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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: LL489

Calculation Name: 6Z4U-AB-Xray188

Preferred Name:

Target Type:

Ligand Name: polyethylene glycol (n=34)

ligand 3-letter code: 15P

PDB ID: 6Z4U

Chain ID: AB

ChEMBL ID:

UniProt ID: P0DTD2

Base Structure: X-ray

Registration Date: 2020-12-21

Reference: K. Kato Y. Handa, Y. Kawashima, K. Fukuzawa, C. Watanabe, T. Honma, , To be published

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHL
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Selected crystal waters in PDB
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandCharge None
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1722981.768238
FMO2-HF: Nuclear repulsion 1655349.584304
FMO2-HF: Total energy -67632.183934
FMO2-MP2: Total energy -67828.500711


3D Structure
Snapshot
 
Ligand structure

15P

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.
-35.569-14.08428.587-12.895-37.172-0.006


Interactive mode: IFIE and PIEDA for fragment #171(B:100:15P )


Summations of interaction energy for fragment #171(B:100:15P )
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.
-35.569-14.08428.587-12.895-37.1720.006
Interaction energy analysis for fragmet #171(B:100:15P )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.018
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].
1A1MET 10.8150.89720.965-0.111-0.1110.0000.0000.0000.000
2A2ASP -1-0.754-0.87019.0810.1300.1300.0000.0000.0000.000
3A3PRO 00.0040.01322.5800.0050.0050.0000.0000.0000.000
4A4LYS 10.9060.92721.712-0.073-0.0730.0000.0000.0000.000
5A5ILE 00.0710.04615.9450.0010.0010.0000.0000.0000.000
6A6SER 0-0.0100.00916.8520.0220.0220.0000.0000.0000.000
7A7GLU -1-0.865-0.89518.2750.0540.0540.0000.0000.0000.000
8A8MET 00.0150.02116.2350.0070.0070.0000.0000.0000.000
9A9HIS 0-0.0070.02717.318-0.008-0.0080.0000.0000.0000.000
10A10PRO 00.0510.01213.419-0.005-0.0050.0000.0000.0000.000
11A11ALA 00.0210.01612.7620.0310.0310.0000.0000.0000.000
12A12LEU 00.0130.01411.6320.0610.0610.0000.0000.0000.000
13A13ARG 10.8250.9008.352-0.256-0.2560.0000.0000.0000.000
14A14LEU 00.0480.0358.3470.2310.2310.0000.0000.0000.000
15A15VAL 0-0.020-0.0092.964-0.888-0.3310.105-0.144-0.518-0.001
16A16ASP -1-0.775-0.8935.878-0.126-0.1260.0000.0000.0000.000
17A17PRO 00.0160.0067.238-0.037-0.0370.0000.0000.0000.000
18A18GLN 0-0.011-0.0098.979-0.018-0.0180.0000.0000.0000.000
19A19ILE 0-0.020-0.0012.862-0.654-0.2130.114-0.095-0.4590.000
20A20GLN 0-0.032-0.0196.2360.4260.4260.0000.0000.0000.000
21A21LEU 00.0100.0032.281-1.092-0.7661.716-0.350-1.692-0.004
22A22ALA 0-0.0100.0055.5880.1300.1300.0000.0000.0000.000
23A23VAL 0-0.008-0.0187.4440.0430.0430.0000.0000.0000.000
24A24THR 00.0210.0129.592-0.080-0.0800.0000.0000.0000.000
25A25ARG 10.9210.95310.256-0.527-0.5270.0000.0000.0000.000
26A26NME 00.0260.03814.791-0.041-0.0410.0000.0000.0000.000
27A38ACE 00.006-0.02817.705-0.193-0.1930.0000.0000.0000.000
28A39PRO 0-0.032-0.03812.7280.2230.2230.0000.0000.0000.000
29A40LYS 10.8510.96512.505-0.379-0.3790.0000.0000.0000.000
30A41VAL 00.0180.0059.4110.0260.0260.0000.0000.0000.000
31A42TYR 0-0.023-0.0158.2580.0140.0140.0000.0000.0000.000
32A43PRO 00.0780.0357.6440.0630.0630.0000.0000.0000.000
33A44ILE 0-0.024-0.0132.433-1.918-0.3360.853-0.672-1.7620.004
34A45ILE 0-0.0040.0126.454-0.182-0.1820.0000.0000.0000.000
35A46LEU 00.0180.0043.485-0.6990.1290.033-0.288-0.5730.002
36A47ARG 10.8710.9177.276-0.603-0.6030.0000.0000.0000.000
37A48LEU 0-0.013-0.0176.9640.0050.0050.0000.0000.0000.000
38A49GLY 00.0410.01910.483-0.078-0.0780.0000.0000.0000.000
39A50SER 0-0.051-0.04310.862-0.069-0.0690.0000.0000.0000.000
40A51PRO 0-0.041-0.0198.8220.0740.0740.0000.0000.0000.000
41A52LEU 00.0160.0122.452-0.725-0.1450.699-0.219-1.060-0.001
42A53SER 0-0.005-0.0025.980-0.129-0.1290.0000.0000.0000.000
43A54LEU 00.0120.0022.983-0.683-0.0130.083-0.154-0.5980.000
44A55ASN 0-0.022-0.0155.6760.1940.1940.0000.0000.0000.000
45A56MET 00.0320.0318.705-0.010-0.0100.0000.0000.0000.000
46A57ALA 00.000-0.00410.3020.0470.0470.0000.0000.0000.000
47A58ARG 10.8770.92013.2790.1770.1770.0000.0000.0000.000
48A59LYS 10.8370.92716.3510.0880.0880.0000.0000.0000.000
49A60THR 0-0.024-0.02819.4430.0000.0000.0000.0000.0000.000
50A61LEU 0-0.0250.00522.1880.0080.0080.0000.0000.0000.000
51A62ASN 0-0.042-0.03822.368-0.009-0.0090.0000.0000.0000.000
52A63SER 00.0300.00525.2750.0080.0080.0000.0000.0000.000
53A64LEU 0-0.055-0.03126.410-0.005-0.0050.0000.0000.0000.000
54A65GLU -1-0.889-0.95927.841-0.057-0.0570.0000.0000.0000.000
55A66ASP -1-0.896-0.91428.796-0.080-0.0800.0000.0000.0000.000
56A67LYS 10.8280.93621.4820.0770.0770.0000.0000.0000.000
57A68ALA 00.0300.02223.141-0.004-0.0040.0000.0000.0000.000
58A69PHE 00.000-0.01017.0950.0000.0000.0000.0000.0000.000
59A70GLN 0-0.0140.00117.494-0.003-0.0030.0000.0000.0000.000
60A71LEU 00.005-0.01412.716-0.013-0.0130.0000.0000.0000.000
61A72THR 0-0.038-0.01512.9320.0380.0380.0000.0000.0000.000
62A73PRO 00.0240.02610.271-0.074-0.0740.0000.0000.0000.000
63A74ILE 00.013-0.0026.9800.0580.0580.0000.0000.0000.000
64A75ALA 0-0.0150.0047.471-0.211-0.2110.0000.0000.0000.000
65A76VAL 00.0310.0192.769-0.3550.0100.122-0.093-0.3940.000
66A77GLN 0-0.009-0.0016.1370.1640.1640.0000.0000.0000.000
67A78MET 0-0.024-0.0196.0370.0500.0500.0000.0000.0000.000
68A79THR 00.0080.0088.369-0.028-0.0280.0000.0000.0000.000
69A80LYS 10.8480.93511.4470.0010.0010.0000.0000.0000.000
70A81LEU 0-0.0110.00113.042-0.014-0.0140.0000.0000.0000.000
71A82ALA 00.010-0.00815.891-0.009-0.0090.0000.0000.0000.000
72A83THR 00.000-0.03119.471-0.001-0.0010.0000.0000.0000.000
73A84THR 00.018-0.00818.9760.0120.0120.0000.0000.0000.000
74A85GLU -1-0.786-0.86619.7050.1720.1720.0000.0000.0000.000
75A86GLU -1-0.776-0.84316.2000.1450.1450.0000.0000.0000.000
76A87LEU 0-0.063-0.01114.0130.0290.0290.0000.0000.0000.000
77A88PRO 00.0190.01913.041-0.026-0.0260.0000.0000.0000.000
78A89ASP -1-0.846-0.92616.1520.2550.2550.0000.0000.0000.000
79A90GLU -1-0.814-0.90713.9370.4330.4330.0000.0000.0000.000
80A91PHE 0-0.052-0.02110.333-0.021-0.0210.0000.0000.0000.000
81A92VAL 00.0170.0085.2990.0050.0050.0000.0000.0000.000
82A93VAL 00.005-0.0027.6870.0250.0250.0000.0000.0000.000
83A94VAL 00.0010.0082.328-1.172-0.4491.805-0.516-2.012-0.001
84A95THR 0-0.053-0.0305.305-0.0560.032-0.001-0.005-0.0820.000
85A96VAL 0-0.059-0.0316.196-0.216-0.2160.0000.0000.0000.000
86A97LYS 00.0340.0318.4920.0610.0610.0000.0000.0000.000
87B2ASP 0-0.058-0.03423.282-0.010-0.0100.0000.0000.0000.000
88B3PRO 00.0540.02221.3320.0050.0050.0000.0000.0000.000
89B4LYS 10.9480.99821.5480.0960.0960.0000.0000.0000.000
90B5ILE 00.022-0.01416.393-0.006-0.0060.0000.0000.0000.000
91B6SER 0-0.038-0.01917.605-0.010-0.0100.0000.0000.0000.000
92B7GLU -1-0.899-0.96118.527-0.124-0.1240.0000.0000.0000.000
93B8MET 0-0.111-0.02216.313-0.002-0.0020.0000.0000.0000.000
94B9HIS 00.0470.03715.214-0.035-0.0350.0000.0000.0000.000
95B10PRO 00.005-0.03011.4400.0080.0080.0000.0000.0000.000
96B11ALA 00.0430.04511.5230.0180.0180.0000.0000.0000.000
97B12LEU 00.0240.00810.978-0.002-0.0020.0000.0000.0000.000
98B13ARG 10.8750.9476.3930.4210.4210.0000.0000.0000.000
99B14LEU 00.0450.0357.6210.0330.0330.0000.0000.0000.000
100B15VAL 0-0.022-0.0162.883-0.9010.0040.260-0.223-0.942-0.002
101B16ASP -1-0.763-0.8745.4990.4670.4670.0000.0000.0000.000
102B17PRO 0-0.009-0.0017.089-0.015-0.0150.0000.0000.0000.000
103B18GLN 0-0.052-0.0159.357-0.084-0.0840.0000.0000.0000.000
104B19ILE 0-0.052-0.0304.215-0.2760.1070.001-0.046-0.3390.000
105B20GLN 0-0.029-0.0136.123-0.231-0.2310.0000.0000.0000.000
106B21LEU 00.0120.0012.621-1.529-0.2540.587-0.347-1.515-0.003
107B22ALA 0-0.012-0.0056.1050.0540.0540.0000.0000.0000.000
108B23VAL 00.1300.0306.499-0.065-0.0650.0000.0000.0000.000
109B24THR 00.5030.5489.0170.0960.0960.0000.0000.0000.000
110B25NME 00.3290.41111.014-0.014-0.0140.0000.0000.0000.000
111B38ACE 0-1.680-1.70815.7890.1070.1070.0000.0000.0000.000
112B39PRO 00.1280.04413.295-0.143-0.1430.0000.0000.0000.000
113B40LYS 11.4571.62512.8330.2010.2010.0000.0000.0000.000
114B41VAL 0-0.031-0.0249.772-0.043-0.0430.0000.0000.0000.000
115B42TYR 00.0300.0238.2360.0220.0220.0000.0000.0000.000
116B43PRO 00.0450.0217.932-0.042-0.0420.0000.0000.0000.000
117B44ILE 00.0040.0022.506-1.581-0.2720.706-0.422-1.594-0.001
118B45ILE 00.0050.0075.8330.0200.0200.0000.0000.0000.000
119B46LEU 00.0130.0082.166-0.315-0.7013.713-0.679-2.6480.001
120B47ARG 10.8710.9286.3160.0700.0700.0000.0000.0000.000
121B48LEU 0-0.015-0.0194.337-0.175-0.009-0.001-0.009-0.1570.000
122B49GLY 00.0580.0338.793-0.078-0.0780.0000.0000.0000.000
123B50SER 0-0.022-0.00810.282-0.012-0.0120.0000.0000.0000.000
124B51PRO 0-0.020-0.0046.1510.0190.0190.0000.0000.0000.000
125B52LEU 00.0450.0222.352-2.210-0.9954.234-1.355-4.0940.000
126B53SER 00.0220.0072.392-4.014-2.2701.504-1.379-1.869-0.012
127B54LEU 00.0290.0032.032-1.019-0.6554.798-0.974-4.188-0.001
128B55ASN 0-0.015-0.0103.9210.0800.2840.010-0.011-0.2020.000
129B56MET 0-0.0330.0017.2800.0520.0520.0000.0000.0000.000
130B57ALA 0-0.005-0.0039.910-0.071-0.0710.0000.0000.0000.000
131B58ARG 10.9140.93013.079-0.513-0.5130.0000.0000.0000.000
132B59LYS 10.8370.94116.546-0.235-0.2350.0000.0000.0000.000
133B60THR 0-0.055-0.03119.236-0.005-0.0050.0000.0000.0000.000
134B61LEU 00.0150.01121.839-0.017-0.0170.0000.0000.0000.000
135B62ASN 00.020-0.00423.9030.0220.0220.0000.0000.0000.000
136B63SER 0-0.035-0.00825.940-0.010-0.0100.0000.0000.0000.000
137B64LEU 0-0.007-0.02028.6900.0030.0030.0000.0000.0000.000
138B65GLU -1-0.937-0.95230.5600.0890.0890.0000.0000.0000.000
139B66ASP -1-0.899-0.93726.8260.1510.1510.0000.0000.0000.000
140B67LYS 10.7770.87221.682-0.162-0.1620.0000.0000.0000.000
141B68ALA 00.0220.02221.673-0.001-0.0010.0000.0000.0000.000
142B69PHE 00.015-0.01316.5320.0110.0110.0000.0000.0000.000
143B70GLN 0-0.016-0.00115.334-0.036-0.0360.0000.0000.0000.000
144B71LEU 0-0.016-0.01110.9260.0460.0460.0000.0000.0000.000
145B72THR 0-0.023-0.00510.612-0.082-0.0820.0000.0000.0000.000
146B73PRO 00.0330.0127.0720.1170.1170.0000.0000.0000.000
147B74ILE 0-0.014-0.0084.544-0.381-0.229-0.001-0.012-0.1390.000
148B75ALA 0-0.0130.0033.1660.1111.5260.113-0.637-0.8900.001
149B76VAL 0-0.013-0.0072.343-9.617-6.2344.748-2.679-5.4510.019
150B77GLN 00.0630.0323.529-2.257-1.7660.011-0.219-0.281-0.001
151B78MET 0-0.044-0.0282.381-0.8520.1721.448-0.682-1.7900.003
152B79THR 00.0120.0137.039-0.152-0.1520.0000.0000.0000.000
153B80LYS 10.8990.94810.5120.3660.3660.0000.0000.0000.000
154B81LEU 00.0220.02112.0190.0200.0200.0000.0000.0000.000
155B82ALA 00.001-0.00314.633-0.015-0.0150.0000.0000.0000.000
156B83THR 0-0.081-0.07918.3480.0030.0030.0000.0000.0000.000
157B84THR 00.001-0.00118.060-0.002-0.0020.0000.0000.0000.000
158B85GLU -1-0.810-0.92818.799-0.082-0.0820.0000.0000.0000.000
159B86GLU -1-0.801-0.87515.581-0.081-0.0810.0000.0000.0000.000
160B87LEU 0-0.050-0.00813.3430.0050.0050.0000.0000.0000.000
161B88PRO 00.0100.00111.9750.0070.0070.0000.0000.0000.000
162B89ASP -1-0.826-0.90815.237-0.093-0.0930.0000.0000.0000.000
163B90GLU -1-0.798-0.88213.813-0.196-0.1960.0000.0000.0000.000
164B91PHE 0-0.037-0.01410.0260.0210.0210.0000.0000.0000.000
165B92VAL 00.0330.0215.080-0.053-0.0530.0000.0000.0000.000
166B93VAL 0-0.012-0.0177.8460.1380.1380.0000.0000.0000.000
167B94VAL 00.0010.0072.501-2.344-0.7080.928-0.684-1.8790.003
168B95THR 0-0.063-0.0405.2740.1370.182-0.001-0.001-0.0440.000
169B96VAL 0-0.042-0.0216.354-0.037-0.0370.0000.0000.0000.000
170B97LYS 00.1310.0748.430-0.062-0.0620.0000.0000.0000.000
172A102HOH 0-0.013-0.0167.072-0.019-0.0190.0000.0000.0000.000
173A104HOH 0-0.012-0.02221.4260.0030.0030.0000.0000.0000.000
174A105HOH 0-0.019-0.02320.5610.0000.0000.0000.0000.0000.000
175A106HOH 0-0.071-0.05916.620-0.010-0.0100.0000.0000.0000.000
176A108HOH 00.002-0.01013.902-0.018-0.0180.0000.0000.0000.000
177A111HOH 0-0.010-0.00817.2540.0000.0000.0000.0000.0000.000
178A113HOH 00.005-0.00622.000-0.004-0.0040.0000.0000.0000.000
179A114HOH 0-0.028-0.03216.3400.0000.0000.0000.0000.0000.000
180A115HOH 0-0.019-0.02919.274-0.004-0.0040.0000.0000.0000.000
181A116HOH 0-0.005-0.0286.6670.1180.1180.0000.0000.0000.000
182A118HOH 0-0.063-0.05430.7000.0010.0010.0000.0000.0000.000
183A121HOH 00.0360.02115.0240.0020.0020.0000.0000.0000.000
184A123HOH 0-0.032-0.02715.5790.0010.0010.0000.0000.0000.000
185A124HOH 00.0310.02312.382-0.013-0.0130.0000.0000.0000.000
186A128HOH 0-0.011-0.01115.143-0.001-0.0010.0000.0000.0000.000
187B202HOH 00.007-0.00213.007-0.023-0.0230.0000.0000.0000.000
188B203HOH 0-0.0040.0025.9210.0020.0020.0000.0000.0000.000
189B207HOH 0-0.010-0.0057.7130.0590.0590.0000.0000.0000.000
190B208HOH 0-0.006-0.0246.541-0.042-0.0420.0000.0000.0000.000