Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: XNN5Q

Calculation Name: 4JLP-B-Xray25

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-diphosphate

ligand 3-letter code: ADP

PDB ID: 4JLP

Chain ID: B

ChEMBL ID:

UniProt ID: O66490

Base Structure: X-ray

Registration Date: 2018-07-25

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 Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge ADP=-3
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2519172.147137
FMO2-HF: Nuclear repulsion 2434381.76488
FMO2-HF: Total energy -84790.382257
FMO2-MP2: Total energy -85037.994797


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-26.072-21.72327.052-13.03-18.374-0.078
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.023
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].
3B3LEU00.000-0.0032.674-1.904-0.0793.150-1.365-3.6100.009
4B4VAL00.0210.0194.670-0.217-0.185-0.001-0.009-0.0230.000
5B5PHE0-0.026-0.0077.4680.0500.0500.0000.0000.0000.000
6B6LEU00.0320.01310.835-0.093-0.0930.0000.0000.0000.000
7B7GLY00.0640.01613.9920.0190.0190.0000.0000.0000.000
8B8PRO00.0350.04217.454-0.002-0.0020.0000.0000.0000.000
9B9PRO0-0.051-0.03320.0900.0270.0270.0000.0000.0000.000
10B10GLY00.0460.00321.342-0.011-0.0110.0000.0000.0000.000
11B11ALA00.0070.00518.133-0.003-0.0030.0000.0000.0000.000
12B12GLY00.0100.00118.4280.0050.0050.0000.0000.0000.000
13B13LYS10.8650.94414.081-0.298-0.2980.0000.0000.0000.000
14B14GLY00.0830.04514.0490.0500.0500.0000.0000.0000.000
15B15THR0-0.072-0.04015.7190.0080.0080.0000.0000.0000.000
16B16GLN00.0420.01312.3620.0340.0340.0000.0000.0000.000
17B17ALA00.0190.02410.9510.0880.0880.0000.0000.0000.000
18B18LYS10.9540.97711.954-0.237-0.2370.0000.0000.0000.000
19B19ARG10.8000.90214.029-0.299-0.2990.0000.0000.0000.000
20B20LEU00.0470.0276.204-0.132-0.1320.0000.0000.0000.000
21B21ALA0-0.0010.0069.9490.0000.0000.0000.0000.0000.000
22B22LYS10.9030.95410.925-0.255-0.2550.0000.0000.0000.000
23B23GLU-1-0.919-0.96912.7350.1950.1950.0000.0000.0000.000
24B24LYS10.8860.9417.971-0.403-0.4030.0000.0000.0000.000
25B25GLY00.0100.0268.277-0.039-0.0390.0000.0000.0000.000
26B26PHE0-0.027-0.0133.061-2.258-0.9870.717-0.462-1.5270.004
27B27VAL00.014-0.0027.270-0.010-0.0100.0000.0000.0000.000
28B28HIS0-0.080-0.0629.0230.0240.0240.0000.0000.0000.000
29B29ILE00.0240.01410.657-0.045-0.0450.0000.0000.0000.000
30B30SER00.0310.03112.8820.0130.0130.0000.0000.0000.000
31B31THR00.0480.00715.533-0.020-0.0200.0000.0000.0000.000
32B32GLY0-0.029-0.00917.950-0.020-0.0200.0000.0000.0000.000
33B33ASP-1-0.868-0.94518.6510.2110.2110.0000.0000.0000.000
34B34ILE00.0230.01916.344-0.017-0.0170.0000.0000.0000.000
35B35LEU00.011-0.00720.780-0.015-0.0150.0000.0000.0000.000
36B36ARG10.8650.91721.159-0.192-0.1920.0000.0000.0000.000
37B37GLU-1-0.818-0.87523.4980.1110.1110.0000.0000.0000.000
38B38ALA0-0.021-0.00724.981-0.011-0.0110.0000.0000.0000.000
39B39VAL0-0.024-0.02526.608-0.009-0.0090.0000.0000.0000.000
40B40GLN0-0.026-0.00228.794-0.004-0.0040.0000.0000.0000.000
41B41LYS10.8160.88627.458-0.111-0.1110.0000.0000.0000.000
42B42GLY0-0.0210.01330.400-0.005-0.0050.0000.0000.0000.000
43B43THR00.0210.00327.305-0.005-0.0050.0000.0000.0000.000
44B44PRO00.016-0.01129.8360.0000.0000.0000.0000.0000.000
45B45LEU00.0480.03723.783-0.002-0.0020.0000.0000.0000.000
46B46GLY00.0460.01728.2240.0010.0010.0000.0000.0000.000
47B47LYS10.8880.93029.261-0.076-0.0760.0000.0000.0000.000
48B48LYS10.9641.00630.082-0.087-0.0870.0000.0000.0000.000
49B49ALA00.0260.00226.9110.0000.0000.0000.0000.0000.000
50B50LYS10.8990.94528.876-0.082-0.0820.0000.0000.0000.000
51B51GLU-1-0.904-0.96031.0400.0850.0850.0000.0000.0000.000
52B52TYR00.0200.01628.720-0.002-0.0020.0000.0000.0000.000
53B53MET0-0.018-0.01424.7810.0020.0020.0000.0000.0000.000
54B54GLU-1-0.898-0.93628.4050.0910.0910.0000.0000.0000.000
55B55ARG10.9170.96531.404-0.085-0.0850.0000.0000.0000.000
56B56GLY0-0.036-0.02028.057-0.001-0.0010.0000.0000.0000.000
57B57GLU-1-0.966-0.98527.7900.0960.0960.0000.0000.0000.000
58B58LEU0-0.045-0.02922.5720.0070.0070.0000.0000.0000.000
59B59VAL0-0.002-0.00124.344-0.009-0.0090.0000.0000.0000.000
60B60PRO0-0.015-0.01024.9290.0050.0050.0000.0000.0000.000
61B61ASP-1-0.752-0.88723.1990.1410.1410.0000.0000.0000.000
62B62ASP-1-0.894-0.93522.9650.1190.1190.0000.0000.0000.000
63B63LEU0-0.070-0.03924.1090.0040.0040.0000.0000.0000.000
64B64ILE0-0.021-0.00919.0580.0070.0070.0000.0000.0000.000
65B65ILE00.0210.00119.0760.0150.0150.0000.0000.0000.000
66B66ALA00.0480.03419.1210.0130.0130.0000.0000.0000.000
67B67LEU0-0.0030.00318.9880.0080.0080.0000.0000.0000.000
68B68ILE0-0.045-0.03713.9950.0140.0140.0000.0000.0000.000
69B69GLU-1-0.953-0.99315.2350.2100.2100.0000.0000.0000.000
70B70GLU-1-1.028-1.00016.7350.1640.1640.0000.0000.0000.000
71B71VAL0-0.062-0.03614.3210.0010.0010.0000.0000.0000.000
72B72PHE0-0.029-0.0057.412-0.025-0.0250.0000.0000.0000.000
73B73PRO0-0.0090.0088.205-0.029-0.0290.0000.0000.0000.000
74B74LYS10.9110.9369.701-0.141-0.1410.0000.0000.0000.000
75B75HIS00.0160.0097.5880.1320.1320.0000.0000.0000.000
76B76GLY00.0290.0155.811-0.060-0.0600.0000.0000.0000.000
77B77ASN00.0340.0351.816-3.220-9.22714.989-5.072-3.909-0.028
78B78VAL00.0090.0113.4010.5541.1540.011-0.161-0.4510.000
79B79ILE0-0.0190.0004.966-0.199-0.216-0.001-0.0170.0350.000
80B80PHE00.0210.0067.361-0.069-0.0690.0000.0000.0000.000
81B81ASP-1-0.824-0.9129.9520.4680.4680.0000.0000.0000.000
82B82GLY0-0.014-0.01612.725-0.044-0.0440.0000.0000.0000.000
83B83PHE00.0000.02013.183-0.036-0.0360.0000.0000.0000.000
84B84PRO00.0800.04312.7160.0330.0330.0000.0000.0000.000
85B85ARG10.8450.89215.673-0.202-0.2020.0000.0000.0000.000
86B86THR00.0370.02618.837-0.009-0.0090.0000.0000.0000.000
87B87VAL00.0820.02619.1540.0110.0110.0000.0000.0000.000
88B88LYS10.9510.98619.901-0.099-0.0990.0000.0000.0000.000
89B89GLN0-0.006-0.00417.7730.0210.0210.0000.0000.0000.000
90B90ALA0-0.002-0.00415.4830.0140.0140.0000.0000.0000.000
91B91GLU-1-0.899-0.95015.7270.1140.1140.0000.0000.0000.000
92B92ALA00.0390.01617.3640.0030.0030.0000.0000.0000.000
93B93LEU0-0.045-0.01510.6620.0170.0170.0000.0000.0000.000
94B94ASP-1-0.828-0.91212.6910.1910.1910.0000.0000.0000.000
95B95GLU-1-0.945-0.95813.7260.1550.1550.0000.0000.0000.000
96B96MET0-0.057-0.03212.1900.0070.0070.0000.0000.0000.000
97B97LEU0-0.042-0.0388.1480.0420.0420.0000.0000.0000.000
98B98GLU-1-0.870-0.91511.4050.2130.2130.0000.0000.0000.000
99B99LYS10.8870.94013.247-0.176-0.1760.0000.0000.0000.000
100B100LYS10.8540.93511.170-0.402-0.4020.0000.0000.0000.000
101B101GLY0-0.0070.01310.9290.1050.1050.0000.0000.0000.000
102B102LEU0-0.078-0.0385.7870.2310.2310.0000.0000.0000.000
103B103LYS11.0090.9976.3570.1240.1240.0000.0000.0000.000
104B104VAL00.0080.0015.5320.0290.0290.0000.0000.0000.000
105B105ASP-1-0.870-0.9242.323-5.906-3.3743.636-3.063-3.105-0.032
106B106HIS00.0310.0112.990-0.9480.1290.620-0.288-1.4100.003
107B107VAL0-0.012-0.0036.2550.0580.0580.0000.0000.0000.000
108B108LEU00.0100.0096.658-0.062-0.0620.0000.0000.0000.000
109B109LEU00.002-0.00610.456-0.057-0.0570.0000.0000.0000.000
110B110PHE0-0.043-0.03611.642-0.021-0.0210.0000.0000.0000.000
111B111GLU-1-0.864-0.86416.1140.1280.1280.0000.0000.0000.000
112B112VAL0-0.024-0.02319.357-0.001-0.0010.0000.0000.0000.000
113B113PRO00.0900.04422.363-0.001-0.0010.0000.0000.0000.000
114B114ASP-1-0.799-0.91725.9380.1310.1310.0000.0000.0000.000
115B115GLU-1-0.952-0.97527.4130.0880.0880.0000.0000.0000.000
116B116VAL00.0320.01724.8960.0000.0000.0000.0000.0000.000
117B117VAL0-0.029-0.01422.5270.0050.0050.0000.0000.0000.000
118B118ILE00.0270.00925.3460.0020.0020.0000.0000.0000.000
119B119GLU-1-0.892-0.93528.6890.0980.0980.0000.0000.0000.000
120B120ARG10.8080.90820.801-0.205-0.2050.0000.0000.0000.000
121B121LEU0-0.039-0.03424.1380.0040.0040.0000.0000.0000.000
122B122SER00.0180.01927.185-0.004-0.0040.0000.0000.0000.000
123B123GLY00.0110.00929.790-0.007-0.0070.0000.0000.0000.000
124B124ARG10.8050.88422.073-0.176-0.1760.0000.0000.0000.000
125B125ARG10.8140.90127.860-0.111-0.1110.0000.0000.0000.000
126B126ILE0-0.0130.00025.0990.0100.0100.0000.0000.0000.000
127B127ASN00.0990.05227.989-0.013-0.0130.0000.0000.0000.000
128B128PRO0-0.077-0.04028.5910.0070.0070.0000.0000.0000.000
129B129GLU-1-0.877-0.93430.3190.0800.0800.0000.0000.0000.000
130B130THR0-0.017-0.00926.4110.0010.0010.0000.0000.0000.000
131B131GLY0-0.0040.00124.7070.0090.0090.0000.0000.0000.000
132B132GLU-1-0.990-0.99023.8570.1520.1520.0000.0000.0000.000
133B133VAL0-0.053-0.04321.862-0.007-0.0070.0000.0000.0000.000
134B134TYR00.0300.01724.5070.0010.0010.0000.0000.0000.000
135B135HIS0-0.049-0.03326.4720.0040.0040.0000.0000.0000.000
136B136VAL0-0.031-0.01828.333-0.005-0.0050.0000.0000.0000.000
137B137LYS10.9510.98830.679-0.094-0.0940.0000.0000.0000.000
138B138TYR0-0.025-0.03226.187-0.003-0.0030.0000.0000.0000.000
139B139ASN0-0.018-0.00824.406-0.005-0.0050.0000.0000.0000.000
140B140PRO00.0440.03027.7140.0050.0050.0000.0000.0000.000
141B141PRO0-0.0130.01030.6240.0010.0010.0000.0000.0000.000
142B142PRO00.0310.00930.680-0.005-0.0050.0000.0000.0000.000
143B143PRO00.0490.01533.8180.0000.0000.0000.0000.0000.000
144B144GLY0-0.012-0.00637.444-0.001-0.0010.0000.0000.0000.000
145B145VAL0-0.0260.00131.7260.0000.0000.0000.0000.0000.000
146B146LYS10.9380.97635.036-0.072-0.0720.0000.0000.0000.000
147B147VAL00.0330.02231.1150.0050.0050.0000.0000.0000.000
148B148ILE0-0.077-0.05331.216-0.007-0.0070.0000.0000.0000.000
149B149GLN00.0130.00031.3180.0020.0020.0000.0000.0000.000
150B150LYS10.9330.96427.682-0.120-0.1200.0000.0000.0000.000
151B151GLU-1-0.742-0.87830.8760.0840.0840.0000.0000.0000.000
152B152ASP-1-0.887-0.94626.7770.1320.1320.0000.0000.0000.000
153B153ASP-1-0.857-0.89327.0710.1510.1510.0000.0000.0000.000
154B154LYS10.8340.90729.823-0.088-0.0880.0000.0000.0000.000
155B155PRO00.018-0.00932.7700.0030.0030.0000.0000.0000.000
156B156GLU-1-0.917-0.94433.9390.0800.0800.0000.0000.0000.000
157B157VAL00.0560.03129.3600.0030.0030.0000.0000.0000.000
158B158ILE0-0.022-0.00529.0180.0080.0080.0000.0000.0000.000
159B159LYS10.8620.91729.322-0.074-0.0740.0000.0000.0000.000
160B160LYS10.9921.01330.114-0.091-0.0910.0000.0000.0000.000
161B161ARG10.9510.97322.456-0.157-0.1570.0000.0000.0000.000
162B162LEU0-0.037-0.02025.2870.0100.0100.0000.0000.0000.000
163B163GLU-1-0.868-0.91626.9220.0900.0900.0000.0000.0000.000
164B164VAL00.0140.01124.6080.0000.0000.0000.0000.0000.000
165B165TYR0-0.014-0.01019.0740.0110.0110.0000.0000.0000.000
166B166ARG10.8970.93523.519-0.107-0.1070.0000.0000.0000.000
167B167GLU-1-0.900-0.93125.7980.0900.0900.0000.0000.0000.000
168B168GLN0-0.027-0.02224.123-0.003-0.0030.0000.0000.0000.000
169B169THR0-0.085-0.05418.6500.0060.0060.0000.0000.0000.000
170B170ALA00.0110.00819.6790.0130.0130.0000.0000.0000.000
171B171PRO00.0530.03020.8280.0040.0040.0000.0000.0000.000
172B172LEU0-0.019-0.02016.131-0.005-0.0050.0000.0000.0000.000
173B173ILE0-0.0070.00116.6080.0140.0140.0000.0000.0000.000
174B174GLU-1-0.649-0.70917.3880.0870.0870.0000.0000.0000.000
175B175TYR0-0.108-0.05415.146-0.017-0.0170.0000.0000.0000.000
176B176TYR00.0580.00012.330-0.002-0.0020.0000.0000.0000.000
177B177LYS10.9140.95514.252-0.129-0.1290.0000.0000.0000.000
178B178LYS10.9080.95816.512-0.096-0.0960.0000.0000.0000.000
179B179LYS10.8760.95513.089-0.115-0.1150.0000.0000.0000.000
180B180GLY00.0080.02113.372-0.035-0.0350.0000.0000.0000.000
181B181ILE0-0.036-0.0168.674-0.034-0.0340.0000.0000.0000.000
182B182LEU0-0.0280.0089.7150.1490.1490.0000.0000.0000.000
183B183ARG10.9380.9877.387-0.321-0.3210.0000.0000.0000.000
184B184ILE00.0140.01712.1350.0830.0830.0000.0000.0000.000
185B185ILE00.0050.00911.776-0.001-0.0010.0000.0000.0000.000
186B186ASP-1-0.763-0.85314.8740.1510.1510.0000.0000.0000.000
187B187ALA0-0.027-0.01817.1530.0090.0090.0000.0000.0000.000
188B188SER0-0.064-0.07318.544-0.015-0.0150.0000.0000.0000.000
189B189LYS10.9210.97819.072-0.160-0.1600.0000.0000.0000.000
190B190PRO00.0230.00521.1860.0170.0170.0000.0000.0000.000
191B191VAL00.019-0.00318.0450.0200.0200.0000.0000.0000.000
192B192GLU-1-0.809-0.89717.4050.2280.2280.0000.0000.0000.000
193B193GLU-1-0.841-0.94417.0310.1590.1590.0000.0000.0000.000
194B194VAL0-0.067-0.01714.5330.0230.0230.0000.0000.0000.000
195B195TYR00.009-0.00111.3610.1250.1250.0000.0000.0000.000
196B196ARG10.9130.94812.020-0.014-0.0140.0000.0000.0000.000
197B197GLN00.0410.02311.905-0.022-0.0220.0000.0000.0000.000
198B198VAL0-0.021-0.0088.1920.0610.0610.0000.0000.0000.000
199B199LEU0-0.082-0.0607.6700.3600.3600.0000.0000.0000.000
200B200GLU-1-0.939-0.9567.068-0.108-0.1080.0000.0000.0000.000
201B201VAL0-0.059-0.0276.067-0.227-0.2270.0000.0000.0000.000
202B202ILE0-0.108-0.0612.805-0.4470.1732.207-0.726-2.100-0.001
203B203GLY-1-0.919-0.9322.351-11.684-9.2681.724-1.867-2.274-0.033
204B301ADP-3-2.589-2.64037.0660.0750.0750.0000.0000.0000.000
205B302ADP-3-2.729-2.78536.3920.0720.0720.0000.0000.0000.000
206A402HOH0-0.174-0.13422.8130.0030.0030.0000.0000.0000.000
207A464HOH0-0.050-0.04814.2250.0010.0010.0000.0000.0000.000
208A500HOH0-0.074-0.10223.0280.0010.0010.0000.0000.0000.000
209A528HOH0-0.001-0.01323.9070.0030.0030.0000.0000.0000.000
210A733HOH0-0.079-0.10122.0160.0010.0010.0000.0000.0000.000
211B401HOH0-0.089-0.06735.0990.0000.0000.0000.0000.0000.000
212B404HOH0-0.026-0.03243.8160.0000.0000.0000.0000.0000.000
213B405HOH0-0.064-0.03835.684-0.001-0.0010.0000.0000.0000.000
214B406HOH0-0.066-0.05036.890-0.001-0.0010.0000.0000.0000.000
215B411HOH0-0.027-0.01643.887-0.001-0.0010.0000.0000.0000.000
216B431HOH00.014-0.01236.5970.0020.0020.0000.0000.0000.000
217B445HOH0-0.083-0.05936.1580.0020.0020.0000.0000.0000.000
218B447HOH0-0.020-0.02535.4740.0000.0000.0000.0000.0000.000
219B452HOH0-0.038-0.03241.1440.0000.0000.0000.0000.0000.000
220B453HOH0-0.088-0.08635.5000.0000.0000.0000.0000.0000.000
221B460HOH00.0370.02818.710-0.007-0.0070.0000.0000.0000.000
222B477HOH0-0.080-0.07140.9760.0000.0000.0000.0000.0000.000
223B506HOH0-0.097-0.08439.706-0.001-0.0010.0000.0000.0000.000
224B511HOH00.000-0.01324.201-0.001-0.0010.0000.0000.0000.000
225B583HOH00.0470.03222.6940.0020.0020.0000.0000.0000.000
226B597HOH0-0.015-0.00923.219-0.006-0.0060.0000.0000.0000.000
227B645HOH0-0.019-0.03214.415-0.008-0.0080.0000.0000.0000.000
228B763HOH0-0.041-0.02038.7560.0010.0010.0000.0000.0000.000
229B767HOH00.0240.01535.1290.0000.0000.0000.0000.0000.000