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: 9GR52

Calculation Name: 4REG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4REG

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U333

Base Structure: X-ray

Registration Date: 2023-03-14

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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3769960.366537
FMO2-HF: Nuclear repulsion 3662615.199692
FMO2-HF: Total energy -107345.166845
FMO2-MP2: Total energy -107664.484216


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:MET)


Summations of interaction energy for fragment #1(A:1: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.
-33.21-26.30518.584-10.122-15.367-0.054
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.010
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].
3A3VAL00.0680.0593.912-1.5980.469-0.018-1.047-1.0010.001
4A4ARG10.7310.8586.259-0.872-0.8720.0000.0000.0000.000
5A5ILE00.0260.0049.9520.0250.0250.0000.0000.0000.000
6A6SER0-0.029-0.03113.039-0.032-0.0320.0000.0000.0000.000
7A7GLY00.0810.04016.708-0.004-0.0040.0000.0000.0000.000
8A8ARG10.7060.83619.708-0.155-0.1550.0000.0000.0000.000
9A9ILE0-0.008-0.00422.4880.0150.0150.0000.0000.0000.000
10A10ARG10.9851.01025.021-0.152-0.1520.0000.0000.0000.000
11A11LEU0-0.043-0.00527.5120.0160.0160.0000.0000.0000.000
12A12ASN00.047-0.00130.548-0.017-0.0170.0000.0000.0000.000
13A13ALA00.0470.03733.6320.0020.0020.0000.0000.0000.000
14A14HIS10.8750.92432.765-0.163-0.1630.0000.0000.0000.000
15A29ILE00.0530.02727.6520.0040.0040.0000.0000.0000.000
16A30THR0-0.041-0.03228.449-0.009-0.0090.0000.0000.0000.000
17A31LYS10.9360.97029.453-0.163-0.1630.0000.0000.0000.000
18A32THR0-0.059-0.02630.236-0.004-0.0040.0000.0000.0000.000
19A33LYS10.8450.90832.664-0.109-0.1090.0000.0000.0000.000
20A34VAL00.0140.00728.9270.0040.0040.0000.0000.0000.000
21A35THR00.0150.01532.255-0.003-0.0030.0000.0000.0000.000
22A36VAL0-0.039-0.01829.0810.0040.0040.0000.0000.0000.000
23A37ARG10.9270.96228.974-0.111-0.1110.0000.0000.0000.000
24A38THR0-0.071-0.02730.3720.0080.0080.0000.0000.0000.000
25A39GLU-1-0.906-0.96129.9390.0460.0460.0000.0000.0000.000
26A40ASN0-0.006-0.01034.044-0.002-0.0020.0000.0000.0000.000
27A41GLY00.0170.02437.3580.0000.0000.0000.0000.0000.000
28A42TRP0-0.040-0.03533.0100.0030.0030.0000.0000.0000.000
29A43THR00.0310.01636.624-0.003-0.0030.0000.0000.0000.000
30A44VAL0-0.055-0.02335.2720.0060.0060.0000.0000.0000.000
31A45VAL00.0520.02935.125-0.003-0.0030.0000.0000.0000.000
32A46GLU-1-0.856-0.92035.0640.1120.1120.0000.0000.0000.000
33A47VAL00.0150.01731.754-0.003-0.0030.0000.0000.0000.000
34A48PRO0-0.014-0.01333.2860.0050.0050.0000.0000.0000.000
35A49ALA00.0290.01528.2670.0030.0030.0000.0000.0000.000
36A50ILE00.006-0.00225.636-0.004-0.0040.0000.0000.0000.000
37A51THR00.0090.02124.4030.0220.0220.0000.0000.0000.000
38A52GLY00.0940.04320.4360.0080.0080.0000.0000.0000.000
39A53ASN0-0.057-0.04919.8510.0680.0680.0000.0000.0000.000
40A54MET00.0050.02121.4000.0080.0080.0000.0000.0000.000
41A55LEU00.0440.02717.8200.0130.0130.0000.0000.0000.000
42A56LYS10.8100.89616.239-0.572-0.5720.0000.0000.0000.000
43A57HIS00.0210.01317.6570.0610.0610.0000.0000.0000.000
44A58TRP00.0600.01919.9260.0150.0150.0000.0000.0000.000
45A59HIS00.0430.02710.916-0.102-0.1020.0000.0000.0000.000
46A60PHE0-0.032-0.02215.8150.0510.0510.0000.0000.0000.000
47A61VAL00.011-0.00417.3370.0090.0090.0000.0000.0000.000
48A62GLY00.0320.01117.093-0.008-0.0080.0000.0000.0000.000
49A63PHE0-0.047-0.02711.4900.0060.0060.0000.0000.0000.000
50A64VAL00.0100.00215.1170.0100.0100.0000.0000.0000.000
51A65ASP-1-0.781-0.86718.3290.3890.3890.0000.0000.0000.000
52A66TYR0-0.010-0.00715.107-0.040-0.0400.0000.0000.0000.000
53A67PHE00.0170.01112.926-0.024-0.0240.0000.0000.0000.000
54A68LYS10.8100.91016.336-0.448-0.4480.0000.0000.0000.000
55A69THR0-0.073-0.02918.296-0.049-0.0490.0000.0000.0000.000
56A70THR0-0.038-0.01713.938-0.023-0.0230.0000.0000.0000.000
57A71PRO00.014-0.01215.540-0.012-0.0120.0000.0000.0000.000
58A72TYR0-0.018-0.02313.127-0.032-0.0320.0000.0000.0000.000
59A73GLY00.0250.03216.8200.0290.0290.0000.0000.0000.000
60A74VAL0-0.020-0.01518.786-0.005-0.0050.0000.0000.0000.000
61A75ASN0-0.023-0.02615.895-0.093-0.0930.0000.0000.0000.000
62A76LEU00.0080.01017.5120.0890.0890.0000.0000.0000.000
63A77THR0-0.041-0.05320.331-0.068-0.0680.0000.0000.0000.000
64A78GLU-1-0.797-0.88023.1200.2730.2730.0000.0000.0000.000
65A79ARG10.7610.82825.139-0.282-0.2820.0000.0000.0000.000
66A80ALA00.0180.01120.677-0.007-0.0070.0000.0000.0000.000
67A81LEU0-0.0050.00922.7980.0090.0090.0000.0000.0000.000
68A82ARG10.7940.87324.503-0.270-0.2700.0000.0000.0000.000
69A83TYR0-0.058-0.06221.925-0.031-0.0310.0000.0000.0000.000
70A84ASN00.0280.03524.3310.0050.0050.0000.0000.0000.000
71A85GLY00.0590.01522.8750.0210.0210.0000.0000.0000.000
72A86THR0-0.064-0.04423.6940.0020.0020.0000.0000.0000.000
73A87ARG10.7850.90918.919-0.559-0.5590.0000.0000.0000.000
74A88PHE00.0460.00022.2300.0290.0290.0000.0000.0000.000
75A89GLY00.0330.01726.210-0.008-0.0080.0000.0000.0000.000
76A90GLN0-0.007-0.01629.7480.0050.0050.0000.0000.0000.000
77A91GLY00.0420.02130.932-0.008-0.0080.0000.0000.0000.000
78A92GLU-1-0.790-0.83929.3050.2400.2400.0000.0000.0000.000
79A93THR00.031-0.00629.4460.0010.0010.0000.0000.0000.000
80A94THR0-0.038-0.02128.3660.0020.0020.0000.0000.0000.000
81A95ALA00.0160.01025.2890.0030.0030.0000.0000.0000.000
82A96THR0-0.0110.01227.0050.0010.0010.0000.0000.0000.000
83A97LYS10.8380.92720.497-0.371-0.3710.0000.0000.0000.000
84A98ALA00.0110.00023.395-0.030-0.0300.0000.0000.0000.000
85A99ASN0-0.013-0.01423.9430.0020.0020.0000.0000.0000.000
86A100GLY00.0110.01926.748-0.021-0.0210.0000.0000.0000.000
87A101ALA0-0.002-0.00126.913-0.010-0.0100.0000.0000.0000.000
88A102THR0-0.019-0.01427.9180.0130.0130.0000.0000.0000.000
89A103VAL00.0240.01922.631-0.010-0.0100.0000.0000.0000.000
90A104GLN00.0380.00626.000-0.013-0.0130.0000.0000.0000.000
91A105LEU0-0.0150.00023.9930.0230.0230.0000.0000.0000.000
92A106ASN00.0640.02325.3730.0020.0020.0000.0000.0000.000
93A107ASP-1-0.794-0.87021.1870.3160.3160.0000.0000.0000.000
94A108GLU-1-0.742-0.84815.3210.5820.5820.0000.0000.0000.000
95A109ALA00.0110.00916.8570.0680.0680.0000.0000.0000.000
96A110THR0-0.025-0.04817.5820.0420.0420.0000.0000.0000.000
97A111ILE0-0.050-0.01019.0160.0170.0170.0000.0000.0000.000
98A112ILE0-0.009-0.00312.9230.0220.0220.0000.0000.0000.000
99A113LYS10.8690.94215.326-0.275-0.2750.0000.0000.0000.000
100A114GLU-1-0.804-0.88416.4330.3780.3780.0000.0000.0000.000
101A115LEU0-0.033-0.01418.120-0.020-0.0200.0000.0000.0000.000
102A116ALA00.0810.03313.9470.0570.0570.0000.0000.0000.000
103A117ASP-1-0.751-0.85514.1430.6740.6740.0000.0000.0000.000
104A118ALA0-0.008-0.01416.377-0.009-0.0090.0000.0000.0000.000
105A119ASP-1-0.834-0.88811.1931.5871.5870.0000.0000.0000.000
106A120VAL00.0410.0339.6990.0500.0500.0000.0000.0000.000
107A121HIS00.0160.01011.752-0.094-0.0940.0000.0000.0000.000
108A122GLY00.0240.03214.773-0.094-0.0940.0000.0000.0000.000
109A123PHE0-0.017-0.01916.371-0.030-0.0300.0000.0000.0000.000
110A124LEU0-0.021-0.01819.907-0.013-0.0130.0000.0000.0000.000
111A125ALA00.0470.02622.985-0.005-0.0050.0000.0000.0000.000
112A126PRO00.0060.00825.594-0.011-0.0110.0000.0000.0000.000
113A127LYS10.8880.95027.899-0.180-0.1800.0000.0000.0000.000
114A128THR0-0.009-0.01926.101-0.012-0.0120.0000.0000.0000.000
115A129GLY00.0130.01926.802-0.002-0.0020.0000.0000.0000.000
116A130ARG10.8100.90122.085-0.227-0.2270.0000.0000.0000.000
117A131ARG10.9440.95319.946-0.297-0.2970.0000.0000.0000.000
118A132ARG10.7330.86610.607-1.084-1.0840.0000.0000.0000.000
119A133VAL0-0.012-0.00614.337-0.009-0.0090.0000.0000.0000.000
120A134SER0-0.014-0.02813.5120.0910.0910.0000.0000.0000.000
121A135LEU00.0050.0057.709-0.081-0.0810.0000.0000.0000.000
122A136VAL0-0.0040.0259.8480.0070.0070.0000.0000.0000.000
123A137LYS10.8370.91511.192-0.707-0.7070.0000.0000.0000.000
124A138ALA00.0280.01313.9010.0460.0460.0000.0000.0000.000
125A139SER0-0.0030.00116.710-0.050-0.0500.0000.0000.0000.000
126A140PHE0-0.023-0.02319.5850.0150.0150.0000.0000.0000.000
127A141ILE00.0100.02022.167-0.001-0.0010.0000.0000.0000.000
128A142LEU0-0.001-0.01024.266-0.014-0.0140.0000.0000.0000.000
129A143PRO0-0.0030.00127.0560.0070.0070.0000.0000.0000.000
130A144THR00.013-0.00526.5420.0030.0030.0000.0000.0000.000
131A145GLU-1-0.783-0.87428.6020.0760.0760.0000.0000.0000.000
132A146ASP-1-0.712-0.85029.2400.1070.1070.0000.0000.0000.000
133A147PHE0-0.046-0.00231.5090.0020.0020.0000.0000.0000.000
134A148ILE0-0.034-0.02931.993-0.003-0.0030.0000.0000.0000.000
135A149LYS10.7580.86133.289-0.071-0.0710.0000.0000.0000.000
136A150GLU-1-0.877-0.92535.4280.0850.0850.0000.0000.0000.000
137A151VAL0-0.103-0.04237.255-0.002-0.0020.0000.0000.0000.000
138A152GLU-1-1.027-1.01539.0150.0600.0600.0000.0000.0000.000
139A185PHE00.0890.02940.1180.0000.0000.0000.0000.0000.000
140A186SER00.003-0.00638.8450.0040.0040.0000.0000.0000.000
141A187ARG10.8530.91338.528-0.072-0.0720.0000.0000.0000.000
142A188GLU-1-0.794-0.88437.9840.0890.0890.0000.0000.0000.000
143A189TYR00.0690.02333.8190.0090.0090.0000.0000.0000.000
144A190ALA0-0.076-0.01933.9740.0120.0120.0000.0000.0000.000
145A191THR0-0.066-0.02333.8030.0060.0060.0000.0000.0000.000
146A192GLY00.0580.01532.5070.0080.0080.0000.0000.0000.000
147A193LEU0-0.039-0.01527.2260.0110.0110.0000.0000.0000.000
148A194TYR0-0.046-0.03926.378-0.006-0.0060.0000.0000.0000.000
149A195GLY00.0880.05623.5280.0110.0110.0000.0000.0000.000
150A196PHE0-0.060-0.05116.5720.0070.0070.0000.0000.0000.000
151A197SER00.0390.01516.3700.0080.0080.0000.0000.0000.000
152A198ILE0-0.014-0.01612.196-0.017-0.0170.0000.0000.0000.000
153A199VAL0-0.011-0.0019.3650.0180.0180.0000.0000.0000.000
154A200LEU00.0300.0146.847-0.017-0.0170.0000.0000.0000.000
155A201ASP-1-0.764-0.8645.6860.5460.5460.0000.0000.0000.000
156A202LEU0-0.002-0.0203.015-0.624-0.0050.064-0.127-0.5560.000
157A203GLY00.0610.0412.5860.4422.0250.956-1.252-1.2870.004
158A204LEU0-0.040-0.0113.0140.414-0.2960.0810.970-0.3410.000
159A205VAL00.0010.0046.088-0.641-0.6410.0000.0000.0000.000
160A206GLY00.0370.0067.7970.2300.2300.0000.0000.0000.000
161A207ILE0-0.0380.0077.721-0.229-0.2290.0000.0000.0000.000
162A208PRO0-0.048-0.00411.2340.0370.0370.0000.0000.0000.000
163A209GLN00.009-0.03511.415-0.138-0.1380.0000.0000.0000.000
164A210GLY0-0.028-0.01014.122-0.071-0.0710.0000.0000.0000.000
165A211LEU0-0.044-0.01716.110-0.053-0.0530.0000.0000.0000.000
166A212PRO00.0700.04112.0730.0350.0350.0000.0000.0000.000
167A213VAL0-0.004-0.00812.7150.0230.0230.0000.0000.0000.000
168A214LYS10.8600.91815.336-0.209-0.2090.0000.0000.0000.000
169A215PHE00.004-0.01317.886-0.028-0.0280.0000.0000.0000.000
170A216GLU-1-0.959-0.95020.6000.0090.0090.0000.0000.0000.000
171A217GLU-1-0.900-0.95121.665-0.090-0.0900.0000.0000.0000.000
172A218ASN0-0.017-0.01923.919-0.009-0.0090.0000.0000.0000.000
173A219GLN00.003-0.00319.320-0.023-0.0230.0000.0000.0000.000
174A220PRO0-0.0110.00516.3140.0330.0330.0000.0000.0000.000
175A221ARG10.9680.97414.263-0.039-0.0390.0000.0000.0000.000
176A222PRO00.0370.0249.6190.0620.0620.0000.0000.0000.000
177A223ASN0-0.031-0.00811.944-0.008-0.0080.0000.0000.0000.000
178A224ILE0-0.007-0.0127.5030.1300.1300.0000.0000.0000.000
179A225VAL0-0.058-0.02511.375-0.166-0.1660.0000.0000.0000.000
180A226ILE0-0.015-0.0039.205-0.013-0.0130.0000.0000.0000.000
181A227ASP-1-0.719-0.82911.1330.3810.3810.0000.0000.0000.000
182A228PRO00.0120.0017.6180.2160.2160.0000.0000.0000.000
183A229ASN0-0.032-0.0307.2730.0510.0510.0000.0000.0000.000
184A230GLU-1-0.739-0.8489.7950.8510.8510.0000.0000.0000.000
185A231ARG10.7920.8773.798-5.364-4.6900.129-0.250-0.5540.002
186A232LYS10.9140.9425.6650.5360.5360.0000.0000.0000.000
187A233ALA00.0360.0256.5760.2210.2210.0000.0000.0000.000
188A234ARG10.7150.8239.090-1.091-1.0910.0000.0000.0000.000
189A235ILE00.0300.0072.969-1.119-0.6181.428-0.366-1.5630.002
190A236GLU-1-0.787-0.8836.8790.4090.4090.0000.0000.0000.000
191A237SER0-0.054-0.0289.228-0.197-0.1970.0000.0000.0000.000
192A238ALA0-0.035-0.0267.777-0.180-0.1800.0000.0000.0000.000
193A239LEU00.0100.0115.213-0.133-0.1330.0000.0000.0000.000
194A240LYS10.9220.9448.954-0.943-0.9430.0000.0000.0000.000
195A241ALA0-0.022-0.01012.443-0.140-0.1400.0000.0000.0000.000
196A242LEU00.016-0.00810.018-0.101-0.1010.0000.0000.0000.000
197A243ILE00.0350.03113.841-0.085-0.0850.0000.0000.0000.000
198A244PRO0-0.0140.00516.461-0.053-0.0530.0000.0000.0000.000
199A245MET0-0.104-0.02014.176-0.008-0.0080.0000.0000.0000.000
200A246LEU00.011-0.00715.901-0.040-0.0400.0000.0000.0000.000
201A247SER0-0.040-0.01519.392-0.055-0.0550.0000.0000.0000.000
202A248GLY00.013-0.00522.045-0.032-0.0320.0000.0000.0000.000
203A249TYR0-0.057-0.01824.406-0.016-0.0160.0000.0000.0000.000
204A260VAL0-0.060-0.04827.604-0.005-0.0050.0000.0000.0000.000
205A261PHE00.0270.02221.341-0.007-0.0070.0000.0000.0000.000
206A262LYS10.8480.94126.099-0.181-0.1810.0000.0000.0000.000
207A263VAL00.0550.02119.939-0.003-0.0030.0000.0000.0000.000
208A264GLU-1-0.832-0.89023.3610.1730.1730.0000.0000.0000.000
209A265GLU-1-0.761-0.86322.0860.1500.1500.0000.0000.0000.000
210A266LEU0-0.045-0.02715.2620.0400.0400.0000.0000.0000.000
211A267VAL00.0570.04014.811-0.030-0.0300.0000.0000.0000.000
212A268ALA0-0.014-0.01510.8760.0660.0660.0000.0000.0000.000
213A269ILE00.0040.0059.130-0.144-0.1440.0000.0000.0000.000
214A270ALA00.0230.0155.1660.3120.3120.0000.0000.0000.000
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