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: 2JL3R

Calculation Name: 4GM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IL98

Base Structure: X-ray

Registration Date: 2023-06-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015421.290736
FMO2-HF: Nuclear repulsion 1943040.422507
FMO2-HF: Total energy -72380.868229
FMO2-MP2: Total energy -72594.472863


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:61:PRO)


Summations of interaction energy for fragment #1(A:61:PRO)
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.
-2.2874.3113.036-3.358-6.2750.003
Interaction energy analysis for fragmet #1(A:61:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : 0.053
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].
3A63LEU00.0040.0092.419-3.8080.3780.851-2.066-2.9700.005
4A64LEU00.0180.0292.280-1.3300.6302.185-1.186-2.959-0.002
5A65LEU00.0730.0424.1530.7991.2510.000-0.106-0.3460.000
6A66SER0-0.068-0.0366.2260.6750.6750.0000.0000.0000.000
7A67LYS10.8450.9027.8001.0041.0040.0000.0000.0000.000
8A68ARG10.7950.8789.0150.4860.4860.0000.0000.0000.000
9A69ILE0-0.024-0.0035.9320.1940.1940.0000.0000.0000.000
10A70ILE00.0180.0085.705-0.536-0.5360.0000.0000.0000.000
11A71PHE0-0.041-0.0285.4030.0410.0410.0000.0000.0000.000
12A72LEU00.0230.0326.9420.4520.4520.0000.0000.0000.000
13A73SER0-0.014-0.0128.655-0.026-0.0260.0000.0000.0000.000
14A74SER00.000-0.00910.3410.0360.0360.0000.0000.0000.000
15A75PRO00.0180.03512.968-0.040-0.0400.0000.0000.0000.000
16A76ILE0-0.014-0.00214.0990.0760.0760.0000.0000.0000.000
17A77TYR00.005-0.02313.360-0.038-0.0380.0000.0000.0000.000
18A78PRO00.0230.00314.5740.0280.0280.0000.0000.0000.000
19A79HIS00.0630.03910.144-0.104-0.1040.0000.0000.0000.000
20A80ILE0-0.030-0.0059.5680.0510.0510.0000.0000.0000.000
21A81SER0-0.012-0.03611.032-0.013-0.0130.0000.0000.0000.000
22A82GLU-1-0.852-0.91712.0020.2950.2950.0000.0000.0000.000
23A83GLN0-0.012-0.0047.4090.1650.1650.0000.0000.0000.000
24A84ILE0-0.0230.0018.817-0.106-0.1060.0000.0000.0000.000
25A85ILE00.0310.01310.466-0.104-0.1040.0000.0000.0000.000
26A86SER0-0.027-0.0239.887-0.059-0.0590.0000.0000.0000.000
27A87GLN0-0.056-0.0455.325-0.391-0.3910.0000.0000.0000.000
28A88LEU00.0080.0049.131-0.097-0.0970.0000.0000.0000.000
29A89LEU00.0100.00912.525-0.026-0.0260.0000.0000.0000.000
30A90TYR00.000-0.0039.3900.0060.0060.0000.0000.0000.000
31A91LEU00.0100.0058.822-0.030-0.0300.0000.0000.0000.000
32A92GLU-1-0.711-0.81712.667-0.134-0.1340.0000.0000.0000.000
33A93TYR0-0.044-0.02615.3950.0300.0300.0000.0000.0000.000
34A94GLU-1-0.829-0.86113.008-0.390-0.3900.0000.0000.0000.000
35A95SER0-0.027-0.05015.5020.0250.0250.0000.0000.0000.000
36A96LYS10.7740.88517.5740.1320.1320.0000.0000.0000.000
37A97ARG10.9790.98620.3750.1160.1160.0000.0000.0000.000
38A98LYS10.8400.92414.9790.3620.3620.0000.0000.0000.000
39A99PRO00.0110.00916.131-0.025-0.0250.0000.0000.0000.000
40A100ILE0-0.0030.01410.824-0.059-0.0590.0000.0000.0000.000
41A101HIS00.0030.01510.5320.1060.1060.0000.0000.0000.000
42A102LEU00.0510.0239.653-0.089-0.0890.0000.0000.0000.000
43A103TYR00.013-0.0039.1460.0620.0620.0000.0000.0000.000
44A104ILE0-0.011-0.00810.4650.0910.0910.0000.0000.0000.000
45A105ASN0-0.039-0.02412.618-0.047-0.0470.0000.0000.0000.000
46A106SER0-0.019-0.02813.9790.0380.0380.0000.0000.0000.000
47A107THR0-0.012-0.03715.823-0.027-0.0270.0000.0000.0000.000
48A108GLY00.0380.02817.771-0.023-0.0230.0000.0000.0000.000
49A109ASP-1-0.795-0.87618.3460.1710.1710.0000.0000.0000.000
50A110ILE0-0.0070.00020.418-0.006-0.0060.0000.0000.0000.000
51A111ASP-1-0.772-0.87819.0900.2660.2660.0000.0000.0000.000
52A112ASN0-0.021-0.01821.710-0.028-0.0280.0000.0000.0000.000
53A113ASN0-0.0040.00324.658-0.006-0.0060.0000.0000.0000.000
54A114LYS10.8690.93424.488-0.131-0.1310.0000.0000.0000.000
55A115ILE00.0390.02323.9560.0090.0090.0000.0000.0000.000
56A116ILE0-0.049-0.01718.019-0.003-0.0030.0000.0000.0000.000
57A117ASN00.002-0.03417.6590.0010.0010.0000.0000.0000.000
58A118LEU0-0.016-0.01320.818-0.012-0.0120.0000.0000.0000.000
59A119ASN00.0510.04121.463-0.020-0.0200.0000.0000.0000.000
60A120GLY00.0520.02520.282-0.004-0.0040.0000.0000.0000.000
61A121ILE0-0.004-0.00321.091-0.003-0.0030.0000.0000.0000.000
62A122THR00.0340.00523.162-0.009-0.0090.0000.0000.0000.000
63A123ASP-1-0.811-0.85617.9620.1610.1610.0000.0000.0000.000
64A124VAL0-0.017-0.02118.712-0.007-0.0070.0000.0000.0000.000
65A125ILE0-0.029-0.00919.768-0.017-0.0170.0000.0000.0000.000
66A126SER0-0.012-0.01719.405-0.015-0.0150.0000.0000.0000.000
67A127ILE0-0.043-0.01714.909-0.010-0.0100.0000.0000.0000.000
68A128VAL0-0.008-0.01317.730-0.022-0.0220.0000.0000.0000.000
69A129ASP-1-0.814-0.87220.412-0.009-0.0090.0000.0000.0000.000
70A130VAL0-0.017-0.01316.219-0.012-0.0120.0000.0000.0000.000
71A131ILE0-0.042-0.02415.803-0.020-0.0200.0000.0000.0000.000
72A132ASN0-0.076-0.05219.108-0.014-0.0140.0000.0000.0000.000
73A133TYR0-0.105-0.06221.514-0.001-0.0010.0000.0000.0000.000
74A134ILE0-0.067-0.01716.531-0.008-0.0080.0000.0000.0000.000
75A135SER0-0.037-0.02620.5140.0060.0060.0000.0000.0000.000
76A136SER0-0.056-0.04916.783-0.010-0.0100.0000.0000.0000.000
77A137ASP-1-0.748-0.84718.369-0.104-0.1040.0000.0000.0000.000
78A138VAL00.001-0.00114.871-0.035-0.0350.0000.0000.0000.000
79A139TYR0-0.045-0.02215.2450.0240.0240.0000.0000.0000.000
80A140THR0-0.002-0.01414.422-0.027-0.0270.0000.0000.0000.000
81A141TYR0-0.012-0.01413.1380.0060.0060.0000.0000.0000.000
82A142CYS0-0.0100.00814.2370.0330.0330.0000.0000.0000.000
83A143LEU0-0.005-0.01811.718-0.018-0.0180.0000.0000.0000.000
84A144GLY00.0090.00615.5850.0120.0120.0000.0000.0000.000
85A145LYS10.9090.98117.118-0.216-0.2160.0000.0000.0000.000
86A146ALA00.0730.03217.0920.0200.0200.0000.0000.0000.000
87A147TYR0-0.0050.00219.137-0.012-0.0120.0000.0000.0000.000
88A148GLY00.0910.04920.8380.0150.0150.0000.0000.0000.000
89A149ILE0-0.015-0.00418.922-0.009-0.0090.0000.0000.0000.000
90A150ALA00.0270.01216.984-0.004-0.0040.0000.0000.0000.000
91A151CYS0-0.0370.00918.342-0.017-0.0170.0000.0000.0000.000
92A152ILE00.0160.01521.216-0.014-0.0140.0000.0000.0000.000
93A153LEU00.0000.02314.068-0.013-0.0130.0000.0000.0000.000
94A154ALA00.0280.00317.500-0.021-0.0210.0000.0000.0000.000
95A155SER0-0.0200.00218.415-0.021-0.0210.0000.0000.0000.000
96A156SER0-0.016-0.03219.442-0.008-0.0080.0000.0000.0000.000
97A157GLY0-0.0120.00918.649-0.009-0.0090.0000.0000.0000.000
98A158LYS10.7960.88219.2900.1010.1010.0000.0000.0000.000
99A159LYS10.8220.88721.7230.0160.0160.0000.0000.0000.000
100A160GLY00.0080.00624.773-0.005-0.0050.0000.0000.0000.000
101A161TYR0-0.061-0.03819.771-0.001-0.0010.0000.0000.0000.000
102A162ARG10.7410.85919.0900.0080.0080.0000.0000.0000.000
103A163PHE00.0250.00617.9080.0040.0040.0000.0000.0000.000
104A164SER00.0340.00518.7920.0170.0170.0000.0000.0000.000
105A165LEU0-0.0100.00416.499-0.012-0.0120.0000.0000.0000.000
106A166LYS11.0101.00420.1980.0110.0110.0000.0000.0000.000
107A167ASN0-0.010-0.01522.382-0.003-0.0030.0000.0000.0000.000
108A168SER0-0.057-0.02918.8720.0120.0120.0000.0000.0000.000
109A169SER0-0.031-0.00521.421-0.008-0.0080.0000.0000.0000.000
110A170PHE00.010-0.02020.2720.0150.0150.0000.0000.0000.000
111A171CYS0-0.056-0.02423.461-0.004-0.0040.0000.0000.0000.000
112A172LEU0-0.0080.00824.6340.0070.0070.0000.0000.0000.000
113A173ASN00.0520.00825.036-0.004-0.0040.0000.0000.0000.000
114A174GLN00.0350.03328.501-0.005-0.0050.0000.0000.0000.000
115A175SER0-0.016-0.01930.9940.0060.0060.0000.0000.0000.000
116A176TYR0-0.095-0.08224.226-0.008-0.0080.0000.0000.0000.000
117A177SER0-0.010-0.02129.955-0.005-0.0050.0000.0000.0000.000
118A178ILE0-0.0030.00826.4780.0000.0000.0000.0000.0000.000
119A179ILE00.0110.01029.910-0.003-0.0030.0000.0000.0000.000
120A180PRO0-0.008-0.00828.1060.0020.0020.0000.0000.0000.000
121A181PHE00.0000.00530.547-0.005-0.0050.0000.0000.0000.000
122A182ASN0-0.020-0.01030.386-0.006-0.0060.0000.0000.0000.000
123A183GLN00.0480.02333.5660.0020.0020.0000.0000.0000.000
124A184ALA00.0230.02334.6350.0000.0000.0000.0000.0000.000
125A185THR0-0.009-0.01735.919-0.002-0.0020.0000.0000.0000.000
126A186ASN00.0080.00637.524-0.003-0.0030.0000.0000.0000.000
127A187ILE00.0970.04537.7850.0010.0010.0000.0000.0000.000
128A188GLU-1-0.854-0.89939.0110.0270.0270.0000.0000.0000.000
129A189ILE0-0.020-0.02235.035-0.001-0.0010.0000.0000.0000.000
130A190GLN00.0800.04033.095-0.003-0.0030.0000.0000.0000.000
131A191ASN0-0.036-0.03134.8030.0020.0020.0000.0000.0000.000
132A192LYS10.8900.93636.730-0.027-0.0270.0000.0000.0000.000
133A193GLU-1-0.908-0.94029.9640.0550.0550.0000.0000.0000.000
134A194ILE0-0.0020.00331.9550.0010.0010.0000.0000.0000.000
135A195MET00.0020.00132.8170.0000.0000.0000.0000.0000.000
136A196ASN0-0.058-0.04232.454-0.004-0.0040.0000.0000.0000.000
137A197THR0-0.025-0.01227.409-0.001-0.0010.0000.0000.0000.000
138A198LYS10.8610.91429.547-0.051-0.0510.0000.0000.0000.000
139A199LYS10.8290.89631.897-0.020-0.0200.0000.0000.0000.000
140A200LYS10.9880.98727.830-0.034-0.0340.0000.0000.0000.000
141A201VAL00.0140.01526.387-0.003-0.0030.0000.0000.0000.000
142A202ILE00.0380.02528.303-0.002-0.0020.0000.0000.0000.000
143A203GLU-1-0.820-0.87430.8250.0120.0120.0000.0000.0000.000
144A204ILE0-0.008-0.00424.290-0.005-0.0050.0000.0000.0000.000
145A205ILE00.0340.01626.504-0.005-0.0050.0000.0000.0000.000
146A206SER0-0.003-0.00528.136-0.004-0.0040.0000.0000.0000.000
147A207LYS10.9150.97524.7410.0070.0070.0000.0000.0000.000
148A208ASN0-0.043-0.03923.471-0.012-0.0120.0000.0000.0000.000
149A209THR0-0.016-0.01527.005-0.003-0.0030.0000.0000.0000.000
150A210GLU-1-0.850-0.88229.443-0.018-0.0180.0000.0000.0000.000
151A211LYS10.8230.90331.729-0.007-0.0070.0000.0000.0000.000
152A212ASP-1-0.874-0.92734.8670.0060.0060.0000.0000.0000.000
153A213THR00.020-0.00334.4870.0020.0020.0000.0000.0000.000
154A214ASN0-0.015-0.00336.3070.0020.0020.0000.0000.0000.000
155A215VAL00.0550.02636.2990.0020.0020.0000.0000.0000.000
156A216ILE0-0.013-0.00531.5800.0030.0030.0000.0000.0000.000
157A217SER00.009-0.01234.1210.0040.0040.0000.0000.0000.000
158A218ASN0-0.078-0.03936.0370.0010.0010.0000.0000.0000.000
159A219VAL0-0.0010.00232.7870.0020.0020.0000.0000.0000.000
160A220LEU00.0140.01829.5530.0030.0030.0000.0000.0000.000
161A221GLU-1-0.850-0.90433.4450.0330.0330.0000.0000.0000.000
162A222ARG10.7960.88634.868-0.034-0.0340.0000.0000.0000.000
163A223ASP-1-0.791-0.87030.1740.0700.0700.0000.0000.0000.000
164A224LYS10.7960.88830.402-0.035-0.0350.0000.0000.0000.000
165A225TYR0-0.003-0.02826.7190.0050.0050.0000.0000.0000.000
166A226PHE00.0030.00326.623-0.007-0.0070.0000.0000.0000.000
167A227ASN00.0420.02126.0770.0040.0040.0000.0000.0000.000
168A228ALA00.0530.01323.951-0.001-0.0010.0000.0000.0000.000
169A229ASP-1-0.883-0.94525.355-0.004-0.0040.0000.0000.0000.000
170A230GLU-1-0.825-0.90528.8520.0260.0260.0000.0000.0000.000
171A231ALA0-0.026-0.00724.8000.0000.0000.0000.0000.0000.000
172A232VAL0-0.0050.00226.106-0.003-0.0030.0000.0000.0000.000
173A233ASP-1-0.937-0.95428.0180.0020.0020.0000.0000.0000.000
174A234PHE00.014-0.01329.382-0.001-0.0010.0000.0000.0000.000
175A235LYS10.8700.93128.2160.0100.0100.0000.0000.0000.000
176A236LEU0-0.018-0.00924.435-0.001-0.0010.0000.0000.0000.000
177A237ILE0-0.052-0.03020.4620.0010.0010.0000.0000.0000.000
178A238ASP-1-0.788-0.86323.436-0.036-0.0360.0000.0000.0000.000
179A239HIS0-0.017-0.00723.1990.0030.0030.0000.0000.0000.000
180A240ILE00.006-0.00122.8660.0030.0030.0000.0000.0000.000
181A241LEU0-0.064-0.02717.439-0.008-0.0080.0000.0000.0000.000
182A242GLU-1-0.923-0.96621.820-0.033-0.0330.0000.0000.0000.000
183A243LYS10.9350.97321.3990.0650.0650.0000.0000.0000.000