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: PGQJ1

Calculation Name: 3SEE-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SEE

Chain ID: A

ChEMBL ID:

UniProt ID: Q89ZG6

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandCharge NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2542983.721755
FMO2-HF: Nuclear repulsion 2459632.734315
FMO2-HF: Total energy -83350.98744
FMO2-MP2: Total energy -83594.852149


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:19:ACE)


Summations of interaction energy for fragment #1(A:19:ACE)
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.
-0.4760.8670.731-0.928-1.1460.002
Interaction energy analysis for fragmet #1(A:19:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.007
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].
3A21ASN00.0170.0083.8410.9121.848-0.012-0.407-0.517-0.001
4A22LEU00.0370.0115.699-0.081-0.0810.0000.0000.0000.000
5A23ILE0-0.066-0.0178.6670.1060.1060.0000.0000.0000.000
6A24LYS10.9530.98310.4900.4510.4510.0000.0000.0000.000
7A25ASN00.019-0.00914.1080.0460.0460.0000.0000.0000.000
8A26GLU-1-0.886-0.93213.112-0.431-0.4310.0000.0000.0000.000
9A27LYS10.9040.94214.7240.3790.3790.0000.0000.0000.000
10A28PHE0-0.024-0.00518.4390.0240.0240.0000.0000.0000.000
11A29ALA00.0170.02120.1980.0170.0170.0000.0000.0000.000
12A30THR0-0.031-0.00121.4990.0110.0110.0000.0000.0000.000
13A31GLU-1-0.889-0.94823.256-0.100-0.1000.0000.0000.0000.000
14A32VAL0-0.040-0.02322.694-0.005-0.0050.0000.0000.0000.000
15A33THR00.0410.00225.6600.0070.0070.0000.0000.0000.000
16A34ASN00.0060.01725.1290.0150.0150.0000.0000.0000.000
17A35LYS10.9330.98027.1770.0460.0460.0000.0000.0000.000
18A36VAL0-0.005-0.00126.3950.0010.0010.0000.0000.0000.000
19A37THR0-0.019-0.01929.4050.0020.0020.0000.0000.0000.000
20A38ASN00.0420.00428.5220.0040.0040.0000.0000.0000.000
21A39PRO00.0600.03123.836-0.005-0.0050.0000.0000.0000.000
22A40SER00.032-0.01224.463-0.006-0.0060.0000.0000.0000.000
23A41LYS10.8540.92726.1220.0370.0370.0000.0000.0000.000
24A42ALA0-0.0240.01523.014-0.004-0.0040.0000.0000.0000.000
25A43THR00.0430.02221.0020.0110.0110.0000.0000.0000.000
26A44ALA0-0.017-0.00817.047-0.004-0.0040.0000.0000.0000.000
27A45GLY0-0.0030.00315.434-0.011-0.0110.0000.0000.0000.000
28A46GLU-1-0.912-0.95016.356-0.181-0.1810.0000.0000.0000.000
29A47TRP0-0.055-0.05016.9040.0210.0210.0000.0000.0000.000
30A48PHE0-0.021-0.00620.9280.0080.0080.0000.0000.0000.000
31A49ILE0-0.004-0.00524.1250.0040.0040.0000.0000.0000.000
32A50MET0-0.0350.00427.0030.0030.0030.0000.0000.0000.000
33A51ASN00.026-0.02528.7380.0040.0040.0000.0000.0000.000
34A52ASN0-0.035-0.02632.269-0.002-0.0020.0000.0000.0000.000
35A53GLU-1-0.839-0.92834.373-0.014-0.0140.0000.0000.0000.000
36A54ALA00.0140.01436.564-0.002-0.0020.0000.0000.0000.000
37A55ASP-1-0.578-0.64339.421-0.031-0.0310.0000.0000.0000.000
38A56GLY00.0590.04039.9910.0020.0020.0000.0000.0000.000
39A57VAL00.0160.05436.7870.0000.0000.0000.0000.0000.000
40A58THR00.1900.13933.271-0.001-0.0010.0000.0000.0000.000
41A59THR00.085-0.06933.7560.0000.0000.0000.0000.0000.000
42A60ILE0-0.0150.03727.5380.0000.0000.0000.0000.0000.000
43A61ALA00.001-0.00329.831-0.001-0.0010.0000.0000.0000.000
44A62TRP00.0410.01424.5530.0050.0050.0000.0000.0000.000
45A63GLH0-0.081-0.09927.6330.0110.0110.0000.0000.0000.000
46A64GLN0-0.013-0.01227.558-0.003-0.0030.0000.0000.0000.000
47A65THR0-0.039-0.03726.7620.0070.0070.0000.0000.0000.000
48A66GLY00.0160.02229.7530.0070.0070.0000.0000.0000.000
49A67ASP-1-0.842-0.90827.422-0.069-0.0690.0000.0000.0000.000
50A68ALA00.000-0.02326.775-0.009-0.0090.0000.0000.0000.000
51A69LYS10.8880.94321.5260.0940.0940.0000.0000.0000.000
52A70TYR0-0.031-0.01419.548-0.007-0.0070.0000.0000.0000.000
53A71PRO00.0440.04622.7700.0070.0070.0000.0000.0000.000
54A72ASN00.0510.04023.1410.0170.0170.0000.0000.0000.000
55A73ALA0-0.0190.00323.361-0.008-0.0080.0000.0000.0000.000
56A74MET0-0.0100.02823.3130.0010.0010.0000.0000.0000.000
57A75LYS10.9440.97425.6790.0600.0600.0000.0000.0000.000
58A76ILE0-0.015-0.01425.7160.0000.0000.0000.0000.0000.000
59A77ASP-1-0.837-0.90829.851-0.034-0.0340.0000.0000.0000.000
60A78ASN0-0.051-0.04332.389-0.002-0.0020.0000.0000.0000.000
61A79SER0-0.014-0.03135.5830.0040.0040.0000.0000.0000.000
62A80GLY0-0.0170.00338.7230.0020.0020.0000.0000.0000.000
63A81ALA0-0.043-0.01337.6220.0020.0020.0000.0000.0000.000
64A82GLU-1-0.866-0.91939.778-0.013-0.0130.0000.0000.0000.000
65A83LYS10.8330.90638.3420.0160.0160.0000.0000.0000.000
66A84ASN00.0290.01534.896-0.003-0.0030.0000.0000.0000.000
67A85THR00.0050.00532.2860.0020.0020.0000.0000.0000.000
68A86SER0-0.019-0.01533.1430.0040.0040.0000.0000.0000.000
69A87TRP00.0820.03427.328-0.004-0.0040.0000.0000.0000.000
70A88TYR00.0310.01528.188-0.004-0.0040.0000.0000.0000.000
71A89LYS10.8630.94330.0460.0110.0110.0000.0000.0000.000
72A90ALA00.0220.01030.346-0.004-0.0040.0000.0000.0000.000
73A91PHE0-0.037-0.02124.0570.0040.0040.0000.0000.0000.000
74A92LEU00.0080.02321.328-0.002-0.0020.0000.0000.0000.000
75A93GLY00.0420.00921.2430.0070.0070.0000.0000.0000.000
76A94GLN00.0240.01414.985-0.047-0.0470.0000.0000.0000.000
77A95ARG10.7570.84817.5230.0750.0750.0000.0000.0000.000
78A96ILE0-0.017-0.02311.884-0.034-0.0340.0000.0000.0000.000
79A97THR00.030-0.00214.8840.0250.0250.0000.0000.0000.000
80A98ASP-1-0.932-0.96310.178-0.341-0.3410.0000.0000.0000.000
81A99GLY0-0.0300.00611.6270.0150.0150.0000.0000.0000.000
82A100LEU0-0.089-0.0489.9200.0210.0210.0000.0000.0000.000
83A101GLU-1-0.882-0.9597.0860.9560.9560.0000.0000.0000.000
84A102LYS10.8870.94111.220-0.196-0.1960.0000.0000.0000.000
85A103GLY00.003-0.00111.1410.0670.0670.0000.0000.0000.000
86A104ILE0-0.0030.00510.611-0.094-0.0940.0000.0000.0000.000
87A105TYR00.0480.0207.7280.2060.2060.0000.0000.0000.000
88A106VAL0-0.072-0.0218.982-0.072-0.0720.0000.0000.0000.000
89A107LEU00.0470.01510.477-0.048-0.0480.0000.0000.0000.000
90A108THR0-0.037-0.03712.3090.0180.0180.0000.0000.0000.000
91A109PHE0-0.0080.00514.574-0.040-0.0400.0000.0000.0000.000
92A110TYR00.0050.01016.9990.0250.0250.0000.0000.0000.000
93A111ALA00.024-0.00520.500-0.007-0.0070.0000.0000.0000.000
94A112LYS10.9460.99323.8720.0600.0600.0000.0000.0000.000
95A113ALA00.0270.01027.482-0.001-0.0010.0000.0000.0000.000
96A114LYS10.9751.00630.5750.0290.0290.0000.0000.0000.000
97A115GLU-1-0.847-0.93034.073-0.022-0.0220.0000.0000.0000.000
98A116ALA00.0070.00733.4680.0000.0000.0000.0000.0000.000
99A117GLY0-0.039-0.02232.5340.0020.0020.0000.0000.0000.000
100A118THR0-0.051-0.03730.5400.0030.0030.0000.0000.0000.000
101A119PRO0-0.056-0.02728.616-0.001-0.0010.0000.0000.0000.000
102A120VAL0-0.0070.01023.487-0.005-0.0050.0000.0000.0000.000
103A121SER0-0.025-0.04723.9660.0070.0070.0000.0000.0000.000
104A122VAL00.0120.02018.021-0.012-0.0120.0000.0000.0000.000
105A123TYR0-0.018-0.02520.7940.0110.0110.0000.0000.0000.000
106A124ILE00.0230.01314.877-0.015-0.0150.0000.0000.0000.000
107A125LYS10.8210.92319.1110.0090.0090.0000.0000.0000.000
108A126GLN00.0530.02120.615-0.003-0.0030.0000.0000.0000.000
109A127THR0-0.074-0.05520.516-0.003-0.0030.0000.0000.0000.000
110A128ASN00.0140.03523.072-0.003-0.0030.0000.0000.0000.000
111A129GLU-1-0.774-0.84025.7470.0270.0270.0000.0000.0000.000
112A130GLU-1-0.868-0.92727.7110.0070.0070.0000.0000.0000.000
113A131LYS10.8980.94030.513-0.002-0.0020.0000.0000.0000.000
114A132ASN00.0240.01133.8760.0000.0000.0000.0000.0000.000
115A133ASP-1-0.806-0.89535.2620.0210.0210.0000.0000.0000.000
116A134ASN0-0.037-0.03038.653-0.003-0.0030.0000.0000.0000.000
117A135GLY00.0040.00938.689-0.002-0.0020.0000.0000.0000.000
118A136LYS10.8500.93136.146-0.019-0.0190.0000.0000.0000.000
119A137LEU0-0.047-0.03231.1320.0010.0010.0000.0000.0000.000
120A138ASN00.0380.02328.9850.0000.0000.0000.0000.0000.000
121A139THR0-0.124-0.07627.820-0.006-0.0060.0000.0000.0000.000
122A140THR00.0180.00022.9010.0060.0060.0000.0000.0000.000
123A141PHE0-0.025-0.03221.871-0.011-0.0110.0000.0000.0000.000
124A142PHE00.0660.03116.0020.0090.0090.0000.0000.0000.000
125A143MET00.0080.02519.319-0.019-0.0190.0000.0000.0000.000
126A144ARG10.7960.88318.637-0.049-0.0490.0000.0000.0000.000
127A145ARG10.9600.95715.295-0.266-0.2660.0000.0000.0000.000
128A146ASP-1-0.930-0.96618.9080.1220.1220.0000.0000.0000.000
129A147TYR0-0.147-0.05321.948-0.016-0.0160.0000.0000.0000.000
130A148ASP-1-0.756-0.87724.3970.0870.0870.0000.0000.0000.000
131A149ALA0-0.036-0.03427.442-0.007-0.0070.0000.0000.0000.000
132A150ASP-1-0.925-0.95230.2740.0580.0580.0000.0000.0000.000
133A151ALA0-0.019-0.00930.150-0.005-0.0050.0000.0000.0000.000
134A152GLN0-0.028-0.01026.517-0.003-0.0030.0000.0000.0000.000
135A153PRO00.0600.03831.388-0.001-0.0010.0000.0000.0000.000
136A154ASN0-0.049-0.04833.809-0.003-0.0030.0000.0000.0000.000
137A155ALA0-0.0190.00028.602-0.004-0.0040.0000.0000.0000.000
138A156SER0-0.010-0.01227.0230.0030.0030.0000.0000.0000.000
139A157GLY00.0870.02825.3350.0030.0030.0000.0000.0000.000
140A158ALA00.0060.02422.7530.0100.0100.0000.0000.0000.000
141A159GLN0-0.044-0.04622.116-0.001-0.0010.0000.0000.0000.000
142A160TYR0-0.0100.00421.0520.0040.0040.0000.0000.0000.000
143A161ASN00.0200.01823.154-0.014-0.0140.0000.0000.0000.000
144A162PHE00.0120.00923.4110.0070.0070.0000.0000.0000.000
145A163LYS10.9590.97825.507-0.017-0.0170.0000.0000.0000.000
146A164ILE00.0420.02726.1190.0020.0020.0000.0000.0000.000
147A165LYS10.8900.94828.3700.0030.0030.0000.0000.0000.000
148A166ASP-1-0.827-0.91330.280-0.012-0.0120.0000.0000.0000.000
149A167ALA00.0110.01031.067-0.002-0.0020.0000.0000.0000.000
150A168ASP-1-0.919-0.96231.926-0.036-0.0360.0000.0000.0000.000
151A169LYS10.8620.91828.1100.0200.0200.0000.0000.0000.000
152A170TRP0-0.079-0.04223.7320.0010.0010.0000.0000.0000.000
153A171THR0-0.057-0.03623.9690.0060.0060.0000.0000.0000.000
154A172LYS10.9210.97014.8560.0480.0480.0000.0000.0000.000
155A173VAL0-0.0010.00519.2760.0160.0160.0000.0000.0000.000
156A174VAL0-0.004-0.02014.924-0.014-0.0140.0000.0000.0000.000
157A175VAL00.0080.00915.8370.0070.0070.0000.0000.0000.000
158A176TYR00.0120.00111.5740.0250.0250.0000.0000.0000.000
159A177TYR0-0.025-0.01613.933-0.034-0.0340.0000.0000.0000.000
160A178ASP-1-0.830-0.92013.8890.3130.3130.0000.0000.0000.000
161A179MET0-0.025-0.00712.284-0.023-0.0230.0000.0000.0000.000
162A180GLY00.0040.00515.096-0.017-0.0170.0000.0000.0000.000
163A181GLN0-0.0350.00017.144-0.034-0.0340.0000.0000.0000.000
164A182VAL0-0.009-0.00119.680-0.004-0.0040.0000.0000.0000.000
165A183VAL0-0.022-0.01022.184-0.002-0.0020.0000.0000.0000.000
166A184ASN00.0360.02525.280-0.005-0.0050.0000.0000.0000.000
167A185ALA00.021-0.00727.741-0.007-0.0070.0000.0000.0000.000
168A186ILE00.0090.01426.6580.0040.0040.0000.0000.0000.000
169A187SER0-0.0210.00328.5400.0010.0010.0000.0000.0000.000
170A188SER00.0240.02530.7230.0040.0040.0000.0000.0000.000
171A189LYS11.0761.03932.095-0.048-0.0480.0000.0000.0000.000
172A190LYS10.9170.96133.600-0.030-0.0300.0000.0000.0000.000
173A191SER0-0.095-0.05935.167-0.003-0.0030.0000.0000.0000.000
174A192ASN00.0280.00633.072-0.003-0.0030.0000.0000.0000.000
175A193PRO0-0.028-0.02435.4270.0030.0030.0000.0000.0000.000
176A194ALA00.0330.03035.8010.0020.0020.0000.0000.0000.000
177A195LEU0-0.076-0.01429.0750.0020.0020.0000.0000.0000.000
178A196GLU-1-0.963-0.99130.0560.0540.0540.0000.0000.0000.000
179A197VAL0-0.027-0.02624.300-0.002-0.0020.0000.0000.0000.000
180A198SER0-0.018-0.00724.955-0.002-0.0020.0000.0000.0000.000
181A199ASP-1-0.844-0.92322.0380.1510.1510.0000.0000.0000.000
182A200THR0-0.113-0.07118.099-0.018-0.0180.0000.0000.0000.000
183A201ASP-1-0.817-0.91620.4430.1140.1140.0000.0000.0000.000
184A202ASP-1-0.881-0.95018.3650.1890.1890.0000.0000.0000.000
185A203ASP-1-0.959-0.96918.2520.0940.0940.0000.0000.0000.000
186A204ALA0-0.050-0.03319.629-0.019-0.0190.0000.0000.0000.000
187A205ALA00.004-0.01419.3480.0010.0010.0000.0000.0000.000
188A206ILE0-0.030-0.01418.340-0.010-0.0100.0000.0000.0000.000
189A207LEU0-0.0030.00914.204-0.009-0.0090.0000.0000.0000.000
190A208LYS10.9320.96814.628-0.065-0.0650.0000.0000.0000.000
191A209ASP-1-0.768-0.84516.756-0.072-0.0720.0000.0000.0000.000
192A210CYS0-0.0230.01715.6470.0140.0140.0000.0000.0000.000
193A211TYR00.020-0.00117.870-0.024-0.0240.0000.0000.0000.000
194A212VAL00.0080.01414.8420.0230.0230.0000.0000.0000.000
195A213ALA00.0110.01118.152-0.015-0.0150.0000.0000.0000.000
196A214ILE00.0070.00318.0210.0110.0110.0000.0000.0000.000
197A215LEU0-0.017-0.01622.154-0.004-0.0040.0000.0000.0000.000
198A216GLY00.0660.01925.8530.0020.0020.0000.0000.0000.000
199A217GLN0-0.0280.00128.6050.0010.0010.0000.0000.0000.000
200A218ASN0-0.0070.00131.5170.0020.0020.0000.0000.0000.000
201A219LYS10.9300.95734.1740.0050.0050.0000.0000.0000.000
202A220GLY00.0120.00637.4610.0010.0010.0000.0000.0000.000
203A221GLY00.0150.04134.042-0.001-0.0010.0000.0000.0000.000
204A222VAL0-0.006-0.01432.054-0.003-0.0030.0000.0000.0000.000
205A223VAL0-0.022-0.01526.2810.0020.0020.0000.0000.0000.000
206A224GLU-1-0.868-0.87226.903-0.067-0.0670.0000.0000.0000.000
207A225ILE00.0100.00620.7690.0040.0040.0000.0000.0000.000
208A226SER0-0.007-0.03820.750-0.015-0.0150.0000.0000.0000.000
209A227ASP-1-0.894-0.95115.433-0.246-0.2460.0000.0000.0000.000
210A228VAL00.0040.00514.3240.0230.0230.0000.0000.0000.000
211A229THR0-0.038-0.0238.980-0.107-0.1070.0000.0000.0000.000
212A230LEU00.0220.0189.6680.1000.1000.0000.0000.0000.000
213A231LYS10.8910.9562.516-2.219-1.9510.745-0.508-0.5050.003
214A232LYS10.9801.0094.577-1.248-1.175-0.001-0.010-0.0620.000
215A233LYS0-0.013-0.0074.9590.8240.890-0.001-0.003-0.0620.000
216A234NA+10.1590.39737.4210.0390.0390.0000.0000.0000.000