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: 5341Z

Calculation Name: 3KEY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KEY

Chain ID: A

ChEMBL ID:

UniProt ID: P38960

Base Structure: X-ray

Registration Date: 2023-06-19

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1821224.403405
FMO2-HF: Nuclear repulsion 1750959.948546
FMO2-HF: Total energy -70264.45486
FMO2-MP2: Total energy -70470.066408


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:312:ARG)


Summations of interaction energy for fragment #1(A:312:ARG)
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.
75.55981.6491.123-3.242-3.971-0.02
Interaction energy analysis for fragmet #1(A:312:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.981 / q_NPA : 0.975
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].
3A314SER00.0730.0413.821-4.098-1.889-0.022-1.078-1.110-0.001
4A315ALA00.0600.0186.054-2.732-2.7320.0000.0000.0000.000
5A316LYS10.8800.9447.06223.73923.7390.0000.0000.0000.000
6A317SER00.0600.0157.3512.2782.2780.0000.0000.0000.000
7A318ASN0-0.023-0.0072.574-16.131-12.9010.740-1.888-2.081-0.021
8A319LEU00.0360.0285.4231.6861.6860.0000.0000.0000.000
9A320MET0-0.0010.0048.9842.2382.2380.0000.0000.0000.000
10A321LEU0-0.045-0.0304.8111.5291.5290.0000.0000.0000.000
11A322ILE00.0040.0187.5311.8551.8550.0000.0000.0000.000
12A323LEU0-0.020-0.0219.7932.0902.0900.0000.0000.0000.000
13A324LEU0-0.047-0.01711.5731.2751.2750.0000.0000.0000.000
14A325GLY00.0080.00711.9941.1841.1840.0000.0000.0000.000
15A326LEU00.0040.01713.2851.1531.1530.0000.0000.0000.000
16A327GLN0-0.0070.00415.8781.1781.1780.0000.0000.0000.000
17A328MET0-0.001-0.00218.3330.7630.7630.0000.0000.0000.000
18A329LYS10.9770.97520.19810.62610.6260.0000.0000.0000.000
19A330GLU-1-0.865-0.92821.807-11.524-11.5240.0000.0000.0000.000
20A331ILE00.0050.00417.608-0.142-0.1420.0000.0000.0000.000
21A332SER00.0760.05821.294-0.197-0.1970.0000.0000.0000.000
22A333ASN00.0590.01420.326-1.175-1.1750.0000.0000.0000.000
23A334SER0-0.020-0.02320.127-0.458-0.4580.0000.0000.0000.000
24A335ASP-1-0.899-0.94920.982-13.051-13.0510.0000.0000.0000.000
25A336LEU0-0.018-0.01114.191-0.734-0.7340.0000.0000.0000.000
26A337TYR0-0.027-0.02115.975-1.215-1.2150.0000.0000.0000.000
27A338LYS10.9380.96717.23112.28512.2850.0000.0000.0000.000
28A339LEU00.0070.02714.026-0.117-0.1170.0000.0000.0000.000
29A340LYS11.0120.99612.90618.94118.9410.0000.0000.0000.000
30A341GLU-1-0.913-0.9728.065-30.525-30.5250.0000.0000.0000.000
31A342VAL00.0220.0169.429-2.666-2.6660.0000.0000.0000.000
32A343ARG10.9090.96311.43816.80616.8060.0000.0000.0000.000
33A344SER0-0.0290.0018.4910.2770.2770.0000.0000.0000.000
34A345VAL0-0.034-0.0136.220-1.366-1.3660.0000.0000.0000.000
35A346VAL0-0.010-0.0088.3250.3200.3200.0000.0000.0000.000
36A347THR00.0340.01411.8921.2531.2530.0000.0000.0000.000
37A348SER0-0.049-0.0207.2341.5901.5900.0000.0000.0000.000
38A349LEU0-0.028-0.01510.1310.6100.6100.0000.0000.0000.000
39A350ALA00.0580.02811.5271.2151.2150.0000.0000.0000.000
40A351SER0-0.050-0.01712.5121.3021.3020.0000.0000.0000.000
41A352PHE00.0030.00112.6690.6680.6680.0000.0000.0000.000
42A353LEU00.013-0.00714.6660.8770.8770.0000.0000.0000.000
43A354PHE0-0.013-0.01417.4580.9870.9870.0000.0000.0000.000
44A355GLN0-0.036-0.02716.7430.6180.6180.0000.0000.0000.000
45A356GLN0-0.038-0.01117.5600.2230.2230.0000.0000.0000.000
46A357GLN00.0020.03620.4050.8730.8730.0000.0000.0000.000
47A358ASN00.0210.01423.535-0.046-0.0460.0000.0000.0000.000
48A359VAL00.0950.03626.5910.0280.0280.0000.0000.0000.000
49A360GLY0-0.027-0.01329.3840.2030.2030.0000.0000.0000.000
50A361VAL0-0.085-0.03526.2280.1830.1830.0000.0000.0000.000
51A362MET0-0.008-0.01426.093-0.524-0.5240.0000.0000.0000.000
52A363LYS10.9220.97424.09612.42812.4280.0000.0000.0000.000
53A364SER00.0320.01324.364-0.381-0.3810.0000.0000.0000.000
54A365PHE00.0770.01615.561-0.166-0.1660.0000.0000.0000.000
55A366ASP-1-0.872-0.93119.777-13.653-13.6530.0000.0000.0000.000
56A367SER0-0.027-0.02020.983-0.237-0.2370.0000.0000.0000.000
57A368LEU00.0080.01018.644-0.268-0.2680.0000.0000.0000.000
58A369GLU-1-0.859-0.94416.008-17.776-17.7760.0000.0000.0000.000
59A370LYS10.8890.94416.98212.08512.0850.0000.0000.0000.000
60A371GLU-1-0.960-0.97119.343-14.067-14.0670.0000.0000.0000.000
61A372ALA00.0350.01413.932-0.364-0.3640.0000.0000.0000.000
62A373PHE0-0.023-0.02314.783-0.995-0.9950.0000.0000.0000.000
63A374ARG10.9810.99015.85213.63213.6320.0000.0000.0000.000
64A375ASP-1-0.874-0.93816.049-16.262-16.2620.0000.0000.0000.000
65A376LEU0-0.100-0.05610.798-0.673-0.6730.0000.0000.0000.000
66A377VAL00.0210.01314.240-0.328-0.3280.0000.0000.0000.000
67A378ASN00.0390.01216.5990.4490.4490.0000.0000.0000.000
68A379ARG10.8990.95711.99622.00822.0080.0000.0000.0000.000
69A380LEU0-0.008-0.00612.2750.0190.0190.0000.0000.0000.000
70A381VAL00.0120.00816.2740.4720.4720.0000.0000.0000.000
71A382SER0-0.049-0.01819.7290.6660.6660.0000.0000.0000.000
72A383GLN0-0.035-0.00915.050-0.700-0.7000.0000.0000.0000.000
73A384GLY00.0700.02319.5720.0920.0920.0000.0000.0000.000
74A385LEU0-0.082-0.03214.0760.0400.0400.0000.0000.0000.000
75A386ILE0-0.0060.00016.359-0.188-0.1880.0000.0000.0000.000
76A387GLY00.0530.02919.1580.2510.2510.0000.0000.0000.000
77A388LEU0-0.0310.00522.387-0.279-0.2790.0000.0000.0000.000
78A389LYS10.9060.94724.40811.63211.6320.0000.0000.0000.000
79A390ASP-1-0.820-0.90026.668-9.546-9.5460.0000.0000.0000.000
80A391LYS10.9030.95127.54210.86110.8610.0000.0000.0000.000
81A392THR0-0.024-0.00228.984-0.073-0.0730.0000.0000.0000.000
82A393SER0-0.035-0.00528.668-0.138-0.1380.0000.0000.0000.000
83A394GLU-1-0.873-0.94024.473-12.238-12.2380.0000.0000.0000.000
84A395THR0-0.023-0.02723.917-0.679-0.6790.0000.0000.0000.000
85A396PHE0-0.041-0.03819.9970.1330.1330.0000.0000.0000.000
86A397ASP-1-0.850-0.95021.983-12.578-12.5780.0000.0000.0000.000
87A398LEU0-0.017-0.02916.859-0.646-0.6460.0000.0000.0000.000
88A399LEU0-0.006-0.00919.132-0.574-0.5740.0000.0000.0000.000
89A400PRO0-0.0040.01120.523-0.157-0.1570.0000.0000.0000.000
90A401LEU00.0240.01913.312-0.254-0.2540.0000.0000.0000.000
91A402LYS10.8350.89216.81015.70915.7090.0000.0000.0000.000
92A403ASN00.0390.02718.4250.0580.0580.0000.0000.0000.000
93A404LEU0-0.023-0.01018.2480.1800.1800.0000.0000.0000.000
94A405PHE0-0.015-0.02311.121-0.656-0.6560.0000.0000.0000.000
95A406GLU-1-0.895-0.92617.035-13.212-13.2120.0000.0000.0000.000
96A407TYR0-0.075-0.03720.0780.6270.6270.0000.0000.0000.000
97A408ALA00.006-0.00817.0390.3890.3890.0000.0000.0000.000
98A409GLU-1-0.871-0.94916.146-17.222-17.2220.0000.0000.0000.000
99A410LYS10.9250.96118.90512.71312.7130.0000.0000.0000.000
100A411ARG10.9050.96721.13012.64012.6400.0000.0000.0000.000
101A412ILE00.0590.01315.8020.3940.3940.0000.0000.0000.000
102A413SER0-0.016-0.00220.1230.5660.5660.0000.0000.0000.000
103A414VAL0-0.020-0.02422.2390.3680.3680.0000.0000.0000.000
104A415LEU0-0.001-0.00721.5310.3610.3610.0000.0000.0000.000
105A416MET00.0190.01818.8810.0420.0420.0000.0000.0000.000
106A417LYS10.9110.96723.10111.88211.8820.0000.0000.0000.000
107A418LEU0-0.033-0.00126.4820.3910.3910.0000.0000.0000.000
108A419GLN0-0.0290.00025.2080.3760.3760.0000.0000.0000.000
109A420CYS0-0.037-0.00524.8830.2000.2000.0000.0000.0000.000
110A421TYR00.0520.02722.871-0.585-0.5850.0000.0000.0000.000
111A422THR00.0340.01621.942-0.421-0.4210.0000.0000.0000.000
112A423GLY00.0030.00822.5210.5500.5500.0000.0000.0000.000
113A424THR00.0200.02522.540-0.413-0.4130.0000.0000.0000.000
114A425VAL0-0.096-0.03821.0600.2400.2400.0000.0000.0000.000
115A426GLN00.0090.00123.236-0.133-0.1330.0000.0000.0000.000
116A427LEU00.006-0.01222.647-0.148-0.1480.0000.0000.0000.000
117A428SER00.0550.02124.996-0.068-0.0680.0000.0000.0000.000
118A429HIS00.0010.00427.4270.0860.0860.0000.0000.0000.000
119A430VAL0-0.030-0.01022.3170.0190.0190.0000.0000.0000.000
120A431GLN0-0.048-0.03525.6220.3180.3180.0000.0000.0000.000
121A432GLU-1-0.909-0.94527.384-9.366-9.3660.0000.0000.0000.000
122A433LYS10.8920.95327.38210.62410.6240.0000.0000.0000.000
123A434LEU0-0.059-0.04422.9680.0110.0110.0000.0000.0000.000
124A435HIS00.0390.03727.130-0.035-0.0350.0000.0000.0000.000
125A436LEU0-0.043-0.01922.559-0.193-0.1930.0000.0000.0000.000
126A437PRO00.032-0.00626.155-0.317-0.3170.0000.0000.0000.000
127A438TYR0-0.012-0.01124.654-0.031-0.0310.0000.0000.0000.000
128A439ILE0-0.0270.03020.219-0.507-0.5070.0000.0000.0000.000
129A440THR00.0610.02619.9460.1960.1960.0000.0000.0000.000
130A441THR00.0530.01620.005-0.582-0.5820.0000.0000.0000.000
131A442ASN00.012-0.00215.729-0.817-0.8170.0000.0000.0000.000
132A443GLY00.0100.01815.132-1.266-1.2660.0000.0000.0000.000
133A444ILE00.0390.01115.722-0.929-0.9290.0000.0000.0000.000
134A445VAL00.0080.00812.455-0.580-0.5800.0000.0000.0000.000
135A446ASP-1-0.871-0.94511.131-25.958-25.9580.0000.0000.0000.000
136A447VAL0-0.0100.00511.269-1.705-1.7050.0000.0000.0000.000
137A448PHE00.0570.00913.082-0.361-0.3610.0000.0000.0000.000
138A449LYS10.9450.9838.49924.21224.2120.0000.0000.0000.000
139A450GLU-1-0.898-0.9606.540-39.698-39.6980.0000.0000.0000.000
140A451CYS0-0.0130.0109.581-0.058-0.0580.0000.0000.0000.000
141A452LEU00.0420.02212.0960.4980.4980.0000.0000.0000.000
142A453LYS10.8780.9552.56049.80350.4540.405-0.276-0.7800.002
143A454ARG10.9080.9458.72526.52526.5250.0000.0000.0000.000
144A455THR00.0370.01511.4271.1941.1940.0000.0000.0000.000
145A456LYS10.9280.96910.57021.15221.1520.0000.0000.0000.000
146A457LYS10.8780.9356.82833.78933.7890.0000.0000.0000.000
147A458GLN0-0.037-0.02012.5820.9770.9770.0000.0000.0000.000
148A459TYR00.0100.02215.9731.1731.1730.0000.0000.0000.000
149A460PRO00.0040.01415.6690.2250.2250.0000.0000.0000.000
150A461GLU-1-0.901-0.95117.149-13.710-13.7100.0000.0000.0000.000
151A462VAL0-0.008-0.01119.6530.5910.5910.0000.0000.0000.000
152A463LEU0-0.007-0.01014.3550.1740.1740.0000.0000.0000.000
153A464LYS10.9390.98716.11612.85812.8580.0000.0000.0000.000
154A465ASN0-0.120-0.09013.716-2.236-2.2360.0000.0000.0000.000
155A466TRP00.0180.0168.5550.3710.3710.0000.0000.0000.000
156A467TRP00.0060.00212.955-1.021-1.0210.0000.0000.0000.000
157A468ILE0-0.070-0.03713.1080.3000.3000.0000.0000.0000.000
158A469ASP-1-0.808-0.87615.020-15.002-15.0020.0000.0000.0000.000
159A470LEU0-0.077-0.04917.191-0.109-0.1090.0000.0000.0000.000
160A471ASP-1-0.860-0.93419.683-11.943-11.9430.0000.0000.0000.000
161A480ASN00.008-0.01822.894-0.162-0.1620.0000.0000.0000.000
162A481SER00.0400.02024.0600.0010.0010.0000.0000.0000.000
163A482GLY00.019-0.00623.0510.1740.1740.0000.0000.0000.000
164A483ILE0-0.069-0.00717.388-0.328-0.3280.0000.0000.0000.000
165A484LEU00.0620.03619.6470.4270.4270.0000.0000.0000.000
166A485LEU0-0.074-0.04716.990-0.849-0.8490.0000.0000.0000.000
167A486HIS00.003-0.00317.5880.8970.8970.0000.0000.0000.000
168A487LEU0-0.056-0.04617.210-1.142-1.1420.0000.0000.0000.000
169A488GLU-1-0.821-0.90918.048-13.441-13.4410.0000.0000.0000.000
170A489TYR0-0.018-0.04518.723-0.758-0.7580.0000.0000.0000.000
171A490ALA0-0.064-0.02119.5310.1570.1570.0000.0000.0000.000
172A491ALA00.033-0.00121.2760.3550.3550.0000.0000.0000.000
173A492ALA0-0.028-0.00623.9430.3360.3360.0000.0000.0000.000
174A493TYR0-0.031-0.01623.8390.3700.3700.0000.0000.0000.000
175A494SER0-0.0250.00425.6210.3220.3220.0000.0000.0000.000