FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 9GZL2

Calculation Name: 3FBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FBQ

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F7

Base Structure: X-ray

Registration Date: 2023-06-19

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 288
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3776437.400886
FMO2-HF: Nuclear repulsion 3663585.774112
FMO2-HF: Total energy -112851.626774
FMO2-MP2: Total energy -113182.270166


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-0.8450.9770.105-0.571-1.3540.001
Interaction energy analysis for fragmet #1(A:4:PRO)
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 : -0.032
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].
3A6VAL0-0.0070.0093.377-0.7110.7810.098-0.484-1.1050.001
4A7GLY0-0.012-0.0053.261-0.370-0.1560.008-0.080-0.1420.000
5A8ASP-1-0.788-0.9124.267-0.0330.083-0.001-0.007-0.1070.000
6A9ILE0-0.022-0.0207.0730.0520.0520.0000.0000.0000.000
7A10PHE00.0290.0049.3440.0530.0530.0000.0000.0000.000
8A11ARG10.8990.93911.5970.2850.2850.0000.0000.0000.000
9A12PHE0-0.050-0.0169.8270.0060.0060.0000.0000.0000.000
10A13LEU00.0270.01111.9540.0410.0410.0000.0000.0000.000
11A14ASP-1-0.876-0.91614.719-0.110-0.1100.0000.0000.0000.000
12A15ASN0-0.065-0.04415.7720.0060.0060.0000.0000.0000.000
13A16GLY00.0230.01219.6930.0100.0100.0000.0000.0000.000
14A17ARG10.8910.94622.2420.0780.0780.0000.0000.0000.000
15A18THR0-0.004-0.00118.919-0.004-0.0040.0000.0000.0000.000
16A19GLY00.0290.00719.9740.0130.0130.0000.0000.0000.000
17A20LEU0-0.029-0.00620.224-0.001-0.0010.0000.0000.0000.000
18A21TYR0-0.026-0.05015.7230.0030.0030.0000.0000.0000.000
19A22GLU-1-0.917-0.92415.764-0.146-0.1460.0000.0000.0000.000
20A23ASN0-0.043-0.03315.484-0.022-0.0220.0000.0000.0000.000
21A24TYR00.0490.00215.2640.0140.0140.0000.0000.0000.000
22A25LYS10.8190.8986.3970.1200.1200.0000.0000.0000.000
23A26GLU-1-0.974-0.97112.279-0.091-0.0910.0000.0000.0000.000
24A27PHE0-0.035-0.02914.0240.0270.0270.0000.0000.0000.000
25A28SER0-0.042-0.03612.7840.0090.0090.0000.0000.0000.000
26A29THR0-0.079-0.03114.3270.0110.0110.0000.0000.0000.000
27A30GLU-1-0.822-0.9077.2290.4120.4120.0000.0000.0000.000
28A31LEU0-0.022-0.04011.5030.0030.0030.0000.0000.0000.000
29A32ASN0-0.077-0.0186.8480.0670.0670.0000.0000.0000.000
30A33MET00.0190.03010.059-0.009-0.0090.0000.0000.0000.000
31A34THR0-0.029-0.03310.4090.0010.0010.0000.0000.0000.000
32A35ARG10.8230.90113.022-0.111-0.1110.0000.0000.0000.000
33A36GLU-1-0.937-0.97513.5260.1390.1390.0000.0000.0000.000
34A37SER00.0330.04016.5920.0010.0010.0000.0000.0000.000
35A38ASN0-0.037-0.03418.9940.0010.0010.0000.0000.0000.000
36A39GLY00.0310.01517.884-0.007-0.0070.0000.0000.0000.000
37A40VAL0-0.017-0.00115.610-0.002-0.0020.0000.0000.0000.000
38A41LYS10.9200.9607.323-0.326-0.3260.0000.0000.0000.000
39A42VAL00.0250.00612.322-0.019-0.0190.0000.0000.0000.000
40A43THR0-0.043-0.0238.3510.0570.0570.0000.0000.0000.000
41A44ILE00.0200.01411.205-0.049-0.0490.0000.0000.0000.000
42A45ASN0-0.018-0.0287.100-0.151-0.1510.0000.0000.0000.000
43A46ASP-1-0.790-0.8758.959-0.054-0.0540.0000.0000.0000.000
44A47VAL00.002-0.00811.552-0.020-0.0200.0000.0000.0000.000
45A48ILE00.0250.04115.3360.0010.0010.0000.0000.0000.000
46A49SER00.0400.00418.115-0.003-0.0030.0000.0000.0000.000
47A50ASP-1-0.822-0.94421.841-0.046-0.0460.0000.0000.0000.000
48A51GLY0-0.0330.01124.3180.0020.0020.0000.0000.0000.000
49A52ARG10.7470.85426.5830.0240.0240.0000.0000.0000.000
50A53THR00.0380.01123.3920.0030.0030.0000.0000.0000.000
51A54LEU0-0.0220.01020.1800.0020.0020.0000.0000.0000.000
52A55SER0-0.007-0.00717.613-0.003-0.0030.0000.0000.0000.000
53A56ILE0-0.002-0.00915.3650.0100.0100.0000.0000.0000.000
54A57THR00.0320.0299.744-0.029-0.0290.0000.0000.0000.000
55A58TYR0-0.0220.00011.4390.0580.0580.0000.0000.0000.000
56A59SER0-0.002-0.0117.920-0.148-0.1480.0000.0000.0000.000
57A60LEU00.0030.00510.1620.0650.0650.0000.0000.0000.000
58A61GLU-1-0.825-0.9067.5570.1630.1630.0000.0000.0000.000
59A62SER0-0.025-0.00611.5880.0220.0220.0000.0000.0000.000
60A63GLU-1-0.881-0.93614.2580.0800.0800.0000.0000.0000.000
61A64GLN0-0.054-0.04816.739-0.007-0.0070.0000.0000.0000.000
62A65ASP-1-0.869-0.92617.941-0.039-0.0390.0000.0000.0000.000
63A66LEU00.0170.00615.0800.0050.0050.0000.0000.0000.000
64A67GLY00.0280.01319.0110.0010.0010.0000.0000.0000.000
65A68ASP-1-0.880-0.91318.884-0.087-0.0870.0000.0000.0000.000
66A69ASP-1-0.911-0.94720.145-0.090-0.0900.0000.0000.0000.000
67A70PRO0-0.095-0.03917.6610.0110.0110.0000.0000.0000.000
68A71ILE00.0330.01320.875-0.006-0.0060.0000.0000.0000.000
69A72ILE0-0.033-0.02217.7040.0080.0080.0000.0000.0000.000
70A73LEU00.0200.02321.788-0.001-0.0010.0000.0000.0000.000
71A74GLY00.0600.02524.1490.0060.0060.0000.0000.0000.000
72A75GLY0-0.0050.00924.624-0.005-0.0050.0000.0000.0000.000
73A76LEU0-0.025-0.00320.4360.0070.0070.0000.0000.0000.000
74A77ASP-1-0.901-0.94823.721-0.005-0.0050.0000.0000.0000.000
75A78ILE0-0.010-0.02025.1840.0040.0040.0000.0000.0000.000
76A79MET0-0.043-0.02727.7500.0000.0000.0000.0000.0000.000
77A80ASP-1-0.923-0.95930.5400.0030.0030.0000.0000.0000.000
78A81ALA0-0.0020.00530.320-0.002-0.0020.0000.0000.0000.000
79A82HIS0-0.0070.00632.2100.0000.0000.0000.0000.0000.000
80A83GLY0-0.0020.01134.6810.0010.0010.0000.0000.0000.000
81A84SER0-0.022-0.04329.2070.0000.0000.0000.0000.0000.000
82A85SER0-0.010-0.01529.4690.0010.0010.0000.0000.0000.000
83A86GLY00.0420.01425.5500.0010.0010.0000.0000.0000.000
84A87SER0-0.0010.01023.0850.0020.0020.0000.0000.0000.000
85A88GLY00.0240.00820.1540.0020.0020.0000.0000.0000.000
86A89LYS10.9030.97117.5820.1410.1410.0000.0000.0000.000
87A90MET00.013-0.00615.256-0.001-0.0010.0000.0000.0000.000
88A91THR00.0090.01012.4410.0170.0170.0000.0000.0000.000
89A92LYS10.8330.91713.1140.0680.0680.0000.0000.0000.000
90A93VAL0-0.009-0.0067.356-0.024-0.0240.0000.0000.0000.000
91A94THR0-0.077-0.0479.7310.0270.0270.0000.0000.0000.000
92A95GLU-1-0.775-0.89212.018-0.033-0.0330.0000.0000.0000.000
93A96LYS10.7780.90511.9970.0180.0180.0000.0000.0000.000
94A97LYS10.8600.9197.110-0.045-0.0450.0000.0000.0000.000
95A98TYR00.040-0.01510.800-0.025-0.0250.0000.0000.0000.000
96A99VAL00.0010.0037.676-0.018-0.0180.0000.0000.0000.000
97A100GLY00.0440.00910.9410.0190.0190.0000.0000.0000.000
98A101MET0-0.026-0.00313.175-0.008-0.0080.0000.0000.0000.000
99A102VAL0-0.036-0.02015.6290.0070.0070.0000.0000.0000.000
100A103THR00.0460.01518.7700.0030.0030.0000.0000.0000.000
101A104THR00.0150.00621.2350.0010.0010.0000.0000.0000.000
102A105THR0-0.014-0.00624.4780.0000.0000.0000.0000.0000.000
103A106HIS00.0060.01327.3690.0020.0020.0000.0000.0000.000
104A107HIS0-0.026-0.02930.1670.0000.0000.0000.0000.0000.000
105A108ASP-1-0.808-0.86933.265-0.006-0.0060.0000.0000.0000.000
106A109SER0-0.017-0.01834.497-0.002-0.0020.0000.0000.0000.000
107A110ASN0-0.046-0.01835.409-0.002-0.0020.0000.0000.0000.000
108A111LYS10.8920.95530.0250.0180.0180.0000.0000.0000.000
109A112LYS10.8390.91628.8900.0070.0070.0000.0000.0000.000
110A113ASP-1-0.867-0.93128.343-0.006-0.0060.0000.0000.0000.000
111A114LYS10.9080.94926.494-0.014-0.0140.0000.0000.0000.000
112A115VAL00.0410.03024.383-0.001-0.0010.0000.0000.0000.000
113A116ASN00.017-0.00724.7060.0060.0060.0000.0000.0000.000
114A117PHE00.0310.01418.897-0.004-0.0040.0000.0000.0000.000
115A118ARG10.8790.92323.749-0.013-0.0130.0000.0000.0000.000
116A119TRP00.0220.01815.313-0.002-0.0020.0000.0000.0000.000
117A120ASN00.015-0.00821.6250.0130.0130.0000.0000.0000.000
118A121ILE0-0.031-0.00618.170-0.005-0.0050.0000.0000.0000.000
119A122GLU-1-0.913-0.98622.4400.0080.0080.0000.0000.0000.000
120A123GLY0-0.005-0.01323.2750.0020.0020.0000.0000.0000.000
121A124ILE0-0.0250.00818.566-0.005-0.0050.0000.0000.0000.000
122A125GLU-1-0.876-0.93922.046-0.015-0.0150.0000.0000.0000.000
123A126ILE0-0.040-0.02021.090-0.005-0.0050.0000.0000.0000.000
124A127PRO00.1010.04623.9040.0050.0050.0000.0000.0000.000
125A128ASP-1-0.850-0.90923.412-0.043-0.0430.0000.0000.0000.000
126A129ARG10.7920.84921.8180.0320.0320.0000.0000.0000.000
127A130LYS10.8190.92526.9740.0240.0240.0000.0000.0000.000
128A131LYS10.9350.99523.2690.0030.0030.0000.0000.0000.000
129A132SER00.0430.02625.128-0.003-0.0030.0000.0000.0000.000
130A133ILE0-0.051-0.02120.0420.0030.0030.0000.0000.0000.000
131A134GLN00.0400.01523.717-0.003-0.0030.0000.0000.0000.000
132A135GLY00.005-0.01123.7180.0040.0040.0000.0000.0000.000
133A136HIS00.0550.03623.514-0.003-0.0030.0000.0000.0000.000
134A137TRP0-0.079-0.02717.2860.0050.0050.0000.0000.0000.000
135A138ASN00.0080.00720.369-0.010-0.0100.0000.0000.0000.000
136A139PHE0-0.009-0.00615.0120.0120.0120.0000.0000.0000.000
137A140ALA0-0.0010.00220.386-0.010-0.0100.0000.0000.0000.000
138A141LEU0-0.0110.00518.2260.0070.0070.0000.0000.0000.000
139A142THR0-0.020-0.00922.648-0.006-0.0060.0000.0000.0000.000
140A143VAL00.0170.01419.3710.0060.0060.0000.0000.0000.000
141A144LYS10.8230.90922.278-0.002-0.0020.0000.0000.0000.000
142A145SER0-0.007-0.00822.369-0.001-0.0010.0000.0000.0000.000
143A146MET0-0.0250.01620.5970.0020.0020.0000.0000.0000.000
144A147ASP-1-0.870-0.93323.869-0.010-0.0100.0000.0000.0000.000
145A148SER00.0720.03026.842-0.003-0.0030.0000.0000.0000.000
146A149LYS10.9290.96229.1290.0240.0240.0000.0000.0000.000
147A150GLU-1-0.809-0.90932.397-0.022-0.0220.0000.0000.0000.000
148A151ARG10.8110.91234.5490.0230.0230.0000.0000.0000.000
149A152THR00.0360.00637.736-0.001-0.0010.0000.0000.0000.000
150A153ILE0-0.081-0.03037.9370.0010.0010.0000.0000.0000.000
151A154GLY00.0680.03541.5610.0000.0000.0000.0000.0000.000
152A155GLY0-0.007-0.00343.448-0.001-0.0010.0000.0000.0000.000
153A156SER00.007-0.01644.1580.0000.0000.0000.0000.0000.000
154A157SER0-0.041-0.01345.5520.0000.0000.0000.0000.0000.000
155A158GLU-1-0.932-0.96646.662-0.017-0.0170.0000.0000.0000.000
156A159LYS10.9420.93448.7040.0200.0200.0000.0000.0000.000
157A160GLU-1-0.816-0.87249.670-0.019-0.0190.0000.0000.0000.000
158A161GLY0-0.072-0.03751.0190.0010.0010.0000.0000.0000.000
159A162ILE0-0.001-0.02245.9550.0010.0010.0000.0000.0000.000
160A163LYS10.8200.91946.6240.0170.0170.0000.0000.0000.000
161A164ALA00.0420.03141.4770.0000.0000.0000.0000.0000.000
162A165ASN0-0.072-0.05442.7710.0010.0010.0000.0000.0000.000
163A166MET00.0240.01438.854-0.001-0.0010.0000.0000.0000.000
164A167GLU-1-0.783-0.83938.551-0.019-0.0190.0000.0000.0000.000
165A168LYS10.7870.87934.6720.0210.0210.0000.0000.0000.000
166A169VAL00.0230.03133.275-0.002-0.0020.0000.0000.0000.000
167A170ALA0-0.013-0.01730.6710.0030.0030.0000.0000.0000.000
168A171MET00.0040.00928.838-0.003-0.0030.0000.0000.0000.000
169A172SER00.0410.01824.0520.0030.0030.0000.0000.0000.000
170A173PRO0-0.004-0.01522.460-0.001-0.0010.0000.0000.0000.000
171A174VAL0-0.0170.01018.530-0.005-0.0050.0000.0000.0000.000
172A175SER0-0.0120.01021.674-0.007-0.0070.0000.0000.0000.000
173A176PHE0-0.038-0.02924.0690.0080.0080.0000.0000.0000.000
174A177ILE0-0.003-0.00126.660-0.002-0.0020.0000.0000.0000.000
175A178LEU0-0.0130.00129.7180.0040.0040.0000.0000.0000.000
176A179TYR00.008-0.00432.005-0.001-0.0010.0000.0000.0000.000
177A180TYR0-0.006-0.02534.0540.0010.0010.0000.0000.0000.000
178A181ASN0-0.011-0.00337.9730.0000.0000.0000.0000.0000.000
179A182GLN0-0.0220.00840.226-0.001-0.0010.0000.0000.0000.000
180A183GLU-1-0.807-0.88642.745-0.016-0.0160.0000.0000.0000.000
181A184VAL00.0530.02445.8900.0000.0000.0000.0000.0000.000
182A185SER0-0.0010.00948.5880.0010.0010.0000.0000.0000.000
183A186LYS11.0170.99052.4490.0110.0110.0000.0000.0000.000
184A187GLY0-0.076-0.04354.9410.0000.0000.0000.0000.0000.000
185A188ALA00.0950.04250.5860.0000.0000.0000.0000.0000.000
186A189ARG10.7590.84748.5180.0150.0150.0000.0000.0000.000
187A190LYS10.8700.94751.1500.0130.0130.0000.0000.0000.000
188A191GLU-1-0.927-0.95552.583-0.017-0.0170.0000.0000.0000.000
189A192TRP0-0.043-0.01347.679-0.001-0.0010.0000.0000.0000.000
190A193ASP-1-0.844-0.92747.111-0.017-0.0170.0000.0000.0000.000
191A194SER0-0.051-0.03341.567-0.001-0.0010.0000.0000.0000.000
192A195VAL0-0.035-0.00842.881-0.001-0.0010.0000.0000.0000.000
193A196ASP-1-0.853-0.89836.812-0.035-0.0350.0000.0000.0000.000
194A197VAL0-0.010-0.00739.0650.0000.0000.0000.0000.0000.000
195A198GLU-1-0.868-0.91232.935-0.047-0.0470.0000.0000.0000.000
196A199LEU0-0.0220.00234.4330.0020.0020.0000.0000.0000.000
197A200THR0-0.047-0.01333.403-0.003-0.0030.0000.0000.0000.000
198A201VAL00.0160.00031.7990.0030.0030.0000.0000.0000.000
199A202LYS10.9270.96332.8200.0420.0420.0000.0000.0000.000
200A203ASP-1-0.681-0.80032.816-0.044-0.0440.0000.0000.0000.000
201A204ASP-1-0.845-0.89935.660-0.032-0.0320.0000.0000.0000.000
202A205LEU0-0.091-0.04234.0720.0010.0010.0000.0000.0000.000
203A206GLY00.0200.01135.543-0.001-0.0010.0000.0000.0000.000
204A207ASN0-0.094-0.05630.549-0.004-0.0040.0000.0000.0000.000
205A208ASP-1-0.904-0.95630.320-0.051-0.0510.0000.0000.0000.000
206A209TYR0-0.065-0.05027.626-0.004-0.0040.0000.0000.0000.000
207A210SER00.010-0.00924.4530.0050.0050.0000.0000.0000.000
208A211GLY00.014-0.01925.6080.0000.0000.0000.0000.0000.000
209A212GLU-1-0.938-0.94622.210-0.098-0.0980.0000.0000.0000.000
210A213GLY00.0280.02426.3200.0030.0030.0000.0000.0000.000
211A214ASN00.0130.01026.422-0.007-0.0070.0000.0000.0000.000
212A215GLY00.0250.02528.2180.0030.0030.0000.0000.0000.000
213A216GLY00.0290.00331.2230.0000.0000.0000.0000.0000.000
214A217SER0-0.069-0.03635.0130.0010.0010.0000.0000.0000.000
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