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: 6694Z

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 OptAll
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 -1353344.673185
FMO2-HF: Nuclear repulsion 1271228.971972
FMO2-HF: Total energy -82115.701214
FMO2-MP2: Total energy -82359.12366


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.
-158.712-158.41529.264-16.516-13.044-0.157
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 : 0.885 / q_NPA : 0.917
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].
3A3144ILE0-0.015-0.0053.0534.4778.6270.026-2.173-2.0020.007
4A3145GLU-1-0.784-0.8861.700-141.570-147.01429.196-13.544-10.208-0.158
5A3146ASP-1-0.802-0.9053.405-56.125-54.5340.042-0.799-0.834-0.006
6A3147LYS10.8690.9275.61034.55834.5580.0000.0000.0000.000
7A3148ILE0-0.0060.0057.8913.7213.7210.0000.0000.0000.000
8A3149GLU-1-0.914-0.9508.387-28.375-28.3750.0000.0000.0000.000
9A3150GLU-1-0.815-0.8969.805-18.015-18.0150.0000.0000.0000.000
10A3151ILE0-0.043-0.02511.8402.3802.3800.0000.0000.0000.000
11A3152LEU00.0090.00112.2961.8271.8270.0000.0000.0000.000
12A3153SER0-0.0040.00914.0352.0412.0410.0000.0000.0000.000
13A3154LYS10.8310.88415.54719.87719.8770.0000.0000.0000.000
14A3155ILE0-0.0120.00417.1041.0591.0590.0000.0000.0000.000
15A3156TYR00.0670.04518.7201.0281.0280.0000.0000.0000.000
16A3157HIS0-0.018-0.00618.0411.5831.5830.0000.0000.0000.000
17A3158ILE0-0.008-0.00121.3990.8550.8550.0000.0000.0000.000
18A3159GLU-1-0.913-0.96322.161-13.398-13.3980.0000.0000.0000.000
19A3160ASN0-0.056-0.03823.3931.1001.1000.0000.0000.0000.000
20A3161GLU-1-0.817-0.89426.256-10.343-10.3430.0000.0000.0000.000
21A3162ILE0-0.019-0.00927.7750.6190.6190.0000.0000.0000.000
22A3163ALA0-0.034-0.01929.1530.4940.4940.0000.0000.0000.000
23A3164ARG10.8400.90629.10210.83510.8350.0000.0000.0000.000
24A3165ILE00.0340.00830.7740.4180.4180.0000.0000.0000.000
25A3166LYS10.9540.97931.59410.29110.2910.0000.0000.0000.000
26A3167LYS10.9440.97733.5379.6839.6830.0000.0000.0000.000
27A3168LEU00.0060.01135.4480.2800.2800.0000.0000.0000.000
28A3169ILE00.0320.01736.8710.2590.2590.0000.0000.0000.000
29A3170LYS10.8950.94739.7137.4657.4650.0000.0000.0000.000
30A3171ALA0-0.014-0.00641.2020.2230.2230.0000.0000.0000.000
31A3172VAL00.0540.02042.4810.2110.2110.0000.0000.0000.000
32A3173GLY00.0270.01344.0220.1830.1830.0000.0000.0000.000
33A3174ASN00.006-0.00244.9590.1910.1910.0000.0000.0000.000
34A3175GLN00.0240.03346.8780.0560.0560.0000.0000.0000.000
35A3176VAL00.0170.02148.2420.1740.1740.0000.0000.0000.000
36A3177VAL00.0580.03350.0890.1430.1430.0000.0000.0000.000
37A3178THR0-0.014-0.00951.1790.1650.1650.0000.0000.0000.000
38A3179THR0-0.035-0.01752.3890.1520.1520.0000.0000.0000.000
39A3180GLN0-0.010-0.01053.5690.0610.0610.0000.0000.0000.000
40A3181THR0-0.008-0.01355.7510.1350.1350.0000.0000.0000.000
41A3182THR0-0.027-0.02356.8680.1190.1190.0000.0000.0000.000
42A3183LEU0-0.0160.00758.8990.1080.1080.0000.0000.0000.000
43A3184VAL0-0.002-0.00160.5950.0990.0990.0000.0000.0000.000
44A3185ASN0-0.008-0.01761.4270.1310.1310.0000.0000.0000.000
45A3186SER0-0.064-0.03362.5350.0830.0830.0000.0000.0000.000
46A3187LEU0-0.039-0.00364.0020.0780.0780.0000.0000.0000.000
47A3188GLY00.0670.05166.6300.0980.0980.0000.0000.0000.000
48A3189GLY00.0290.00068.425-0.029-0.0290.0000.0000.0000.000
49A3190ASN0-0.040-0.02569.4190.0020.0020.0000.0000.0000.000
50A3191ALA00.0060.02364.985-0.031-0.0310.0000.0000.0000.000
51A3192LYS10.8630.90662.8355.0365.0360.0000.0000.0000.000
52A3193VAL00.0180.00656.2720.0050.0050.0000.0000.0000.000
53A3194ASN0-0.038-0.01358.9560.1300.1300.0000.0000.0000.000
54A3195ALA00.024-0.00156.576-0.095-0.0950.0000.0000.0000.000
55A3196ASP-1-0.834-0.88854.991-5.662-5.6620.0000.0000.0000.000
56A3197GLY0-0.0030.00254.050-0.095-0.0950.0000.0000.0000.000
57A3198THR0-0.075-0.05654.9930.0350.0350.0000.0000.0000.000
58A3199ILE0-0.001-0.01957.269-0.014-0.0140.0000.0000.0000.000
59A3200THR0-0.0380.01660.5720.0430.0430.0000.0000.0000.000
60A3201GLY00.0500.01364.287-0.015-0.0150.0000.0000.0000.000
61A3202PRO0-0.0170.00065.8620.0220.0220.0000.0000.0000.000
62A3203THR0-0.031-0.02969.0810.0250.0250.0000.0000.0000.000
63A3204TYR0-0.046-0.03369.5800.0270.0270.0000.0000.0000.000
64A3205ASN0-0.046-0.02775.101-0.005-0.0050.0000.0000.0000.000
65A3206VAL00.0220.02278.5050.0520.0520.0000.0000.0000.000
66A3207ALA00.009-0.00580.9500.0050.0050.0000.0000.0000.000
67A3208GLN0-0.014-0.00284.3090.0140.0140.0000.0000.0000.000
68A3209GLY00.0230.02382.3130.0260.0260.0000.0000.0000.000
69A3210ASN0-0.024-0.01577.264-0.040-0.0400.0000.0000.0000.000
70A3211GLN00.0080.00075.549-0.018-0.0180.0000.0000.0000.000
71A3212THR00.0190.01070.512-0.021-0.0210.0000.0000.0000.000
72A3213ASN0-0.039-0.03569.950-0.079-0.0790.0000.0000.0000.000
73A3214VAL00.0750.02069.6910.0660.0660.0000.0000.0000.000
74A3215GLY00.0230.02872.0290.0560.0560.0000.0000.0000.000
75A3216ASP-1-0.806-0.88773.652-4.254-4.2540.0000.0000.0000.000
76A3217ALA0-0.031-0.01875.2210.0690.0690.0000.0000.0000.000
77A3218LEU00.000-0.00974.0610.0630.0630.0000.0000.0000.000
78A3219THR00.004-0.00377.2620.0630.0630.0000.0000.0000.000
79A3220ALA00.0010.00379.6950.0660.0660.0000.0000.0000.000
80A3221LEU0-0.025-0.01878.8510.0620.0620.0000.0000.0000.000
81A3222ASP-1-0.875-0.93381.861-3.822-3.8220.0000.0000.0000.000
82A3223ASN0-0.017-0.01983.3340.0940.0940.0000.0000.0000.000
83A3224ALA0-0.0080.00985.4180.0610.0610.0000.0000.0000.000
84A3225ILE0-0.0040.00085.1800.0570.0570.0000.0000.0000.000
85A3226ASN0-0.016-0.00586.3730.0860.0860.0000.0000.0000.000
86A3227THR0-0.033-0.01689.6760.0620.0620.0000.0000.0000.000
87A3228ALA00.0150.00490.7910.0490.0490.0000.0000.0000.000
88A3229ALA0-0.0120.00491.6800.0470.0470.0000.0000.0000.000
89A3230THR0-0.053-0.03193.5020.0500.0500.0000.0000.0000.000
90A3231THR0-0.010-0.02295.6000.0300.0300.0000.0000.0000.000
91A3232SER0-0.044-0.02695.2650.0340.0340.0000.0000.0000.000
92A3233LYS10.8320.93497.9353.2893.2890.0000.0000.0000.000
93A3234SER00.011-0.00299.9890.0340.0340.0000.0000.0000.000
94A3235THR0-0.078-0.041103.4280.0100.0100.0000.0000.0000.000
95A3236VAL00.0170.014106.6890.0080.0080.0000.0000.0000.000
96A3237SER0-0.0030.000110.415-0.005-0.0050.0000.0000.0000.000
97A3238ASN0-0.020-0.018113.487-0.014-0.0140.0000.0000.0000.000
98A3239GLY00.0560.024117.289-0.009-0.0090.0000.0000.0000.000
99A3240GLN00.014-0.004120.2220.0010.0010.0000.0000.0000.000
100A3241ASN0-0.013-0.010123.7150.0060.0060.0000.0000.0000.000
101A3242ILE0-0.0070.014118.7070.0010.0010.0000.0000.0000.000
102A3243VAL00.0030.003118.7450.0010.0010.0000.0000.0000.000
103A3244VAL0-0.024-0.019112.964-0.008-0.0080.0000.0000.0000.000
104A3245SER0-0.056-0.028114.137-0.002-0.0020.0000.0000.0000.000
105A3246LYS10.8500.915104.4713.0813.0810.0000.0000.0000.000
106A3247SER00.0110.006108.315-0.002-0.0020.0000.0000.0000.000
107A3248LYS10.8200.884100.5093.2093.2090.0000.0000.0000.000
108A3249ASN00.0030.021101.9050.0530.0530.0000.0000.0000.000
109A3250ALA00.014-0.009100.758-0.018-0.0180.0000.0000.0000.000
110A3251ASP-1-0.814-0.86896.637-3.323-3.3230.0000.0000.0000.000
111A3252GLY00.0140.01796.586-0.038-0.0380.0000.0000.0000.000
112A3253SER0-0.058-0.04198.6990.0200.0200.0000.0000.0000.000
113A3254ASP-1-0.823-0.911100.077-3.178-3.1780.0000.0000.0000.000
114A3255ASN0-0.035-0.027103.6450.0130.0130.0000.0000.0000.000
115A3256TYR00.018-0.011104.9700.0040.0040.0000.0000.0000.000
116A3257GLU-1-0.832-0.875110.260-2.836-2.8360.0000.0000.0000.000
117A3258VAL00.012-0.005113.3560.0090.0090.0000.0000.0000.000
118A3259SER0-0.032-0.016116.3030.0140.0140.0000.0000.0000.000
119A3260THR00.003-0.001120.104-0.009-0.0090.0000.0000.0000.000
120A3261ALA0-0.019-0.004123.390-0.009-0.0090.0000.0000.0000.000
121A3262LYS10.9330.954125.3212.5802.5800.0000.0000.0000.000
122A3263ASP-1-0.895-0.930128.293-2.482-2.4820.0000.0000.0000.000
123A3264LEU0-0.033-0.022127.647-0.021-0.0210.0000.0000.0000.000
124A3265THR0-0.038-0.032129.8200.0240.0240.0000.0000.0000.000
125A3266VAL0-0.0090.002129.241-0.026-0.0260.0000.0000.0000.000
126A3267ASP-1-0.871-0.925131.414-2.469-2.4690.0000.0000.0000.000
127A3268SER0-0.080-0.055133.4290.0250.0250.0000.0000.0000.000
128A3269VAL00.0120.011132.761-0.023-0.0230.0000.0000.0000.000
129A3270LYS10.8790.931133.7192.4232.4230.0000.0000.0000.000
130A3271ALA00.0210.012133.806-0.022-0.0220.0000.0000.0000.000
131A3272GLY00.0380.022135.2370.0190.0190.0000.0000.0000.000
132A3273ASP-1-0.903-0.957137.068-2.346-2.3460.0000.0000.0000.000
133A3274THR0-0.0140.011139.6440.0240.0240.0000.0000.0000.000
134A3275VAL0-0.032-0.024138.390-0.026-0.0260.0000.0000.0000.000
135A3276LEU00.0300.022136.8430.0210.0210.0000.0000.0000.000
136A3277ASN00.024-0.004137.752-0.013-0.0130.0000.0000.0000.000
137A3278ASN00.0460.023139.0860.0060.0060.0000.0000.0000.000
138A3279ALA0-0.0230.000140.6440.0130.0130.0000.0000.0000.000
139A3280GLY00.0080.003142.8700.0220.0220.0000.0000.0000.000
140A3281ILE00.0010.000141.810-0.021-0.0210.0000.0000.0000.000
141A3282THR0-0.053-0.033143.2480.0230.0230.0000.0000.0000.000
142A3283ILE00.0090.010143.156-0.019-0.0190.0000.0000.0000.000
143A3284GLY00.0420.014143.3870.0190.0190.0000.0000.0000.000
144A3285ASN0-0.044-0.028144.513-0.011-0.0110.0000.0000.0000.000
145A3286ASN0-0.004-0.009145.9520.0050.0050.0000.0000.0000.000
146A3287ALA00.0060.016147.9550.0190.0190.0000.0000.0000.000
147A3288VAL00.004-0.001148.5420.0200.0200.0000.0000.0000.000
148A3289VAL0-0.012-0.003147.879-0.020-0.0200.0000.0000.0000.000
149A3290LEU00.0140.007147.0380.0190.0190.0000.0000.0000.000
150A3291ASN00.0740.050147.144-0.011-0.0110.0000.0000.0000.000
151A3292ASN00.0240.001147.8030.0080.0080.0000.0000.0000.000
152A3293THR0-0.075-0.041149.5920.0140.0140.0000.0000.0000.000
153A3294GLY00.0540.017152.2050.0210.0210.0000.0000.0000.000
154A3295LEU0-0.0020.016151.333-0.019-0.0190.0000.0000.0000.000
155A3296THR0-0.025-0.036152.6950.0220.0220.0000.0000.0000.000
156A3297ILE00.0110.016152.639-0.019-0.0190.0000.0000.0000.000
157A3298SER00.0090.014152.7840.0220.0220.0000.0000.0000.000
158A3299GLY00.0110.004154.7200.0000.0000.0000.0000.0000.000
159A3300GLY0-0.046-0.027157.6820.0150.0150.0000.0000.0000.000
160A3301PRO00.0070.013158.0330.0040.0040.0000.0000.0000.000
161A3302SER0-0.013-0.011157.362-0.017-0.0170.0000.0000.0000.000
162A3303VAL00.007-0.004156.8710.0160.0160.0000.0000.0000.000
163A3304THR0-0.014-0.006156.182-0.017-0.0170.0000.0000.0000.000
164A3305LEU00.0260.003154.6910.0130.0130.0000.0000.0000.000
165A3306ALA0-0.032-0.001158.6390.0110.0110.0000.0000.0000.000
166A3307GLY00.0040.012161.1370.0180.0180.0000.0000.0000.000
167A3308ILE0-0.039-0.023161.100-0.016-0.0160.0000.0000.0000.000
168A3309ASP-1-0.853-0.915161.698-2.000-2.0000.0000.0000.0000.000
169A3310ALA00.0160.003162.032-0.012-0.0120.0000.0000.0000.000
170A3311GLY00.0270.013161.984-0.004-0.0040.0000.0000.0000.000
171A3312ASN0-0.084-0.045162.8510.0090.0090.0000.0000.0000.000
172A3313LYS10.8650.934160.9652.0352.0350.0000.0000.0000.000
173A3314THR00.0070.004166.3660.0010.0010.0000.0000.0000.000
174A3315ILE00.0470.028165.818-0.013-0.0130.0000.0000.0000.000
175A3316GLN0-0.046-0.034165.7000.0120.0120.0000.0000.0000.000
176A3317ASN0-0.019-0.020164.0790.0020.0020.0000.0000.0000.000
177A3318VAL00.0150.027167.619-0.006-0.0060.0000.0000.0000.000
178A3319ALA00.0280.015169.0840.0140.0140.0000.0000.0000.000
179A3320ASN0-0.037-0.023170.9210.0010.0010.0000.0000.0000.000
180A3321ALA00.0220.020173.663-0.005-0.0050.0000.0000.0000.000
181A3322VAL0-0.048-0.033174.0740.0130.0130.0000.0000.0000.000
182A3323ASN0-0.048-0.040171.3550.0150.0150.0000.0000.0000.000
183A3324ALA0-0.026-0.023175.2130.0010.0010.0000.0000.0000.000
184A3325THR00.007-0.002171.8860.0050.0050.0000.0000.0000.000
185A3326ASP-1-0.794-0.850171.399-1.926-1.9260.0000.0000.0000.000
186A3327ALA0-0.009-0.013170.4260.0100.0100.0000.0000.0000.000
187A3328VAL00.0270.017172.3450.0000.0000.0000.0000.0000.000
188A3329ASN0-0.004-0.002173.5220.0050.0050.0000.0000.0000.000
189A3330LYS10.8430.887175.2761.8321.8320.0000.0000.0000.000
190A3331GLY00.0150.013177.0970.0120.0120.0000.0000.0000.000
191A3332GLN00.029-0.002176.5630.0050.0050.0000.0000.0000.000
192A3333MET0-0.0100.007179.7520.0080.0080.0000.0000.0000.000
193A3334LYS10.8240.909181.3101.7851.7850.0000.0000.0000.000
194A3335GLN00.0550.043182.9270.0230.0230.0000.0000.0000.000
195A3336ILE00.0090.018183.9920.0130.0130.0000.0000.0000.000
196A3337GLU-1-0.736-0.875183.053-1.789-1.7890.0000.0000.0000.000
197A3338ASP-1-0.861-0.938186.719-1.754-1.7540.0000.0000.0000.000
198A3339LYS10.8380.904188.1041.7571.7570.0000.0000.0000.000
199A3340ILE00.0090.009189.4950.0090.0090.0000.0000.0000.000
200A3341GLU-1-0.840-0.893191.749-1.681-1.6810.0000.0000.0000.000
201A3342GLU-1-0.831-0.888193.559-1.659-1.6590.0000.0000.0000.000
202A3343ILE0-0.027-0.013194.3070.0130.0130.0000.0000.0000.000
203A3344LEU00.0180.007194.1690.0110.0110.0000.0000.0000.000
204A3345SER00.020-0.015197.3080.0140.0140.0000.0000.0000.000
205A3346LYS10.7570.872198.4471.6671.6670.0000.0000.0000.000
206A3347ILE0-0.008-0.004199.2330.0110.0110.0000.0000.0000.000
207A3348TYR00.0460.034201.8030.0110.0110.0000.0000.0000.000
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209A3350ILE0-0.016-0.001204.5090.0120.0120.0000.0000.0000.000
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