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: 3JR6L

Calculation Name: 4G54-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G54

Chain ID: A

ChEMBL ID:

UniProt ID: A0A3Q0

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 OptHSide
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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2886277.11429
FMO2-HF: Nuclear repulsion 2792900.81308
FMO2-HF: Total energy -93376.30121
FMO2-MP2: Total energy -93646.229672


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:343:TRP)


Summations of interaction energy for fragment #1(A:343:TRP)
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.
-33.239-13.63124.542-12.967-31.188-0.037
Interaction energy analysis for fragmet #1(A:343:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.046
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].
3A345GLY00.0090.0102.842-2.571-0.1370.261-1.242-1.454-0.007
4A346GLU-1-0.865-0.9264.043-1.930-1.4500.000-0.096-0.3850.000
5A347SER00.011-0.0092.261-1.9860.2911.552-1.781-2.049-0.001
6A348ALA00.0100.0123.0851.8221.1140.0440.953-0.2890.000
7A349VAL0-0.016-0.0123.836-0.0480.2520.002-0.044-0.2580.000
8A350ALA0-0.047-0.0242.981-2.095-0.0761.974-0.971-3.0220.009
9A351ARG10.8510.9395.021-1.196-1.015-0.001-0.033-0.1480.000
10A352MET0-0.069-0.0058.150-0.451-0.4510.0000.0000.0000.000
11A353THR00.0690.0175.4690.4600.4600.0000.0000.0000.000
12A354THR0-0.033-0.0166.970-0.164-0.1640.0000.0000.0000.000
13A355ARG10.9090.9269.687-0.056-0.0560.0000.0000.0000.000
14A356ALA00.0370.02311.1630.0170.0170.0000.0000.0000.000
15A357GLN00.0400.01510.7480.0190.0190.0000.0000.0000.000
16A358GLY00.0400.00211.5450.0160.0160.0000.0000.0000.000
17A359LEU00.006-0.01412.346-0.015-0.0150.0000.0000.0000.000
18A360GLU-1-0.902-0.94015.5020.0000.0000.0000.0000.0000.000
19A361GLU-1-0.771-0.86814.8360.0750.0750.0000.0000.0000.000
20A362LEU0-0.012-0.00915.671-0.014-0.0140.0000.0000.0000.000
21A363TYR0-0.010-0.02617.461-0.016-0.0160.0000.0000.0000.000
22A364LYS10.8410.93418.118-0.058-0.0580.0000.0000.0000.000
23A365LEU0-0.0170.00417.992-0.010-0.0100.0000.0000.0000.000
24A366TRP0-0.038-0.02321.161-0.012-0.0120.0000.0000.0000.000
25A367GLY00.0090.00824.346-0.006-0.0060.0000.0000.0000.000
26A368TYR0-0.035-0.02624.628-0.008-0.0080.0000.0000.0000.000
27A369ARG10.9080.95323.7110.0120.0120.0000.0000.0000.000
28A370ALA0-0.022-0.00521.129-0.002-0.0020.0000.0000.0000.000
29A371THR0-0.039-0.05322.897-0.007-0.0070.0000.0000.0000.000
30A372ARG10.9940.97619.6190.0610.0610.0000.0000.0000.000
31A373ILE00.0620.02221.1910.0010.0010.0000.0000.0000.000
32A374ASP-1-0.729-0.77622.4050.0170.0170.0000.0000.0000.000
33A375THR0-0.044-0.02817.0830.0060.0060.0000.0000.0000.000
34A376MET0-0.0160.00016.9890.0030.0030.0000.0000.0000.000
35A377CYS0-0.078-0.03117.0790.0180.0180.0000.0000.0000.000
36A378GLU-1-0.885-0.93319.0280.0130.0130.0000.0000.0000.000
37A379GLN0-0.042-0.01821.698-0.002-0.0020.0000.0000.0000.000
38A380PRO0-0.013-0.02525.061-0.002-0.0020.0000.0000.0000.000
39A381SER00.0290.01525.743-0.001-0.0010.0000.0000.0000.000
40A382THR00.0330.01425.583-0.002-0.0020.0000.0000.0000.000
41A383SER0-0.018-0.01426.005-0.003-0.0030.0000.0000.0000.000
42A384ILE00.0250.01528.5770.0020.0020.0000.0000.0000.000
43A385PHE00.0000.01323.3270.0020.0020.0000.0000.0000.000
44A386GLN0-0.043-0.00924.004-0.004-0.0040.0000.0000.0000.000
45A388GLN00.0230.02319.081-0.003-0.0030.0000.0000.0000.000
46A389VAL00.0270.01913.5320.0100.0100.0000.0000.0000.000
47A390ARG10.8010.88115.337-0.109-0.1090.0000.0000.0000.000
48A391GLN0-0.020-0.01012.6930.0200.0200.0000.0000.0000.000
49A392LEU0-0.029-0.01414.482-0.015-0.0150.0000.0000.0000.000
50A393ASN00.004-0.00214.6520.0120.0120.0000.0000.0000.000
51A394TRP00.0840.00414.6250.0010.0010.0000.0000.0000.000
52A395GLN00.0100.02216.252-0.010-0.0100.0000.0000.0000.000
53A396GLU-1-0.838-0.93418.5140.1040.1040.0000.0000.0000.000
54A397LEU0-0.040-0.01112.768-0.005-0.0050.0000.0000.0000.000
55A398GLN0-0.024-0.03216.964-0.012-0.0120.0000.0000.0000.000
56A399GLN0-0.060-0.01319.327-0.010-0.0100.0000.0000.0000.000
57A400THR0-0.051-0.02517.637-0.003-0.0030.0000.0000.0000.000
58A401PRO00.0330.03020.672-0.004-0.0040.0000.0000.0000.000
59A402HIS10.7610.87420.417-0.078-0.0780.0000.0000.0000.000
60A403PRO00.0240.01917.6340.0080.0080.0000.0000.0000.000
61A404LEU0-0.0070.01214.701-0.003-0.0030.0000.0000.0000.000
62A405LEU0-0.047-0.00510.4950.0210.0210.0000.0000.0000.000
63A406LEU00.0110.0048.400-0.045-0.0450.0000.0000.0000.000
64A407THR0-0.044-0.0495.7080.1680.1680.0000.0000.0000.000
65A408LEU0-0.015-0.0102.207-1.159-0.4681.844-0.725-1.8100.003
66A409GLN0-0.035-0.0522.603-3.978-1.7511.553-1.407-2.373-0.019
67A410HIS00.009-0.0082.531-6.341-2.2236.023-3.249-6.892-0.003
68A411GLU-1-0.900-0.9454.3093.1193.5500.008-0.011-0.4290.001
69A412GLY0-0.0150.0027.010-0.447-0.4470.0000.0000.0000.000
70A413GLN0-0.0250.0022.087-10.815-10.3785.729-2.227-3.939-0.016
71A414ARG10.7810.8492.449-0.3651.1471.111-0.725-1.898-0.004
72A415ALA00.0260.0322.737-1.891-0.2702.182-0.768-3.0350.000
73A416TYR0-0.0240.0023.833-0.953-0.7710.0040.062-0.2480.000
74A417VAL00.0440.0316.9910.0540.0540.0000.0000.0000.000
75A418VAL00.0040.0079.103-0.109-0.1090.0000.0000.0000.000
76A419LEU00.0010.01512.527-0.011-0.0110.0000.0000.0000.000
77A420LEU0-0.033-0.02813.680-0.013-0.0130.0000.0000.0000.000
78A421GLU-1-0.852-0.94516.8350.0000.0000.0000.0000.0000.000
79A422VAL00.0120.00416.4420.0010.0010.0000.0000.0000.000
80A423ASP-1-0.779-0.85518.064-0.004-0.0040.0000.0000.0000.000
81A424PRO00.006-0.02318.7350.0000.0000.0000.0000.0000.000
82A425GLU-1-0.939-0.96119.109-0.014-0.0140.0000.0000.0000.000
83A426ARG10.7450.85315.761-0.017-0.0170.0000.0000.0000.000
84A427VAL0-0.008-0.00611.6830.0240.0240.0000.0000.0000.000
85A428VAL0-0.046-0.01414.312-0.031-0.0310.0000.0000.0000.000
86A429LEU0-0.007-0.0158.8040.0400.0400.0000.0000.0000.000
87A430LEU0-0.010-0.00812.766-0.049-0.0490.0000.0000.0000.000
88A431THR00.0530.0229.4560.0420.0420.0000.0000.0000.000
89A432GLY00.000-0.02411.7430.0610.0610.0000.0000.0000.000
90A433GLU-1-0.878-0.92613.044-0.094-0.0940.0000.0000.0000.000
91A434GLN0-0.011-0.01111.013-0.036-0.0360.0000.0000.0000.000
92A435ARG10.8950.94513.6230.0590.0590.0000.0000.0000.000
93A436LEU0-0.031-0.0198.861-0.045-0.0450.0000.0000.0000.000
94A437THR00.0100.01212.7410.0530.0530.0000.0000.0000.000
95A438PHE0-0.034-0.0095.7130.0090.0090.0000.0000.0000.000
96A439THR00.0700.01511.9680.0690.0690.0000.0000.0000.000
97A440VAL00.0350.01612.236-0.017-0.0170.0000.0000.0000.000
98A441SER00.006-0.00112.3440.0330.0330.0000.0000.0000.000
99A442GLN0-0.0010.0158.7840.1930.1930.0000.0000.0000.000
100A443LEU00.0240.0227.712-0.094-0.0940.0000.0000.0000.000
101A444MET0-0.017-0.0187.8400.0550.0550.0000.0000.0000.000
102A445SER0-0.094-0.0347.1860.0030.0030.0000.0000.0000.000
103A446LEU00.0170.0112.315-1.1690.0042.257-0.657-2.7730.000
104A447TRP0-0.058-0.0184.286-0.2000.033-0.001-0.046-0.1860.000
105A448ARG10.9160.9566.307-1.271-1.2710.0000.0000.0000.000
106A449GLY00.0860.0359.092-0.014-0.0140.0000.0000.0000.000
107A450GLU-1-0.744-0.7999.5370.1590.1590.0000.0000.0000.000
108A451VAL00.0160.01810.2810.0260.0260.0000.0000.0000.000
109A452THR0-0.018-0.01912.148-0.022-0.0220.0000.0000.0000.000
110A453ASP-1-0.747-0.83214.4150.1010.1010.0000.0000.0000.000
111A454LEU00.0410.00717.811-0.007-0.0070.0000.0000.0000.000
112A455TRP0-0.024-0.00920.3430.0030.0030.0000.0000.0000.000
113A456PRO00.0000.01423.867-0.002-0.0020.0000.0000.0000.000
114A457MET0-0.043-0.00727.2900.0020.0020.0000.0000.0000.000
115A458PRO00.0460.01729.555-0.001-0.0010.0000.0000.0000.000
116A459LEU00.0330.02332.845-0.002-0.0020.0000.0000.0000.000
117A460ARG10.8280.88327.422-0.030-0.0300.0000.0000.0000.000
118A461GLU-1-0.912-0.95334.1520.0180.0180.0000.0000.0000.000
119A462THR0-0.088-0.05337.6810.0010.0010.0000.0000.0000.000
120A463LEU00.0290.02539.445-0.002-0.0020.0000.0000.0000.000
121A464ARG10.9370.94342.129-0.018-0.0180.0000.0000.0000.000
122A465LEU00.0310.00845.346-0.001-0.0010.0000.0000.0000.000
123A466GLY0-0.020-0.00548.6610.0000.0000.0000.0000.0000.000
124A467MET0-0.0450.01243.5080.0000.0000.0000.0000.0000.000
125A468HIS0-0.019-0.00447.6070.0000.0000.0000.0000.0000.000
126A469GLY00.0750.03345.6340.0000.0000.0000.0000.0000.000
127A470GLU-1-0.855-0.93740.2450.0100.0100.0000.0000.0000.000
128A471ALA0-0.037-0.03039.8650.0010.0010.0000.0000.0000.000
129A472ILE0-0.029-0.01140.3160.0020.0020.0000.0000.0000.000
130A473GLU-1-0.802-0.87142.4910.0090.0090.0000.0000.0000.000
131A474VAL0-0.037-0.02736.1510.0010.0010.0000.0000.0000.000
132A475LEU0-0.021-0.00938.0200.0020.0020.0000.0000.0000.000
133A476ASP-1-0.743-0.86239.0380.0140.0140.0000.0000.0000.000
134A477GLN0-0.010-0.01438.2590.0000.0000.0000.0000.0000.000
135A478LEU0-0.048-0.03132.7140.0010.0010.0000.0000.0000.000
136A479LEU0-0.006-0.00635.7260.0020.0020.0000.0000.0000.000
137A480ALA00.0240.01537.9890.0010.0010.0000.0000.0000.000
138A481LYS10.8830.96431.377-0.023-0.0230.0000.0000.0000.000
139A482ALA0-0.081-0.05733.5960.0010.0010.0000.0000.0000.000
140A483LEU0-0.046-0.02934.5750.0010.0010.0000.0000.0000.000
141A484ASN0-0.089-0.02635.023-0.002-0.0020.0000.0000.0000.000
142A485ASP-1-0.762-0.84837.9470.0150.0150.0000.0000.0000.000
143A486GLU-1-0.877-0.93941.1220.0090.0090.0000.0000.0000.000
144A487PRO0-0.055-0.02141.9720.0010.0010.0000.0000.0000.000
145A488LEU00.002-0.02243.786-0.001-0.0010.0000.0000.0000.000
146A489LYS10.7160.86845.594-0.010-0.0100.0000.0000.0000.000
147A490THR00.0000.00146.272-0.001-0.0010.0000.0000.0000.000
148A491THR0-0.010-0.02846.1220.0010.0010.0000.0000.0000.000
149A492GLN0-0.015-0.01747.6760.0010.0010.0000.0000.0000.000
150A493PHE00.0070.01842.8040.0000.0000.0000.0000.0000.000
151A494ASN00.0480.02147.6140.0010.0010.0000.0000.0000.000
152A495ALA00.055-0.00149.1470.0010.0010.0000.0000.0000.000
153A496GLU-1-0.891-0.93948.6120.0120.0120.0000.0000.0000.000
154A497LEU00.014-0.00443.0120.0010.0010.0000.0000.0000.000
155A498MET0-0.051-0.01044.7550.0010.0010.0000.0000.0000.000
156A499GLN0-0.042-0.01845.3610.0000.0000.0000.0000.0000.000
157A500ARG10.8090.87841.916-0.015-0.0150.0000.0000.0000.000
158A501VAL0-0.032-0.01340.2750.0020.0020.0000.0000.0000.000
159A502GLU-1-0.822-0.91340.7060.0210.0210.0000.0000.0000.000
160A503TRP0-0.0110.00740.7630.0010.0010.0000.0000.0000.000
161A504PHE00.002-0.00332.8130.0020.0020.0000.0000.0000.000
162A505GLN0-0.022-0.03437.1950.0010.0010.0000.0000.0000.000
163A506ARG10.8750.92737.934-0.023-0.0230.0000.0000.0000.000
164A507TRP0-0.017-0.00733.1500.0020.0020.0000.0000.0000.000
165A508GLN0-0.0060.00731.6590.0050.0050.0000.0000.0000.000
166A509ALA00.0040.01634.0260.0030.0030.0000.0000.0000.000
167A510MET0-0.107-0.06334.0830.0040.0040.0000.0000.0000.000
168A511THR00.018-0.00337.181-0.001-0.0010.0000.0000.0000.000
169A512GLU-1-0.835-0.89640.6410.0260.0260.0000.0000.0000.000
170A513ASP-1-0.873-0.92642.3280.0250.0250.0000.0000.0000.000
171A514GLY00.0520.02543.346-0.001-0.0010.0000.0000.0000.000
172A515ILE0-0.052-0.03241.856-0.001-0.0010.0000.0000.0000.000
173A516ALA00.0190.00738.8570.0020.0020.0000.0000.0000.000
174A517GLY00.0430.01138.358-0.001-0.0010.0000.0000.0000.000
175A518GLN00.0270.00830.6470.0000.0000.0000.0000.0000.000
176A519ARG10.9420.97532.187-0.042-0.0420.0000.0000.0000.000
177A520THR00.0180.00632.8730.0030.0030.0000.0000.0000.000
178A521LEU00.0570.02734.0520.0010.0010.0000.0000.0000.000
179A522ALA0-0.051-0.01529.1300.0010.0010.0000.0000.0000.000
180A523ARG10.8630.92328.949-0.043-0.0430.0000.0000.0000.000
181A524LEU00.0290.01129.7560.0010.0010.0000.0000.0000.000
182A525GLN0-0.011-0.02429.765-0.001-0.0010.0000.0000.0000.000
183A526HIS0-0.105-0.05021.593-0.003-0.0030.0000.0000.0000.000
184A527MET0-0.029-0.01425.7040.0030.0030.0000.0000.0000.000
185A528VAL0-0.0220.00127.792-0.001-0.0010.0000.0000.0000.000
186A529SER0-0.035-0.03027.8470.0020.0020.0000.0000.0000.000
187A530LEU00.0230.00530.170-0.001-0.0010.0000.0000.0000.000
188A531SER0-0.005-0.00131.049-0.002-0.0020.0000.0000.0000.000
189A532GLU-1-0.769-0.88127.0420.0320.0320.0000.0000.0000.000
190A533PRO00.0320.01326.707-0.001-0.0010.0000.0000.0000.000
191A534TRP00.0510.03022.142-0.002-0.0020.0000.0000.0000.000
192A535ARG10.8850.93023.650-0.030-0.0300.0000.0000.0000.000
193A536ALA00.0150.01525.927-0.004-0.0040.0000.0000.0000.000
194A537LEU00.0110.00920.695-0.005-0.0050.0000.0000.0000.000
195A538THR0-0.092-0.04121.805-0.003-0.0030.0000.0000.0000.000
196A539GLN00.033-0.02023.608-0.009-0.0090.0000.0000.0000.000
197A540ALA0-0.0310.00126.074-0.003-0.0030.0000.0000.0000.000
198A541GLU-1-0.807-0.87527.531-0.019-0.0190.0000.0000.0000.000
199A542LYS10.7920.88724.8760.0130.0130.0000.0000.0000.000
200A543GLN0-0.088-0.05629.390-0.003-0.0030.0000.0000.0000.000
201A544GLY00.0090.02432.7910.0030.0030.0000.0000.0000.000
202A546GLU-1-0.895-0.91628.855-0.037-0.0370.0000.0000.0000.000
203A547GLU-1-0.960-0.99625.253-0.047-0.0470.0000.0000.0000.000
204A548GLN00.002-0.01323.7820.0040.0040.0000.0000.0000.000
205A549VAL00.0180.00827.529-0.003-0.0030.0000.0000.0000.000
206A550MET0-0.036-0.00925.647-0.003-0.0030.0000.0000.0000.000
207A551ARG10.9030.95222.0680.0550.0550.0000.0000.0000.000
208A552TYR0-0.018-0.01115.6460.0100.0100.0000.0000.0000.000
209A553PRO0-0.036-0.02617.683-0.011-0.0110.0000.0000.0000.000
210A554GLU-1-0.919-0.95719.739-0.036-0.0360.0000.0000.0000.000
211A555PHE0-0.017-0.02819.7780.0080.0080.0000.0000.0000.000
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