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: 7GLKK

Calculation Name: 3WPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WPR

Chain ID: A

ChEMBL ID:

UniProt ID: K7ZP88

Base Structure: X-ray

Registration Date: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1352001.027133
FMO2-HF: Nuclear repulsion 1269886.445456
FMO2-HF: Total energy -82114.581677
FMO2-MP2: Total energy -82358.144363


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:3142:LYS)


Summations of interaction energy for fragment #1(A:3142:LYS)
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.
-162.357-159.12326.984-16.344-13.876-0.167
Interaction energy analysis for fragmet #1(A:3142:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.900
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].
3A3144ILE00.005-0.0092.6881.0224.2250.167-1.439-1.9320.006
4A3145GLU-1-0.778-0.8681.642-140.173-140.52526.818-14.802-11.665-0.173
5A3146ASP-1-0.799-0.8954.196-51.078-50.695-0.001-0.103-0.2790.000
6A3147LYS10.8450.9226.06832.53532.5350.0000.0000.0000.000
7A3148ILE0-0.024-0.0097.5213.6113.6110.0000.0000.0000.000
8A3149GLU-1-0.902-0.9468.327-30.187-30.1870.0000.0000.0000.000
9A3150GLU-1-0.904-0.95610.111-18.787-18.7870.0000.0000.0000.000
10A3151ILE0-0.058-0.03811.9332.3962.3960.0000.0000.0000.000
11A3152LEU00.005-0.00212.3461.7901.7900.0000.0000.0000.000
12A3153SER00.0140.02114.4721.9411.9410.0000.0000.0000.000
13A3154LYS10.9020.93715.96119.50519.5050.0000.0000.0000.000
14A3155ILE00.0100.01117.4071.0101.0100.0000.0000.0000.000
15A3156TYR00.0280.02619.0541.0041.0040.0000.0000.0000.000
16A3157HIS0-0.012-0.01519.1341.4471.4470.0000.0000.0000.000
17A3158ILE0-0.0020.00221.7090.7890.7890.0000.0000.0000.000
18A3159GLU-1-0.924-0.96122.884-12.966-12.9660.0000.0000.0000.000
19A3160ASN0-0.011-0.01224.5060.8090.8090.0000.0000.0000.000
20A3161GLU-1-0.947-0.97226.406-10.473-10.4730.0000.0000.0000.000
21A3162ILE0-0.029-0.00727.5670.6310.6310.0000.0000.0000.000
22A3163ALA0-0.034-0.01629.6760.5080.5080.0000.0000.0000.000
23A3164ARG10.9650.96830.89110.33910.3390.0000.0000.0000.000
24A3165ILE00.0290.01931.3690.4280.4280.0000.0000.0000.000
25A3166LYS10.9680.98232.2919.9209.9200.0000.0000.0000.000
26A3167LYS10.9210.96235.1339.3679.3670.0000.0000.0000.000
27A3168LEU00.0190.01336.6360.2790.2790.0000.0000.0000.000
28A3169ILE00.0270.01837.3630.2630.2630.0000.0000.0000.000
29A3170LYS10.8650.93540.1357.4177.4170.0000.0000.0000.000
30A3171ALA0-0.004-0.00841.8160.2280.2280.0000.0000.0000.000
31A3172VAL00.0420.01742.8310.2050.2050.0000.0000.0000.000
32A3173GLY00.0340.02144.5870.1830.1830.0000.0000.0000.000
33A3174ASN00.0270.00845.7060.1770.1770.0000.0000.0000.000
34A3175GLN00.0250.02747.7690.0520.0520.0000.0000.0000.000
35A3176VAL00.0240.01448.9560.1750.1750.0000.0000.0000.000
36A3177VAL00.0480.02350.6290.1470.1470.0000.0000.0000.000
37A3178THR0-0.021-0.01951.9200.1550.1550.0000.0000.0000.000
38A3179THR0-0.039-0.02053.1460.1420.1420.0000.0000.0000.000
39A3180GLN0-0.012-0.00654.1950.1230.1230.0000.0000.0000.000
40A3181THR00.0020.00256.4730.1290.1290.0000.0000.0000.000
41A3182THR0-0.023-0.00957.8050.1160.1160.0000.0000.0000.000
42A3183LEU0-0.0200.00559.5760.1070.1070.0000.0000.0000.000
43A3184VAL00.0160.00261.1700.0980.0980.0000.0000.0000.000
44A3185ASN0-0.020-0.02562.0840.1300.1300.0000.0000.0000.000
45A3186SER0-0.067-0.03463.2470.0830.0830.0000.0000.0000.000
46A3187LEU0-0.047-0.00464.5960.0750.0750.0000.0000.0000.000
47A3188GLY00.0710.05667.3850.0980.0980.0000.0000.0000.000
48A3189GLY00.038-0.00268.886-0.034-0.0340.0000.0000.0000.000
49A3190ASN0-0.038-0.01369.531-0.008-0.0080.0000.0000.0000.000
50A3191ALA00.0020.02265.109-0.033-0.0330.0000.0000.0000.000
51A3192LYS10.8950.93263.2604.9704.9700.0000.0000.0000.000
52A3193VAL0-0.0030.00556.543-0.004-0.0040.0000.0000.0000.000
53A3194ASN0-0.019-0.01859.5240.0980.0980.0000.0000.0000.000
54A3195ALA00.0290.00156.596-0.091-0.0910.0000.0000.0000.000
55A3196ASP-1-0.869-0.90854.972-5.594-5.5940.0000.0000.0000.000
56A3197GLY0-0.016-0.00654.142-0.072-0.0720.0000.0000.0000.000
57A3198THR0-0.054-0.03655.0260.0430.0430.0000.0000.0000.000
58A3199ILE00.006-0.00957.3140.0060.0060.0000.0000.0000.000
59A3200THR0-0.047-0.00260.6840.0330.0330.0000.0000.0000.000
60A3201GLY00.0330.00764.449-0.018-0.0180.0000.0000.0000.000
61A3202PRO0-0.0180.00566.2770.0180.0180.0000.0000.0000.000
62A3203THR0-0.057-0.04069.3570.0360.0360.0000.0000.0000.000
63A3204TYR0-0.033-0.03870.1650.0050.0050.0000.0000.0000.000
64A3205ASN0-0.036-0.03775.477-0.001-0.0010.0000.0000.0000.000
65A3206VAL00.0060.02078.9470.0480.0480.0000.0000.0000.000
66A3207ALA0-0.005-0.02181.4050.0070.0070.0000.0000.0000.000
67A3208GLN0-0.025-0.00984.7650.0230.0230.0000.0000.0000.000
68A3209GLY00.0410.03082.4700.0250.0250.0000.0000.0000.000
69A3210ASN0-0.019-0.00777.407-0.038-0.0380.0000.0000.0000.000
70A3211GLN00.0200.01975.793-0.027-0.0270.0000.0000.0000.000
71A3212THR00.0210.01270.879-0.021-0.0210.0000.0000.0000.000
72A3213ASN0-0.025-0.00970.276-0.075-0.0750.0000.0000.0000.000
73A3214VAL00.0710.02070.0280.0610.0610.0000.0000.0000.000
74A3215GLY00.0160.01872.3170.0580.0580.0000.0000.0000.000
75A3216ASP-1-0.819-0.92074.104-4.245-4.2450.0000.0000.0000.000
76A3217ALA0-0.029-0.01775.7450.0710.0710.0000.0000.0000.000
77A3218LEU0-0.003-0.01074.1430.0610.0610.0000.0000.0000.000
78A3219THR00.0230.01978.0840.0630.0630.0000.0000.0000.000
79A3220ALA0-0.036-0.01480.1730.0640.0640.0000.0000.0000.000
80A3221LEU0-0.027-0.02779.4890.0640.0640.0000.0000.0000.000
81A3222ASP-1-0.887-0.92882.135-3.847-3.8470.0000.0000.0000.000
82A3223ASN0-0.018-0.01884.0150.0770.0770.0000.0000.0000.000
83A3224ALA0-0.035-0.01585.9030.0610.0610.0000.0000.0000.000
84A3225ILE00.0310.01486.5320.0590.0590.0000.0000.0000.000
85A3226ASN00.0150.01087.0900.0620.0620.0000.0000.0000.000
86A3227THR0-0.009-0.00790.3970.0620.0620.0000.0000.0000.000
87A3228ALA0-0.013-0.00891.3660.0520.0520.0000.0000.0000.000
88A3229ALA0-0.005-0.00592.4780.0430.0430.0000.0000.0000.000
89A3230THR0-0.068-0.03294.2040.0500.0500.0000.0000.0000.000
90A3231THR0-0.062-0.04295.9640.0400.0400.0000.0000.0000.000
91A3232SER00.0000.01396.0710.0330.0330.0000.0000.0000.000
92A3233LYS10.8770.96098.5883.2823.2820.0000.0000.0000.000
93A3234SER00.0050.003100.6640.0280.0280.0000.0000.0000.000
94A3235THR0-0.063-0.032104.1740.0080.0080.0000.0000.0000.000
95A3236VAL00.0200.012107.2050.0100.0100.0000.0000.0000.000
96A3237SER0-0.018-0.009110.9150.0010.0010.0000.0000.0000.000
97A3238ASN0-0.021-0.006113.983-0.012-0.0120.0000.0000.0000.000
98A3239GLY00.0640.034117.755-0.002-0.0020.0000.0000.0000.000
99A3240GLN00.011-0.022120.4450.0030.0030.0000.0000.0000.000
100A3241ASN0-0.009-0.004123.9300.0020.0020.0000.0000.0000.000
101A3242ILE00.0030.028118.8070.0020.0020.0000.0000.0000.000
102A3243VAL0-0.003-0.003119.0580.0010.0010.0000.0000.0000.000
103A3244VAL0-0.016-0.010113.377-0.008-0.0080.0000.0000.0000.000
104A3245SER0-0.0130.008114.490-0.007-0.0070.0000.0000.0000.000
105A3246LYS10.9590.986105.4033.0603.0600.0000.0000.0000.000
106A3247SER0-0.019-0.005108.6240.0010.0010.0000.0000.0000.000
107A3248LYS10.9560.970101.2143.1853.1850.0000.0000.0000.000
108A3249ASN00.0260.012102.6810.0470.0470.0000.0000.0000.000
109A3250ALA00.007-0.013101.339-0.018-0.0180.0000.0000.0000.000
110A3251ASP-1-0.862-0.90997.094-3.316-3.3160.0000.0000.0000.000
111A3252GLY0-0.023-0.00597.359-0.036-0.0360.0000.0000.0000.000
112A3253SER0-0.091-0.04499.3820.0200.0200.0000.0000.0000.000
113A3254ASP-1-0.915-0.974100.829-3.148-3.1480.0000.0000.0000.000
114A3255ASN0-0.037-0.018104.3950.0210.0210.0000.0000.0000.000
115A3256TYR00.004-0.024106.0760.0120.0120.0000.0000.0000.000
116A3257GLU-1-0.899-0.933110.764-2.827-2.8270.0000.0000.0000.000
117A3258VAL0-0.019-0.017113.9510.0140.0140.0000.0000.0000.000
118A3259SER00.0170.014116.7450.0120.0120.0000.0000.0000.000
119A3260THR00.001-0.009120.391-0.006-0.0060.0000.0000.0000.000
120A3261ALA0-0.044-0.025123.682-0.004-0.0040.0000.0000.0000.000
121A3262LYS10.9410.949125.5992.5732.5730.0000.0000.0000.000
122A3263ASP-1-0.901-0.933128.666-2.467-2.4670.0000.0000.0000.000
123A3264LEU0-0.059-0.027127.807-0.018-0.0180.0000.0000.0000.000
124A3265THR00.0030.000130.0910.0270.0270.0000.0000.0000.000
125A3266VAL0-0.045-0.024129.907-0.025-0.0250.0000.0000.0000.000
126A3267ASP-1-0.844-0.908132.210-2.456-2.4560.0000.0000.0000.000
127A3268SER0-0.107-0.073133.4990.0250.0250.0000.0000.0000.000
128A3269VAL00.0180.020133.183-0.024-0.0240.0000.0000.0000.000
129A3270LYS10.8890.940133.9582.4302.4300.0000.0000.0000.000
130A3271ALA00.0220.006134.157-0.022-0.0220.0000.0000.0000.000
131A3272GLY00.0070.006135.6550.0180.0180.0000.0000.0000.000
132A3273ASP-1-0.885-0.945137.463-2.331-2.3310.0000.0000.0000.000
133A3274THR0-0.0120.007139.9410.0250.0250.0000.0000.0000.000
134A3275VAL0-0.038-0.019138.545-0.026-0.0260.0000.0000.0000.000
135A3276LEU00.0350.028136.9370.0210.0210.0000.0000.0000.000
136A3277ASN00.034-0.009138.012-0.011-0.0110.0000.0000.0000.000
137A3278ASN00.0340.011139.6140.0070.0070.0000.0000.0000.000
138A3279ALA0-0.048-0.012141.2070.0140.0140.0000.0000.0000.000
139A3280GLY00.0380.023143.2150.0220.0220.0000.0000.0000.000
140A3281ILE0-0.015-0.003142.233-0.022-0.0220.0000.0000.0000.000
141A3282THR0-0.037-0.019143.5100.0240.0240.0000.0000.0000.000
142A3283ILE00.0170.012143.546-0.019-0.0190.0000.0000.0000.000
143A3284GLY00.0330.002144.0170.0190.0190.0000.0000.0000.000
144A3285ASN0-0.052-0.029145.182-0.008-0.0080.0000.0000.0000.000
145A3286ASN00.021-0.006146.4960.0020.0020.0000.0000.0000.000
146A3287ALA0-0.0270.008148.3970.0190.0190.0000.0000.0000.000
147A3288VAL00.0180.007149.0850.0200.0200.0000.0000.0000.000
148A3289VAL0-0.010-0.004148.460-0.020-0.0200.0000.0000.0000.000
149A3290LEU00.0100.008147.3630.0180.0180.0000.0000.0000.000
150A3291ASN00.0820.047147.594-0.009-0.0090.0000.0000.0000.000
151A3292ASN0-0.003-0.014148.6880.0150.0150.0000.0000.0000.000
152A3293THR0-0.058-0.027150.3770.0150.0150.0000.0000.0000.000
153A3294GLY00.0480.019152.6230.0190.0190.0000.0000.0000.000
154A3295LEU00.0050.011151.996-0.017-0.0170.0000.0000.0000.000
155A3296THR0-0.015-0.026153.1670.0220.0220.0000.0000.0000.000
156A3297ILE00.0000.010153.256-0.019-0.0190.0000.0000.0000.000
157A3298SER0-0.0050.007153.4300.0220.0220.0000.0000.0000.000
158A3299GLY0-0.004-0.006155.273-0.002-0.0020.0000.0000.0000.000
159A3300GLY0-0.064-0.038158.2840.0110.0110.0000.0000.0000.000
160A3301PRO0-0.0150.002159.1530.0030.0030.0000.0000.0000.000
161A3302SER00.003-0.008157.952-0.016-0.0160.0000.0000.0000.000
162A3303VAL0-0.0070.002157.4260.0160.0160.0000.0000.0000.000
163A3304THR00.0120.005156.504-0.015-0.0150.0000.0000.0000.000
164A3305LEU00.0480.005156.0560.0120.0120.0000.0000.0000.000
165A3306ALA0-0.063-0.013159.1230.0120.0120.0000.0000.0000.000
166A3307GLY00.0020.010161.4860.0170.0170.0000.0000.0000.000
167A3308ILE0-0.039-0.026161.725-0.014-0.0140.0000.0000.0000.000
168A3309ASP-1-0.844-0.896162.069-1.997-1.9970.0000.0000.0000.000
169A3310ALA00.008-0.013162.696-0.011-0.0110.0000.0000.0000.000
170A3311GLY00.005-0.010162.978-0.001-0.0010.0000.0000.0000.000
171A3312ASN0-0.082-0.039163.9090.0060.0060.0000.0000.0000.000
172A3313LYS10.9490.981161.8772.0192.0190.0000.0000.0000.000
173A3314THR0-0.021-0.013166.9270.0010.0010.0000.0000.0000.000
174A3315ILE00.0670.034166.370-0.013-0.0130.0000.0000.0000.000
175A3316GLN0-0.050-0.032166.2440.0140.0140.0000.0000.0000.000
176A3317ASN0-0.030-0.020164.9680.0020.0020.0000.0000.0000.000
177A3318VAL00.0460.043167.585-0.009-0.0090.0000.0000.0000.000
178A3319ALA00.0060.003169.5970.0120.0120.0000.0000.0000.000
179A3320ASN0-0.013-0.011171.3530.0010.0010.0000.0000.0000.000
180A3321ALA00.0270.017174.037-0.005-0.0050.0000.0000.0000.000
181A3322VAL0-0.055-0.018174.2280.0120.0120.0000.0000.0000.000
182A3323ASN0-0.069-0.049172.1880.0170.0170.0000.0000.0000.000
183A3324ALA00.012-0.005175.6950.0010.0010.0000.0000.0000.000
184A3325THR0-0.032-0.015172.2600.0040.0040.0000.0000.0000.000
185A3326ASP-1-0.809-0.874171.802-1.927-1.9270.0000.0000.0000.000
186A3327ALA0-0.017-0.015171.2290.0100.0100.0000.0000.0000.000
187A3328VAL00.0320.023173.1020.0010.0010.0000.0000.0000.000
188A3329ASN0-0.024-0.025173.8520.0070.0070.0000.0000.0000.000
189A3330LYS11.0060.977175.5801.8461.8460.0000.0000.0000.000
190A3331GLY00.0110.011177.6300.0120.0120.0000.0000.0000.000
191A3332GLN00.0570.018176.8080.0040.0040.0000.0000.0000.000
192A3333MET00.0090.021180.4110.0080.0080.0000.0000.0000.000
193A3334LYS10.8480.923182.0041.7851.7850.0000.0000.0000.000
194A3335GLN00.0210.017183.3830.0210.0210.0000.0000.0000.000
195A3336ILE00.0390.015185.2940.0130.0130.0000.0000.0000.000
196A3337GLU-1-0.885-0.955184.365-1.778-1.7780.0000.0000.0000.000
197A3338ASP-1-0.865-0.930187.795-1.746-1.7460.0000.0000.0000.000
198A3339LYS10.8310.919189.3221.7461.7460.0000.0000.0000.000
199A3340ILE00.0150.010190.1620.0110.0110.0000.0000.0000.000
200A3341GLU-1-0.877-0.934192.223-1.680-1.6800.0000.0000.0000.000
201A3342GLU-1-0.812-0.885193.945-1.654-1.6540.0000.0000.0000.000
202A3343ILE0-0.021-0.010195.0860.0130.0130.0000.0000.0000.000
203A3344LEU00.0240.000195.1130.0110.0110.0000.0000.0000.000
204A3345SER00.0010.009197.8780.0130.0130.0000.0000.0000.000
205A3346LYS10.7590.861199.2071.6621.6620.0000.0000.0000.000
206A3347ILE00.004-0.008200.0790.0110.0110.0000.0000.0000.000
207A3348TYR00.0290.024202.2460.0110.0110.0000.0000.0000.000
208A3349HIS0-0.019-0.024202.9080.0140.0140.0000.0000.0000.000
209A3350ILE0-0.0010.006205.9240.0110.0110.0000.0000.0000.000
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