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: YV972

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2211137.913634
FMO2-HF: Nuclear repulsion 2134160.923253
FMO2-HF: Total energy -76976.990381
FMO2-MP2: Total energy -77202.063541


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.
-10.901-3.2795.942-4.732-8.831-0.048
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 : -0.053 / q_NPA : -0.023
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].
3A5LYS10.9690.9753.237-2.0300.4460.064-1.020-1.5190.000
4A6ALA00.0300.0095.1100.3100.372-0.001-0.004-0.0560.000
5A7LEU0-0.015-0.0158.492-0.092-0.0920.0000.0000.0000.000
6A8PHE00.008-0.01211.1950.0850.0850.0000.0000.0000.000
7A9LEU0-0.031-0.02314.298-0.002-0.0020.0000.0000.0000.000
8A10ILE00.0100.01717.3800.0210.0210.0000.0000.0000.000
9A11LEU00.0170.02320.041-0.001-0.0010.0000.0000.0000.000
10A12ASP-1-0.759-0.88623.483-0.136-0.1360.0000.0000.0000.000
11A13GLN0-0.052-0.01126.0740.0110.0110.0000.0000.0000.000
12A14TYR0-0.014-0.01221.0000.0060.0060.0000.0000.0000.000
13A15ALA00.0260.00224.5240.0000.0000.0000.0000.0000.000
14A16ASP-1-0.794-0.87122.708-0.160-0.1600.0000.0000.0000.000
15A17TRP0-0.007-0.02821.714-0.020-0.0200.0000.0000.0000.000
16A18GLU-1-0.796-0.91422.048-0.104-0.1040.0000.0000.0000.000
17A19GLY00.0370.01017.7610.0090.0090.0000.0000.0000.000
18A20VAL00.0110.00616.293-0.036-0.0360.0000.0000.0000.000
19A21TYR00.0160.01316.474-0.025-0.0250.0000.0000.0000.000
20A22LEU00.0050.01213.220-0.007-0.0070.0000.0000.0000.000
21A23ALA00.0110.00411.976-0.042-0.0420.0000.0000.0000.000
22A24SER00.000-0.01211.072-0.093-0.0930.0000.0000.0000.000
23A25ALA0-0.0130.00911.663-0.047-0.0470.0000.0000.0000.000
24A26LEU0-0.008-0.0148.2640.0100.0100.0000.0000.0000.000
25A27ASN00.0310.0026.748-0.339-0.3390.0000.0000.0000.000
26A28GLN0-0.059-0.0317.019-0.150-0.1500.0000.0000.0000.000
27A29ARG10.7740.8916.067-0.357-0.3570.0000.0000.0000.000
28A30GLU-1-0.883-0.9334.620-1.607-1.475-0.001-0.018-0.1120.000
29A31ASP-1-0.834-0.9042.582-1.574-0.0781.782-1.051-2.228-0.011
30A32TRP00.005-0.0152.629-1.381-0.0612.801-1.542-2.580-0.023
31A33SER00.0110.0182.380-3.846-1.7861.297-1.058-2.299-0.014
32A34VAL0-0.022-0.0074.2510.4640.5400.000-0.039-0.0370.000
33A35HIS0-0.038-0.0135.909-0.231-0.2310.0000.0000.0000.000
34A36THR0-0.018-0.0249.9610.0940.0940.0000.0000.0000.000
35A37VAL0-0.009-0.01613.6770.0020.0020.0000.0000.0000.000
36A38SER00.010-0.02415.7720.0270.0270.0000.0000.0000.000
37A39LEU0-0.067-0.03619.5340.0030.0030.0000.0000.0000.000
38A40ASP-1-0.889-0.94022.386-0.128-0.1280.0000.0000.0000.000
39A41PRO00.006-0.02120.199-0.016-0.0160.0000.0000.0000.000
40A42ILE0-0.035-0.02420.358-0.019-0.0190.0000.0000.0000.000
41A43VAL0-0.0160.01920.8480.0150.0150.0000.0000.0000.000
42A44SER0-0.018-0.02523.149-0.014-0.0140.0000.0000.0000.000
43A45SER0-0.050-0.03023.5560.0060.0060.0000.0000.0000.000
44A46ILE00.016-0.01025.3130.0060.0060.0000.0000.0000.000
45A47GLY0-0.045-0.02227.0540.0080.0080.0000.0000.0000.000
46A48GLY0-0.027-0.00927.9180.0040.0040.0000.0000.0000.000
47A49PHE0-0.056-0.03122.812-0.003-0.0030.0000.0000.0000.000
48A50LYS10.9090.96224.0080.1450.1450.0000.0000.0000.000
49A51THR00.0350.01917.724-0.004-0.0040.0000.0000.0000.000
50A52SER0-0.009-0.00617.7260.0260.0260.0000.0000.0000.000
51A53VAL0-0.043-0.02516.355-0.037-0.0370.0000.0000.0000.000
52A54ASP-1-0.821-0.86410.658-0.621-0.6210.0000.0000.0000.000
53A55TYR0-0.017-0.0267.8880.0590.0590.0000.0000.0000.000
54A56ILE00.0360.03514.7890.0110.0110.0000.0000.0000.000
55A57ILE0-0.008-0.01917.8210.0050.0050.0000.0000.0000.000
56A58GLY0-0.107-0.06018.1900.0180.0180.0000.0000.0000.000
57A59LEU0-0.070-0.03816.6950.0140.0140.0000.0000.0000.000
58A60GLU-1-0.841-0.90013.167-0.213-0.2130.0000.0000.0000.000
59A61PRO0-0.031-0.0098.7010.0370.0370.0000.0000.0000.000
60A62ALA00.0450.01511.3350.0030.0030.0000.0000.0000.000
61A63ASN0-0.062-0.04310.553-0.004-0.0040.0000.0000.0000.000
62A64PHE0-0.0130.0017.981-0.062-0.0620.0000.0000.0000.000
63A65ASN00.0120.0006.268-0.296-0.2960.0000.0000.0000.000
64A66LEU00.0330.0359.0650.1090.1090.0000.0000.0000.000
65A67LEU0-0.0150.00911.110-0.094-0.0940.0000.0000.0000.000
66A68VAL0-0.0010.00613.0800.0490.0490.0000.0000.0000.000
67A69MET0-0.042-0.00815.658-0.024-0.0240.0000.0000.0000.000
68A70ILE00.0190.00418.0170.0180.0180.0000.0000.0000.000
69A71GLY00.0230.02120.6940.0050.0050.0000.0000.0000.000
70A72GLY00.006-0.00624.261-0.015-0.0150.0000.0000.0000.000
71A73ASP-1-0.922-0.94826.982-0.077-0.0770.0000.0000.0000.000
72A74SER0-0.012-0.02427.2030.0080.0080.0000.0000.0000.000
73A75TRP0-0.028-0.03321.4290.0050.0050.0000.0000.0000.000
74A76SER0-0.0380.00728.2120.0070.0070.0000.0000.0000.000
75A77ASN0-0.023-0.03427.8230.0020.0020.0000.0000.0000.000
76A78ASP-1-0.853-0.92529.441-0.050-0.0500.0000.0000.0000.000
77A79ASN00.0170.01526.7180.0040.0040.0000.0000.0000.000
78A80LYS11.0040.99526.1660.0580.0580.0000.0000.0000.000
79A81LYS10.9170.95423.5280.0950.0950.0000.0000.0000.000
80A82LEU00.0880.05321.668-0.004-0.0040.0000.0000.0000.000
81A83LEU00.0090.01322.550-0.001-0.0010.0000.0000.0000.000
82A84HIS0-0.019-0.01521.5660.0070.0070.0000.0000.0000.000
83A85PHE00.0180.03214.7960.0130.0130.0000.0000.0000.000
84A86VAL00.0620.02318.9170.0020.0020.0000.0000.0000.000
85A87LYS10.9090.96020.2060.0340.0340.0000.0000.0000.000
86A88THR0-0.015-0.03318.6410.0150.0150.0000.0000.0000.000
87A89ALA0-0.021-0.00916.3320.0140.0140.0000.0000.0000.000
88A90PHE00.0620.01417.6790.0180.0180.0000.0000.0000.000
89A91GLN0-0.050-0.01720.4920.0130.0130.0000.0000.0000.000
90A92LYS10.8150.91814.9140.1010.1010.0000.0000.0000.000
91A93ASN0-0.029-0.01716.7220.0130.0130.0000.0000.0000.000
92A94ILE0-0.0200.00812.7480.0330.0330.0000.0000.0000.000
93A95PRO00.0090.00012.979-0.021-0.0210.0000.0000.0000.000
94A96ILE00.004-0.00214.660-0.052-0.0520.0000.0000.0000.000
95A97ALA00.0070.01116.9650.0250.0250.0000.0000.0000.000
96A98ALA0-0.030-0.02318.499-0.026-0.0260.0000.0000.0000.000
97A99ILE0-0.0030.00421.0930.0150.0150.0000.0000.0000.000
98A100CYS0-0.0010.00623.571-0.005-0.0050.0000.0000.0000.000
99A101GLY00.0240.00826.8850.0060.0060.0000.0000.0000.000
100A102ALA0-0.0090.00922.5650.0050.0050.0000.0000.0000.000
101A103VAL0-0.006-0.01124.5950.0080.0080.0000.0000.0000.000
102A104ASP-1-0.799-0.88826.375-0.042-0.0420.0000.0000.0000.000
103A105PHE0-0.013-0.00725.1610.0060.0060.0000.0000.0000.000
104A106LEU0-0.009-0.01222.5940.0060.0060.0000.0000.0000.000
105A107ALA00.0240.01526.6750.0070.0070.0000.0000.0000.000
106A108LYS10.8920.94430.2700.0520.0520.0000.0000.0000.000
107A109ASN0-0.109-0.06427.9520.0050.0050.0000.0000.0000.000
108A110GLY00.028-0.00229.2030.0020.0020.0000.0000.0000.000
109A111LEU0-0.090-0.03823.9030.0050.0050.0000.0000.0000.000
110A112LEU00.0140.01726.2100.0040.0040.0000.0000.0000.000
111A113ASN0-0.022-0.02628.6050.0030.0030.0000.0000.0000.000
112A114ASN00.0100.00028.3920.0040.0040.0000.0000.0000.000
113A115HIS0-0.019-0.00523.0810.0080.0080.0000.0000.0000.000
114A116SER00.0060.00128.160-0.008-0.0080.0000.0000.0000.000
115A117HIS0-0.017-0.00727.572-0.004-0.0040.0000.0000.0000.000
116A118THR00.0270.01827.7150.0000.0000.0000.0000.0000.000
117A119GLY00.043-0.00328.477-0.004-0.0040.0000.0000.0000.000
118A120ASN00.0210.01129.5510.0020.0020.0000.0000.0000.000
119A121PHE00.0460.00631.8570.0030.0030.0000.0000.0000.000
120A122VAL00.0660.04635.088-0.002-0.0020.0000.0000.0000.000
121A123TYR00.001-0.00835.9930.0000.0000.0000.0000.0000.000
122A124LEU0-0.0340.00033.8270.0010.0010.0000.0000.0000.000
123A125TRP0-0.025-0.05830.1070.0010.0010.0000.0000.0000.000
124A126LYS10.8390.91336.4090.0190.0190.0000.0000.0000.000
125A127ASP-1-0.834-0.88439.644-0.016-0.0160.0000.0000.0000.000
126A128TYR0-0.0210.00032.557-0.001-0.0010.0000.0000.0000.000
127A129LYS10.9790.97937.2730.0190.0190.0000.0000.0000.000
128A130GLN0-0.062-0.03532.2400.0060.0060.0000.0000.0000.000
129A131TYR00.0240.01932.1770.0020.0020.0000.0000.0000.000
130A132LYS10.8270.89534.5170.0040.0040.0000.0000.0000.000
131A133PRO0-0.0420.00833.0850.0030.0030.0000.0000.0000.000
132A134ILE0-0.0070.01831.9310.0000.0000.0000.0000.0000.000
133A135SER0-0.030-0.00931.4380.0020.0020.0000.0000.0000.000
134A136SER00.003-0.00833.725-0.005-0.0050.0000.0000.0000.000
135A137PHE0-0.0160.00932.1900.0030.0030.0000.0000.0000.000
136A138VAL0-0.014-0.02431.6000.0020.0020.0000.0000.0000.000
137A139GLU-1-0.920-0.95232.661-0.008-0.0080.0000.0000.0000.000
138A140LYS10.9000.94330.913-0.015-0.0150.0000.0000.0000.000
139A141GLN0-0.0030.01328.1810.0000.0000.0000.0000.0000.000
140A142ALA00.0250.00224.416-0.008-0.0080.0000.0000.0000.000
141A143VAL0-0.047-0.01325.7270.0090.0090.0000.0000.0000.000
142A144ARG10.9841.00518.752-0.164-0.1640.0000.0000.0000.000
143A145ASP-1-0.772-0.86223.5000.0710.0710.0000.0000.0000.000
144A146LYS10.8470.90521.966-0.078-0.0780.0000.0000.0000.000
145A147ASN00.0180.00816.8710.0220.0220.0000.0000.0000.000
146A148LEU00.0220.01819.016-0.021-0.0210.0000.0000.0000.000
147A149VAL00.0070.00019.3750.0100.0100.0000.0000.0000.000
148A150THR0-0.009-0.00321.527-0.017-0.0170.0000.0000.0000.000
149A151ALA00.0530.00824.1360.0090.0090.0000.0000.0000.000
150A152ASN00.0310.05125.873-0.013-0.0130.0000.0000.0000.000
151A153GLY00.0750.01126.754-0.003-0.0030.0000.0000.0000.000
152A154THR0-0.063-0.03527.370-0.006-0.0060.0000.0000.0000.000
153A155ALA0-0.0060.00426.2430.0030.0030.0000.0000.0000.000
154A156PRO00.0450.03722.3960.0030.0030.0000.0000.0000.000
155A157ILE00.0150.01021.343-0.002-0.0020.0000.0000.0000.000
156A158GLU-1-0.766-0.87121.824-0.023-0.0230.0000.0000.0000.000
157A159PHE00.0090.00018.9260.0150.0150.0000.0000.0000.000
158A160THR0-0.014-0.03216.347-0.004-0.0040.0000.0000.0000.000
159A161ASN0-0.021-0.01417.5800.0140.0140.0000.0000.0000.000
160A162LEU0-0.003-0.00718.9640.0240.0240.0000.0000.0000.000
161A163ILE0-0.006-0.00114.3290.0250.0250.0000.0000.0000.000
162A164LEU0-0.002-0.00813.0010.0290.0290.0000.0000.0000.000
163A165GLU-1-0.906-0.94114.8070.1660.1660.0000.0000.0000.000
164A166MET0-0.126-0.05515.8730.0420.0420.0000.0000.0000.000
165A167ILE0-0.093-0.04010.5750.0020.0020.0000.0000.0000.000
166A168ASP-1-0.935-0.95011.4790.5330.5330.0000.0000.0000.000
167A169PHE0-0.038-0.0219.1140.1280.1280.0000.0000.0000.000
168A170ASP-1-0.831-0.91611.7670.3550.3550.0000.0000.0000.000
169A171THR0-0.024-0.01914.473-0.013-0.0130.0000.0000.0000.000
170A172PRO00.1210.03918.043-0.028-0.0280.0000.0000.0000.000
171A173GLU-1-0.880-0.91320.6730.1500.1500.0000.0000.0000.000
172A174ASN0-0.068-0.05516.863-0.040-0.0400.0000.0000.0000.000
173A175ILE00.0170.02115.835-0.035-0.0350.0000.0000.0000.000
174A176GLU-1-0.840-0.89018.8220.0200.0200.0000.0000.0000.000
175A177LYS10.9130.94821.362-0.110-0.1100.0000.0000.0000.000
176A178MET0-0.0010.00414.168-0.007-0.0070.0000.0000.0000.000
177A179MET0-0.021-0.01117.838-0.029-0.0290.0000.0000.0000.000
178A180TYR00.0040.00721.889-0.008-0.0080.0000.0000.0000.000
179A181MET00.0010.00322.061-0.009-0.0090.0000.0000.0000.000
180A182ASN0-0.051-0.03218.689-0.017-0.0170.0000.0000.0000.000
181A183ARG10.8260.89623.1060.0190.0190.0000.0000.0000.000
182A184TYR0-0.050-0.02726.3680.0000.0000.0000.0000.0000.000
183A185GLY00.0420.03726.9750.0000.0000.0000.0000.0000.000
184A186PHE00.042-0.00826.3430.0080.0080.0000.0000.0000.000
185A187TYR00.0170.00528.1620.0040.0040.0000.0000.0000.000
186A188HIS00.0640.04630.8670.0060.0060.0000.0000.0000.000
187A189PHE0-0.058-0.02723.8100.0070.0070.0000.0000.0000.000
188A190CYS0-0.016-0.03628.8010.0050.0050.0000.0000.0000.000
189A191ASP-1-0.918-0.92730.457-0.002-0.0020.0000.0000.0000.000
190A192LYS10.7640.88828.149-0.025-0.0250.0000.0000.0000.000
191A193TYR0-0.050-0.06326.1730.0060.0060.0000.0000.0000.000
192A194GLY0-0.0240.03129.5710.0050.0050.0000.0000.0000.000
193A195ASN0-0.043-0.04525.613-0.008-0.0080.0000.0000.0000.000