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: Z6GMN

Calculation Name: 5UD9-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5UD9

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2449950.633569
FMO2-HF: Nuclear repulsion 2362345.961196
FMO2-HF: Total energy -87604.672373
FMO2-MP2: Total energy -87858.996372


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.
-13.144-5.10512.444-6.816-13.662-0.039
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 : -0.036 / q_NPA : -0.024
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].
3H4LEU00.0290.0233.711-1.1560.719-0.019-0.829-1.0260.003
4H5ARG10.8330.9025.768-0.631-0.6310.0000.0000.0000.000
5H6GLU-1-0.720-0.8649.778-0.276-0.2760.0000.0000.0000.000
6H7SER0-0.085-0.04312.6500.0430.0430.0000.0000.0000.000
7H8GLY00.0860.01015.987-0.021-0.0210.0000.0000.0000.000
8H9PRO00.0270.02619.2270.0100.0100.0000.0000.0000.000
9H10GLY00.0150.02021.9080.0070.0070.0000.0000.0000.000
10H11LEU0-0.060-0.03723.288-0.006-0.0060.0000.0000.0000.000
11H12VAL00.0040.00125.1330.0010.0010.0000.0000.0000.000
12H13LYS10.8800.94427.9790.0120.0120.0000.0000.0000.000
13H14PRO00.020-0.00931.056-0.004-0.0040.0000.0000.0000.000
14H15SER0-0.080-0.03532.3300.0040.0040.0000.0000.0000.000
15H16GLU-1-0.845-0.91529.716-0.022-0.0220.0000.0000.0000.000
16H17THR0-0.037-0.03226.423-0.005-0.0050.0000.0000.0000.000
17H18LEU00.0080.01820.6430.0060.0060.0000.0000.0000.000
18H19SER0-0.004-0.01520.336-0.003-0.0030.0000.0000.0000.000
19H20LEU0-0.036-0.00116.2640.0110.0110.0000.0000.0000.000
20H21SER0-0.062-0.03514.6370.0050.0050.0000.0000.0000.000
21H22CYS0-0.0560.0108.746-0.004-0.0040.0000.0000.0000.000
22H23THR00.0110.0099.527-0.002-0.0020.0000.0000.0000.000
23H24VAL00.0390.0243.668-0.222-0.0130.007-0.043-0.1730.000
24H25SER00.0200.0154.366-0.1430.026-0.001-0.053-0.1140.000
25H26GLN00.032-0.0022.192-3.705-2.2104.729-2.958-3.266-0.017
26H27ASP-1-0.792-0.8822.168-6.853-3.6163.351-2.568-4.020-0.015
27H28SER0-0.021-0.0093.0591.3220.5060.1011.053-0.337-0.001
28H29ARG10.8850.9575.5700.3790.3790.0000.0000.0000.000
29H30PRO00.0280.0156.186-0.101-0.1010.0000.0000.0000.000
30H31SER00.010-0.0037.2500.0000.0000.0000.0000.0000.000
31H32ASP-1-0.837-0.9278.948-0.307-0.3070.0000.0000.0000.000
32H33HIS00.0150.0205.737-0.005-0.0050.0000.0000.0000.000
33H34SER00.001-0.0019.2030.0650.0650.0000.0000.0000.000
34H35TRP0-0.070-0.0403.685-0.380-0.1400.006-0.041-0.2040.000
35H36THR0-0.034-0.0509.9630.0760.0760.0000.0000.0000.000
36H37TRP0-0.011-0.01511.260-0.038-0.0380.0000.0000.0000.000
37H38VAL0-0.001-0.00113.7890.0140.0140.0000.0000.0000.000
38H39ARG10.7790.86615.8930.1230.1230.0000.0000.0000.000
39H40GLN00.0050.01018.603-0.018-0.0180.0000.0000.0000.000
40H41SER00.0540.03920.9280.0060.0060.0000.0000.0000.000
41H42PRO00.007-0.01224.477-0.006-0.0060.0000.0000.0000.000
42H43GLY00.0220.02925.0700.0050.0050.0000.0000.0000.000
43H44LYS10.8480.91924.6800.0930.0930.0000.0000.0000.000
44H45ALA00.0560.02822.884-0.008-0.0080.0000.0000.0000.000
45H46LEU0-0.0010.00316.0440.0050.0050.0000.0000.0000.000
46H47GLU-1-0.784-0.87119.929-0.122-0.1220.0000.0000.0000.000
47H48TRP00.0070.00215.2770.0060.0060.0000.0000.0000.000
48H49ILE00.002-0.00617.4290.0240.0240.0000.0000.0000.000
49H50GLY00.0710.01517.0680.0240.0240.0000.0000.0000.000
50H51ASP-1-0.878-0.87713.430-0.289-0.2890.0000.0000.0000.000
51H52ILE0-0.0050.00813.1300.0360.0360.0000.0000.0000.000
52H53HIS00.0250.02112.591-0.015-0.0150.0000.0000.0000.000
53H54TYR00.0560.0109.7660.0210.0210.0000.0000.0000.000
54H55ASN0-0.0090.00314.4570.0160.0160.0000.0000.0000.000
55H56GLY00.0010.00817.1750.0150.0150.0000.0000.0000.000
56H57ALA0-0.035-0.01018.4800.0060.0060.0000.0000.0000.000
57H58THR0-0.015-0.02417.446-0.013-0.0130.0000.0000.0000.000
58H59THR0-0.060-0.03617.7420.0140.0140.0000.0000.0000.000
59H60TYR00.031-0.01319.032-0.006-0.0060.0000.0000.0000.000
60H61ASN00.0010.01621.2860.0140.0140.0000.0000.0000.000
61H62PRO00.008-0.00523.0400.0090.0090.0000.0000.0000.000
62H63SER0-0.048-0.03026.2180.0090.0090.0000.0000.0000.000
63H64LEU00.009-0.00122.4910.0060.0060.0000.0000.0000.000
64H65ARG10.9510.98024.6320.1010.1010.0000.0000.0000.000
65H66SER0-0.014-0.00325.9170.0020.0020.0000.0000.0000.000
66H67ARG10.7960.87426.7100.0810.0810.0000.0000.0000.000
67H68VAL0-0.039-0.00621.6010.0020.0020.0000.0000.0000.000
68H69ARG10.8730.93221.3590.0630.0630.0000.0000.0000.000
69H70ILE00.0130.02115.1710.0010.0010.0000.0000.0000.000
70H71GLU-1-0.801-0.87117.068-0.053-0.0530.0000.0000.0000.000
71H72LEU00.004-0.00611.396-0.015-0.0150.0000.0000.0000.000
72H73ASP-1-0.762-0.83014.4770.0480.0480.0000.0000.0000.000
73H74GLN00.022-0.01612.5970.0160.0160.0000.0000.0000.000
74H75SER0-0.077-0.05313.0030.0210.0210.0000.0000.0000.000
75H76ILE0-0.0490.00310.7700.0300.0300.0000.0000.0000.000
76H77PRO00.0000.0107.5830.0740.0740.0000.0000.0000.000
77H78ARG10.8500.8909.184-0.030-0.0300.0000.0000.0000.000
78H79PHE00.0190.0137.696-0.002-0.0020.0000.0000.0000.000
79H80SER0-0.037-0.05812.8500.0000.0000.0000.0000.0000.000
80H81LEU00.0350.02415.719-0.022-0.0220.0000.0000.0000.000
81H82LYS10.8610.92817.7320.0650.0650.0000.0000.0000.000
82H83MET00.0120.00921.528-0.008-0.0080.0000.0000.0000.000
83H84THR00.0160.00124.1330.0060.0060.0000.0000.0000.000
84H85SER00.0320.00727.904-0.003-0.0030.0000.0000.0000.000
85H86MET0-0.0210.02024.319-0.005-0.0050.0000.0000.0000.000
86H87THR00.008-0.01528.9460.0060.0060.0000.0000.0000.000
87H88ALA00.0460.00729.252-0.003-0.0030.0000.0000.0000.000
88H89ALA00.0040.00229.452-0.003-0.0030.0000.0000.0000.000
89H90ASP-1-0.735-0.81125.471-0.084-0.0840.0000.0000.0000.000
90H91THR00.0040.01624.561-0.003-0.0030.0000.0000.0000.000
91H92GLY00.001-0.02322.959-0.003-0.0030.0000.0000.0000.000
92H93MET0-0.0440.01517.0020.0140.0140.0000.0000.0000.000
93H94TYR0-0.018-0.04016.775-0.010-0.0100.0000.0000.0000.000
94H95TYR00.0380.00012.2970.0080.0080.0000.0000.0000.000
95H97ALA00.0370.0047.391-0.075-0.0750.0000.0000.0000.000
96H98ARG10.8160.8802.4010.3571.6701.741-0.772-2.282-0.006
97H99ASN0-0.023-0.0106.381-0.090-0.0900.0000.0000.0000.000
98H100ALA00.0130.0086.1460.0710.0710.0000.0000.0000.000
99H101ILE00.0010.0107.9010.0830.0830.0000.0000.0000.000
100H102ARG10.7650.8927.1200.6880.6880.0000.0000.0000.000
101H103ILE00.026-0.00112.4340.0230.0230.0000.0000.0000.000
102H104TYR0-0.054-0.02115.508-0.008-0.0080.0000.0000.0000.000
103H105GLY00.0460.03018.5740.0160.0160.0000.0000.0000.000
104H106VAL0-0.024-0.01620.313-0.007-0.0070.0000.0000.0000.000
105H107VAL00.0360.00917.783-0.001-0.0010.0000.0000.0000.000
106H108ALA0-0.039-0.02620.497-0.003-0.0030.0000.0000.0000.000
107H109LEU0-0.022-0.01123.6510.0070.0070.0000.0000.0000.000
108H110GLY00.0060.01021.5850.0020.0020.0000.0000.0000.000
109H111GLU-1-0.869-0.91121.185-0.130-0.1300.0000.0000.0000.000
110H112TRP0-0.054-0.04215.193-0.016-0.0160.0000.0000.0000.000
111H113PHE00.0160.01114.4750.0090.0090.0000.0000.0000.000
112H114HIS00.005-0.01511.952-0.021-0.0210.0000.0000.0000.000
113H115TYR0-0.043-0.0269.3880.0410.0410.0000.0000.0000.000
114H116GLY00.0510.02811.1520.0250.0250.0000.0000.0000.000
115H117MET0-0.048-0.0329.125-0.076-0.0760.0000.0000.0000.000
116H118ASP-1-0.779-0.8565.322-1.433-1.4330.0000.0000.0000.000
117H119VAL0-0.0100.0002.237-1.033-0.8102.530-0.604-2.149-0.003
118H120TRP00.016-0.0145.2480.1980.292-0.001-0.001-0.0910.000
119H121GLY00.0050.0096.835-0.139-0.1390.0000.0000.0000.000
120H122GLN0-0.068-0.0518.6730.0230.0230.0000.0000.0000.000
121H123GLY00.0420.03511.8240.0350.0350.0000.0000.0000.000
122H124THR0-0.069-0.04213.9430.0540.0540.0000.0000.0000.000
123H125ALA00.0180.01516.862-0.010-0.0100.0000.0000.0000.000
124H126VAL0-0.028-0.01620.1390.0100.0100.0000.0000.0000.000
125H127THR00.0000.00122.749-0.005-0.0050.0000.0000.0000.000
126H128VAL00.0010.00626.5320.0040.0040.0000.0000.0000.000
127H129SER00.003-0.00729.2270.0010.0010.0000.0000.0000.000
128H130SER00.0660.01432.4920.0010.0010.0000.0000.0000.000
129H131ALA0-0.0060.02734.1320.0030.0030.0000.0000.0000.000
130H132SER00.012-0.00633.608-0.002-0.0020.0000.0000.0000.000
131H133THR0-0.007-0.00228.685-0.002-0.0020.0000.0000.0000.000
132H134LYS10.8000.91031.446-0.012-0.0120.0000.0000.0000.000
133H135GLY00.0870.05030.119-0.002-0.0020.0000.0000.0000.000
134H136PRO0-0.022-0.00928.936-0.002-0.0020.0000.0000.0000.000
135H137SER0-0.029-0.01732.0150.0020.0020.0000.0000.0000.000
136H138VAL0-0.0020.00231.305-0.003-0.0030.0000.0000.0000.000
137H139PHE00.0130.00534.5560.0020.0020.0000.0000.0000.000
138H140PRO0-0.0080.00035.5870.0000.0000.0000.0000.0000.000
139H141LEU0-0.010-0.00434.255-0.003-0.0030.0000.0000.0000.000
140H142ALA00.0360.01336.5680.0020.0020.0000.0000.0000.000
141H143PRO00.0540.03637.172-0.003-0.0030.0000.0000.0000.000
142H144SER0-0.046-0.02138.873-0.001-0.0010.0000.0000.0000.000
143H145SER00.0320.01641.7330.0010.0010.0000.0000.0000.000
144H146LYS10.9380.98344.402-0.018-0.0180.0000.0000.0000.000
145H147SER0-0.0030.00145.0970.0000.0000.0000.0000.0000.000
146H148THR00.030-0.00442.1620.0000.0000.0000.0000.0000.000
147H149SER0-0.0040.00343.4700.0000.0000.0000.0000.0000.000
148H150GLY00.0460.04141.0160.0000.0000.0000.0000.0000.000
149H151GLY00.0230.00838.654-0.001-0.0010.0000.0000.0000.000
150H152THR0-0.064-0.04734.3370.0030.0030.0000.0000.0000.000
151H153ALA00.0330.02135.937-0.004-0.0040.0000.0000.0000.000
152H154ALA00.0070.00734.0030.0030.0030.0000.0000.0000.000
153H155LEU0-0.018-0.00431.843-0.001-0.0010.0000.0000.0000.000
154H156GLY00.0570.00631.7370.0000.0000.0000.0000.0000.000
155H157CYS0-0.092-0.00527.2990.0080.0080.0000.0000.0000.000
156H158LEU00.0430.04231.800-0.003-0.0030.0000.0000.0000.000
157H159VAL0-0.027-0.02329.1020.0040.0040.0000.0000.0000.000
158H160LYS10.8580.90432.342-0.011-0.0110.0000.0000.0000.000
159H161ASP-1-0.785-0.87733.8520.0080.0080.0000.0000.0000.000
160H162TYR0-0.030-0.02927.7370.0050.0050.0000.0000.0000.000
161H163PHE00.0410.02230.264-0.006-0.0060.0000.0000.0000.000
162H164PRO00.0260.01925.9230.0050.0050.0000.0000.0000.000
163H165GLU-1-0.766-0.87124.751-0.015-0.0150.0000.0000.0000.000
164H166PRO0-0.039-0.01720.290-0.005-0.0050.0000.0000.0000.000
165H167VAL0-0.015-0.01123.5940.0090.0090.0000.0000.0000.000
166H168THR0-0.037-0.02119.238-0.005-0.0050.0000.0000.0000.000
167H169VAL0-0.002-0.01222.4570.0080.0080.0000.0000.0000.000
168H170SER0-0.0010.01420.4720.0010.0010.0000.0000.0000.000
169H171TRP00.0210.00122.477-0.008-0.0080.0000.0000.0000.000
170H172ASN00.007-0.00723.5370.0080.0080.0000.0000.0000.000
171H173SER0-0.011-0.01322.8640.0060.0060.0000.0000.0000.000
172H174GLY00.0050.01119.4310.0270.0270.0000.0000.0000.000
173H175ALA0-0.034-0.00919.9550.0060.0060.0000.0000.0000.000
174H176LEU0-0.039-0.01122.300-0.010-0.0100.0000.0000.0000.000
175H177THR00.019-0.00218.579-0.007-0.0070.0000.0000.0000.000
176H178SER00.0340.01121.897-0.020-0.0200.0000.0000.0000.000
177H179GLY00.0450.01923.9760.0030.0030.0000.0000.0000.000
178H180VAL0-0.048-0.01123.610-0.004-0.0040.0000.0000.0000.000
179H181HIS00.0050.00624.854-0.005-0.0050.0000.0000.0000.000
180H182THR00.0060.00124.1950.0080.0080.0000.0000.0000.000
181H183PHE0-0.0190.00526.049-0.009-0.0090.0000.0000.0000.000
182H184PRO00.033-0.00426.6280.0030.0030.0000.0000.0000.000
183H185ALA0-0.0070.00628.0440.0040.0040.0000.0000.0000.000
184H186VAL0-0.0100.00230.039-0.005-0.0050.0000.0000.0000.000
185H187LEU0-0.020-0.01232.6290.0030.0030.0000.0000.0000.000
186H188GLN0-0.047-0.03634.1550.0010.0010.0000.0000.0000.000
187H189SER00.0330.00637.701-0.001-0.0010.0000.0000.0000.000
188H190SER0-0.0030.00038.830-0.001-0.0010.0000.0000.0000.000
189H191GLY00.0130.01036.4190.0010.0010.0000.0000.0000.000
190H192LEU0-0.050-0.01234.094-0.001-0.0010.0000.0000.0000.000
191H193TYR00.0350.01229.347-0.001-0.0010.0000.0000.0000.000
192H194SER00.0170.00232.5620.0060.0060.0000.0000.0000.000
193H195LEU00.0120.03526.505-0.003-0.0030.0000.0000.0000.000
194H196SER00.000-0.01930.6140.0050.0050.0000.0000.0000.000
195H197SER0-0.0160.00726.237-0.001-0.0010.0000.0000.0000.000
196H198VAL00.009-0.01628.6170.0020.0020.0000.0000.0000.000
197H199VAL00.0190.01327.6000.0010.0010.0000.0000.0000.000
198H200THR0-0.023-0.00329.559-0.003-0.0030.0000.0000.0000.000
199H201VAL00.0370.02330.2350.0050.0050.0000.0000.0000.000
200H202PRO00.0700.03731.545-0.006-0.0060.0000.0000.0000.000
201H203SER00.0030.00134.7990.0030.0030.0000.0000.0000.000
202H204SER0-0.0020.00037.4010.0000.0000.0000.0000.0000.000
203H205SER0-0.008-0.01033.8600.0020.0020.0000.0000.0000.000
204H206LEU0-0.0040.00135.9360.0020.0020.0000.0000.0000.000
205H207GLY00.0000.00337.802-0.001-0.0010.0000.0000.0000.000
206H208THR0-0.054-0.03037.0970.0010.0010.0000.0000.0000.000
207H209GLN0-0.045-0.01430.5330.0070.0070.0000.0000.0000.000
208H210THR0-0.0040.00831.859-0.004-0.0040.0000.0000.0000.000
209H211TYR00.0380.00029.6210.0100.0100.0000.0000.0000.000
210H212ILE00.019-0.00428.594-0.006-0.0060.0000.0000.0000.000
211H214ASN00.013-0.01523.6840.0000.0000.0000.0000.0000.000
212H215VAL0-0.0050.00224.536-0.001-0.0010.0000.0000.0000.000
213H216ASN00.0030.00121.0810.0130.0130.0000.0000.0000.000
214H217HIS00.0280.01924.208-0.003-0.0030.0000.0000.0000.000
215H218LYS10.8900.94016.6590.0240.0240.0000.0000.0000.000
216H219PRO00.0270.01622.5550.0030.0030.0000.0000.0000.000
217H220SER0-0.019-0.04024.9590.0010.0010.0000.0000.0000.000
218H221ASN0-0.059-0.01924.1990.0090.0090.0000.0000.0000.000
219H222THR00.0070.02325.9400.0070.0070.0000.0000.0000.000
220H223LYS10.8550.90822.239-0.111-0.1110.0000.0000.0000.000
221H224VAL0-0.003-0.00227.443-0.002-0.0020.0000.0000.0000.000
222H225ASP-1-0.808-0.89726.5160.1010.1010.0000.0000.0000.000
223H226LYS10.8940.94729.456-0.047-0.0470.0000.0000.0000.000
224H227ARG10.9040.93731.815-0.065-0.0650.0000.0000.0000.000
225H228VAL0-0.047-0.02332.852-0.006-0.0060.0000.0000.0000.000
226H229GLU-1-0.836-0.90835.1350.0570.0570.0000.0000.0000.000
227H230PRO00.016-0.00838.056-0.004-0.0040.0000.0000.0000.000
228H231LYS10.8380.91740.867-0.024-0.0240.0000.0000.0000.000
229H232SER00.0210.02243.7880.0000.0000.0000.0000.0000.000