Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QY4NY

Calculation Name: 4OF0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OF0

Chain ID: A

ChEMBL ID:

UniProt ID: B1Q236

Base Structure: X-ray

Registration Date: 2023-06-26

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2465905.804972
FMO2-HF: Nuclear repulsion 2375890.406275
FMO2-HF: Total energy -90015.398697
FMO2-MP2: Total energy -90277.004976


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:23:GLN)


Summations of interaction energy for fragment #1(A:23:GLN)
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.
-53.148-42.05429.556-16.616-24.034-0.009
Interaction energy analysis for fragmet #1(A:23:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.026
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].
3A25ILE00.020-0.0073.808-0.8691.644-0.033-1.399-1.0820.005
4A26VAL0-0.063-0.0136.974-0.121-0.1210.0000.0000.0000.000
5A27GLU-1-0.850-0.9039.1250.2690.2690.0000.0000.0000.000
6A28ALA00.0250.00311.6830.0300.0300.0000.0000.0000.000
7A29PRO00.0130.01612.7720.0610.0610.0000.0000.0000.000
8A30LYS10.9740.99215.938-0.179-0.1790.0000.0000.0000.000
9A31ASP-1-0.823-0.90819.382-0.128-0.1280.0000.0000.0000.000
10A32THR0-0.105-0.05521.9570.0460.0460.0000.0000.0000.000
11A33LEU0-0.017-0.00724.520-0.021-0.0210.0000.0000.0000.000
12A34ALA00.0390.01627.2220.0210.0210.0000.0000.0000.000
13A35ALA0-0.0100.00729.238-0.019-0.0190.0000.0000.0000.000
14A36VAL0-0.028-0.02831.9870.0090.0090.0000.0000.0000.000
15A37GLY0-0.046-0.01932.4330.0020.0020.0000.0000.0000.000
16A38GLU-1-0.911-0.94030.5770.0870.0870.0000.0000.0000.000
17A39THR0-0.010-0.01925.772-0.008-0.0080.0000.0000.0000.000
18A40ALA0-0.0140.00424.2820.0020.0020.0000.0000.0000.000
19A41ILE0-0.013-0.02020.0700.0300.0300.0000.0000.0000.000
20A42LEU0-0.0080.01517.944-0.021-0.0210.0000.0000.0000.000
21A43THR0-0.041-0.04215.9870.0410.0410.0000.0000.0000.000
22A44CYS00.0090.01110.1380.1100.1100.0000.0000.0000.000
23A45ARG10.8310.93410.176-0.580-0.5800.0000.0000.0000.000
24A46VAL0-0.016-0.0074.902-0.281-0.2810.0000.0000.0000.000
25A47GLU-1-0.836-0.9064.0121.7841.9650.000-0.051-0.1300.000
26A48HIS0-0.022-0.0322.232-2.450-0.3072.078-2.051-2.169-0.017
27A49GLN00.0170.0072.112-4.642-2.5536.735-4.575-4.250-0.017
28A50GLN00.0240.0031.835-13.779-18.08613.177-3.368-5.5030.031
29A51GLY00.0300.0372.510-7.953-7.4691.188-0.142-1.5300.010
30A52PRO0-0.028-0.0064.0880.7700.9660.001-0.017-0.1800.000
31A53VAL00.0210.0176.235-0.503-0.5030.0000.0000.0000.000
32A54GLN0-0.009-0.0158.089-0.031-0.0310.0000.0000.0000.000
33A55TRP0-0.021-0.03410.720-0.232-0.2320.0000.0000.0000.000
34A56MET0-0.032-0.00811.025-0.044-0.0440.0000.0000.0000.000
35A57LYS10.7720.86215.1260.1620.1620.0000.0000.0000.000
36A58ASP-1-0.911-0.95618.890-0.343-0.3430.0000.0000.0000.000
37A59ASP-1-0.895-0.93716.057-0.678-0.6780.0000.0000.0000.000
38A60PHE00.0080.00216.433-0.033-0.0330.0000.0000.0000.000
39A61GLY00.0250.01513.7840.0520.0520.0000.0000.0000.000
40A62LEU0-0.058-0.03014.4110.0510.0510.0000.0000.0000.000
41A63GLY00.0220.01514.8450.0620.0620.0000.0000.0000.000
42A64THR0-0.015-0.02010.2910.0220.0220.0000.0000.0000.000
43A65ASP-1-0.828-0.90513.2380.5430.5430.0000.0000.0000.000
44A66ARG10.8490.90313.322-1.024-1.0240.0000.0000.0000.000
45A67ASP-1-0.893-0.93416.4910.7320.7320.0000.0000.0000.000
46A68LYS10.8250.89719.174-0.492-0.4920.0000.0000.0000.000
47A69PRO0-0.073-0.03020.2620.0170.0170.0000.0000.0000.000
48A70LEU00.0080.02416.888-0.001-0.0010.0000.0000.0000.000
49A71PRO00.003-0.00618.739-0.040-0.0400.0000.0000.0000.000
50A72GLY00.0040.02120.448-0.038-0.0380.0000.0000.0000.000
51A73ASN0-0.031-0.03921.661-0.020-0.0200.0000.0000.0000.000
52A74LYS10.9891.00123.733-0.071-0.0710.0000.0000.0000.000
53A75ARG10.7570.85525.900-0.037-0.0370.0000.0000.0000.000
54A76TYR0-0.024-0.03120.3150.0020.0020.0000.0000.0000.000
55A77ARG10.9180.94920.694-0.329-0.3290.0000.0000.0000.000
56A78MET00.0240.03613.1730.0320.0320.0000.0000.0000.000
57A79VAL0-0.037-0.01617.4650.0370.0370.0000.0000.0000.000
58A80GLY00.0470.01716.3630.0240.0240.0000.0000.0000.000
59A81SER0-0.038-0.01816.3400.0510.0510.0000.0000.0000.000
60A82ALA00.0580.01412.8860.0850.0850.0000.0000.0000.000
61A83ALA0-0.031-0.01112.1270.2400.2400.0000.0000.0000.000
62A84ASN0-0.087-0.05712.4940.1310.1310.0000.0000.0000.000
63A85GLY00.0660.0419.5910.0110.0110.0000.0000.0000.000
64A86GLU-1-0.883-0.9289.8650.8030.8030.0000.0000.0000.000
65A87TYR0-0.018-0.0348.7590.1790.1790.0000.0000.0000.000
66A88ASN00.0490.02712.466-0.119-0.1190.0000.0000.0000.000
67A89LEU00.0080.01415.6010.0300.0300.0000.0000.0000.000
68A90GLU-1-0.830-0.89117.8040.2240.2240.0000.0000.0000.000
69A91ILE0-0.0010.00821.419-0.011-0.0110.0000.0000.0000.000
70A92SER00.030-0.00824.272-0.014-0.0140.0000.0000.0000.000
71A93ASN0-0.049-0.02827.692-0.006-0.0060.0000.0000.0000.000
72A94VAL00.0070.01927.194-0.013-0.0130.0000.0000.0000.000
73A95THR0-0.011-0.01929.404-0.011-0.0110.0000.0000.0000.000
74A96LEU00.053-0.00530.087-0.004-0.0040.0000.0000.0000.000
75A97PHE00.0050.01028.696-0.011-0.0110.0000.0000.0000.000
76A98ASP-1-0.724-0.80625.7810.0120.0120.0000.0000.0000.000
77A99ASP-1-0.824-0.90125.355-0.090-0.0900.0000.0000.0000.000
78A100ASP-1-0.788-0.88622.759-0.212-0.2120.0000.0000.0000.000
79A101ASP-1-0.881-0.94720.276-0.257-0.2570.0000.0000.0000.000
80A102PHE0-0.031-0.03617.800-0.010-0.0100.0000.0000.0000.000
81A103ALA00.0010.00313.571-0.025-0.0250.0000.0000.0000.000
82A105GLN00.0650.0337.234-0.090-0.0900.0000.0000.0000.000
83A106ILE0-0.037-0.0172.518-1.5650.1352.562-1.167-3.0950.012
84A107SER0-0.025-0.0364.046-3.437-3.2560.001-0.060-0.1210.000
85A108GLU-1-0.876-0.9442.728-9.855-8.3180.177-0.808-0.907-0.011
86A109SER0-0.036-0.0373.6641.1271.8000.013-0.166-0.5200.000
87A110ASP-1-0.907-0.9494.780-1.439-1.424-0.001-0.002-0.0110.000
88A111HIS0-0.075-0.0457.801-0.002-0.0020.0000.0000.0000.000
89A112ALA0-0.009-0.0083.231-0.6800.0350.205-0.326-0.5940.003
90A113LYS10.9581.0023.5652.2433.0710.057-0.343-0.541-0.001
91A114ALA00.0320.0092.154-12.686-11.7582.770-1.643-2.055-0.025
92A115VAL0-0.091-0.0382.506-0.0061.1380.627-0.496-1.2760.001
93A116VAL00.003-0.0014.9721.4611.535-0.001-0.002-0.0700.000
94A117SER0-0.0090.0018.6540.0460.0460.0000.0000.0000.000
95A118SER0-0.005-0.00510.853-0.054-0.0540.0000.0000.0000.000
96A119LYS10.8290.89914.4270.5650.5650.0000.0000.0000.000
97A120ALA0-0.0030.01917.1830.0280.0280.0000.0000.0000.000
98A121LYS10.8700.96219.6030.1530.1530.0000.0000.0000.000
99A122LEU0-0.032-0.00922.9170.0370.0370.0000.0000.0000.000
100A123THR0-0.026-0.02724.522-0.018-0.0180.0000.0000.0000.000
101A124VAL0-0.025-0.01228.2540.0190.0190.0000.0000.0000.000
102A125LEU0-0.053-0.03030.536-0.013-0.0130.0000.0000.0000.000
103A126VAL0-0.008-0.02233.8570.0080.0080.0000.0000.0000.000
104A127ARG10.8870.93337.185-0.039-0.0390.0000.0000.0000.000
105A128PRO0-0.0060.00139.832-0.001-0.0010.0000.0000.0000.000
106A129THR0-0.034-0.01743.2230.0040.0040.0000.0000.0000.000
107A130PRO00.0420.02046.421-0.003-0.0030.0000.0000.0000.000
108A131PRO0-0.0350.00348.502-0.003-0.0030.0000.0000.0000.000
109A132LYS10.8530.92050.877-0.010-0.0100.0000.0000.0000.000
110A133ILE00.019-0.00254.331-0.003-0.0030.0000.0000.0000.000
111A134VAL0-0.050-0.02957.4690.0010.0010.0000.0000.0000.000
112A135LYS10.8340.92858.820-0.010-0.0100.0000.0000.0000.000
113A136SER0-0.009-0.01662.3250.0000.0000.0000.0000.0000.000
114A137HIS0-0.004-0.01860.7810.0000.0000.0000.0000.0000.000
115A138HIS0-0.0110.02064.8330.0010.0010.0000.0000.0000.000
116A139SER0-0.0230.00066.1560.0000.0000.0000.0000.0000.000
117A140LEU00.015-0.01364.687-0.001-0.0010.0000.0000.0000.000
118A141LYS10.8480.91267.900-0.005-0.0050.0000.0000.0000.000
119A142ALA00.010-0.00169.752-0.001-0.0010.0000.0000.0000.000
120A143ILE0-0.010-0.00271.9030.0010.0010.0000.0000.0000.000
121A144ALA00.0050.00972.858-0.001-0.0010.0000.0000.0000.000
122A145GLY00.0100.00672.4820.0000.0000.0000.0000.0000.000
123A146ASP-1-0.901-0.94972.807-0.008-0.0080.0000.0000.0000.000
124A147PRO0-0.063-0.03268.4980.0010.0010.0000.0000.0000.000
125A148ILE0-0.026-0.00866.0810.0000.0000.0000.0000.0000.000
126A149THR00.002-0.01662.2300.0000.0000.0000.0000.0000.000
127A150GLN0-0.063-0.03360.8520.0030.0030.0000.0000.0000.000
128A151SER00.0320.00957.483-0.001-0.0010.0000.0000.0000.000
129A152CYS0-0.069-0.00653.3310.0010.0010.0000.0000.0000.000
130A153LEU0-0.0110.00551.989-0.003-0.0030.0000.0000.0000.000
131A154SER00.003-0.00247.0300.0040.0040.0000.0000.0000.000
132A155ARG10.8670.90446.8460.0140.0140.0000.0000.0000.000
133A156LYS10.9030.92942.6130.0190.0190.0000.0000.0000.000
134A157GLY00.0610.05041.0500.0050.0050.0000.0000.0000.000
135A158LYS10.8230.94232.1040.0500.0500.0000.0000.0000.000
136A159PRO00.0730.01435.6250.0050.0050.0000.0000.0000.000
137A160PRO00.0430.01238.2420.0070.0070.0000.0000.0000.000
138A161PRO0-0.0020.01242.0040.0010.0010.0000.0000.0000.000
139A162THR0-0.0320.00743.395-0.005-0.0050.0000.0000.0000.000
140A163ILE00.007-0.01345.5840.0050.0050.0000.0000.0000.000
141A164GLY00.0260.02349.283-0.004-0.0040.0000.0000.0000.000
142A165TRP00.000-0.01052.0490.0030.0030.0000.0000.0000.000
143A166ALA00.0100.00155.5830.0000.0000.0000.0000.0000.000
144A167ILE00.0150.02457.5990.0000.0000.0000.0000.0000.000
145A168ALA00.0290.02258.4380.0010.0010.0000.0000.0000.000
146A169SER00.0410.01760.580-0.001-0.0010.0000.0000.0000.000
147A170ASP-1-0.844-0.91658.1240.0250.0250.0000.0000.0000.000
148A171GLU-1-0.865-0.93258.9370.0230.0230.0000.0000.0000.000
149A172HIS0-0.031-0.01854.8500.0000.0000.0000.0000.0000.000
150A173GLY0-0.0040.00354.4330.0010.0010.0000.0000.0000.000
151A174LYS10.8270.90352.099-0.031-0.0310.0000.0000.0000.000
152A175HIS0-0.012-0.00555.7640.0000.0000.0000.0000.0000.000
153A176ILE00.0080.00254.061-0.002-0.0020.0000.0000.0000.000
154A177VAL0-0.022-0.02758.3830.0000.0000.0000.0000.0000.000
155A178SER00.036-0.00660.445-0.001-0.0010.0000.0000.0000.000
156A179TRP0-0.017-0.00851.4890.0000.0000.0000.0000.0000.000
157A180LEU00.0120.01457.199-0.001-0.0010.0000.0000.0000.000
158A181GLY00.0290.02356.448-0.001-0.0010.0000.0000.0000.000
159A182GLU-1-0.879-0.94352.713-0.014-0.0140.0000.0000.0000.000
160A183SER0-0.029-0.02152.0030.0000.0000.0000.0000.0000.000
161A184ARG10.9360.94951.113-0.005-0.0050.0000.0000.0000.000
162A185SER0-0.074-0.03249.6600.0010.0010.0000.0000.0000.000
163A186LYS10.8300.90846.8360.0150.0150.0000.0000.0000.000
164A187PHE0-0.038-0.01046.2710.0030.0030.0000.0000.0000.000
165A195GLU-1-0.823-0.88657.5880.0040.0040.0000.0000.0000.000
166A196ILE0-0.052-0.03758.9010.0000.0000.0000.0000.0000.000
167A197SER0-0.0240.00562.4420.0000.0000.0000.0000.0000.000
168A198GLN0-0.040-0.02763.536-0.001-0.0010.0000.0000.0000.000
169A199GLU-1-0.866-0.92065.725-0.002-0.0020.0000.0000.0000.000
170A200THR0-0.004-0.00962.7010.0000.0000.0000.0000.0000.000
171A201VAL00.0400.02563.1190.0000.0000.0000.0000.0000.000
172A202ILE00.0160.01163.677-0.001-0.0010.0000.0000.0000.000
173A203ALA00.008-0.01861.0170.0010.0010.0000.0000.0000.000
174A204HIS0-0.017-0.00557.7460.0000.0000.0000.0000.0000.000
175A205VAL00.0180.00654.1200.0010.0010.0000.0000.0000.000
176A206ASN00.0000.00155.697-0.004-0.0040.0000.0000.0000.000
177A207GLU-1-0.815-0.89349.493-0.019-0.0190.0000.0000.0000.000
178A208THR00.0130.01351.124-0.003-0.0030.0000.0000.0000.000
179A209THR0-0.011-0.02044.6490.0040.0040.0000.0000.0000.000
180A210GLN0-0.029-0.00847.333-0.004-0.0040.0000.0000.0000.000
181A211VAL00.0050.01141.7110.0030.0030.0000.0000.0000.000
182A212GLU-1-0.769-0.87341.166-0.021-0.0210.0000.0000.0000.000
183A222SER00.020-0.00432.192-0.001-0.0010.0000.0000.0000.000
184A223SER00.0060.01134.2210.0040.0040.0000.0000.0000.000
185A224ILE0-0.034-0.01237.7270.0030.0030.0000.0000.0000.000
186A225TYR00.0320.00838.507-0.004-0.0040.0000.0000.0000.000
187A226SER0-0.061-0.02443.2220.0060.0060.0000.0000.0000.000
188A227ILE00.0080.00446.531-0.004-0.0040.0000.0000.0000.000
189A228MET00.0030.00548.7250.0050.0050.0000.0000.0000.000
190A229SER0-0.012-0.01952.139-0.002-0.0020.0000.0000.0000.000
191A230ASN00.001-0.01253.8920.0040.0040.0000.0000.0000.000
192A231LEU00.0290.04057.576-0.002-0.0020.0000.0000.0000.000
193A232SER0-0.001-0.00559.4590.0010.0010.0000.0000.0000.000
194A233PHE00.005-0.01562.8270.0000.0000.0000.0000.0000.000
195A234ILE00.0270.02964.7990.0000.0000.0000.0000.0000.000
196A235PRO0-0.044-0.00167.5040.0010.0010.0000.0000.0000.000
197A236ARG10.8190.86865.083-0.003-0.0030.0000.0000.0000.000
198A237PRO00.0430.01270.8010.0010.0010.0000.0000.0000.000
199A238GLU-1-0.878-0.93469.4790.0050.0050.0000.0000.0000.000
200A239ASP-1-0.796-0.87766.5360.0050.0050.0000.0000.0000.000
201A240ASP-1-0.813-0.90968.1480.0080.0080.0000.0000.0000.000
202A241HIS0-0.091-0.04369.1820.0020.0020.0000.0000.0000.000
203A242LYS10.8550.94164.600-0.009-0.0090.0000.0000.0000.000
204A243TYR0-0.011-0.01761.219-0.001-0.0010.0000.0000.0000.000
205A244LEU00.0150.02760.0850.0000.0000.0000.0000.0000.000
206A245ILE0-0.025-0.02554.8440.0010.0010.0000.0000.0000.000
207A247ILE0-0.011-0.01949.3180.0030.0030.0000.0000.0000.000
208A248SER00.0260.00846.537-0.005-0.0050.0000.0000.0000.000
209A249GLN00.0330.01443.5800.0090.0090.0000.0000.0000.000
210A250HIS00.0380.02037.6640.0010.0010.0000.0000.0000.000
211A251MET00.0210.01235.2060.0050.0050.0000.0000.0000.000
212A252THR0-0.004-0.03035.9740.0080.0080.0000.0000.0000.000
213A253PHE0-0.078-0.04437.5560.0080.0080.0000.0000.0000.000
214A254PRO00.0720.03535.937-0.004-0.0040.0000.0000.0000.000
215A255ASN0-0.052-0.02739.0740.0010.0010.0000.0000.0000.000
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