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: YZMY2

Calculation Name: 4KXR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KXR

Chain ID: B

ChEMBL ID:

UniProt ID: O53943

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptH
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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1514443.330237
FMO2-HF: Nuclear repulsion 1443528.635057
FMO2-HF: Total energy -70914.69518
FMO2-MP2: Total energy -71118.241066


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.
-5.549-0.5924.875-2.792-7.04-0.011
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 : -0.073 / q_NPA : -0.050
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].
3B3PHE00.0300.0002.620-2.8010.2772.699-1.882-3.895-0.015
4B4GLU-1-0.721-0.8615.471-1.182-1.1820.0000.0000.0000.000
5B5ALA0-0.085-0.0196.7150.3060.3060.0000.0000.0000.000
6B6TYR0-0.100-0.0545.2450.1420.1420.0000.0000.0000.000
7B7PRO00.0520.0429.898-0.035-0.0350.0000.0000.0000.000
8B8PRO00.0870.03912.449-0.003-0.0030.0000.0000.0000.000
9B9GLU-1-0.846-0.89814.251-0.069-0.0690.0000.0000.0000.000
10B10VAL0-0.075-0.0359.9520.0430.0430.0000.0000.0000.000
11B11ASN0-0.014-0.0198.2770.0910.0910.0000.0000.0000.000
12B12SER00.0500.00910.9940.0800.0800.0000.0000.0000.000
13B13ALA0-0.028-0.01514.5440.0360.0360.0000.0000.0000.000
14B14ASN0-0.079-0.0459.6460.0470.0470.0000.0000.0000.000
15B15ILE0-0.0290.00111.0760.0710.0710.0000.0000.0000.000
16B16TYR0-0.043-0.01913.6390.0030.0030.0000.0000.0000.000
17B17ALA0-0.049-0.00116.076-0.005-0.0050.0000.0000.0000.000
18B18GLY0-0.015-0.01116.1300.0270.0270.0000.0000.0000.000
19B19PRO0-0.049-0.03916.547-0.016-0.0160.0000.0000.0000.000
20B20GLY00.0790.05517.620-0.018-0.0180.0000.0000.0000.000
21B21PRO00.0290.00716.8000.0130.0130.0000.0000.0000.000
22B22ASP-1-0.863-0.92717.9220.0350.0350.0000.0000.0000.000
23B23SER0-0.067-0.04617.894-0.007-0.0070.0000.0000.0000.000
24B24MET00.0550.02111.560-0.012-0.0120.0000.0000.0000.000
25B25LEU00.0360.02217.634-0.015-0.0150.0000.0000.0000.000
26B26ALA0-0.082-0.04720.768-0.008-0.0080.0000.0000.0000.000
27B27ALA00.0180.00818.644-0.006-0.0060.0000.0000.0000.000
28B28ALA00.0490.03719.675-0.007-0.0070.0000.0000.0000.000
29B29ARG10.9190.95621.039-0.025-0.0250.0000.0000.0000.000
30B30ALA0-0.0050.00223.190-0.003-0.0030.0000.0000.0000.000
31B31TRP00.0480.00418.538-0.006-0.0060.0000.0000.0000.000
32B32ARG10.9830.99923.187-0.002-0.0020.0000.0000.0000.000
33B33SER0-0.030-0.01525.766-0.002-0.0020.0000.0000.0000.000
34B34LEU00.0120.01424.029-0.001-0.0010.0000.0000.0000.000
35B35ASP-1-0.866-0.92625.599-0.018-0.0180.0000.0000.0000.000
36B36VAL0-0.016-0.01627.429-0.001-0.0010.0000.0000.0000.000
37B37GLU-1-0.940-0.98130.740-0.001-0.0010.0000.0000.0000.000
38B38MET0-0.015-0.02128.4240.0010.0010.0000.0000.0000.000
39B39THR00.0400.03030.340-0.001-0.0010.0000.0000.0000.000
40B40ALA0-0.016-0.00732.5960.0000.0000.0000.0000.0000.000
41B41VAL00.0070.01033.5540.0000.0000.0000.0000.0000.000
42B42GLN00.0550.02032.8930.0000.0000.0000.0000.0000.000
43B43ARG10.8810.92934.2490.0130.0130.0000.0000.0000.000
44B44SER0-0.025-0.01638.1870.0000.0000.0000.0000.0000.000
45B45PHE0-0.023-0.00937.7870.0000.0000.0000.0000.0000.000
46B46ASN00.0110.00139.2650.0000.0000.0000.0000.0000.000
47B47ARG10.9790.99240.8950.0050.0050.0000.0000.0000.000
48B48THR0-0.019-0.00642.9450.0010.0010.0000.0000.0000.000
49B49LEU0-0.018-0.01140.9020.0000.0000.0000.0000.0000.000
50B50LEU00.028-0.00244.3040.0000.0000.0000.0000.0000.000
51B51SER0-0.050-0.01346.7900.0000.0000.0000.0000.0000.000
52B52LEU00.0030.00947.3040.0000.0000.0000.0000.0000.000
53B53MET0-0.038-0.03348.6360.0000.0000.0000.0000.0000.000
54B54ASP-1-0.985-0.98950.538-0.004-0.0040.0000.0000.0000.000
55B55ALA0-0.025-0.00152.7470.0000.0000.0000.0000.0000.000
56B56TRP0-0.070-0.03453.6700.0000.0000.0000.0000.0000.000
57B57ALA00.0560.03954.0600.0000.0000.0000.0000.0000.000
58B58GLY00.026-0.00354.1770.0000.0000.0000.0000.0000.000
59B59PRO0-0.012-0.03153.6200.0000.0000.0000.0000.0000.000
60B60VAL00.0320.03252.0280.0000.0000.0000.0000.0000.000
61B61VAL00.0680.03949.1900.0000.0000.0000.0000.0000.000
62B62MET0-0.025-0.00948.4160.0000.0000.0000.0000.0000.000
63B63GLN00.0660.02947.321-0.001-0.0010.0000.0000.0000.000
64B64LEU0-0.0110.00246.0570.0000.0000.0000.0000.0000.000
65B65MET0-0.043-0.02144.014-0.001-0.0010.0000.0000.0000.000
66B66GLU-1-0.979-0.99342.621-0.006-0.0060.0000.0000.0000.000
67B67ALA0-0.033-0.01441.592-0.001-0.0010.0000.0000.0000.000
68B68ALA00.0360.02239.6700.0000.0000.0000.0000.0000.000
69B69LYS10.9390.98338.1080.0100.0100.0000.0000.0000.000
70B70PRO0-0.019-0.02834.953-0.001-0.0010.0000.0000.0000.000
71B71PHE00.0790.04833.226-0.002-0.0020.0000.0000.0000.000
72B72VAL00.0290.00933.680-0.001-0.0010.0000.0000.0000.000
73B73ARG10.9040.94532.4620.0140.0140.0000.0000.0000.000
74B74TRP00.0280.01727.018-0.001-0.0010.0000.0000.0000.000
75B75LEU0-0.009-0.00329.084-0.001-0.0010.0000.0000.0000.000
76B76THR0-0.034-0.02530.0540.0000.0000.0000.0000.0000.000
77B77ASP-1-0.921-0.96326.228-0.027-0.0270.0000.0000.0000.000
78B78LEU0-0.034-0.00424.926-0.003-0.0030.0000.0000.0000.000
79B79CYS0-0.017-0.01225.3130.0000.0000.0000.0000.0000.000
80B80VAL0-0.0050.00724.266-0.001-0.0010.0000.0000.0000.000
81B81GLN0-0.053-0.03220.0950.0030.0030.0000.0000.0000.000
82B82LEU0-0.016-0.01621.362-0.001-0.0010.0000.0000.0000.000
83B83SER0-0.053-0.01222.7790.0000.0000.0000.0000.0000.000
84B84GLU-1-0.858-0.92018.268-0.057-0.0570.0000.0000.0000.000
85B85VAL0-0.005-0.01317.248-0.003-0.0030.0000.0000.0000.000
86B86GLU-1-0.916-0.97118.004-0.014-0.0140.0000.0000.0000.000
87B87ARG10.8780.94719.4100.0420.0420.0000.0000.0000.000
88B88GLN00.029-0.00514.327-0.004-0.0040.0000.0000.0000.000
89B89ILE0-0.0110.01214.4660.0060.0060.0000.0000.0000.000
90B90HIS0-0.057-0.03815.6020.0190.0190.0000.0000.0000.000
91B91GLU-1-0.938-0.95514.841-0.056-0.0560.0000.0000.0000.000
92B92ILE0-0.0070.00310.4310.0020.0020.0000.0000.0000.000
93B93VAL0-0.024-0.01712.8760.0320.0320.0000.0000.0000.000
94B94ARG10.9360.96715.5230.0330.0330.0000.0000.0000.000
95B95ALA0-0.034-0.01011.559-0.005-0.0050.0000.0000.0000.000
96B96TYR0-0.014-0.00812.494-0.010-0.0100.0000.0000.0000.000
97B97GLU-1-0.939-0.98313.4310.0130.0130.0000.0000.0000.000
98B98TRP0-0.046-0.03115.701-0.014-0.0140.0000.0000.0000.000
99B99ALA00.0540.03711.750-0.017-0.0170.0000.0000.0000.000
100B100HIS0-0.046-0.03013.617-0.015-0.0150.0000.0000.0000.000
101B101HIS0-0.143-0.07116.205-0.006-0.0060.0000.0000.0000.000
102B102ASP-1-0.884-0.94815.281-0.099-0.0990.0000.0000.0000.000
103B103MET0-0.0860.00410.691-0.040-0.0400.0000.0000.0000.000
104B104VAL00.0420.02715.4840.0210.0210.0000.0000.0000.000
105B105PRO0-0.015-0.00217.8270.0120.0120.0000.0000.0000.000
106B106LEU00.0460.00717.767-0.007-0.0070.0000.0000.0000.000
107B107ALA0-0.040-0.01720.672-0.005-0.0050.0000.0000.0000.000
108B108GLN00.006-0.00222.3740.0070.0070.0000.0000.0000.000
109B109ILE00.0680.06017.4050.0000.0000.0000.0000.0000.000
110B110TYR0-0.030-0.03820.5240.0060.0060.0000.0000.0000.000
111B111ASN0-0.010-0.00424.2020.0050.0050.0000.0000.0000.000
112B112ASN00.0550.05423.6760.0020.0020.0000.0000.0000.000
113B113ARG10.8360.90722.1340.0770.0770.0000.0000.0000.000
114B114ALA0-0.029-0.02525.6990.0040.0040.0000.0000.0000.000
115B115GLU-1-0.947-0.98329.029-0.039-0.0390.0000.0000.0000.000
116B116ARG10.8250.89226.1820.0550.0550.0000.0000.0000.000
117B117GLN0-0.076-0.04429.7210.0000.0000.0000.0000.0000.000
118B118ILE00.0400.02431.2260.0030.0030.0000.0000.0000.000
119B119LEU00.0090.01132.4480.0030.0030.0000.0000.0000.000
120B120ILE0-0.032-0.02430.4040.0020.0020.0000.0000.0000.000
121B121ASP-1-0.922-0.95134.509-0.017-0.0170.0000.0000.0000.000
122B122ASN0-0.107-0.04736.9530.0030.0030.0000.0000.0000.000
123B123ASN00.007-0.00735.8010.0010.0010.0000.0000.0000.000
124B124ALA0-0.0150.00638.7650.0000.0000.0000.0000.0000.000
125B125LEU0-0.024-0.02741.7690.0010.0010.0000.0000.0000.000
126B126GLY00.0160.00938.9600.0000.0000.0000.0000.0000.000
127B127GLN0-0.079-0.02038.817-0.002-0.0020.0000.0000.0000.000
128B128PHE00.0390.02435.845-0.001-0.0010.0000.0000.0000.000
129B129THR0-0.020-0.03933.731-0.002-0.0020.0000.0000.0000.000
130B130ALA00.0100.00632.806-0.002-0.0020.0000.0000.0000.000
131B131GLN00.0330.02032.026-0.003-0.0030.0000.0000.0000.000
132B132ILE0-0.028-0.02029.584-0.003-0.0030.0000.0000.0000.000
133B133ALA0-0.015-0.01128.187-0.004-0.0040.0000.0000.0000.000
134B134ASP-1-0.898-0.94227.195-0.060-0.0600.0000.0000.0000.000
135B135LEU0-0.017-0.00526.657-0.007-0.0070.0000.0000.0000.000
136B136ASP-1-0.796-0.88323.900-0.071-0.0710.0000.0000.0000.000
137B137GLN0-0.038-0.00321.402-0.001-0.0010.0000.0000.0000.000
138B138GLU-1-0.852-0.91722.035-0.086-0.0860.0000.0000.0000.000
139B139TYR0-0.139-0.11217.768-0.015-0.0150.0000.0000.0000.000
140B140ASP-1-0.905-0.96918.011-0.165-0.1650.0000.0000.0000.000
141B141ASP-1-0.882-0.93717.259-0.173-0.1730.0000.0000.0000.000
142B142PHE0-0.036-0.02917.162-0.018-0.0180.0000.0000.0000.000
143B143TRP0-0.104-0.07011.4540.0360.0360.0000.0000.0000.000
144B144ASP-1-0.965-0.98312.669-0.412-0.4120.0000.0000.0000.000
145B145GLU-1-0.855-0.91912.833-0.282-0.2820.0000.0000.0000.000
146B146ASP-1-0.762-0.90911.497-0.215-0.2150.0000.0000.0000.000
147B147GLY0-0.058-0.0238.678-0.069-0.0690.0000.0000.0000.000
148B148GLU-1-0.951-0.9828.215-0.611-0.6110.0000.0000.0000.000
149B149VAL00.0610.04310.3410.0140.0140.0000.0000.0000.000
150B150MET0-0.047-0.0375.9400.1950.1950.0000.0000.0000.000
151B151ARG10.8100.9175.7600.6920.6920.0000.0000.0000.000
152B152ASP-1-0.843-0.9336.792-0.271-0.2710.0000.0000.0000.000
153B153TYR0-0.045-0.0208.1670.0880.0880.0000.0000.0000.000
154B154ARG10.9370.9642.356-0.3521.5272.176-0.910-3.1450.004
155B155LEU0-0.018-0.0195.917-0.309-0.3090.0000.0000.0000.000
156B156ARG11.0281.0217.8880.1390.1390.0000.0000.0000.000
157B157VAL0-0.012-0.0026.248-0.034-0.0340.0000.0000.0000.000
158B158SER0-0.031-0.0215.429-0.144-0.1440.0000.0000.0000.000
159B159ASP-1-0.935-0.9587.131-0.265-0.2650.0000.0000.0000.000
160B160ALA0-0.019-0.00910.7390.0220.0220.0000.0000.0000.000
161B161LEU0-0.012-0.0186.5970.0170.0170.0000.0000.0000.000
162B162SER0-0.090-0.02710.4580.0290.0290.0000.0000.0000.000
163B163LYS10.9440.97011.9030.1330.1330.0000.0000.0000.000
164B164LEU0-0.064-0.01613.0830.0260.0260.0000.0000.0000.000
165B165THR0-0.018-0.00114.545-0.005-0.0050.0000.0000.0000.000
166B166PRO00.0200.00216.0030.0090.0090.0000.0000.0000.000
167B167TRP00.0350.01917.9570.0040.0040.0000.0000.0000.000
168B168LYS10.9760.98821.1980.0400.0400.0000.0000.0000.000
169B169ALA00.0190.01224.0950.0020.0020.0000.0000.0000.000
170B170PRO0-0.0010.01126.974-0.001-0.0010.0000.0000.0000.000
171B171PRO0-0.031-0.00130.2190.0010.0010.0000.0000.0000.000
172B172PRO00.017-0.00933.0710.0010.0010.0000.0000.0000.000
173B173ILE00.0030.00136.420-0.001-0.0010.0000.0000.0000.000
174B174ALA0-0.017-0.00239.5870.0000.0000.0000.0000.0000.000