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: YZY92

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2382666.806151
FMO2-HF: Nuclear repulsion 2296002.94829
FMO2-HF: Total energy -86663.857862
FMO2-MP2: Total energy -86904.6299


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.
23.33125.1210-0.86-0.930.004
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 : 0.889 / q_NPA : 0.931
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].
3A100VAL0-0.019-0.0063.7215.0376.8270.000-0.860-0.9300.004
4A101ARG10.9520.9836.50321.15321.1530.0000.0000.0000.000
5A102ILE00.0030.0027.1102.6532.6530.0000.0000.0000.000
6A103LEU0-0.022-0.0049.1010.1930.1930.0000.0000.0000.000
7A104TYR0-0.005-0.02811.036-0.719-0.7190.0000.0000.0000.000
8A105GLN0-0.031-0.01115.4150.7070.7070.0000.0000.0000.000
9A106VAL0-0.030-0.01718.5480.7250.7250.0000.0000.0000.000
10A107GLY0-0.0040.00818.061-0.501-0.5010.0000.0000.0000.000
11A108ASP-1-0.984-0.99113.628-16.387-16.3870.0000.0000.0000.000
12A109SER00.007-0.00812.713-1.483-1.4830.0000.0000.0000.000
13A110GLU-1-0.777-0.86012.982-19.177-19.1770.0000.0000.0000.000
14A111GLU-1-0.873-0.93015.631-12.977-12.9770.0000.0000.0000.000
15A112ASP-1-0.821-0.90417.511-13.859-13.8590.0000.0000.0000.000
16A113LEU0-0.072-0.01616.7330.4710.4710.0000.0000.0000.000
17A114PRO00.0210.02020.4100.1690.1690.0000.0000.0000.000
18A115VAL0-0.003-0.00822.411-0.598-0.5980.0000.0000.0000.000
19A116CYS0-0.0140.01619.1490.7610.7610.0000.0000.0000.000
20A117ALA00.0510.03325.2300.2630.2630.0000.0000.0000.000
21A118PRO0-0.018-0.03927.734-0.368-0.3680.0000.0000.0000.000
22A119ASN0-0.061-0.03228.109-0.032-0.0320.0000.0000.0000.000
23A120ALA00.0460.04525.7680.0330.0330.0000.0000.0000.000
24A121VAL0-0.075-0.04321.252-0.394-0.3940.0000.0000.0000.000
25A122CYS00.0670.00615.7970.5520.5520.0000.0000.0000.000
26A123SER00.003-0.00215.210-0.454-0.4540.0000.0000.0000.000
27A124LYS10.8010.90317.76614.08114.0810.0000.0000.0000.000
28A125ILE00.004-0.00414.064-0.976-0.9760.0000.0000.0000.000
29A126ASP-1-0.815-0.90315.918-13.900-13.9000.0000.0000.0000.000
30A127LEU0-0.031-0.03814.945-1.404-1.4040.0000.0000.0000.000
31A128TYR0-0.031-0.00717.4170.3390.3390.0000.0000.0000.000
32A129GLU-1-0.875-0.93516.891-15.134-15.1340.0000.0000.0000.000
33A130THR0-0.026-0.01910.851-1.184-1.1840.0000.0000.0000.000
34A131PRO0-0.011-0.00411.3000.1500.1500.0000.0000.0000.000
35A132TRP0-0.036-0.01710.965-1.513-1.5130.0000.0000.0000.000
36A133ILE0-0.021-0.01810.1771.2321.2320.0000.0000.0000.000
37A134GLU-1-0.777-0.85912.398-15.396-15.3960.0000.0000.0000.000
38A135ARG10.7450.83012.33519.89519.8950.0000.0000.0000.000
39A136GLN0-0.085-0.05815.7061.1981.1980.0000.0000.0000.000
40A138ARG10.8620.93918.16013.05813.0580.0000.0000.0000.000
41A139CYS00.0510.01719.954-0.032-0.0320.0000.0000.0000.000
42A140PRO00.0330.02621.992-0.054-0.0540.0000.0000.0000.000
43A141ASP-1-0.873-0.93123.562-13.539-13.5390.0000.0000.0000.000
44A142GLY0-0.064-0.02024.4560.5470.5470.0000.0000.0000.000
45A143ARG10.7870.86321.60713.24513.2450.0000.0000.0000.000
46A144THR00.0770.03316.559-0.025-0.0250.0000.0000.0000.000
47A261PRO0-0.035-0.00914.627-1.526-1.5260.0000.0000.0000.000
48A262SER00.0300.00411.1370.7610.7610.0000.0000.0000.000
49A263SER0-0.0140.01011.286-2.087-2.0870.0000.0000.0000.000
50A264LEU00.0780.03710.5231.6471.6470.0000.0000.0000.000
51A265GLY00.0020.01813.4111.3281.3280.0000.0000.0000.000
52A266VAL0-0.017-0.05215.8940.2530.2530.0000.0000.0000.000
53A267GLU-1-0.850-0.92517.178-15.883-15.8830.0000.0000.0000.000
54A268ASP-1-0.800-0.85916.467-17.790-17.7900.0000.0000.0000.000
55A269GLY00.0020.00518.5910.4660.4660.0000.0000.0000.000
56A270HIS0-0.027-0.01819.6001.2231.2230.0000.0000.0000.000
57A271THR0-0.032-0.01418.805-0.555-0.5550.0000.0000.0000.000
58A272ILE0-0.010-0.00221.1000.6690.6690.0000.0000.0000.000
59A273ALA00.0030.00321.657-0.417-0.4170.0000.0000.0000.000
60A274ASP-1-0.752-0.87523.010-10.728-10.7280.0000.0000.0000.000
61A275LYS10.7600.86824.49010.67810.6780.0000.0000.0000.000
62A276THR00.0260.02321.4520.0400.0400.0000.0000.0000.000
63A277ARG10.8270.89519.92812.89012.8900.0000.0000.0000.000
64A278HIS10.7590.86916.93817.32117.3210.0000.0000.0000.000
65A279TYR00.0600.04719.722-0.331-0.3310.0000.0000.0000.000
66A280LYS10.7700.87215.55519.40819.4080.0000.0000.0000.000
67A281MET00.0470.02719.9480.3670.3670.0000.0000.0000.000
68A283GLN00.0390.01322.9270.1090.1090.0000.0000.0000.000
69A284PRO00.0210.01224.277-0.117-0.1170.0000.0000.0000.000
70A285VAL00.0290.01223.9270.6310.6310.0000.0000.0000.000
71A286HIS00.006-0.00626.6390.6530.6530.0000.0000.0000.000
72A287LYS10.8780.94228.48511.33711.3370.0000.0000.0000.000
73A288LEU00.0240.03628.1210.3110.3110.0000.0000.0000.000
74A289PRO00.0380.02931.873-0.025-0.0250.0000.0000.0000.000
75A290VAL0-0.016-0.00133.121-0.199-0.1990.0000.0000.0000.000
76A291CYS0-0.065-0.02932.8770.5110.5110.0000.0000.0000.000
77A292LYS10.7960.89237.4008.0588.0580.0000.0000.0000.000
78A293HIS00.0260.03840.7580.2380.2380.0000.0000.0000.000
79A294PHE0-0.018-0.02942.034-0.189-0.1890.0000.0000.0000.000
80A295ARG10.8260.89739.5248.0128.0120.0000.0000.0000.000
81A296ASP-1-0.720-0.84638.760-7.914-7.9140.0000.0000.0000.000
82A297TYR0-0.025-0.02836.036-0.101-0.1010.0000.0000.0000.000
83A298THR0-0.027-0.04531.451-0.132-0.1320.0000.0000.0000.000
84A299TRP00.032-0.00327.428-0.300-0.3000.0000.0000.0000.000
85A300THR0-0.050-0.01831.4770.3350.3350.0000.0000.0000.000
86A301LEU00.0020.01926.007-0.093-0.0930.0000.0000.0000.000
87A302THR0-0.005-0.01729.5460.4940.4940.0000.0000.0000.000
88A303THR00.0170.00629.322-0.262-0.2620.0000.0000.0000.000
89A304ALA00.0730.01530.8410.3330.3330.0000.0000.0000.000
90A305ALA0-0.017-0.01031.819-0.197-0.1970.0000.0000.0000.000
91A306GLU-1-0.938-0.96232.948-8.105-8.1050.0000.0000.0000.000
92A307LEU0-0.050-0.01629.061-0.120-0.1200.0000.0000.0000.000
93A308ASN0-0.022-0.00724.7070.0820.0820.0000.0000.0000.000
94A309VAL00.0190.01623.106-0.466-0.4660.0000.0000.0000.000
95A310THR0-0.053-0.03624.2000.4990.4990.0000.0000.0000.000
96A311GLU-1-0.771-0.88924.967-11.477-11.4770.0000.0000.0000.000
97A312GLN0-0.028-0.01724.8170.2060.2060.0000.0000.0000.000
98A313ILE00.0230.01926.997-0.331-0.3310.0000.0000.0000.000
99A314VAL0-0.019-0.02127.0680.2470.2470.0000.0000.0000.000
100A315HIS0-0.014-0.01930.2070.1330.1330.0000.0000.0000.000
101A317ARG10.8610.94828.50010.19110.1910.0000.0000.0000.000
102A318CYS00.0660.03131.1910.1900.1900.0000.0000.0000.000
103A319PRO00.0170.00132.129-0.199-0.1990.0000.0000.0000.000
104A320ARG10.9750.98430.7669.7069.7060.0000.0000.0000.000
105A321ASN0-0.017-0.01631.0070.2230.2230.0000.0000.0000.000
106A322SER0-0.053-0.00731.9910.1800.1800.0000.0000.0000.000
107A323VAL00.0290.00630.450-0.310-0.3100.0000.0000.0000.000
108A324THR0-0.021-0.02129.1340.4540.4540.0000.0000.0000.000
109A325TYR0-0.030-0.00431.961-0.034-0.0340.0000.0000.0000.000
110A326LEU00.0440.03932.0150.0920.0920.0000.0000.0000.000
111A327THR0-0.052-0.04534.0660.2580.2580.0000.0000.0000.000
112A328LYS10.8690.93636.9837.7077.7070.0000.0000.0000.000
113A329ARG10.8850.95935.7397.7297.7290.0000.0000.0000.000
114A330GLU-1-0.872-0.92237.853-7.561-7.5610.0000.0000.0000.000
115A331PRO00.0650.02038.152-0.218-0.2180.0000.0000.0000.000
116A332ILE0-0.0150.01134.6880.0090.0090.0000.0000.0000.000
117A333GLY00.017-0.00438.304-0.008-0.0080.0000.0000.0000.000
118A334ASN0-0.033-0.01741.664-0.060-0.0600.0000.0000.0000.000
119A335ASP-1-0.873-0.90839.376-7.581-7.5810.0000.0000.0000.000
120A336SER00.009-0.00836.642-0.047-0.0470.0000.0000.0000.000
121A337PRO00.0110.02037.734-0.007-0.0070.0000.0000.0000.000
122A338GLY00.0380.00735.466-0.256-0.2560.0000.0000.0000.000
123A339TYR0-0.071-0.04434.6230.3050.3050.0000.0000.0000.000
124A340ARG10.8100.89633.7477.9387.9380.0000.0000.0000.000
125A341TYR00.0110.00331.8570.3510.3510.0000.0000.0000.000
126A342LEU00.0080.00533.062-0.280-0.2800.0000.0000.0000.000
127A343PHE00.0210.00829.7220.0640.0640.0000.0000.0000.000
128A344ALA00.0230.00133.8910.0760.0760.0000.0000.0000.000
129A346SER00.0590.03535.4140.2310.2310.0000.0000.0000.000
130A347PRO0-0.048-0.02237.335-0.057-0.0570.0000.0000.0000.000
131A348LEU00.0390.02838.528-0.005-0.0050.0000.0000.0000.000
132A349THR00.0060.00140.0860.0980.0980.0000.0000.0000.000
133A350ARG10.9180.96343.7156.8666.8660.0000.0000.0000.000
134A351LEU00.0410.01845.9570.1860.1860.0000.0000.0000.000
135A352ARG10.9530.97348.6475.9245.9240.0000.0000.0000.000
136A353CYS0-0.0580.01342.908-0.033-0.0330.0000.0000.0000.000
137A354GLN0-0.005-0.01650.9410.2410.2410.0000.0000.0000.000
138A355ARG11.0050.98852.0805.4455.4450.0000.0000.0000.000
139A356LYS10.9670.97749.6316.2106.2100.0000.0000.0000.000
140A357GLN00.0580.04447.201-0.009-0.0090.0000.0000.0000.000
141A358PRO00.0130.00843.7840.0930.0930.0000.0000.0000.000
142A359CYS00.006-0.01745.467-0.063-0.0630.0000.0000.0000.000
143A360LYS10.8510.91641.4857.1977.1970.0000.0000.0000.000
144A361LEU00.0090.00337.5440.1210.1210.0000.0000.0000.000
145A362PHE0-0.0130.00437.559-0.172-0.1720.0000.0000.0000.000
146A363THR0-0.034-0.03431.5740.0140.0140.0000.0000.0000.000
147A364VAL00.0210.02132.910-0.169-0.1690.0000.0000.0000.000
148A365ARG10.8890.91726.70110.89410.8940.0000.0000.0000.000
149A366LYS10.8440.91628.8489.6319.6310.0000.0000.0000.000
150A367ARG10.8010.88621.92212.59412.5940.0000.0000.0000.000
151A368GLN00.0190.00922.906-0.274-0.2740.0000.0000.0000.000
152A369GLU-1-0.925-0.95525.672-9.501-9.5010.0000.0000.0000.000
153A370PHE0-0.011-0.01128.4430.3640.3640.0000.0000.0000.000
154A371LEU0-0.017-0.00225.2810.0870.0870.0000.0000.0000.000
155A372ASP-1-0.783-0.87128.060-9.780-9.7800.0000.0000.0000.000
156A373GLU-1-0.797-0.87226.506-11.435-11.4350.0000.0000.0000.000
157A374VAL00.018-0.00430.2320.1270.1270.0000.0000.0000.000
158A375ASN0-0.059-0.00829.663-0.085-0.0850.0000.0000.0000.000
159A376ILE00.0430.01033.5800.2230.2230.0000.0000.0000.000
160A377ASN00.0190.01634.3340.0330.0330.0000.0000.0000.000
161A378SER00.017-0.00238.2180.2500.2500.0000.0000.0000.000
162A379LEU0-0.060-0.01639.249-0.103-0.1030.0000.0000.0000.000
163A381GLN00.0180.02646.537-0.137-0.1370.0000.0000.0000.000
164A382CYS0-0.042-0.04648.9830.0840.0840.0000.0000.0000.000
165A383PRO00.0350.02252.1270.0210.0210.0000.0000.0000.000
166A384LYS10.9090.94555.6525.7275.7270.0000.0000.0000.000
167A385GLY00.0900.04558.5850.0230.0230.0000.0000.0000.000
168A386HIS0-0.032-0.01854.9280.0240.0240.0000.0000.0000.000
169A387ARG10.7690.85851.9775.7495.7490.0000.0000.0000.000
170A389PRO0-0.0290.00046.157-0.041-0.0410.0000.0000.0000.000
171A390SER0-0.034-0.02144.813-0.168-0.1680.0000.0000.0000.000
172A391HIS00.0600.02641.861-0.316-0.3160.0000.0000.0000.000
173A392HIS00.0410.00938.2350.1760.1760.0000.0000.0000.000
174A393THR00.0070.00541.8360.0650.0650.0000.0000.0000.000
175A394GLN00.0100.03144.3990.0780.0780.0000.0000.0000.000
176A395SER00.0620.02047.386-0.055-0.0550.0000.0000.0000.000
177A396GLY00.0330.00250.1250.0030.0030.0000.0000.0000.000
178A397VAL0-0.052-0.02943.384-0.078-0.0780.0000.0000.0000.000
179A398ILE0-0.0090.01044.7110.1070.1070.0000.0000.0000.000
180A399ALA00.0400.01040.780-0.152-0.1520.0000.0000.0000.000
181A400GLY0-0.037-0.02240.0640.1660.1660.0000.0000.0000.000
182A401GLU-1-0.809-0.88936.228-7.874-7.8740.0000.0000.0000.000
183A402SER0-0.002-0.02834.682-0.069-0.0690.0000.0000.0000.000
184A403PHE00.0070.00026.6100.1340.1340.0000.0000.0000.000
185A404LEU00.0610.00329.590-0.249-0.2490.0000.0000.0000.000
186A405GLU-1-0.852-0.89022.664-12.774-12.7740.0000.0000.0000.000
187A406ASP-1-0.827-0.89024.139-12.576-12.5760.0000.0000.0000.000
188A407ASN0-0.042-0.01625.6180.2980.2980.0000.0000.0000.000
189A408ILE0-0.056-0.03227.8290.1380.1380.0000.0000.0000.000
190A409GLN00.0210.03830.6260.1670.1670.0000.0000.0000.000
191A410THR0-0.053-0.03534.3910.0360.0360.0000.0000.0000.000
192A411TYR00.0340.01536.6710.1360.1360.0000.0000.0000.000
193A412SER0-0.0020.00640.324-0.193-0.1930.0000.0000.0000.000
194A413GLY00.0260.01943.0040.1370.1370.0000.0000.0000.000
195A414TYR0-0.010-0.01445.670-0.074-0.0740.0000.0000.0000.000
196A416MET00.0780.05551.7890.0760.0760.0000.0000.0000.000
197A417ALA00.0280.00553.7400.0010.0010.0000.0000.0000.000
198A418ASN0-0.036-0.02056.710-0.146-0.1460.0000.0000.0000.000
199A419ASP-1-0.820-0.86857.166-5.419-5.4190.0000.0000.0000.000