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: XYNM2

Calculation Name: 3GMG-A-Xray33

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GMG

Chain ID: A

ChEMBL ID:

UniProt ID: P9WFG3

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1362184.880326
FMO2-HF: Nuclear repulsion 1303809.101835
FMO2-HF: Total energy -58375.778491
FMO2-MP2: Total energy -58543.810221


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:148:ACE)


Summations of interaction energy for fragment #1(A:148:ACE)
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.
1.9543.410.503-0.801-1.158-0.004
Interaction energy analysis for fragmet #1(A:148:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.008
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].
3A150ARG11.0050.9973.8501.2642.054-0.010-0.335-0.4450.000
4A151LEU00.0570.0253.693-0.0200.1990.004-0.051-0.1720.000
5A152ALA00.0520.0304.7180.1180.160-0.001-0.008-0.0330.000
6A153ALA00.0410.0276.5410.1970.1970.0000.0000.0000.000
7A154LEU0-0.030-0.0198.6920.1060.1060.0000.0000.0000.000
8A155SER00.022-0.0028.2520.0920.0920.0000.0000.0000.000
9A156ILE00.0280.01810.5860.0370.0370.0000.0000.0000.000
10A157LEU0-0.0290.01112.5990.0400.0400.0000.0000.0000.000
11A158VAL0-0.031-0.01113.4640.0240.0240.0000.0000.0000.000
12A159GLY00.0660.03915.2830.0230.0230.0000.0000.0000.000
13A160ALA0-0.047-0.02212.3710.0190.0190.0000.0000.0000.000
14A161VAL0-0.016-0.01010.0890.0290.0290.0000.0000.0000.000
15A162GLY00.0240.01713.240-0.020-0.0200.0000.0000.0000.000
16A163ALA0-0.018-0.01013.251-0.044-0.0440.0000.0000.0000.000
17A164THR00.002-0.01514.9210.0320.0320.0000.0000.0000.000
18A165GLY00.0360.02516.287-0.046-0.0460.0000.0000.0000.000
19A166PRO00.0380.03218.8790.0230.0230.0000.0000.0000.000
20A167GLY00.0620.01822.068-0.008-0.0080.0000.0000.0000.000
21A168VAL0-0.041-0.01824.5820.0070.0070.0000.0000.0000.000
22A169MET0-0.0050.00626.848-0.002-0.0020.0000.0000.0000.000
23A170ILE0-0.0100.00029.2880.0030.0030.0000.0000.0000.000
24A171THR00.0260.02332.1120.0020.0020.0000.0000.0000.000
25A172ILE0-0.017-0.00834.8290.0000.0000.0000.0000.0000.000
26A173ASP-1-0.810-0.87537.330-0.024-0.0240.0000.0000.0000.000
27A174ASP-1-0.733-0.87140.539-0.023-0.0230.0000.0000.0000.000
28A175PRO00.0200.01142.5910.0020.0020.0000.0000.0000.000
29A176GLY0-0.0490.01545.8600.0010.0010.0000.0000.0000.000
30A177PRO0-0.039-0.01443.7440.0010.0010.0000.0000.0000.000
31A178GLY00.013-0.02744.4850.0010.0010.0000.0000.0000.000
32A179VAL0-0.051-0.02138.5390.0000.0000.0000.0000.0000.000
33A180ALA00.0450.01840.8120.0010.0010.0000.0000.0000.000
34A181PRO00.020-0.00537.280-0.002-0.0020.0000.0000.0000.000
35A182GLU-1-0.872-0.93336.524-0.022-0.0220.0000.0000.0000.000
36A183VAL00.0320.02737.264-0.003-0.0030.0000.0000.0000.000
37A184MET00.0030.00432.433-0.005-0.0050.0000.0000.0000.000
38A185ILE0-0.040-0.02132.575-0.004-0.0040.0000.0000.0000.000
39A186ASP-1-0.812-0.89532.568-0.040-0.0400.0000.0000.0000.000
40A187VAL0-0.020-0.00530.806-0.005-0.0050.0000.0000.0000.000
41A188ILE0-0.022-0.00927.195-0.007-0.0070.0000.0000.0000.000
42A189ASN00.008-0.01328.489-0.010-0.0100.0000.0000.0000.000
43A190GLU-1-0.697-0.81730.204-0.054-0.0540.0000.0000.0000.000
44A191LEU0-0.023-0.01726.846-0.006-0.0060.0000.0000.0000.000
45A192ARG10.8340.91124.8460.0500.0500.0000.0000.0000.000
46A193ALA00.0070.01326.213-0.008-0.0080.0000.0000.0000.000
47A194ALA0-0.034-0.00628.157-0.005-0.0050.0000.0000.0000.000
48A195GLY00.0260.02124.211-0.008-0.0080.0000.0000.0000.000
49A196ALA0-0.0130.00422.435-0.016-0.0160.0000.0000.0000.000
50A197GLU-1-0.844-0.90217.467-0.253-0.2530.0000.0000.0000.000
51A198ALA0-0.018-0.01517.676-0.006-0.0060.0000.0000.0000.000
52A199ILE00.0210.01019.7170.0020.0020.0000.0000.0000.000
53A200GLN0-0.011-0.01522.2240.0000.0000.0000.0000.0000.000
54A201ILE00.0120.00624.370-0.002-0.0020.0000.0000.0000.000
55A202ASN00.0260.02326.6530.0060.0060.0000.0000.0000.000
56A203ASP-1-0.708-0.83629.641-0.018-0.0180.0000.0000.0000.000
57A204ALA0-0.031-0.01632.182-0.001-0.0010.0000.0000.0000.000
58A205HIS0-0.036-0.00933.0380.0010.0010.0000.0000.0000.000
59A206ARG10.8330.91129.8840.0130.0130.0000.0000.0000.000
60A207SER00.0390.01425.468-0.003-0.0030.0000.0000.0000.000
61A208VAL0-0.039-0.01425.4890.0070.0070.0000.0000.0000.000
62A209ARG10.7790.88415.4720.0940.0940.0000.0000.0000.000
63A210VAL00.0280.01622.5550.0090.0090.0000.0000.0000.000
64A211GLY00.0430.01221.577-0.011-0.0110.0000.0000.0000.000
65A212VAL00.0160.01222.1700.0020.0020.0000.0000.0000.000
66A213ASP-1-0.782-0.86324.031-0.008-0.0080.0000.0000.0000.000
67A214THR0-0.046-0.03525.7270.0020.0020.0000.0000.0000.000
68A215TRP00.0100.01427.476-0.002-0.0020.0000.0000.0000.000
69A216VAL00.028-0.00131.2550.0000.0000.0000.0000.0000.000
70A217VAL00.0150.01833.8400.0000.0000.0000.0000.0000.000
71A218GLY00.0120.01037.263-0.001-0.0010.0000.0000.0000.000
72A219VAL0-0.001-0.00940.0640.0000.0000.0000.0000.0000.000
73A220PRO00.0170.01541.3580.0000.0000.0000.0000.0000.000
74A221GLY00.0230.00441.5510.0020.0020.0000.0000.0000.000
75A222SER0-0.040-0.01539.4700.0010.0010.0000.0000.0000.000
76A223LEU00.0380.03935.8900.0010.0010.0000.0000.0000.000
77A224THR0-0.018-0.01933.7960.0010.0010.0000.0000.0000.000
78A225VAL00.0370.00928.967-0.001-0.0010.0000.0000.0000.000
79A226ASP-1-0.709-0.81726.479-0.017-0.0170.0000.0000.0000.000
80A227THR0-0.073-0.04329.0940.0050.0050.0000.0000.0000.000
81A228LYS10.8790.95425.8370.0070.0070.0000.0000.0000.000
82A229VAL00.0020.01131.855-0.003-0.0030.0000.0000.0000.000
83A230LEU0-0.067-0.01230.8500.0000.0000.0000.0000.0000.000
84A231SER00.001-0.00635.1930.0010.0010.0000.0000.0000.000
85A232PRO0-0.0390.02737.183-0.002-0.0020.0000.0000.0000.000
86A233PRO00.0340.00737.4190.0020.0020.0000.0000.0000.000
87A234TYR0-0.017-0.03733.4800.0010.0010.0000.0000.0000.000
88A235SER0-0.005-0.00430.150-0.003-0.0030.0000.0000.0000.000
89A236ILE0-0.014-0.00927.8630.0010.0010.0000.0000.0000.000
90A237LEU0-0.0220.00124.279-0.002-0.0020.0000.0000.0000.000
91A238ALA00.029-0.00323.5530.0010.0010.0000.0000.0000.000
92A239ILE0-0.0190.01317.9830.0010.0010.0000.0000.0000.000
93A240GLY00.035-0.00121.506-0.002-0.0020.0000.0000.0000.000
94A241ASP-1-0.784-0.88422.645-0.127-0.1270.0000.0000.0000.000
95A242PRO0-0.034-0.00824.9240.0120.0120.0000.0000.0000.000
96A243PRO00.0400.02327.7100.0100.0100.0000.0000.0000.000
97A244THR0-0.010-0.02328.0030.0100.0100.0000.0000.0000.000
98A245LEU0-0.029-0.00524.7480.0080.0080.0000.0000.0000.000
99A246ALA00.008-0.00229.3100.0070.0070.0000.0000.0000.000
100A247ALA0-0.022-0.01232.5170.0070.0070.0000.0000.0000.000
101A248ALA00.0100.00731.5900.0050.0050.0000.0000.0000.000
102A249MET0-0.018-0.00331.5210.0060.0060.0000.0000.0000.000
103A250ASN0-0.056-0.02534.9860.0070.0070.0000.0000.0000.000
104A251ILE0-0.0180.02635.4060.0020.0020.0000.0000.0000.000
105A252PRO00.006-0.00439.0270.0010.0010.0000.0000.0000.000
106A253GLY0-0.017-0.01541.729-0.001-0.0010.0000.0000.0000.000
107A254GLY00.0350.04138.6320.0010.0010.0000.0000.0000.000
108A255ALA00.002-0.01836.1490.0030.0030.0000.0000.0000.000
109A256GLN00.0140.00038.1090.0040.0040.0000.0000.0000.000
110A257ASP-1-0.791-0.89239.483-0.034-0.0340.0000.0000.0000.000
111A258GLY00.0250.01641.5590.0030.0030.0000.0000.0000.000
112A259VAL00.0080.00538.6530.0020.0020.0000.0000.0000.000
113A260LYS10.8430.93841.9760.0390.0390.0000.0000.0000.000
114A261ARG10.9120.97544.2000.0290.0290.0000.0000.0000.000
115A262VAL0-0.0390.00444.0270.0020.0020.0000.0000.0000.000
116A263GLY00.0370.04147.0660.0010.0010.0000.0000.0000.000
117A264GLY00.0620.05343.2490.0000.0000.0000.0000.0000.000
118A265ARG10.9300.97241.8010.0320.0320.0000.0000.0000.000
119A266MET00.0070.01335.604-0.001-0.0010.0000.0000.0000.000
120A267VAL0-0.0270.00336.0200.0010.0010.0000.0000.0000.000
121A268VAL00.0050.00232.409-0.002-0.0020.0000.0000.0000.000
122A269GLN0-0.061-0.02830.9830.0060.0060.0000.0000.0000.000
123A270GLN00.0230.00329.464-0.010-0.0100.0000.0000.0000.000
124A271ALA00.0230.01826.6060.0060.0060.0000.0000.0000.000
125A272ASP-1-0.827-0.90524.920-0.128-0.1280.0000.0000.0000.000
126A273ARG10.7740.86820.0550.1110.1110.0000.0000.0000.000
127A274VAL0-0.0090.01921.7800.0170.0170.0000.0000.0000.000
128A275ASP-1-0.771-0.85719.636-0.147-0.1470.0000.0000.0000.000
129A276VAL0-0.0090.01018.7970.0180.0180.0000.0000.0000.000
130A277THR0-0.001-0.00517.945-0.010-0.0100.0000.0000.0000.000
131A278ALA0-0.0120.01419.0350.0150.0150.0000.0000.0000.000
132A279LEU0-0.0100.00315.924-0.011-0.0110.0000.0000.0000.000
133A280ARG10.7540.86318.5380.0240.0240.0000.0000.0000.000
134A281GLN0-0.015-0.01719.5030.0200.0200.0000.0000.0000.000
135A282PRO0-0.0230.01919.191-0.007-0.0070.0000.0000.0000.000
136A283LYS10.9140.93522.099-0.005-0.0050.0000.0000.0000.000
137A284GLN0-0.008-0.00223.729-0.001-0.0010.0000.0000.0000.000
138A285HIS0-0.033-0.02521.433-0.008-0.0080.0000.0000.0000.000
139A286GLN0-0.005-0.00525.2720.0060.0060.0000.0000.0000.000
140A287TYR00.0240.00027.5900.0030.0030.0000.0000.0000.000
141A288ALA00.0270.02823.7020.0030.0030.0000.0000.0000.000
142A289GLN00.013-0.00121.6760.0080.0080.0000.0000.0000.000
143A290PRO0-0.017-0.00616.759-0.011-0.0110.0000.0000.0000.000
144A291VAL00.0160.00717.9120.0030.0030.0000.0000.0000.000
145A292NME00.0130.01416.3540.0120.0120.0000.0000.0000.000
146A1HOH00.0410.02122.2930.0040.0040.0000.0000.0000.000
147A2HOH00.000-0.01141.4820.0000.0000.0000.0000.0000.000
148A3HOH00.0080.00619.633-0.002-0.0020.0000.0000.0000.000
149A7HOH00.002-0.00233.0410.0020.0020.0000.0000.0000.000
150A8HOH00.0350.06226.2090.0030.0030.0000.0000.0000.000
151A11HOH00.0230.00041.4810.0000.0000.0000.0000.0000.000
152A14HOH00.006-0.00620.253-0.004-0.0040.0000.0000.0000.000
153A15HOH00.0230.01833.944-0.002-0.0020.0000.0000.0000.000
154A16HOH0-0.007-0.00423.972-0.002-0.0020.0000.0000.0000.000
155A18HOH00.0110.00641.1320.0010.0010.0000.0000.0000.000
156A19HOH00.0050.01740.4460.0000.0000.0000.0000.0000.000
157A23HOH00.0370.02243.165-0.001-0.0010.0000.0000.0000.000
158A24HOH0-0.004-0.00720.7700.0040.0040.0000.0000.0000.000
159A25HOH00.0240.01628.701-0.003-0.0030.0000.0000.0000.000
160A26HOH00.0260.01938.0080.0000.0000.0000.0000.0000.000
161A27HOH0-0.015-0.02222.0570.0040.0040.0000.0000.0000.000
162A30HOH0-0.018-0.02344.9230.0000.0000.0000.0000.0000.000
163A31HOH0-0.006-0.01617.012-0.004-0.0040.0000.0000.0000.000
164A32HOH00.003-0.00216.9700.0070.0070.0000.0000.0000.000
165A33HOH0-0.025-0.01539.1680.0010.0010.0000.0000.0000.000
166A36HOH00.0320.0332.9600.4100.8150.510-0.407-0.508-0.004
167A37HOH0-0.024-0.01918.7600.0060.0060.0000.0000.0000.000
168A38HOH0-0.021-0.01828.0980.0010.0010.0000.0000.0000.000
169A40HOH0-0.015-0.01216.5020.0090.0090.0000.0000.0000.000
170A41HOH0-0.087-0.09427.1310.0000.0000.0000.0000.0000.000
171A44HOH0-0.004-0.01135.1110.0000.0000.0000.0000.0000.000
172A45HOH0-0.025-0.02036.4930.0020.0020.0000.0000.0000.000
173A48HOH0-0.033-0.03218.389-0.007-0.0070.0000.0000.0000.000
174A49HOH0-0.018-0.00333.6180.0010.0010.0000.0000.0000.000
175A52HOH00.0290.02735.1280.0010.0010.0000.0000.0000.000
176A53HOH00.008-0.00422.657-0.003-0.0030.0000.0000.0000.000
177A54HOH0-0.035-0.02434.5350.0000.0000.0000.0000.0000.000
178A56HOH0-0.031-0.02239.6950.0010.0010.0000.0000.0000.000
179A58HOH00.0320.01933.994-0.001-0.0010.0000.0000.0000.000
180A59HOH0-0.034-0.01929.966-0.001-0.0010.0000.0000.0000.000
181A62HOH0-0.024-0.02143.9560.0000.0000.0000.0000.0000.000
182A68HOH0-0.082-0.05620.4020.0050.0050.0000.0000.0000.000
183A70HOH0-0.034-0.02726.953-0.003-0.0030.0000.0000.0000.000
184A71HOH0-0.008-0.01634.5870.0000.0000.0000.0000.0000.000
185A72HOH0-0.016-0.00418.8200.0000.0000.0000.0000.0000.000
186A74HOH0-0.043-0.04532.2860.0010.0010.0000.0000.0000.000
187A75HOH0-0.038-0.03345.7260.0000.0000.0000.0000.0000.000
188A76HOH0-0.064-0.03922.846-0.001-0.0010.0000.0000.0000.000
189A84HOH0-0.027-0.01929.492-0.001-0.0010.0000.0000.0000.000
190A85HOH0-0.0010.01539.1060.0000.0000.0000.0000.0000.000
191A86HOH00.0280.02021.642-0.005-0.0050.0000.0000.0000.000
192A87HOH0-0.039-0.02127.2410.0020.0020.0000.0000.0000.000
193A88HOH00.0520.03328.4810.0010.0010.0000.0000.0000.000
194A93HOH0-0.016-0.00737.0320.0000.0000.0000.0000.0000.000
195A99HOH0-0.019-0.01836.6110.0010.0010.0000.0000.0000.000
196A100HOH0-0.039-0.03631.7020.0010.0010.0000.0000.0000.000
197A101HOH0-0.010-0.00942.2490.0010.0010.0000.0000.0000.000
198A108HOH0-0.026-0.01937.2520.0010.0010.0000.0000.0000.000
199A118HOH0-0.021-0.01930.393-0.002-0.0020.0000.0000.0000.000
200A119HOH0-0.015-0.01737.8430.0000.0000.0000.0000.0000.000
201A124HOH0-0.047-0.04536.6150.0000.0000.0000.0000.0000.000
202A125HOH0-0.044-0.04244.2330.0010.0010.0000.0000.0000.000
203A127HOH0-0.003-0.00935.303-0.001-0.0010.0000.0000.0000.000
204A301HOH0-0.027-0.01116.7030.0080.0080.0000.0000.0000.000
205A303HOH00.0180.01013.751-0.002-0.0020.0000.0000.0000.000
206A304HOH00.0510.03021.473-0.003-0.0030.0000.0000.0000.000
207A305HOH0-0.042-0.03148.2870.0000.0000.0000.0000.0000.000
208A306HOH00.0010.00727.857-0.003-0.0030.0000.0000.0000.000
209A307HOH00.000-0.00545.8690.0000.0000.0000.0000.0000.000
210A308HOH0-0.021-0.02141.1790.0010.0010.0000.0000.0000.000
211A310HOH00.0180.00336.5210.0010.0010.0000.0000.0000.000
212A311HOH0-0.038-0.02024.5480.0000.0000.0000.0000.0000.000
213A312HOH0-0.048-0.03346.1460.0000.0000.0000.0000.0000.000
214A313HOH0-0.028-0.02422.983-0.007-0.0070.0000.0000.0000.000
215A314HOH0-0.051-0.03643.6620.0000.0000.0000.0000.0000.000
216A315HOH0-0.047-0.03739.100-0.001-0.0010.0000.0000.0000.000
217A317HOH0-0.041-0.02237.3760.0010.0010.0000.0000.0000.000
218A318HOH0-0.048-0.04244.6000.0000.0000.0000.0000.0000.000
219A319HOH0-0.025-0.0189.2610.0410.0410.0000.0000.0000.000
220A320HOH00.0310.02334.744-0.002-0.0020.0000.0000.0000.000
221A321HOH0-0.027-0.01823.8820.0030.0030.0000.0000.0000.000
222A322HOH0-0.030-0.03422.846-0.001-0.0010.0000.0000.0000.000
223A323HOH0-0.046-0.03045.8570.0010.0010.0000.0000.0000.000
224A324HOH0-0.047-0.03745.085-0.001-0.0010.0000.0000.0000.000
225A326HOH0-0.042-0.03010.6360.0240.0240.0000.0000.0000.000
226A327HOH00.0270.02323.7620.0020.0020.0000.0000.0000.000
227A329HOH0-0.034-0.02337.1720.0000.0000.0000.0000.0000.000
228A330HOH0-0.034-0.03540.7900.0010.0010.0000.0000.0000.000
229A331HOH0-0.060-0.05717.6970.0070.0070.0000.0000.0000.000
230A332HOH0-0.039-0.03634.416-0.001-0.0010.0000.0000.0000.000
231A333HOH0-0.020-0.02447.8870.0000.0000.0000.0000.0000.000
232A335HOH0-0.025-0.02429.3640.0000.0000.0000.0000.0000.000
233A337HOH0-0.055-0.02918.487-0.002-0.0020.0000.0000.0000.000
234A339HOH0-0.012-0.00923.5190.0020.0020.0000.0000.0000.000
235B22HOH00.0070.00424.3620.0010.0010.0000.0000.0000.000