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: YY482

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1822343.680161
FMO2-HF: Nuclear repulsion 1752078.158317
FMO2-HF: Total energy -70265.521844
FMO2-MP2: Total energy -70471.117705


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.
55.4359.3776.356-4.818-5.484-0.047
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 : 0.975 / q_NPA : 0.972
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].
3A314SER00.0850.0533.689-5.661-3.223-0.001-1.204-1.233-0.001
4A315ALA00.0790.0375.441-3.858-3.8580.0000.0000.0000.000
5A316LYS10.8540.9006.46524.07024.0700.0000.0000.0000.000
6A317SER00.0370.0067.0071.7541.7540.0000.0000.0000.000
7A318ASN0-0.055-0.0271.978-28.100-26.9336.354-3.567-3.954-0.046
8A319LEU00.0600.0365.1721.8821.930-0.001-0.002-0.0450.000
9A320MET0-0.014-0.0028.6822.3732.3730.0000.0000.0000.000
10A321LEU0-0.049-0.0284.9751.6121.6120.0000.0000.0000.000
11A322ILE00.0060.0197.1411.8021.8020.0000.0000.0000.000
12A323LEU0-0.012-0.0189.5682.1942.1940.0000.0000.0000.000
13A324LEU0-0.046-0.01611.5481.3311.3310.0000.0000.0000.000
14A325GLY00.0110.01011.8691.2561.2560.0000.0000.0000.000
15A326LEU00.0130.02513.1831.1831.1830.0000.0000.0000.000
16A327GLN0-0.016-0.00115.7001.2511.2510.0000.0000.0000.000
17A328MET0-0.005-0.00318.6390.7240.7240.0000.0000.0000.000
18A329LYS10.9870.99020.03010.64010.6400.0000.0000.0000.000
19A330GLU-1-0.829-0.89721.558-11.592-11.5920.0000.0000.0000.000
20A331ILE00.0060.00217.322-0.127-0.1270.0000.0000.0000.000
21A332SER00.0640.02821.009-0.183-0.1830.0000.0000.0000.000
22A333ASN00.0690.01319.970-1.315-1.3150.0000.0000.0000.000
23A334SER0-0.008-0.00819.754-0.480-0.4800.0000.0000.0000.000
24A335ASP-1-0.837-0.89920.680-13.128-13.1280.0000.0000.0000.000
25A336LEU0-0.0080.00313.939-0.721-0.7210.0000.0000.0000.000
26A337TYR0-0.014-0.01315.605-1.242-1.2420.0000.0000.0000.000
27A338LYS10.8540.92016.85512.62612.6260.0000.0000.0000.000
28A339LEU0-0.0060.01813.784-0.085-0.0850.0000.0000.0000.000
29A340LYS11.0160.99812.58219.42319.4230.0000.0000.0000.000
30A341GLU-1-0.908-0.9658.355-30.083-30.0830.0000.0000.0000.000
31A342VAL00.0150.0069.038-2.839-2.8390.0000.0000.0000.000
32A343ARG10.8820.92911.06717.05317.0530.0000.0000.0000.000
33A344SER0-0.0260.0018.4660.2180.2180.0000.0000.0000.000
34A345VAL0-0.028-0.0145.669-1.318-1.3180.0000.0000.0000.000
35A346VAL0-0.018-0.0107.9630.5090.5090.0000.0000.0000.000
36A347THR00.009-0.00911.5630.7870.7870.0000.0000.0000.000
37A348SER0-0.045-0.0108.014-0.082-0.0820.0000.0000.0000.000
38A349LEU0-0.014-0.0079.9560.8410.8410.0000.0000.0000.000
39A350ALA00.0520.02511.1801.3471.3470.0000.0000.0000.000
40A351SER0-0.061-0.03212.3141.2191.2190.0000.0000.0000.000
41A352PHE0-0.004-0.00112.3940.6640.6640.0000.0000.0000.000
42A353LEU0-0.002-0.01514.3880.9990.9990.0000.0000.0000.000
43A354PHE0-0.010-0.01017.1410.9760.9760.0000.0000.0000.000
44A355GLN0-0.024-0.02215.9670.8350.8350.0000.0000.0000.000
45A356GLN0-0.040-0.00917.4070.1540.1540.0000.0000.0000.000
46A357GLN0-0.0080.02920.1850.7900.7900.0000.0000.0000.000
47A358ASN00.0160.01123.2370.1140.1140.0000.0000.0000.000
48A359VAL00.0890.03226.4120.0320.0320.0000.0000.0000.000
49A360GLY0-0.018-0.00629.1470.1990.1990.0000.0000.0000.000
50A361VAL0-0.077-0.03426.0210.1610.1610.0000.0000.0000.000
51A362MET00.002-0.00825.825-0.506-0.5060.0000.0000.0000.000
52A363LYS10.8470.93023.00413.16413.1640.0000.0000.0000.000
53A364SER00.0360.00924.114-0.400-0.4000.0000.0000.0000.000
54A365PHE00.0720.01815.274-0.181-0.1810.0000.0000.0000.000
55A366ASP-1-0.799-0.88019.497-13.668-13.6680.0000.0000.0000.000
56A367SER0-0.014-0.00320.635-0.197-0.1970.0000.0000.0000.000
57A368LEU00.0100.00018.366-0.298-0.2980.0000.0000.0000.000
58A369GLU-1-0.802-0.88215.528-18.700-18.7000.0000.0000.0000.000
59A370LYS10.8170.89316.55112.34112.3410.0000.0000.0000.000
60A371GLU-1-0.823-0.88218.948-13.759-13.7590.0000.0000.0000.000
61A372ALA00.0200.00513.507-0.327-0.3270.0000.0000.0000.000
62A373PHE0-0.010-0.01414.126-1.072-1.0720.0000.0000.0000.000
63A374ARG10.9000.93315.32914.15014.1500.0000.0000.0000.000
64A375ASP-1-0.810-0.88715.450-16.552-16.5520.0000.0000.0000.000
65A376LEU0-0.079-0.0389.833-0.577-0.5770.0000.0000.0000.000
66A377VAL00.0150.00913.626-0.298-0.2980.0000.0000.0000.000
67A378ASN00.0370.01316.0950.5010.5010.0000.0000.0000.000
68A379ARG10.8350.90712.65820.73620.7360.0000.0000.0000.000
69A380LEU0-0.014-0.00712.0260.0570.0570.0000.0000.0000.000
70A381VAL00.0130.00616.0670.5100.5100.0000.0000.0000.000
71A382SER0-0.023-0.00519.3010.6790.6790.0000.0000.0000.000
72A383GLN0-0.0350.00515.092-0.776-0.7760.0000.0000.0000.000
73A384GLY00.0790.02819.4480.1060.1060.0000.0000.0000.000
74A385LEU0-0.089-0.03613.9670.0040.0040.0000.0000.0000.000
75A386ILE0-0.004-0.00215.831-0.201-0.2010.0000.0000.0000.000
76A387GLY00.0530.03118.9720.2650.2650.0000.0000.0000.000
77A388LEU0-0.0360.00022.148-0.301-0.3010.0000.0000.0000.000
78A389LYS10.8450.90924.14811.92911.9290.0000.0000.0000.000
79A390ASP-1-0.775-0.86226.392-9.745-9.7450.0000.0000.0000.000
80A391LYS10.8050.89126.28111.20011.2000.0000.0000.0000.000
81A392THR0-0.006-0.00228.656-0.031-0.0310.0000.0000.0000.000
82A393SER0-0.061-0.04628.410-0.125-0.1250.0000.0000.0000.000
83A394GLU-1-0.826-0.89724.148-12.416-12.4160.0000.0000.0000.000
84A395THR0-0.018-0.01723.589-0.738-0.7380.0000.0000.0000.000
85A396PHE0-0.034-0.03119.5540.1290.1290.0000.0000.0000.000
86A397ASP-1-0.828-0.94121.713-12.580-12.5800.0000.0000.0000.000
87A398LEU0-0.019-0.03016.688-0.634-0.6340.0000.0000.0000.000
88A399LEU0-0.006-0.00819.000-0.581-0.5810.0000.0000.0000.000
89A400PRO00.0000.01120.421-0.120-0.1200.0000.0000.0000.000
90A401LEU00.0230.02013.151-0.238-0.2380.0000.0000.0000.000
91A402LYS10.8560.89417.05415.76415.7640.0000.0000.0000.000
92A403ASN00.0140.01218.379-0.030-0.0300.0000.0000.0000.000
93A404LEU0-0.013-0.00418.2780.1940.1940.0000.0000.0000.000
94A405PHE0-0.003-0.02011.511-0.602-0.6020.0000.0000.0000.000
95A406GLU-1-0.834-0.89017.413-13.070-13.0700.0000.0000.0000.000
96A407TYR0-0.065-0.03120.4430.5980.5980.0000.0000.0000.000
97A408ALA00.010-0.00516.9430.3840.3840.0000.0000.0000.000
98A409GLU-1-0.882-0.95115.662-18.032-18.0320.0000.0000.0000.000
99A410LYS10.8440.91118.91113.12213.1220.0000.0000.0000.000
100A411ARG10.9150.97321.04612.57012.5700.0000.0000.0000.000
101A412ILE00.0430.00715.6960.3870.3870.0000.0000.0000.000
102A413SER00.0140.01320.0000.6100.6100.0000.0000.0000.000
103A414VAL0-0.033-0.02522.1190.3650.3650.0000.0000.0000.000
104A415LEU00.0110.00021.4530.3480.3480.0000.0000.0000.000
105A416MET00.0210.01718.931-0.026-0.0260.0000.0000.0000.000
106A417LYS10.8880.95623.20912.20012.2000.0000.0000.0000.000
107A418LEU0-0.033-0.00226.5300.3900.3900.0000.0000.0000.000
108A419GLN0-0.034-0.00725.3390.3430.3430.0000.0000.0000.000
109A420CYS0-0.0090.00724.7350.3250.3250.0000.0000.0000.000
110A421TYR00.0480.03422.974-0.585-0.5850.0000.0000.0000.000
111A422THR00.0210.00721.953-0.412-0.4120.0000.0000.0000.000
112A423GLY0-0.0040.00622.5360.5380.5380.0000.0000.0000.000
113A424THR00.0020.01822.556-0.417-0.4170.0000.0000.0000.000
114A425VAL0-0.089-0.04021.0210.2270.2270.0000.0000.0000.000
115A426GLN00.0170.00723.255-0.130-0.1300.0000.0000.0000.000
116A427LEU0-0.001-0.01322.973-0.146-0.1460.0000.0000.0000.000
117A428SER00.0500.02025.016-0.086-0.0860.0000.0000.0000.000
118A429HIS00.0100.00527.3820.0420.0420.0000.0000.0000.000
119A430VAL0-0.034-0.01322.1560.0090.0090.0000.0000.0000.000
120A431GLN0-0.039-0.02325.5410.2850.2850.0000.0000.0000.000
121A432GLU-1-0.897-0.94127.318-9.383-9.3830.0000.0000.0000.000
122A433LYS10.8900.94927.36110.50010.5000.0000.0000.0000.000
123A434LEU0-0.055-0.04223.081-0.001-0.0010.0000.0000.0000.000
124A435HIS00.0300.03327.129-0.071-0.0710.0000.0000.0000.000
125A436LEU0-0.040-0.01622.417-0.205-0.2050.0000.0000.0000.000
126A437PRO00.044-0.00126.095-0.327-0.3270.0000.0000.0000.000
127A438TYR0-0.012-0.00824.571-0.052-0.0520.0000.0000.0000.000
128A439ILE0-0.0300.01919.579-0.534-0.5340.0000.0000.0000.000
129A440THR00.0400.02119.9720.1840.1840.0000.0000.0000.000
130A441THR00.0760.02419.705-0.605-0.6050.0000.0000.0000.000
131A442ASN00.010-0.00315.828-0.702-0.7020.0000.0000.0000.000
132A443GLY00.0040.01115.132-1.331-1.3310.0000.0000.0000.000
133A444ILE00.0380.01315.664-0.959-0.9590.0000.0000.0000.000
134A445VAL00.0140.00912.525-0.639-0.6390.0000.0000.0000.000
135A446ASP-1-0.823-0.90210.963-26.515-26.5150.0000.0000.0000.000
136A447VAL00.0030.01111.194-1.706-1.7060.0000.0000.0000.000
137A448PHE00.0760.02412.993-0.376-0.3760.0000.0000.0000.000
138A449LYS10.8760.9498.36224.68524.6850.0000.0000.0000.000
139A450GLU-1-0.817-0.9076.602-39.016-39.0160.0000.0000.0000.000
140A451CYS0-0.0090.0089.487-0.079-0.0790.0000.0000.0000.000
141A452LEU00.0470.03512.0570.5130.5130.0000.0000.0000.000
142A453LYS10.8140.9053.66446.54046.8340.004-0.045-0.2520.000
143A454ARG10.8570.9249.19126.22326.2230.0000.0000.0000.000
144A455THR00.019-0.00911.3231.1871.1870.0000.0000.0000.000
145A456LYS10.9110.94510.98920.48320.4830.0000.0000.0000.000
146A457LYS10.8900.9427.04632.23932.2390.0000.0000.0000.000
147A458GLN0-0.031-0.01512.6660.9000.9000.0000.0000.0000.000
148A459TYR00.0030.01415.9681.1341.1340.0000.0000.0000.000
149A460PRO00.0090.02115.7500.1610.1610.0000.0000.0000.000
150A461GLU-1-0.894-0.95217.233-13.740-13.7400.0000.0000.0000.000
151A462VAL0-0.023-0.02119.7590.5890.5890.0000.0000.0000.000
152A463LEU0-0.018-0.00914.8520.1740.1740.0000.0000.0000.000
153A464LYS10.8560.92616.22812.73712.7370.0000.0000.0000.000
154A465ASN0-0.110-0.06813.781-2.184-2.1840.0000.0000.0000.000
155A466TRP00.0220.0168.8470.2830.2830.0000.0000.0000.000
156A467TRP00.0010.00112.965-0.880-0.8800.0000.0000.0000.000
157A468ILE0-0.063-0.03112.9720.3290.3290.0000.0000.0000.000
158A469ASP-1-0.811-0.88215.036-14.908-14.9080.0000.0000.0000.000
159A470LEU0-0.062-0.04317.047-0.107-0.1070.0000.0000.0000.000
160A471ASP-1-0.869-0.94119.702-11.536-11.5360.0000.0000.0000.000
161A480ASN0-0.004-0.01822.840-0.441-0.4410.0000.0000.0000.000
162A481SER00.0570.02524.0800.0030.0030.0000.0000.0000.000
163A482GLY00.006-0.01023.0700.1860.1860.0000.0000.0000.000
164A483ILE0-0.060-0.00517.366-0.318-0.3180.0000.0000.0000.000
165A484LEU00.0340.02219.6060.4430.4430.0000.0000.0000.000
166A485LEU0-0.060-0.03117.006-0.827-0.8270.0000.0000.0000.000
167A486HIS00.0300.00917.6080.8750.8750.0000.0000.0000.000
168A487LEU0-0.049-0.03917.247-1.111-1.1110.0000.0000.0000.000
169A488GLU-1-0.747-0.86018.191-13.253-13.2530.0000.0000.0000.000
170A489TYR0-0.015-0.04318.854-0.741-0.7410.0000.0000.0000.000
171A490ALA0-0.059-0.02019.5560.1660.1660.0000.0000.0000.000
172A491ALA00.0410.00221.3770.3450.3450.0000.0000.0000.000
173A492ALA0-0.028-0.00724.0220.3270.3270.0000.0000.0000.000
174A493TYR0-0.027-0.02123.9490.3560.3560.0000.0000.0000.000
175A494SER0-0.0350.00225.7240.2950.2950.0000.0000.0000.000