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: VQVZ1

Calculation Name: 3F5D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5D

Chain ID: A

ChEMBL ID:

UniProt ID: P96658

Base Structure: X-ray

Registration Date: 2023-09-22

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2212191.101049
FMO2-HF: Nuclear repulsion 2135213.528785
FMO2-HF: Total energy -76977.572263
FMO2-MP2: Total energy -77202.574424


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-9.75-2.214.966-4.53-7.976-0.041
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.010
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].
3A5LYS10.9740.9843.880-1.4100.289-0.013-0.686-1.0000.002
4A6ALA00.0290.0105.5030.3350.3350.0000.0000.0000.000
5A7LEU0-0.027-0.0138.840-0.094-0.0940.0000.0000.0000.000
6A8PHE00.0310.00011.5520.0800.0800.0000.0000.0000.000
7A9LEU0-0.041-0.02514.619-0.006-0.0060.0000.0000.0000.000
8A10ILE00.0180.01217.5970.0180.0180.0000.0000.0000.000
9A11LEU00.0000.01120.1890.0040.0040.0000.0000.0000.000
10A12ASP-1-0.731-0.85023.688-0.114-0.1140.0000.0000.0000.000
11A13GLN0-0.040-0.00326.4970.0100.0100.0000.0000.0000.000
12A14TYR0-0.038-0.01920.4720.0070.0070.0000.0000.0000.000
13A15ALA00.0420.01024.776-0.002-0.0020.0000.0000.0000.000
14A16ASP-1-0.805-0.87522.631-0.133-0.1330.0000.0000.0000.000
15A17TRP0-0.007-0.02421.729-0.019-0.0190.0000.0000.0000.000
16A18GLU-1-0.793-0.91222.403-0.065-0.0650.0000.0000.0000.000
17A19GLY00.0230.00818.2510.0100.0100.0000.0000.0000.000
18A20VAL00.0140.00916.688-0.023-0.0230.0000.0000.0000.000
19A21TYR00.0060.00916.420-0.032-0.0320.0000.0000.0000.000
20A22LEU00.0150.01913.145-0.005-0.0050.0000.0000.0000.000
21A23ALA00.001-0.00112.269-0.037-0.0370.0000.0000.0000.000
22A24SER0-0.017-0.03311.341-0.093-0.0930.0000.0000.0000.000
23A25ALA0-0.0070.01112.017-0.050-0.0500.0000.0000.0000.000
24A26LEU0-0.011-0.0108.2130.0100.0100.0000.0000.0000.000
25A27ASN00.0250.0006.871-0.353-0.3530.0000.0000.0000.000
26A28GLN0-0.049-0.0297.520-0.137-0.1370.0000.0000.0000.000
27A29ARG10.7460.8626.173-0.400-0.4000.0000.0000.0000.000
28A30GLU-1-0.859-0.9274.400-2.077-1.890-0.001-0.028-0.1570.000
29A31ASP-1-0.836-0.8952.672-1.6460.0871.496-1.124-2.105-0.012
30A32TRP0-0.016-0.0192.703-0.3171.6371.782-1.576-2.160-0.017
31A33SER00.0030.0032.331-4.096-2.1801.702-1.082-2.537-0.014
32A34VAL0-0.040-0.0134.4150.4370.4880.000-0.034-0.0170.000
33A35HIS0-0.042-0.0236.490-0.165-0.1650.0000.0000.0000.000
34A36THR0-0.010-0.02310.3690.0920.0920.0000.0000.0000.000
35A37VAL0-0.014-0.01813.9710.0000.0000.0000.0000.0000.000
36A38SER00.011-0.01916.1380.0230.0230.0000.0000.0000.000
37A39LEU0-0.065-0.03619.9680.0060.0060.0000.0000.0000.000
38A40ASP-1-0.885-0.93322.552-0.101-0.1010.0000.0000.0000.000
39A41PRO00.007-0.01620.551-0.014-0.0140.0000.0000.0000.000
40A42ILE0-0.024-0.02120.505-0.020-0.0200.0000.0000.0000.000
41A43VAL0-0.0130.01521.1180.0150.0150.0000.0000.0000.000
42A44SER0-0.045-0.05223.400-0.015-0.0150.0000.0000.0000.000
43A45SER0-0.075-0.05423.6790.0030.0030.0000.0000.0000.000
44A46ILE00.011-0.00225.5480.0060.0060.0000.0000.0000.000
45A47GLY0-0.031-0.01427.2380.0070.0070.0000.0000.0000.000
46A48GLY0-0.020-0.00528.2050.0000.0000.0000.0000.0000.000
47A49PHE0-0.017-0.00623.237-0.004-0.0040.0000.0000.0000.000
48A50LYS10.8740.92723.9260.1300.1300.0000.0000.0000.000
49A51THR00.0120.02218.065-0.016-0.0160.0000.0000.0000.000
50A52SER00.0190.00518.0260.0220.0220.0000.0000.0000.000
51A53VAL0-0.042-0.01316.468-0.031-0.0310.0000.0000.0000.000
52A54ASP-1-0.823-0.86710.753-0.544-0.5440.0000.0000.0000.000
53A55TYR0-0.002-0.0208.3860.0520.0520.0000.0000.0000.000
54A56ILE00.0320.02715.3340.0110.0110.0000.0000.0000.000
55A57ILE0-0.009-0.01218.3490.0070.0070.0000.0000.0000.000
56A58GLY0-0.129-0.08918.8830.0160.0160.0000.0000.0000.000
57A59LEU0-0.035-0.00317.1500.0110.0110.0000.0000.0000.000
58A60GLU-1-0.816-0.88913.557-0.137-0.1370.0000.0000.0000.000
59A61PRO0-0.032-0.0069.2080.0330.0330.0000.0000.0000.000
60A62ALA00.0460.00711.8210.0030.0030.0000.0000.0000.000
61A63ASN0-0.060-0.03311.071-0.001-0.0010.0000.0000.0000.000
62A64PHE0-0.006-0.0028.253-0.059-0.0590.0000.0000.0000.000
63A65ASN0-0.001-0.0046.558-0.235-0.2350.0000.0000.0000.000
64A66LEU00.0400.0339.4260.0990.0990.0000.0000.0000.000
65A67LEU0-0.055-0.00811.335-0.094-0.0940.0000.0000.0000.000
66A68VAL00.0100.00513.4200.0410.0410.0000.0000.0000.000
67A69MET0-0.039-0.01116.041-0.028-0.0280.0000.0000.0000.000
68A70ILE00.0360.01318.6600.0150.0150.0000.0000.0000.000
69A71GLY00.0090.01421.4050.0010.0010.0000.0000.0000.000
70A72GLY00.0610.02024.722-0.014-0.0140.0000.0000.0000.000
71A73ASP-1-0.899-0.94827.371-0.057-0.0570.0000.0000.0000.000
72A74SER0-0.051-0.04527.3450.0080.0080.0000.0000.0000.000
73A75TRP0-0.019-0.02721.9520.0060.0060.0000.0000.0000.000
74A76SER0-0.039-0.00628.4420.0080.0080.0000.0000.0000.000
75A77ASN0-0.013-0.00928.3800.0010.0010.0000.0000.0000.000
76A78ASP-1-0.812-0.90230.525-0.022-0.0220.0000.0000.0000.000
77A79ASN00.0140.02427.2020.0050.0050.0000.0000.0000.000
78A80LYS10.9080.93826.7780.0250.0250.0000.0000.0000.000
79A81LYS10.9070.94923.1780.0800.0800.0000.0000.0000.000
80A82LEU00.0770.04622.0980.0010.0010.0000.0000.0000.000
81A83LEU00.0130.01122.9920.0030.0030.0000.0000.0000.000
82A84HIS00.0310.02122.1420.0050.0050.0000.0000.0000.000
83A85PHE00.0260.03214.9740.0150.0150.0000.0000.0000.000
84A86VAL00.0650.02819.4550.0080.0080.0000.0000.0000.000
85A87LYS10.8880.94520.8420.0030.0030.0000.0000.0000.000
86A88THR0-0.001-0.02319.0910.0140.0140.0000.0000.0000.000
87A89ALA0-0.024-0.01217.0040.0150.0150.0000.0000.0000.000
88A90PHE00.0560.01018.2790.0210.0210.0000.0000.0000.000
89A91GLN0-0.059-0.02621.0700.0110.0110.0000.0000.0000.000
90A92LYS10.8330.92215.2030.0110.0110.0000.0000.0000.000
91A93ASN0-0.033-0.00917.0200.0170.0170.0000.0000.0000.000
92A94ILE0-0.0040.01813.1820.0350.0350.0000.0000.0000.000
93A95PRO00.0190.00712.743-0.033-0.0330.0000.0000.0000.000
94A96ILE0-0.0030.00114.801-0.048-0.0480.0000.0000.0000.000
95A97ALA00.0160.01417.3880.0190.0190.0000.0000.0000.000
96A98ALA0-0.034-0.01318.979-0.023-0.0230.0000.0000.0000.000
97A99ILE0-0.0150.00321.5360.0130.0130.0000.0000.0000.000
98A100CYS0-0.0100.01223.979-0.007-0.0070.0000.0000.0000.000
99A101GLY00.027-0.00327.2740.0050.0050.0000.0000.0000.000
100A102ALA0-0.0030.01422.8800.0040.0040.0000.0000.0000.000
101A103VAL0-0.004-0.01024.9220.0080.0080.0000.0000.0000.000
102A104ASP-1-0.764-0.87026.508-0.016-0.0160.0000.0000.0000.000
103A105PHE0-0.006-0.00625.3270.0040.0040.0000.0000.0000.000
104A106LEU0-0.012-0.01822.8710.0050.0050.0000.0000.0000.000
105A107ALA00.0190.01627.0900.0070.0070.0000.0000.0000.000
106A108LYS10.8070.88730.7290.0280.0280.0000.0000.0000.000
107A109ASN0-0.067-0.04628.2630.0030.0030.0000.0000.0000.000
108A110GLY00.0290.01129.6790.0030.0030.0000.0000.0000.000
109A111LEU0-0.068-0.02924.1530.0060.0060.0000.0000.0000.000
110A112LEU00.0140.01526.4880.0080.0080.0000.0000.0000.000
111A113ASN0-0.028-0.01328.6860.0020.0020.0000.0000.0000.000
112A114ASN00.0190.00628.4040.0010.0010.0000.0000.0000.000
113A115HIS0-0.055-0.02923.0360.0100.0100.0000.0000.0000.000
114A116SER00.017-0.01028.164-0.011-0.0110.0000.0000.0000.000
115A117HIS0-0.0090.00627.719-0.002-0.0020.0000.0000.0000.000
116A118THR00.015-0.00727.985-0.003-0.0030.0000.0000.0000.000
117A119GLY00.033-0.00428.859-0.001-0.0010.0000.0000.0000.000
118A120ASN0-0.023-0.01729.8340.0010.0010.0000.0000.0000.000
119A121PHE00.0400.00632.3050.0020.0020.0000.0000.0000.000
120A122VAL00.0560.04335.575-0.002-0.0020.0000.0000.0000.000
121A123TYR00.003-0.01136.4310.0000.0000.0000.0000.0000.000
122A124LEU0-0.030-0.00534.2280.0000.0000.0000.0000.0000.000
123A125TRP0-0.031-0.05630.3190.0020.0020.0000.0000.0000.000
124A126LYS10.8380.91036.6500.0060.0060.0000.0000.0000.000
125A127ASP-1-0.821-0.87939.936-0.002-0.0020.0000.0000.0000.000
126A128TYR0-0.022-0.00132.994-0.001-0.0010.0000.0000.0000.000
127A129LYS10.9740.98237.4150.0020.0020.0000.0000.0000.000
128A130GLN0-0.047-0.01632.2050.0060.0060.0000.0000.0000.000
129A131TYR0-0.008-0.00132.5830.0030.0030.0000.0000.0000.000
130A132LYS10.8220.88234.681-0.017-0.0170.0000.0000.0000.000
131A133PRO0-0.0130.01833.1480.0030.0030.0000.0000.0000.000
132A134ILE0-0.0060.00331.837-0.001-0.0010.0000.0000.0000.000
133A135SER0-0.038-0.00631.6420.0010.0010.0000.0000.0000.000
134A136SER0-0.031-0.03434.036-0.004-0.0040.0000.0000.0000.000
135A137PHE00.0220.02732.4510.0040.0040.0000.0000.0000.000
136A138VAL0-0.016-0.00731.8810.0010.0010.0000.0000.0000.000
137A139GLU-1-0.912-0.94832.7380.0100.0100.0000.0000.0000.000
138A140LYS10.8970.94130.988-0.033-0.0330.0000.0000.0000.000
139A141GLN00.0050.01128.1940.0000.0000.0000.0000.0000.000
140A142ALA00.016-0.00424.545-0.007-0.0070.0000.0000.0000.000
141A143VAL0-0.040-0.01025.8410.0060.0060.0000.0000.0000.000
142A144ARG10.9170.96718.674-0.218-0.2180.0000.0000.0000.000
143A145ASP-1-0.751-0.84123.6890.0990.0990.0000.0000.0000.000
144A146LYS10.8530.90822.476-0.107-0.1070.0000.0000.0000.000
145A147ASN00.0020.00617.3030.0240.0240.0000.0000.0000.000
146A148LEU00.0030.00519.113-0.015-0.0150.0000.0000.0000.000
147A149VAL00.011-0.00119.2810.0060.0060.0000.0000.0000.000
148A150THR0-0.022-0.01321.723-0.016-0.0160.0000.0000.0000.000
149A151ALA00.0530.01424.3000.0070.0070.0000.0000.0000.000
150A152ASN00.0370.05226.107-0.012-0.0120.0000.0000.0000.000
151A153GLY00.0870.01927.065-0.002-0.0020.0000.0000.0000.000
152A154THR0-0.054-0.03227.808-0.006-0.0060.0000.0000.0000.000
153A155ALA00.0020.01626.3140.0000.0000.0000.0000.0000.000
154A156PRO00.0370.02422.0000.0080.0080.0000.0000.0000.000
155A157ILE0-0.0050.01520.987-0.002-0.0020.0000.0000.0000.000
156A158GLU-1-0.767-0.87521.6190.0040.0040.0000.0000.0000.000
157A159PHE00.0170.00219.1480.0190.0190.0000.0000.0000.000
158A160THR0-0.013-0.02916.1760.0040.0040.0000.0000.0000.000
159A161ASN0-0.024-0.01817.4630.0170.0170.0000.0000.0000.000
160A162LEU0-0.019-0.00718.7200.0280.0280.0000.0000.0000.000
161A163ILE0-0.001-0.00514.3230.0280.0280.0000.0000.0000.000
162A164LEU0-0.013-0.01012.8540.0430.0430.0000.0000.0000.000
163A165GLU-1-0.856-0.93314.6100.2150.2150.0000.0000.0000.000
164A166MET0-0.137-0.04815.6450.0190.0190.0000.0000.0000.000
165A167ILE0-0.082-0.04210.5350.0110.0110.0000.0000.0000.000
166A168ASP-1-0.927-0.95411.1370.6570.6570.0000.0000.0000.000
167A169PHE0-0.0120.0068.9780.1240.1240.0000.0000.0000.000
168A170ASP-1-0.811-0.89411.1850.3630.3630.0000.0000.0000.000
169A171THR0-0.014-0.02314.063-0.007-0.0070.0000.0000.0000.000
170A172PRO00.0830.03617.702-0.032-0.0320.0000.0000.0000.000
171A173GLU-1-0.849-0.90620.3440.1720.1720.0000.0000.0000.000
172A174ASN0-0.036-0.01516.999-0.060-0.0600.0000.0000.0000.000
173A175ILE00.0200.01115.752-0.039-0.0390.0000.0000.0000.000
174A176GLU-1-0.809-0.86218.8460.0260.0260.0000.0000.0000.000
175A177LYS10.8850.92721.097-0.118-0.1180.0000.0000.0000.000
176A178MET0-0.019-0.00814.031-0.008-0.0080.0000.0000.0000.000
177A179MET0-0.029-0.01517.604-0.030-0.0300.0000.0000.0000.000
178A180TYR00.0060.00321.772-0.009-0.0090.0000.0000.0000.000
179A181MET00.0010.00021.863-0.010-0.0100.0000.0000.0000.000
180A182ASN0-0.031-0.02518.517-0.020-0.0200.0000.0000.0000.000
181A183ARG10.8270.90422.883-0.005-0.0050.0000.0000.0000.000
182A184TYR0-0.041-0.01826.3680.0020.0020.0000.0000.0000.000
183A185GLY00.0320.02426.355-0.002-0.0020.0000.0000.0000.000
184A186PHE00.029-0.01125.9780.0080.0080.0000.0000.0000.000
185A187TYR00.0170.00827.8610.0040.0040.0000.0000.0000.000
186A188HIS00.0810.04030.6700.0060.0060.0000.0000.0000.000
187A189PHE0-0.042-0.01123.4400.0070.0070.0000.0000.0000.000
188A190CYS0-0.027-0.01928.5390.0050.0050.0000.0000.0000.000
189A191ASP-1-0.918-0.95330.420-0.002-0.0020.0000.0000.0000.000
190A192LYS10.7560.88927.782-0.032-0.0320.0000.0000.0000.000
191A193TYR0-0.064-0.07425.8770.0060.0060.0000.0000.0000.000
192A194GLY0-0.0170.02029.1500.0040.0040.0000.0000.0000.000
193A195ASN0-0.044-0.03525.638-0.006-0.0060.0000.0000.0000.000