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: G61R1

Calculation Name: 4ONS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ONS

Chain ID: A

ChEMBL ID:

UniProt ID: Q61301

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2359187.64076
FMO2-HF: Nuclear repulsion 2268832.33017
FMO2-HF: Total energy -90355.31059
FMO2-MP2: Total energy -90616.643558


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:18:GLU)


Summations of interaction energy for fragment #1(A:18:GLU)
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.
-110.557-112.26921.404-11.116-8.5760.117
Interaction energy analysis for fragmet #1(A:18:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.893 / q_NPA : -0.936
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].
3A20ARG10.8080.8851.707-123.276-124.98821.404-11.116-8.5760.117
4A21THR00.0820.0215.682-1.214-1.2140.0000.0000.0000.000
5A22LEU00.0000.0088.774-2.201-2.2010.0000.0000.0000.000
6A23THR0-0.032-0.03510.054-2.688-2.6880.0000.0000.0000.000
7A24VAL00.0630.02811.503-1.392-1.3920.0000.0000.0000.000
8A25GLU-1-0.774-0.88611.88120.74520.7450.0000.0000.0000.000
9A26ARG10.9070.95314.116-21.531-21.5310.0000.0000.0000.000
10A27LEU0-0.016-0.00116.033-1.040-1.0400.0000.0000.0000.000
11A28LEU00.0230.01317.635-0.912-0.9120.0000.0000.0000.000
12A29GLU-1-0.862-0.89819.18012.48812.4880.0000.0000.0000.000
13A30PRO00.0290.01120.847-0.718-0.7180.0000.0000.0000.000
14A31LEU0-0.0030.00222.925-0.635-0.6350.0000.0000.0000.000
15A32VAL00.0060.00421.476-0.593-0.5930.0000.0000.0000.000
16A33THR0-0.024-0.02624.596-0.683-0.6830.0000.0000.0000.000
17A34GLN0-0.036-0.01026.502-0.243-0.2430.0000.0000.0000.000
18A35VAL0-0.017-0.00627.450-0.449-0.4490.0000.0000.0000.000
19A36THR0-0.045-0.02627.517-0.266-0.2660.0000.0000.0000.000
20A37THR0-0.037-0.02030.170-0.150-0.1500.0000.0000.0000.000
21A38LEU0-0.062-0.03232.662-0.164-0.1640.0000.0000.0000.000
22A39VAL00.0100.01536.151-0.234-0.2340.0000.0000.0000.000
23A52GLY00.0490.02549.166-0.073-0.0730.0000.0000.0000.000
24A53ARG10.8880.93943.926-6.679-6.6790.0000.0000.0000.000
25A54SER0-0.025-0.00845.160-0.146-0.1460.0000.0000.0000.000
26A55LYS11.0060.98245.366-5.815-5.8150.0000.0000.0000.000
27A56LYS10.9750.97045.350-6.165-6.1650.0000.0000.0000.000
28A57ALA00.0260.02441.8950.1060.1060.0000.0000.0000.000
29A58HIS00.028-0.00740.6960.2350.2350.0000.0000.0000.000
30A59VAL0-0.0070.01540.7030.1060.1060.0000.0000.0000.000
31A60LEU0-0.0120.00638.8410.1390.1390.0000.0000.0000.000
32A61ALA00.0380.01936.5490.2170.2170.0000.0000.0000.000
33A62ALA00.0150.01035.8570.2010.2010.0000.0000.0000.000
34A63SER0-0.035-0.03436.1970.1100.1100.0000.0000.0000.000
35A64VAL00.0070.01231.2680.1770.1770.0000.0000.0000.000
36A65GLU-1-0.826-0.88931.7009.5599.5590.0000.0000.0000.000
37A66GLN0-0.021-0.01232.0410.3030.3030.0000.0000.0000.000
38A67ALA00.0100.00031.1650.1510.1510.0000.0000.0000.000
39A68THR0-0.036-0.03026.8580.4330.4330.0000.0000.0000.000
40A69GLN0-0.018-0.02927.6230.4970.4970.0000.0000.0000.000
41A70ASN0-0.049-0.03328.9750.0440.0440.0000.0000.0000.000
42A71PHE0-0.010-0.00621.4840.1780.1780.0000.0000.0000.000
43A72LEU00.001-0.00723.1710.4350.4350.0000.0000.0000.000
44A73GLU-1-0.860-0.90124.6209.7759.7750.0000.0000.0000.000
45A74LYS10.8440.90025.546-9.822-9.8220.0000.0000.0000.000
46A75GLY00.0410.03121.4480.3400.3400.0000.0000.0000.000
47A76GLU-1-0.831-0.90420.63111.95511.9550.0000.0000.0000.000
48A77GLN0-0.119-0.05422.2190.0340.0340.0000.0000.0000.000
49A78ILE00.0240.00018.9880.1210.1210.0000.0000.0000.000
50A79ALA00.0080.00817.5340.5460.5460.0000.0000.0000.000
51A80LYS10.9080.96718.127-10.584-10.5840.0000.0000.0000.000
52A81GLU-1-0.915-0.96620.40911.63111.6310.0000.0000.0000.000
53A82SER0-0.0050.01514.969-0.037-0.0370.0000.0000.0000.000
54A83GLN0-0.004-0.00416.623-0.385-0.3850.0000.0000.0000.000
55A84ASP-1-0.862-0.92011.62120.00820.0080.0000.0000.0000.000
56A85LEU00.017-0.0037.350-0.458-0.4580.0000.0000.0000.000
57A86LYS10.8750.93410.922-15.531-15.5310.0000.0000.0000.000
58A87GLU-1-0.919-0.96211.19218.85418.8540.0000.0000.0000.000
59A88GLU-1-0.842-0.9188.31624.62324.6230.0000.0000.0000.000
60A89LEU00.011-0.00410.681-0.757-0.7570.0000.0000.0000.000
61A90VAL0-0.009-0.00713.880-0.922-0.9220.0000.0000.0000.000
62A91ALA0-0.0040.00212.401-0.836-0.8360.0000.0000.0000.000
63A92ALA0-0.001-0.00213.389-0.544-0.5440.0000.0000.0000.000
64A93VAL0-0.0020.00015.086-0.680-0.6800.0000.0000.0000.000
65A94GLU-1-0.832-0.90717.54811.92211.9220.0000.0000.0000.000
66A95ASP-1-0.898-0.93916.35014.85714.8570.0000.0000.0000.000
67A96VAL00.0060.00318.414-0.635-0.6350.0000.0000.0000.000
68A97ARG10.8130.88720.802-12.151-12.1510.0000.0000.0000.000
69A98LYS10.8590.92319.420-13.773-13.7730.0000.0000.0000.000
70A99GLN0-0.030-0.02319.781-1.028-1.0280.0000.0000.0000.000
71A100GLY00.0260.01523.803-0.417-0.4170.0000.0000.0000.000
72A101GLU-1-0.818-0.89726.4589.0759.0750.0000.0000.0000.000
73A102THR0-0.041-0.01925.865-0.422-0.4220.0000.0000.0000.000
74A103MET0-0.039-0.00327.945-0.335-0.3350.0000.0000.0000.000
75A104ARG10.8490.93529.645-9.309-9.3090.0000.0000.0000.000
76A105ILE0-0.014-0.01730.782-0.355-0.3550.0000.0000.0000.000
77A106ALA0-0.0020.00431.952-0.277-0.2770.0000.0000.0000.000
78A107SER0-0.008-0.04333.030-0.265-0.2650.0000.0000.0000.000
79A108SER0-0.033-0.01035.495-0.274-0.2740.0000.0000.0000.000
80A109GLU-1-0.875-0.93336.9507.4017.4010.0000.0000.0000.000
81A110PHE0-0.031-0.01237.623-0.225-0.2250.0000.0000.0000.000
82A111ALA0-0.025-0.01239.411-0.186-0.1860.0000.0000.0000.000
83A112ASP-1-0.813-0.90341.5246.8226.8220.0000.0000.0000.000
84A113ASP-1-0.847-0.90543.0056.8596.8590.0000.0000.0000.000
85A114PRO0-0.0090.00142.4800.0850.0850.0000.0000.0000.000
86A115CYS0-0.023-0.02543.545-0.006-0.0060.0000.0000.0000.000
87A116SER0-0.011-0.00242.0300.0780.0780.0000.0000.0000.000
88A117SER00.0540.00140.3530.1020.1020.0000.0000.0000.000
89A118VAL00.0230.01337.3820.2320.2320.0000.0000.0000.000
90A119LYS10.8930.94036.414-7.045-7.0450.0000.0000.0000.000
91A120ARG10.8980.97636.291-7.489-7.4890.0000.0000.0000.000
92A121GLY00.003-0.00534.4180.2110.2110.0000.0000.0000.000
93A122THR0-0.038-0.04431.8680.3790.3790.0000.0000.0000.000
94A123MET00.0130.03131.1850.2170.2170.0000.0000.0000.000
95A124VAL00.0020.00230.9170.2700.2700.0000.0000.0000.000
96A125ARG10.9180.95628.069-9.374-9.3740.0000.0000.0000.000
97A126ALA00.0320.02626.6710.4280.4280.0000.0000.0000.000
98A127ALA00.0340.00426.5130.3150.3150.0000.0000.0000.000
99A128ARG10.8610.93124.417-10.734-10.7340.0000.0000.0000.000
100A129ALA00.0180.02522.4040.5630.5630.0000.0000.0000.000
101A130LEU00.0350.01921.7060.5510.5510.0000.0000.0000.000
102A131LEU00.015-0.00522.3960.4030.4030.0000.0000.0000.000
103A132SER0-0.024-0.01519.1870.4580.4580.0000.0000.0000.000
104A133ALA00.0420.03317.8120.8740.8740.0000.0000.0000.000
105A134VAL0-0.035-0.01818.0040.5080.5080.0000.0000.0000.000
106A135THR0-0.037-0.04017.4460.2750.2750.0000.0000.0000.000
107A136ARG10.8550.9278.960-22.710-22.7100.0000.0000.0000.000
108A137LEU00.0100.00514.0511.0251.0250.0000.0000.0000.000
109A138LEU0-0.028-0.01415.8350.2970.2970.0000.0000.0000.000
110A139ILE0-0.017-0.00211.5990.4180.4180.0000.0000.0000.000
111A140LEU00.001-0.0069.3821.0941.0940.0000.0000.0000.000
112A141ALA0-0.022-0.01912.3950.4140.4140.0000.0000.0000.000
113A142ASP-1-0.912-0.94714.67418.61018.6100.0000.0000.0000.000
114A143MET0-0.025-0.0187.0990.4430.4430.0000.0000.0000.000
115A144ALA0-0.021-0.00611.4400.9300.9300.0000.0000.0000.000
116A145ASP-1-0.890-0.93713.35714.85714.8570.0000.0000.0000.000
117A146VAL0-0.043-0.02312.676-0.612-0.6120.0000.0000.0000.000
118A147MET0-0.022-0.0128.7110.7930.7930.0000.0000.0000.000
119A148ARG10.9370.97013.193-15.148-15.1480.0000.0000.0000.000
120A149LEU0-0.053-0.01416.735-0.949-0.9490.0000.0000.0000.000
121A150LEU0-0.013-0.01312.858-0.812-0.8120.0000.0000.0000.000
122A151SER0-0.017-0.01116.434-0.476-0.4760.0000.0000.0000.000
123A152HIS00.0260.00217.406-0.327-0.3270.0000.0000.0000.000
124A153LEU0-0.063-0.02617.279-0.657-0.6570.0000.0000.0000.000
125A154LYS10.8940.92715.639-17.743-17.7430.0000.0000.0000.000
126A155ILE00.0690.04819.595-0.575-0.5750.0000.0000.0000.000
127A156VAL0-0.036-0.02922.446-0.676-0.6760.0000.0000.0000.000
128A157GLU-1-0.826-0.88719.85515.14615.1460.0000.0000.0000.000
129A158GLU-1-0.894-0.95720.09813.98713.9870.0000.0000.0000.000
130A159ALA0-0.046-0.01924.375-0.533-0.5330.0000.0000.0000.000
131A160LEU0-0.054-0.04527.016-0.559-0.5590.0000.0000.0000.000
132A161GLU-1-0.893-0.94323.82512.21112.2110.0000.0000.0000.000
133A162ALA0-0.025-0.00428.054-0.353-0.3530.0000.0000.0000.000
134A163VAL0-0.052-0.03730.696-0.394-0.3940.0000.0000.0000.000
135A164LYS10.8430.94728.632-10.765-10.7650.0000.0000.0000.000
136A165ASN0-0.053-0.03728.773-0.432-0.4320.0000.0000.0000.000
137A166ALA00.0680.05333.027-0.101-0.1010.0000.0000.0000.000
138A167THR0-0.026-0.02036.044-0.054-0.0540.0000.0000.0000.000
139A168ASN0-0.006-0.01639.097-0.245-0.2450.0000.0000.0000.000
140A169GLU-1-0.728-0.86441.1447.3707.3700.0000.0000.0000.000
141A170GLN0-0.0170.00442.3610.0080.0080.0000.0000.0000.000
142A171ASP-1-0.806-0.89937.2388.3698.3690.0000.0000.0000.000
143A172LEU00.0440.03937.2420.1990.1990.0000.0000.0000.000
144A173ALA0-0.0100.00037.6680.1550.1550.0000.0000.0000.000
145A174ASN0-0.054-0.03835.866-0.037-0.0370.0000.0000.0000.000
146A175ARG10.8390.90733.089-8.829-8.8290.0000.0000.0000.000
147A176PHE00.005-0.00233.2630.2700.2700.0000.0000.0000.000
148A177LYS10.8820.93635.224-7.672-7.6720.0000.0000.0000.000
149A178GLU-1-0.855-0.92031.2609.3849.3840.0000.0000.0000.000
150A179PHE00.0920.04728.9760.1910.1910.0000.0000.0000.000
151A180GLY00.0230.01830.4310.2210.2210.0000.0000.0000.000
152A181LYS10.8960.94632.119-8.737-8.7370.0000.0000.0000.000
153A182GLU-1-0.809-0.92026.52911.16911.1690.0000.0000.0000.000
154A183MET0-0.031-0.00227.4140.3990.3990.0000.0000.0000.000
155A184VAL0-0.041-0.02129.0130.1160.1160.0000.0000.0000.000
156A185LYS10.8850.94626.864-10.931-10.9310.0000.0000.0000.000
157A186LEU00.0460.03222.7920.3170.3170.0000.0000.0000.000
158A187ASN0-0.047-0.04125.9920.3050.3050.0000.0000.0000.000
159A188TYR0-0.0020.01926.4120.0100.0100.0000.0000.0000.000
160A189VAL00.0440.01821.501-0.091-0.0910.0000.0000.0000.000
161A190ALA00.0290.00824.4920.1860.1860.0000.0000.0000.000
162A191ALA0-0.038-0.01425.407-0.082-0.0820.0000.0000.0000.000
163A192ARG10.9430.95925.973-11.653-11.6530.0000.0000.0000.000
164A193ARG10.8900.94919.742-15.053-15.0530.0000.0000.0000.000
165A194GLN00.0440.02924.5540.2160.2160.0000.0000.0000.000
166A195GLN0-0.060-0.03527.238-0.118-0.1180.0000.0000.0000.000
167A196GLU-1-0.893-0.92923.24013.07613.0760.0000.0000.0000.000
168A197LEU0-0.0360.01423.0140.1780.1780.0000.0000.0000.000
169A198LYS10.9560.97926.313-11.758-11.7580.0000.0000.0000.000
170A199ASP-1-0.805-0.90926.23711.28311.2830.0000.0000.0000.000
171A200PRO0-0.007-0.01528.2150.0940.0940.0000.0000.0000.000
172A201HIS00.0170.00727.107-0.497-0.4970.0000.0000.0000.000
173A202CYS0-0.003-0.01324.5810.2960.2960.0000.0000.0000.000
174A203ARG10.8200.90026.326-10.287-10.2870.0000.0000.0000.000
175A204ASP-1-0.904-0.94528.7659.8139.8130.0000.0000.0000.000
176A205GLU-1-0.891-0.93923.89113.00513.0050.0000.0000.0000.000
177A206MET0-0.028-0.00322.9900.1160.1160.0000.0000.0000.000
178A207ALA0-0.035-0.02126.324-0.072-0.0720.0000.0000.0000.000
179A208ALA00.0060.01528.546-0.303-0.3030.0000.0000.0000.000
180A209ALA00.0230.01724.671-0.213-0.2130.0000.0000.0000.000
181A210ARG10.9100.93126.772-10.875-10.8750.0000.0000.0000.000
182A211GLY0-0.024-0.00828.048-0.311-0.3110.0000.0000.0000.000
183A212ALA0-0.041-0.02528.277-0.342-0.3420.0000.0000.0000.000
184A213LEU00.0310.01525.546-0.260-0.2600.0000.0000.0000.000
185A214LYS10.9450.98028.840-9.085-9.0850.0000.0000.0000.000
186A215LYS10.9720.98732.161-9.108-9.1080.0000.0000.0000.000
187A216ASN00.053-0.00130.456-0.455-0.4550.0000.0000.0000.000
188A217ALA00.0700.05730.807-0.066-0.0660.0000.0000.0000.000
189A218THR0-0.071-0.04232.332-0.260-0.2600.0000.0000.0000.000
190A219MET0-0.022-0.00834.685-0.195-0.1950.0000.0000.0000.000
191A220LEU00.0500.03030.255-0.167-0.1670.0000.0000.0000.000
192A221TYR0-0.0090.01834.289-0.166-0.1660.0000.0000.0000.000
193A222THR0-0.012-0.02037.019-0.250-0.2500.0000.0000.0000.000
194A223ALA0-0.014-0.00435.900-0.187-0.1870.0000.0000.0000.000
195A224SER00.002-0.03035.2350.0030.0030.0000.0000.0000.000
196A225GLN0-0.070-0.04537.500-0.184-0.1840.0000.0000.0000.000
197A226ALA0-0.049-0.03140.919-0.187-0.1870.0000.0000.0000.000
198A227PHE0-0.012-0.01138.092-0.069-0.0690.0000.0000.0000.000
199A228LEU0-0.028-0.00440.076-0.094-0.0940.0000.0000.0000.000
200A229ARG10.8170.90042.606-7.072-7.0720.0000.0000.0000.000
201A230HIS0-0.019-0.00244.209-0.188-0.1880.0000.0000.0000.000
202A231PRO00.0460.02942.1880.1540.1540.0000.0000.0000.000
203A232ASP-1-0.905-0.94542.3387.0267.0260.0000.0000.0000.000
204A233VAL0-0.053-0.01343.266-0.034-0.0340.0000.0000.0000.000
205A234ALA00.0470.01340.1990.1730.1730.0000.0000.0000.000
206A235ALA00.018-0.00539.0160.2390.2390.0000.0000.0000.000
207A236THR00.0110.00338.9850.2320.2320.0000.0000.0000.000
208A237ARG10.9750.99932.917-8.896-8.8960.0000.0000.0000.000
209A238ALA0-0.016-0.00634.9160.3010.3010.0000.0000.0000.000
210A239ASN00.000-0.00734.3080.3490.3490.0000.0000.0000.000
211A240ARG10.8410.93533.231-9.012-9.0120.0000.0000.0000.000
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