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: 226MR

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1352753.972604
FMO2-HF: Nuclear repulsion 1270638.606971
FMO2-HF: Total energy -82115.365633
FMO2-MP2: Total energy -82358.838954


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.
-158.79-157.45426.749-15.365-12.72-0.155
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 : 0.864 / q_NPA : 0.907
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].
3A3144ILE00.016-0.0022.6541.2294.3630.164-1.411-1.8870.006
4A3145GLU-1-0.791-0.8801.782-141.232-143.46126.585-13.826-10.530-0.160
5A3146ASP-1-0.824-0.9054.123-51.353-50.9220.000-0.128-0.303-0.001
6A3147LYS10.8450.9165.98133.47733.4770.0000.0000.0000.000
7A3148ILE0-0.020-0.0087.7573.6263.6260.0000.0000.0000.000
8A3149GLU-1-0.914-0.9518.694-28.431-28.4310.0000.0000.0000.000
9A3150GLU-1-0.824-0.89910.038-18.080-18.0800.0000.0000.0000.000
10A3151ILE0-0.059-0.03811.7252.4162.4160.0000.0000.0000.000
11A3152LEU00.0120.00312.3871.8051.8050.0000.0000.0000.000
12A3153SER00.0070.01714.4121.9931.9930.0000.0000.0000.000
13A3154LYS10.8350.88715.68819.68619.6860.0000.0000.0000.000
14A3155ILE00.0020.00617.1631.0471.0470.0000.0000.0000.000
15A3156TYR00.0390.03519.1080.9590.9590.0000.0000.0000.000
16A3157HIS0-0.013-0.01418.9231.5251.5250.0000.0000.0000.000
17A3158ILE0-0.015-0.00621.5300.8160.8160.0000.0000.0000.000
18A3159GLU-1-0.922-0.96022.943-13.091-13.0910.0000.0000.0000.000
19A3160ASN0-0.028-0.02023.9940.9710.9710.0000.0000.0000.000
20A3161GLU-1-0.853-0.91726.550-10.267-10.2670.0000.0000.0000.000
21A3162ILE0-0.017-0.00628.1800.6230.6230.0000.0000.0000.000
22A3163ALA0-0.031-0.01529.7110.5060.5060.0000.0000.0000.000
23A3164ARG10.8790.92629.59010.72410.7240.0000.0000.0000.000
24A3165ILE00.0350.01231.2550.4230.4230.0000.0000.0000.000
25A3166LYS10.9580.98132.28010.07310.0730.0000.0000.0000.000
26A3167LYS10.9330.96734.7379.4799.4790.0000.0000.0000.000
27A3168LEU00.0000.01036.0580.2830.2830.0000.0000.0000.000
28A3169ILE00.0360.01737.4620.2630.2630.0000.0000.0000.000
29A3170LYS10.8880.94440.1957.4287.4280.0000.0000.0000.000
30A3171ALA0-0.008-0.00541.7500.2330.2330.0000.0000.0000.000
31A3172VAL00.0470.01942.8680.2080.2080.0000.0000.0000.000
32A3173GLY00.0360.02244.6150.1850.1850.0000.0000.0000.000
33A3174ASN00.012-0.00145.4910.1930.1930.0000.0000.0000.000
34A3175GLN00.0220.02647.5130.0540.0540.0000.0000.0000.000
35A3176VAL00.0230.01848.8890.1760.1760.0000.0000.0000.000
36A3177VAL00.0440.02550.5590.1450.1450.0000.0000.0000.000
37A3178THR0-0.013-0.01051.8340.1600.1600.0000.0000.0000.000
38A3179THR0-0.038-0.02153.0060.1460.1460.0000.0000.0000.000
39A3180GLN00.0000.00054.4910.0950.0950.0000.0000.0000.000
40A3181THR0-0.012-0.01056.3900.1280.1280.0000.0000.0000.000
41A3182THR0-0.025-0.01857.5980.1150.1150.0000.0000.0000.000
42A3183LEU0-0.0180.01159.5100.1090.1090.0000.0000.0000.000
43A3184VAL00.009-0.00361.2040.1000.1000.0000.0000.0000.000
44A3185ASN0-0.021-0.02362.1600.1250.1250.0000.0000.0000.000
45A3186SER0-0.060-0.03463.1640.0830.0830.0000.0000.0000.000
46A3187LEU0-0.048-0.00564.6170.0760.0760.0000.0000.0000.000
47A3188GLY00.0680.05567.3960.0990.0990.0000.0000.0000.000
48A3189GLY00.0390.00168.993-0.035-0.0350.0000.0000.0000.000
49A3190ASN0-0.048-0.01969.721-0.005-0.0050.0000.0000.0000.000
50A3191ALA00.0150.03165.326-0.034-0.0340.0000.0000.0000.000
51A3192LYS10.8900.92563.4404.9964.9960.0000.0000.0000.000
52A3193VAL0-0.0010.00356.7430.0000.0000.0000.0000.0000.000
53A3194ASN0-0.025-0.01159.7550.0930.0930.0000.0000.0000.000
54A3195ALA00.0320.00156.811-0.092-0.0920.0000.0000.0000.000
55A3196ASP-1-0.863-0.89555.190-5.610-5.6100.0000.0000.0000.000
56A3197GLY0-0.011-0.00354.367-0.073-0.0730.0000.0000.0000.000
57A3198THR0-0.062-0.04455.2490.0440.0440.0000.0000.0000.000
58A3199ILE00.004-0.01157.4950.0020.0020.0000.0000.0000.000
59A3200THR0-0.048-0.00660.9050.0450.0450.0000.0000.0000.000
60A3201GLY00.0350.00464.671-0.017-0.0170.0000.0000.0000.000
61A3202PRO0-0.0200.00366.4970.0190.0190.0000.0000.0000.000
62A3203THR0-0.017-0.02869.5500.0280.0280.0000.0000.0000.000
63A3204TYR0-0.076-0.05370.1750.0100.0100.0000.0000.0000.000
64A3205ASN0-0.040-0.03775.619-0.005-0.0050.0000.0000.0000.000
65A3206VAL00.0190.02479.1130.0470.0470.0000.0000.0000.000
66A3207ALA00.000-0.01681.4730.0050.0050.0000.0000.0000.000
67A3208GLN0-0.018-0.00484.8310.0110.0110.0000.0000.0000.000
68A3209GLY00.0420.03182.6770.0260.0260.0000.0000.0000.000
69A3210ASN0-0.034-0.01677.693-0.034-0.0340.0000.0000.0000.000
70A3211GLN00.0130.01375.973-0.025-0.0250.0000.0000.0000.000
71A3212THR00.0350.01771.102-0.020-0.0200.0000.0000.0000.000
72A3213ASN0-0.046-0.03270.360-0.079-0.0790.0000.0000.0000.000
73A3214VAL00.0720.02069.8840.0620.0620.0000.0000.0000.000
74A3215GLY00.0270.02472.2600.0590.0590.0000.0000.0000.000
75A3216ASP-1-0.805-0.89674.023-4.246-4.2460.0000.0000.0000.000
76A3217ALA0-0.029-0.01775.7510.0720.0720.0000.0000.0000.000
77A3218LEU00.001-0.00774.2040.0620.0620.0000.0000.0000.000
78A3219THR00.0160.00877.8220.0620.0620.0000.0000.0000.000
79A3220ALA0-0.0130.00480.1440.0680.0680.0000.0000.0000.000
80A3221LEU0-0.019-0.01879.3220.0630.0630.0000.0000.0000.000
81A3222ASP-1-0.899-0.93682.127-3.824-3.8240.0000.0000.0000.000
82A3223ASN0-0.031-0.03783.6710.0950.0950.0000.0000.0000.000
83A3224ALA0-0.018-0.00485.8290.0610.0610.0000.0000.0000.000
84A3225ILE00.0090.00485.8910.0580.0580.0000.0000.0000.000
85A3226ASN00.0080.01286.8510.0760.0760.0000.0000.0000.000
86A3227THR0-0.016-0.00790.2660.0610.0610.0000.0000.0000.000
87A3228ALA00.0070.00891.2340.0490.0490.0000.0000.0000.000
88A3229ALA0-0.0090.00992.3400.0460.0460.0000.0000.0000.000
89A3230THR0-0.076-0.04894.1100.0500.0500.0000.0000.0000.000
90A3231THR0-0.010-0.01996.2420.0300.0300.0000.0000.0000.000
91A3232SER0-0.057-0.02995.7680.0330.0330.0000.0000.0000.000
92A3233LYS10.8440.93098.4993.2743.2740.0000.0000.0000.000
93A3234SER00.0120.008100.5710.0280.0280.0000.0000.0000.000
94A3235THR0-0.079-0.043104.0830.0110.0110.0000.0000.0000.000
95A3236VAL00.0150.008107.1110.0100.0100.0000.0000.0000.000
96A3237SER0-0.003-0.001110.8210.0010.0010.0000.0000.0000.000
97A3238ASN0-0.035-0.019113.887-0.013-0.0130.0000.0000.0000.000
98A3239GLY00.0730.040117.659-0.002-0.0020.0000.0000.0000.000
99A3240GLN00.011-0.018120.3520.0010.0010.0000.0000.0000.000
100A3241ASN0-0.017-0.009123.8380.0030.0030.0000.0000.0000.000
101A3242ILE00.0070.031118.7850.0020.0020.0000.0000.0000.000
102A3243VAL0-0.006-0.002119.0610.0010.0010.0000.0000.0000.000
103A3244VAL0-0.014-0.010113.291-0.008-0.0080.0000.0000.0000.000
104A3245SER0-0.0210.010114.389-0.007-0.0070.0000.0000.0000.000
105A3246LYS10.8780.935104.7103.0793.0790.0000.0000.0000.000
106A3247SER0-0.0010.002108.5190.0000.0000.0000.0000.0000.000
107A3248LYS10.8430.909101.0003.2013.2010.0000.0000.0000.000
108A3249ASN00.0230.014102.5560.0490.0490.0000.0000.0000.000
109A3250ALA00.016-0.008101.274-0.018-0.0180.0000.0000.0000.000
110A3251ASP-1-0.834-0.88097.170-3.310-3.3100.0000.0000.0000.000
111A3252GLY00.0100.01497.258-0.036-0.0360.0000.0000.0000.000
112A3253SER0-0.059-0.04299.2790.0210.0210.0000.0000.0000.000
113A3254ASP-1-0.846-0.925100.730-3.159-3.1590.0000.0000.0000.000
114A3255ASN0-0.036-0.016104.2960.0150.0150.0000.0000.0000.000
115A3256TYR00.034-0.002105.6670.0070.0070.0000.0000.0000.000
116A3257GLU-1-0.882-0.927110.667-2.831-2.8310.0000.0000.0000.000
117A3258VAL0-0.013-0.017113.8550.0140.0140.0000.0000.0000.000
118A3259SER00.0190.016116.6510.0140.0140.0000.0000.0000.000
119A3260THR0-0.002-0.005120.296-0.007-0.0070.0000.0000.0000.000
120A3261ALA0-0.046-0.031123.587-0.004-0.0040.0000.0000.0000.000
121A3262LYS10.9400.953125.5012.5782.5780.0000.0000.0000.000
122A3263ASP-1-0.901-0.938128.567-2.473-2.4730.0000.0000.0000.000
123A3264LEU0-0.055-0.023127.712-0.018-0.0180.0000.0000.0000.000
124A3265THR00.0040.000129.9970.0270.0270.0000.0000.0000.000
125A3266VAL0-0.036-0.023129.785-0.025-0.0250.0000.0000.0000.000
126A3267ASP-1-0.857-0.911131.817-2.466-2.4660.0000.0000.0000.000
127A3268SER0-0.092-0.069133.4110.0240.0240.0000.0000.0000.000
128A3269VAL00.0110.015133.042-0.024-0.0240.0000.0000.0000.000
129A3270LYS10.8830.940133.8782.4272.4270.0000.0000.0000.000
130A3271ALA00.0260.007134.077-0.022-0.0220.0000.0000.0000.000
131A3272GLY00.0220.014135.5870.0180.0180.0000.0000.0000.000
132A3273ASP-1-0.891-0.947137.387-2.335-2.3350.0000.0000.0000.000
133A3274THR0-0.0140.007139.8600.0250.0250.0000.0000.0000.000
134A3275VAL0-0.043-0.022138.536-0.026-0.0260.0000.0000.0000.000
135A3276LEU00.0310.027137.1420.0210.0210.0000.0000.0000.000
136A3277ASN00.030-0.011137.928-0.011-0.0110.0000.0000.0000.000
137A3278ASN00.0390.019139.5290.0040.0040.0000.0000.0000.000
138A3279ALA0-0.038-0.010141.1210.0140.0140.0000.0000.0000.000
139A3280GLY00.0330.021143.1260.0220.0220.0000.0000.0000.000
140A3281ILE0-0.018-0.009142.198-0.022-0.0220.0000.0000.0000.000
141A3282THR0-0.039-0.020143.4260.0230.0230.0000.0000.0000.000
142A3283ILE00.0210.013143.466-0.019-0.0190.0000.0000.0000.000
143A3284GLY00.0390.006143.9440.0190.0190.0000.0000.0000.000
144A3285ASN0-0.052-0.030145.107-0.012-0.0120.0000.0000.0000.000
145A3286ASN00.005-0.011146.4240.0030.0030.0000.0000.0000.000
146A3287ALA0-0.0140.012148.3220.0190.0190.0000.0000.0000.000
147A3288VAL00.0120.004149.0070.0200.0200.0000.0000.0000.000
148A3289VAL0-0.015-0.007148.314-0.020-0.0200.0000.0000.0000.000
149A3290LEU00.0140.012147.1920.0180.0180.0000.0000.0000.000
150A3291ASN00.0810.045147.509-0.009-0.0090.0000.0000.0000.000
151A3292ASN00.011-0.003148.5630.0090.0090.0000.0000.0000.000
152A3293THR0-0.063-0.035150.2890.0150.0150.0000.0000.0000.000
153A3294GLY00.0480.021152.5350.0190.0190.0000.0000.0000.000
154A3295LEU0-0.0040.006151.772-0.017-0.0170.0000.0000.0000.000
155A3296THR0-0.010-0.024153.0850.0210.0210.0000.0000.0000.000
156A3297ILE00.0020.011153.175-0.019-0.0190.0000.0000.0000.000
157A3298SER00.0030.011153.2710.0220.0220.0000.0000.0000.000
158A3299GLY0-0.005-0.004155.197-0.002-0.0020.0000.0000.0000.000
159A3300GLY0-0.070-0.044158.2060.0110.0110.0000.0000.0000.000
160A3301PRO0-0.0200.004158.9760.0030.0030.0000.0000.0000.000
161A3302SER0-0.004-0.010157.774-0.017-0.0170.0000.0000.0000.000
162A3303VAL0-0.0030.001157.4320.0160.0160.0000.0000.0000.000
163A3304THR00.0130.005156.319-0.015-0.0150.0000.0000.0000.000
164A3305LEU00.0460.011155.5710.0120.0120.0000.0000.0000.000
165A3306ALA0-0.062-0.015159.0340.0120.0120.0000.0000.0000.000
166A3307GLY00.0050.011161.3970.0180.0180.0000.0000.0000.000
167A3308ILE0-0.044-0.028161.638-0.014-0.0140.0000.0000.0000.000
168A3309ASP-1-0.846-0.906161.986-1.998-1.9980.0000.0000.0000.000
169A3310ALA00.006-0.010162.613-0.011-0.0110.0000.0000.0000.000
170A3311GLY00.013-0.002162.899-0.002-0.0020.0000.0000.0000.000
171A3312ASN0-0.087-0.046163.8300.0080.0080.0000.0000.0000.000
172A3313LYS10.9520.986161.5252.0252.0250.0000.0000.0000.000
173A3314THR0-0.005-0.004166.8490.0010.0010.0000.0000.0000.000
174A3315ILE00.0490.026166.037-0.013-0.0130.0000.0000.0000.000
175A3316GLN0-0.048-0.033166.1290.0110.0110.0000.0000.0000.000
176A3317ASN0-0.027-0.021164.8200.0020.0020.0000.0000.0000.000
177A3318VAL00.0410.039167.496-0.008-0.0080.0000.0000.0000.000
178A3319ALA00.0040.002169.5000.0120.0120.0000.0000.0000.000
179A3320ASN0-0.025-0.023171.2600.0020.0020.0000.0000.0000.000
180A3321ALA00.0120.015173.942-0.005-0.0050.0000.0000.0000.000
181A3322VAL0-0.041-0.027174.1650.0120.0120.0000.0000.0000.000
182A3323ASN0-0.064-0.050171.8200.0170.0170.0000.0000.0000.000
183A3324ALA00.006-0.008175.5970.0010.0010.0000.0000.0000.000
184A3325THR0-0.024-0.013172.1900.0050.0050.0000.0000.0000.000
185A3326ASP-1-0.799-0.859171.905-1.926-1.9260.0000.0000.0000.000
186A3327ALA0-0.010-0.012171.1100.0100.0100.0000.0000.0000.000
187A3328VAL00.0290.023173.0110.0010.0010.0000.0000.0000.000
188A3329ASN0-0.021-0.012173.8270.0070.0070.0000.0000.0000.000
189A3330LYS10.9260.944175.4921.8291.8290.0000.0000.0000.000
190A3331GLY00.0210.012177.5410.0130.0130.0000.0000.0000.000
191A3332GLN00.0420.010176.8620.0050.0050.0000.0000.0000.000
192A3333MET00.0050.021180.3960.0080.0080.0000.0000.0000.000
193A3334LYS10.8480.911181.9201.7831.7830.0000.0000.0000.000
194A3335GLN00.0320.033183.3530.0200.0200.0000.0000.0000.000
195A3336ILE00.0490.023184.8690.0130.0130.0000.0000.0000.000
196A3337GLU-1-0.815-0.928183.591-1.785-1.7850.0000.0000.0000.000
197A3338ASP-1-0.884-0.937187.501-1.751-1.7510.0000.0000.0000.000
198A3339LYS10.8470.922188.8541.7511.7510.0000.0000.0000.000
199A3340ILE00.0060.007190.2220.0100.0100.0000.0000.0000.000
200A3341GLU-1-0.860-0.924192.140-1.679-1.6790.0000.0000.0000.000
201A3342GLU-1-0.813-0.884193.861-1.656-1.6560.0000.0000.0000.000
202A3343ILE0-0.030-0.014194.7180.0130.0130.0000.0000.0000.000
203A3344LEU00.0230.003194.8280.0110.0110.0000.0000.0000.000
204A3345SER00.0050.006197.8440.0130.0130.0000.0000.0000.000
205A3346LYS10.7580.864198.8751.6641.6640.0000.0000.0000.000
206A3347ILE00.011-0.001199.7430.0110.0110.0000.0000.0000.000
207A3348TYR00.0320.029202.1720.0110.0110.0000.0000.0000.000
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