.7230.0000.0000.0000.000
112H113ALA0-0.045-0.01717.574-0.096-0.0960.0000.0000.0000.000
113H114SER0-0.018-0.00119.895-0.490-0.4900.0000.0000.0000.000
114H115VAL00.0160.00623.280-0.059-0.0590.0000.0000.0000.000
115H116THR0-0.011-0.00326.258-0.245-0.2450.0000.0000.0000.000
116H117VAL0-0.013-0.00529.902-0.028-0.0280.0000.0000.0000.000
117H118SER0-0.003-0.01832.700-0.274-0.2740.0000.0000.0000.000
118H119SER00.0340.01535.8750.1050.1050.0000.0000.0000.000
119H120ALA0-0.0150.00437.447-0.065-0.0650.0000.0000.0000.000
120H121LYS10.9280.95736.822-7.829-7.8290.0000.0000.0000.000
121H122THR00.0170.00331.8570.0880.0880.0000.0000.0000.000
122H123THR0-0.005-0.00234.550-0.373-0.3730.0000.0000.0000.000
123H124PRO00.0200.03733.1250.2020.2020.0000.0000.0000.000
124H125LYN00.009-0.03128.844-0.137-0.1370.0000.0000.0000.000
125H126LEU00.0100.02833.661-0.085-0.0850.0000.0000.0000.000
126H127VAL0-0.011-0.00532.2370.0030.0030.0000.0000.0000.000
127H128TYR00.015-0.01135.117-0.197-0.1970.0000.0000.0000.000
128H129PRO0-0.0150.00135.9340.2800.2800.0000.0000.0000.000
129H130LEU0-0.007-0.01336.942-0.252-0.2520.0000.0000.0000.000
130H131ALA00.0340.01037.8300.2250.2250.0000.0000.0000.000
131H132PRO00.0280.02939.899-0.216-0.2160.0000.0000.0000.000
132H141VAL0-0.006-0.01636.013-0.052-0.0520.0000.0000.0000.000
133H142THR0-0.015-0.00435.5430.3270.3270.0000.0000.0000.000
134H143LEU00.0000.00234.278-0.299-0.2990.0000.0000.0000.000
135H144GLY00.0540.02433.6800.3530.3530.0000.0000.0000.000
136H145CYS0-0.055-0.01328.1930.1520.1520.0000.0000.0000.000
137H146LEU00.0330.01033.9900.0990.0990.0000.0000.0000.000
138H147VAL0-0.003-0.01130.626-0.118-0.1180.0000.0000.0000.000
139H148LYS10.9290.95033.940-7.840-7.8400.0000.0000.0000.000
140H149GLY00.0410.02136.6000.0010.0010.0000.0000.0000.000
141H150TYR00.014-0.00630.216-0.141-0.1410.0000.0000.0000.000
142H151PHE00.0330.03133.091-0.061-0.0610.0000.0000.0000.000
143H152PRO0-0.060-0.01829.135-0.070-0.0700.0000.0000.0000.000
144H153GLU-1-0.784-0.88727.66810.95210.9520.0000.0000.0000.000
145H154PRO0-0.024-0.01023.3820.0630.0630.0000.0000.0000.000
146H155VAL00.013-0.01526.231-0.126-0.1260.0000.0000.0000.000
147H156THR0-0.036-0.01020.6190.4470.4470.0000.0000.0000.000
148H157VAL0-0.023-0.03123.930-0.397-0.3970.0000.0000.0000.000
149H158THR00.0090.01521.0020.3300.3300.0000.0000.0000.000
150H159TRP00.006-0.00823.941-0.356-0.3560.0000.0000.0000.000
151H160ASN0-0.049-0.02424.415-0.131-0.1310.0000.0000.0000.000
152H161SER00.0150.01719.9840.4370.4370.0000.0000.0000.000
153H169HIS00.0070.00228.1940.3810.3810.0000.0000.0000.000
154H170THR00.012-0.01926.461-0.455-0.4550.0000.0000.0000.000
155H171PHE0-0.0200.00528.8190.2010.2010.0000.0000.0000.000
156H172PRO00.019-0.00330.1320.1270.1270.0000.0000.0000.000
157H173ALA00.0010.00930.954-0.303-0.3030.0000.0000.0000.000
158H174VAL0-0.007-0.00632.751-0.078-0.0780.0000.0000.0000.000
159H175LEU0-0.036-0.01436.183-0.029-0.0290.0000.0000.0000.000
160H176GLN0-0.031-0.03337.736-0.126-0.1260.0000.0000.0000.000
161H177SER00.0240.00641.071-0.031-0.0310.0000.0000.0000.000
162H178GLY00.0150.01539.573-0.069-0.0690.0000.0000.0000.000
163H179LEU0-0.039-0.00837.1980.2050.2050.0000.0000.0000.000
164H180TYR00.027-0.00133.008-0.135-0.1350.0000.0000.0000.000
165H181THR0-0.025-0.01135.374-0.190-0.1900.0000.0000.0000.000
166H182LEU00.0290.02628.6900.0440.0440.0000.0000.0000.000
167H183THR00.000-0.01232.317-0.280-0.2800.0000.0000.0000.000
168H184SER0-0.0030.01729.2740.1640.1640.0000.0000.0000.000
169H185SER0-0.010-0.01031.125-0.337-0.3370.0000.0000.0000.000
170H186VAL0-0.0060.01228.5870.2910.2910.0000.0000.0000.000
171H187THR00.0420.01830.638-0.336-0.3360.0000.0000.0000.000
172H196VAL00.006-0.00430.3010.0900.0900.0000.0000.0000.000
173H197THR0-0.017-0.02428.273-0.228-0.2280.0000.0000.0000.000
174H199ASN0-0.015-0.02024.574-0.077-0.0770.0000.0000.0000.000
175H200VAL00.000-0.01025.5670.2900.2900.0000.0000.0000.000
176H201ALA00.0400.02323.686-0.099-0.0990.0000.0000.0000.000
177H202HIS00.0040.00625.7500.0100.0100.0000.0000.0000.000
178H203PRO00.0500.02023.187-0.281-0.2810.0000.0000.0000.000
179H204ALA00.0160.02425.563-0.172-0.1720.0000.0000.0000.000
180H205SER00.0010.00728.335-0.350-0.3500.0000.0000.0000.000
181H206SER0-0.068-0.02427.241-0.125-0.1250.0000.0000.0000.000
182H207THR0-0.069-0.03228.317-0.152-0.1520.0000.0000.0000.000
183H208LYS10.9350.93225.029-11.247-11.2470.0000.0000.0000.000
184H209VAL00.015-0.01127.487-0.438-0.4380.0000.0000.0000.000
185H210ASP-1-0.787-0.82626.95011.54311.5430.0000.0000.0000.000
186H211LYS10.8460.95129.790-9.044-9.0440.0000.0000.0000.000
187H212LYS10.9260.98031.388-9.616-9.6160.0000.0000.0000.000