Manual

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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: PL7Q9

Calculation Name: 1L7L-A-Xray30

Preferred Name: PA-I galactophilic lectin

Target Type: SINGLE PROTEIN

Ligand Name: calcium ion

ligand 3-letter code: CA

PDB ID: 1L7L

Chain ID: A

ChEMBL ID: CHEMBL3351196

UniProt ID: Q05097

Base Structure: X-ray

Registration Date: 2018-09-06

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 205
LigandCharge CA+=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1129908.05812
FMO2-HF: Nuclear repulsion 1078157.124832
FMO2-HF: Total energy -51750.933287
FMO2-MP2: Total energy -51897.698621


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-35.372-29.2123.01-4.321-4.852-0.039
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.919
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].
3A3LYS10.9981.0083.79330.42432.107-0.022-0.813-0.849-0.002
4A4GLY00.0200.0246.2571.1211.1210.0000.0000.0000.000
5A5GLU-1-0.856-0.8919.924-17.379-17.3790.0000.0000.0000.000
6A6VAL0-0.0090.00112.677-0.376-0.3760.0000.0000.0000.000
7A7LEU00.018-0.00115.2070.7200.7200.0000.0000.0000.000
8A8ALA00.0510.01318.901-0.027-0.0270.0000.0000.0000.000
9A9ASN00.1080.10721.395-0.291-0.2910.0000.0000.0000.000
10A10ASN00.0540.10117.7571.0651.0650.0000.0000.0000.000
11A11GLU-1-0.730-0.82820.505-12.158-12.1580.0000.0000.0000.000
12A12ALA0-0.0160.00320.803-0.048-0.0480.0000.0000.0000.000
13A13GLY00.0130.02417.391-0.447-0.4470.0000.0000.0000.000
14A14GLN0-0.073-0.04312.1981.5771.5770.0000.0000.0000.000
15A15VAL00.0320.02011.893-1.259-1.2590.0000.0000.0000.000
16A16THR0-0.024-0.0217.105-2.856-2.8560.0000.0000.0000.000
17A17SER0-0.038-0.0174.729-3.208-3.162-0.001-0.011-0.0350.000
18A18ILE0-0.010-0.0062.515-6.267-5.8790.670-0.383-0.675-0.003
19A19ILE00.0080.0046.2235.4625.4620.0000.0000.0000.000
20A20TYR0-0.025-0.0188.801-1.740-1.7400.0000.0000.0000.000
21A21ASN0-0.021-0.03510.2753.4863.4860.0000.0000.0000.000
22A22PRO00.0330.00312.855-0.400-0.4000.0000.0000.0000.000
23A23GLY00.0800.05515.289-0.203-0.2030.0000.0000.0000.000
24A24ASP-1-0.719-0.8249.811-30.652-30.6520.0000.0000.0000.000
25A25VAL0-0.0190.03710.7731.7181.7180.0000.0000.0000.000
26A26ILE0-0.050-0.0217.208-4.109-4.1090.0000.0000.0000.000
27A27THR00.002-0.0177.2754.7194.7190.0000.0000.0000.000
28A28ILE0-0.045-0.0216.824-5.114-5.1140.0000.0000.0000.000
29A29VAL00.0230.0228.3632.6932.6930.0000.0000.0000.000
30A30ALA0-0.004-0.0029.643-1.947-1.9470.0000.0000.0000.000
31A31ALA0-0.017-0.01212.3861.3691.3690.0000.0000.0000.000
32A32GLY00.0240.01314.900-0.562-0.5620.0000.0000.0000.000
33A33TRP00.0010.00217.8440.3720.3720.0000.0000.0000.000
34A34ALA00.0650.02720.696-0.138-0.1380.0000.0000.0000.000
35A35SER00.2260.19122.5820.4030.4030.0000.0000.0000.000
36A36TYR00.9040.74025.720-0.238-0.2380.0000.0000.0000.000
37A37GLY00.2580.05127.4400.2970.2970.0000.0000.0000.000
38A38PRO00.1130.19930.0590.2080.2080.0000.0000.0000.000
39A39THR00.0430.03230.389-0.346-0.3460.0000.0000.0000.000
40A40GLN0-0.0180.02929.208-0.034-0.0340.0000.0000.0000.000
41A41LYS10.8620.92024.13611.40611.4060.0000.0000.0000.000
42A42TRP0-0.017-0.00124.5360.1670.1670.0000.0000.0000.000
43A43GLY00.0760.03420.606-0.439-0.4390.0000.0000.0000.000
44A44PRO00.012-0.00316.3750.4080.4080.0000.0000.0000.000
45A45GLN0-0.0010.00818.699-0.503-0.5030.0000.0000.0000.000
46A46GLY00.0180.03121.3570.4020.4020.0000.0000.0000.000
47A47ASP-1-0.737-0.84323.800-9.944-9.9440.0000.0000.0000.000
48A48ARG10.8980.93027.54310.05010.0500.0000.0000.0000.000
49A49GLU-1-0.798-0.90029.174-8.836-8.8360.0000.0000.0000.000
50A50HIS00.8090.89430.2600.3770.3770.0000.0000.0000.000
51A51PRO00.0280.03531.548-0.234-0.2340.0000.0000.0000.000
52A52ASP-1-0.692-0.79929.786-10.697-10.6970.0000.0000.0000.000
53A53GLN0-0.0090.00831.6560.1660.1660.0000.0000.0000.000
54A54GLY00.0350.01531.3060.1510.1510.0000.0000.0000.000
55A55LEU0-0.0420.00426.121-0.197-0.1970.0000.0000.0000.000
56A56ILE0-0.0040.01721.0000.1060.1060.0000.0000.0000.000
57A57CYS0-0.0350.01421.038-0.214-0.2140.0000.0000.0000.000
58A58HIS10.8240.89423.98210.91010.9100.0000.0000.0000.000
59A59ASP-1-0.808-0.88023.501-11.759-11.7590.0000.0000.0000.000
60A60ALA0-0.013-0.01221.896-0.411-0.4110.0000.0000.0000.000
61A61PHE00.0270.02923.9530.3950.3950.0000.0000.0000.000
62A62CYS00.4890.50224.356-0.649-0.6490.0000.0000.0000.000
63A63GLY00.016-0.00323.4540.1570.1570.0000.0000.0000.000
64A64ALA0-0.0280.00520.578-0.449-0.4490.0000.0000.0000.000
65A65LEU0-0.031-0.01212.863-0.111-0.1110.0000.0000.0000.000
66A66VAL0-0.006-0.00317.0090.1800.1800.0000.0000.0000.000
67A67MET0-0.0120.00012.507-1.786-1.7860.0000.0000.0000.000
68A68LYS10.9590.99114.87516.08616.0860.0000.0000.0000.000
69A69ILE00.0360.01912.377-1.644-1.6440.0000.0000.0000.000
70A70GLY00.0200.01414.5161.1831.1830.0000.0000.0000.000
71A71ASN0-0.050-0.02916.464-0.357-0.3570.0000.0000.0000.000
72A72SER0-0.018-0.00317.9800.4650.4650.0000.0000.0000.000
73A73GLY00.0350.01519.9250.1590.1590.0000.0000.0000.000
74A74THR0-0.051-0.04419.177-0.765-0.7650.0000.0000.0000.000
75A75ILE00.0450.03316.0920.6360.6360.0000.0000.0000.000
76A76PRO00.0160.00017.259-0.890-0.8900.0000.0000.0000.000
77A77VAL00.0070.01512.773-0.741-0.7410.0000.0000.0000.000
78A78ASN00.0110.00115.6690.3590.3590.0000.0000.0000.000
79A79THR00.014-0.00415.710-0.849-0.8490.0000.0000.0000.000
80A80GLY0-0.001-0.00212.630-1.235-1.2350.0000.0000.0000.000
81A81LEU0-0.0260.00811.8831.3801.3800.0000.0000.0000.000
82A82PHE00.022-0.00511.483-2.110-2.1100.0000.0000.0000.000
83A83ARG10.9340.97911.70022.07022.0700.0000.0000.0000.000
84A84TRP00.0340.01712.0241.0951.0950.0000.0000.0000.000
85A85VAL00.0380.02012.439-1.776-1.7760.0000.0000.0000.000
86A86ALA0-0.0110.00014.3260.9310.9310.0000.0000.0000.000
87A87PRO00.0300.01115.9850.5440.5440.0000.0000.0000.000
88A88ASN00.0610.01618.958-0.991-0.9910.0000.0000.0000.000
89A89ASN0-0.042-0.02920.8350.1890.1890.0000.0000.0000.000
90A90VAL0-0.0140.03315.7190.0130.0130.0000.0000.0000.000
91A91GLN0-0.023-0.01414.634-0.232-0.2320.0000.0000.0000.000
92A92GLY00.0480.01113.5381.3221.3220.0000.0000.0000.000
93A93ALA00.0140.00310.939-1.796-1.7960.0000.0000.0000.000
94A94ILE00.0180.0297.6982.1032.1030.0000.0000.0000.000
95A95THR00.0000.00910.687-1.759-1.7590.0000.0000.0000.000
96A96LEU0-0.027-0.0149.5680.7720.7720.0000.0000.0000.000
97A97ILE00.0330.00013.6410.5320.5320.0000.0000.0000.000
98A98TYR00.5080.51417.3400.0490.0490.0000.0000.0000.000
99A99ASN00.0440.00919.8620.3600.3600.0000.0000.0000.000
100A100ASP-10.142-0.14622.483-10.900-10.9000.0000.0000.0000.000
101A101VAL00.4860.50525.832-0.192-0.1920.0000.0000.0000.000
102A102PRO00.4260.48927.121-0.010-0.0100.0000.0000.0000.000
103A103GLY00.1180.06228.6150.4710.4710.0000.0000.0000.000
104A104THR00.4630.40229.4440.2980.2980.0000.0000.0000.000
105A105TYR01.0340.80322.2910.1390.1390.0000.0000.0000.000
106A106GLY00.1920.17527.175-0.243-0.2430.0000.0000.0000.000
107A107ASN00.1530.08429.492-0.286-0.2860.0000.0000.0000.000
108A108ASN00.4100.17324.5760.6600.6600.0000.0000.0000.000
109A109SER00.0570.14525.0910.0560.0560.0000.0000.0000.000
110A110GLY00.0560.02322.181-0.099-0.0990.0000.0000.0000.000
111A111SER0-0.049-0.05717.153-0.067-0.0670.0000.0000.0000.000
112A112PHE00.0030.01914.7080.2540.2540.0000.0000.0000.000
113A113SER0-0.032-0.00811.647-1.726-1.7260.0000.0000.0000.000
114A114VAL00.007-0.0088.4890.6530.6530.0000.0000.0000.000
115A115ASN0-0.006-0.0045.016-6.364-6.3640.0000.0000.0000.000
116A116ILE00.0400.0164.1784.3164.488-0.001-0.042-0.1290.000
117A117GLY0-0.009-0.0122.540-24.460-21.5202.063-2.602-2.402-0.028
118A118LYS10.7970.8973.58844.88644.9150.0140.089-0.1320.000
119A119ASP-1-0.772-0.8695.792-33.037-33.0370.0000.0000.0000.000
120A120GLN0-0.007-0.0138.4780.8450.8450.0000.0000.0000.000
121A121SER-1-0.876-0.90711.395-20.492-20.4920.0000.0000.0000.000
122A201CA+2-6.221-5.01029.35921.70621.7060.0000.0000.0000.000
123A203HOH0-0.034-0.03222.1940.1890.1890.0000.0000.0000.000
124A204HOH0-0.007-0.03022.3060.0920.0920.0000.0000.0000.000
125A205HOH0-0.002-0.01122.5290.1510.1510.0000.0000.0000.000
126A206HOH0-0.017-0.01819.022-0.210-0.2100.0000.0000.0000.000
127A207HOH0-0.019-0.00410.193-0.795-0.7950.0000.0000.0000.000
128A208HOH0-0.008-0.00422.3020.0410.0410.0000.0000.0000.000
129A209HOH0-0.038-0.02827.276-0.125-0.1250.0000.0000.0000.000
130A210HOH0-0.015-0.01424.101-0.162-0.1620.0000.0000.0000.000
131A211HOH0-0.006-0.0209.887-0.587-0.5870.0000.0000.0000.000
132A212HOH00.006-0.00926.9090.0340.0340.0000.0000.0000.000
133A213HOH0-0.006-0.01322.703-0.275-0.2750.0000.0000.0000.000
134A214HOH0-0.037-0.02912.4340.4290.4290.0000.0000.0000.000
135A215HOH0-0.023-0.02830.712-0.110-0.1100.0000.0000.0000.000
136A216HOH0-0.055-0.04924.7290.1080.1080.0000.0000.0000.000
137A217HOH00.0320.01816.1920.2800.2800.0000.0000.0000.000
138A219HOH00.0230.01124.8890.1130.1130.0000.0000.0000.000
139A220HOH0-0.016-0.01627.198-0.017-0.0170.0000.0000.0000.000
140A221HOH0-0.043-0.0352.807-5.392-4.5480.288-0.542-0.589-0.006
141A222HOH0-0.025-0.01931.6830.0020.0020.0000.0000.0000.000
142A223HOH0-0.004-0.01128.2260.0810.0810.0000.0000.0000.000
143A224HOH00.002-0.00730.815-0.076-0.0760.0000.0000.0000.000
144A225HOH00.005-0.00815.4850.1260.1260.0000.0000.0000.000
145A226HOH0-0.008-0.00613.7110.0180.0180.0000.0000.0000.000
146A227HOH00.0030.00618.8060.2470.2470.0000.0000.0000.000
147A228HOH0-0.019-0.01128.681-0.159-0.1590.0000.0000.0000.000
148A229HOH0-0.041-0.03916.4360.3930.3930.0000.0000.0000.000
149A230HOH0-0.040-0.02724.425-0.140-0.1400.0000.0000.0000.000
150A231HOH00.0340.01923.5650.0230.0230.0000.0000.0000.000
151A232HOH0-0.047-0.02731.920-0.096-0.0960.0000.0000.0000.000
152A233HOH00.0210.0045.589-0.565-0.5650.0000.0000.0000.000
153A234HOH00.0110.01317.7960.1440.1440.0000.0000.0000.000
154A237HOH0-0.041-0.02815.0050.2830.2830.0000.0000.0000.000
155A239HOH00.0160.01515.917-0.590-0.5900.0000.0000.0000.000
156A240HOH00.0110.00526.8550.0460.0460.0000.0000.0000.000
157A241HOH0-0.009-0.01318.451-0.235-0.2350.0000.0000.0000.000
158A243HOH0-0.059-0.05032.2550.0750.0750.0000.0000.0000.000
159A244HOH0-0.040-0.02721.5600.2530.2530.0000.0000.0000.000
160A245HOH0-0.021-0.0109.844-0.390-0.3900.0000.0000.0000.000
161A246HOH0-0.032-0.02317.6520.1490.1490.0000.0000.0000.000
162A247HOH0-0.002-0.00431.440-0.106-0.1060.0000.0000.0000.000
163A248HOH00.003-0.00133.6480.0140.0140.0000.0000.0000.000
164A249HOH0-0.032-0.01714.295-0.004-0.0040.0000.0000.0000.000
165A250HOH0-0.039-0.03929.4930.1120.1120.0000.0000.0000.000
166A251HOH0-0.0110.00928.580-0.147-0.1470.0000.0000.0000.000
167A253HOH00.0290.01631.894-0.089-0.0890.0000.0000.0000.000
168A254HOH0-0.040-0.02815.4920.4020.4020.0000.0000.0000.000
169A256HOH0-0.015-0.01617.7250.0730.0730.0000.0000.0000.000
170A257HOH00.0090.00517.2310.2910.2910.0000.0000.0000.000
171A258HOH0-0.038-0.02835.3350.0960.0960.0000.0000.0000.000
172A259HOH0-0.024-0.01933.975-0.020-0.0200.0000.0000.0000.000
173A260HOH0-0.043-0.02632.6610.0820.0820.0000.0000.0000.000
174A261HOH0-0.055-0.0369.4010.8630.8630.0000.0000.0000.000
175A262HOH00.0290.02033.1160.1020.1020.0000.0000.0000.000
176A263HOH0-0.022-0.03028.871-0.156-0.1560.0000.0000.0000.000
177A265HOH0-0.025-0.02212.693-0.080-0.0800.0000.0000.0000.000
178A266HOH00.0290.01716.434-0.506-0.5060.0000.0000.0000.000
179A267HOH0-0.021-0.01922.509-0.225-0.2250.0000.0000.0000.000
180A268HOH0-0.009-0.00128.6360.0970.0970.0000.0000.0000.000
181A269HOH00.0380.02128.9320.0440.0440.0000.0000.0000.000
182A273HOH0-0.037-0.03329.528-0.021-0.0210.0000.0000.0000.000
183A274HOH0-0.037-0.0299.3130.4150.4150.0000.0000.0000.000
184A275HOH0-0.054-0.04022.392-0.253-0.2530.0000.0000.0000.000
185A276HOH0-0.034-0.02428.3560.1280.1280.0000.0000.0000.000
186A278HOH0-0.009-0.00811.430-0.461-0.4610.0000.0000.0000.000
187A280HOH0-0.047-0.03215.641-0.004-0.0040.0000.0000.0000.000
188A281HOH0-0.023-0.02416.782-0.069-0.0690.0000.0000.0000.000
189A282HOH0-0.003-0.00218.0390.1830.1830.0000.0000.0000.000
190A284HOH0-0.0120.0005.573-1.267-1.2670.0000.0000.0000.000
191A285HOH0-0.041-0.03333.1870.0340.0340.0000.0000.0000.000
192A286HOH0-0.013-0.01032.9610.0730.0730.0000.0000.0000.000
193A288HOH00.0140.00830.419-0.139-0.1390.0000.0000.0000.000
194A289HOH0-0.043-0.04129.906-0.111-0.1110.0000.0000.0000.000
195A290HOH0-0.018-0.02519.3690.0700.0700.0000.0000.0000.000
196A292HOH0-0.045-0.03019.5570.3260.3260.0000.0000.0000.000
197A293HOH00.0200.01415.103-0.351-0.3510.0000.0000.0000.000
198A295HOH0-0.004-0.00213.8830.7060.7060.0000.0000.0000.000
199A297HOH0-0.047-0.02727.3850.0840.0840.0000.0000.0000.000
200A299HOH0-0.013-0.00922.6540.2230.2230.0000.0000.0000.000
201A300HOH0-0.031-0.02027.061-0.043-0.0430.0000.0000.0000.000
202A302HOH0-0.008-0.0124.3694.9204.978-0.001-0.017-0.0410.000
203A306HOH0-0.023-0.03630.2990.0870.0870.0000.0000.0000.000
204A307HOH0-0.0030.02031.961-0.017-0.0170.0000.0000.0000.000
205A308HOH0-0.004-0.00628.235-0.073-0.0730.0000.0000.0000.000