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: JQG19

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2886573.521377
FMO2-HF: Nuclear repulsion 2793199.204594
FMO2-HF: Total energy -93374.316783
FMO2-MP2: Total energy -93644.568121


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.
-30.083-8.37119-12.11-28.6-0.023
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 : -0.009 / q_NPA : -0.030
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].
3A345GLY00.0040.0032.783-2.960-0.4310.307-1.334-1.501-0.007
4A346GLU-1-0.885-0.9383.865-1.996-1.4520.001-0.106-0.4390.000
5A347SER0-0.004-0.0172.258-2.3790.2361.833-2.116-2.331-0.001
6A348ALA00.0360.0223.0411.8981.0350.0581.124-0.3190.000
7A349VAL0-0.011-0.0033.633-0.1170.2170.003-0.039-0.2990.000
8A350ALA0-0.061-0.0352.939-2.194-0.1752.174-0.968-3.2250.008
9A351ARG10.9290.9924.990-1.273-1.077-0.001-0.030-0.1640.000
10A352MET0-0.071-0.0037.839-0.430-0.4300.0000.0000.0000.000
11A353THR00.0600.0145.5730.4300.4300.0000.0000.0000.000
12A354THR0-0.023-0.0066.921-0.083-0.0830.0000.0000.0000.000
13A355ARG10.9420.9509.700-0.028-0.0280.0000.0000.0000.000
14A356ALA00.0350.02611.2580.0150.0150.0000.0000.0000.000
15A357GLN00.0440.01810.776-0.015-0.0150.0000.0000.0000.000
16A358GLY00.029-0.01011.5950.0170.0170.0000.0000.0000.000
17A359LEU00.009-0.01312.390-0.008-0.0080.0000.0000.0000.000
18A360GLU-1-0.960-0.96815.567-0.064-0.0640.0000.0000.0000.000
19A361GLU-1-0.788-0.89614.872-0.015-0.0150.0000.0000.0000.000
20A362LEU0-0.012-0.01115.691-0.009-0.0090.0000.0000.0000.000
21A363TYR00.014-0.01417.500-0.010-0.0100.0000.0000.0000.000
22A364LYS10.8960.97118.7770.0320.0320.0000.0000.0000.000
23A365LEU0-0.0190.00318.416-0.006-0.0060.0000.0000.0000.000
24A366TRP0-0.033-0.02220.947-0.007-0.0070.0000.0000.0000.000
25A367GLY00.0060.00624.384-0.002-0.0020.0000.0000.0000.000
26A368TYR0-0.032-0.02224.666-0.004-0.0040.0000.0000.0000.000
27A369ARG10.9520.97923.7440.0400.0400.0000.0000.0000.000
28A370ALA0-0.019-0.00221.1920.0010.0010.0000.0000.0000.000
29A371THR0-0.036-0.03322.944-0.008-0.0080.0000.0000.0000.000
30A372ARG11.0030.97020.1860.0890.0890.0000.0000.0000.000
31A373ILE00.0520.02521.2760.0010.0010.0000.0000.0000.000
32A374ASP-1-0.726-0.81722.505-0.010-0.0100.0000.0000.0000.000
33A375THR0-0.058-0.03217.1520.0070.0070.0000.0000.0000.000
34A376MET0-0.006-0.00317.0860.0000.0000.0000.0000.0000.000
35A377CYS0-0.100-0.04017.1830.0140.0140.0000.0000.0000.000
36A378GLU-1-0.879-0.93019.1490.0050.0050.0000.0000.0000.000
37A379GLN0-0.051-0.00621.8300.0010.0010.0000.0000.0000.000
38A380PRO0-0.015-0.03225.1960.0000.0000.0000.0000.0000.000
39A381SER00.0310.01225.855-0.001-0.0010.0000.0000.0000.000
40A382THR00.0550.03325.5750.0000.0000.0000.0000.0000.000
41A383SER0-0.030-0.01626.049-0.003-0.0030.0000.0000.0000.000
42A384ILE00.0250.01528.6800.0030.0030.0000.0000.0000.000
43A385PHE0-0.0020.00823.3080.0020.0020.0000.0000.0000.000
44A386GLN0-0.073-0.03024.064-0.001-0.0010.0000.0000.0000.000
45A388GLN00.0410.04119.204-0.001-0.0010.0000.0000.0000.000
46A389VAL00.0180.01213.8040.0040.0040.0000.0000.0000.000
47A390ARG10.8270.89215.459-0.069-0.0690.0000.0000.0000.000
48A391GLN0-0.011-0.00412.7640.0170.0170.0000.0000.0000.000
49A392LEU0-0.024-0.01214.570-0.011-0.0110.0000.0000.0000.000
50A393ASN00.0300.02014.7170.0070.0070.0000.0000.0000.000
51A394TRP00.0750.00014.686-0.003-0.0030.0000.0000.0000.000
52A395GLN00.0080.01416.301-0.013-0.0130.0000.0000.0000.000
53A396GLU-1-0.886-0.96718.6340.0720.0720.0000.0000.0000.000
54A397LEU0-0.038-0.00712.946-0.005-0.0050.0000.0000.0000.000
55A398GLN0-0.015-0.02217.056-0.013-0.0130.0000.0000.0000.000
56A399GLN0-0.028-0.00119.410-0.009-0.0090.0000.0000.0000.000
57A400THR0-0.070-0.03717.7800.0020.0020.0000.0000.0000.000
58A401PRO00.0320.03320.791-0.005-0.0050.0000.0000.0000.000
59A402HIS10.7570.86720.298-0.037-0.0370.0000.0000.0000.000
60A403PRO00.0190.01117.8190.0060.0060.0000.0000.0000.000
61A404LEU0-0.0020.02214.7440.0020.0020.0000.0000.0000.000
62A405LEU0-0.051-0.01410.4890.0100.0100.0000.0000.0000.000
63A406LEU00.0130.0098.534-0.030-0.0300.0000.0000.0000.000
64A407THR0-0.054-0.0635.7910.1390.1390.0000.0000.0000.000
65A408LEU0-0.015-0.0112.331-1.178-0.2421.136-0.546-1.5250.002
66A409GLN0-0.047-0.0632.741-3.612-1.3031.004-1.283-2.030-0.016
67A410HIS00.0310.0202.589-6.418-2.7436.954-3.461-7.168-0.003
68A411GLU-1-0.934-0.9714.2373.4423.8020.0090.012-0.3810.001
69A412GLY0-0.0140.0047.055-0.344-0.3440.0000.0000.0000.000
70A413GLN0-0.037-0.0062.468-6.619-4.7811.702-1.323-2.216-0.002
71A414ARG10.8410.9032.570-0.4821.0120.683-0.607-1.571-0.003
72A415ALA00.0180.0282.849-2.392-0.4981.571-0.844-2.621-0.001
73A416TYR0-0.0190.0073.864-0.725-0.5470.0030.043-0.2240.000
74A417VAL00.0410.0277.0340.0400.0400.0000.0000.0000.000
75A418VAL00.0070.0099.257-0.085-0.0850.0000.0000.0000.000
76A419LEU0-0.0010.01312.645-0.019-0.0190.0000.0000.0000.000
77A420LEU0-0.035-0.02613.813-0.004-0.0040.0000.0000.0000.000
78A421GLU-1-0.901-0.97716.935-0.046-0.0460.0000.0000.0000.000
79A422VAL0-0.002-0.00416.551-0.009-0.0090.0000.0000.0000.000
80A423ASP-1-0.848-0.90118.152-0.056-0.0560.0000.0000.0000.000
81A424PRO00.005-0.02018.788-0.005-0.0050.0000.0000.0000.000
82A425GLU-1-0.939-0.96919.057-0.062-0.0620.0000.0000.0000.000
83A426ARG10.8450.94515.7600.0330.0330.0000.0000.0000.000
84A427VAL0-0.019-0.03011.7360.0310.0310.0000.0000.0000.000
85A428VAL0-0.0190.00014.355-0.038-0.0380.0000.0000.0000.000
86A429LEU0-0.006-0.0178.9630.0430.0430.0000.0000.0000.000
87A430LEU0-0.010-0.01012.883-0.044-0.0440.0000.0000.0000.000
88A431THR00.0510.0269.4540.0390.0390.0000.0000.0000.000
89A432GLY0-0.008-0.02911.7910.0410.0410.0000.0000.0000.000
90A433GLU-1-0.950-0.97713.019-0.178-0.1780.0000.0000.0000.000
91A434GLN0-0.008-0.00211.115-0.044-0.0440.0000.0000.0000.000
92A435ARG10.9120.94613.5740.1200.1200.0000.0000.0000.000
93A436LEU0-0.028-0.0158.624-0.041-0.0410.0000.0000.0000.000
94A437THR00.0080.00912.6620.0590.0590.0000.0000.0000.000
95A438PHE0-0.030-0.0085.8250.0070.0070.0000.0000.0000.000
96A439THR00.0710.02411.9170.0840.0840.0000.0000.0000.000
97A440VAL00.0450.02012.183-0.034-0.0340.0000.0000.0000.000
98A441SER0-0.032-0.01712.2620.0050.0050.0000.0000.0000.000
99A442GLN00.0370.0238.7520.2060.2060.0000.0000.0000.000
100A443LEU00.0320.0287.620-0.154-0.1540.0000.0000.0000.000
101A444MET0-0.031-0.0207.8430.0280.0280.0000.0000.0000.000
102A445SER0-0.095-0.0347.1030.0020.0020.0000.0000.0000.000
103A446LEU00.0260.0202.400-1.4140.0131.564-0.589-2.403-0.001
104A447TRP0-0.050-0.0234.298-0.1380.089-0.001-0.043-0.1830.000
105A448ARG10.9200.9546.795-1.135-1.1350.0000.0000.0000.000
106A449GLY00.0730.0269.1160.0050.0050.0000.0000.0000.000
107A450GLU-1-0.799-0.8509.6280.1430.1430.0000.0000.0000.000
108A451VAL00.0120.01310.4030.0110.0110.0000.0000.0000.000
109A452THR0-0.029-0.01712.429-0.010-0.0100.0000.0000.0000.000
110A453ASP-1-0.733-0.81914.5290.0530.0530.0000.0000.0000.000
111A454LEU00.0420.01417.914-0.003-0.0030.0000.0000.0000.000
112A455TRP0-0.023-0.00620.4350.0000.0000.0000.0000.0000.000
113A456PRO00.0030.01323.9540.0000.0000.0000.0000.0000.000
114A457MET0-0.024-0.00627.3770.0030.0030.0000.0000.0000.000
115A458PRO00.0390.01129.6550.0000.0000.0000.0000.0000.000
116A459LEU00.0320.02232.942-0.001-0.0010.0000.0000.0000.000
117A460ARG10.8420.90327.556-0.010-0.0100.0000.0000.0000.000
118A461GLU-1-0.918-0.95434.2710.0080.0080.0000.0000.0000.000
119A462THR0-0.088-0.05537.8050.0000.0000.0000.0000.0000.000
120A463LEU00.0340.03239.616-0.001-0.0010.0000.0000.0000.000
121A464ARG10.9440.94342.245-0.010-0.0100.0000.0000.0000.000
122A465LEU00.0320.01245.463-0.001-0.0010.0000.0000.0000.000
123A466GLY0-0.024-0.00848.7730.0000.0000.0000.0000.0000.000
124A467MET0-0.0440.00543.7770.0000.0000.0000.0000.0000.000
125A468HIS0-0.021-0.00747.659-0.001-0.0010.0000.0000.0000.000
126A469GLY00.0730.03545.7330.0000.0000.0000.0000.0000.000
127A470GLU-1-0.866-0.94040.447-0.005-0.0050.0000.0000.0000.000
128A471ALA0-0.040-0.02739.9460.0000.0000.0000.0000.0000.000
129A472ILE0-0.031-0.01540.4120.0010.0010.0000.0000.0000.000
130A473GLU-1-0.819-0.89742.580-0.004-0.0040.0000.0000.0000.000
131A474VAL0-0.043-0.02636.1850.0000.0000.0000.0000.0000.000
132A475LEU0-0.025-0.01438.1740.0010.0010.0000.0000.0000.000
133A476ASP-1-0.747-0.86539.1860.0000.0000.0000.0000.0000.000
134A477GLN00.000-0.00638.399-0.001-0.0010.0000.0000.0000.000
135A478LEU0-0.056-0.03232.9710.0000.0000.0000.0000.0000.000
136A479LEU0-0.002-0.00735.8690.0010.0010.0000.0000.0000.000
137A480ALA00.0170.01038.1300.0000.0000.0000.0000.0000.000
138A481LYS10.9180.98431.6710.0040.0040.0000.0000.0000.000
139A482ALA0-0.082-0.06033.7260.0000.0000.0000.0000.0000.000
140A483LEU0-0.056-0.03234.7090.0010.0010.0000.0000.0000.000
141A484ASN0-0.090-0.03035.122-0.002-0.0020.0000.0000.0000.000
142A485ASP-1-0.733-0.83738.0750.0000.0000.0000.0000.0000.000
143A486GLU-1-0.943-0.97741.259-0.007-0.0070.0000.0000.0000.000
144A487PRO0-0.064-0.02742.0540.0010.0010.0000.0000.0000.000
145A488LEU0-0.015-0.01943.9310.0000.0000.0000.0000.0000.000
146A489LYS10.8280.91345.7590.0060.0060.0000.0000.0000.000
147A490THR0-0.008-0.00346.3210.0000.0000.0000.0000.0000.000
148A491THR00.0040.01046.2320.0000.0000.0000.0000.0000.000
149A492GLN0-0.009-0.02747.7700.0010.0010.0000.0000.0000.000
150A493PHE00.0010.01842.9630.0000.0000.0000.0000.0000.000
151A494ASN00.0510.02047.7150.0010.0010.0000.0000.0000.000
152A495ALA00.043-0.00549.2890.0010.0010.0000.0000.0000.000
153A496GLU-1-0.886-0.94348.6690.0010.0010.0000.0000.0000.000
154A497LEU00.0260.00643.2200.0000.0000.0000.0000.0000.000
155A498MET0-0.047-0.00944.8930.0000.0000.0000.0000.0000.000
156A499GLN0-0.0090.00845.4930.0000.0000.0000.0000.0000.000
157A500ARG10.8190.88941.821-0.001-0.0010.0000.0000.0000.000
158A501VAL0-0.033-0.01540.3780.0010.0010.0000.0000.0000.000
159A502GLU-1-0.862-0.93940.8340.0110.0110.0000.0000.0000.000
160A503TRP0-0.0190.00440.8610.0010.0010.0000.0000.0000.000
161A504PHE00.006-0.00132.9520.0010.0010.0000.0000.0000.000
162A505GLN0-0.033-0.02537.3140.0010.0010.0000.0000.0000.000
163A506ARG10.9560.99038.046-0.012-0.0120.0000.0000.0000.000
164A507TRP0-0.038-0.02033.2830.0020.0020.0000.0000.0000.000
165A508GLN00.0030.01131.6550.0040.0040.0000.0000.0000.000
166A509ALA0-0.0090.01234.1320.0030.0030.0000.0000.0000.000
167A510MET0-0.091-0.04634.3170.0030.0030.0000.0000.0000.000
168A511THR00.009-0.02137.289-0.001-0.0010.0000.0000.0000.000
169A512GLU-1-0.902-0.95340.7510.0150.0150.0000.0000.0000.000
170A513ASP-1-0.884-0.94342.5690.0150.0150.0000.0000.0000.000
171A514GLY00.0460.02343.495-0.001-0.0010.0000.0000.0000.000
172A515ILE0-0.061-0.03241.866-0.001-0.0010.0000.0000.0000.000
173A516ALA00.0130.00738.9560.0010.0010.0000.0000.0000.000
174A517GLY00.0380.00338.4830.0000.0000.0000.0000.0000.000
175A518GLN00.0200.00830.7700.0000.0000.0000.0000.0000.000
176A519ARG10.9810.97831.885-0.030-0.0300.0000.0000.0000.000
177A520THR00.0220.01833.0020.0010.0010.0000.0000.0000.000
178A521LEU00.0560.02434.1880.0000.0000.0000.0000.0000.000
179A522ALA0-0.052-0.01529.1850.0000.0000.0000.0000.0000.000
180A523ARG10.8500.91828.968-0.027-0.0270.0000.0000.0000.000
181A524LEU00.0400.02129.8910.0000.0000.0000.0000.0000.000
182A525GLN0-0.006-0.02129.854-0.003-0.0030.0000.0000.0000.000
183A526HIS0-0.116-0.06021.747-0.003-0.0030.0000.0000.0000.000
184A527MET0-0.040-0.01725.8450.0010.0010.0000.0000.0000.000
185A528VAL0-0.0010.01827.930-0.002-0.0020.0000.0000.0000.000
186A529SER0-0.018-0.00927.8760.0020.0020.0000.0000.0000.000
187A530LEU00.006-0.01530.323-0.002-0.0020.0000.0000.0000.000
188A531SER0-0.021-0.01531.201-0.002-0.0020.0000.0000.0000.000
189A532GLU-1-0.820-0.90027.0950.0020.0020.0000.0000.0000.000
190A533PRO00.0320.01726.784-0.002-0.0020.0000.0000.0000.000
191A534TRP00.0620.03922.234-0.004-0.0040.0000.0000.0000.000
192A535ARG10.8970.92623.7880.0030.0030.0000.0000.0000.000
193A536ALA00.0120.00926.062-0.004-0.0040.0000.0000.0000.000
194A537LEU00.0040.00720.545-0.005-0.0050.0000.0000.0000.000
195A538THR0-0.087-0.03721.941-0.006-0.0060.0000.0000.0000.000
196A539GLN00.058-0.01523.724-0.009-0.0090.0000.0000.0000.000
197A540ALA0-0.093-0.01325.588-0.001-0.0010.0000.0000.0000.000
198A541GLU-1-0.782-0.86927.318-0.051-0.0510.0000.0000.0000.000
199A542LYS10.8060.89324.6660.0540.0540.0000.0000.0000.000
200A543GLN0-0.069-0.05329.243-0.001-0.0010.0000.0000.0000.000
201A544GLY00.0080.02632.6520.0040.0040.0000.0000.0000.000
202A546GLU-1-0.941-0.94128.757-0.068-0.0680.0000.0000.0000.000
203A547GLU-1-0.958-0.98725.245-0.090-0.0900.0000.0000.0000.000
204A548GLN00.000-0.02623.4870.0070.0070.0000.0000.0000.000
205A549VAL00.0240.01727.461-0.002-0.0020.0000.0000.0000.000
206A550MET0-0.049-0.01225.715-0.002-0.0020.0000.0000.0000.000
207A551ARG10.9230.96521.8330.1020.1020.0000.0000.0000.000
208A552TYR0-0.027-0.00615.5380.0060.0060.0000.0000.0000.000
209A553PRO0-0.018-0.02117.672-0.009-0.0090.0000.0000.0000.000
210A554GLU-1-0.921-0.95519.705-0.092-0.0920.0000.0000.0000.000
211A555PHE0-0.028-0.03319.9150.0080.0080.0000.0000.0000.000
212A556PRO00.0100.01125.266-0.005-0.0050.0000.0000.0000.000
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