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: 4NM7N

Calculation Name: 2QWU-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QWU

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NEC5

Base Structure: X-ray

Registration Date: 2021-09-06

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 209
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2227710.096056
FMO2-HF: Nuclear repulsion 2148218.963538
FMO2-HF: Total energy -79491.132518
FMO2-MP2: Total energy -79716.617523


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:2:ACE )


Summations of interaction energy for fragment #1(A:2: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.
-1.5840.257-0.007-0.963-0.87-0.004
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.022
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].
3A4SER 0-0.005-0.0033.824-0.2011.665-0.007-0.934-0.924-0.004
4A5GLU -1-0.876-0.9304.823-2.416-2.4760.000-0.0230.0830.000
5A6MET 0-0.0080.0017.723-0.103-0.1030.0000.0000.0000.000
6A7ILE 0-0.045-0.02010.7280.0460.0460.0000.0000.0000.000
7A8THR 00.0520.0297.6660.0170.0170.0000.0000.0000.000
8A9ARG 10.9300.9428.8590.5030.5030.0000.0000.0000.000
9A10GLN 00.0590.0259.9980.1340.1340.0000.0000.0000.000
10A11GLN 00.0680.05211.8210.0010.0010.0000.0000.0000.000
11A12VAL 0-0.039-0.01813.6190.0810.0810.0000.0000.0000.000
12A13THR 0-0.085-0.04914.1050.0670.0670.0000.0000.0000.000
13A14SER 0-0.074-0.06215.5000.0450.0450.0000.0000.0000.000
14A15GLY 0-0.0050.01617.7120.0290.0290.0000.0000.0000.000
15A16GLU -1-0.953-0.96315.166-0.433-0.4330.0000.0000.0000.000
16A17THR 0-0.017-0.01218.6980.0180.0180.0000.0000.0000.000
17A18ILE 00.0100.02316.211-0.049-0.0490.0000.0000.0000.000
18A19HIS 0-0.007-0.02016.3400.0490.0490.0000.0000.0000.000
19A20VAL 00.0670.02815.810-0.044-0.0440.0000.0000.0000.000
20A21ARG 10.8750.92016.8660.2540.2540.0000.0000.0000.000
21A22THR 00.0080.00117.191-0.019-0.0190.0000.0000.0000.000
22A23ASP -1-0.892-0.93819.373-0.100-0.1000.0000.0000.0000.000
23A24PRO 00.000-0.01521.7320.0030.0030.0000.0000.0000.000
24A25THR 00.0350.02725.3640.0020.0020.0000.0000.0000.000
25A26ALA 00.0050.01720.9500.0080.0080.0000.0000.0000.000
26A27CYS 0-0.0140.00523.0050.0050.0050.0000.0000.0000.000
27A28ILE 00.0140.02625.0680.0070.0070.0000.0000.0000.000
28A29GLY 00.0240.00925.604-0.002-0.0020.0000.0000.0000.000
29A30SER 00.009-0.00124.654-0.001-0.0010.0000.0000.0000.000
30A31HIS 0-0.053-0.03920.1020.0070.0070.0000.0000.0000.000
31A32PRO 00.0210.00316.020-0.003-0.0030.0000.0000.0000.000
32A33ASN 00.0340.03315.620-0.002-0.0020.0000.0000.0000.000
33A34CYS 00.0310.00514.6770.0160.0160.0000.0000.0000.000
34A35ARG 10.8020.89816.6340.0510.0510.0000.0000.0000.000
35A36MET 00.0010.00819.479-0.007-0.0070.0000.0000.0000.000
36A37PHE 0-0.003-0.00921.9500.0030.0030.0000.0000.0000.000
37A38ILE 0-0.0060.00225.645-0.001-0.0010.0000.0000.0000.000
38A39ASP -1-0.823-0.91128.326-0.040-0.0400.0000.0000.0000.000
39A40SER 0-0.021-0.02031.4530.0040.0040.0000.0000.0000.000
40A41LEU 00.0680.02531.810-0.005-0.0050.0000.0000.0000.000
41A42THR 0-0.047-0.00834.2510.0050.0050.0000.0000.0000.000
42A43ILE 00.0540.02134.457-0.004-0.0040.0000.0000.0000.000
43A44ALA 00.0390.02937.8410.0030.0030.0000.0000.0000.000
44A45GLY 0-0.025-0.02440.4830.0030.0030.0000.0000.0000.000
45A46GLU -1-0.924-0.96341.019-0.034-0.0340.0000.0000.0000.000
46A47LYS 10.9280.96139.3140.0310.0310.0000.0000.0000.000
47A48LEU 00.001-0.00335.5720.0020.0020.0000.0000.0000.000
48A49ASP -1-0.906-0.94337.974-0.030-0.0300.0000.0000.0000.000
49A50LYS 10.9040.95433.7840.0280.0280.0000.0000.0000.000
50A51ASN 0-0.014-0.02835.8960.0010.0010.0000.0000.0000.000
51A52ILE 00.0130.01130.4560.0010.0010.0000.0000.0000.000
52A53VAL 00.0310.01231.781-0.001-0.0010.0000.0000.0000.000
53A54ALA 0-0.043-0.00927.1570.0000.0000.0000.0000.0000.000
54A55ILE 00.0320.01924.6410.0040.0040.0000.0000.0000.000
55A56ASP -1-0.802-0.92022.610-0.050-0.0500.0000.0000.0000.000
56A57GLY 0-0.005-0.00619.5460.0070.0070.0000.0000.0000.000
57A58GLY 0-0.072-0.05120.5330.0070.0070.0000.0000.0000.000
58A59GLU -1-0.936-0.95721.549-0.008-0.0080.0000.0000.0000.000
59A60ASP -1-0.867-0.92725.1620.0180.0180.0000.0000.0000.000
60A61VAL 00.038-0.00926.932-0.003-0.0030.0000.0000.0000.000
61A62THR 0-0.095-0.04129.465-0.002-0.0020.0000.0000.0000.000
62A63LYS 10.9060.94531.071-0.017-0.0170.0000.0000.0000.000
63A64ALA 0-0.0030.02530.609-0.002-0.0020.0000.0000.0000.000
64A65ASP -1-0.885-0.94032.667-0.007-0.0070.0000.0000.0000.000
65A66SER 0-0.101-0.04435.488-0.003-0.0030.0000.0000.0000.000
66A67ALA 00.0070.00334.351-0.001-0.0010.0000.0000.0000.000
67A68THR 0-0.051-0.04129.721-0.001-0.0010.0000.0000.0000.000
68A69ALA 0-0.045-0.02829.387-0.003-0.0030.0000.0000.0000.000
69A70ALA 0-0.0110.00631.4220.0030.0030.0000.0000.0000.000
70A71ALA 0-0.034-0.01830.4000.0000.0000.0000.0000.0000.000
71A72SER 00.005-0.00425.824-0.002-0.0020.0000.0000.0000.000
72A73VAL 0-0.005-0.01623.1280.0010.0010.0000.0000.0000.000
73A74ILE 0-0.0120.00622.948-0.007-0.0070.0000.0000.0000.000
74A75ARG 10.9530.95821.4960.1350.1350.0000.0000.0000.000
75A76MET 0-0.0170.00621.1710.0190.0190.0000.0000.0000.000
76A77SER 0-0.0220.00420.688-0.035-0.0350.0000.0000.0000.000
77A78ILE 00.0230.00721.2880.0240.0240.0000.0000.0000.000
78A79THR 00.011-0.00221.524-0.022-0.0220.0000.0000.0000.000
79A80PRO 0-0.014-0.00721.3050.0230.0230.0000.0000.0000.000
80A81GLY 00.0410.03124.4750.0010.0010.0000.0000.0000.000
81A82SER 0-0.063-0.03627.9410.0020.0020.0000.0000.0000.000
82A83ILE 0-0.001-0.00330.1170.0050.0050.0000.0000.0000.000
83A84ASN 00.0310.01630.9630.0000.0000.0000.0000.0000.000
84A85PRO 00.0070.02026.533-0.002-0.0020.0000.0000.0000.000
85A86THR 0-0.0100.00927.1020.0130.0130.0000.0000.0000.000
86A87ILE 0-0.026-0.02225.788-0.013-0.0130.0000.0000.0000.000
87A88SER 0-0.0010.01825.9310.0070.0070.0000.0000.0000.000
88A89ILE 0-0.020-0.02325.570-0.012-0.0120.0000.0000.0000.000
89A90THR 00.0100.00125.7710.0040.0040.0000.0000.0000.000
90A91LEU 0-0.006-0.01026.414-0.005-0.0050.0000.0000.0000.000
91A92GLY 00.0390.03528.7490.0030.0030.0000.0000.0000.000
92A93VAL 00.0160.00330.1350.0020.0020.0000.0000.0000.000
93A94LEU 00.0220.02033.4640.0010.0010.0000.0000.0000.000
94A95ILE 00.0520.02736.0520.0020.0020.0000.0000.0000.000
95A96LYS 11.0081.00239.4780.0250.0250.0000.0000.0000.000
96A97SER 00.0530.00542.503-0.002-0.0020.0000.0000.0000.000
97A98ASN 0-0.020-0.02343.787-0.001-0.0010.0000.0000.0000.000
98A99VAL 00.0590.03641.1890.0000.0000.0000.0000.0000.000
99A100ARG 10.9650.99939.9120.0430.0430.0000.0000.0000.000
100A101THR 0-0.019-0.00341.610-0.001-0.0010.0000.0000.0000.000
101A102LYS 10.8440.91644.6570.0310.0310.0000.0000.0000.000
102A103ILE 00.0300.02638.7090.0000.0000.0000.0000.0000.000
103A104GLU -1-0.883-0.95440.460-0.048-0.0480.0000.0000.0000.000
104A105GLU -1-0.858-0.93642.248-0.034-0.0340.0000.0000.0000.000
105A106LYS 10.8730.95543.5600.0380.0380.0000.0000.0000.000
106A107VAL 00.023-0.00339.006-0.001-0.0010.0000.0000.0000.000
107A108SER 00.0030.00542.088-0.001-0.0010.0000.0000.0000.000
108A109SER 00.006-0.00844.2170.0010.0010.0000.0000.0000.000
109A110ILE 0-0.030-0.01043.0180.0010.0010.0000.0000.0000.000
110A111LEU 0-0.036-0.01640.160-0.001-0.0010.0000.0000.0000.000
111A112GLN 0-0.065-0.04343.3800.0010.0010.0000.0000.0000.000
112A113ALA 0-0.0440.01646.7850.0010.0010.0000.0000.0000.000
113A114SER 0-0.003-0.01246.0180.0000.0000.0000.0000.0000.000
114A115ALA 00.0280.01441.038-0.001-0.0010.0000.0000.0000.000
115A116THR 0-0.022-0.01139.563-0.001-0.0010.0000.0000.0000.000
116A117ASP -1-0.845-0.92040.133-0.046-0.0460.0000.0000.0000.000
117A118MET 0-0.111-0.04136.8520.0020.0020.0000.0000.0000.000
118A119LYS 10.9010.95137.0820.0540.0540.0000.0000.0000.000
119A120ILE 00.0100.00632.4020.0030.0030.0000.0000.0000.000
120A121LYS 10.8550.92133.3600.0550.0550.0000.0000.0000.000
121A122LEU 00.003-0.01027.3380.0030.0030.0000.0000.0000.000
122A123GLY 00.0010.01231.0750.0020.0020.0000.0000.0000.000
123A124ASN 0-0.049-0.03728.572-0.009-0.0090.0000.0000.0000.000
124A125SER 00.0130.01223.716-0.002-0.0020.0000.0000.0000.000
125A126ASN 0-0.042-0.01321.133-0.003-0.0030.0000.0000.0000.000
126A127LYS 10.9610.95421.4460.0360.0360.0000.0000.0000.000
127A128LYS 10.8900.97318.7160.0010.0010.0000.0000.0000.000
128A129GLN 00.0440.03017.114-0.018-0.0180.0000.0000.0000.000
129A130GLU -1-0.774-0.89611.101-0.390-0.3900.0000.0000.0000.000
130A131TYR 0-0.022-0.00912.7100.0130.0130.0000.0000.0000.000
131A132LYS 10.7550.8759.6530.2370.2370.0000.0000.0000.000
132A133THR 0-0.010-0.0214.2970.0890.1240.000-0.006-0.0290.000
133A134ASP -1-0.800-0.8617.6340.2650.2650.0000.0000.0000.000
134A135GLU -1-0.962-0.97110.4560.2600.2600.0000.0000.0000.000
135A136ALA 00.0020.01012.940-0.031-0.0310.0000.0000.0000.000
136A137TRP 0-0.014-0.00413.555-0.018-0.0180.0000.0000.0000.000
137A138GLY 0-0.007-0.00914.8780.0100.0100.0000.0000.0000.000
138A139ILE 0-0.0350.00015.714-0.004-0.0040.0000.0000.0000.000
139A140MET 0-0.0060.00513.651-0.027-0.0270.0000.0000.0000.000
140A141ILE 00.0580.00215.476-0.018-0.0180.0000.0000.0000.000
141A142ASP -1-0.919-0.93518.726-0.069-0.0690.0000.0000.0000.000
142A143LEU 00.013-0.01421.924-0.001-0.0010.0000.0000.0000.000
143A144SER 0-0.018-0.01624.7000.0090.0090.0000.0000.0000.000
144A145ASN 0-0.066-0.02527.4670.0010.0010.0000.0000.0000.000
145A146LEU 00.0330.05026.0530.0020.0020.0000.0000.0000.000
146A147GLU -1-0.923-0.97129.674-0.054-0.0540.0000.0000.0000.000
147A148LEU 0-0.025-0.00728.213-0.005-0.0050.0000.0000.0000.000
148A149TYR 0-0.024-0.01332.4590.0070.0070.0000.0000.0000.000
149A150PRO 00.0100.00734.380-0.006-0.0060.0000.0000.0000.000
150A151ILE 00.0060.01931.9000.0030.0030.0000.0000.0000.000
151A152SER 0-0.022-0.03036.2020.0050.0050.0000.0000.0000.000
152A153ALA 00.0670.02038.791-0.002-0.0020.0000.0000.0000.000
153A154LYS 10.9260.95540.4230.0510.0510.0000.0000.0000.000
154A155ALA 0-0.025-0.00135.103-0.001-0.0010.0000.0000.0000.000
155A156PHE 0-0.0130.00235.225-0.004-0.0040.0000.0000.0000.000
156A157SER 00.0190.02034.3530.0050.0050.0000.0000.0000.000
157A158ILE 00.011-0.00134.666-0.004-0.0040.0000.0000.0000.000
158A159SER 00.0000.01533.9160.0030.0030.0000.0000.0000.000
159A160ILE 00.000-0.00734.813-0.003-0.0030.0000.0000.0000.000
160A161GLU -1-0.946-0.96834.278-0.061-0.0610.0000.0000.0000.000
161A162PRO 0-0.069-0.02735.321-0.001-0.0010.0000.0000.0000.000
162A163THR 00.001-0.00532.228-0.001-0.0010.0000.0000.0000.000
163A164GLU -1-0.843-0.94835.284-0.030-0.0300.0000.0000.0000.000
164A165LEU 0-0.030-0.01429.2310.0020.0020.0000.0000.0000.000
165A166MET 0-0.035-0.01031.8070.0010.0010.0000.0000.0000.000
166A167GLY 0-0.0040.01334.1820.0030.0030.0000.0000.0000.000
167A168VAL 0-0.041-0.02637.642-0.002-0.0020.0000.0000.0000.000
168A169SER 0-0.013-0.02539.5670.0020.0020.0000.0000.0000.000
169A170LYS 10.9600.95741.0380.0140.0140.0000.0000.0000.000
170A171ASP -1-0.826-0.88142.850-0.022-0.0220.0000.0000.0000.000
171A172GLY 0-0.065-0.03044.224-0.001-0.0010.0000.0000.0000.000
172A173MET 0-0.078-0.03439.462-0.003-0.0030.0000.0000.0000.000
173A174ARG 10.9350.97037.8530.0320.0320.0000.0000.0000.000
174A175TYR 00.0250.01927.546-0.001-0.0010.0000.0000.0000.000
175A176HIS 0-0.020-0.02734.4980.0010.0010.0000.0000.0000.000
176A177ILE 00.0200.00628.845-0.003-0.0030.0000.0000.0000.000
177A178ILE 0-0.005-0.00131.5400.0020.0020.0000.0000.0000.000
178A179SER 0-0.020-0.00330.167-0.009-0.0090.0000.0000.0000.000
179A180ILE 0-0.005-0.00630.2440.0060.0060.0000.0000.0000.000
180A181ASP -1-0.883-0.95029.435-0.117-0.1170.0000.0000.0000.000
181A182GLY 00.0340.00830.9490.0060.0060.0000.0000.0000.000
182A183LEU 0-0.032-0.01530.2190.0080.0080.0000.0000.0000.000
183A184THR 00.006-0.01530.333-0.006-0.0060.0000.0000.0000.000
184A185THR 0-0.011-0.02628.2870.0030.0030.0000.0000.0000.000
185A186SER 00.0150.00131.572-0.003-0.0030.0000.0000.0000.000
186A187GLN 0-0.043-0.00426.3660.0080.0080.0000.0000.0000.000
187A188GLY 00.0770.02228.470-0.006-0.0060.0000.0000.0000.000
188A189SER 0-0.045-0.02723.810-0.008-0.0080.0000.0000.0000.000
189A190LEU 00.0550.02821.7510.0110.0110.0000.0000.0000.000
190A191PRO 0-0.0020.01620.422-0.016-0.0160.0000.0000.0000.000
191A192VAL 00.0340.00915.247-0.005-0.0050.0000.0000.0000.000
192A193CYS 0-0.067-0.03711.9210.0490.0490.0000.0000.0000.000
193A194CYS 0-0.079-0.0139.075-0.012-0.0120.0000.0000.0000.000
194A195ALA 00.0970.0454.8810.1120.1120.0000.0000.0000.000
195A196ALA 00.0140.0146.9290.1700.1700.0000.0000.0000.000
196A197SER 0-0.056-0.0768.893-0.085-0.0850.0000.0000.0000.000
197A198THR 0-0.010-0.01411.787-0.010-0.0100.0000.0000.0000.000
198A199ASP -1-0.889-0.9238.310-0.189-0.1890.0000.0000.0000.000
199A200LYS 10.9580.95311.906-0.009-0.0090.0000.0000.0000.000
200A201GLY 0-0.020-0.01215.281-0.004-0.0040.0000.0000.0000.000
201A202VAL 0-0.0240.00016.9680.0090.0090.0000.0000.0000.000
202A203ALA 00.0450.03318.361-0.009-0.0090.0000.0000.0000.000
203A204LYS 10.8790.94519.9360.1330.1330.0000.0000.0000.000
204A205ILE 0-0.012-0.02222.529-0.013-0.0130.0000.0000.0000.000
205A206GLY 00.0500.02524.8230.0020.0020.0000.0000.0000.000
206A207TYR 0-0.027-0.02128.4190.0010.0010.0000.0000.0000.000
207A208ILE 0-0.012-0.00327.699-0.001-0.0010.0000.0000.0000.000
208A209ALA 0-0.029-0.01032.0780.0020.0020.0000.0000.0000.000
209A210NME 00.0110.01535.4740.0000.0000.0000.0000.0000.000