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: 7GKRK

Calculation Name: 4GHU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VCF0

Base Structure: X-ray

Registration Date: 2023-03-14

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1976233.867334
FMO2-HF: Nuclear repulsion 1899363.088191
FMO2-HF: Total energy -76870.779143
FMO2-MP2: Total energy -77090.582991


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:376:ASN)


Summations of interaction energy for fragment #1(A:376:ASN)
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.
-17.105-11.6174.592-3.463-6.6190.024
Interaction energy analysis for fragmet #1(A:376:ASN)
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 : -0.010
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].
3A378GLY00.0980.0723.019-3.849-1.4280.186-1.113-1.4950.004
4A379LEU0-0.011-0.0142.355-10.822-8.4664.396-2.128-4.6240.020
5A380LEU0-0.018-0.0123.560-2.691-1.9800.010-0.222-0.5000.000
6A381GLU-1-0.916-0.9616.0952.6372.6370.0000.0000.0000.000
7A382SER0-0.017-0.0096.955-0.916-0.9160.0000.0000.0000.000
8A383GLN0-0.051-0.0338.071-0.610-0.6100.0000.0000.0000.000
9A384LEU00.0420.02510.124-0.195-0.1950.0000.0000.0000.000
10A385SER00.0150.02211.626-0.216-0.2160.0000.0000.0000.000
11A386ARG10.9250.96312.493-0.458-0.4580.0000.0000.0000.000
12A387HIS0-0.047-0.03013.362-0.066-0.0660.0000.0000.0000.000
13A388ASP-1-0.900-0.93516.0340.4970.4970.0000.0000.0000.000
14A389GLN00.0180.00016.887-0.053-0.0530.0000.0000.0000.000
15A390MET0-0.059-0.03018.926-0.062-0.0620.0000.0000.0000.000
16A391LEU0-0.002-0.01119.165-0.045-0.0450.0000.0000.0000.000
17A392SER00.0400.03021.970-0.029-0.0290.0000.0000.0000.000
18A393VAL0-0.049-0.02323.461-0.030-0.0300.0000.0000.0000.000
19A394HIS0-0.033-0.03923.719-0.016-0.0160.0000.0000.0000.000
20A395ASP-1-0.886-0.93426.2500.1890.1890.0000.0000.0000.000
21A396ILE00.0020.01027.613-0.012-0.0120.0000.0000.0000.000
22A397ARG10.8920.94327.737-0.112-0.1120.0000.0000.0000.000
23A398LEU00.003-0.00829.124-0.016-0.0160.0000.0000.0000.000
24A399ALA00.0650.04932.284-0.009-0.0090.0000.0000.0000.000
25A400ASP-1-0.911-0.96434.1240.1220.1220.0000.0000.0000.000
26A401MET0-0.119-0.07333.117-0.013-0.0130.0000.0000.0000.000
27A402ASP-1-0.858-0.91036.2930.0940.0940.0000.0000.0000.000
28A403LEU0-0.045-0.02638.094-0.007-0.0070.0000.0000.0000.000
29A404ARG10.9080.95338.152-0.064-0.0640.0000.0000.0000.000
30A405PHE00.0330.01138.148-0.008-0.0080.0000.0000.0000.000
31A406GLN00.0230.02542.523-0.004-0.0040.0000.0000.0000.000
32A407VAL0-0.036-0.01744.527-0.004-0.0040.0000.0000.0000.000
33A408LEU0-0.046-0.02644.168-0.004-0.0040.0000.0000.0000.000
34A409GLU-1-0.955-0.97645.1190.0520.0520.0000.0000.0000.000
35A410THR0-0.125-0.06048.519-0.002-0.0020.0000.0000.0000.000
36A411ALA00.0170.02050.2050.0000.0000.0000.0000.0000.000
37A412SER0-0.058-0.05151.988-0.003-0.0030.0000.0000.0000.000
38A413TYR00.030-0.00950.6020.0010.0010.0000.0000.0000.000
39A414ASN00.0470.02657.257-0.001-0.0010.0000.0000.0000.000
40A415GLY00.0430.02359.773-0.001-0.0010.0000.0000.0000.000
41A416VAL0-0.039-0.01060.5200.0010.0010.0000.0000.0000.000
42A417LEU00.0090.04054.8970.0000.0000.0000.0000.0000.000
43A418ILE0-0.011-0.02457.360-0.001-0.0010.0000.0000.0000.000
44A419TRP00.0410.01351.9650.0000.0000.0000.0000.0000.000
45A420LYS10.9460.98253.239-0.061-0.0610.0000.0000.0000.000
46A421ILE0-0.0080.00053.0600.0030.0030.0000.0000.0000.000
47A422ARG11.0080.99050.304-0.077-0.0770.0000.0000.0000.000
48A423ASP-1-0.821-0.88549.1340.0930.0930.0000.0000.0000.000
49A424TYR0-0.041-0.05352.5960.0020.0020.0000.0000.0000.000
50A425LYS10.9410.96855.078-0.072-0.0720.0000.0000.0000.000
51A426ARG10.9010.93146.740-0.104-0.1040.0000.0000.0000.000
52A427ARG10.9520.97946.987-0.089-0.0890.0000.0000.0000.000
53A428LYS10.8690.94652.133-0.069-0.0690.0000.0000.0000.000
54A429GLN00.026-0.00953.0250.0020.0020.0000.0000.0000.000
55A430GLU-1-0.880-0.93447.3780.1130.1130.0000.0000.0000.000
56A431ALA00.0030.01551.0650.0020.0020.0000.0000.0000.000
57A432VAL0-0.060-0.03053.437-0.001-0.0010.0000.0000.0000.000
58A433MET0-0.076-0.03751.1820.0000.0000.0000.0000.0000.000
59A434GLY0-0.005-0.00451.4870.0030.0030.0000.0000.0000.000
60A435LYS10.8910.96346.473-0.115-0.1150.0000.0000.0000.000
61A436THR00.017-0.00247.2430.0040.0040.0000.0000.0000.000
62A437LEU0-0.035-0.00549.052-0.005-0.0050.0000.0000.0000.000
63A438SER0-0.029-0.01051.038-0.005-0.0050.0000.0000.0000.000
64A439LEU0-0.016-0.00949.3540.0040.0040.0000.0000.0000.000
65A440TYR00.0600.00648.999-0.003-0.0030.0000.0000.0000.000
66A441SER0-0.046-0.02250.2510.0020.0020.0000.0000.0000.000
67A442GLN00.0290.01849.2390.0050.0050.0000.0000.0000.000
68A443PRO0-0.004-0.01548.545-0.002-0.0020.0000.0000.0000.000
69A444PHE0-0.042-0.01051.599-0.001-0.0010.0000.0000.0000.000
70A445TYR00.0420.01149.6880.0010.0010.0000.0000.0000.000
71A446THR0-0.009-0.01256.4510.0000.0000.0000.0000.0000.000
72A447GLY00.0750.02658.049-0.002-0.0020.0000.0000.0000.000
73A448TYR0-0.040-0.01954.4400.0010.0010.0000.0000.0000.000
74A449PHE0-0.0110.00152.1360.0010.0010.0000.0000.0000.000
75A450GLY0-0.0050.01255.578-0.001-0.0010.0000.0000.0000.000
76A451TYR0-0.006-0.04955.9120.0010.0010.0000.0000.0000.000
77A452LYS10.9610.98747.358-0.052-0.0520.0000.0000.0000.000
78A453MET0-0.063-0.01054.3590.0000.0000.0000.0000.0000.000
79A454CYS00.0040.00951.3330.0010.0010.0000.0000.0000.000
80A455ALA0-0.0030.01754.482-0.002-0.0020.0000.0000.0000.000
81A456ARG10.9380.96851.273-0.071-0.0710.0000.0000.0000.000
82A457VAL0-0.0070.00254.675-0.003-0.0030.0000.0000.0000.000
83A458TYR00.0470.01954.9590.0040.0040.0000.0000.0000.000
84A459LEU0-0.002-0.00754.148-0.003-0.0030.0000.0000.0000.000
85A460ASN00.0430.01457.278-0.003-0.0030.0000.0000.0000.000
86A461GLY00.0310.03458.943-0.001-0.0010.0000.0000.0000.000
87A462ASP-1-0.918-0.99958.5440.0670.0670.0000.0000.0000.000
88A463GLY00.0230.01760.307-0.003-0.0030.0000.0000.0000.000
89A464MET0-0.015-0.02362.7520.0010.0010.0000.0000.0000.000
90A465GLY00.0390.02864.432-0.001-0.0010.0000.0000.0000.000
91A466LYS10.9000.95957.595-0.071-0.0710.0000.0000.0000.000
92A467GLY0-0.039-0.01961.413-0.001-0.0010.0000.0000.0000.000
93A468THR00.0310.02562.670-0.001-0.0010.0000.0000.0000.000
94A469HIS0-0.043-0.03264.228-0.003-0.0030.0000.0000.0000.000
95A470LEU0-0.0040.02559.8560.0030.0030.0000.0000.0000.000
96A471SER0-0.051-0.04360.165-0.002-0.0020.0000.0000.0000.000
97A472LEU0-0.019-0.01459.2090.0030.0030.0000.0000.0000.000
98A473PHE0-0.029-0.00858.144-0.002-0.0020.0000.0000.0000.000
99A474PHE00.0360.00258.5960.0010.0010.0000.0000.0000.000
100A475VAL00.010-0.00953.4690.0010.0010.0000.0000.0000.000
101A476ILE00.0260.02856.082-0.001-0.0010.0000.0000.0000.000
102A477MET0-0.026-0.02948.6590.0030.0030.0000.0000.0000.000
103A478ARG10.9420.97145.739-0.056-0.0560.0000.0000.0000.000
104A479GLY0-0.021-0.01950.3290.0020.0020.0000.0000.0000.000
105A480GLU-1-0.935-0.97846.5470.0350.0350.0000.0000.0000.000
106A481TYR00.0340.01050.409-0.002-0.0020.0000.0000.0000.000
107A482ASP-1-0.788-0.89353.9870.0340.0340.0000.0000.0000.000
108A483ALA0-0.087-0.04155.271-0.001-0.0010.0000.0000.0000.000
109A484LEU00.001-0.00156.987-0.002-0.0020.0000.0000.0000.000
110A485LEU0-0.0480.00057.370-0.001-0.0010.0000.0000.0000.000
111A486PRO00.0030.00560.8640.0000.0000.0000.0000.0000.000
112A487TRP0-0.0360.00857.3330.0030.0030.0000.0000.0000.000
113A488PRO00.0440.00062.993-0.001-0.0010.0000.0000.0000.000
114A489PHE0-0.035-0.00761.176-0.001-0.0010.0000.0000.0000.000
115A490LYS10.9780.98063.446-0.022-0.0220.0000.0000.0000.000
116A491GLN0-0.006-0.01664.252-0.001-0.0010.0000.0000.0000.000
117A492LYS10.9800.98766.333-0.027-0.0270.0000.0000.0000.000
118A493VAL00.0380.02963.1410.0000.0000.0000.0000.0000.000
119A494THR0-0.052-0.02465.639-0.001-0.0010.0000.0000.0000.000
120A495LEU0-0.029-0.01262.0270.0010.0010.0000.0000.0000.000
121A496MET00.034-0.00963.837-0.001-0.0010.0000.0000.0000.000
122A497LEU00.0000.01062.2470.0020.0020.0000.0000.0000.000
123A498MET0-0.061-0.03563.156-0.002-0.0020.0000.0000.0000.000
124A499ASP-1-0.732-0.83264.9490.0430.0430.0000.0000.0000.000
125A500GLN0-0.102-0.07860.975-0.002-0.0020.0000.0000.0000.000
126A501GLY00.0190.00966.0490.0000.0000.0000.0000.0000.000
127A502SER0-0.042-0.03369.371-0.001-0.0010.0000.0000.0000.000
128A503SER0-0.013-0.01171.783-0.001-0.0010.0000.0000.0000.000
129A504ARG10.8730.95765.786-0.040-0.0400.0000.0000.0000.000
130A505ARG10.9790.97871.384-0.036-0.0360.0000.0000.0000.000
131A506HIS00.013-0.00168.1390.0030.0030.0000.0000.0000.000
132A507LEU00.0070.01967.804-0.001-0.0010.0000.0000.0000.000
133A508GLY00.002-0.02167.6890.0010.0010.0000.0000.0000.000
134A509ASP-1-0.837-0.89868.3420.0350.0350.0000.0000.0000.000
135A510ALA0-0.077-0.03968.2680.0010.0010.0000.0000.0000.000
136A511PHE00.0160.01363.7360.0000.0000.0000.0000.0000.000
137A512LYS10.8900.93268.726-0.027-0.0270.0000.0000.0000.000
138A513PRO0-0.037-0.01165.3340.0000.0000.0000.0000.0000.000
139A514ASP-1-0.829-0.92167.4050.0320.0320.0000.0000.0000.000
140A515PRO0-0.021-0.02066.8280.0010.0010.0000.0000.0000.000
141A516ASN00.0040.00266.845-0.001-0.0010.0000.0000.0000.000
142A517SER00.0150.03063.8560.0020.0020.0000.0000.0000.000
143A518SER00.008-0.01159.918-0.001-0.0010.0000.0000.0000.000
144A519SER0-0.031-0.03859.4310.0010.0010.0000.0000.0000.000
145A520PHE0-0.022-0.00959.6300.0010.0010.0000.0000.0000.000
146A521LYS10.9661.01055.268-0.048-0.0480.0000.0000.0000.000
147A522LYS10.9840.99754.825-0.029-0.0290.0000.0000.0000.000
148A523PRO00.0000.01653.3640.0010.0010.0000.0000.0000.000
149A524THR0-0.030-0.01352.606-0.001-0.0010.0000.0000.0000.000
150A525GLY00.0020.00149.1870.0010.0010.0000.0000.0000.000
151A526GLU-1-0.929-0.97543.7330.0730.0730.0000.0000.0000.000
152A527MET0-0.019-0.00248.249-0.003-0.0030.0000.0000.0000.000
153A528ASN0-0.046-0.02151.5500.0020.0020.0000.0000.0000.000
154A529ILE00.0110.00354.6090.0030.0030.0000.0000.0000.000
155A530ALA0-0.0090.01256.076-0.003-0.0030.0000.0000.0000.000
156A531SER00.0140.00657.7770.0000.0000.0000.0000.0000.000
157A532GLY00.0210.00161.4960.0000.0000.0000.0000.0000.000
158A533CYS0-0.0080.01163.409-0.001-0.0010.0000.0000.0000.000
159A534PRO00.0690.02063.2250.0020.0020.0000.0000.0000.000
160A535VAL00.0240.02664.3020.0020.0020.0000.0000.0000.000
161A536PHE0-0.058-0.00564.606-0.001-0.0010.0000.0000.0000.000
162A537VAL00.0490.02065.008-0.002-0.0020.0000.0000.0000.000
163A538ALA00.0350.02265.9630.0020.0020.0000.0000.0000.000
164A539GLN00.006-0.01861.6680.0000.0000.0000.0000.0000.000
165A540THR00.0180.01665.4090.0000.0000.0000.0000.0000.000
166A541VAL00.0330.01468.2600.0000.0000.0000.0000.0000.000
167A542LEU0-0.030-0.01361.719-0.001-0.0010.0000.0000.0000.000
168A543GLU-1-0.878-0.94061.7430.0650.0650.0000.0000.0000.000
169A544ASN0-0.045-0.00965.3660.0010.0010.0000.0000.0000.000
170A545GLY00.0070.02868.058-0.002-0.0020.0000.0000.0000.000
171A546THR0-0.041-0.04567.4880.0010.0010.0000.0000.0000.000
172A547TYR0-0.009-0.00864.7350.0000.0000.0000.0000.0000.000
173A548ILE0-0.0150.00860.1650.0010.0010.0000.0000.0000.000
174A549LYS10.9470.97361.202-0.048-0.0480.0000.0000.0000.000
175A550ASP-1-0.878-0.94457.5080.0590.0590.0000.0000.0000.000
176A551ASP-1-0.857-0.93054.9200.0790.0790.0000.0000.0000.000
177A552THR0-0.062-0.02955.7330.0040.0040.0000.0000.0000.000
178A553ILE0-0.0050.00057.219-0.003-0.0030.0000.0000.0000.000
179A554PHE00.013-0.00657.2770.0020.0020.0000.0000.0000.000
180A555ILE00.0180.01557.639-0.002-0.0020.0000.0000.0000.000
181A556LYS10.9190.96459.501-0.036-0.0360.0000.0000.0000.000
182A557VAL00.0070.01159.5380.0000.0000.0000.0000.0000.000
183A558ILE0-0.024-0.01461.948-0.001-0.0010.0000.0000.0000.000
184A559VAL0-0.006-0.00661.0940.0000.0000.0000.0000.0000.000
185A560ASP-1-0.879-0.93964.2380.0230.0230.0000.0000.0000.000
186A561THR00.003-0.00762.9300.0000.0000.0000.0000.0000.000
187A562SER0-0.053-0.02766.086-0.001-0.0010.0000.0000.0000.000
188A563ASP-1-0.937-0.96268.4620.0200.0200.0000.0000.0000.000
189A564LEU0-0.0330.00163.986-0.001-0.0010.0000.0000.0000.000
190A565PRO0-0.0080.00464.0230.0000.0000.0000.0000.0000.000