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: MV75Z

Calculation Name: 3QIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QIV

Chain ID: A

ChEMBL ID:

UniProt ID: Q743I2

Base Structure: X-ray

Registration Date: 2023-09-20

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2069475.161792
FMO2-HF: Nuclear repulsion 1995395.320408
FMO2-HF: Total energy -74079.841384
FMO2-MP2: Total energy -74293.834938


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.927-11.31717.136-5.087-12.659-0.078
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.027
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].
3A3PHE0-0.044-0.0383.171-0.7961.3660.009-0.991-1.1800.001
4A4GLU-1-0.844-0.9002.7010.1521.2420.131-0.273-0.948-0.001
5A5ASN0-0.117-0.0574.591-0.253-0.203-0.001-0.013-0.0350.000
6A6LYS10.8040.9087.8220.1870.1870.0000.0000.0000.000
7A7VAL0-0.011-0.0069.7410.1000.1000.0000.0000.0000.000
8A8GLY0-0.007-0.00912.144-0.034-0.0340.0000.0000.0000.000
9A9ILE0-0.0100.00013.0350.0070.0070.0000.0000.0000.000
10A10VAL00.0090.00614.034-0.004-0.0040.0000.0000.0000.000
11A11THR00.0350.01816.881-0.004-0.0040.0000.0000.0000.000
12A12GLY0-0.012-0.00820.5340.0000.0000.0000.0000.0000.000
13A13SER0-0.005-0.02616.986-0.004-0.0040.0000.0000.0000.000
14A14GLY00.0150.00418.064-0.010-0.0100.0000.0000.0000.000
15A15GLY00.0330.01019.880-0.003-0.0030.0000.0000.0000.000
16A16GLY0-0.013-0.00420.1260.0050.0050.0000.0000.0000.000
17A17ILE00.012-0.00216.359-0.009-0.0090.0000.0000.0000.000
18A18GLY00.0350.02416.752-0.002-0.0020.0000.0000.0000.000
19A19GLN0-0.024-0.01315.1680.0220.0220.0000.0000.0000.000
20A20ALA00.0040.00513.698-0.009-0.0090.0000.0000.0000.000
21A21TYR0-0.028-0.04312.442-0.008-0.0080.0000.0000.0000.000
22A22ALA00.0150.00511.3280.0190.0190.0000.0000.0000.000
23A23GLU-1-0.769-0.8799.948-0.207-0.2070.0000.0000.0000.000
24A24ALA0-0.031-0.0128.012-0.016-0.0160.0000.0000.0000.000
25A25LEU0-0.015-0.0106.5990.1550.1550.0000.0000.0000.000
26A26ALA00.0110.0146.0380.4320.4320.0000.0000.0000.000
27A27ARG10.7580.8643.8620.2360.6610.001-0.070-0.3560.000
28A28GLU-1-0.763-0.8692.124-9.928-9.11010.867-5.229-6.456-0.053
29A29GLY00.0570.0042.420-0.236-3.3396.0140.567-3.478-0.025
30A30ALA0-0.040-0.0043.842-0.549-1.3810.1150.922-0.2060.000
31A31ALA00.0060.0047.333-0.025-0.0250.0000.0000.0000.000
32A32VAL0-0.043-0.0309.751-0.047-0.0470.0000.0000.0000.000
33A33VAL0-0.025-0.02112.484-0.024-0.0240.0000.0000.0000.000
34A34VAL00.0030.00414.878-0.001-0.0010.0000.0000.0000.000
35A35ALA00.0340.01117.236-0.001-0.0010.0000.0000.0000.000
36A36ASP-1-0.805-0.91320.810-0.045-0.0450.0000.0000.0000.000
37A37ILE00.0080.01723.3950.0020.0020.0000.0000.0000.000
38A38ASN0-0.050-0.03025.0420.0000.0000.0000.0000.0000.000
39A39ALA00.0380.00423.985-0.004-0.0040.0000.0000.0000.000
40A40GLU-1-0.898-0.93923.080-0.066-0.0660.0000.0000.0000.000
41A41ALA0-0.013-0.00522.395-0.007-0.0070.0000.0000.0000.000
42A42ALA00.023-0.00219.437-0.009-0.0090.0000.0000.0000.000
43A43GLU-1-0.786-0.85018.240-0.078-0.0780.0000.0000.0000.000
44A44ALA0-0.025-0.01018.588-0.011-0.0110.0000.0000.0000.000
45A45VAL0-0.007-0.00814.351-0.017-0.0170.0000.0000.0000.000
46A46ALA00.0170.00814.154-0.023-0.0230.0000.0000.0000.000
47A47LYS10.8270.89013.7680.0720.0720.0000.0000.0000.000
48A48GLN0-0.058-0.02010.7070.0070.0070.0000.0000.0000.000
49A49ILE00.0310.0138.656-0.047-0.0470.0000.0000.0000.000
50A50VAL0-0.036-0.0119.081-0.080-0.0800.0000.0000.0000.000
51A51ALA0-0.054-0.02510.837-0.033-0.0330.0000.0000.0000.000
52A52ASP-1-0.849-0.9217.506-0.596-0.5960.0000.0000.0000.000
53A53GLY0-0.066-0.0197.002-0.249-0.2490.0000.0000.0000.000
54A54GLY00.0080.0165.839-0.045-0.0450.0000.0000.0000.000
55A55THR0-0.032-0.0226.7500.0800.0800.0000.0000.0000.000
56A56ALA00.011-0.0059.5440.0520.0520.0000.0000.0000.000
57A57ILE0-0.0390.00012.409-0.018-0.0180.0000.0000.0000.000
58A58SER0-0.003-0.01616.2420.0060.0060.0000.0000.0000.000
59A59VAL0-0.036-0.03019.1870.0060.0060.0000.0000.0000.000
60A60ALA00.0180.01522.299-0.002-0.0020.0000.0000.0000.000
61A61VAL0-0.027-0.03723.6170.0030.0030.0000.0000.0000.000
62A62ASP-1-0.776-0.83426.590-0.020-0.0200.0000.0000.0000.000
63A63VAL00.0230.00424.8650.0020.0020.0000.0000.0000.000
64A64SER0-0.035-0.03527.8820.0020.0020.0000.0000.0000.000
65A65ASP-1-0.813-0.90430.812-0.011-0.0110.0000.0000.0000.000
66A66PRO0-0.033-0.02430.1470.0000.0000.0000.0000.0000.000
67A67GLU-1-0.832-0.89129.977-0.006-0.0060.0000.0000.0000.000
68A68SER00.0210.01728.891-0.001-0.0010.0000.0000.0000.000
69A69ALA00.0260.00725.9100.0000.0000.0000.0000.0000.000
70A70LYS10.7960.86225.2970.0070.0070.0000.0000.0000.000
71A71ALA00.0110.01325.9900.0010.0010.0000.0000.0000.000
72A72MET00.0120.02821.435-0.001-0.0010.0000.0000.0000.000
73A73ALA00.0000.01021.4590.0020.0020.0000.0000.0000.000
74A74ASP-1-0.817-0.92221.9230.0000.0000.0000.0000.0000.000
75A75ARG10.8100.88920.2480.0220.0220.0000.0000.0000.000
76A76THR00.003-0.01216.9360.0020.0020.0000.0000.0000.000
77A77LEU0-0.091-0.03518.8130.0060.0060.0000.0000.0000.000
78A78ALA0-0.050-0.02421.0510.0030.0030.0000.0000.0000.000
79A79GLU-1-0.799-0.85917.349-0.017-0.0170.0000.0000.0000.000
80A80PHE00.013-0.00814.0330.0120.0120.0000.0000.0000.000
81A81GLY00.0030.01716.1960.0060.0060.0000.0000.0000.000
82A82GLY0-0.054-0.06017.465-0.002-0.0020.0000.0000.0000.000
83A83ILE0-0.021-0.01616.0120.0030.0030.0000.0000.0000.000
84A84ASP-1-0.754-0.82912.475-0.012-0.0120.0000.0000.0000.000
85A85TYR0-0.007-0.0138.814-0.032-0.0320.0000.0000.0000.000
86A86LEU0-0.031-0.01214.2740.0100.0100.0000.0000.0000.000
87A87VAL00.0080.00914.181-0.002-0.0020.0000.0000.0000.000
88A88ASN0-0.024-0.02417.320-0.001-0.0010.0000.0000.0000.000
89A89ASN00.011-0.01419.3780.0020.0020.0000.0000.0000.000
90A90ALA0-0.0270.00321.359-0.002-0.0020.0000.0000.0000.000
91A91ALA00.0210.01424.3480.0030.0030.0000.0000.0000.000
92A92ILE0-0.051-0.01727.425-0.003-0.0030.0000.0000.0000.000
93A93PHE00.0560.00825.4370.0030.0030.0000.0000.0000.000
94A94GLY0-0.019-0.00831.397-0.001-0.0010.0000.0000.0000.000
95A95GLY0-0.001-0.00634.4200.0000.0000.0000.0000.0000.000
96A96MET00.0660.01335.8890.0010.0010.0000.0000.0000.000
97A97LYS10.8960.96336.6630.0220.0220.0000.0000.0000.000
98A98LEU0-0.040-0.02236.8930.0010.0010.0000.0000.0000.000
99A99ASP-1-0.885-0.93040.350-0.010-0.0100.0000.0000.0000.000
100A100PHE0-0.044-0.02243.0290.0010.0010.0000.0000.0000.000
101A101LEU00.010-0.00941.4070.0000.0000.0000.0000.0000.000
102A102LEU0-0.026-0.00845.2660.0000.0000.0000.0000.0000.000
103A103THR0-0.017-0.01447.6430.0000.0000.0000.0000.0000.000
104A104ILE0-0.078-0.00740.191-0.001-0.0010.0000.0000.0000.000
105A105ASP-1-0.791-0.89842.559-0.014-0.0140.0000.0000.0000.000
106A106PRO00.0220.00142.6710.0000.0000.0000.0000.0000.000
107A107GLU-1-0.813-0.88741.217-0.010-0.0100.0000.0000.0000.000
108A108TYR00.0120.00334.860-0.001-0.0010.0000.0000.0000.000
109A109TYR00.0150.00137.6670.0000.0000.0000.0000.0000.000
110A110LYS10.8420.89438.1360.0100.0100.0000.0000.0000.000
111A111LYS10.8170.88633.1560.0170.0170.0000.0000.0000.000
112A112PHE0-0.004-0.01833.7180.0000.0000.0000.0000.0000.000
113A113MET0-0.035-0.01433.2840.0000.0000.0000.0000.0000.000
114A114SER0-0.024-0.02933.6360.0000.0000.0000.0000.0000.000
115A115VAL0-0.019-0.02628.2860.0000.0000.0000.0000.0000.000
116A116ASN0-0.0120.00328.826-0.002-0.0020.0000.0000.0000.000
117A117LEU0-0.069-0.02329.5730.0010.0010.0000.0000.0000.000
118A118ASP-1-0.809-0.87930.244-0.007-0.0070.0000.0000.0000.000
119A119GLY00.0280.01627.8260.0010.0010.0000.0000.0000.000
120A120ALA00.0300.01424.7710.0000.0000.0000.0000.0000.000
121A121LEU00.0090.02125.4570.0010.0010.0000.0000.0000.000
122A122TRP0-0.030-0.02227.9120.0020.0020.0000.0000.0000.000
123A123CYS00.0170.01022.7990.0000.0000.0000.0000.0000.000
124A124THR00.0330.00223.2580.0010.0010.0000.0000.0000.000
125A125ARG10.8700.93024.3030.0040.0040.0000.0000.0000.000
126A126ALA0-0.0150.00924.6570.0010.0010.0000.0000.0000.000
127A127VAL00.0420.01620.1050.0010.0010.0000.0000.0000.000
128A128TYR00.0430.03022.2210.0010.0010.0000.0000.0000.000
129A129LYS10.8780.95023.5200.0000.0000.0000.0000.0000.000
130A130LYS10.7910.89721.7230.0020.0020.0000.0000.0000.000
131A131MET00.0470.03616.9100.0020.0020.0000.0000.0000.000
132A132THR0-0.026-0.03520.0900.0010.0010.0000.0000.0000.000
133A133LYS10.8880.94822.703-0.007-0.0070.0000.0000.0000.000
134A134ARG10.8240.89413.338-0.012-0.0120.0000.0000.0000.000
135A135GLY00.0050.02117.977-0.002-0.0020.0000.0000.0000.000
136A136GLY00.007-0.00118.3690.0030.0030.0000.0000.0000.000
137A137GLY00.0240.01015.663-0.002-0.0020.0000.0000.0000.000
138A138ALA0-0.057-0.00914.2820.0050.0050.0000.0000.0000.000
139A139ILE00.009-0.00216.100-0.002-0.0020.0000.0000.0000.000
140A140VAL00.0120.01315.0620.0040.0040.0000.0000.0000.000
141A141ASN0-0.009-0.01418.227-0.004-0.0040.0000.0000.0000.000
142A142GLN00.0780.05619.1630.0060.0060.0000.0000.0000.000
143A143SER00.000-0.00722.093-0.001-0.0010.0000.0000.0000.000
144A144SER0-0.036-0.02724.8740.0000.0000.0000.0000.0000.000
145A156LEU00.0470.00834.9630.0000.0000.0000.0000.0000.000
146A157ALA00.0400.02534.162-0.001-0.0010.0000.0000.0000.000
147A158LYS10.9440.97526.8530.0080.0080.0000.0000.0000.000
148A159VAL00.001-0.00629.7130.0010.0010.0000.0000.0000.000
149A160GLY00.0140.01731.7000.0010.0010.0000.0000.0000.000
150A161ILE00.0400.03125.4900.0010.0010.0000.0000.0000.000
151A162ASN00.0240.02627.155-0.001-0.0010.0000.0000.0000.000
152A163GLY00.0430.02128.2190.0020.0020.0000.0000.0000.000
153A164LEU00.0080.00227.8810.0010.0010.0000.0000.0000.000
154A165THR00.0070.00023.4690.0000.0000.0000.0000.0000.000
155A166GLN00.0070.00026.1480.0010.0010.0000.0000.0000.000
156A167GLN0-0.061-0.02128.3790.0030.0030.0000.0000.0000.000
157A168LEU00.0570.02425.7640.0010.0010.0000.0000.0000.000
158A169SER00.0190.01524.8600.0010.0010.0000.0000.0000.000
159A170ARG10.8100.91425.905-0.008-0.0080.0000.0000.0000.000
160A171GLU-1-0.888-0.93829.2400.0040.0040.0000.0000.0000.000
161A172LEU0-0.058-0.03922.9160.0000.0000.0000.0000.0000.000
162A173GLY00.0480.02625.5410.0010.0010.0000.0000.0000.000
163A174GLY0-0.032-0.02626.753-0.001-0.0010.0000.0000.0000.000
164A175ARG10.8440.93023.842-0.006-0.0060.0000.0000.0000.000
165A176ASN0-0.006-0.00918.2130.0020.0020.0000.0000.0000.000
166A177ILE0-0.0260.00419.344-0.004-0.0040.0000.0000.0000.000
167A178ARG10.8060.91813.9290.0090.0090.0000.0000.0000.000
168A179ILE0-0.019-0.01619.320-0.005-0.0050.0000.0000.0000.000
169A180ASN0-0.003-0.01817.7730.0090.0090.0000.0000.0000.000
170A181ALA0-0.0030.00320.678-0.004-0.0040.0000.0000.0000.000
171A182ILE00.0450.03416.3510.0050.0050.0000.0000.0000.000
172A183ALA0-0.012-0.01721.018-0.003-0.0030.0000.0000.0000.000
173A184PRO00.0000.01322.4170.0040.0040.0000.0000.0000.000
174A216PRO0-0.012-0.02719.0000.0020.0020.0000.0000.0000.000
175A217ASP-1-0.870-0.93813.832-0.076-0.0760.0000.0000.0000.000
176A218ASP-1-0.861-0.92813.8630.0030.0030.0000.0000.0000.000
177A219LEU0-0.058-0.02815.0120.0070.0070.0000.0000.0000.000
178A220VAL00.0090.00210.2990.0040.0040.0000.0000.0000.000
179A221GLY00.0450.03210.355-0.010-0.0100.0000.0000.0000.000
180A222MET0-0.032-0.01111.2780.0090.0090.0000.0000.0000.000
181A223CYS0-0.048-0.02613.1160.0030.0030.0000.0000.0000.000
182A224LEU00.0460.0176.6340.0070.0070.0000.0000.0000.000
183A225PHE0-0.0060.0039.489-0.029-0.0290.0000.0000.0000.000
184A226LEU0-0.019-0.00110.9040.0040.0040.0000.0000.0000.000
185A227LEU0-0.0120.00010.7070.0120.0120.0000.0000.0000.000
186A228SER0-0.047-0.0288.5030.0120.0120.0000.0000.0000.000
187A229ASP-1-0.809-0.8979.853-0.075-0.0750.0000.0000.0000.000
188A230GLU-1-0.825-0.9178.1660.1820.1820.0000.0000.0000.000
189A231ALA0-0.042-0.00212.3790.0050.0050.0000.0000.0000.000
190A232SER0-0.004-0.01814.637-0.011-0.0110.0000.0000.0000.000
191A233TRP0-0.045-0.02516.749-0.012-0.0120.0000.0000.0000.000
192A234ILE0-0.037-0.00516.558-0.003-0.0030.0000.0000.0000.000
193A235THR00.0460.01418.850-0.010-0.0100.0000.0000.0000.000
194A236GLY0-0.023-0.00221.5920.0030.0030.0000.0000.0000.000
195A237GLN0-0.058-0.02921.6750.0000.0000.0000.0000.0000.000
196A238ILE0-0.030-0.02722.637-0.004-0.0040.0000.0000.0000.000
197A239PHE00.0260.01519.6640.0030.0030.0000.0000.0000.000
198A240ASN0-0.027-0.01822.029-0.007-0.0070.0000.0000.0000.000
199A241VAL00.0030.01119.5120.0020.0020.0000.0000.0000.000