Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6NL3Z

Calculation Name: 3FTJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FTJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q2EHL8

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378885.306434
FMO2-HF: Nuclear repulsion 2297622.497707
FMO2-HF: Total energy -81262.808727
FMO2-MP2: Total energy -81503.977326


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(A:307:GLN)


Summations of interaction energy for fragment #1(A:307:GLN)
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.
-6.577-2.5521.603-2.419-3.211-0.002
Interaction energy analysis for fragmet #1(A:307:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.014
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].
3A309ILE00.0410.0283.889-2.892-0.580-0.015-1.162-1.1350.001
4A310LEU00.0670.0122.302-2.166-1.3241.561-0.984-1.420-0.002
5A311GLU-1-0.841-0.8983.506-6.393-5.6410.058-0.252-0.559-0.001
6A312ASN0-0.0460.0044.5881.2981.417-0.001-0.021-0.0970.000
7A313ILE0-0.0070.0027.3130.1810.1810.0000.0000.0000.000
8A314ARG10.8460.8867.1502.8102.8100.0000.0000.0000.000
9A315GLY00.0510.03511.1120.0130.0130.0000.0000.0000.000
10A316ILE0-0.018-0.00312.1140.0770.0770.0000.0000.0000.000
11A317GLY00.0510.02714.9060.0510.0510.0000.0000.0000.000
12A318THR0-0.046-0.03413.6070.0300.0300.0000.0000.0000.000
13A319ASN00.0130.00016.3510.0100.0100.0000.0000.0000.000
14A320THR00.0250.01519.7010.0120.0120.0000.0000.0000.000
15A321MET0-0.032-0.00220.2070.0170.0170.0000.0000.0000.000
16A322THR0-0.0010.00222.427-0.008-0.0080.0000.0000.0000.000
17A323ILE0-0.027-0.00524.4630.0190.0190.0000.0000.0000.000
18A324PHE00.0380.00023.685-0.008-0.0080.0000.0000.0000.000
19A325ASN00.0210.00728.7040.0070.0070.0000.0000.0000.000
20A326GLY00.012-0.00630.3780.0040.0040.0000.0000.0000.000
21A327ASN0-0.028-0.03829.700-0.003-0.0030.0000.0000.0000.000
22A328GLY00.0720.02925.8950.0100.0100.0000.0000.0000.000
23A329PHE00.0220.00121.744-0.004-0.0040.0000.0000.0000.000
24A330GLY00.0020.00925.3160.0020.0020.0000.0000.0000.000
25A331ASP-1-0.766-0.83826.3210.0790.0790.0000.0000.0000.000
26A332ARG10.9400.95326.115-0.123-0.1230.0000.0000.0000.000
27A333ARG10.9210.98331.384-0.060-0.0600.0000.0000.0000.000
28A334SER0-0.003-0.03832.414-0.009-0.0090.0000.0000.0000.000
29A335ARG10.9040.96227.621-0.041-0.0410.0000.0000.0000.000
30A336HIS0-0.038-0.01532.412-0.009-0.0090.0000.0000.0000.000
31A337ILE0-0.050-0.02035.792-0.005-0.0050.0000.0000.0000.000
32A338GLN00.0300.01035.903-0.002-0.0020.0000.0000.0000.000
33A339ASN00.0110.00536.447-0.006-0.0060.0000.0000.0000.000
34A340LEU0-0.0430.00230.995-0.002-0.0020.0000.0000.0000.000
35A341LYS10.8520.91735.6580.0070.0070.0000.0000.0000.000
36A342ILE00.0660.03037.067-0.003-0.0030.0000.0000.0000.000
37A343SER00.008-0.00838.718-0.003-0.0030.0000.0000.0000.000
38A344ASP-1-0.754-0.84435.341-0.012-0.0120.0000.0000.0000.000
39A345ALA00.0400.02334.029-0.003-0.0030.0000.0000.0000.000
40A346ASN00.0300.01735.071-0.004-0.0040.0000.0000.0000.000
41A347THR00.001-0.00737.002-0.003-0.0030.0000.0000.0000.000
42A348LEU00.003-0.00630.436-0.001-0.0010.0000.0000.0000.000
43A349SER0-0.050-0.03833.165-0.006-0.0060.0000.0000.0000.000
44A350LYS10.9180.96234.7800.0430.0430.0000.0000.0000.000
45A351GLN0-0.034-0.00532.1060.0050.0050.0000.0000.0000.000
46A352SER00.0450.01832.673-0.005-0.0050.0000.0000.0000.000
47A353TYR0-0.004-0.00627.839-0.007-0.0070.0000.0000.0000.000
48A354ILE0-0.056-0.03527.642-0.005-0.0050.0000.0000.0000.000
49A355GLN00.0700.06127.055-0.003-0.0030.0000.0000.0000.000
50A356SER00.002-0.00428.9040.0020.0020.0000.0000.0000.000
51A357VAL0-0.006-0.00929.2340.0030.0030.0000.0000.0000.000
52A358THR0-0.0120.01029.118-0.003-0.0030.0000.0000.0000.000
53A359PRO0-0.008-0.01230.6250.0060.0060.0000.0000.0000.000
54A360ASN00.0220.00628.737-0.002-0.0020.0000.0000.0000.000
55A361THR00.0090.00632.4680.0110.0110.0000.0000.0000.000
56A362SER00.0120.01332.919-0.004-0.0040.0000.0000.0000.000
57A363SER0-0.028-0.00635.7040.0060.0060.0000.0000.0000.000
58A364SER00.0190.00236.295-0.003-0.0030.0000.0000.0000.000
59A365GLY0-0.045-0.03438.1020.0040.0040.0000.0000.0000.000
60A366ILE0-0.013-0.00141.047-0.001-0.0010.0000.0000.0000.000
61A367LEU0-0.024-0.00239.805-0.002-0.0020.0000.0000.0000.000
62A368VAL00.0100.00043.5290.0010.0010.0000.0000.0000.000
63A369VAL00.004-0.00543.469-0.003-0.0030.0000.0000.0000.000
64A370GLY00.0070.01146.6620.0000.0000.0000.0000.0000.000
65A371ASN00.009-0.00850.1300.0010.0010.0000.0000.0000.000
66A372LYS10.8220.91743.8970.0460.0460.0000.0000.0000.000
67A373SER0-0.002-0.01345.928-0.001-0.0010.0000.0000.0000.000
68A374PHE00.0320.02040.5030.0010.0010.0000.0000.0000.000
69A375THR00.0470.01240.3400.0010.0010.0000.0000.0000.000
70A376SER0-0.040-0.01336.5460.0010.0010.0000.0000.0000.000
71A377ALA00.0240.02636.250-0.003-0.0030.0000.0000.0000.000
72A378ASN0-0.014-0.00833.4420.0100.0100.0000.0000.0000.000
73A379LEU00.0060.01635.163-0.008-0.0080.0000.0000.0000.000
74A380TYR0-0.024-0.02730.3470.0070.0070.0000.0000.0000.000
75A381GLY00.003-0.01134.946-0.004-0.0040.0000.0000.0000.000
76A382ILE0-0.045-0.02331.2830.0040.0040.0000.0000.0000.000
77A383GLY00.010-0.00332.9480.0020.0020.0000.0000.0000.000
78A384GLU-1-0.825-0.91832.981-0.105-0.1050.0000.0000.0000.000
79A385GLN0-0.020-0.03229.6000.0020.0020.0000.0000.0000.000
80A386TYR0-0.0230.00227.756-0.012-0.0120.0000.0000.0000.000
81A387PHE00.039-0.00727.392-0.005-0.0050.0000.0000.0000.000
82A388ASP-1-0.888-0.92626.814-0.217-0.2170.0000.0000.0000.000
83A389VAL0-0.025-0.02324.476-0.021-0.0210.0000.0000.0000.000
84A390GLU-1-0.906-0.96122.812-0.123-0.1230.0000.0000.0000.000
85A391GLY00.0250.02622.766-0.012-0.0120.0000.0000.0000.000
86A392LEU0-0.053-0.00823.810-0.008-0.0080.0000.0000.0000.000
87A393LYS10.8690.89623.8220.2630.2630.0000.0000.0000.000
88A394LEU00.0140.00527.9750.0120.0120.0000.0000.0000.000
89A395LYN00.0020.03528.049-0.021-0.0210.0000.0000.0000.000
90A396GLN0-0.019-0.02533.1060.0100.0100.0000.0000.0000.000
91A397GLY0-0.0030.00236.8790.0030.0030.0000.0000.0000.000
92A398ARG10.7830.84437.6910.0810.0810.0000.0000.0000.000
93A399LEU00.0600.03232.0200.0050.0050.0000.0000.0000.000
94A400LEU0-0.041-0.02835.5610.0060.0060.0000.0000.0000.000
95A401THR0-0.009-0.02737.202-0.006-0.0060.0000.0000.0000.000
96A402GLU-1-0.868-0.93739.425-0.076-0.0760.0000.0000.0000.000
97A403ASP-1-0.830-0.91140.941-0.058-0.0580.0000.0000.0000.000
98A404ASP-1-0.797-0.86140.915-0.073-0.0730.0000.0000.0000.000
99A405VAL0-0.035-0.01438.4320.0050.0050.0000.0000.0000.000
100A406ASP-1-0.846-0.89941.584-0.054-0.0540.0000.0000.0000.000
101A407GLN0-0.049-0.01344.8320.0070.0070.0000.0000.0000.000
102A408SER0-0.071-0.02544.0310.0050.0050.0000.0000.0000.000
103A409ASN0-0.011-0.00144.2090.0070.0070.0000.0000.0000.000
104A410GLN0-0.039-0.03143.8650.0000.0000.0000.0000.0000.000
105A411VAL0-0.032-0.01041.4640.0010.0010.0000.0000.0000.000
106A412VAL0-0.012-0.00338.5260.0010.0010.0000.0000.0000.000
107A413VAL00.0160.02734.381-0.001-0.0010.0000.0000.0000.000
108A414LEU0-0.030-0.02735.8210.0040.0040.0000.0000.0000.000
109A415ASP-1-0.691-0.81729.809-0.108-0.1080.0000.0000.0000.000
110A416GLU-1-0.842-0.92629.652-0.139-0.1390.0000.0000.0000.000
111A417SER0-0.031-0.03229.8890.0130.0130.0000.0000.0000.000
112A418ALA00.0020.00431.8860.0100.0100.0000.0000.0000.000
113A419LYS10.8460.91534.8700.0900.0900.0000.0000.0000.000
114A420LYS10.9570.97232.2290.0820.0820.0000.0000.0000.000
115A421ALA0-0.012-0.01335.6890.0050.0050.0000.0000.0000.000
116A422ILE0-0.0140.00737.3840.0050.0050.0000.0000.0000.000
117A423PHE0-0.018-0.02039.6080.0040.0040.0000.0000.0000.000
118A424ALA00.0410.03538.755-0.001-0.0010.0000.0000.0000.000
119A425ASN00.0130.00739.041-0.010-0.0100.0000.0000.0000.000
120A426GLU-1-0.838-0.89441.150-0.053-0.0530.0000.0000.0000.000
121A427ASN00.0480.01841.812-0.009-0.0090.0000.0000.0000.000
122A428PRO0-0.0070.00739.2300.0060.0060.0000.0000.0000.000
123A429LEU00.0110.00939.9160.0030.0030.0000.0000.0000.000
124A430GLY0-0.0010.00143.4870.0030.0030.0000.0000.0000.000
125A431LYS10.8310.91945.2580.0610.0610.0000.0000.0000.000
126A432THR0-0.024-0.01245.819-0.002-0.0020.0000.0000.0000.000
127A433VAL00.0030.00141.5380.0010.0010.0000.0000.0000.000
128A434ILE0-0.015-0.01144.8820.0000.0000.0000.0000.0000.000
129A435PHE00.0380.03239.9770.0010.0010.0000.0000.0000.000
130A436ASN00.0280.00443.1480.0010.0010.0000.0000.0000.000
131A437LYS10.9530.96746.3400.0140.0140.0000.0000.0000.000
132A438ARG10.8940.96246.3080.0260.0260.0000.0000.0000.000
133A439PRO0-0.010-0.00346.684-0.002-0.0020.0000.0000.0000.000
134A440PHE00.0090.00342.5630.0000.0000.0000.0000.0000.000
135A441ARG10.9760.99345.2490.0610.0610.0000.0000.0000.000
136A442VAL00.006-0.00340.319-0.003-0.0030.0000.0000.0000.000
137A443ILE0-0.042-0.02939.8410.0010.0010.0000.0000.0000.000
138A444GLY00.0500.02837.753-0.005-0.0050.0000.0000.0000.000
139A445VAL0-0.059-0.01633.5020.0090.0090.0000.0000.0000.000
140A446VAL00.0310.01829.975-0.007-0.0070.0000.0000.0000.000
141A447SER00.0060.00726.3260.0000.0000.0000.0000.0000.000
142A448ASP-1-0.918-0.95426.136-0.140-0.1400.0000.0000.0000.000
143A449GLN0-0.058-0.02222.832-0.029-0.0290.0000.0000.0000.000
144A458SER00.008-0.01029.1500.0020.0020.0000.0000.0000.000
145A459LEU0-0.012-0.01331.4220.0050.0050.0000.0000.0000.000
146A460ASN00.0000.01629.3970.0140.0140.0000.0000.0000.000
147A461LEU0-0.021-0.01633.350-0.005-0.0050.0000.0000.0000.000
148A462TYR00.034-0.00629.7070.0050.0050.0000.0000.0000.000
149A463SER00.009-0.00935.172-0.001-0.0010.0000.0000.0000.000
150A464PRO00.0660.03837.002-0.001-0.0010.0000.0000.0000.000
151A465TYR0-0.004-0.01536.2390.0090.0090.0000.0000.0000.000
152A466SER0-0.027-0.02838.1580.0050.0050.0000.0000.0000.000
153A467THR00.017-0.00641.7160.0050.0050.0000.0000.0000.000
154A468VAL00.0020.00738.6720.0040.0040.0000.0000.0000.000
155A469LEU0-0.031-0.00439.6300.0040.0040.0000.0000.0000.000
156A470ASN0-0.021-0.01842.7080.0060.0060.0000.0000.0000.000
157A471LYS10.8200.91645.1860.0400.0400.0000.0000.0000.000
158A472ILE0-0.069-0.02142.1180.0010.0010.0000.0000.0000.000
159A473THR0-0.006-0.01340.2850.0020.0020.0000.0000.0000.000
160A474GLY00.0090.02643.7550.0040.0040.0000.0000.0000.000
161A475GLY0-0.007-0.00943.8130.0000.0000.0000.0000.0000.000
162A476SER00.0350.00842.128-0.002-0.0020.0000.0000.0000.000
163A477ARG10.8460.90939.261-0.006-0.0060.0000.0000.0000.000
164A478ILE00.0030.00334.223-0.002-0.0020.0000.0000.0000.000
165A479GLY00.0600.03233.1640.0060.0060.0000.0000.0000.000
166A480SER0-0.036-0.03728.4460.0080.0080.0000.0000.0000.000
167A481ILE0-0.005-0.00329.241-0.004-0.0040.0000.0000.0000.000
168A482THR0-0.0020.01924.3220.0130.0130.0000.0000.0000.000
169A483VAL0-0.022-0.01825.4890.0000.0000.0000.0000.0000.000
170A484LYS10.8440.91623.2520.2140.2140.0000.0000.0000.000
171A485ILE0-0.019-0.01622.9320.0120.0120.0000.0000.0000.000
172A486SER00.0140.00024.689-0.021-0.0210.0000.0000.0000.000
173A487ASP-1-0.827-0.91222.718-0.257-0.2570.0000.0000.0000.000
174A488ASP-1-0.921-0.94923.053-0.177-0.1770.0000.0000.0000.000
175A489VAL0-0.031-0.00724.5500.0180.0180.0000.0000.0000.000
176A490ASN00.014-0.00320.8370.0020.0020.0000.0000.0000.000
177A491SER00.0850.03419.0240.0280.0280.0000.0000.0000.000
178A492THR00.0600.02919.1910.0090.0090.0000.0000.0000.000
179A493VAL0-0.030-0.01821.5940.0150.0150.0000.0000.0000.000
180A494ALA00.0420.03824.1290.0060.0060.0000.0000.0000.000
181A495GLU-1-0.844-0.92121.1410.0520.0520.0000.0000.0000.000
182A496LYS10.9360.96824.750-0.036-0.0360.0000.0000.0000.000
183A497SER0-0.018-0.01027.1020.0040.0040.0000.0000.0000.000
184A498LEU00.0130.01526.2230.0020.0020.0000.0000.0000.000
185A499THR0-0.029-0.02926.9550.0070.0070.0000.0000.0000.000
186A500GLU-1-0.809-0.89329.6300.0390.0390.0000.0000.0000.000
187A501LEU00.0040.02232.6630.0010.0010.0000.0000.0000.000
188A502LEU00.014-0.00630.3780.0010.0010.0000.0000.0000.000
189A503LYS10.7700.86031.751-0.037-0.0370.0000.0000.0000.000
190A504SER0-0.0020.00135.0380.0010.0010.0000.0000.0000.000
191A505LEU0-0.039-0.01736.726-0.001-0.0010.0000.0000.0000.000
192A506HIS10.7420.85835.028-0.010-0.0100.0000.0000.0000.000
193A507GLY00.0140.02238.4680.0030.0030.0000.0000.0000.000
194A508LYS10.8210.90137.001-0.022-0.0220.0000.0000.0000.000
195A509LYS10.9270.95127.674-0.075-0.0750.0000.0000.0000.000
196A510ASP-1-0.779-0.86332.1380.0340.0340.0000.0000.0000.000
197A511PHE0-0.0080.00529.053-0.005-0.0050.0000.0000.0000.000
198A512PHE0-0.041-0.00523.7120.0120.0120.0000.0000.0000.000
199A513ILE00.0350.01522.564-0.016-0.0160.0000.0000.0000.000
200A514MET0-0.032-0.00320.1570.0260.0260.0000.0000.0000.000
201A515ASN00.033-0.00617.885-0.014-0.0140.0000.0000.0000.000
202A516SER00.0300.02212.3910.0510.0510.0000.0000.0000.000
203A517ASP-1-0.809-0.91213.2930.3340.3340.0000.0000.0000.000
204A518THR00.0440.01914.9880.0630.0630.0000.0000.0000.000
205A519ILE0-0.0110.00911.7310.0490.0490.0000.0000.0000.000
206A520LYS10.8000.9049.790-0.440-0.4400.0000.0000.0000.000
207A521GLN0-0.018-0.00911.8380.1390.1390.0000.0000.0000.000
208A522THR0-0.042-0.02614.6950.0090.0090.0000.0000.0000.000
209A523ILE0-0.052-0.0198.3010.0220.0220.0000.0000.0000.000
210A524GLU-1-0.849-0.93610.6580.8360.8360.0000.0000.0000.000
211A525ASN0-0.065-0.03012.122-0.036-0.0360.0000.0000.0000.000
212A526THR0-0.075-0.03512.836-0.101-0.1010.0000.0000.0000.000
213A527THR0-0.028-0.01413.0530.0870.0870.0000.0000.0000.000
214A528GLY0-0.0070.00211.6680.0140.0140.0000.0000.0000.000