FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 523YZ

Calculation Name: 3CGU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CGU

Chain ID: A

ChEMBL ID:

UniProt ID: Q00805

Base Structure: X-ray

Registration Date: 2023-06-21

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2376324.353135
FMO2-HF: Nuclear repulsion 2289661.289536
FMO2-HF: Total energy -86663.063599
FMO2-MP2: Total energy -86903.700004


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(A:98:ARG)


Summations of interaction energy for fragment #1(A:98:ARG)
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.
20.81622.79-0.011-0.954-1.010.005
Interaction energy analysis for fragmet #1(A:98:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.943 / q_NPA : 0.972
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].
3A100VAL0-0.028-0.0053.8273.2185.192-0.011-0.954-1.0100.005
4A101ARG10.9560.9855.96420.21420.2140.0000.0000.0000.000
5A102ILE00.003-0.0066.4382.0862.0860.0000.0000.0000.000
6A103LEU0-0.0140.0048.7600.2600.2600.0000.0000.0000.000
7A104TYR00.007-0.00710.598-0.718-0.7180.0000.0000.0000.000
8A105GLN0-0.0040.01315.0390.6930.6930.0000.0000.0000.000
9A106VAL0-0.019-0.01518.2310.6670.6670.0000.0000.0000.000
10A107GLY0-0.0010.01017.992-0.422-0.4220.0000.0000.0000.000
11A108ASP-1-0.998-1.00913.842-15.804-15.8040.0000.0000.0000.000
12A109SER00.0450.00712.572-1.322-1.3220.0000.0000.0000.000
13A110GLU-1-0.812-0.88612.759-18.211-18.2110.0000.0000.0000.000
14A111GLU-1-0.937-0.97115.256-12.775-12.7750.0000.0000.0000.000
15A112ASP-1-0.858-0.91117.461-13.503-13.5030.0000.0000.0000.000
16A113LEU0-0.091-0.02716.1460.4840.4840.0000.0000.0000.000
17A114PRO00.0210.02219.7750.2760.2760.0000.0000.0000.000
18A115VAL0-0.026-0.02622.003-0.558-0.5580.0000.0000.0000.000
19A116CYS00.0230.02518.7880.6660.6660.0000.0000.0000.000
20A117ALA00.0350.03924.8500.2440.2440.0000.0000.0000.000
21A118PRO0-0.008-0.04127.267-0.341-0.3410.0000.0000.0000.000
22A119ASN0-0.054-0.02527.814-0.061-0.0610.0000.0000.0000.000
23A120ALA00.0780.06025.3910.1620.1620.0000.0000.0000.000
24A121VAL0-0.057-0.03220.767-0.410-0.4100.0000.0000.0000.000
25A122CYS00.0390.00015.4890.3600.3600.0000.0000.0000.000
26A123SER00.0130.00814.991-0.455-0.4550.0000.0000.0000.000
27A124LYS10.8470.94016.81413.87613.8760.0000.0000.0000.000
28A125ILE0-0.009-0.00513.777-0.688-0.6880.0000.0000.0000.000
29A126ASP-1-0.829-0.91015.695-13.763-13.7630.0000.0000.0000.000
30A127LEU0-0.028-0.03814.960-1.218-1.2180.0000.0000.0000.000
31A128TYR0-0.0210.00317.0680.3340.3340.0000.0000.0000.000
32A129GLU-1-0.870-0.93317.186-14.383-14.3830.0000.0000.0000.000
33A130THR0-0.057-0.03011.043-0.985-0.9850.0000.0000.0000.000
34A131PRO0-0.016-0.01811.5190.3280.3280.0000.0000.0000.000
35A132TRP00.0050.00410.909-1.960-1.9600.0000.0000.0000.000
36A133ILE0-0.008-0.0109.5931.4981.4980.0000.0000.0000.000
37A134GLU-1-0.787-0.89011.954-15.175-15.1750.0000.0000.0000.000
38A135ARG10.7300.82912.09019.10019.1000.0000.0000.0000.000
39A136GLN0-0.079-0.06015.2481.1671.1670.0000.0000.0000.000
40A138ARG10.9680.98617.67412.81612.8160.0000.0000.0000.000
41A139CYS00.023-0.00919.5460.0260.0260.0000.0000.0000.000
42A140PRO00.0410.03821.582-0.105-0.1050.0000.0000.0000.000
43A141ASP-1-0.917-0.93422.789-13.282-13.2820.0000.0000.0000.000
44A142GLY0-0.012-0.02724.3200.5500.5500.0000.0000.0000.000
45A143ARG10.8050.89022.03012.72512.7250.0000.0000.0000.000
46A144THR00.0830.02916.246-0.074-0.0740.0000.0000.0000.000
47A261PRO0-0.032-0.00514.697-1.289-1.2890.0000.0000.0000.000
48A262SER00.0380.00210.6080.2270.2270.0000.0000.0000.000
49A263SER0-0.0120.01211.816-1.690-1.6900.0000.0000.0000.000
50A264LEU00.0810.03910.5221.3371.3370.0000.0000.0000.000
51A265GLY0-0.020-0.00613.9371.2291.2290.0000.0000.0000.000
52A266VAL0-0.038-0.04516.5320.1050.1050.0000.0000.0000.000
53A267GLU-1-0.861-0.94117.654-14.811-14.8110.0000.0000.0000.000
54A268ASP-1-0.812-0.87717.118-16.904-16.9040.0000.0000.0000.000
55A269GLY00.0320.02819.1900.4470.4470.0000.0000.0000.000
56A270HIS0-0.054-0.04219.9780.9760.9760.0000.0000.0000.000
57A271THR0-0.0240.00119.397-0.404-0.4040.0000.0000.0000.000
58A272ILE0-0.019-0.00621.7220.5840.5840.0000.0000.0000.000
59A273ALA0-0.0050.00122.979-0.406-0.4060.0000.0000.0000.000
60A274ASP-1-0.761-0.89823.699-10.539-10.5390.0000.0000.0000.000
61A275LYS10.7730.87424.75710.61210.6120.0000.0000.0000.000
62A276THR00.0350.02521.129-0.149-0.1490.0000.0000.0000.000
63A277ARG10.8340.89720.07712.55812.5580.0000.0000.0000.000
64A278HIS10.7920.90817.64116.71716.7170.0000.0000.0000.000
65A279TYR00.0430.02719.363-0.385-0.3850.0000.0000.0000.000
66A280LYS10.7970.89516.05718.86018.8600.0000.0000.0000.000
67A281MET00.0380.02019.7640.3560.3560.0000.0000.0000.000
68A283GLN00.0270.02522.463-0.179-0.1790.0000.0000.0000.000
69A284PRO00.0280.00824.853-0.096-0.0960.0000.0000.0000.000
70A285VAL00.0330.01024.5260.5350.5350.0000.0000.0000.000
71A286HIS00.015-0.00827.1590.6330.6330.0000.0000.0000.000
72A287LYS10.8690.94029.41811.01811.0180.0000.0000.0000.000
73A288LEU00.0290.04028.5150.3040.3040.0000.0000.0000.000
74A289PRO00.0420.03032.475-0.034-0.0340.0000.0000.0000.000
75A290VAL0-0.003-0.00433.967-0.195-0.1950.0000.0000.0000.000
76A291CYS0-0.093-0.04432.7610.4440.4440.0000.0000.0000.000
77A292LYS10.8960.94137.8447.7827.7820.0000.0000.0000.000
78A293HIS00.0260.03441.3070.2480.2480.0000.0000.0000.000
79A294PHE0-0.022-0.02241.868-0.167-0.1670.0000.0000.0000.000
80A295ARG10.8070.88039.3987.8147.8140.0000.0000.0000.000
81A296ASP-1-0.763-0.86438.745-7.666-7.6660.0000.0000.0000.000
82A297TYR0-0.051-0.05335.674-0.134-0.1340.0000.0000.0000.000
83A298THR0-0.018-0.02631.762-0.133-0.1330.0000.0000.0000.000
84A299TRP00.0430.00727.412-0.299-0.2990.0000.0000.0000.000
85A300THR0-0.047-0.00631.2280.2660.2660.0000.0000.0000.000
86A301LEU0-0.008-0.00725.913-0.167-0.1670.0000.0000.0000.000
87A302THR00.010-0.00229.4530.4580.4580.0000.0000.0000.000
88A303THR00.000-0.00129.121-0.244-0.2440.0000.0000.0000.000
89A304ALA00.0590.00930.2720.3190.3190.0000.0000.0000.000
90A305ALA0-0.014-0.00231.252-0.159-0.1590.0000.0000.0000.000
91A306GLU-1-0.931-0.96632.273-8.083-8.0830.0000.0000.0000.000
92A307LEU0-0.033-0.00528.436-0.134-0.1340.0000.0000.0000.000
93A308ASN0-0.019-0.00224.7020.0410.0410.0000.0000.0000.000
94A309VAL00.0340.01722.701-0.427-0.4270.0000.0000.0000.000
95A310THR0-0.059-0.02724.1090.4880.4880.0000.0000.0000.000
96A311GLU-1-0.837-0.92424.639-11.075-11.0750.0000.0000.0000.000
97A312GLN0-0.041-0.02124.6150.1630.1630.0000.0000.0000.000
98A313ILE00.0170.01426.537-0.316-0.3160.0000.0000.0000.000
99A314VAL0-0.031-0.03926.7880.2260.2260.0000.0000.0000.000
100A315HIS0-0.014-0.01129.7730.1120.1120.0000.0000.0000.000
101A317ARG10.8500.93229.4419.9599.9590.0000.0000.0000.000
102A318CYS00.0720.03932.0240.1170.1170.0000.0000.0000.000
103A319PRO00.0070.00232.650-0.233-0.2330.0000.0000.0000.000
104A320ARG10.9750.97931.0749.5799.5790.0000.0000.0000.000
105A321ASN0-0.020-0.02031.6810.1750.1750.0000.0000.0000.000
106A322SER0-0.0310.01332.8440.2440.2440.0000.0000.0000.000
107A323VAL00.0330.01230.477-0.314-0.3140.0000.0000.0000.000
108A324THR0-0.0010.00029.0800.4170.4170.0000.0000.0000.000
109A325TYR0-0.031-0.00831.856-0.048-0.0480.0000.0000.0000.000
110A326LEU00.0440.03331.9660.0990.0990.0000.0000.0000.000
111A327THR0-0.076-0.05134.0570.2610.2610.0000.0000.0000.000
112A328LYS10.9230.96636.9527.4637.4630.0000.0000.0000.000
113A329ARG10.9090.97135.4577.6167.6160.0000.0000.0000.000
114A330GLU-1-0.905-0.94337.606-7.432-7.4320.0000.0000.0000.000
115A331PRO00.0570.01937.999-0.214-0.2140.0000.0000.0000.000
116A332ILE0-0.0230.00734.0520.0520.0520.0000.0000.0000.000
117A333GLY00.004-0.01538.0130.0240.0240.0000.0000.0000.000
118A334ASN0-0.035-0.01241.423-0.077-0.0770.0000.0000.0000.000
119A335ASP-1-0.900-0.94239.404-7.366-7.3660.0000.0000.0000.000
120A336SER00.0090.00536.331-0.135-0.1350.0000.0000.0000.000
121A337PRO00.0320.03137.5940.0530.0530.0000.0000.0000.000
122A338GLY00.0570.01435.222-0.242-0.2420.0000.0000.0000.000
123A339TYR0-0.071-0.04734.4480.2830.2830.0000.0000.0000.000
124A340ARG10.8180.90033.7377.7727.7720.0000.0000.0000.000
125A341TYR00.0210.00531.5020.3000.3000.0000.0000.0000.000
126A342LEU00.0070.00932.878-0.230-0.2300.0000.0000.0000.000
127A343PHE00.0280.01529.5820.1050.1050.0000.0000.0000.000
128A344ALA00.0110.00133.7400.0990.0990.0000.0000.0000.000
129A346SER00.0400.03135.6990.2330.2330.0000.0000.0000.000
130A347PRO0-0.039-0.02037.663-0.069-0.0690.0000.0000.0000.000
131A348LEU00.0450.03439.348-0.041-0.0410.0000.0000.0000.000
132A349THR00.0050.00540.8250.0610.0610.0000.0000.0000.000
133A350ARG10.9360.96444.4906.7346.7340.0000.0000.0000.000
134A351LEU00.0530.01846.2940.1590.1590.0000.0000.0000.000
135A352ARG10.9520.97849.2295.8665.8660.0000.0000.0000.000
136A353CYS0-0.0370.00842.860-0.006-0.0060.0000.0000.0000.000
137A354GLN00.007-0.00150.8630.2300.2300.0000.0000.0000.000
138A355ARG11.0331.00351.6345.3825.3820.0000.0000.0000.000
139A356LYS10.9510.96949.4276.1136.1130.0000.0000.0000.000
140A357GLN00.0260.02247.100-0.052-0.0520.0000.0000.0000.000
141A358PRO00.0200.01243.5980.0890.0890.0000.0000.0000.000
142A359CYS00.003-0.01145.516-0.044-0.0440.0000.0000.0000.000
143A360LYS10.8620.92841.5787.0697.0690.0000.0000.0000.000
144A361LEU00.0060.00837.6740.1060.1060.0000.0000.0000.000
145A362PHE0-0.016-0.00137.464-0.135-0.1350.0000.0000.0000.000
146A363THR0-0.020-0.01931.5460.0270.0270.0000.0000.0000.000
147A364VAL00.0060.00933.111-0.138-0.1380.0000.0000.0000.000
148A365ARG10.9010.92826.59610.71910.7190.0000.0000.0000.000
149A366LYS10.8810.92828.9179.3559.3550.0000.0000.0000.000
150A367ARG10.7980.89622.14612.08012.0800.0000.0000.0000.000
151A368GLN00.009-0.00323.298-0.243-0.2430.0000.0000.0000.000
152A369GLU-1-0.936-0.95525.985-9.417-9.4170.0000.0000.0000.000
153A370PHE0-0.019-0.01428.3350.3550.3550.0000.0000.0000.000
154A371LEU0-0.0110.00325.4680.0780.0780.0000.0000.0000.000
155A372ASP-1-0.802-0.88228.622-9.448-9.4480.0000.0000.0000.000
156A373GLU-1-0.788-0.86026.567-11.156-11.1560.0000.0000.0000.000
157A374VAL00.012-0.00630.3670.0580.0580.0000.0000.0000.000
158A375ASN0-0.077-0.02329.541-0.122-0.1220.0000.0000.0000.000
159A376ILE00.0220.00733.4690.2070.2070.0000.0000.0000.000
160A377ASN00.0120.01134.254-0.025-0.0250.0000.0000.0000.000
161A378SER00.020-0.00538.1680.2470.2470.0000.0000.0000.000
162A379LEU0-0.058-0.01739.382-0.059-0.0590.0000.0000.0000.000
163A381GLN0-0.0160.00446.518-0.104-0.1040.0000.0000.0000.000
164A382CYS0-0.030-0.03548.7750.0720.0720.0000.0000.0000.000
165A383PRO0-0.0050.00151.8710.0230.0230.0000.0000.0000.000
166A384LYS10.9800.97255.5525.6425.6420.0000.0000.0000.000
167A385GLY00.0640.03758.1860.0420.0420.0000.0000.0000.000
168A386HIS0-0.038-0.01954.6710.0380.0380.0000.0000.0000.000
169A387ARG10.8470.93251.7965.7105.7100.0000.0000.0000.000
170A389PRO00.0150.02446.248-0.025-0.0250.0000.0000.0000.000
171A390SER0-0.062-0.04244.720-0.149-0.1490.0000.0000.0000.000
172A391HIS00.0550.02341.969-0.306-0.3060.0000.0000.0000.000
173A392HIS00.0470.00938.2360.1620.1620.0000.0000.0000.000
174A393THR00.0100.01242.1340.0930.0930.0000.0000.0000.000
175A394GLN00.0250.03644.4630.0490.0490.0000.0000.0000.000
176A395SER00.0550.02347.412-0.063-0.0630.0000.0000.0000.000
177A396GLY00.022-0.00450.0010.0050.0050.0000.0000.0000.000
178A397VAL0-0.050-0.03443.468-0.080-0.0800.0000.0000.0000.000
179A398ILE0-0.0210.00544.5320.0710.0710.0000.0000.0000.000
180A399ALA00.016-0.00440.960-0.141-0.1410.0000.0000.0000.000
181A400GLY0-0.029-0.01540.0710.1310.1310.0000.0000.0000.000
182A401GLU-1-0.841-0.91335.958-7.756-7.7560.0000.0000.0000.000
183A402SER0-0.013-0.03934.749-0.069-0.0690.0000.0000.0000.000
184A403PHE0-0.004-0.00926.7240.0900.0900.0000.0000.0000.000
185A404LEU00.0760.01529.893-0.216-0.2160.0000.0000.0000.000
186A405GLU-1-0.942-0.94123.007-12.293-12.2930.0000.0000.0000.000
187A406ASP-1-0.802-0.87923.745-12.318-12.3180.0000.0000.0000.000
188A407ASN0-0.046-0.02025.7310.3070.3070.0000.0000.0000.000
189A408ILE0-0.047-0.02428.0570.1330.1330.0000.0000.0000.000
190A409GLN00.0400.05130.5790.1690.1690.0000.0000.0000.000
191A410THR0-0.055-0.03934.3160.0600.0600.0000.0000.0000.000
192A411TYR00.0330.02436.6710.1520.1520.0000.0000.0000.000
193A412SER00.0160.01240.234-0.178-0.1780.0000.0000.0000.000
194A413GLY00.0220.02042.7420.1380.1380.0000.0000.0000.000
195A414TYR0-0.021-0.02645.522-0.057-0.0570.0000.0000.0000.000
196A416MET00.0500.03151.5530.0660.0660.0000.0000.0000.000
197A417ALA00.0350.00853.822-0.003-0.0030.0000.0000.0000.000
198A418ASN0-0.027-0.02956.789-0.139-0.1390.0000.0000.0000.000
199A419ASP-1-0.886-0.91557.275-5.291-5.2910.0000.0000.0000.000