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: 1734Z

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 OptAll
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 -1521543.079371
FMO2-HF: Nuclear repulsion 1450627.339446
FMO2-HF: Total energy -70915.739925
FMO2-MP2: Total energy -71119.379828


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.
-5.093-1.699.343-4.247-8.497-0.014
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 : -0.022 / q_NPA : -0.008
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].
3B3PHE00.0620.0202.979-3.1850.6382.407-2.291-3.938-0.015
4B4GLU-1-0.701-0.8375.534-2.650-2.6500.0000.0000.0000.000
5B5ALA0-0.087-0.0276.7510.2970.2970.0000.0000.0000.000
6B6TYR0-0.099-0.0524.8810.2020.2020.0000.0000.0000.000
7B7PRO00.0480.04110.056-0.028-0.0280.0000.0000.0000.000
8B8PRO00.0530.03012.5640.0380.0380.0000.0000.0000.000
9B9GLU-1-0.817-0.90514.139-0.083-0.0830.0000.0000.0000.000
10B10VAL0-0.070-0.03610.1530.0690.0690.0000.0000.0000.000
11B11ASN0-0.014-0.0178.3450.1760.1760.0000.0000.0000.000
12B12SER00.049-0.00110.7690.1380.1380.0000.0000.0000.000
13B13ALA0-0.042-0.02114.1810.0600.0600.0000.0000.0000.000
14B14ASN0-0.085-0.0509.0970.0410.0410.0000.0000.0000.000
15B15ILE0-0.031-0.00310.8950.1560.1560.0000.0000.0000.000
16B16TYR0-0.048-0.03313.5520.0050.0050.0000.0000.0000.000
17B17ALA0-0.0340.00616.056-0.028-0.0280.0000.0000.0000.000
18B18GLY00.014-0.00515.5240.0700.0700.0000.0000.0000.000
19B19PRO0-0.082-0.04316.008-0.037-0.0370.0000.0000.0000.000
20B20GLY00.0600.04617.637-0.030-0.0300.0000.0000.0000.000
21B21PRO00.0610.01716.9470.0220.0220.0000.0000.0000.000
22B22ASP-1-0.833-0.91617.9600.1800.1800.0000.0000.0000.000
23B23SER0-0.006-0.00617.241-0.010-0.0100.0000.0000.0000.000
24B24MET00.0370.02211.781-0.021-0.0210.0000.0000.0000.000
25B25LEU00.0870.04217.466-0.020-0.0200.0000.0000.0000.000
26B26ALA0-0.105-0.03020.884-0.022-0.0220.0000.0000.0000.000
27B27ALA00.0340.01418.365-0.015-0.0150.0000.0000.0000.000
28B28ALA00.0150.01119.683-0.014-0.0140.0000.0000.0000.000
29B29ARG10.8180.88021.093-0.192-0.1920.0000.0000.0000.000
30B30ALA00.0030.00823.185-0.013-0.0130.0000.0000.0000.000
31B31TRP00.041-0.00418.606-0.017-0.0170.0000.0000.0000.000
32B32ARG10.8650.92523.405-0.147-0.1470.0000.0000.0000.000
33B33SER0-0.003-0.00726.115-0.010-0.0100.0000.0000.0000.000
34B34LEU0-0.0040.00423.836-0.008-0.0080.0000.0000.0000.000
35B35ASP-1-0.841-0.92725.8480.1170.1170.0000.0000.0000.000
36B36VAL0-0.0170.00627.707-0.010-0.0100.0000.0000.0000.000
37B37GLU-1-0.908-0.95430.9790.0840.0840.0000.0000.0000.000
38B38MET0-0.011-0.01028.371-0.007-0.0070.0000.0000.0000.000
39B39THR0-0.010-0.01830.665-0.007-0.0070.0000.0000.0000.000
40B40ALA0-0.005-0.00132.881-0.007-0.0070.0000.0000.0000.000
41B41VAL00.0100.01333.855-0.006-0.0060.0000.0000.0000.000
42B42GLN00.0080.00633.273-0.006-0.0060.0000.0000.0000.000
43B43ARG10.8860.92434.242-0.078-0.0780.0000.0000.0000.000
44B44SER0-0.030-0.02338.519-0.005-0.0050.0000.0000.0000.000
45B45PHE00.0040.01237.820-0.004-0.0040.0000.0000.0000.000
46B46ASN00.0330.01339.463-0.004-0.0040.0000.0000.0000.000
47B47ARG10.9680.98641.133-0.051-0.0510.0000.0000.0000.000
48B48THR0-0.039-0.01242.987-0.003-0.0030.0000.0000.0000.000
49B49LEU0-0.016-0.00940.689-0.002-0.0020.0000.0000.0000.000
50B50LEU00.017-0.00244.327-0.002-0.0020.0000.0000.0000.000
51B51SER0-0.040-0.03646.987-0.002-0.0020.0000.0000.0000.000
52B52LEU00.0030.00647.449-0.002-0.0020.0000.0000.0000.000
53B53MET0-0.037-0.03448.744-0.001-0.0010.0000.0000.0000.000
54B54ASP-1-0.974-0.97950.6240.0330.0330.0000.0000.0000.000
55B55ALA0-0.012-0.00952.934-0.001-0.0010.0000.0000.0000.000
56B56TRP0-0.064-0.03853.530-0.001-0.0010.0000.0000.0000.000
57B57ALA00.0380.03554.2220.0000.0000.0000.0000.0000.000
58B58GLY00.0270.00454.181-0.002-0.0020.0000.0000.0000.000
59B59PRO00.009-0.01353.5170.0010.0010.0000.0000.0000.000
60B60VAL00.0260.02252.0560.0010.0010.0000.0000.0000.000
61B61VAL00.0400.03049.4950.0020.0020.0000.0000.0000.000
62B62MET0-0.042-0.01048.6710.0010.0010.0000.0000.0000.000
63B63GLN00.0660.02647.5420.0010.0010.0000.0000.0000.000
64B64LEU0-0.0060.01045.5070.0020.0020.0000.0000.0000.000
65B65MET0-0.017-0.00344.2410.0040.0040.0000.0000.0000.000
66B66GLU-1-0.995-1.01042.8800.0410.0410.0000.0000.0000.000
67B67ALA0-0.014-0.00941.9360.0020.0020.0000.0000.0000.000
68B68ALA00.0370.01640.0610.0030.0030.0000.0000.0000.000
69B69LYS10.9380.98138.524-0.044-0.0440.0000.0000.0000.000
70B70PRO0-0.025-0.02635.4480.0030.0030.0000.0000.0000.000
71B71PHE00.0760.03933.5800.0040.0040.0000.0000.0000.000
72B72VAL00.0260.01434.1550.0040.0040.0000.0000.0000.000
73B73ARG10.8850.95933.159-0.060-0.0600.0000.0000.0000.000
74B74TRP00.0240.00427.205-0.001-0.0010.0000.0000.0000.000
75B75LEU00.0350.01629.5040.0060.0060.0000.0000.0000.000
76B76THR0-0.039-0.03430.7390.0020.0020.0000.0000.0000.000
77B77ASP-1-0.873-0.91926.5200.1140.1140.0000.0000.0000.000
78B78LEU00.0230.01924.8260.0080.0080.0000.0000.0000.000
79B79CYS0-0.0070.00025.5990.0080.0080.0000.0000.0000.000
80B80VAL0-0.023-0.00124.8520.0040.0040.0000.0000.0000.000
81B81GLN0-0.016-0.00720.153-0.008-0.0080.0000.0000.0000.000
82B82LEU0-0.017-0.01221.6750.0150.0150.0000.0000.0000.000
83B83SER0-0.0440.00022.8960.0100.0100.0000.0000.0000.000
84B84GLU-1-0.805-0.86519.0160.1690.1690.0000.0000.0000.000
85B85VAL00.019-0.00217.4060.0190.0190.0000.0000.0000.000
86B86GLU-1-0.822-0.89318.2850.1850.1850.0000.0000.0000.000
87B87ARG10.8310.89119.790-0.135-0.1350.0000.0000.0000.000
88B88GLN00.0520.00214.9840.0290.0290.0000.0000.0000.000
89B89ILE00.0070.01115.0420.0460.0460.0000.0000.0000.000
90B90HIS0-0.068-0.04716.0530.0200.0200.0000.0000.0000.000
91B91GLU-1-0.928-0.94615.4430.2140.2140.0000.0000.0000.000
92B92ILE00.001-0.00110.8080.0220.0220.0000.0000.0000.000
93B93VAL0-0.035-0.01813.2230.0430.0430.0000.0000.0000.000
94B94ARG10.9140.95615.944-0.197-0.1970.0000.0000.0000.000
95B95ALA0-0.016-0.00111.944-0.021-0.0210.0000.0000.0000.000
96B96TYR0-0.020-0.01012.462-0.016-0.0160.0000.0000.0000.000
97B97GLU-1-0.936-0.98213.7450.1830.1830.0000.0000.0000.000
98B98TRP0-0.030-0.02915.519-0.027-0.0270.0000.0000.0000.000
99B99ALA00.0510.03311.716-0.035-0.0350.0000.0000.0000.000
100B100HIS0-0.032-0.03713.575-0.046-0.0460.0000.0000.0000.000
101B101HIS0-0.184-0.09216.307-0.036-0.0360.0000.0000.0000.000
102B102ASP-1-0.855-0.91915.4860.0180.0180.0000.0000.0000.000
103B103MET0-0.0540.01410.671-0.071-0.0710.0000.0000.0000.000
104B104VAL00.0530.03815.4750.0220.0220.0000.0000.0000.000
105B105PRO00.0000.00418.0080.0210.0210.0000.0000.0000.000
106B106LEU00.011-0.00517.046-0.017-0.0170.0000.0000.0000.000
107B107ALA0-0.040-0.01420.318-0.015-0.0150.0000.0000.0000.000
108B108GLN00.0340.01222.4640.0050.0050.0000.0000.0000.000
109B109ILE00.0410.04417.319-0.009-0.0090.0000.0000.0000.000
110B110TYR0-0.032-0.03320.0670.0020.0020.0000.0000.0000.000
111B111ASN0-0.080-0.04124.0990.0050.0050.0000.0000.0000.000
112B112ASN00.0420.02323.799-0.004-0.0040.0000.0000.0000.000
113B113ARG10.8010.87921.6930.1480.1480.0000.0000.0000.000
114B114ALA0-0.023-0.01325.5030.0020.0020.0000.0000.0000.000
115B115GLU-1-0.898-0.95428.850-0.060-0.0600.0000.0000.0000.000
116B116ARG10.8490.90626.1240.1350.1350.0000.0000.0000.000
117B117GLN0-0.078-0.05229.549-0.006-0.0060.0000.0000.0000.000
118B118ILE00.0250.01231.1190.0030.0030.0000.0000.0000.000
119B119LEU0-0.0020.00832.0030.0030.0030.0000.0000.0000.000
120B120ILE0-0.016-0.01729.9980.0010.0010.0000.0000.0000.000
121B121ASP-1-0.903-0.93534.357-0.050-0.0500.0000.0000.0000.000
122B122ASN0-0.083-0.04836.8980.0070.0070.0000.0000.0000.000
123B123ASN0-0.045-0.02235.9320.0030.0030.0000.0000.0000.000
124B124ALA0-0.0010.00238.504-0.002-0.0020.0000.0000.0000.000
125B125LEU0-0.025-0.01541.5530.0010.0010.0000.0000.0000.000
126B126GLY0-0.0050.00238.8500.0000.0000.0000.0000.0000.000
127B127GLN0-0.054-0.02938.514-0.006-0.0060.0000.0000.0000.000
128B128PHE00.0350.02335.8310.0000.0000.0000.0000.0000.000
129B129THR0-0.030-0.03533.633-0.005-0.0050.0000.0000.0000.000
130B130ALA0-0.0160.00232.711-0.007-0.0070.0000.0000.0000.000
131B131GLN00.0760.03531.789-0.005-0.0050.0000.0000.0000.000
132B132ILE0-0.047-0.01729.827-0.003-0.0030.0000.0000.0000.000
133B133ALA00.0020.00228.068-0.008-0.0080.0000.0000.0000.000
134B134ASP-1-0.905-0.95527.098-0.138-0.1380.0000.0000.0000.000
135B135LEU00.0080.00326.616-0.009-0.0090.0000.0000.0000.000
136B136ASP-1-0.795-0.85523.798-0.164-0.1640.0000.0000.0000.000
137B137GLN0-0.065-0.02821.761-0.014-0.0140.0000.0000.0000.000
138B138GLU-1-0.844-0.90721.999-0.141-0.1410.0000.0000.0000.000
139B139TYR0-0.119-0.08017.765-0.016-0.0160.0000.0000.0000.000
140B140ASP-1-0.890-0.96217.903-0.351-0.3510.0000.0000.0000.000
141B141ASP-1-0.863-0.92917.297-0.316-0.3160.0000.0000.0000.000
142B142PHE0-0.037-0.03317.584-0.010-0.0100.0000.0000.0000.000
143B143TRP0-0.058-0.04311.7010.0840.0840.0000.0000.0000.000
144B144ASP-1-0.973-0.97712.764-0.762-0.7620.0000.0000.0000.000
145B145GLU-1-0.916-0.94712.972-0.304-0.3040.0000.0000.0000.000
146B146ASP-1-0.741-0.88011.566-0.132-0.1320.0000.0000.0000.000
147B147GLY0-0.032-0.0148.8150.0030.0030.0000.0000.0000.000
148B148GLU-1-0.830-0.8928.508-0.708-0.7080.0000.0000.0000.000
149B149VAL00.0510.02010.2970.0570.0570.0000.0000.0000.000
150B150MET0-0.018-0.0186.1070.3030.3030.0000.0000.0000.000
151B151ARG10.7160.8395.7331.1451.1450.0000.0000.0000.000
152B152ASP-1-0.760-0.8676.7770.1760.1760.0000.0000.0000.000
153B153TYR0-0.030-0.0048.2780.1820.1820.0000.0000.0000.000
154B154ARG10.8890.9372.1811.2760.8566.936-1.956-4.5590.001
155B155LEU0-0.036-0.0136.2810.0200.0200.0000.0000.0000.000
156B156ARG10.8790.9208.821-0.080-0.0800.0000.0000.0000.000
157B157VAL0-0.012-0.0026.814-0.092-0.0920.0000.0000.0000.000
158B158SER0-0.012-0.0076.726-0.095-0.0950.0000.0000.0000.000
159B159ASP-1-0.912-0.9548.2660.0950.0950.0000.0000.0000.000
160B160ALA0-0.056-0.02311.702-0.067-0.0670.0000.0000.0000.000
161B161LEU0-0.008-0.0167.055-0.069-0.0690.0000.0000.0000.000
162B162SER0-0.086-0.04311.100-0.080-0.0800.0000.0000.0000.000
163B163LYS10.8530.93412.711-0.300-0.3000.0000.0000.0000.000
164B164LEU0-0.074-0.01914.033-0.033-0.0330.0000.0000.0000.000
165B165THR00.0140.00515.1530.0060.0060.0000.0000.0000.000
166B166PRO00.0170.01016.330-0.002-0.0020.0000.0000.0000.000
167B167TRP00.0110.01317.976-0.023-0.0230.0000.0000.0000.000
168B168LYS10.8430.89721.218-0.128-0.1280.0000.0000.0000.000
169B169ALA00.0170.01324.257-0.002-0.0020.0000.0000.0000.000
170B170PRO0-0.0020.01026.930-0.004-0.0040.0000.0000.0000.000
171B171PRO0-0.031-0.00430.387-0.002-0.0020.0000.0000.0000.000
172B172PRO00.005-0.00933.2840.0000.0000.0000.0000.0000.000
173B173ILE0-0.002-0.00236.656-0.001-0.0010.0000.0000.0000.000
174B174ALA0-0.0080.00239.888-0.002-0.0020.0000.0000.0000.000