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

tag_button

FMODB ID: YV8G2

Calculation Name: 4ANN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ANN

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G185

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1923728.480864
FMO2-HF: Nuclear repulsion 1852595.852703
FMO2-HF: Total energy -71132.62816
FMO2-MP2: Total energy -71343.717822


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:30:LEU)


Summations of interaction energy for fragment #1(A:30: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.
-10.297-3.2132.705-4.109-5.68-0.02
Interaction energy analysis for fragmet #1(A:30:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.028
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].
3A32MET0-0.080-0.0112.843-3.1170.337-0.014-1.663-1.777-0.003
4A33ARG10.8580.9143.912-0.925-0.6950.000-0.117-0.113-0.001
5A34GLU-1-0.889-0.9576.6160.2880.2880.0000.0000.0000.000
6A35ILE0-0.042-0.0149.645-0.057-0.0570.0000.0000.0000.000
7A36PRO00.0500.01712.9240.0400.0400.0000.0000.0000.000
8A37LYS10.8460.92215.840-0.036-0.0360.0000.0000.0000.000
9A38SER0-0.059-0.01318.983-0.008-0.0080.0000.0000.0000.000
10A39SER0-0.060-0.03717.136-0.010-0.0100.0000.0000.0000.000
11A40ILE0-0.0030.01017.302-0.012-0.0120.0000.0000.0000.000
12A41LYS10.9640.99120.8240.0810.0810.0000.0000.0000.000
13A42PRO00.0730.02124.258-0.002-0.0020.0000.0000.0000.000
14A43GLU-1-0.896-0.95625.922-0.047-0.0470.0000.0000.0000.000
15A44HIS0-0.014-0.02822.791-0.005-0.0050.0000.0000.0000.000
16A45PHE00.0340.01221.768-0.005-0.0050.0000.0000.0000.000
17A46HIS0-0.056-0.00521.920-0.004-0.0040.0000.0000.0000.000
18A47LEU0-0.011-0.02722.153-0.001-0.0010.0000.0000.0000.000
19A48MET00.0010.01317.651-0.018-0.0180.0000.0000.0000.000
20A49TYR00.0650.03717.684-0.014-0.0140.0000.0000.0000.000
21A50LEU0-0.025-0.00919.064-0.007-0.0070.0000.0000.0000.000
22A51LEU0-0.042-0.02813.566-0.017-0.0170.0000.0000.0000.000
23A52GLU-1-0.861-0.91614.195-0.063-0.0630.0000.0000.0000.000
24A53GLN0-0.073-0.01616.1330.0270.0270.0000.0000.0000.000
25A54HIS0-0.034-0.02817.932-0.019-0.0190.0000.0000.0000.000
26A55SER00.012-0.00417.2640.0120.0120.0000.0000.0000.000
27A56PRO0-0.008-0.00517.621-0.013-0.0130.0000.0000.0000.000
28A57TYR00.003-0.01116.9480.0050.0050.0000.0000.0000.000
29A58PHE0-0.053-0.02512.041-0.018-0.0180.0000.0000.0000.000
30A59ILE0-0.0070.0138.5910.0440.0440.0000.0000.0000.000
31A60ASP-1-0.863-0.91511.831-0.143-0.1430.0000.0000.0000.000
32A61ALA00.022-0.00111.293-0.052-0.0520.0000.0000.0000.000
33A62GLU-1-0.908-0.94412.0990.0450.0450.0000.0000.0000.000
34A63LEU0-0.039-0.01712.526-0.008-0.0080.0000.0000.0000.000
35A64THR0-0.049-0.02813.1090.0470.0470.0000.0000.0000.000
36A65GLU-1-0.873-0.93715.119-0.007-0.0070.0000.0000.0000.000
37A66LEU0-0.036-0.00713.7350.0170.0170.0000.0000.0000.000
38A67ARG10.9120.93317.648-0.132-0.1320.0000.0000.0000.000
39A68ASP-1-0.855-0.93318.6960.0330.0330.0000.0000.0000.000
40A69SER0-0.022-0.01213.689-0.013-0.0130.0000.0000.0000.000
41A70PHE00.0410.02414.5710.0190.0190.0000.0000.0000.000
42A71GLN0-0.045-0.03310.0910.0260.0260.0000.0000.0000.000
43A72ILE0-0.009-0.0028.6280.0170.0170.0000.0000.0000.000
44A73HIS0-0.011-0.0087.8500.1070.1070.0000.0000.0000.000
45A74TYR00.0060.0035.105-0.022-0.0220.0000.0000.0000.000
46A75ASP-1-0.787-0.8718.4610.1330.1330.0000.0000.0000.000
47A76ILE0-0.063-0.0325.081-0.125-0.1250.0000.0000.0000.000
48A77ASN00.004-0.0088.9130.0650.0650.0000.0000.0000.000
49A78ASP-1-0.868-0.95612.096-0.020-0.0200.0000.0000.0000.000
50A79ASN0-0.208-0.11714.4370.0210.0210.0000.0000.0000.000
51A80HIS0-0.0010.01011.430-0.008-0.0080.0000.0000.0000.000
52A81THR0-0.043-0.01611.7570.0090.0090.0000.0000.0000.000
53A82PRO00.0510.0217.905-0.029-0.0290.0000.0000.0000.000
54A83PHE00.0330.0059.6860.0950.0950.0000.0000.0000.000
55A84ASP-1-0.853-0.9428.111-0.544-0.5440.0000.0000.0000.000
56A85ASN0-0.044-0.02110.8710.0330.0330.0000.0000.0000.000
57A86ILE0-0.012-0.00713.2990.0440.0440.0000.0000.0000.000
58A87LYS10.9250.97711.6060.3930.3930.0000.0000.0000.000
59A88SER0-0.038-0.01116.6010.0140.0140.0000.0000.0000.000
60A89PHE0-0.030-0.00817.6150.0170.0170.0000.0000.0000.000
61A90THR0-0.003-0.01720.8510.0000.0000.0000.0000.0000.000
62A91LYS10.9620.98823.5030.0860.0860.0000.0000.0000.000
63A92ASN00.0380.00724.749-0.010-0.0100.0000.0000.0000.000
64A93GLU-1-0.766-0.85922.626-0.111-0.1110.0000.0000.0000.000
65A94LYS10.8250.91919.1970.1480.1480.0000.0000.0000.000
66A95LEU00.013-0.00220.734-0.016-0.0160.0000.0000.0000.000
67A96ARG10.8170.90422.9990.1140.1140.0000.0000.0000.000
68A97TYR00.0120.01016.7960.0040.0040.0000.0000.0000.000
69A98LEU0-0.012-0.01717.455-0.017-0.0170.0000.0000.0000.000
70A99LEU00.0050.01819.837-0.011-0.0110.0000.0000.0000.000
71A100ASN0-0.032-0.02120.1810.0080.0080.0000.0000.0000.000
72A101ILE0-0.0050.00315.804-0.006-0.0060.0000.0000.0000.000
73A102LYS11.0031.01118.3250.1260.1260.0000.0000.0000.000
74A103ASN00.008-0.00220.0640.0170.0170.0000.0000.0000.000
75A104LEU00.0170.00814.0130.0070.0070.0000.0000.0000.000
76A105GLU-1-0.920-0.95618.428-0.181-0.1810.0000.0000.0000.000
77A106GLU-1-0.963-0.97921.082-0.124-0.1240.0000.0000.0000.000
78A107VAL0-0.033-0.02116.6050.0140.0140.0000.0000.0000.000
79A108ASN00.0190.01619.800-0.004-0.0040.0000.0000.0000.000
80A109ARG10.8890.96421.7390.1480.1480.0000.0000.0000.000
81A110THR0-0.122-0.07020.5100.0100.0100.0000.0000.0000.000
82A111ARG10.9620.97221.6170.1100.1100.0000.0000.0000.000
83A112TYR0-0.071-0.05016.4450.0060.0060.0000.0000.0000.000
84A113THR0-0.026-0.01015.2790.0030.0030.0000.0000.0000.000
85A114PHE00.0410.01412.244-0.020-0.0200.0000.0000.0000.000
86A115VAL00.0220.0188.8150.0450.0450.0000.0000.0000.000
87A116LEU00.0090.01710.550-0.043-0.0430.0000.0000.0000.000
88A117ALA00.0550.0037.6080.0480.0480.0000.0000.0000.000
89A118PRO00.009-0.0017.419-0.021-0.0210.0000.0000.0000.000
90A119ASP-1-0.894-0.9402.842-6.133-3.1450.459-1.619-1.828-0.017
91A120GLU-1-0.840-0.8954.278-1.076-0.892-0.001-0.035-0.1480.000
92A121LEU0-0.066-0.0117.0220.1610.1610.0000.0000.0000.000
93A122PHE00.0260.0065.133-0.017-0.0170.0000.0000.0000.000
94A123PHE0-0.012-0.01510.7780.0320.0320.0000.0000.0000.000
95A124THR00.0770.04514.4520.0130.0130.0000.0000.0000.000
96A125ARG10.9530.97316.9150.0700.0700.0000.0000.0000.000
97A126ASP-1-0.911-0.95319.585-0.092-0.0920.0000.0000.0000.000
98A127GLY0-0.045-0.01218.5730.0040.0040.0000.0000.0000.000
99A128LEU0-0.029-0.01418.863-0.007-0.0070.0000.0000.0000.000
100A129PRO0-0.0280.00515.068-0.012-0.0120.0000.0000.0000.000
101A130ILE0-0.025-0.00411.9800.0270.0270.0000.0000.0000.000
102A131ALA00.0260.01210.582-0.060-0.0600.0000.0000.0000.000
103A132LYS10.8960.9502.0761.2821.5102.261-0.675-1.8140.001
104A133THR0-0.090-0.0686.0250.0500.0500.0000.0000.0000.000
105A134ARG10.8550.9178.5150.3370.3370.0000.0000.0000.000
106A135GLY00.0050.01912.2540.0010.0010.0000.0000.0000.000
107A136LEU0-0.069-0.04314.6350.0180.0180.0000.0000.0000.000
108A137GLN00.0760.03018.3460.0060.0060.0000.0000.0000.000
109A138ASN0-0.108-0.06021.0150.0100.0100.0000.0000.0000.000
110A139VAL0-0.086-0.04719.6190.0140.0140.0000.0000.0000.000
111A140VAL00.0290.01714.9160.0100.0100.0000.0000.0000.000
112A141ASP-1-0.848-0.89714.021-0.222-0.2220.0000.0000.0000.000
113A142PRO0-0.011-0.02811.105-0.009-0.0090.0000.0000.0000.000
114A143LEU00.0240.02913.6180.0230.0230.0000.0000.0000.000
115A144PRO0-0.0100.01115.830-0.027-0.0270.0000.0000.0000.000
116A145VAL00.0420.01715.3120.0110.0110.0000.0000.0000.000
117A146SER0-0.014-0.01118.3870.0080.0080.0000.0000.0000.000
118A147GLU-1-0.851-0.92520.569-0.149-0.1490.0000.0000.0000.000
119A148ALA0-0.024-0.02022.127-0.007-0.0070.0000.0000.0000.000
120A149GLU-1-0.843-0.93815.865-0.309-0.3090.0000.0000.0000.000
121A150PHE00.0380.01616.943-0.030-0.0300.0000.0000.0000.000
122A151LEU0-0.010-0.00218.266-0.014-0.0140.0000.0000.0000.000
123A152THR00.0050.00017.8100.0040.0040.0000.0000.0000.000
124A153ARG10.8860.94710.5650.4300.4300.0000.0000.0000.000
125A154TYR0-0.046-0.04215.593-0.018-0.0180.0000.0000.0000.000
126A155LYS10.8270.90017.6440.1600.1600.0000.0000.0000.000
127A156ALA00.0320.02715.3200.0080.0080.0000.0000.0000.000
128A157LEU00.0140.00811.708-0.002-0.0020.0000.0000.0000.000
129A158VAL00.0030.00115.4520.0140.0140.0000.0000.0000.000
130A159ILE0-0.022-0.01418.5750.0160.0160.0000.0000.0000.000
131A160CYS0-0.046-0.02213.8400.0020.0020.0000.0000.0000.000
132A161ALA0-0.0040.00515.9460.0110.0110.0000.0000.0000.000
133A162PHE0-0.040-0.03016.9210.0260.0260.0000.0000.0000.000
134A163ASN0-0.013-0.00318.4260.0240.0240.0000.0000.0000.000
135A164GLU-1-0.918-0.96215.509-0.149-0.1490.0000.0000.0000.000
136A165LYS10.8810.94015.0700.1120.1120.0000.0000.0000.000
137A166GLN0-0.068-0.02016.502-0.001-0.0010.0000.0000.0000.000
138A167SER00.0160.01412.956-0.044-0.0440.0000.0000.0000.000
139A168PHE00.048-0.00310.2960.0250.0250.0000.0000.0000.000
140A169ASP-1-0.824-0.9079.460-0.634-0.6340.0000.0000.0000.000
141A170ALA0-0.038-0.02512.3810.0470.0470.0000.0000.0000.000
142A171LEU0-0.089-0.05115.7130.0280.0280.0000.0000.0000.000
143A172VAL0-0.029-0.02213.6490.0250.0250.0000.0000.0000.000
144A173GLU-1-0.958-0.96712.950-0.323-0.3230.0000.0000.0000.000
145A174GLY0-0.0150.01217.2300.0250.0250.0000.0000.0000.000
146A175ASN0-0.065-0.03720.492-0.001-0.0010.0000.0000.0000.000
147A176LEU00.0710.02220.3560.0080.0080.0000.0000.0000.000
148A177GLU-1-0.871-0.94723.330-0.111-0.1110.0000.0000.0000.000
149A178LEU0-0.116-0.04626.3430.0100.0100.0000.0000.0000.000
150A179HIS0-0.055-0.02421.5130.0020.0020.0000.0000.0000.000
151A180LYS10.8860.94325.2450.0960.0960.0000.0000.0000.000
152A181GLY00.0690.02525.084-0.006-0.0060.0000.0000.0000.000
153A182THR0-0.071-0.02625.0260.0110.0110.0000.0000.0000.000
154A183PRO00.0460.00027.595-0.004-0.0040.0000.0000.0000.000
155A184PHE0-0.006-0.00322.5980.0010.0010.0000.0000.0000.000
156A185GLU-1-0.738-0.86622.040-0.155-0.1550.0000.0000.0000.000
157A186THR00.0190.00725.020-0.004-0.0040.0000.0000.0000.000
158A187LYS10.9610.98127.9280.0930.0930.0000.0000.0000.000
159A188VAL0-0.0220.00722.033-0.001-0.0010.0000.0000.0000.000
160A189ILE0-0.018-0.02123.043-0.005-0.0050.0000.0000.0000.000
161A190GLU-1-0.876-0.93225.082-0.101-0.1010.0000.0000.0000.000
162A191ALA0-0.072-0.00626.1710.0060.0060.0000.0000.0000.000
163A192ALA00.005-0.00727.127-0.007-0.0070.0000.0000.0000.000
164A193THR00.0300.00427.383-0.002-0.0020.0000.0000.0000.000
165A194LEU00.0700.03922.426-0.002-0.0020.0000.0000.0000.000
166A195ASP-1-0.879-0.93025.631-0.118-0.1180.0000.0000.0000.000
167A196LEU0-0.051-0.03328.7030.0040.0040.0000.0000.0000.000
168A197LEU0-0.019-0.00221.7170.0030.0030.0000.0000.0000.000
169A198THR0-0.012-0.01226.011-0.004-0.0040.0000.0000.0000.000
170A199ALA00.0230.02126.8550.0030.0030.0000.0000.0000.000
171A200PHE00.0160.00626.0560.0040.0040.0000.0000.0000.000
172A201LEU0-0.019-0.02522.5840.0030.0030.0000.0000.0000.000
173A202ASP-1-0.909-0.96826.844-0.107-0.1070.0000.0000.0000.000
174A203GLU-1-0.968-0.97529.619-0.084-0.0840.0000.0000.0000.000
175A204GLN0-0.115-0.04827.1310.0060.0060.0000.0000.0000.000
176A205TYR0-0.114-0.04626.2690.0050.0050.0000.0000.0000.000