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: G64K1

Calculation Name: 5U3J-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U3J

Chain ID: H

ChEMBL ID:

UniProt ID: V9QIE5

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2397490.620656
FMO2-HF: Nuclear repulsion 2308626.600252
FMO2-HF: Total energy -88864.020404
FMO2-MP2: Total energy -89123.089361


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.
-65.238-62.4620.002-1.038-1.740.002
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 : -0.905 / q_NPA : -0.961
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].
3H3GLN0-0.055-0.0163.873-7.062-5.0510.002-0.765-1.2480.002
4H4LEU00.0400.0095.545-1.882-1.8820.0000.0000.0000.000
5H5VAL00.008-0.0037.994-0.075-0.0750.0000.0000.0000.000
6H6GLU-1-0.774-0.88310.61718.79718.7970.0000.0000.0000.000
7H7SER0-0.037-0.03814.4060.0910.0910.0000.0000.0000.000
8H8GLY00.0280.01317.272-0.247-0.2470.0000.0000.0000.000
9H9GLY0-0.0130.00720.365-0.583-0.5830.0000.0000.0000.000
10H10GLY00.015-0.00222.1870.1180.1180.0000.0000.0000.000
11H11LEU0-0.049-0.01425.320-0.156-0.1560.0000.0000.0000.000
12H12VAL00.0210.01429.049-0.014-0.0140.0000.0000.0000.000
13H13LYS10.8450.92231.294-8.350-8.3500.0000.0000.0000.000
14H14PRO00.025-0.00534.7050.1130.1130.0000.0000.0000.000
15H15GLY0-0.0100.00836.325-0.162-0.1620.0000.0000.0000.000
16H16GLY00.0000.00734.328-0.011-0.0110.0000.0000.0000.000
17H17SER0-0.022-0.02231.224-0.024-0.0240.0000.0000.0000.000
18H18LEU0-0.012-0.00625.114-0.058-0.0580.0000.0000.0000.000
19H19ARG10.8930.93123.117-11.374-11.3740.0000.0000.0000.000
20H20LEU0-0.0090.01719.9720.2690.2690.0000.0000.0000.000
21H21SER0-0.025-0.02017.779-0.143-0.1430.0000.0000.0000.000
22H22CYS0-0.0080.00412.8830.4910.4910.0000.0000.0000.000
23H23ALA00.0270.04210.664-0.792-0.7920.0000.0000.0000.000
24H24ALA00.0250.0038.9820.9850.9850.0000.0000.0000.000
25H25SER0-0.009-0.0163.569-1.307-0.7790.001-0.205-0.3240.000
26H26GLY00.0360.0114.2460.8430.9240.000-0.054-0.0270.000
27H27PHE00.002-0.0024.986-1.339-1.183-0.001-0.014-0.1410.000
28H28THR00.0280.0118.638-0.069-0.0690.0000.0000.0000.000
29H29PHE00.0690.04811.600-1.422-1.4220.0000.0000.0000.000
30H30SER00.0230.00913.149-0.877-0.8770.0000.0000.0000.000
31H31ASN0-0.035-0.01015.694-1.876-1.8760.0000.0000.0000.000
32H32THR00.0280.01313.953-0.205-0.2050.0000.0000.0000.000
33H33TRP0-0.023-0.00616.577-0.553-0.5530.0000.0000.0000.000
34H34MET0-0.0190.02213.3481.1561.1560.0000.0000.0000.000
35H35SER0-0.009-0.02117.799-1.121-1.1210.0000.0000.0000.000
36H36TRP0-0.019-0.01117.6540.8270.8270.0000.0000.0000.000
37H37VAL00.0350.01519.384-0.777-0.7770.0000.0000.0000.000
38H38ARG10.7360.82820.372-10.053-10.0530.0000.0000.0000.000
39H39GLN00.001-0.00421.7460.3370.3370.0000.0000.0000.000
40H40ALA00.0360.03024.0170.0690.0690.0000.0000.0000.000
41H41PRO00.009-0.00826.8130.1250.1250.0000.0000.0000.000
42H42GLY00.0140.00127.363-0.397-0.3970.0000.0000.0000.000
43H43LYS10.8770.94827.555-9.724-9.7240.0000.0000.0000.000
44H44GLY00.0610.03426.1750.3670.3670.0000.0000.0000.000
45H45LEU0-0.0040.00020.335-0.058-0.0580.0000.0000.0000.000
46H46GLU-1-0.823-0.88024.2289.8529.8520.0000.0000.0000.000
47H47TRP00.0320.01722.8740.0520.0520.0000.0000.0000.000
48H48VAL0-0.021-0.01323.684-0.481-0.4810.0000.0000.0000.000
49H49GLY00.046-0.00523.901-0.569-0.5690.0000.0000.0000.000
50H50ARG10.7670.89722.372-10.909-10.9090.0000.0000.0000.000
51H51ILE0-0.041-0.02420.640-0.609-0.6090.0000.0000.0000.000
52H52SER00.0370.02921.2510.5450.5450.0000.0000.0000.000
53H52ARG10.8460.91119.395-13.464-13.4640.0000.0000.0000.000
54H52ASN00.021-0.01920.604-1.081-1.0810.0000.0000.0000.000
55H52LYS10.8660.93022.751-12.018-12.0180.0000.0000.0000.000
56H53ASP-1-0.806-0.88323.93911.92911.9290.0000.0000.0000.000
57H54GLY00.0120.00626.487-0.338-0.3380.0000.0000.0000.000
58H55ALA0-0.027-0.00924.596-0.229-0.2290.0000.0000.0000.000
59H56LYS10.9440.98225.564-9.601-9.6010.0000.0000.0000.000
60H57THR00.0340.02025.2750.3120.3120.0000.0000.0000.000
61H58GLU-1-0.867-0.89826.79110.15510.1550.0000.0000.0000.000
62H59TYR00.0260.01527.0230.4330.4330.0000.0000.0000.000
63H60ALA00.0700.04028.347-0.381-0.3810.0000.0000.0000.000
64H61ALA0-0.012-0.02430.082-0.122-0.1220.0000.0000.0000.000
65H62PRO00.0180.01530.896-0.172-0.1720.0000.0000.0000.000
66H63VAL00.0140.01228.150-0.083-0.0830.0000.0000.0000.000
67H64ARG10.8920.95331.414-8.946-8.9460.0000.0000.0000.000
68H65GLY00.0160.01133.093-0.236-0.2360.0000.0000.0000.000
69H66ARG10.7300.84431.839-9.217-9.2170.0000.0000.0000.000
70H67PHE00.003-0.00526.8470.1370.1370.0000.0000.0000.000
71H68THR0-0.040-0.02627.488-0.308-0.3080.0000.0000.0000.000
72H69ILE0-0.0040.01421.9980.2310.2310.0000.0000.0000.000
73H70SER0-0.003-0.00822.689-0.255-0.2550.0000.0000.0000.000
74H71ARG10.7390.84116.770-14.923-14.9230.0000.0000.0000.000
75H72ASP-1-0.803-0.90718.12613.62113.6210.0000.0000.0000.000
76H73ASP-1-0.745-0.87116.25915.98715.9870.0000.0000.0000.000
77H74SER0-0.0300.00516.5650.0850.0850.0000.0000.0000.000
78H75ARG10.8440.92714.351-16.121-16.1210.0000.0000.0000.000
79H76ASP-1-0.844-0.91711.11721.62421.6240.0000.0000.0000.000
80H77THR0-0.033-0.01512.2351.0511.0510.0000.0000.0000.000
81H78LEU0-0.0150.00114.927-0.948-0.9480.0000.0000.0000.000
82H79TYR0-0.063-0.06217.3140.3240.3240.0000.0000.0000.000
83H80LEU00.0190.00620.478-0.211-0.2110.0000.0000.0000.000
84H81GLN00.0140.02723.2330.1100.1100.0000.0000.0000.000
85H82MET0-0.0210.00125.530-0.111-0.1110.0000.0000.0000.000
86H82THR0-0.008-0.03228.644-0.186-0.1860.0000.0000.0000.000
87H82SER00.0480.02032.464-0.069-0.0690.0000.0000.0000.000
88H82LEU0-0.0370.00628.864-0.021-0.0210.0000.0000.0000.000
89H83LYS10.9140.94932.768-8.511-8.5110.0000.0000.0000.000
90H84ILE00.0420.02332.6230.2650.2650.0000.0000.0000.000
91H85GLU-1-0.834-0.92832.3468.5598.5590.0000.0000.0000.000
92H86ASP-1-0.765-0.82329.0029.7259.7250.0000.0000.0000.000
93H87SER0-0.0190.00127.7210.4460.4460.0000.0000.0000.000
94H88GLY00.011-0.00725.463-0.179-0.1790.0000.0000.0000.000
95H89ARG10.7950.91015.662-15.811-15.8110.0000.0000.0000.000
96H90TYR0-0.015-0.03420.239-0.344-0.3440.0000.0000.0000.000
97H91PHE0-0.003-0.01015.1960.4060.4060.0000.0000.0000.000
98H92CYS0-0.031-0.01313.767-0.869-0.8690.0000.0000.0000.000
99H93THR0-0.038-0.03114.1290.2670.2670.0000.0000.0000.000
100H94ALA00.0520.02512.463-0.722-0.7220.0000.0000.0000.000
101H95ASP-1-0.807-0.88714.46415.26515.2650.0000.0000.0000.000
102H96LEU0-0.025-0.01214.3520.2750.2750.0000.0000.0000.000
103H97GLY0-0.012-0.02018.293-0.592-0.5920.0000.0000.0000.000
104H98GLU-1-0.910-0.92721.77013.06913.0690.0000.0000.0000.000
105H99PRO0-0.029-0.02523.571-0.509-0.5090.0000.0000.0000.000
106H100VAL00.0030.01027.0140.0270.0270.0000.0000.0000.000
107H100VAL00.0280.01028.771-0.236-0.2360.0000.0000.0000.000
108H100SER0-0.028-0.01131.446-0.289-0.2890.0000.0000.0000.000
109H100ARG10.8790.92533.723-8.561-8.5610.0000.0000.0000.000
110H100PHE00.0540.02835.7960.0760.0760.0000.0000.0000.000
111H100PHE0-0.015-0.02037.6470.0430.0430.0000.0000.0000.000
112H100GLU-1-0.830-0.89634.4228.4968.4960.0000.0000.0000.000
113H100TRP0-0.037-0.00633.1490.2340.2340.0000.0000.0000.000
114H100GLY0-0.0060.00631.538-0.202-0.2020.0000.0000.0000.000
115H100SER0-0.075-0.04430.7160.2640.2640.0000.0000.0000.000
116H100TYR00.013-0.01025.5210.2140.2140.0000.0000.0000.000
117H100TYR00.0030.00224.749-0.218-0.2180.0000.0000.0000.000
118H100TYR0-0.061-0.08421.0250.3720.3720.0000.0000.0000.000
119H100TYR0-0.087-0.06115.754-0.779-0.7790.0000.0000.0000.000
120H100MET00.0110.00517.4390.1760.1760.0000.0000.0000.000
121H101ASP-1-0.852-0.89412.35220.75620.7560.0000.0000.0000.000
122H102LEU00.0330.0277.5720.7310.7310.0000.0000.0000.000
123H103TRP0-0.024-0.03511.138-1.596-1.5960.0000.0000.0000.000
124H104GLY00.0400.03410.0332.0412.0410.0000.0000.0000.000
125H105LYS10.9420.9608.016-28.041-28.0410.0000.0000.0000.000
126H106GLY00.0230.02512.363-1.306-1.3060.0000.0000.0000.000
127H107THR0-0.036-0.01815.669-0.073-0.0730.0000.0000.0000.000
128H108THR0-0.018-0.01818.273-0.245-0.2450.0000.0000.0000.000
129H109VAL00.0010.00821.979-0.083-0.0830.0000.0000.0000.000
130H110THR0-0.046-0.02825.309-0.108-0.1080.0000.0000.0000.000
131H111VAL00.0450.02528.787-0.104-0.1040.0000.0000.0000.000
132H112SER00.023-0.00231.798-0.309-0.3090.0000.0000.0000.000
133H113SER00.0500.00534.9230.1080.1080.0000.0000.0000.000
134H114ALA0-0.0140.02736.725-0.145-0.1450.0000.0000.0000.000
135H115SER00.014-0.00837.0040.2020.2020.0000.0000.0000.000
136H116THR0-0.034-0.01835.580-0.030-0.0300.0000.0000.0000.000
137H117LYS10.8300.91837.425-7.399-7.3990.0000.0000.0000.000
138H118GLY00.0770.04438.3520.1910.1910.0000.0000.0000.000
139H119PRO0-0.054-0.01838.185-0.153-0.1530.0000.0000.0000.000
140H120SER0-0.015-0.00140.745-0.123-0.1230.0000.0000.0000.000
141H121VAL0-0.009-0.00243.0050.0660.0660.0000.0000.0000.000
142H122PHE00.008-0.00344.700-0.178-0.1780.0000.0000.0000.000
143H123PRO0-0.004-0.01546.4330.1160.1160.0000.0000.0000.000
144H124LEU0-0.049-0.00544.046-0.074-0.0740.0000.0000.0000.000
145H125ALA00.0110.00148.1910.0430.0430.0000.0000.0000.000
146H126PRO00.0300.04150.588-0.020-0.0200.0000.0000.0000.000
147H127SER00.0540.01052.209-0.133-0.1330.0000.0000.0000.000
148H128SER00.0210.01155.0200.0850.0850.0000.0000.0000.000
149H129LYS10.9220.95654.877-5.392-5.3920.0000.0000.0000.000
150H130SER0-0.031-0.00849.7750.1120.1120.0000.0000.0000.000
151H131THR0-0.003-0.02251.4760.0830.0830.0000.0000.0000.000
152H132SER0-0.026-0.01851.341-0.013-0.0130.0000.0000.0000.000
153H133GLY00.0430.03353.1940.0610.0610.0000.0000.0000.000
154H134GLY00.0520.03154.374-0.038-0.0380.0000.0000.0000.000
155H135THR0-0.067-0.03248.1060.1170.1170.0000.0000.0000.000
156H136ALA00.0180.00950.401-0.099-0.0990.0000.0000.0000.000
157H137ALA00.0050.01246.3900.1500.1500.0000.0000.0000.000
158H138LEU00.0020.02445.967-0.170-0.1700.0000.0000.0000.000
159H139GLY00.0550.00244.2400.1890.1890.0000.0000.0000.000
160H140CYS0-0.0750.00441.737-0.081-0.0810.0000.0000.0000.000
161H141LEU00.0410.04441.9730.1960.1960.0000.0000.0000.000
162H142VAL0-0.017-0.01938.236-0.115-0.1150.0000.0000.0000.000
163H143LYS10.9090.91239.598-6.749-6.7490.0000.0000.0000.000
164H144ASP-1-0.802-0.87540.7276.9966.9960.0000.0000.0000.000
165H145TYR00.0020.02133.680-0.209-0.2090.0000.0000.0000.000
166H146PHE00.0410.01533.4300.1420.1420.0000.0000.0000.000
167H147PRO00.0290.01130.546-0.140-0.1400.0000.0000.0000.000
168H148GLU-1-0.807-0.92828.6999.4959.4950.0000.0000.0000.000
169H149PRO0-0.013-0.00727.943-0.114-0.1140.0000.0000.0000.000
170H150VAL00.0020.00830.016-0.192-0.1920.0000.0000.0000.000
171H151THR0-0.058-0.02630.6380.2830.2830.0000.0000.0000.000
172H152VAL00.008-0.01633.315-0.254-0.2540.0000.0000.0000.000
173H153SER0-0.018-0.00335.3810.2480.2480.0000.0000.0000.000
174H154TRP00.0180.00737.676-0.298-0.2980.0000.0000.0000.000
175H155ASN00.013-0.01441.0530.1120.1120.0000.0000.0000.000
176H156SER0-0.022-0.02140.769-0.022-0.0220.0000.0000.0000.000
177H157GLY00.0150.01638.0530.1370.1370.0000.0000.0000.000
178H158ALA0-0.023-0.00238.6930.0960.0960.0000.0000.0000.000
179H159LEU0-0.039-0.01140.956-0.073-0.0730.0000.0000.0000.000
180H160THR00.0180.00036.3420.0490.0490.0000.0000.0000.000
181H161SER00.0170.00737.2070.1850.1850.0000.0000.0000.000
182H162GLY00.0340.01139.710-0.158-0.1580.0000.0000.0000.000
183H163VAL0-0.036-0.00636.946-0.137-0.1370.0000.0000.0000.000
184H164HIS00.0250.01536.3480.3590.3590.0000.0000.0000.000
185H165THR00.006-0.00734.162-0.322-0.3220.0000.0000.0000.000
186H166PHE0-0.0170.01033.8130.2460.2460.0000.0000.0000.000
187H167PRO00.031-0.00130.6780.0410.0410.0000.0000.0000.000
188H168ALA0-0.0250.01031.934-0.305-0.3050.0000.0000.0000.000
189H169VAL0-0.014-0.01033.3240.1270.1270.0000.0000.0000.000
190H170LEU0-0.038-0.01433.222-0.129-0.1290.0000.0000.0000.000
191H171GLN0-0.017-0.01735.860-0.270-0.2700.0000.0000.0000.000
192H172SER00.022-0.00439.2230.0710.0710.0000.0000.0000.000
193H173SER0-0.0040.00441.404-0.011-0.0110.0000.0000.0000.000
194H174GLY00.0080.00837.830-0.015-0.0150.0000.0000.0000.000
195H175LEU0-0.046-0.01937.0750.2080.2080.0000.0000.0000.000
196H176TYR00.0200.01030.590-0.064-0.0640.0000.0000.0000.000
197H177SER0-0.003-0.00636.563-0.280-0.2800.0000.0000.0000.000
198H178LEU00.0350.03734.0870.1130.1130.0000.0000.0000.000
199H179SER0-0.012-0.02737.671-0.344-0.3440.0000.0000.0000.000
200H180SER0-0.0120.00537.8300.1550.1550.0000.0000.0000.000
201H181VAL00.023-0.00739.490-0.239-0.2390.0000.0000.0000.000
202H182VAL00.0080.00440.7240.1940.1940.0000.0000.0000.000
203H183THR0-0.012-0.00143.049-0.145-0.1450.0000.0000.0000.000
204H184VAL00.0090.00545.1920.0980.0980.0000.0000.0000.000
205H185PRO00.0850.03447.976-0.084-0.0840.0000.0000.0000.000
206H186SER0-0.030-0.00551.242-0.019-0.0190.0000.0000.0000.000
207H187SER00.014-0.00154.137-0.027-0.0270.0000.0000.0000.000
208H188SER0-0.029-0.01651.701-0.019-0.0190.0000.0000.0000.000
209H189LEU00.0220.00352.0630.0250.0250.0000.0000.0000.000
210H190GLY0-0.0160.00154.865-0.095-0.0950.0000.0000.0000.000
211H191THR0-0.0090.00155.510-0.057-0.0570.0000.0000.0000.000
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