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: R5N38

Calculation Name: 3WPR-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1355193.384372
FMO2-HF: Nuclear repulsion 1272908.116091
FMO2-HF: Total energy -82285.268281
FMO2-MP2: Total energy -82529.316355


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:3141:ACE )


Summations of interaction energy for fragment #1(A:3141:ACE )
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.
-2.437-0.0971.37-1.894-1.816-0.017
Interaction energy analysis for fragmet #1(A:3141:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.036
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].
3A3143GLN 00.0780.0453.8331.0031.711-0.006-0.306-0.3960.000
4A3144ILE 0-0.015-0.0176.9720.2800.2800.0000.0000.0000.000
5A3145GLU -1-0.876-0.9422.522-4.564-3.0301.376-1.584-1.325-0.017
6A3146ASP -1-0.797-0.8945.073-0.0740.0240.000-0.004-0.0950.000
7A3147LYS 10.8390.9187.9100.5150.5150.0000.0000.0000.000
8A3148ILE 0-0.025-0.01010.5280.0890.0890.0000.0000.0000.000
9A3149GLU -1-0.902-0.9449.0890.1410.1410.0000.0000.0000.000
10A3150GLU -1-0.903-0.95511.846-0.019-0.0190.0000.0000.0000.000
11A3151ILE 0-0.062-0.03913.7650.0300.0300.0000.0000.0000.000
12A3152LEU 00.006-0.00114.0940.0240.0240.0000.0000.0000.000
13A3153SER 00.0130.02115.9180.0220.0220.0000.0000.0000.000
14A3154LYS 10.9030.93617.6000.1040.1040.0000.0000.0000.000
15A3155ILE 00.0080.01019.7210.0070.0070.0000.0000.0000.000
16A3156TYR 00.0290.02620.5990.0110.0110.0000.0000.0000.000
17A3157HIS 0-0.012-0.01420.3370.0040.0040.0000.0000.0000.000
18A3158ILE 0-0.0030.00123.8680.0030.0030.0000.0000.0000.000
19A3159GLU -1-0.923-0.96124.860-0.037-0.0370.0000.0000.0000.000
20A3160ASN 0-0.014-0.01325.4490.0020.0020.0000.0000.0000.000
21A3161GLU -1-0.943-0.97027.825-0.009-0.0090.0000.0000.0000.000
22A3162ILE 0-0.031-0.00829.5440.0020.0020.0000.0000.0000.000
23A3163ALA 0-0.033-0.01631.1620.0020.0020.0000.0000.0000.000
24A3164ARG 10.9640.96831.784-0.001-0.0010.0000.0000.0000.000
25A3165ILE 00.0280.01933.1360.0010.0010.0000.0000.0000.000
26A3166LYS 10.9680.98234.2930.0220.0220.0000.0000.0000.000
27A3167LYS 10.9210.96236.1300.0010.0010.0000.0000.0000.000
28A3168LEU 00.0200.01337.9890.0010.0010.0000.0000.0000.000
29A3169ILE 00.0260.01839.3410.0010.0010.0000.0000.0000.000
30A3170LYS 10.8670.93641.7090.0080.0080.0000.0000.0000.000
31A3171ALA 0-0.005-0.00843.1710.0010.0010.0000.0000.0000.000
32A3172VAL 00.0420.01744.2750.0010.0010.0000.0000.0000.000
33A3173GLY 00.0320.02146.1910.0000.0000.0000.0000.0000.000
34A3174ASN 00.0270.00847.020-0.001-0.0010.0000.0000.0000.000
35A3175GLN 00.0260.02749.1390.0000.0000.0000.0000.0000.000
36A3176VAL 00.0230.01450.5260.0000.0000.0000.0000.0000.000
37A3177VAL 00.0490.02352.2460.0000.0000.0000.0000.0000.000
38A3178THR 0-0.021-0.01953.2360.0000.0000.0000.0000.0000.000
39A3179THR 0-0.036-0.01954.5540.0010.0010.0000.0000.0000.000
40A3180GLN 0-0.016-0.00856.2220.0000.0000.0000.0000.0000.000
41A3181THR 00.0000.00258.0310.0000.0000.0000.0000.0000.000
42A3182THR 0-0.020-0.00859.1370.0000.0000.0000.0000.0000.000
43A3183LEU 0-0.0200.00561.0520.0000.0000.0000.0000.0000.000
44A3184VAL 00.0130.00162.7780.0000.0000.0000.0000.0000.000
45A3185ASN 0-0.018-0.02463.4270.0000.0000.0000.0000.0000.000
46A3186SER 0-0.067-0.03464.6110.0000.0000.0000.0000.0000.000
47A3187LEU 0-0.047-0.00566.2550.0000.0000.0000.0000.0000.000
48A3188GLY 00.0710.05768.9310.0000.0000.0000.0000.0000.000
49A3189GLY 00.036-0.00370.5980.0000.0000.0000.0000.0000.000
50A3190ASN 0-0.036-0.01271.3310.0000.0000.0000.0000.0000.000
51A3191ALA 00.0010.02266.9570.0000.0000.0000.0000.0000.000
52A3192LYS 10.8950.93165.1060.0070.0070.0000.0000.0000.000
53A3193VAL 0-0.0050.00558.4820.0000.0000.0000.0000.0000.000
54A3194ASN 0-0.018-0.01861.6780.0010.0010.0000.0000.0000.000
55A3195ALA 00.0300.00158.8120.0000.0000.0000.0000.0000.000
56A3196ASP -1-0.869-0.90857.315-0.010-0.0100.0000.0000.0000.000
57A3197GLY 0-0.016-0.00656.483-0.001-0.0010.0000.0000.0000.000
58A3198THR 0-0.056-0.03757.3300.0010.0010.0000.0000.0000.000
59A3199ILE 00.009-0.00859.2910.0000.0000.0000.0000.0000.000
60A3200THR 0-0.051-0.00462.8360.0000.0000.0000.0000.0000.000
61A3201GLY 00.0350.00866.6180.0000.0000.0000.0000.0000.000
62A3202PRO 0-0.0190.00568.3190.0000.0000.0000.0000.0000.000
63A3203THR 0-0.056-0.04071.2700.0000.0000.0000.0000.0000.000
64A3204TYR 0-0.038-0.04071.7620.0000.0000.0000.0000.0000.000
65A3205ASN 0-0.029-0.03477.3170.0000.0000.0000.0000.0000.000
66A3206VAL 00.0060.01980.6070.0000.0000.0000.0000.0000.000
67A3207ALA 0-0.006-0.02183.1390.0000.0000.0000.0000.0000.000
68A3208GLN 0-0.027-0.00986.5020.0000.0000.0000.0000.0000.000
69A3209GLY 00.0420.03184.4720.0000.0000.0000.0000.0000.000
70A3210ASN 0-0.019-0.00879.5130.0000.0000.0000.0000.0000.000
71A3211GLN 00.0190.01877.6610.0000.0000.0000.0000.0000.000
72A3212THR 00.0210.01173.0060.0000.0000.0000.0000.0000.000
73A3213ASN 0-0.025-0.00972.1080.0000.0000.0000.0000.0000.000
74A3214VAL 00.0720.02071.4900.0000.0000.0000.0000.0000.000
75A3215GLY 00.0160.01973.8850.0000.0000.0000.0000.0000.000
76A3216ASP -1-0.818-0.92075.612-0.004-0.0040.0000.0000.0000.000
77A3217ALA 0-0.030-0.01877.3990.0000.0000.0000.0000.0000.000
78A3218LEU 0-0.003-0.01075.5030.0000.0000.0000.0000.0000.000
79A3219THR 00.0270.02179.5640.0000.0000.0000.0000.0000.000
80A3220ALA 0-0.039-0.01581.7620.0000.0000.0000.0000.0000.000
81A3221LEU 0-0.028-0.02780.9100.0000.0000.0000.0000.0000.000
82A3222ASP -1-0.884-0.92783.517-0.002-0.0020.0000.0000.0000.000
83A3223ASN 0-0.017-0.01885.4050.0000.0000.0000.0000.0000.000
84A3224ALA 0-0.034-0.01687.3960.0000.0000.0000.0000.0000.000
85A3225ILE 00.0300.01487.8400.0000.0000.0000.0000.0000.000
86A3226ASN 00.0160.01188.4440.0000.0000.0000.0000.0000.000
87A3227THR 0-0.011-0.00891.7710.0000.0000.0000.0000.0000.000
88A3228ALA 0-0.011-0.00792.7560.0000.0000.0000.0000.0000.000
89A3229ALA 0-0.005-0.00493.7750.0000.0000.0000.0000.0000.000
90A3230THR 0-0.068-0.03295.5330.0000.0000.0000.0000.0000.000
91A3231THR 0-0.065-0.04497.4280.0000.0000.0000.0000.0000.000
92A3232SER 00.0020.01497.4650.0000.0000.0000.0000.0000.000
93A3233LYS 10.8780.96199.9600.0010.0010.0000.0000.0000.000
94A3234SER 00.0030.002101.9750.0000.0000.0000.0000.0000.000
95A3235THR 0-0.061-0.031105.5050.0000.0000.0000.0000.0000.000
96A3236VAL 00.0190.012108.5100.0000.0000.0000.0000.0000.000
97A3237SER 0-0.022-0.010112.2060.0000.0000.0000.0000.0000.000
98A3238ASN 0-0.020-0.006115.2850.0000.0000.0000.0000.0000.000
99A3239GLY 00.0640.034119.0470.0000.0000.0000.0000.0000.000
100A3240GLN 00.011-0.022121.7910.0000.0000.0000.0000.0000.000
101A3241ASN 0-0.009-0.003125.2470.0000.0000.0000.0000.0000.000
102A3242ILE 00.0030.029120.0690.0000.0000.0000.0000.0000.000
103A3243VAL 0-0.002-0.003120.1930.0000.0000.0000.0000.0000.000
104A3244VAL 0-0.017-0.010114.6020.0000.0000.0000.0000.0000.000
105A3245SER 0-0.0150.007115.6040.0000.0000.0000.0000.0000.000
106A3246LYS 10.9620.987106.5880.0010.0010.0000.0000.0000.000
107A3247SER 0-0.021-0.006109.6620.0000.0000.0000.0000.0000.000
108A3248LYS 10.9560.969102.2650.0000.0000.0000.0000.0000.000
109A3249ASN 00.0250.011103.7070.0000.0000.0000.0000.0000.000
110A3250ALA 00.008-0.012102.2000.0000.0000.0000.0000.0000.000
111A3251ASP -1-0.863-0.90898.0800.0000.0000.0000.0000.0000.000
112A3252GLY 0-0.022-0.00598.3630.0000.0000.0000.0000.0000.000
113A3253SER 0-0.091-0.044100.3980.0000.0000.0000.0000.0000.000
114A3254ASP -1-0.914-0.973101.923-0.001-0.0010.0000.0000.0000.000
115A3255ASN 0-0.040-0.019105.5150.0000.0000.0000.0000.0000.000
116A3256TYR 00.008-0.022107.3080.0000.0000.0000.0000.0000.000
117A3257GLU -1-0.899-0.934111.9140.0000.0000.0000.0000.0000.000
118A3258VAL 0-0.020-0.017115.0610.0000.0000.0000.0000.0000.000
119A3259SER 00.0150.012117.9080.0000.0000.0000.0000.0000.000
120A3260THR 00.002-0.009121.5310.0000.0000.0000.0000.0000.000
121A3261ALA 0-0.043-0.025124.8590.0000.0000.0000.0000.0000.000
122A3262LYS 10.9400.949126.7720.0000.0000.0000.0000.0000.000
123A3263ASP -1-0.902-0.933129.7940.0000.0000.0000.0000.0000.000
124A3264LEU 0-0.058-0.027129.0400.0000.0000.0000.0000.0000.000
125A3265THR 00.002-0.001131.3790.0000.0000.0000.0000.0000.000
126A3266VAL 0-0.045-0.023131.2400.0000.0000.0000.0000.0000.000
127A3267ASP -1-0.845-0.909133.560-0.001-0.0010.0000.0000.0000.000
128A3268SER 0-0.109-0.073134.8700.0000.0000.0000.0000.0000.000
129A3269VAL 00.0200.020134.4660.0000.0000.0000.0000.0000.000
130A3270LYS 10.8900.941135.2640.0000.0000.0000.0000.0000.000
131A3271ALA 00.0210.005135.4300.0000.0000.0000.0000.0000.000
132A3272GLY 00.0070.006136.9080.0000.0000.0000.0000.0000.000
133A3273ASP -1-0.886-0.945138.7120.0000.0000.0000.0000.0000.000
134A3274THR 0-0.0120.007141.1950.0000.0000.0000.0000.0000.000
135A3275VAL 0-0.035-0.017139.8840.0000.0000.0000.0000.0000.000
136A3276LEU 00.0330.027138.1980.0000.0000.0000.0000.0000.000
137A3277ASN 00.038-0.008139.3440.0000.0000.0000.0000.0000.000
138A3278ASN 00.0310.010140.9740.0000.0000.0000.0000.0000.000
139A3279ALA 0-0.050-0.012142.5960.0000.0000.0000.0000.0000.000
140A3280GLY 00.0380.023144.5710.0000.0000.0000.0000.0000.000
141A3281ILE 0-0.013-0.003143.5050.0000.0000.0000.0000.0000.000
142A3282THR 0-0.037-0.019144.8170.0000.0000.0000.0000.0000.000
143A3283ILE 00.0170.012144.8490.0000.0000.0000.0000.0000.000
144A3284GLY 00.0330.001145.3120.0000.0000.0000.0000.0000.000
145A3285ASN 0-0.050-0.028146.5260.0000.0000.0000.0000.0000.000
146A3286ASN 00.020-0.007147.8400.0000.0000.0000.0000.0000.000
147A3287ALA 0-0.0300.008149.7280.0000.0000.0000.0000.0000.000
148A3288VAL 00.0180.007150.3890.0000.0000.0000.0000.0000.000
149A3289VAL 0-0.009-0.003149.7630.0000.0000.0000.0000.0000.000
150A3290LEU 00.0080.007148.6100.0000.0000.0000.0000.0000.000
151A3291ASN 00.0880.049148.9100.0000.0000.0000.0000.0000.000
152A3292ASN 0-0.007-0.015150.0560.0000.0000.0000.0000.0000.000
153A3293THR 0-0.059-0.028151.7310.0000.0000.0000.0000.0000.000
154A3294GLY 00.0470.019153.9550.0000.0000.0000.0000.0000.000
155A3295LEU 00.0050.010153.2430.0000.0000.0000.0000.0000.000
156A3296THR 0-0.015-0.026154.4710.0000.0000.0000.0000.0000.000
157A3297ILE 00.0010.010154.5650.0000.0000.0000.0000.0000.000
158A3298SER 0-0.0030.008154.7850.0000.0000.0000.0000.0000.000
159A3299GLY 0-0.005-0.006156.6100.0000.0000.0000.0000.0000.000
160A3300GLY 0-0.064-0.038159.5970.0000.0000.0000.0000.0000.000
161A3301PRO 0-0.0170.001160.3910.0000.0000.0000.0000.0000.000
162A3302SER 00.005-0.007159.2380.0000.0000.0000.0000.0000.000
163A3303VAL 0-0.0090.001158.6740.0000.0000.0000.0000.0000.000
164A3304THR 00.0140.005157.8340.0000.0000.0000.0000.0000.000
165A3305LEU 00.0480.005157.4260.0000.0000.0000.0000.0000.000
166A3306ALA 0-0.065-0.013160.4620.0000.0000.0000.0000.0000.000
167A3307GLY 00.0030.010162.8140.0000.0000.0000.0000.0000.000
168A3308ILE 0-0.039-0.026163.0310.0000.0000.0000.0000.0000.000
169A3309ASP -1-0.845-0.896163.3840.0000.0000.0000.0000.0000.000
170A3310ALA 00.009-0.013163.9720.0000.0000.0000.0000.0000.000
171A3311GLY 00.005-0.009164.2680.0000.0000.0000.0000.0000.000
172A3312ASN 0-0.082-0.039165.2060.0000.0000.0000.0000.0000.000
173A3313LYS 10.9480.981163.1100.0000.0000.0000.0000.0000.000
174A3314THR 0-0.021-0.013168.1670.0000.0000.0000.0000.0000.000
175A3315ILE 00.0680.035167.5350.0000.0000.0000.0000.0000.000
176A3316GLN 0-0.050-0.033167.3480.0000.0000.0000.0000.0000.000
177A3317ASN 0-0.030-0.020166.0240.0000.0000.0000.0000.0000.000
178A3318VAL 00.0440.042168.6480.0000.0000.0000.0000.0000.000
179A3319ALA 00.0100.004170.6590.0000.0000.0000.0000.0000.000
180A3320ASN 0-0.014-0.012172.3960.0000.0000.0000.0000.0000.000
181A3321ALA 00.0260.017175.0890.0000.0000.0000.0000.0000.000
182A3322VAL 0-0.053-0.018175.2690.0000.0000.0000.0000.0000.000
183A3323ASN 0-0.069-0.049173.2650.0000.0000.0000.0000.0000.000
184A3324ALA 00.011-0.005176.8030.0000.0000.0000.0000.0000.000
185A3325THR 0-0.031-0.014173.4300.0000.0000.0000.0000.0000.000
186A3326ASP -1-0.808-0.874172.9310.0000.0000.0000.0000.0000.000
187A3327ALA 0-0.017-0.015172.4040.0000.0000.0000.0000.0000.000
188A3328VAL 00.0310.022174.2630.0000.0000.0000.0000.0000.000
189A3329ASN 0-0.024-0.025174.9200.0000.0000.0000.0000.0000.000
190A3330LYS 11.0090.977176.6970.0000.0000.0000.0000.0000.000
191A3331GLY 00.0110.011178.7140.0000.0000.0000.0000.0000.000
192A3332GLN 00.0560.018177.8980.0000.0000.0000.0000.0000.000
193A3333MET 00.0070.020181.5680.0000.0000.0000.0000.0000.000
194A3334LYS 10.8500.923183.1090.0000.0000.0000.0000.0000.000
195A3335GLN 00.0260.019184.4370.0000.0000.0000.0000.0000.000
196A3336ILE 00.0350.014186.4430.0000.0000.0000.0000.0000.000
197A3337GLU -1-0.884-0.955185.5200.0000.0000.0000.0000.0000.000
198A3338ASP -1-0.863-0.928188.8580.0000.0000.0000.0000.0000.000
199A3339LYS 10.8330.917190.3810.0000.0000.0000.0000.0000.000
200A3340ILE 0-0.0110.001191.3280.0000.0000.0000.0000.0000.000
201A3341GLU -1-0.885-0.941193.3370.0000.0000.0000.0000.0000.000
202A3342GLU -1-0.847-0.917195.0570.0000.0000.0000.0000.0000.000
203A3343ILE 0-0.040-0.024196.2330.0000.0000.0000.0000.0000.000
204A3344LEU 00.0290.004196.2810.0000.0000.0000.0000.0000.000
205A3345SER 00.0140.021199.0020.0000.0000.0000.0000.0000.000
206A3346LYS 10.8260.907200.7710.0000.0000.0000.0000.0000.000
207A3347ILE 00.000-0.010201.2590.0000.0000.0000.0000.0000.000
208A3348TYR 00.0320.025203.3870.0000.0000.0000.0000.0000.000
209A3349HIS 0-0.017-0.023203.9690.0000.0000.0000.0000.0000.000
210A3350ILE 00.0000.006207.0450.0000.0000.0000.0000.0000.000
211A3351GLU -1-0.941-0.968206.1150.0000.0000.0000.0000.0000.000
212A3352ASN 0-0.043-0.028209.3900.0000.0000.0000.0000.0000.000
213A3353GLU -1-0.892-0.941211.2840.0000.0000.0000.0000.0000.000
214A3354ILE 0-0.013-0.004212.4130.0000.0000.0000.0000.0000.000
215A3355ALA 0-0.031-0.020213.8280.0000.0000.0000.0000.0000.000
216A3356ARG 10.9700.995215.4340.0000.0000.0000.0000.0000.000
217A3357ILE 00.0260.007217.1950.0000.0000.0000.0000.0000.000
218A3358LYS 10.9570.979214.7800.0000.0000.0000.0000.0000.000
219A3359LYS 10.9320.972219.7130.0000.0000.0000.0000.0000.000
220A3360LEU 00.004-0.016221.0290.0000.0000.0000.0000.0000.000
221A3361ILE 00.0230.025222.6630.0000.0000.0000.0000.0000.000
222A3362LYS 10.9180.960224.1120.0000.0000.0000.0000.0000.000
223A3363LEU 0-0.035-0.033224.9420.0000.0000.0000.0000.0000.000
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