FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 6Y5KZ

Calculation Name: 5B23-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B23

Chain ID: B

ChEMBL ID:

UniProt ID: Q8XN25

Base Structure: X-ray

Registration Date: 2023-09-23

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2178796.574982
FMO2-HF: Nuclear repulsion 2103805.666424
FMO2-HF: Total energy -74990.908557
FMO2-MP2: Total energy -75212.92811


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:67:SER)


Summations of interaction energy for fragment #1(B:67:SER)
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.
-10.847-8.2515.602-3.569-4.630.015
Interaction energy analysis for fragmet #1(B:67:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.001
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].
3B69LYS10.9590.9752.498-3.853-1.4850.353-1.079-1.6420.002
4B70ASN00.0090.0002.003-4.306-4.4825.232-2.394-2.6620.012
5B71LEU00.0770.0343.735-1.060-0.7240.018-0.095-0.2600.001
6B72LYS10.8770.9376.159-0.683-0.6830.0000.0000.0000.000
7B73ASN0-0.069-0.0325.914-0.361-0.3610.0000.0000.0000.000
8B74ILE0-0.0320.0077.086-0.167-0.1670.0000.0000.0000.000
9B75ASN0-0.021-0.02810.011-0.058-0.0580.0000.0000.0000.000
10B76PRO00.0150.00911.2950.0220.0220.0000.0000.0000.000
11B77ASP-1-0.848-0.87212.7440.2160.2160.0000.0000.0000.000
12B78TYR0-0.007-0.0027.825-0.124-0.1240.0000.0000.0000.000
13B79ARG10.7800.88411.945-0.219-0.2190.0000.0000.0000.000
14B80PHE0-0.011-0.01510.1230.0620.0620.0000.0000.0000.000
15B81TRP0-0.021-0.0228.889-0.094-0.0940.0000.0000.0000.000
16B82ILE00.001-0.00411.3710.0250.0250.0000.0000.0000.000
17B83LYS10.9260.97213.944-0.006-0.0060.0000.0000.0000.000
18B84VAL0-0.011-0.00616.1650.0100.0100.0000.0000.0000.000
19B85GLU-1-0.875-0.92019.882-0.021-0.0210.0000.0000.0000.000
20B86GLY00.0680.03621.3720.0020.0020.0000.0000.0000.000
21B87THR0-0.057-0.03521.4600.0000.0000.0000.0000.0000.000
22B88ASN0-0.070-0.05820.1110.0020.0020.0000.0000.0000.000
23B89ILE0-0.023-0.01318.087-0.007-0.0070.0000.0000.0000.000
24B90ASP-1-0.820-0.91213.206-0.035-0.0350.0000.0000.0000.000
25B91PHE0-0.041-0.00113.661-0.033-0.0330.0000.0000.0000.000
26B92PRO0-0.0160.01010.5250.0400.0400.0000.0000.0000.000
27B93VAL0-0.0040.00412.324-0.012-0.0120.0000.0000.0000.000
28B94VAL0-0.028-0.02613.5300.0450.0450.0000.0000.0000.000
29B95GLN0-0.027-0.00915.5800.0040.0040.0000.0000.0000.000
30B96GLY00.0310.01418.3120.0150.0150.0000.0000.0000.000
31B97LYS10.9050.93421.027-0.142-0.1420.0000.0000.0000.000
32B98ASP-1-0.773-0.86923.7840.0780.0780.0000.0000.0000.000
33B99ASN0-0.013-0.02324.3650.0130.0130.0000.0000.0000.000
34B100ASP-1-0.852-0.93026.2860.0500.0500.0000.0000.0000.000
35B101PHE0-0.066-0.03619.975-0.005-0.0050.0000.0000.0000.000
36B102TYR0-0.038-0.07217.373-0.005-0.0050.0000.0000.0000.000
37B103LEU00.0040.02322.045-0.008-0.0080.0000.0000.0000.000
38B104HIS00.0060.01124.521-0.009-0.0090.0000.0000.0000.000
39B105HIS10.7950.88220.847-0.072-0.0720.0000.0000.0000.000
40B106ASN00.0480.04017.7950.0120.0120.0000.0000.0000.000
41B107PHE00.0620.0209.6560.0010.0010.0000.0000.0000.000
42B108ASN00.0200.01313.6780.0540.0540.0000.0000.0000.000
43B109LYS10.9330.97915.490-0.191-0.1910.0000.0000.0000.000
44B110GLU-1-0.886-0.92718.7180.0420.0420.0000.0000.0000.000
45B111LYS10.9430.96021.083-0.051-0.0510.0000.0000.0000.000
46B112SER0-0.007-0.01621.587-0.006-0.0060.0000.0000.0000.000
47B113PHE00.0170.01324.0350.0040.0040.0000.0000.0000.000
48B114SER00.015-0.00222.8670.0000.0000.0000.0000.0000.000
49B115GLY0-0.0410.00422.2800.0000.0000.0000.0000.0000.000
50B116SER0-0.042-0.05817.206-0.007-0.0070.0000.0000.0000.000
51B117ILE0-0.0110.00717.2630.0000.0000.0000.0000.0000.000
52B118PHE0-0.031-0.01217.5780.0140.0140.0000.0000.0000.000
53B119VAL0-0.021-0.00617.889-0.009-0.0090.0000.0000.0000.000
54B120ASP-1-0.779-0.89420.2840.0790.0790.0000.0000.0000.000
55B121SER0-0.0100.00822.4530.0080.0080.0000.0000.0000.000
56B122GLU-1-0.895-0.94523.4230.0900.0900.0000.0000.0000.000
57B123ASN0-0.144-0.08121.216-0.003-0.0030.0000.0000.0000.000
58B124ASN0-0.001-0.00721.4570.0240.0240.0000.0000.0000.000
59B125LEU00.032-0.00715.425-0.005-0.0050.0000.0000.0000.000
60B126ASN0-0.100-0.04917.2090.0030.0030.0000.0000.0000.000
61B127ASP-1-0.874-0.92419.5920.0730.0730.0000.0000.0000.000
62B128ASP-1-0.793-0.87422.9230.0780.0780.0000.0000.0000.000
63B129SER0-0.012-0.01623.4300.0010.0010.0000.0000.0000.000
64B130ASN00.0030.01025.047-0.001-0.0010.0000.0000.0000.000
65B131ILE0-0.042-0.01318.8670.0070.0070.0000.0000.0000.000
66B132VAL00.0380.01822.301-0.005-0.0050.0000.0000.0000.000
67B133VAL0-0.032-0.02319.1000.0100.0100.0000.0000.0000.000
68B134TYR00.0200.01022.014-0.014-0.0140.0000.0000.0000.000
69B135GLY00.0520.00221.9830.0040.0040.0000.0000.0000.000
70B136HIS00.0310.02123.410-0.006-0.0060.0000.0000.0000.000
71B137ASN0-0.010-0.02725.296-0.007-0.0070.0000.0000.0000.000
72B138MET0-0.039-0.01426.9500.0000.0000.0000.0000.0000.000
73B139ARG10.9350.95829.500-0.007-0.0070.0000.0000.0000.000
74B140ASN0-0.001-0.00526.067-0.001-0.0010.0000.0000.0000.000
75B141ASP-1-0.870-0.91526.056-0.019-0.0190.0000.0000.0000.000
76B142THR00.0150.02422.922-0.004-0.0040.0000.0000.0000.000
77B143MET0-0.039-0.02518.3740.0090.0090.0000.0000.0000.000
78B144PHE00.0630.03619.571-0.002-0.0020.0000.0000.0000.000
79B145ALA0-0.014-0.00323.6400.0010.0010.0000.0000.0000.000
80B146GLN0-0.004-0.00724.4200.0020.0020.0000.0000.0000.000
81B147ILE00.0660.04623.543-0.001-0.0010.0000.0000.0000.000
82B148LYS10.9070.93926.8880.0000.0000.0000.0000.0000.000
83B149HIS00.0050.01427.5930.0010.0010.0000.0000.0000.000
84B150PHE00.0160.01825.041-0.001-0.0010.0000.0000.0000.000
85B151LYS10.8390.91430.634-0.007-0.0070.0000.0000.0000.000
86B152ASN0-0.035-0.01333.345-0.001-0.0010.0000.0000.0000.000
87B153GLU-1-0.865-0.92033.9590.0000.0000.0000.0000.0000.000
88B154ASN0-0.017-0.02334.9810.0000.0000.0000.0000.0000.000
89B155PHE00.0120.00526.389-0.001-0.0010.0000.0000.0000.000
90B156PHE00.0270.01030.2890.0010.0010.0000.0000.0000.000
91B157ASN00.001-0.00330.6470.0020.0020.0000.0000.0000.000
92B158ALA0-0.052-0.02230.2620.0000.0000.0000.0000.0000.000
93B159ASN0-0.082-0.03525.453-0.001-0.0010.0000.0000.0000.000
94B160LYS11.0020.99626.0300.0060.0060.0000.0000.0000.000
95B161TYR0-0.0200.00021.1330.0020.0020.0000.0000.0000.000
96B162VAL0-0.0050.00418.725-0.002-0.0020.0000.0000.0000.000
97B163THR0-0.039-0.03013.7850.0000.0000.0000.0000.0000.000
98B164LEU0-0.0130.00013.8860.0040.0040.0000.0000.0000.000
99B165TYR0-0.029-0.0055.084-0.120-0.052-0.001-0.001-0.0660.000
100B166ARG10.9950.9829.313-0.135-0.1350.0000.0000.0000.000
101B167GLU-1-0.961-0.9696.8670.4970.4970.0000.0000.0000.000
102B168GLY0-0.009-0.0175.432-0.343-0.3430.0000.0000.0000.000
103B169LYS10.9000.9386.199-0.184-0.1840.0000.0000.0000.000
104B170LYS10.9510.9769.8670.0400.0400.0000.0000.0000.000
105B171SER00.0160.01912.180-0.030-0.0300.0000.0000.0000.000
106B172THR0-0.017-0.02215.4980.0080.0080.0000.0000.0000.000
107B173PHE00.0290.02217.404-0.001-0.0010.0000.0000.0000.000
108B174GLU-1-0.864-0.95621.5580.0070.0070.0000.0000.0000.000
109B175ILE0-0.055-0.02424.7740.0020.0020.0000.0000.0000.000
110B176PHE0-0.015-0.00427.044-0.004-0.0040.0000.0000.0000.000
111B177SER0-0.001-0.01129.856-0.002-0.0020.0000.0000.0000.000
112B178VAL00.0060.00930.1290.0030.0030.0000.0000.0000.000
113B179TYR00.0100.00032.268-0.002-0.0020.0000.0000.0000.000
114B180GLN0-0.012-0.00633.4100.0000.0000.0000.0000.0000.000
115B181GLH0-0.001-0.04435.772-0.001-0.0010.0000.0000.0000.000
116B182ASN00.0200.01336.4490.0020.0020.0000.0000.0000.000
117B183ALA00.0070.00134.7240.0010.0010.0000.0000.0000.000
118B184LYS10.9460.96835.776-0.030-0.0300.0000.0000.0000.000
119B185ASP-1-0.883-0.93238.3300.0240.0240.0000.0000.0000.000
120B186LEU00.020-0.00131.5750.0010.0010.0000.0000.0000.000
121B187GLU-1-0.950-0.97333.4590.0390.0390.0000.0000.0000.000
122B188SER0-0.066-0.01834.5000.0020.0020.0000.0000.0000.000
123B189GLU-1-0.875-0.90435.6170.0250.0250.0000.0000.0000.000
124B190ILE0-0.031-0.01628.8770.0010.0010.0000.0000.0000.000
125B191LYS10.9620.98830.989-0.033-0.0330.0000.0000.0000.000
126B192THR0-0.0040.00925.974-0.001-0.0010.0000.0000.0000.000
127B193LYS10.8720.92726.077-0.076-0.0760.0000.0000.0000.000
128B194PHE00.032-0.00929.080-0.004-0.0040.0000.0000.0000.000
129B195SER0-0.163-0.11231.4540.0020.0020.0000.0000.0000.000
130B196ASN00.0230.00634.859-0.001-0.0010.0000.0000.0000.000
131B197LYS11.0741.02234.300-0.019-0.0190.0000.0000.0000.000
132B198GLU-1-0.924-0.95635.3010.0220.0220.0000.0000.0000.000
133B199ASP-1-0.814-0.84236.3090.0290.0290.0000.0000.0000.000
134B200TYR0-0.075-0.04827.9840.0010.0010.0000.0000.0000.000
135B201GLU-1-0.901-0.95934.0370.0190.0190.0000.0000.0000.000
136B202LYS10.8780.94435.789-0.025-0.0250.0000.0000.0000.000
137B203TYR00.0070.00730.2460.0000.0000.0000.0000.0000.000
138B204LEU00.016-0.00629.9780.0000.0000.0000.0000.0000.000
139B205LYS10.9630.98933.679-0.017-0.0170.0000.0000.0000.000
140B206GLU-1-0.885-0.96036.9890.0230.0230.0000.0000.0000.000
141B207GLN00.0050.02631.8220.0000.0000.0000.0000.0000.000
142B208GLU-1-0.868-0.94134.4050.0140.0140.0000.0000.0000.000
143B209SER0-0.120-0.04735.167-0.002-0.0020.0000.0000.0000.000
144B210LYS10.8950.94635.933-0.024-0.0240.0000.0000.0000.000
145B211SER0-0.060-0.03334.6240.0000.0000.0000.0000.0000.000
146B212LEU0-0.065-0.04135.771-0.001-0.0010.0000.0000.0000.000
147B213PHE0-0.0090.00134.545-0.002-0.0020.0000.0000.0000.000
148B214LYS10.9381.01035.432-0.007-0.0070.0000.0000.0000.000
149B215ARG10.8230.91328.958-0.009-0.0090.0000.0000.0000.000
150B216ASP-1-0.916-0.97033.7760.0030.0030.0000.0000.0000.000
151B217GLY0-0.036-0.02733.7550.0000.0000.0000.0000.0000.000
152B218ILE0-0.0130.00729.797-0.001-0.0010.0000.0000.0000.000
153B219ASP-1-0.966-1.00430.5180.0120.0120.0000.0000.0000.000
154B220LEU0-0.0050.01630.2750.0020.0020.0000.0000.0000.000
155B221ASN00.0650.03130.6060.0000.0000.0000.0000.0000.000
156B222SER0-0.022-0.00930.9880.0020.0020.0000.0000.0000.000
157B223ASN0-0.057-0.04229.2050.0040.0040.0000.0000.0000.000
158B224ASP-1-0.839-0.90026.9140.0260.0260.0000.0000.0000.000
159B225ARG10.8930.96118.126-0.090-0.0900.0000.0000.0000.000
160B226ILE0-0.022-0.01024.144-0.001-0.0010.0000.0000.0000.000
161B227LEU0-0.025-0.00619.4940.0100.0100.0000.0000.0000.000
162B228THR00.001-0.01223.108-0.010-0.0100.0000.0000.0000.000
163B229LEU0-0.027-0.01121.1040.0070.0070.0000.0000.0000.000
164B230ILE00.0360.01824.697-0.007-0.0070.0000.0000.0000.000
165B231THR00.005-0.02326.1080.0010.0010.0000.0000.0000.000
166B232CYS0-0.040-0.00328.0000.0010.0010.0000.0000.0000.000
167B233GLY00.0300.02630.970-0.002-0.0020.0000.0000.0000.000
168B234TYR0-0.094-0.08331.6500.0010.0010.0000.0000.0000.000
169B235ASP-1-0.819-0.90136.8910.0060.0060.0000.0000.0000.000
170B236PHE0-0.0050.00338.5560.0000.0000.0000.0000.0000.000
171B237VAL00.009-0.00639.1460.0010.0010.0000.0000.0000.000
172B238ASN0-0.026-0.01836.8770.0010.0010.0000.0000.0000.000
173B239ALA00.0170.02736.4770.0020.0020.0000.0000.0000.000
174B240ARG10.9300.95629.098-0.034-0.0340.0000.0000.0000.000
175B241ILE0-0.037-0.01730.332-0.002-0.0020.0000.0000.0000.000
176B242VAL00.0080.00629.1400.0030.0030.0000.0000.0000.000
177B243VAL00.0120.00325.987-0.004-0.0040.0000.0000.0000.000
178B244VAL0-0.015-0.00226.7160.0060.0060.0000.0000.0000.000
179B245ALA00.018-0.00123.627-0.005-0.0050.0000.0000.0000.000
180B246LYS10.8710.94624.912-0.013-0.0130.0000.0000.0000.000
181B247GLU-1-0.929-0.96718.7620.0650.0650.0000.0000.0000.000
182B248ILE0-0.028-0.01321.756-0.005-0.0050.0000.0000.0000.000
183B249ASP-1-0.993-0.99020.0220.0010.0010.0000.0000.0000.000