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: G6VQ1

Calculation Name: 4E16-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E16

Chain ID: A

ChEMBL ID:

UniProt ID: Q180S3

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2680268.67925
FMO2-HF: Nuclear repulsion 2589874.370455
FMO2-HF: Total energy -90394.308795
FMO2-MP2: Total energy -90656.363859


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.
-26.278-15.8469.197-5.955-13.674-0.026
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 : 0.000 / 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].
3A3LYS10.7860.8922.520-16.063-11.4163.216-2.147-5.7150.012
4A4VAL00.0640.0323.5740.1270.3010.0070.070-0.2520.000
5A5HIS10.8040.8836.225-0.901-0.9010.0000.0000.0000.000
6A6PHE00.0150.0089.222-0.061-0.0610.0000.0000.0000.000
7A7VAL0-0.013-0.01812.2310.0810.0810.0000.0000.0000.000
8A8GLY00.0130.02315.201-0.039-0.0390.0000.0000.0000.000
9A9ALA0-0.015-0.02418.8510.0190.0190.0000.0000.0000.000
10A10GLY0-0.0010.01621.1890.0030.0030.0000.0000.0000.000
11A11PRO0-0.051-0.03324.260-0.010-0.0100.0000.0000.0000.000
12A12GLY00.021-0.00427.156-0.008-0.0080.0000.0000.0000.000
13A13ASP-1-0.857-0.92128.4080.0670.0670.0000.0000.0000.000
14A14LYS10.8660.91326.646-0.058-0.0580.0000.0000.0000.000
15A15GLU-1-0.948-0.97925.6720.0940.0940.0000.0000.0000.000
16A16LEU0-0.065-0.02326.6290.0070.0070.0000.0000.0000.000
17A17ILE0-0.0510.00119.0030.0070.0070.0000.0000.0000.000
18A18THR00.0300.00418.8720.0150.0150.0000.0000.0000.000
19A19LEU00.0470.02518.9500.0120.0120.0000.0000.0000.000
20A20LYS10.9460.96512.765-0.544-0.5440.0000.0000.0000.000
21A21GLY00.0570.01915.3680.0340.0340.0000.0000.0000.000
22A22TYR00.0730.04216.9690.0080.0080.0000.0000.0000.000
23A23LYS10.9220.97914.817-0.271-0.2710.0000.0000.0000.000
24A24LEU0-0.0140.00610.3860.0110.0110.0000.0000.0000.000
25A25LEU00.006-0.00713.950-0.010-0.0100.0000.0000.0000.000
26A26SER0-0.007-0.02016.500-0.010-0.0100.0000.0000.0000.000
27A27ASN0-0.095-0.06513.561-0.018-0.0180.0000.0000.0000.000
28A28ALA0-0.0180.01612.8450.0310.0310.0000.0000.0000.000
29A29ASP-1-0.808-0.88511.8510.2800.2800.0000.0000.0000.000
30A30VAL0-0.011-0.00411.315-0.032-0.0320.0000.0000.0000.000
31A31VAL00.0220.00912.6830.0070.0070.0000.0000.0000.000
32A32ILE00.0190.01512.547-0.013-0.0130.0000.0000.0000.000
33A33TYR00.0500.02716.1180.0040.0040.0000.0000.0000.000
34A34ALA00.0460.02219.244-0.014-0.0140.0000.0000.0000.000
35A35GLY00.0130.00021.8610.0070.0070.0000.0000.0000.000
36A36SER0-0.048-0.02724.7840.0060.0060.0000.0000.0000.000
37A37LEU0-0.022-0.01624.8330.0040.0040.0000.0000.0000.000
38A38VAL0-0.0100.00721.3710.0060.0060.0000.0000.0000.000
39A39ASN0-0.025-0.03424.726-0.008-0.0080.0000.0000.0000.000
40A40PRO00.016-0.00325.4550.0060.0060.0000.0000.0000.000
41A41GLU-1-0.798-0.86825.8990.0570.0570.0000.0000.0000.000
42A42LEU0-0.019-0.00422.3580.0070.0070.0000.0000.0000.000
43A43LEU0-0.020-0.02220.7650.0110.0110.0000.0000.0000.000
44A44GLU-1-0.877-0.92322.8720.0630.0630.0000.0000.0000.000
45A45TYR0-0.074-0.05421.6380.0050.0050.0000.0000.0000.000
46A46CYS0-0.065-0.02518.4040.0120.0120.0000.0000.0000.000
47A47LYS10.8530.92014.739-0.248-0.2480.0000.0000.0000.000
48A48GLU-1-0.932-0.96020.6870.0650.0650.0000.0000.0000.000
49A49ASP-1-0.956-0.96920.3320.0790.0790.0000.0000.0000.000
50A50CYS0-0.108-0.04316.3380.0070.0070.0000.0000.0000.000
51A51GLN0-0.0030.00115.432-0.006-0.0060.0000.0000.0000.000
52A52ILE00.0290.00616.514-0.007-0.0070.0000.0000.0000.000
53A53HIS00.0440.02315.672-0.019-0.0190.0000.0000.0000.000
54A54ASN00.0290.00618.895-0.001-0.0010.0000.0000.0000.000
55A55SER00.041-0.00418.405-0.002-0.0020.0000.0000.0000.000
56A56ALA0-0.052-0.02720.238-0.005-0.0050.0000.0000.0000.000
57A57HIS0-0.089-0.04323.228-0.001-0.0010.0000.0000.0000.000
58A58MET00.0120.04116.8420.0040.0040.0000.0000.0000.000
59A59ASP-1-0.888-0.93820.371-0.150-0.1500.0000.0000.0000.000
60A60LEU00.018-0.01515.886-0.008-0.0080.0000.0000.0000.000
61A61GLN0-0.048-0.03214.719-0.030-0.0300.0000.0000.0000.000
62A62GLU-1-0.856-0.93315.804-0.127-0.1270.0000.0000.0000.000
63A63ILE0-0.013-0.01613.422-0.002-0.0020.0000.0000.0000.000
64A64ILE0-0.018-0.01410.775-0.034-0.0340.0000.0000.0000.000
65A65ASP-1-0.785-0.86610.748-0.376-0.3760.0000.0000.0000.000
66A66VAL00.0210.03111.7920.0020.0020.0000.0000.0000.000
67A67MET0-0.091-0.0508.1370.0030.0030.0000.0000.0000.000
68A68ARG10.8060.8996.9050.2950.2950.0000.0000.0000.000
69A69GLU-1-0.879-0.9397.439-0.083-0.0830.0000.0000.0000.000
70A70GLY0-0.018-0.0018.6710.1400.1400.0000.0000.0000.000
71A71ILE0-0.042-0.0362.361-0.681-0.2251.111-0.289-1.277-0.004
72A72GLU-1-0.905-0.9615.1610.4010.481-0.0010.000-0.0790.000
73A73ASN0-0.094-0.0457.4670.1140.1140.0000.0000.0000.000
74A74ASN0-0.130-0.0626.4870.5630.5630.0000.0000.0000.000
75A75LYS10.9390.9837.800-0.288-0.2880.0000.0000.0000.000
76A76SER0-0.0110.0087.6640.0340.0340.0000.0000.0000.000
77A77VAL00.0220.0117.435-0.097-0.0970.0000.0000.0000.000
78A78VAL0-0.010-0.0149.1220.0320.0320.0000.0000.0000.000
79A79ARG10.8070.91711.8720.0590.0590.0000.0000.0000.000
80A80LEU00.0150.00013.6740.0280.0280.0000.0000.0000.000
81A81GLN0-0.003-0.01916.627-0.047-0.0470.0000.0000.0000.000
82A82THR00.006-0.01019.1020.0220.0220.0000.0000.0000.000
83A83GLY0-0.0010.01722.378-0.005-0.0050.0000.0000.0000.000
84A84ASP-1-0.814-0.89420.3610.1050.1050.0000.0000.0000.000
85A85PHE00.041-0.00315.751-0.021-0.0210.0000.0000.0000.000
86A86SER0-0.079-0.06020.234-0.021-0.0210.0000.0000.0000.000
87A87ILE0-0.035-0.01921.662-0.009-0.0090.0000.0000.0000.000
88A88TYR0-0.032-0.02724.9960.0020.0020.0000.0000.0000.000
89A89GLY00.0730.04920.9010.0020.0020.0000.0000.0000.000
90A90SER0-0.033-0.02219.874-0.003-0.0030.0000.0000.0000.000
91A91ILE00.0490.03014.332-0.017-0.0170.0000.0000.0000.000
92A92ARG10.8410.90615.3840.1180.1180.0000.0000.0000.000
93A93GLU-1-0.907-0.94716.121-0.187-0.1870.0000.0000.0000.000
94A94GLN00.0470.00613.061-0.039-0.0390.0000.0000.0000.000
95A95VAL0-0.0180.00911.155-0.091-0.0910.0000.0000.0000.000
96A96GLU-1-0.852-0.91911.560-0.334-0.3340.0000.0000.0000.000
97A97ASP-1-0.801-0.89712.832-0.469-0.4690.0000.0000.0000.000
98A98LEU00.0400.0107.020-0.044-0.0440.0000.0000.0000.000
99A99ASN0-0.029-0.0108.135-0.342-0.3420.0000.0000.0000.000
100A100LYS10.7960.8999.8860.3250.3250.0000.0000.0000.000
101A101LEU0-0.017-0.0128.4500.0580.0580.0000.0000.0000.000
102A102ASN0-0.107-0.0426.911-0.040-0.0400.0000.0000.0000.000
103A103ILE00.0180.0143.113-1.369-0.8100.053-0.106-0.5070.000
104A104ASP-1-0.795-0.8882.174-8.044-3.9854.790-3.347-5.502-0.033
105A105TYR0-0.026-0.0223.516-0.3490.1080.021-0.136-0.342-0.001
106A106ASP-1-0.874-0.9285.8761.9471.9470.0000.0000.0000.000
107A107CYS00.0050.0148.829-0.178-0.1780.0000.0000.0000.000
108A108THR0-0.053-0.03212.4680.1030.1030.0000.0000.0000.000
109A109PRO00.0320.01314.867-0.034-0.0340.0000.0000.0000.000
110A110GLY00.0080.00418.5050.0190.0190.0000.0000.0000.000
111A111VAL00.0100.00221.480-0.008-0.0080.0000.0000.0000.000
112A112SER00.0640.02625.286-0.011-0.0110.0000.0000.0000.000
113A113SER00.0800.02826.8470.0020.0020.0000.0000.0000.000
114A114PHE00.0170.00928.5040.0000.0000.0000.0000.0000.000
115A115LEU0-0.0030.01827.517-0.001-0.0010.0000.0000.0000.000
116A116GLY00.0410.02030.6780.0010.0010.0000.0000.0000.000
117A117ALA0-0.006-0.02032.044-0.001-0.0010.0000.0000.0000.000
118A118ALA0-0.018-0.00434.864-0.002-0.0020.0000.0000.0000.000
119A119SER00.0180.00333.5580.0000.0000.0000.0000.0000.000
120A120SER0-0.049-0.02735.886-0.002-0.0020.0000.0000.0000.000
121A121LEU0-0.061-0.05137.562-0.003-0.0030.0000.0000.0000.000
122A122GLY0-0.0270.00739.254-0.002-0.0020.0000.0000.0000.000
123A123VAL0-0.093-0.03739.325-0.003-0.0030.0000.0000.0000.000
124A124GLU-1-0.905-0.95838.4630.0440.0440.0000.0000.0000.000
125A125TYR0-0.052-0.06134.353-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.039-0.00637.363-0.002-0.0020.0000.0000.0000.000
127A127VAL00.0770.04039.9240.0020.0020.0000.0000.0000.000
128A128PRO00.0380.00042.974-0.002-0.0020.0000.0000.0000.000
129A129GLU-1-0.946-0.97145.5040.0190.0190.0000.0000.0000.000
130A130ILE0-0.072-0.00945.986-0.002-0.0020.0000.0000.0000.000
131A131SER0-0.050-0.04142.112-0.001-0.0010.0000.0000.0000.000
132A132GLN00.0280.01240.6630.0020.0020.0000.0000.0000.000
133A133SER0-0.040-0.02537.8210.0010.0010.0000.0000.0000.000
134A134VAL00.0170.00235.0900.0000.0000.0000.0000.0000.000
135A135ILE0-0.0290.01135.7400.0000.0000.0000.0000.0000.000
136A136ILE00.0220.01130.8620.0010.0010.0000.0000.0000.000
137A137THR0-0.014-0.01433.254-0.004-0.0040.0000.0000.0000.000
138A138ARG10.8530.90228.0430.0300.0300.0000.0000.0000.000
139A139MET0-0.076-0.01634.541-0.002-0.0020.0000.0000.0000.000
140A140GLU-1-0.771-0.84832.093-0.028-0.0280.0000.0000.0000.000
141A141GLY0-0.009-0.01736.5360.0020.0020.0000.0000.0000.000
142A142ARG10.7520.84539.6770.0140.0140.0000.0000.0000.000
143A143THR00.022-0.00236.920-0.003-0.0030.0000.0000.0000.000
144A144PRO0-0.0160.01238.8310.0020.0020.0000.0000.0000.000
145A145VAL00.0460.01737.047-0.002-0.0020.0000.0000.0000.000
146A146PRO00.0140.02236.9340.0020.0020.0000.0000.0000.000
147A147GLU-1-0.771-0.91740.044-0.012-0.0120.0000.0000.0000.000
148A148LYS10.8760.94739.1180.0210.0210.0000.0000.0000.000
149A149GLU-1-0.935-0.97233.934-0.021-0.0210.0000.0000.0000.000
150A150SER0-0.0370.00738.2400.0010.0010.0000.0000.0000.000
151A151ILE00.0560.00938.6290.0020.0020.0000.0000.0000.000
152A152GLN00.0350.01841.6670.0020.0020.0000.0000.0000.000
153A153SER0-0.066-0.02142.2180.0020.0020.0000.0000.0000.000
154A154TYR00.018-0.00935.7090.0020.0020.0000.0000.0000.000
155A155ALA00.0270.00541.9310.0020.0020.0000.0000.0000.000
156A156LYS10.9460.98944.7920.0050.0050.0000.0000.0000.000
157A157HIS0-0.036-0.00642.1380.0010.0010.0000.0000.0000.000
158A158GLN0-0.060-0.04745.3520.0020.0020.0000.0000.0000.000
159A159THR00.0540.04140.7700.0020.0020.0000.0000.0000.000
160A160SER0-0.054-0.01539.690-0.002-0.0020.0000.0000.0000.000
161A161MET0-0.048-0.01638.562-0.001-0.0010.0000.0000.0000.000
162A162VAL0-0.0040.00033.7270.0010.0010.0000.0000.0000.000
163A163ILE0-0.002-0.00835.715-0.003-0.0030.0000.0000.0000.000
164A164PHE00.0180.01429.5390.0010.0010.0000.0000.0000.000
165A165LEU0-0.0010.00234.477-0.004-0.0040.0000.0000.0000.000
166A166SER00.0780.01236.2380.0010.0010.0000.0000.0000.000
167A167VAL00.0230.03037.9190.0000.0000.0000.0000.0000.000
168A168GLN00.0320.01741.113-0.001-0.0010.0000.0000.0000.000
169A169GLU-1-0.843-0.92140.697-0.013-0.0130.0000.0000.0000.000
170A170ILE00.004-0.00243.2200.0000.0000.0000.0000.0000.000
171A171GLU-1-0.842-0.91444.710-0.002-0.0020.0000.0000.0000.000
172A172LYS10.9440.97744.3750.0110.0110.0000.0000.0000.000
173A173VAL00.0250.01441.5170.0000.0000.0000.0000.0000.000
174A174VAL00.0370.02244.3880.0010.0010.0000.0000.0000.000
175A175SER0-0.005-0.00847.3340.0000.0000.0000.0000.0000.000
176A176LYS10.8830.93443.7010.0100.0100.0000.0000.0000.000
177A177LEU00.0130.01043.1040.0000.0000.0000.0000.0000.000
178A178LEU0-0.029-0.00946.9150.0010.0010.0000.0000.0000.000
179A179GLU-1-0.952-0.96349.199-0.007-0.0070.0000.0000.0000.000
180A180GLY0-0.097-0.05147.749-0.001-0.0010.0000.0000.0000.000
181A181GLY0-0.006-0.00248.8270.0010.0010.0000.0000.0000.000
182A182TYR0-0.063-0.01243.8740.0000.0000.0000.0000.0000.000
183A183PRO00.0520.02450.102-0.001-0.0010.0000.0000.0000.000
184A184LYS10.9430.96552.088-0.002-0.0020.0000.0000.0000.000
185A185ASP-1-0.810-0.88453.2660.0090.0090.0000.0000.0000.000
186A186THR0-0.040-0.02847.6000.0010.0010.0000.0000.0000.000
187A187PRO0-0.020-0.00747.590-0.001-0.0010.0000.0000.0000.000
188A188ILE0-0.005-0.00943.7430.0000.0000.0000.0000.0000.000
189A189ALA0-0.033-0.01142.1460.0000.0000.0000.0000.0000.000
190A190VAL00.0040.01140.561-0.001-0.0010.0000.0000.0000.000
191A191ILE00.0270.01537.0620.0010.0010.0000.0000.0000.000
192A192TYR0-0.017-0.02336.788-0.001-0.0010.0000.0000.0000.000
193A193LYS10.8160.89832.252-0.019-0.0190.0000.0000.0000.000
194A194ALA00.0360.02232.8560.0020.0020.0000.0000.0000.000
195A195THR0-0.007-0.02131.2070.0050.0050.0000.0000.0000.000
196A196TRP0-0.0320.01028.4170.0020.0020.0000.0000.0000.000
197A197ALA00.0520.01833.369-0.001-0.0010.0000.0000.0000.000
198A198ASP-1-0.853-0.92535.3920.0210.0210.0000.0000.0000.000
199A199GLU-1-0.857-0.88036.2430.0330.0330.0000.0000.0000.000
200A200LYS10.8920.93237.777-0.014-0.0140.0000.0000.0000.000
201A201ILE00.0320.01140.320-0.001-0.0010.0000.0000.0000.000
202A202VAL0-0.037-0.01242.529-0.001-0.0010.0000.0000.0000.000
203A203LYS10.9950.98844.752-0.020-0.0200.0000.0000.0000.000
204A204GLY0-0.043-0.03746.935-0.001-0.0010.0000.0000.0000.000
205A205THR0-0.004-0.00849.1510.0010.0010.0000.0000.0000.000
206A206LEU00.0460.00647.015-0.001-0.0010.0000.0000.0000.000
207A207SER0-0.123-0.05850.322-0.001-0.0010.0000.0000.0000.000
208A208ASP-1-0.760-0.84551.7750.0080.0080.0000.0000.0000.000
209A209ILE00.0690.03645.9880.0000.0000.0000.0000.0000.000
210A210ALA00.0250.01148.4590.0000.0000.0000.0000.0000.000
211A211VAL0-0.007-0.01649.5320.0000.0000.0000.0000.0000.000
212A212LYS10.8860.95249.407-0.010-0.0100.0000.0000.0000.000
213A213VAL00.0010.00644.6330.0010.0010.0000.0000.0000.000
214A214LYS10.8270.90547.0110.0000.0000.0000.0000.0000.000
215A215GLU-1-0.942-0.97049.1340.0060.0060.0000.0000.0000.000
216A216ASN00.0240.01845.9990.0020.0020.0000.0000.0000.000
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