FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 4LJ2N

Calculation Name: 2ZYZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZYZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZVI1

Base Structure: X-ray

Registration Date: 2023-09-27

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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945569.457975
FMO2-HF: Nuclear repulsion 1873847.788066
FMO2-HF: Total energy -71721.669909
FMO2-MP2: Total energy -71933.263235


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.
-9.61-4.6414.25-4.12-15.099-0.042
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 : -0.046 / q_NPA : -0.012
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].
3B3GLY0-0.011-0.0033.760-2.639-0.719-0.040-0.942-0.938-0.001
4B4TYR00.0080.0046.9070.4650.4650.0000.0000.0000.000
5B5LEU0-0.018-0.01010.408-0.115-0.1150.0000.0000.0000.000
6B6ARG10.8440.89812.316-0.046-0.0460.0000.0000.0000.000
7B7GLY00.0080.01216.351-0.033-0.0330.0000.0000.0000.000
8B8LEU0-0.023-0.02617.6710.0150.0150.0000.0000.0000.000
9B9ALA0-0.043-0.01514.876-0.023-0.0230.0000.0000.0000.000
10B10VAL00.0310.0208.5920.0330.0330.0000.0000.0000.000
11B11ILE0-0.015-0.00911.292-0.094-0.0940.0000.0000.0000.000
12B12VAL00.0060.0025.6890.0710.0710.0000.0000.0000.000
13B13GLU-1-0.811-0.8897.6640.0500.0500.0000.0000.0000.000
14B14ASP-1-0.855-0.9193.527-2.938-2.2990.008-0.294-0.353-0.002
15B15VAL00.0460.0016.518-0.365-0.3650.0000.0000.0000.000
16B16GLU-1-0.824-0.8967.247-0.930-0.9300.0000.0000.0000.000
17B17PHE0-0.038-0.0102.870-3.091-1.1923.425-1.514-3.809-0.015
18B18ALA0-0.0060.0025.4520.0850.0850.0000.0000.0000.000
19B19ARG10.8470.9047.9450.6690.6690.0000.0000.0000.000
20B20ARG10.8360.9074.9912.0662.0660.0000.0000.0000.000
21B21LEU00.0440.0285.2760.2310.2310.0000.0000.0000.000
22B22TYR0-0.086-0.0468.5340.2070.2070.0000.0000.0000.000
23B23LYS10.8530.91511.9640.7680.7680.0000.0000.0000.000
24B24GLU-1-0.884-0.9368.174-1.269-1.2690.0000.0000.0000.000
25B25GLY00.0840.03311.026-0.038-0.0380.0000.0000.0000.000
26B26PHE00.0090.00213.3420.0760.0760.0000.0000.0000.000
27B27TYR0-0.033-0.00410.3330.0620.0620.0000.0000.0000.000
28B28GLY00.0320.01112.083-0.065-0.0650.0000.0000.0000.000
29B29ARG10.8570.90713.3230.2640.2640.0000.0000.0000.000
30B30PHE00.0670.04311.877-0.010-0.0100.0000.0000.0000.000
31B31LEU0-0.0200.01415.6170.0500.0500.0000.0000.0000.000
32B32GLY00.0180.00218.031-0.012-0.0120.0000.0000.0000.000
33B33TYR00.008-0.01218.5120.0090.0090.0000.0000.0000.000
34B34ASP-1-0.858-0.93920.615-0.185-0.1850.0000.0000.0000.000
35B35LYS10.8320.90221.7320.1810.1810.0000.0000.0000.000
36B36VAL00.0300.04617.2140.0070.0070.0000.0000.0000.000
37B37LYS10.8530.91719.7100.2280.2280.0000.0000.0000.000
38B38ARG10.9320.94615.9290.4690.4690.0000.0000.0000.000
39B39ASP-1-0.882-0.94017.685-0.330-0.3300.0000.0000.0000.000
40B40GLU-1-0.792-0.87420.027-0.247-0.2470.0000.0000.0000.000
41B41VAL0-0.012-0.00313.5010.0000.0000.0000.0000.0000.000
42B42GLU-1-0.832-0.91014.109-0.663-0.6630.0000.0000.0000.000
43B43LYS10.9100.96616.5630.2870.2870.0000.0000.0000.000
44B44ILE0-0.0110.01515.2980.0370.0370.0000.0000.0000.000
45B45ASN00.015-0.00414.181-0.081-0.0810.0000.0000.0000.000
46B46ALA0-0.0150.00714.0050.0570.0570.0000.0000.0000.000
47B47PRO00.0560.02711.685-0.079-0.0790.0000.0000.0000.000
48B48LEU0-0.049-0.0139.0620.0460.0460.0000.0000.0000.000
49B49ILE0-0.021-0.01011.194-0.014-0.0140.0000.0000.0000.000
50B50LEU0-0.0080.0017.847-0.020-0.0200.0000.0000.0000.000
51B51GLY00.0140.00012.3530.0670.0670.0000.0000.0000.000
52B52LEU00.0530.01613.263-0.028-0.0280.0000.0000.0000.000
53B53TYR00.006-0.00113.6840.0160.0160.0000.0000.0000.000
54B54GLU-1-0.792-0.88511.585-0.385-0.3850.0000.0000.0000.000
55B55ALA00.0210.0098.952-0.032-0.0320.0000.0000.0000.000
56B56LEU00.0470.0269.0000.1160.1160.0000.0000.0000.000
57B57TYR0-0.012-0.02910.7530.0530.0530.0000.0000.0000.000
58B58LEU0-0.021-0.0236.0600.0100.0100.0000.0000.0000.000
59B59ALA0-0.0070.0036.4100.3810.3810.0000.0000.0000.000
60B60GLU-1-0.852-0.9207.3960.3750.3750.0000.0000.0000.000
61B61LYS10.7930.8817.9400.1250.1250.0000.0000.0000.000
62B62GLY00.0350.0694.988-0.427-0.4270.0000.0000.0000.000
63B63ARG10.7620.8532.563-1.2250.4831.937-0.974-2.671-0.010
64B64LEU0-0.043-0.0352.037-3.279-4.0226.777-1.961-4.073-0.013
65B65LYS10.8600.9232.414-1.473-1.9232.1431.592-3.286-0.001
66B66VAL0-0.004-0.0014.782-0.831-0.8340.000-0.0270.0310.000
67B67MET0-0.0010.0127.4960.3430.3430.0000.0000.0000.000
68B68GLY00.0310.00310.035-0.182-0.1820.0000.0000.0000.000
69B69GLU-1-0.921-0.98113.7940.2040.2040.0000.0000.0000.000
70B70ASP-1-0.843-0.88116.3270.4350.4350.0000.0000.0000.000
71B71GLY0-0.022-0.01613.4440.0120.0120.0000.0000.0000.000
72B72ARG10.8300.90613.181-0.339-0.3390.0000.0000.0000.000
73B73GLU-1-0.810-0.9017.3322.5562.5560.0000.0000.0000.000
74B74VAL0-0.045-0.03210.447-0.153-0.1530.0000.0000.0000.000
75B75ALA0-0.0060.00110.6390.1020.1020.0000.0000.0000.000
76B76PRO00.027-0.0099.903-0.119-0.1190.0000.0000.0000.000
77B77GLU-1-0.818-0.93712.3600.1340.1340.0000.0000.0000.000
78B78GLU-1-0.858-0.91214.7980.4900.4900.0000.0000.0000.000
79B79LEU0-0.046-0.02310.116-0.064-0.0640.0000.0000.0000.000
80B80ALA0-0.001-0.00614.847-0.058-0.0580.0000.0000.0000.000
81B81ALA0-0.028-0.00417.461-0.033-0.0330.0000.0000.0000.000
82B82LEU00.0220.01416.541-0.023-0.0230.0000.0000.0000.000
83B83GLY00.019-0.01618.511-0.024-0.0240.0000.0000.0000.000
84B84ARG10.7480.84719.898-0.151-0.1510.0000.0000.0000.000
85B85GLU-1-0.949-0.96222.6230.1100.1100.0000.0000.0000.000
86B86ARG10.9070.95121.753-0.093-0.0930.0000.0000.0000.000
87B87MET0-0.069-0.01719.147-0.017-0.0170.0000.0000.0000.000
88B88ARG10.9770.98324.358-0.009-0.0090.0000.0000.0000.000
89B89ASN0-0.025-0.04026.108-0.010-0.0100.0000.0000.0000.000
90B90PHE00.0040.03516.664-0.011-0.0110.0000.0000.0000.000
91B91ASP-1-0.760-0.85921.5800.0800.0800.0000.0000.0000.000
92B92GLU-1-0.845-0.92422.4300.0110.0110.0000.0000.0000.000
93B93ILE0-0.011-0.00421.247-0.012-0.0120.0000.0000.0000.000
94B94TYR0-0.035-0.05114.340-0.043-0.0430.0000.0000.0000.000
95B95LYS10.9160.97819.174-0.020-0.0200.0000.0000.0000.000
96B96ILE00.0070.00521.348-0.014-0.0140.0000.0000.0000.000
97B97TYR0-0.003-0.00614.076-0.029-0.0290.0000.0000.0000.000
98B98LYS10.8810.92714.8810.0020.0020.0000.0000.0000.000
99B99TYR0-0.0120.00117.931-0.021-0.0210.0000.0000.0000.000
100B100PHE00.0320.00520.677-0.009-0.0090.0000.0000.0000.000
101B101ARG10.8400.92114.3390.3600.3600.0000.0000.0000.000
102B102ASP-1-0.789-0.85815.058-0.166-0.1660.0000.0000.0000.000
103B103LEU0-0.048-0.01316.991-0.008-0.0080.0000.0000.0000.000
104B104GLY00.0030.01217.323-0.001-0.0010.0000.0000.0000.000
105B105TYR0-0.028-0.00118.388-0.012-0.0120.0000.0000.0000.000
106B106VAL0-0.021-0.01517.235-0.016-0.0160.0000.0000.0000.000
107B107VAL0-0.0100.00517.5920.0280.0280.0000.0000.0000.000
108B108LYS10.7810.88815.1420.3720.3720.0000.0000.0000.000
109B109SER00.0500.01919.7940.0270.0270.0000.0000.0000.000
110B110GLY00.0660.02921.701-0.007-0.0070.0000.0000.0000.000
111B111LEU00.0230.02024.8120.0060.0060.0000.0000.0000.000
112B112LYS10.9140.96526.0720.1340.1340.0000.0000.0000.000
113B113PHE0-0.041-0.03225.7070.0010.0010.0000.0000.0000.000
114B114GLY00.0130.02029.8510.0050.0050.0000.0000.0000.000
115B115ALA0-0.058-0.03428.5130.0060.0060.0000.0000.0000.000
116B116LEU00.0080.01924.143-0.001-0.0010.0000.0000.0000.000
117B117PHE0-0.006-0.02020.308-0.009-0.0090.0000.0000.0000.000
118B118SER0-0.027-0.00823.1660.0020.0020.0000.0000.0000.000
119B119VAL00.0060.00022.258-0.016-0.0160.0000.0000.0000.000
120B120TYR0-0.026-0.01021.8250.0130.0130.0000.0000.0000.000
121B121GLU-1-0.831-0.92022.266-0.173-0.1730.0000.0000.0000.000
122B122LYS10.8810.94521.9360.1810.1810.0000.0000.0000.000
123B123GLY00.0590.01020.839-0.033-0.0330.0000.0000.0000.000
124B124PRO0-0.052-0.02220.3880.0190.0190.0000.0000.0000.000
125B125GLY0-0.0100.02423.0660.0200.0200.0000.0000.0000.000
126B126ILE0-0.046-0.02723.163-0.017-0.0170.0000.0000.0000.000
127B127ASP-1-0.857-0.97424.886-0.168-0.1680.0000.0000.0000.000
128B128HIS0-0.080-0.00526.986-0.013-0.0130.0000.0000.0000.000
129B129ALA00.0120.00726.999-0.010-0.0100.0000.0000.0000.000
130B130PRO0-0.031-0.02226.3340.0030.0030.0000.0000.0000.000
131B131MET0-0.0070.01526.9740.0120.0120.0000.0000.0000.000
132B132VAL0-0.010-0.01727.288-0.004-0.0040.0000.0000.0000.000
133B133VAL0-0.007-0.00225.8710.0060.0060.0000.0000.0000.000
134B134VAL0-0.003-0.00928.0120.0010.0010.0000.0000.0000.000
135B135PHE00.0300.01227.667-0.001-0.0010.0000.0000.0000.000
136B136LEU0-0.025-0.00829.6880.0010.0010.0000.0000.0000.000
137B137GLU-1-0.884-0.94030.978-0.019-0.0190.0000.0000.0000.000
138B138PRO00.028-0.00430.419-0.001-0.0010.0000.0000.0000.000
139B139ASP-1-0.832-0.86733.4820.0100.0100.0000.0000.0000.000
140B140LYS10.8670.96535.8870.0210.0210.0000.0000.0000.000
141B141GLY00.0410.02037.868-0.002-0.0020.0000.0000.0000.000
142B142ILE0-0.016-0.01437.745-0.002-0.0020.0000.0000.0000.000
143B143SER0-0.023-0.01540.5720.0010.0010.0000.0000.0000.000
144B144ALA00.0880.02342.506-0.002-0.0020.0000.0000.0000.000
145B145THR00.007-0.00642.664-0.003-0.0030.0000.0000.0000.000
146B146ASP-1-0.786-0.88938.323-0.031-0.0310.0000.0000.0000.000
147B147ILE00.0200.02738.641-0.004-0.0040.0000.0000.0000.000
148B148THR0-0.012-0.01140.004-0.003-0.0030.0000.0000.0000.000
149B149ARG10.8700.93336.1550.0350.0350.0000.0000.0000.000
150B150GLY00.0490.02035.755-0.003-0.0030.0000.0000.0000.000
151B151GLY0-0.013-0.00836.316-0.005-0.0050.0000.0000.0000.000
152B152ARG10.8780.93238.6310.0530.0530.0000.0000.0000.000
153B153LEU00.0060.00232.677-0.002-0.0020.0000.0000.0000.000
154B154SER0-0.040-0.01633.889-0.008-0.0080.0000.0000.0000.000
155B155HIS0-0.002-0.01032.280-0.003-0.0030.0000.0000.0000.000
156B156SER00.0020.02034.951-0.001-0.0010.0000.0000.0000.000
157B157VAL00.0610.02036.9240.0040.0040.0000.0000.0000.000
158B158ARG10.9320.95038.4890.0860.0860.0000.0000.0000.000
159B159LYS10.8890.96438.4330.0570.0570.0000.0000.0000.000
160B160THR00.0400.02034.8190.0030.0030.0000.0000.0000.000
161B161TRP0-0.0230.01232.921-0.005-0.0050.0000.0000.0000.000
162B162THR00.0250.00729.3780.0010.0010.0000.0000.0000.000
163B163LEU0-0.0240.00331.149-0.001-0.0010.0000.0000.0000.000
164B164ALA00.0160.00027.192-0.002-0.0020.0000.0000.0000.000
165B165THR0-0.004-0.01329.3100.0050.0050.0000.0000.0000.000
166B166VAL0-0.003-0.00425.880-0.002-0.0020.0000.0000.0000.000
167B167LEU00.0140.01929.1900.0040.0040.0000.0000.0000.000
168B168ARG10.8230.86231.463-0.011-0.0110.0000.0000.0000.000
169B169GLN0-0.036-0.00932.4660.0020.0020.0000.0000.0000.000
170B170THR00.0660.01631.6970.0040.0040.0000.0000.0000.000
171B171GLY0-0.027-0.00228.1880.0030.0030.0000.0000.0000.000
172B172GLU-1-0.919-0.96527.375-0.035-0.0350.0000.0000.0000.000
173B173VAL0-0.042-0.02324.1960.0030.0030.0000.0000.0000.000
174B174VAL00.0300.02227.626-0.004-0.0040.0000.0000.0000.000
175B175LEU0-0.032-0.01826.329-0.001-0.0010.0000.0000.0000.000
176B176LEU00.0010.00630.7840.0010.0010.0000.0000.0000.000
177B177GLY00.0210.01533.625-0.004-0.0040.0000.0000.0000.000
178B178PHE00.0120.00535.0130.0050.0050.0000.0000.0000.000
179B179GLY00.051-0.00837.237-0.006-0.0060.0000.0000.0000.000
180B180TRP0-0.058-0.02239.8080.0030.0030.0000.0000.0000.000
181B181ALA00.0490.01943.180-0.002-0.0020.0000.0000.0000.000
182B182ARG10.8950.94846.1190.0550.0550.0000.0000.0000.000
183B183LEU00.0800.05748.7560.0000.0000.0000.0000.0000.000