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: XR838

Calculation Name: 2GDG-A-Xray26

Preferred Name: Macrophage migration inhibitory factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GDG

Chain ID: A

ChEMBL ID: CHEMBL1926491

UniProt ID: P34884

Base Structure: X-ray

Registration Date: 2018-07-26

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 223
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1097427.324238
FMO2-HF: Nuclear repulsion 1045009.388617
FMO2-HF: Total energy -52417.93562
FMO2-MP2: Total energy -52565.862769


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:PRO)


Summations of interaction energy for fragment #1(A:1: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.
-52.451-37.31214.462-12.49-17.108-0.131
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.881
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].
3A3PHE00.0380.0223.7213.0234.923-0.039-0.728-1.132-0.004
4A4ILE00.0050.0016.1881.4701.4700.0000.0000.0000.000
5A5VAL00.0350.0209.8860.8000.8000.0000.0000.0000.000
6A6ASN00.0150.02112.8891.6131.6130.0000.0000.0000.000
7A7THR00.025-0.01316.4690.3650.3650.0000.0000.0000.000
8A8ASN00.0610.05219.233-0.453-0.4530.0000.0000.0000.000
9A9VAL00.0030.00520.8780.6440.6440.0000.0000.0000.000
10A10PRO00.0710.03922.235-0.403-0.4030.0000.0000.0000.000
11A11ARG10.9170.91720.64014.52014.5200.0000.0000.0000.000
12A12ALA0-0.0120.03922.461-0.409-0.4090.0000.0000.0000.000
13A13SER00.021-0.01523.5180.3820.3820.0000.0000.0000.000
14A14VAL0-0.0410.00617.370-0.385-0.3850.0000.0000.0000.000
15A15PRO00.0410.03118.6440.1760.1760.0000.0000.0000.000
16A16GLU-1-0.916-0.96519.004-14.646-14.6460.0000.0000.0000.000
17A17GLY00.0510.04717.057-0.038-0.0380.0000.0000.0000.000
18A18PHE0-0.015-0.01914.321-1.274-1.2740.0000.0000.0000.000
19A19LEU00.0680.02111.806-1.269-1.2690.0000.0000.0000.000
20A20SER00.0290.04810.782-1.903-1.9030.0000.0000.0000.000
21A21GLU-1-0.797-0.89411.779-19.848-19.8480.0000.0000.0000.000
22A22LEU0-0.007-0.0028.623-1.551-1.5510.0000.0000.0000.000
23A23THR0-0.010-0.0157.018-3.976-3.9760.0000.0000.0000.000
24A24GLN00.0730.0587.416-3.777-3.7770.0000.0000.0000.000
25A25GLN0-0.021-0.0259.509-0.146-0.1460.0000.0000.0000.000
26A26LEU0-0.015-0.0254.216-0.658-0.505-0.001-0.014-0.1380.000
27A27ALA0-0.0030.0415.036-3.796-3.675-0.001-0.005-0.1140.000
28A28GLN0-0.001-0.0076.0530.3500.3500.0000.0000.0000.000
29A29ALA00.0090.0257.2541.1151.1150.0000.0000.0000.000
30A30THR0-0.028-0.0392.831-4.744-3.2710.175-0.650-0.998-0.006
31A31GLY00.0350.0355.1330.6960.729-0.001-0.002-0.0290.000
32A32LYS10.8300.9102.23748.56648.7903.291-0.923-2.592-0.002
33A33PRO00.0160.0114.6361.3771.466-0.001-0.012-0.0760.000
34A34ALA00.0820.0254.416-8.025-7.920-0.001-0.011-0.0930.000
35A35GLN0-0.050-0.0136.058-1.672-1.6720.0000.0000.0000.000
36A36TYR0-0.001-0.0033.3120.4161.4310.086-0.368-0.733-0.002
37A37ILE0-0.0550.0061.975-42.556-37.8155.860-5.461-5.140-0.069
38A38ALA00.0280.0263.55712.32313.0230.009-0.216-0.493-0.001
39A39VAL00.006-0.0075.459-4.602-4.6020.0000.0000.0000.000
40A40HIS0-0.008-0.0018.0192.5202.5200.0000.0000.0000.000
41A41VAL00.0370.01611.066-0.248-0.2480.0000.0000.0000.000
42A42VAL0-0.029-0.00113.9390.7730.7730.0000.0000.0000.000
43A43PRO0-0.0030.01117.0830.3010.3010.0000.0000.0000.000
44A44ASP-1-0.735-0.81820.104-12.558-12.5580.0000.0000.0000.000
45A45GLN0-0.0310.01419.6970.3900.3900.0000.0000.0000.000
46A46LEU00.0620.04923.0630.3710.3710.0000.0000.0000.000
47A47MET0-0.090-0.03218.978-0.363-0.3630.0000.0000.0000.000
48A48THR0-0.020-0.02224.5750.5330.5330.0000.0000.0000.000
49A49PHE00.0340.02219.475-0.412-0.4120.0000.0000.0000.000
50A50SER0-0.007-0.01624.8690.2440.2440.0000.0000.0000.000
51A51GLY00.0180.02527.4610.4150.4150.0000.0000.0000.000
52A52THR00.0230.00628.5660.2550.2550.0000.0000.0000.000
53A53ASN00.0370.00027.697-0.348-0.3480.0000.0000.0000.000
54A54ASP-1-0.712-0.80727.649-10.291-10.2910.0000.0000.0000.000
55A55PRO0-0.023-0.01623.774-0.406-0.4060.0000.0000.0000.000
56A56CYS0-0.0120.01921.4640.0730.0730.0000.0000.0000.000
57A57ALA00.0410.01616.193-0.367-0.3670.0000.0000.0000.000
58A58LEU00.0190.02216.0490.0630.0630.0000.0000.0000.000
59A59CYS0-0.0110.00810.883-0.437-0.4370.0000.0000.0000.000
60A60SER0-0.0040.0019.0691.7491.7490.0000.0000.0000.000
61A61LEU0-0.025-0.0013.129-2.518-2.1490.062-0.085-0.3450.000
62A62HIS00.0460.0704.1800.6080.874-0.001-0.082-0.1840.000
63A63SER0-0.032-0.0502.373-30.357-26.6175.005-4.012-4.733-0.047
64A64ILE00.0230.0443.4597.7918.0010.0190.079-0.3080.000
65A65GLY00.0540.0415.4640.0980.0980.0000.0000.0000.000
66A66LYS10.8040.8675.04625.05825.0580.0000.0000.0000.000
67A67ILE00.0480.0445.300-0.703-0.7030.0000.0000.0000.000
68A68GLY00.0580.0248.7821.8261.8260.0000.0000.0000.000
69A69GLY00.0540.05012.529-0.064-0.0640.0000.0000.0000.000
70A70ALA0-0.044-0.07914.822-0.029-0.0290.0000.0000.0000.000
71A71GLN00.027-0.0019.531-1.038-1.0380.0000.0000.0000.000
72A72ASN00.1000.0509.682-2.522-2.5220.0000.0000.0000.000
73A73ARG10.9070.96211.21015.84315.8430.0000.0000.0000.000
74A74ASN00.0210.05411.8921.5471.5470.0000.0000.0000.000
75A75TYR0-0.021-0.0176.616-0.724-0.7240.0000.0000.0000.000
76A76SER00.0640.05610.3880.1640.1640.0000.0000.0000.000
77A77LYS10.9520.98413.06416.41216.4120.0000.0000.0000.000
78A78LEU0-0.0030.0069.5200.5870.5870.0000.0000.0000.000
79A79LEU00.0180.0057.9950.3750.3750.0000.0000.0000.000
80A80CYS00.0370.02912.3580.7670.7670.0000.0000.0000.000
81A81GLY00.0290.01415.9070.9970.9970.0000.0000.0000.000
82A82LEU0-0.0010.01111.9320.4930.4930.0000.0000.0000.000
83A83LEU00.005-0.00513.7920.5070.5070.0000.0000.0000.000
84A84SER0-0.0040.01416.7850.9260.9260.0000.0000.0000.000
85A85ASP-1-0.803-0.88819.171-13.717-13.7170.0000.0000.0000.000
86A86ARG10.7660.85916.89816.66116.6610.0000.0000.0000.000
87A87LEU0-0.030-0.01116.7300.3220.3220.0000.0000.0000.000
88A88HIS00.0400.07720.4210.3890.3890.0000.0000.0000.000
89A89ILE0-0.0170.01918.3910.4110.4110.0000.0000.0000.000
90A90SER00.0540.00421.030-0.334-0.3340.0000.0000.0000.000
91A91PRO00.0540.01919.476-0.370-0.3700.0000.0000.0000.000
92A92ASP-1-0.767-0.82619.873-12.027-12.0270.0000.0000.0000.000
93A93ARG10.7360.86021.62511.97311.9730.0000.0000.0000.000
94A94VAL00.011-0.00615.360-0.503-0.5030.0000.0000.0000.000
95A95TYR0-0.0020.01616.1490.2490.2490.0000.0000.0000.000
96A96ILE0-0.027-0.0309.818-0.823-0.8230.0000.0000.0000.000
97A97ASN0-0.048-0.01311.8011.0241.0240.0000.0000.0000.000
98A98TYR00.015-0.0187.343-2.939-2.9390.0000.0000.0000.000
99A99TYR0-0.0210.0047.3892.6522.6520.0000.0000.0000.000
100A100ASP-1-0.732-0.8396.799-33.354-33.3540.0000.0000.0000.000
101A101MET0-0.053-0.0146.0653.6923.6920.0000.0000.0000.000
102A102ASN00.0660.0338.239-1.620-1.6200.0000.0000.0000.000
103A103ALA00.0610.0168.997-1.387-1.3870.0000.0000.0000.000
104A104ALA00.0410.02510.050-0.395-0.3950.0000.0000.0000.000
105A105ASN0-0.021-0.01711.2282.0122.0120.0000.0000.0000.000
106A106VAL0-0.041-0.0165.666-1.964-1.9640.0000.0000.0000.000
107A107GLY00.0170.0069.0611.0611.0610.0000.0000.0000.000
108A108TRP00.008-0.0127.858-3.019-3.0190.0000.0000.0000.000
109A109ASN00.0220.03810.0092.4192.4190.0000.0000.0000.000
110A110GLY00.0390.02212.9461.2391.2390.0000.0000.0000.000
111A111SER00.0410.04913.5432.0762.0760.0000.0000.0000.000
112A112THR0-0.037-0.04611.368-1.440-1.4400.0000.0000.0000.000
113A113PHE0-0.0110.0145.720-1.277-1.2770.0000.0000.0000.000
114A114ALA-1-0.871-0.93010.577-20.840-20.8400.0000.0000.0000.000
115A115HOH0-0.028-0.02816.9130.4450.4450.0000.0000.0000.000
116A116HOH0-0.038-0.03611.9020.5760.5760.0000.0000.0000.000
117A117HOH00.0280.02424.6130.1480.1480.0000.0000.0000.000
118A118HOH0-0.028-0.02818.396-0.178-0.1780.0000.0000.0000.000
119A119HOH00.0640.04211.295-0.224-0.2240.0000.0000.0000.000
120A120HOH00.0220.00811.2700.4250.4250.0000.0000.0000.000
121A121HOH00.0530.03711.749-0.491-0.4910.0000.0000.0000.000
122A122HOH0-0.023-0.01326.6690.0690.0690.0000.0000.0000.000
123A123HOH00.0130.00024.503-0.080-0.0800.0000.0000.0000.000
124A124HOH0-0.041-0.0357.3031.3791.3790.0000.0000.0000.000
125A126HOH0-0.056-0.05118.457-0.139-0.1390.0000.0000.0000.000
126A127HOH0-0.070-0.0519.0900.7720.7720.0000.0000.0000.000
127A128HOH0-0.012-0.02312.1480.6640.6640.0000.0000.0000.000
128A129HOH00.0030.01412.397-0.333-0.3330.0000.0000.0000.000
129A130HOH0-0.0010.00315.048-0.193-0.1930.0000.0000.0000.000
130A131HOH00.0130.01522.959-0.265-0.2650.0000.0000.0000.000
131A132HOH0-0.018-0.01821.2810.0580.0580.0000.0000.0000.000
132A133HOH0-0.048-0.02913.087-0.061-0.0610.0000.0000.0000.000
133A134HOH0-0.038-0.03117.4940.1840.1840.0000.0000.0000.000
134A135HOH0-0.055-0.05215.1020.0290.0290.0000.0000.0000.000
135A136HOH0-0.035-0.0706.4981.8521.8520.0000.0000.0000.000
136A137HOH00.0290.02211.103-0.252-0.2520.0000.0000.0000.000
137A138HOH0-0.010-0.01626.776-0.166-0.1660.0000.0000.0000.000
138A139HOH0-0.040-0.0289.865-0.810-0.8100.0000.0000.0000.000
139A140HOH0-0.031-0.02311.585-0.148-0.1480.0000.0000.0000.000
140A141HOH0-0.028-0.02624.976-0.098-0.0980.0000.0000.0000.000
141A142HOH00.0420.0219.268-0.760-0.7600.0000.0000.0000.000
142A143HOH0-0.050-0.04722.5650.2430.2430.0000.0000.0000.000
143A144HOH0-0.002-0.0077.296-0.441-0.4410.0000.0000.0000.000
144A145HOH00.0110.00326.787-0.148-0.1480.0000.0000.0000.000
145A146HOH0-0.011-0.00224.110-0.228-0.2280.0000.0000.0000.000
146A147HOH0-0.004-0.00926.2910.0330.0330.0000.0000.0000.000
147A148HOH0-0.005-0.00910.4140.8370.8370.0000.0000.0000.000
148A149HOH00.0150.00611.056-0.543-0.5430.0000.0000.0000.000
149A150HOH00.0010.00726.6370.1020.1020.0000.0000.0000.000
150A151HOH00.0140.00414.350-0.442-0.4420.0000.0000.0000.000
151A152HOH0-0.015-0.00911.8550.1950.1950.0000.0000.0000.000
152A153HOH0-0.057-0.02926.4420.1460.1460.0000.0000.0000.000
153A154HOH00.0250.0178.964-1.373-1.3730.0000.0000.0000.000
154A155HOH00.0160.01815.370-0.124-0.1240.0000.0000.0000.000
155A156HOH0-0.037-0.02522.1380.0160.0160.0000.0000.0000.000
156A157HOH00.0480.04113.144-0.531-0.5310.0000.0000.0000.000
157A158HOH0-0.035-0.0247.9461.1111.1110.0000.0000.0000.000
158A159HOH0-0.007-0.02126.5840.0220.0220.0000.0000.0000.000
159A160HOH0-0.004-0.00810.786-0.851-0.8510.0000.0000.0000.000
160A161HOH0-0.021-0.01615.062-0.127-0.1270.0000.0000.0000.000
161A162HOH00.0250.0198.536-0.707-0.7070.0000.0000.0000.000
162A163HOH0-0.028-0.02223.9010.0750.0750.0000.0000.0000.000
163A164HOH0-0.028-0.01930.2370.1090.1090.0000.0000.0000.000
164A165HOH00.0320.01920.022-0.292-0.2920.0000.0000.0000.000
165A166HOH0-0.021-0.00525.5910.0270.0270.0000.0000.0000.000
166A167HOH0-0.039-0.02710.1860.3640.3640.0000.0000.0000.000
167A168HOH0-0.057-0.06215.7140.4370.4370.0000.0000.0000.000
168A169HOH0-0.041-0.02623.3260.0710.0710.0000.0000.0000.000
169A170HOH0-0.008-0.0187.1441.3571.3570.0000.0000.0000.000
170A172HOH0-0.027-0.01631.2130.0510.0510.0000.0000.0000.000
171A173HOH0-0.020-0.00215.6730.1500.1500.0000.0000.0000.000
172A174HOH0-0.020-0.02115.3590.4370.4370.0000.0000.0000.000
173A175HOH00.0300.02216.007-0.405-0.4050.0000.0000.0000.000
174A176HOH0-0.045-0.05022.9710.1060.1060.0000.0000.0000.000
175A177HOH0-0.048-0.0339.616-0.037-0.0370.0000.0000.0000.000
176A179HOH0-0.034-0.01720.6800.0550.0550.0000.0000.0000.000
177A181HOH0-0.0110.01430.017-0.113-0.1130.0000.0000.0000.000
178A182HOH0-0.043-0.06926.0210.1830.1830.0000.0000.0000.000
179A183HOH0-0.056-0.04026.669-0.056-0.0560.0000.0000.0000.000
180A184HOH0-0.021-0.03120.184-0.316-0.3160.0000.0000.0000.000
181A185HOH0-0.026-0.01714.6990.0410.0410.0000.0000.0000.000
182A186HOH00.0260.02120.195-0.012-0.0120.0000.0000.0000.000
183A187HOH00.0350.02123.084-0.147-0.1470.0000.0000.0000.000
184A189HOH0-0.009-0.01616.8300.2850.2850.0000.0000.0000.000
185A191HOH0-0.012-0.0127.7391.8711.8710.0000.0000.0000.000
186A192HOH0-0.061-0.03511.159-0.738-0.7380.0000.0000.0000.000
187A194HOH0-0.031-0.02515.7940.1460.1460.0000.0000.0000.000
188A195HOH0-0.034-0.02811.4670.6340.6340.0000.0000.0000.000
189A196HOH0-0.0130.00219.6180.0830.0830.0000.0000.0000.000
190A197HOH00.0320.01116.867-0.021-0.0210.0000.0000.0000.000
191A199HOH0-0.0130.00417.667-0.448-0.4480.0000.0000.0000.000
192A200HOH0-0.036-0.03011.0790.3170.3170.0000.0000.0000.000
193A201HOH00.0390.0308.741-0.209-0.2090.0000.0000.0000.000
194A202HOH0-0.079-0.06928.751-0.097-0.0970.0000.0000.0000.000
195A203HOH0-0.051-0.04222.4670.2410.2410.0000.0000.0000.000
196A204HOH0-0.040-0.03610.0930.5800.5800.0000.0000.0000.000
197A205HOH0-0.011-0.02826.262-0.117-0.1170.0000.0000.0000.000
198A206HOH0-0.044-0.03426.529-0.051-0.0510.0000.0000.0000.000
199A232HOH00.0310.01919.973-0.204-0.2040.0000.0000.0000.000
200A237HOH0-0.004-0.00913.3910.5260.5260.0000.0000.0000.000
201A239HOH0-0.031-0.02217.8220.2940.2940.0000.0000.0000.000
202A242HOH00.0180.01510.130-0.549-0.5490.0000.0000.0000.000
203A245HOH00.0000.00725.2320.1110.1110.0000.0000.0000.000
204A247HOH00.0020.0169.938-0.062-0.0620.0000.0000.0000.000
205A251HOH0-0.031-0.01027.2260.1620.1620.0000.0000.0000.000
206A252HOH00.0170.01127.699-0.145-0.1450.0000.0000.0000.000
207A253HOH0-0.040-0.03516.1600.4010.4010.0000.0000.0000.000
208A256HOH00.0320.02216.751-0.384-0.3840.0000.0000.0000.000
209A258HOH00.0150.0299.1160.0050.0050.0000.0000.0000.000
210A259HOH00.0310.01714.493-0.528-0.5280.0000.0000.0000.000
211A263HOH0-0.032-0.02132.9390.0770.0770.0000.0000.0000.000
212A264HOH0-0.023-0.02323.4080.1940.1940.0000.0000.0000.000
213A266HOH0-0.021-0.02924.3220.1400.1400.0000.0000.0000.000
214A267HOH0-0.029-0.02420.8630.2910.2910.0000.0000.0000.000
215A269HOH0-0.062-0.05512.1730.5940.5940.0000.0000.0000.000
216A272HOH0-0.056-0.03725.8240.1060.1060.0000.0000.0000.000
217A278HOH0-0.036-0.02227.1720.0210.0210.0000.0000.0000.000
218A279HOH0-0.021-0.02125.6780.1070.1070.0000.0000.0000.000
219B116HOH00.004-0.00526.8630.0440.0440.0000.0000.0000.000
220B117HOH0-0.003-0.00223.1220.1720.1720.0000.0000.0000.000
221B137HOH0-0.028-0.00815.0040.0140.0140.0000.0000.0000.000
222C163HOH00.007-0.0107.8260.8590.8590.0000.0000.0000.000
223C186HOH0-0.008-0.00410.7510.9720.9720.0000.0000.0000.000