FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 17J5Z

Calculation Name: 5T11-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T11

Chain ID: J

ChEMBL ID:

UniProt ID: B2T2U6

Base Structure: X-ray

Registration Date: 2023-06-21

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 139
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1103377.174467
FMO2-HF: Nuclear repulsion 1052951.201001
FMO2-HF: Total energy -50425.973466
FMO2-MP2: Total energy -50574.904925


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(J:4:MET)


Summations of interaction energy for fragment #1(J:4: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.
-5.5580.0230.408-2.358-3.632-0.005
Interaction energy analysis for fragmet #1(J:4:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.006
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].
3J6THR0-0.092-0.0403.092-2.3130.1540.121-1.379-1.210-0.004
4J7VAL00.0330.0025.4220.0450.0450.0000.0000.0000.000
5J8ARG10.8900.9528.0490.0470.0470.0000.0000.0000.000
6J9GLN0-0.003-0.00911.274-0.002-0.0020.0000.0000.0000.000
7J10THR00.0000.01214.6820.0010.0010.0000.0000.0000.000
8J11SER0-0.004-0.00718.165-0.009-0.0090.0000.0000.0000.000
9J12GLY00.0470.01820.5040.0040.0040.0000.0000.0000.000
10J13PRO0-0.0160.01222.135-0.003-0.0030.0000.0000.0000.000
11J14ALA0-0.028-0.02922.785-0.006-0.0060.0000.0000.0000.000
12J15LEU00.0230.02721.7300.0050.0050.0000.0000.0000.000
13J16ALA00.0360.00824.751-0.004-0.0040.0000.0000.0000.000
14J17ARG10.9700.97826.3490.0360.0360.0000.0000.0000.000
15J18GLY0-0.038-0.02927.4750.0020.0020.0000.0000.0000.000
16J19ASP-1-0.829-0.90227.122-0.029-0.0290.0000.0000.0000.000
17J20LYS10.8970.96227.6520.0160.0160.0000.0000.0000.000
18J21VAL00.0140.01823.2750.0010.0010.0000.0000.0000.000
19J22ALA0-0.014-0.00826.6100.0010.0010.0000.0000.0000.000
20J23VAL00.005-0.00321.961-0.001-0.0010.0000.0000.0000.000
21J24VAL0-0.010-0.01824.6080.0020.0020.0000.0000.0000.000
22J25SER0-0.008-0.01225.0200.0000.0000.0000.0000.0000.000
23J26ILE0-0.0320.00319.0190.0000.0000.0000.0000.0000.000
24J27ALA00.0020.01322.5420.0020.0020.0000.0000.0000.000
25J28ASN00.025-0.00720.7780.0010.0010.0000.0000.0000.000
26J29TYR0-0.033-0.01119.3810.0000.0000.0000.0000.0000.000
27J30THR0-0.045-0.02216.8170.0010.0010.0000.0000.0000.000
28J31GLU-1-0.917-0.96419.4310.0140.0140.0000.0000.0000.000
29J32THR0-0.065-0.05117.763-0.001-0.0010.0000.0000.0000.000
30J33PRO00.010-0.00220.8840.0000.0000.0000.0000.0000.000
31J34ASP-1-0.840-0.91722.8830.0120.0120.0000.0000.0000.000
32J35ALA00.000-0.00118.4660.0000.0000.0000.0000.0000.000
33J36GLY00.0320.01719.4890.0010.0010.0000.0000.0000.000
34J37HIS00.0040.00521.366-0.002-0.0020.0000.0000.0000.000
35J38SER0-0.040-0.01718.617-0.001-0.0010.0000.0000.0000.000
36J39ALA0-0.003-0.00517.1950.0000.0000.0000.0000.0000.000
37J40GLU-1-0.814-0.90918.105-0.005-0.0050.0000.0000.0000.000
38J41SER0-0.007-0.00421.037-0.005-0.0050.0000.0000.0000.000
39J42ILE0-0.031-0.01114.351-0.004-0.0040.0000.0000.0000.000
40J43ALA00.0250.03516.958-0.009-0.0090.0000.0000.0000.000
41J44ALA00.0280.00817.897-0.008-0.0080.0000.0000.0000.000
42J45ASN0-0.005-0.01619.448-0.005-0.0050.0000.0000.0000.000
43J46THR0-0.055-0.03114.468-0.007-0.0070.0000.0000.0000.000
44J47LEU0-0.001-0.00317.336-0.009-0.0090.0000.0000.0000.000
45J48ARG10.8960.94319.8190.0160.0160.0000.0000.0000.000
46J49ALA0-0.031-0.00617.855-0.002-0.0020.0000.0000.0000.000
47J50GLY0-0.0090.00118.824-0.007-0.0070.0000.0000.0000.000
48J51GLY00.0120.00319.349-0.002-0.0020.0000.0000.0000.000
49J52ILE0-0.019-0.01022.1130.0030.0030.0000.0000.0000.000
50J53ALA0-0.051-0.02624.5310.0020.0020.0000.0000.0000.000
51J54ASP-1-0.883-0.94427.727-0.016-0.0160.0000.0000.0000.000
52J55VAL00.0440.02323.242-0.001-0.0010.0000.0000.0000.000
53J56ARG10.8300.90626.5740.0150.0150.0000.0000.0000.000
54J57ILE00.0330.01923.932-0.001-0.0010.0000.0000.0000.000
55J58ALA0-0.033-0.01127.2390.0000.0000.0000.0000.0000.000
56J59PRO0-0.015-0.00429.3620.0010.0010.0000.0000.0000.000
57J60ALA00.0200.01330.4740.0010.0010.0000.0000.0000.000
58J78LYS11.0020.97333.7380.0000.0000.0000.0000.0000.000
59J79ALA00.0980.06131.7490.0000.0000.0000.0000.0000.000
60J80MET00.005-0.00630.243-0.001-0.0010.0000.0000.0000.000
61J81GLU-1-0.973-0.97833.704-0.004-0.0040.0000.0000.0000.000
62J82TRP00.0990.05030.052-0.001-0.0010.0000.0000.0000.000
63J83ALA00.0440.04431.320-0.001-0.0010.0000.0000.0000.000
64J84ARG10.9640.97933.0810.0060.0060.0000.0000.0000.000
65J85SER0-0.067-0.04536.0080.0000.0000.0000.0000.0000.000
66J86GLN0-0.042-0.00233.2070.0000.0000.0000.0000.0000.000
67J87ASN0-0.045-0.02034.322-0.001-0.0010.0000.0000.0000.000
68J88ALA0-0.025-0.01229.777-0.001-0.0010.0000.0000.0000.000
69J89ARG10.9230.96229.6060.0250.0250.0000.0000.0000.000
70J90TYR0-0.004-0.01525.583-0.001-0.0010.0000.0000.0000.000
71J91VAL00.003-0.00725.9510.0010.0010.0000.0000.0000.000
72J92LEU0-0.0390.00418.539-0.002-0.0020.0000.0000.0000.000
73J93SER00.0230.00422.2070.0030.0030.0000.0000.0000.000
74J94GLY00.0430.00819.398-0.005-0.0050.0000.0000.0000.000
75J95ALA0-0.0030.01618.5000.0030.0030.0000.0000.0000.000
76J96VAL0-0.027-0.00915.756-0.001-0.0010.0000.0000.0000.000
77J97GLU-1-0.811-0.90214.4880.0110.0110.0000.0000.0000.000
78J98GLU-1-0.934-0.97510.322-0.070-0.0700.0000.0000.0000.000
79J99TRP00.036-0.00113.4930.0150.0150.0000.0000.0000.000
80J100ARG10.9611.00013.1750.0070.0070.0000.0000.0000.000
81J101TYR00.0550.04412.6440.0150.0150.0000.0000.0000.000
82J102LYS10.8470.9228.0110.2770.2770.0000.0000.0000.000
83J103THR0-0.022-0.01113.0690.0140.0140.0000.0000.0000.000
84J104GLY00.0490.02515.615-0.007-0.0070.0000.0000.0000.000
85J105VAL00.013-0.00317.1040.0020.0020.0000.0000.0000.000
86J106ASP-1-0.932-0.95914.8220.0160.0160.0000.0000.0000.000
87J107GLY0-0.0070.01213.053-0.012-0.0120.0000.0000.0000.000
88J108GLU-1-0.838-0.9307.412-0.255-0.2550.0000.0000.0000.000
89J109PRO0-0.070-0.0169.140-0.026-0.0260.0000.0000.0000.000
90J110VAL0-0.019-0.0047.1490.0070.0070.0000.0000.0000.000
91J111VAL0-0.004-0.0168.4840.0490.0490.0000.0000.0000.000
92J112GLY0-0.002-0.0089.199-0.041-0.0410.0000.0000.0000.000
93J113VAL0-0.020-0.00211.4980.0110.0110.0000.0000.0000.000
94J114THR0-0.025-0.02312.958-0.013-0.0130.0000.0000.0000.000
95J115PHE0-0.008-0.02013.7850.0010.0010.0000.0000.0000.000
96J116GLU-1-0.918-0.97117.738-0.008-0.0080.0000.0000.0000.000
97J117LEU0-0.019-0.01620.8050.0000.0000.0000.0000.0000.000
98J118ILE0-0.026-0.02322.7020.0000.0000.0000.0000.0000.000
99J119ASP-1-0.801-0.85526.441-0.020-0.0200.0000.0000.0000.000
100J120VAL0-0.024-0.01929.1080.0030.0030.0000.0000.0000.000
101J121SER0-0.137-0.10631.8250.0020.0020.0000.0000.0000.000
102J122ASN00.028-0.00532.0240.0010.0010.0000.0000.0000.000
103J123GLY0-0.068-0.02631.5390.0010.0010.0000.0000.0000.000
104J124ALA00.0060.01229.6610.0010.0010.0000.0000.0000.000
105J125VAL00.0310.01623.244-0.002-0.0020.0000.0000.0000.000
106J126VAL0-0.028-0.01424.4550.0000.0000.0000.0000.0000.000
107J127TRP00.014-0.01615.154-0.002-0.0020.0000.0000.0000.000
108J128SER00.0020.02118.8040.0070.0070.0000.0000.0000.000
109J129ALA0-0.008-0.00413.330-0.012-0.0120.0000.0000.0000.000
110J130THR00.0370.02211.3580.0170.0170.0000.0000.0000.000
111J131GLY0-0.031-0.0258.738-0.043-0.0430.0000.0000.0000.000
112J132THR00.0220.0156.996-0.031-0.0310.0000.0000.0000.000
113J133ARG10.9100.9513.659-2.326-1.0190.224-0.354-1.1760.001
114J134THR00.0000.0143.086-0.8020.1030.044-0.321-0.6280.000
115J135GLY0-0.043-0.0213.5450.0790.9810.019-0.304-0.618-0.002
116J136TRP0-0.007-0.0225.360-0.644-0.6440.0000.0000.0000.000
117J137SER00.1170.0588.085-0.011-0.0110.0000.0000.0000.000
118J138ARG10.9620.99711.345-0.127-0.1270.0000.0000.0000.000
119J139SER0-0.069-0.0349.2450.0820.0820.0000.0000.0000.000
120J140GLY00.0880.04011.374-0.033-0.0330.0000.0000.0000.000
121J141LEU00.041-0.00411.4600.0540.0540.0000.0000.0000.000
122J142SER00.0250.01612.2640.0230.0230.0000.0000.0000.000
123J143SER00.0080.00410.420-0.011-0.0110.0000.0000.0000.000
124J144VAL0-0.004-0.0046.9750.0430.0430.0000.0000.0000.000
125J145ALA00.0370.0238.3470.0140.0140.0000.0000.0000.000
126J146THR00.0110.00011.005-0.037-0.0370.0000.0000.0000.000
127J147SER0-0.039-0.0236.602-0.062-0.0620.0000.0000.0000.000
128J148LEU0-0.082-0.0246.115-0.086-0.0860.0000.0000.0000.000
129J149ILE00.0550.0247.753-0.087-0.0870.0000.0000.0000.000
130J150ALA00.0290.02110.418-0.024-0.0240.0000.0000.0000.000
131J151LYS10.9370.9664.9150.6090.6090.0000.0000.0000.000
132J152VAL0-0.015-0.0038.924-0.020-0.0200.0000.0000.0000.000
133J153LEU00.0470.01410.8370.0010.0010.0000.0000.0000.000
134J154SER0-0.0090.00211.4720.0030.0030.0000.0000.0000.000
135J155PRO0-0.049-0.02613.2260.0080.0080.0000.0000.0000.000
136J156LEU0-0.024-0.00316.4420.0120.0120.0000.0000.0000.000
137J157GLN0-0.031-0.00415.249-0.003-0.0030.0000.0000.0000.000
138J158ALA0-0.043-0.01219.3200.0020.0020.0000.0000.0000.000
139J159ARG10.8380.92519.6890.0730.0730.0000.0000.0000.000