FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: KG893

Calculation Name: 3R89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R89

Chain ID: A

ChEMBL ID:

UniProt ID: C7RH50

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptAll
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 289
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4305715.406111
FMO2-HF: Nuclear repulsion 4190411.192749
FMO2-HF: Total energy -115304.213362
FMO2-MP2: Total energy -115639.533446


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-1.969-0.666-0.011-0.676-0.6160.001
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.024
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].
3A0ALA0-0.0040.0073.852-0.2811.022-0.011-0.676-0.6160.001
4A1MET0-0.0050.0006.6290.5500.5500.0000.0000.0000.000
5A2LYS10.8750.9498.1940.9310.9310.0000.0000.0000.000
6A3ILE00.0540.02311.438-0.162-0.1620.0000.0000.0000.000
7A4ILE0-0.0030.01413.715-0.021-0.0210.0000.0000.0000.000
8A5ASP-1-0.768-0.8649.330-1.248-1.2480.0000.0000.0000.000
9A6LYS10.8260.8949.5780.6160.6160.0000.0000.0000.000
10A7LEU0-0.0050.01111.2160.0420.0420.0000.0000.0000.000
11A8TYR00.0040.00410.0630.0400.0400.0000.0000.0000.000
12A9GLU-1-0.791-0.9045.871-3.419-3.4190.0000.0000.0000.000
13A10LYS10.8370.9319.6500.7310.7310.0000.0000.0000.000
14A11VAL00.0250.01012.6300.0980.0980.0000.0000.0000.000
15A12SER0-0.088-0.04510.6200.0800.0800.0000.0000.0000.000
16A13LYS10.7430.8667.3391.4671.4670.0000.0000.0000.000
17A14ASN0-0.020-0.01413.1740.0520.0520.0000.0000.0000.000
18A15GLY00.0310.02916.2800.0450.0450.0000.0000.0000.000
19A16PHE00.002-0.01418.252-0.030-0.0300.0000.0000.0000.000
20A17VAL00.0030.01120.1120.0120.0120.0000.0000.0000.000
21A18CYS0-0.0170.00021.053-0.029-0.0290.0000.0000.0000.000
22A19ILE00.0200.01123.2580.0250.0250.0000.0000.0000.000
23A20GLY00.0410.02025.727-0.008-0.0080.0000.0000.0000.000
24A21LEU00.0360.02826.5630.0150.0150.0000.0000.0000.000
25A22ASP-1-0.820-0.86829.982-0.137-0.1370.0000.0000.0000.000
26A23SER0-0.027-0.05432.7150.0060.0060.0000.0000.0000.000
27A24SER00.013-0.01035.0590.0010.0010.0000.0000.0000.000
28A25ILE00.0580.02838.8200.0010.0010.0000.0000.0000.000
29A26ASP-1-0.869-0.91041.133-0.059-0.0590.0000.0000.0000.000
30A27TYR0-0.090-0.05035.7160.0040.0040.0000.0000.0000.000
31A28ILE0-0.0120.01637.4820.0000.0000.0000.0000.0000.000
32A29PRO00.0190.00838.4720.0030.0030.0000.0000.0000.000
33A30GLU-1-0.948-0.97541.455-0.039-0.0390.0000.0000.0000.000
34A31ASN00.005-0.02341.929-0.002-0.0020.0000.0000.0000.000
35A32MET00.0190.02635.455-0.001-0.0010.0000.0000.0000.000
36A33LYS10.8690.93840.2150.0500.0500.0000.0000.0000.000
37A34ALA00.0020.01041.9810.0010.0010.0000.0000.0000.000
38A35GLY0-0.050-0.03143.5190.0000.0000.0000.0000.0000.000
39A36LYS10.8270.93338.6690.0450.0450.0000.0000.0000.000
40A37SER0-0.034-0.03341.0870.0000.0000.0000.0000.0000.000
41A38VAL00.011-0.00840.412-0.001-0.0010.0000.0000.0000.000
42A39SER0-0.055-0.05537.061-0.003-0.0030.0000.0000.0000.000
43A40GLU-1-0.815-0.90536.445-0.051-0.0510.0000.0000.0000.000
44A41ALA0-0.0280.00536.761-0.001-0.0010.0000.0000.0000.000
45A42LEU0-0.003-0.01535.417-0.003-0.0030.0000.0000.0000.000
46A43PHE00.0060.01328.879-0.004-0.0040.0000.0000.0000.000
47A44SER0-0.027-0.03332.045-0.002-0.0020.0000.0000.0000.000
48A45TYR0-0.033-0.03532.920-0.002-0.0020.0000.0000.0000.000
49A46ASN00.006-0.01229.602-0.001-0.0010.0000.0000.0000.000
50A47LYS10.8610.94427.4490.0660.0660.0000.0000.0000.000
51A48GLU-1-0.796-0.88427.983-0.069-0.0690.0000.0000.0000.000
52A49ILE0-0.002-0.01227.572-0.002-0.0020.0000.0000.0000.000
53A50ILE00.0070.03423.145-0.007-0.0070.0000.0000.0000.000
54A51ASP-1-0.791-0.85923.792-0.105-0.1050.0000.0000.0000.000
55A52GLN0-0.074-0.03324.6470.0060.0060.0000.0000.0000.000
56A53THR0-0.018-0.04223.617-0.003-0.0030.0000.0000.0000.000
57A54TYR00.0260.02718.179-0.012-0.0120.0000.0000.0000.000
58A55ASP-1-0.802-0.85517.507-0.170-0.1700.0000.0000.0000.000
59A56VAL0-0.048-0.02318.344-0.001-0.0010.0000.0000.0000.000
60A57CYS0-0.042-0.01519.6260.0110.0110.0000.0000.0000.000
61A58ALA00.0220.03116.317-0.022-0.0220.0000.0000.0000.000
62A59ILE0-0.041-0.02816.880-0.048-0.0480.0000.0000.0000.000
63A60TYR00.0390.00719.6700.0320.0320.0000.0000.0000.000
64A61LYS10.7820.87923.2830.1460.1460.0000.0000.0000.000
65A62LEU00.0220.01826.2880.0150.0150.0000.0000.0000.000
66A63GLN0-0.104-0.06329.4660.0030.0030.0000.0000.0000.000
67A64ILE00.0220.02131.9430.0090.0090.0000.0000.0000.000
68A65ALA00.0600.03633.9610.0070.0070.0000.0000.0000.000
69A66TYR0-0.018-0.00335.5860.0080.0080.0000.0000.0000.000
70A67TYR0-0.027-0.01431.9400.0080.0080.0000.0000.0000.000
71A68GLU-1-0.783-0.90236.629-0.101-0.1010.0000.0000.0000.000
72A69SER0-0.103-0.05139.2240.0060.0060.0000.0000.0000.000
73A70TYR00.010-0.00339.2150.0060.0060.0000.0000.0000.000
74A71GLY00.0120.01241.7210.0030.0030.0000.0000.0000.000
75A72ILE0-0.003-0.01439.957-0.004-0.0040.0000.0000.0000.000
76A73GLU-1-0.714-0.81439.048-0.062-0.0620.0000.0000.0000.000
77A74GLY00.0280.00437.833-0.003-0.0030.0000.0000.0000.000
78A75MET0-0.019-0.01733.768-0.006-0.0060.0000.0000.0000.000
79A76ILE0-0.0080.00634.290-0.006-0.0060.0000.0000.0000.000
80A77ALA00.0400.02133.523-0.004-0.0040.0000.0000.0000.000
81A78TYR0-0.037-0.00729.015-0.008-0.0080.0000.0000.0000.000
82A79ARG10.8380.90929.8180.0750.0750.0000.0000.0000.000
83A80ASP-1-0.819-0.88228.695-0.092-0.0920.0000.0000.0000.000
84A81THR0-0.052-0.04327.413-0.001-0.0010.0000.0000.0000.000
85A82LEU0-0.008-0.00725.125-0.012-0.0120.0000.0000.0000.000
86A83SER0-0.060-0.03524.040-0.017-0.0170.0000.0000.0000.000
87A84TYR0-0.002-0.04123.535-0.004-0.0040.0000.0000.0000.000
88A85LEU0-0.040-0.02921.858-0.006-0.0060.0000.0000.0000.000
89A86ARG10.8200.88819.2850.2330.2330.0000.0000.0000.000
90A87GLU-1-0.906-0.93818.903-0.112-0.1120.0000.0000.0000.000
91A88LYS10.7780.89619.0810.1420.1420.0000.0000.0000.000
92A89ASP-1-0.897-0.93612.758-0.571-0.5710.0000.0000.0000.000
93A90LEU0-0.055-0.01815.508-0.073-0.0730.0000.0000.0000.000
94A91LEU00.0230.02514.2360.0160.0160.0000.0000.0000.000
95A92SER00.019-0.02318.3530.0430.0430.0000.0000.0000.000
96A93ILE0-0.002-0.01122.012-0.012-0.0120.0000.0000.0000.000
97A94GLY00.1090.04724.3760.0210.0210.0000.0000.0000.000
98A95ASP-1-0.792-0.86927.537-0.157-0.1570.0000.0000.0000.000
99A96VAL00.020-0.01229.6520.0140.0140.0000.0000.0000.000
100A97LYS10.7990.88631.7450.1520.1520.0000.0000.0000.000
101A98ARG10.8580.93732.6680.1300.1300.0000.0000.0000.000
102A99SER00.021-0.00333.868-0.005-0.0050.0000.0000.0000.000
103A100ASP-1-0.904-0.94635.634-0.103-0.1030.0000.0000.0000.000
104A101ILE00.0660.02734.868-0.008-0.0080.0000.0000.0000.000
105A102ALA00.006-0.00834.7480.0040.0040.0000.0000.0000.000
106A103ALA0-0.0060.00334.244-0.005-0.0050.0000.0000.0000.000
107A104SER00.0390.01635.372-0.001-0.0010.0000.0000.0000.000
108A105ALA00.0000.01032.019-0.003-0.0030.0000.0000.0000.000
109A106LYS10.8340.90728.0190.1510.1510.0000.0000.0000.000
110A107MET0-0.048-0.01731.063-0.002-0.0020.0000.0000.0000.000
111A108TYR00.018-0.00131.852-0.001-0.0010.0000.0000.0000.000
112A109ALA0-0.016-0.00327.184-0.007-0.0070.0000.0000.0000.000
113A110LYS10.8310.90127.3800.1190.1190.0000.0000.0000.000
114A111ALA0-0.035-0.01728.644-0.001-0.0010.0000.0000.0000.000
115A112HIS00.007-0.01027.8880.0090.0090.0000.0000.0000.000
116A113PHE00.0140.02423.174-0.017-0.0170.0000.0000.0000.000
117A114GLU-1-0.754-0.85123.501-0.151-0.1510.0000.0000.0000.000
118A115GLY00.0050.00525.7860.0060.0060.0000.0000.0000.000
119A116ASP-1-0.876-0.95127.275-0.102-0.1020.0000.0000.0000.000
120A117PHE0-0.052-0.03328.8880.0010.0010.0000.0000.0000.000
121A118GLU-1-0.857-0.89620.646-0.239-0.2390.0000.0000.0000.000
122A119THR0-0.032-0.02723.451-0.007-0.0070.0000.0000.0000.000
123A120ASP-1-0.774-0.85718.402-0.342-0.3420.0000.0000.0000.000
124A121PHE0-0.001-0.00417.059-0.022-0.0220.0000.0000.0000.000
125A122ILE00.0170.02222.3350.0230.0230.0000.0000.0000.000
126A123THR0-0.020-0.01826.108-0.005-0.0050.0000.0000.0000.000
127A124LEU0-0.023-0.00228.0260.0110.0110.0000.0000.0000.000
128A125ASN00.026-0.01130.894-0.005-0.0050.0000.0000.0000.000
129A126PRO00.0130.00832.4810.0040.0040.0000.0000.0000.000
130A127TYR0-0.056-0.02434.2780.0060.0060.0000.0000.0000.000
131A128MET0-0.015-0.00337.6790.0050.0050.0000.0000.0000.000
132A129GLY00.0560.04636.9190.0060.0060.0000.0000.0000.000
133A130MET0-0.0210.01130.901-0.004-0.0040.0000.0000.0000.000
134A131ASP-1-0.817-0.90832.277-0.122-0.1220.0000.0000.0000.000
135A132SER0-0.037-0.04033.7120.0000.0000.0000.0000.0000.000
136A133ILE0-0.023-0.02727.742-0.008-0.0080.0000.0000.0000.000
137A134GLU-1-0.872-0.95728.312-0.155-0.1550.0000.0000.0000.000
138A135PRO0-0.058-0.02228.152-0.007-0.0070.0000.0000.0000.000
139A136TYR00.0390.01025.896-0.001-0.0010.0000.0000.0000.000
140A137GLU-1-0.716-0.82323.713-0.235-0.2350.0000.0000.0000.000
141A138GLU-1-0.871-0.90522.531-0.196-0.1960.0000.0000.0000.000
142A139TYR0-0.049-0.06721.636-0.001-0.0010.0000.0000.0000.000
143A140ILE0-0.035-0.00619.297-0.024-0.0240.0000.0000.0000.000
144A141GLU-1-0.957-0.98617.966-0.320-0.3200.0000.0000.0000.000
145A142LYS10.8480.93417.1500.1860.1860.0000.0000.0000.000
146A143GLY0-0.0280.00114.110-0.025-0.0250.0000.0000.0000.000
147A144ASP-1-0.824-0.92713.282-0.656-0.6560.0000.0000.0000.000
148A145LYS10.7500.87815.4800.3310.3310.0000.0000.0000.000
149A146GLY00.0300.00918.771-0.024-0.0240.0000.0000.0000.000
150A147VAL0-0.058-0.02820.5190.0310.0310.0000.0000.0000.000
151A148PHE0-0.014-0.00620.849-0.017-0.0170.0000.0000.0000.000
152A149VAL00.0280.00925.9350.0190.0190.0000.0000.0000.000
153A150LEU0-0.053-0.03628.976-0.001-0.0010.0000.0000.0000.000
154A151LEU0-0.0150.02030.5230.0030.0030.0000.0000.0000.000
155A152ARG10.7910.86932.9070.1170.1170.0000.0000.0000.000
156A153THR0-0.042-0.06833.490-0.005-0.0050.0000.0000.0000.000
157A154SER00.0330.00535.7790.0050.0050.0000.0000.0000.000
158A155ASN0-0.0370.00637.5250.0100.0100.0000.0000.0000.000
159A156PRO00.019-0.01340.3220.0000.0000.0000.0000.0000.000
160A157GLY00.1120.04443.8610.0000.0000.0000.0000.0000.000
161A158ALA0-0.0010.01539.7490.0010.0010.0000.0000.0000.000
162A159LYS10.8310.89841.5990.0810.0810.0000.0000.0000.000
163A160ASP-1-0.897-0.93144.634-0.069-0.0690.0000.0000.0000.000
164A161PHE0-0.018-0.02942.9580.0010.0010.0000.0000.0000.000
165A162GLU-1-0.752-0.82437.651-0.115-0.1150.0000.0000.0000.000
166A163VAL00.006-0.00740.338-0.003-0.0030.0000.0000.0000.000
167A164LEU0-0.0130.01742.0960.0030.0030.0000.0000.0000.000
168A165PRO0-0.001-0.00943.795-0.003-0.0030.0000.0000.0000.000
169A166VAL00.0090.00642.7390.0030.0030.0000.0000.0000.000
170A167ASP-1-0.873-0.93142.913-0.085-0.0850.0000.0000.0000.000
171A168GLY0-0.025-0.00644.4910.0000.0000.0000.0000.0000.000
172A169GLU-1-0.834-0.88638.161-0.103-0.1030.0000.0000.0000.000
173A170GLU-1-0.790-0.88639.331-0.093-0.0930.0000.0000.0000.000
174A171PHE0-0.014-0.00439.298-0.006-0.0060.0000.0000.0000.000
175A172PHE00.0450.00434.681-0.004-0.0040.0000.0000.0000.000
176A173TYR00.0220.00233.419-0.012-0.0120.0000.0000.0000.000
177A174LYS10.8030.89534.6650.0880.0880.0000.0000.0000.000
178A175VAL0-0.0080.00232.769-0.004-0.0040.0000.0000.0000.000
179A176GLY00.0560.00930.845-0.009-0.0090.0000.0000.0000.000
180A177ASP-1-0.792-0.84929.883-0.152-0.1520.0000.0000.0000.000
181A178LYS10.9260.96030.3460.1240.1240.0000.0000.0000.000
182A179MET00.0090.01627.607-0.010-0.0100.0000.0000.0000.000
183A180ARG10.8140.88425.4360.1540.1540.0000.0000.0000.000
184A181GLU-1-0.851-0.92825.243-0.195-0.1950.0000.0000.0000.000
185A182LEU0-0.056-0.02326.013-0.005-0.0050.0000.0000.0000.000
186A183ASN00.001-0.00820.696-0.034-0.0340.0000.0000.0000.000
187A184GLU-1-0.800-0.88320.779-0.325-0.3250.0000.0000.0000.000
188A185LYS10.7560.88520.5880.2020.2020.0000.0000.0000.000
189A186TYR0-0.042-0.05217.782-0.018-0.0180.0000.0000.0000.000
190A187ILE0-0.0220.01215.499-0.069-0.0690.0000.0000.0000.000
191A188GLY0-0.006-0.01512.465-0.024-0.0240.0000.0000.0000.000
192A189LYS10.8780.9207.2191.2161.2160.0000.0000.0000.000
193A190SER0-0.026-0.02610.1170.1320.1320.0000.0000.0000.000
194A191GLY0-0.026-0.00112.0230.1100.1100.0000.0000.0000.000
195A192PHE00.0260.01915.1000.0670.0670.0000.0000.0000.000
196A193GLY00.0250.00216.002-0.065-0.0650.0000.0000.0000.000
197A194PRO0-0.055-0.02216.8720.0080.0080.0000.0000.0000.000
198A195ILE0-0.012-0.00418.8080.0310.0310.0000.0000.0000.000
199A196GLY00.0740.04022.6000.0050.0050.0000.0000.0000.000
200A197LEU0-0.038-0.01923.6150.0240.0240.0000.0000.0000.000
201A198VAL0-0.048-0.02426.522-0.007-0.0070.0000.0000.0000.000
202A199VAL00.0190.00228.1910.0130.0130.0000.0000.0000.000
203A200GLY0-0.031-0.02729.815-0.003-0.0030.0000.0000.0000.000
204A201ALA00.0240.01231.3600.0010.0010.0000.0000.0000.000
205A202THR0-0.077-0.07832.9470.0050.0050.0000.0000.0000.000
206A203HIS0-0.020-0.02136.3500.0070.0070.0000.0000.0000.000
207A204SER0-0.006-0.01834.784-0.004-0.0040.0000.0000.0000.000
208A205GLU-1-0.888-0.94334.552-0.083-0.0830.0000.0000.0000.000
209A206GLU-1-0.782-0.83135.499-0.106-0.1060.0000.0000.0000.000
210A207VAL0-0.019-0.01331.114-0.007-0.0070.0000.0000.0000.000
211A208GLU-1-0.739-0.85130.677-0.109-0.1090.0000.0000.0000.000
212A209LYS10.7470.88231.0500.0930.0930.0000.0000.0000.000
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