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: YY5L2

Calculation Name: 4D9O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D9O

Chain ID: A

ChEMBL ID:

UniProt ID: Q91DD5

Base Structure: X-ray

Registration Date: 2023-06-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2314162.147482
FMO2-HF: Nuclear repulsion 2234502.548358
FMO2-HF: Total energy -79659.599124
FMO2-MP2: Total energy -79893.073785


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:10:MET)


Summations of interaction energy for fragment #1(A:10: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.
1.3613.164-0.017-0.879-0.9070.002
Interaction energy analysis for fragmet #1(A:10:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.011
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].
3A12PRO0-0.020-0.0013.8091.6003.403-0.017-0.879-0.9070.002
4A13PRO00.0620.0435.2830.3500.3500.0000.0000.0000.000
5A14LYS11.0020.9877.472-0.635-0.6350.0000.0000.0000.000
6A15LYS10.9510.96311.123-0.305-0.3050.0000.0000.0000.000
7A16ASP-1-0.812-0.9078.471-0.182-0.1820.0000.0000.0000.000
8A17MET0-0.019-0.0068.962-0.084-0.0840.0000.0000.0000.000
9A18GLU-1-0.888-0.93412.4040.0320.0320.0000.0000.0000.000
10A19LYS10.8630.92913.7970.0130.0130.0000.0000.0000.000
11A20GLY0-0.0030.01014.526-0.014-0.0140.0000.0000.0000.000
12A21VAL00.0250.00815.814-0.002-0.0020.0000.0000.0000.000
13A22ILE0-0.026-0.01118.3470.0090.0090.0000.0000.0000.000
14A23PHE00.005-0.01418.547-0.001-0.0010.0000.0000.0000.000
15A24SER0-0.030-0.01319.954-0.002-0.0020.0000.0000.0000.000
16A25ASP-1-0.880-0.93621.588-0.115-0.1150.0000.0000.0000.000
17A26LEU0-0.018-0.01423.8290.0100.0100.0000.0000.0000.000
18A27CYS0-0.0370.00323.5470.0080.0080.0000.0000.0000.000
19A28ASN0-0.0260.00023.074-0.012-0.0120.0000.0000.0000.000
20A29PHE00.0050.00426.9740.0090.0090.0000.0000.0000.000
21A30LEU0-0.020-0.00428.127-0.002-0.0020.0000.0000.0000.000
22A31ILE00.0210.00931.0140.0100.0100.0000.0000.0000.000
23A32THR0-0.033-0.01433.513-0.004-0.0040.0000.0000.0000.000
24A33GLN0-0.004-0.01236.2170.0030.0030.0000.0000.0000.000
25A34THR00.0550.03039.109-0.001-0.0010.0000.0000.0000.000
26A35LEU0-0.006-0.01441.3830.0010.0010.0000.0000.0000.000
27A36GLN0-0.017-0.01542.6260.0000.0000.0000.0000.0000.000
28A37GLY0-0.043-0.03743.9860.0030.0030.0000.0000.0000.000
29A38TRP00.0040.00638.9330.0000.0000.0000.0000.0000.000
30A39LYS10.8720.94334.9020.0740.0740.0000.0000.0000.000
31A40VAL0-0.029-0.02334.103-0.007-0.0070.0000.0000.0000.000
32A41TYR0-0.0030.00326.6300.0080.0080.0000.0000.0000.000
33A42TRP00.025-0.01528.772-0.005-0.0050.0000.0000.0000.000
34A43ALA00.0240.01727.2020.0080.0080.0000.0000.0000.000
35A44GLY00.0500.02027.6370.0100.0100.0000.0000.0000.000
36A45ILE0-0.047-0.01828.2110.0090.0090.0000.0000.0000.000
37A46GLU-1-0.864-0.93232.011-0.077-0.0770.0000.0000.0000.000
38A47PHE00.018-0.00133.7890.0060.0060.0000.0000.0000.000
39A48ASP-1-0.855-0.91437.688-0.065-0.0650.0000.0000.0000.000
40A49VAL00.0060.00539.7820.0040.0040.0000.0000.0000.000
41A50SER00.0150.00842.450-0.001-0.0010.0000.0000.0000.000
42A51GLN00.0750.03143.851-0.004-0.0040.0000.0000.0000.000
43A52LYS10.9670.97846.7850.0430.0430.0000.0000.0000.000
44A53GLY0-0.119-0.04949.8720.0000.0000.0000.0000.0000.000
45A54MET00.1110.05049.0470.0010.0010.0000.0000.0000.000
46A55ALA00.0360.03552.4200.0010.0010.0000.0000.0000.000
47A56LEU0-0.005-0.00255.8240.0010.0010.0000.0000.0000.000
48A57LEU00.0320.01651.3340.0010.0010.0000.0000.0000.000
49A58THR00.018-0.01554.3020.0010.0010.0000.0000.0000.000
50A59ARG10.9330.97556.8580.0330.0330.0000.0000.0000.000
51A60LEU0-0.046-0.01657.9480.0010.0010.0000.0000.0000.000
52A61LYS10.8330.93955.2980.0400.0400.0000.0000.0000.000
53A62THR0-0.057-0.01959.6170.0010.0010.0000.0000.0000.000
54A70ALA00.018-0.00564.0420.0000.0000.0000.0000.0000.000
55A71MET00.0610.03263.2650.0000.0000.0000.0000.0000.000
56A72THR00.0310.00859.7250.0000.0000.0000.0000.0000.000
57A73ARG10.9550.97860.6620.0280.0280.0000.0000.0000.000
58A74ASN0-0.008-0.02562.086-0.001-0.0010.0000.0000.0000.000
59A75LEU00.0280.02959.9210.0000.0000.0000.0000.0000.000
60A76PHE0-0.022-0.00455.4740.0000.0000.0000.0000.0000.000
61A77PRO00.0630.02558.832-0.001-0.0010.0000.0000.0000.000
62A78HIS00.0170.01254.3400.0000.0000.0000.0000.0000.000
63A79LEU00.0160.00752.770-0.002-0.0020.0000.0000.0000.000
64A80PHE0-0.045-0.03656.118-0.001-0.0010.0000.0000.0000.000
65A81GLN0-0.035-0.00159.0720.0000.0000.0000.0000.0000.000
66A82ASN00.0530.02956.5030.0000.0000.0000.0000.0000.000
67A83PRO0-0.041-0.02857.936-0.001-0.0010.0000.0000.0000.000
68A84ASN0-0.017-0.01555.321-0.002-0.0020.0000.0000.0000.000
69A85SER0-0.0390.00253.276-0.002-0.0020.0000.0000.0000.000
70A86VAL0-0.014-0.01949.1430.0000.0000.0000.0000.0000.000
71A87ILE0-0.018-0.00349.8590.0000.0000.0000.0000.0000.000
72A88GLN0-0.020-0.00444.208-0.001-0.0010.0000.0000.0000.000
73A89SER00.0210.02742.3290.0030.0030.0000.0000.0000.000
74A90PRO00.0790.01944.2220.0000.0000.0000.0000.0000.000
75A91ILE00.0090.01538.2150.0010.0010.0000.0000.0000.000
76A92TRP00.009-0.00139.752-0.001-0.0010.0000.0000.0000.000
77A93ALA00.0520.01841.1610.0010.0010.0000.0000.0000.000
78A94LEU0-0.0080.00737.1880.0020.0020.0000.0000.0000.000
79A95ARG10.8020.90333.3930.0950.0950.0000.0000.0000.000
80A96VAL00.0390.02537.6670.0000.0000.0000.0000.0000.000
81A97ILE0-0.012-0.00539.9740.0020.0020.0000.0000.0000.000
82A98LEU0-0.049-0.01834.3000.0020.0020.0000.0000.0000.000
83A99ALA00.0170.01035.7930.0010.0010.0000.0000.0000.000
84A100ALA00.0310.01136.8270.0020.0020.0000.0000.0000.000
85A101GLY00.0380.02537.8180.0030.0030.0000.0000.0000.000
86A102LEU0-0.058-0.03431.8670.0020.0020.0000.0000.0000.000
87A103GLN0-0.003-0.01035.1630.0050.0050.0000.0000.0000.000
88A104ASP-1-0.924-0.96237.624-0.023-0.0230.0000.0000.0000.000
89A105GLN00.013-0.00131.359-0.002-0.0020.0000.0000.0000.000
90A106LEU0-0.071-0.04134.1490.0030.0030.0000.0000.0000.000
91A107LEU0-0.039-0.02335.4220.0020.0020.0000.0000.0000.000
92A108ASP-1-0.927-0.93837.559-0.007-0.0070.0000.0000.0000.000
93A109HIS0-0.135-0.06032.3390.0030.0030.0000.0000.0000.000
94A110SER00.0370.01334.434-0.001-0.0010.0000.0000.0000.000
95A111LEU0-0.011-0.01732.218-0.001-0.0010.0000.0000.0000.000
96A112VAL0-0.039-0.01431.003-0.004-0.0040.0000.0000.0000.000
97A113GLU-1-0.842-0.91428.443-0.003-0.0030.0000.0000.0000.000
98A114PRO0-0.004-0.01823.903-0.006-0.0060.0000.0000.0000.000
99A115LEU0-0.031-0.02326.066-0.010-0.0100.0000.0000.0000.000
100A116THR00.0680.04027.717-0.005-0.0050.0000.0000.0000.000
101A117GLY00.0160.01728.324-0.004-0.0040.0000.0000.0000.000
102A118ALA0-0.050-0.03625.449-0.007-0.0070.0000.0000.0000.000
103A119LEU0-0.013-0.00227.376-0.007-0.0070.0000.0000.0000.000
104A120GLY00.0600.03430.610-0.002-0.0020.0000.0000.0000.000
105A121LEU00.002-0.00326.936-0.005-0.0050.0000.0000.0000.000
106A122ILE0-0.032-0.02026.060-0.005-0.0050.0000.0000.0000.000
107A123SER0-0.010-0.00230.111-0.002-0.0020.0000.0000.0000.000
108A124ASP-1-0.836-0.92133.238-0.070-0.0700.0000.0000.0000.000
109A125TRP0-0.084-0.03129.413-0.001-0.0010.0000.0000.0000.000
110A126LEU0-0.046-0.02432.308-0.001-0.0010.0000.0000.0000.000
111A127LEU00.0380.01934.5390.0010.0010.0000.0000.0000.000
112A128THR0-0.060-0.02936.3340.0010.0010.0000.0000.0000.000
113A129THR0-0.079-0.03034.054-0.005-0.0050.0000.0000.0000.000
114A130THR00.001-0.01936.5630.0010.0010.0000.0000.0000.000
115A131SER0-0.0110.00731.544-0.005-0.0050.0000.0000.0000.000
116A132THR00.0530.01331.1860.0030.0030.0000.0000.0000.000
117A133HIS0-0.019-0.01022.686-0.013-0.0130.0000.0000.0000.000
118A134PHE00.0210.02226.6110.0030.0030.0000.0000.0000.000
119A135ASN00.015-0.01923.987-0.029-0.0290.0000.0000.0000.000
120A136LEU00.0170.03222.5900.0040.0040.0000.0000.0000.000
121A137ARG10.9300.94221.4530.2040.2040.0000.0000.0000.000
122A138THR00.0220.02522.5050.0000.0000.0000.0000.0000.000
123A139ARG10.9640.96417.0200.2990.2990.0000.0000.0000.000
124A140SER00.0380.02818.9460.0090.0090.0000.0000.0000.000
125A141VAL00.0860.04620.8100.0090.0090.0000.0000.0000.000
126A142LYS10.9120.95817.3890.2930.2930.0000.0000.0000.000
127A143ASP-1-0.862-0.93515.587-0.191-0.1910.0000.0000.0000.000
128A144GLN0-0.040-0.02217.2500.0300.0300.0000.0000.0000.000
129A145LEU00.0050.00719.2780.0140.0140.0000.0000.0000.000
130A146SER0-0.029-0.02718.6630.0110.0110.0000.0000.0000.000
131A147LEU00.0840.02320.162-0.010-0.0100.0000.0000.0000.000
132A148ARG10.9700.98521.858-0.025-0.0250.0000.0000.0000.000
133A149MET0-0.0440.00922.785-0.003-0.0030.0000.0000.0000.000
134A150LEU00.0400.02323.647-0.002-0.0020.0000.0000.0000.000
135A151SER0-0.011-0.00825.801-0.004-0.0040.0000.0000.0000.000
136A152LEU00.0280.00627.8740.0000.0000.0000.0000.0000.000
137A153ILE00.0230.02827.140-0.001-0.0010.0000.0000.0000.000
138A154ARG10.8390.91927.8330.0470.0470.0000.0000.0000.000
139A155SER0-0.018-0.00531.5240.0010.0010.0000.0000.0000.000
140A156ASN0-0.002-0.01533.1960.0020.0020.0000.0000.0000.000
141A157ILE00.0150.02733.516-0.001-0.0010.0000.0000.0000.000
142A158LEU00.003-0.00335.1120.0000.0000.0000.0000.0000.000
143A159GLN0-0.0030.00537.6820.0000.0000.0000.0000.0000.000
144A160PHE00.0280.01039.0520.0010.0010.0000.0000.0000.000
145A161ILE00.004-0.00938.1910.0000.0000.0000.0000.0000.000
146A162ASN0-0.034-0.02641.1970.0020.0020.0000.0000.0000.000
147A163LYS10.9260.97842.8130.0190.0190.0000.0000.0000.000
148A164LEU0-0.016-0.00843.1900.0000.0000.0000.0000.0000.000
149A165ASP-1-0.960-0.98545.788-0.023-0.0230.0000.0000.0000.000
150A166ALA00.0010.01547.6010.0010.0010.0000.0000.0000.000
151A167LEU0-0.079-0.01148.8840.0010.0010.0000.0000.0000.000
152A168HIS00.0160.00251.6710.0000.0000.0000.0000.0000.000
153A169VAL0-0.036-0.02954.922-0.001-0.0010.0000.0000.0000.000
154A170VAL0-0.005-0.00556.2980.0010.0010.0000.0000.0000.000
155A171ASN0-0.033-0.03358.3070.0000.0000.0000.0000.0000.000
156A172TYR00.014-0.00461.6680.0000.0000.0000.0000.0000.000
157A173ASN0-0.0060.00063.679-0.001-0.0010.0000.0000.0000.000
158A174GLY00.0140.01860.7770.0010.0010.0000.0000.0000.000
159A175LEU0-0.0260.00658.2600.0000.0000.0000.0000.0000.000
160A176LEU00.0140.00451.201-0.001-0.0010.0000.0000.0000.000
161A177SER00.0440.01954.070-0.001-0.0010.0000.0000.0000.000
162A178SER0-0.020-0.01651.081-0.001-0.0010.0000.0000.0000.000
163A179ILE00.0170.01645.4520.0020.0020.0000.0000.0000.000
164A180GLU-1-0.953-0.97347.895-0.030-0.0300.0000.0000.0000.000
165A181ILE0-0.029-0.01241.4850.0010.0010.0000.0000.0000.000
166A182GLY00.0240.01544.853-0.002-0.0020.0000.0000.0000.000
167A183THR0-0.003-0.00540.3560.0000.0000.0000.0000.0000.000
168A184SER0-0.030-0.02741.8130.0010.0010.0000.0000.0000.000
169A185THR0-0.042-0.02240.7600.0010.0010.0000.0000.0000.000
170A186HIS00.0160.00740.964-0.001-0.0010.0000.0000.0000.000
171A187THR00.0400.03344.4100.0030.0030.0000.0000.0000.000
172A188ILE0-0.009-0.00341.249-0.002-0.0020.0000.0000.0000.000
173A189ILE00.0300.02145.7730.0020.0020.0000.0000.0000.000
174A190ILE0-0.020-0.01243.647-0.002-0.0020.0000.0000.0000.000
175A191THR00.0320.00548.1740.0030.0030.0000.0000.0000.000
176A192ARG10.8200.91350.7250.0240.0240.0000.0000.0000.000
177A193THR0-0.019-0.02752.4890.0010.0010.0000.0000.0000.000
178A194ASN00.043-0.00454.2440.0000.0000.0000.0000.0000.000
179A195MET0-0.073-0.03153.886-0.001-0.0010.0000.0000.0000.000
180A196GLY00.0010.01450.383-0.002-0.0020.0000.0000.0000.000
181A197PHE00.0300.01347.0680.0010.0010.0000.0000.0000.000
182A198LEU0-0.027-0.00348.686-0.003-0.0030.0000.0000.0000.000
183A199VAL0-0.0060.00444.2810.0010.0010.0000.0000.0000.000
184A200GLU-1-0.841-0.94747.717-0.036-0.0360.0000.0000.0000.000
185A201VAL00.0150.00643.5490.0000.0000.0000.0000.0000.000
186A202GLN0-0.032-0.02346.872-0.001-0.0010.0000.0000.0000.000
187A203GLU-1-0.898-0.94144.556-0.053-0.0530.0000.0000.0000.000
188A217VAL0-0.0130.00650.2480.0000.0000.0000.0000.0000.000
189A218LYS10.9430.98643.7410.0610.0610.0000.0000.0000.000
190A219PHE00.0450.00448.4090.0010.0010.0000.0000.0000.000
191A220SER0-0.024-0.04046.606-0.002-0.0020.0000.0000.0000.000
192A221LEU0-0.0230.00148.5510.0020.0020.0000.0000.0000.000
193A222LEU0-0.0090.00742.532-0.002-0.0020.0000.0000.0000.000
194A223HIS00.000-0.00546.6970.0010.0010.0000.0000.0000.000
195A224GLU-1-0.764-0.89846.484-0.030-0.0300.0000.0000.0000.000
196A225SER0-0.060-0.04046.4930.0000.0000.0000.0000.0000.000
197A226ALA00.0140.01641.8070.0000.0000.0000.0000.0000.000
198A227PHE0-0.001-0.02240.284-0.002-0.0020.0000.0000.0000.000
199A228LYS10.9200.97343.1550.0290.0290.0000.0000.0000.000
200A229PRO00.0060.00840.2390.0020.0020.0000.0000.0000.000
201A230PHE0-0.041-0.01136.3150.0020.0020.0000.0000.0000.000
202A231THR0-0.0230.01141.1150.0020.0020.0000.0000.0000.000