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

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FMODB ID: RY1J8

Calculation Name: 2FBE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FBE

Chain ID: A

ChEMBL ID:

UniProt ID: A6NLU0

Base Structure: X-ray

Registration Date: 2023-09-26

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2110574.641914
FMO2-HF: Nuclear repulsion 2035608.867696
FMO2-HF: Total energy -74965.774218
FMO2-MP2: Total energy -75181.58397


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-3.8080.5613.667-4.078-3.956-0.029
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.005
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].
3A3LEU0-0.063-0.0153.1531.2622.6630.017-0.642-0.7760.000
4A4GLY00.0370.0165.1690.0160.035-0.001-0.006-0.0110.000
5A5SER0-0.031-0.0117.5730.3080.3080.0000.0000.0000.000
6A6PRO00.0380.0017.166-0.058-0.0580.0000.0000.0000.000
7A7GLU-1-0.866-0.9368.266-0.691-0.6910.0000.0000.0000.000
8A8PHE0-0.002-0.01510.2240.1300.1300.0000.0000.0000.000
9A9GLN0-0.014-0.0096.2660.0830.0830.0000.0000.0000.000
10A10VAL0-0.061-0.0309.4250.1630.1630.0000.0000.0000.000
11A11ASP-1-0.808-0.87311.598-0.141-0.1410.0000.0000.0000.000
12A12MET0-0.059-0.01912.4350.0530.0530.0000.0000.0000.000
13A13THR00.0450.02814.3990.0150.0150.0000.0000.0000.000
14A14PHE0-0.020-0.01116.498-0.022-0.0220.0000.0000.0000.000
15A15ASP-1-0.830-0.89419.614-0.068-0.0680.0000.0000.0000.000
16A16VAL00.023-0.00423.1420.0050.0050.0000.0000.0000.000
17A17ASP-1-0.799-0.87725.751-0.029-0.0290.0000.0000.0000.000
18A18THR00.024-0.02424.573-0.001-0.0010.0000.0000.0000.000
19A19ALA0-0.048-0.00524.9690.0020.0020.0000.0000.0000.000
20A20ASN00.0520.02426.3150.0070.0070.0000.0000.0000.000
21A21ASN00.041-0.00228.6410.0020.0020.0000.0000.0000.000
22A22TYR0-0.060-0.01029.9510.0030.0030.0000.0000.0000.000
23A23LEU0-0.0270.00823.9760.0070.0070.0000.0000.0000.000
24A24ILE0-0.024-0.00224.126-0.006-0.0060.0000.0000.0000.000
25A25ILE0-0.046-0.03820.7830.0050.0050.0000.0000.0000.000
26A26SER0-0.033-0.02518.817-0.002-0.0020.0000.0000.0000.000
27A27GLU-1-0.857-0.95321.6450.0710.0710.0000.0000.0000.000
28A28ASP-1-0.854-0.90716.4940.0680.0680.0000.0000.0000.000
29A29LEU0-0.045-0.02118.570-0.019-0.0190.0000.0000.0000.000
30A30ARG10.8370.88412.5600.0430.0430.0000.0000.0000.000
31A31SER00.0340.00514.9120.0370.0370.0000.0000.0000.000
32A32PHE0-0.048-0.01517.303-0.015-0.0150.0000.0000.0000.000
33A33ARG10.9530.98219.846-0.072-0.0720.0000.0000.0000.000
34A34SER0-0.0020.00422.559-0.006-0.0060.0000.0000.0000.000
35A35GLY0-0.053-0.05225.9420.0100.0100.0000.0000.0000.000
36A36ASP-1-0.857-0.89729.0440.0450.0450.0000.0000.0000.000
37A37LEU0-0.0020.00931.289-0.004-0.0040.0000.0000.0000.000
38A38SER00.0360.01132.771-0.001-0.0010.0000.0000.0000.000
39A39GLN0-0.003-0.00429.289-0.001-0.0010.0000.0000.0000.000
40A40ASN0-0.021-0.01832.832-0.005-0.0050.0000.0000.0000.000
41A41ARG10.8740.94926.700-0.003-0.0030.0000.0000.0000.000
42A42LYS10.8360.89630.4840.0260.0260.0000.0000.0000.000
43A43GLU-1-0.947-0.94634.218-0.025-0.0250.0000.0000.0000.000
44A44GLN00.001-0.02732.1420.0030.0030.0000.0000.0000.000
45A45ALA00.0530.03633.6290.0000.0000.0000.0000.0000.000
46A46GLU-1-0.886-0.94329.052-0.050-0.0500.0000.0000.0000.000
47A47ARG10.7730.89028.6270.0210.0210.0000.0000.0000.000
48A48PHE00.0130.01524.9510.0000.0000.0000.0000.0000.000
49A49ASP-1-0.782-0.87530.104-0.019-0.0190.0000.0000.0000.000
50A50THR0-0.074-0.05132.6240.0050.0050.0000.0000.0000.000
51A51ALA0-0.022-0.00627.5640.0050.0050.0000.0000.0000.000
52A52LEU0-0.022-0.01125.642-0.001-0.0010.0000.0000.0000.000
53A53CYS0-0.014-0.01123.2080.0010.0010.0000.0000.0000.000
54A54VAL00.0130.00220.7910.0040.0040.0000.0000.0000.000
55A55LEU00.0030.00820.592-0.010-0.0100.0000.0000.0000.000
56A56GLY00.0270.00717.7260.0070.0070.0000.0000.0000.000
57A57THR0-0.018-0.02618.6400.0060.0060.0000.0000.0000.000
58A58PRO0-0.039-0.01716.5290.0050.0050.0000.0000.0000.000
59A59ARG10.9260.94419.7530.1180.1180.0000.0000.0000.000
60A60PHE0-0.0040.00915.097-0.003-0.0030.0000.0000.0000.000
61A61THR00.0660.02820.5760.0050.0050.0000.0000.0000.000
62A62SER00.0170.00721.5640.0040.0040.0000.0000.0000.000
63A63GLY00.0250.02619.065-0.010-0.0100.0000.0000.0000.000
64A64ARG10.8430.92813.7130.5860.5860.0000.0000.0000.000
65A65HIS10.8260.88913.0660.3970.3970.0000.0000.0000.000
66A66TYR0-0.006-0.0383.083-0.2050.1240.015-0.144-0.2000.000
67A67TRP00.0260.0258.2800.0020.0020.0000.0000.0000.000
68A68GLU-1-0.782-0.8832.415-4.195-2.0292.087-2.226-2.026-0.025
69A69VAL00.0110.0037.2930.0700.0700.0000.0000.0000.000
70A70ASP-1-0.752-0.8529.7510.6930.6930.0000.0000.0000.000
71A71VAL0-0.004-0.00710.979-0.048-0.0480.0000.0000.0000.000
72A72GLY00.0330.01613.164-0.021-0.0210.0000.0000.0000.000
73A73THR0-0.031-0.03714.724-0.003-0.0030.0000.0000.0000.000
74A74SER0-0.0070.00617.581-0.026-0.0260.0000.0000.0000.000
75A75GLN00.013-0.00818.987-0.001-0.0010.0000.0000.0000.000
76A76VAL0-0.042-0.01121.677-0.012-0.0120.0000.0000.0000.000
77A77TRP00.002-0.01314.358-0.003-0.0030.0000.0000.0000.000
78A78ASP-1-0.780-0.86518.751-0.036-0.0360.0000.0000.0000.000
79A79VAL0-0.023-0.01112.7580.0010.0010.0000.0000.0000.000
80A80GLY00.0680.03315.361-0.009-0.0090.0000.0000.0000.000
81A81VAL0-0.0520.00516.261-0.010-0.0100.0000.0000.0000.000
82A82CYS0-0.0190.01218.8010.0160.0160.0000.0000.0000.000
83A83LYS10.9080.94522.5800.1000.1000.0000.0000.0000.000
84A84GLU-1-0.757-0.86425.279-0.089-0.0890.0000.0000.0000.000
85A85SER0-0.090-0.06126.6790.0100.0100.0000.0000.0000.000
86A86VAL0-0.0260.00526.3820.0060.0060.0000.0000.0000.000
87A87ASN0-0.021-0.02329.4030.0030.0030.0000.0000.0000.000
88A88ARG10.8310.91827.1150.0730.0730.0000.0000.0000.000
89A89GLN0-0.018-0.00930.6840.0020.0020.0000.0000.0000.000
90A90GLY0-0.0010.00733.868-0.002-0.0020.0000.0000.0000.000
91A91LYS10.8440.90432.3710.0330.0330.0000.0000.0000.000
92A92ILE00.0110.01026.718-0.003-0.0030.0000.0000.0000.000
93A93GLU-1-0.900-0.94028.704-0.041-0.0410.0000.0000.0000.000
94A94LEU00.0030.00622.888-0.006-0.0060.0000.0000.0000.000
95A95SER00.0610.03225.940-0.004-0.0040.0000.0000.0000.000
96A96SER00.0580.02424.270-0.002-0.0020.0000.0000.0000.000
97A97GLU-1-0.984-0.99425.783-0.083-0.0830.0000.0000.0000.000
98A98HIS0-0.063-0.03228.4030.0030.0030.0000.0000.0000.000
99A99GLY0-0.020-0.01526.4610.0010.0010.0000.0000.0000.000
100A100PHE00.003-0.00823.235-0.010-0.0100.0000.0000.0000.000
101A101LEU0-0.0210.00719.7630.0040.0040.0000.0000.0000.000
102A102THR0-0.021-0.03718.110-0.014-0.0140.0000.0000.0000.000
103A103VAL00.0280.01915.2200.0050.0050.0000.0000.0000.000
104A104GLY00.0360.01417.4750.0060.0060.0000.0000.0000.000
105A105CYS0-0.076-0.00918.2480.0060.0060.0000.0000.0000.000
106A106ARG10.8220.87320.2060.0130.0130.0000.0000.0000.000
107A107GLU-1-0.880-0.95823.5050.0460.0460.0000.0000.0000.000
108A108GLY00.0200.01025.259-0.006-0.0060.0000.0000.0000.000
109A109LYS10.8490.92118.208-0.149-0.1490.0000.0000.0000.000
110A110VAL00.0200.02621.550-0.004-0.0040.0000.0000.0000.000
111A111PHE00.009-0.01616.2290.0010.0010.0000.0000.0000.000
112A112ALA0-0.002-0.00720.422-0.006-0.0060.0000.0000.0000.000
113A113ALA00.0470.03619.175-0.003-0.0030.0000.0000.0000.000
114A114SER0-0.016-0.00320.7550.0040.0040.0000.0000.0000.000
115A115THR0-0.046-0.03922.637-0.007-0.0070.0000.0000.0000.000
116A116VAL00.0050.01025.0700.0080.0080.0000.0000.0000.000
117A117PRO00.0120.00328.8680.0000.0000.0000.0000.0000.000
118A118MET00.0060.02925.297-0.007-0.0070.0000.0000.0000.000
119A119THR0-0.016-0.00322.2320.0060.0060.0000.0000.0000.000
120A120PRO00.000-0.00822.631-0.001-0.0010.0000.0000.0000.000
121A121LEU0-0.008-0.00517.656-0.012-0.0120.0000.0000.0000.000
122A122TRP0-0.047-0.01819.5870.0180.0180.0000.0000.0000.000
123A123VAL00.0190.01414.462-0.016-0.0160.0000.0000.0000.000
124A124SER00.0260.01313.0580.0190.0190.0000.0000.0000.000
125A125PRO00.0700.02415.1850.0110.0110.0000.0000.0000.000
126A126GLN0-0.036-0.02513.579-0.029-0.0290.0000.0000.0000.000
127A127LEU0-0.0190.01010.2510.0800.0800.0000.0000.0000.000
128A128HIS10.8730.9239.133-0.748-0.7480.0000.0000.0000.000
129A129ARG10.8460.9154.901-0.998-0.9980.0000.0000.0000.000
130A130VAL00.0300.0337.8950.0180.0180.0000.0000.0000.000
131A131GLY00.0230.0046.019-0.019-0.0190.0000.0000.0000.000
132A132ILE0-0.0040.0016.7840.0450.0450.0000.0000.0000.000
133A133PHE0-0.014-0.0109.003-0.106-0.1060.0000.0000.0000.000
134A134LEU00.0110.01311.1210.0790.0790.0000.0000.0000.000
135A135ASP-1-0.802-0.90614.738-0.441-0.4410.0000.0000.0000.000
136A136VAL00.0180.00216.8300.0350.0350.0000.0000.0000.000
137A137GLY0-0.031-0.00319.9550.0280.0280.0000.0000.0000.000
138A138MET0-0.024-0.00918.7380.0300.0300.0000.0000.0000.000
139A139ARG10.9190.97220.9160.1780.1780.0000.0000.0000.000
140A140SER00.0240.00818.0160.0050.0050.0000.0000.0000.000
141A141ILE0-0.018-0.00614.498-0.025-0.0250.0000.0000.0000.000
142A142ALA0-0.0130.01712.4060.0400.0400.0000.0000.0000.000
143A143PHE00.0190.00810.951-0.053-0.0530.0000.0000.0000.000
144A144TYR00.0110.0007.196-0.021-0.0210.0000.0000.0000.000
145A145ASN00.0200.0238.1860.2090.2090.0000.0000.0000.000
146A146VAL0-0.009-0.0292.474-0.421-0.4881.531-0.817-0.647-0.002
147A147SER0-0.094-0.0503.5200.1040.6250.018-0.243-0.296-0.002
148A148ASP-1-0.836-0.9296.0930.1100.1100.0000.0000.0000.000
149A149GLY0-0.0060.0096.136-0.241-0.2410.0000.0000.0000.000
150A150CYS0-0.056-0.0077.027-0.011-0.0110.0000.0000.0000.000
151A151HIS00.0110.02110.309-0.017-0.0170.0000.0000.0000.000
152A152ILE0-0.063-0.02511.2360.0710.0710.0000.0000.0000.000
153A153TYR00.019-0.00214.0380.0300.0300.0000.0000.0000.000
154A154THR00.014-0.02714.960-0.064-0.0640.0000.0000.0000.000
155A155PHE0-0.039-0.00816.9570.0290.0290.0000.0000.0000.000
156A156ILE00.019-0.01219.445-0.031-0.0310.0000.0000.0000.000
157A157GLU-1-0.949-0.96521.968-0.128-0.1280.0000.0000.0000.000
158A158ILE0-0.0190.00219.7770.0150.0150.0000.0000.0000.000
159A159PRO0-0.005-0.00723.974-0.004-0.0040.0000.0000.0000.000
160A160VAL0-0.014-0.01923.114-0.008-0.0080.0000.0000.0000.000
161A161CYS0-0.024-0.01325.8160.0030.0030.0000.0000.0000.000
162A162GLU-1-0.779-0.85426.636-0.098-0.0980.0000.0000.0000.000
163A163PRO0-0.015-0.01824.108-0.011-0.0110.0000.0000.0000.000
164A164TRP0-0.018-0.00719.9850.0090.0090.0000.0000.0000.000
165A165ARG10.7480.83820.4260.0990.0990.0000.0000.0000.000
166A166PRO0-0.016-0.00815.6060.0050.0050.0000.0000.0000.000
167A167PHE00.0470.00217.5010.0230.0230.0000.0000.0000.000
168A168PHE0-0.005-0.01513.804-0.010-0.0100.0000.0000.0000.000
169A169ALA00.0470.02318.6770.0030.0030.0000.0000.0000.000
170A170HIS00.0190.01019.758-0.005-0.0050.0000.0000.0000.000
171A171LYS10.9540.97721.827-0.032-0.0320.0000.0000.0000.000
172A172ARG10.7430.86324.235-0.057-0.0570.0000.0000.0000.000
173A173GLY0-0.015-0.00525.608-0.007-0.0070.0000.0000.0000.000
174A174SER0-0.029-0.04326.809-0.003-0.0030.0000.0000.0000.000
175A175GLN00.014-0.00928.8310.0030.0030.0000.0000.0000.000
176A176ASP-1-0.811-0.88929.3010.0770.0770.0000.0000.0000.000
177A177ASP-1-0.846-0.89123.5570.1180.1180.0000.0000.0000.000
178A178GLN0-0.014-0.01623.261-0.010-0.0100.0000.0000.0000.000
179A179SER0-0.060-0.01819.6100.0110.0110.0000.0000.0000.000
180A180ILE0-0.012-0.01816.624-0.021-0.0210.0000.0000.0000.000
181A181LEU0-0.0330.00215.1740.0230.0230.0000.0000.0000.000
182A182SER0-0.0030.00012.854-0.001-0.0010.0000.0000.0000.000
183A183ILE0-0.034-0.01511.3830.0090.0090.0000.0000.0000.000
184A184CYS0-0.083-0.0526.6310.1520.1520.0000.0000.0000.000
185A185SER0-0.049-0.0557.476-0.153-0.1530.0000.0000.0000.000
186A186VAL0-0.017-0.0187.927-0.022-0.0220.0000.0000.0000.000
187A187ILE00.0110.0357.452-0.098-0.0980.0000.0000.0000.000
188A188ASN00.0950.0839.7320.0520.0520.0000.0000.0000.000