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: XM99Z

Calculation Name: 3LHC-A-Xray29

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LHC

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

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 188
LigandCharge NA+=1,PO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -722225.812047
FMO2-HF: Nuclear repulsion 675664.653274
FMO2-HF: Total energy -46561.158773
FMO2-MP2: Total energy -46688.23191


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-228.778-226.01519.612-14.421-7.954-0.154
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.869
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].
3A3LYS10.9280.9482.89364.66066.4200.003-0.670-1.0930.000
4A4PHE00.0710.0396.5204.1014.1010.0000.0000.0000.000
5A5SER0-0.022-0.0059.1781.5331.5330.0000.0000.0000.000
6A6GLN00.0380.0219.6153.1083.1080.0000.0000.0000.000
7A7THR00.0270.03511.2211.8751.8750.0000.0000.0000.000
8A22CYS0-0.054-0.01013.043-0.076-0.0760.0000.0000.0000.000
9A9TYR00.0230.01915.1430.3710.3710.0000.0000.0000.000
10A10ASN00.003-0.01418.4050.0070.0070.0000.0000.0000.000
11A11SER00.0140.02815.7610.0800.0800.0000.0000.0000.000
12A12ALA00.0000.01918.1700.6800.6800.0000.0000.0000.000
13A13ILE00.0180.00715.761-0.760-0.7600.0000.0000.0000.000
14A14GLN00.0180.01419.2500.5290.5290.0000.0000.0000.000
15A15GLY0-0.015-0.00421.222-0.091-0.0910.0000.0000.0000.000
16A16SER00.005-0.01118.067-0.189-0.1890.0000.0000.0000.000
17A17VAL00.0180.02016.874-1.117-1.1170.0000.0000.0000.000
18A18LEU0-0.0140.01112.1040.3430.3430.0000.0000.0000.000
19A19THR0-0.005-0.01415.9920.0270.0270.0000.0000.0000.000
20A20SER0-0.001-0.02514.966-0.225-0.2250.0000.0000.0000.000
21A21THR0-0.0030.00417.0380.3930.3930.0000.0000.0000.000
22A23GLU-1-0.786-0.88915.190-17.322-17.3220.0000.0000.0000.000
23A24ARG10.9310.97414.80914.27014.2700.0000.0000.0000.000
24A25THR00.025-0.01515.224-0.074-0.0740.0000.0000.0000.000
25A26ASN0-0.072-0.03016.864-0.157-0.1570.0000.0000.0000.000
26A27GLY00.0530.04819.5470.7350.7350.0000.0000.0000.000
27A28GLY0-0.012-0.00521.1770.2250.2250.0000.0000.0000.000
28A29TYR0-0.007-0.01818.103-0.377-0.3770.0000.0000.0000.000
29A30ASN0-0.051-0.03817.4591.5161.5160.0000.0000.0000.000
30A31THR0-0.0030.01418.182-0.908-0.9080.0000.0000.0000.000
31A32SER0-0.073-0.01515.5220.2930.2930.0000.0000.0000.000
32A33SER00.0690.01916.574-0.027-0.0270.0000.0000.0000.000
33A34ILE0-0.0190.00310.499-0.303-0.3030.0000.0000.0000.000
34A35ASP-1-0.764-0.85014.714-15.427-15.4270.0000.0000.0000.000
35A36LEU0-0.019-0.02211.308-0.861-0.8610.0000.0000.0000.000
36A37ASN00.0520.02814.300-0.730-0.7300.0000.0000.0000.000
37A38SER0-0.0010.00815.3900.2320.2320.0000.0000.0000.000
38A39VAL0-0.073-0.0338.987-0.466-0.4660.0000.0000.0000.000
39A40ILE0-0.014-0.00910.601-1.898-1.8980.0000.0000.0000.000
40A41ALA00.0280.03213.0261.2891.2890.0000.0000.0000.000
41A42ALA0-0.005-0.01115.697-0.518-0.5180.0000.0000.0000.000
42A43VAL0-0.021-0.02016.8390.5950.5950.0000.0000.0000.000
43A44ASP-1-0.937-0.97819.412-12.277-12.2770.0000.0000.0000.000
44A45GLY00.0240.02122.1160.0790.0790.0000.0000.0000.000
45A46SER0-0.072-0.02817.202-0.457-0.4570.0000.0000.0000.000
46A47LEU00.0320.02414.8050.0020.0020.0000.0000.0000.000
47A48LYS10.8840.95212.32217.38617.3860.0000.0000.0000.000
48A49TRP00.0530.0317.5940.1880.1880.0000.0000.0000.000
49A50PRO00.0230.0307.8951.9141.9140.0000.0000.0000.000
50A51SER00.0230.0199.784-1.275-1.2750.0000.0000.0000.000
51A52ASN00.0850.06610.5842.2752.2750.0000.0000.0000.000
52A53PHE00.0750.02012.827-0.423-0.4230.0000.0000.0000.000
53A54ILE00.007-0.00213.2190.1870.1870.0000.0000.0000.000
54A55GLH0-0.075-0.0377.4801.1041.1040.0000.0000.0000.000
55A56ALA00.0010.01711.800-0.504-0.5040.0000.0000.0000.000
56A72CYS0-0.044-0.00214.2960.4640.4640.0000.0000.0000.000
57A58ARG10.9290.91917.37911.80911.8090.0000.0000.0000.000
58A59ASN00.035-0.01720.0210.2460.2460.0000.0000.0000.000
59A60THR00.0620.08920.2790.3110.3110.0000.0000.0000.000
60A61GLN00.0100.01923.3530.1150.1150.0000.0000.0000.000
61A62LEU00.0390.03726.984-0.211-0.2110.0000.0000.0000.000
62A63ALA0-0.033-0.01829.4100.2220.2220.0000.0000.0000.000
63A64GLY0-0.012-0.01131.7550.0180.0180.0000.0000.0000.000
64A65SER0-0.015-0.02334.363-0.070-0.0700.0000.0000.0000.000
65A66SER00.0260.00931.638-0.008-0.0080.0000.0000.0000.000
66A67GLU-1-0.825-0.89229.483-9.607-9.6070.0000.0000.0000.000
67A68LEU0-0.0010.01921.732-0.010-0.0100.0000.0000.0000.000
68A69ALA00.0070.00026.183-0.050-0.0500.0000.0000.0000.000
69A70ALA00.023-0.00521.511-0.292-0.2920.0000.0000.0000.000
70A71GLU-1-0.780-0.84222.470-10.756-10.7560.0000.0000.0000.000
71A73LYS10.9660.99214.09317.85317.8530.0000.0000.0000.000
72A74THR00.0350.02717.566-0.631-0.6310.0000.0000.0000.000
73A75ALA00.0480.01316.873-0.463-0.4630.0000.0000.0000.000
74A76ALA0-0.013-0.00317.939-0.351-0.3510.0000.0000.0000.000
75A77GLY00.0060.00918.1490.0700.0700.0000.0000.0000.000
76A78GLN0-0.0340.00419.186-0.082-0.0820.0000.0000.0000.000
77A79PHE0-0.013-0.02117.272-0.419-0.4190.0000.0000.0000.000
78A80VAL00.0060.01322.1380.5680.5680.0000.0000.0000.000
79A81SER00.0120.00823.708-0.223-0.2230.0000.0000.0000.000
80A82THR0-0.0200.00422.0150.2230.2230.0000.0000.0000.000
81A83LYS10.9390.95725.4649.3039.3030.0000.0000.0000.000
82A84ILE00.0050.02223.331-0.081-0.0810.0000.0000.0000.000
83A85ASN00.0360.02126.641-0.070-0.0700.0000.0000.0000.000
84A86LEU0-0.001-0.00124.657-0.183-0.1830.0000.0000.0000.000
85A87ASP-1-0.800-0.91028.012-8.713-8.7130.0000.0000.0000.000
86A88ASP-1-0.884-0.91228.023-9.590-9.5900.0000.0000.0000.000
87A89HIS10.8050.86226.02010.67910.6790.0000.0000.0000.000
88A90ILE0-0.0440.01324.509-0.215-0.2150.0000.0000.0000.000
89A91ALA00.0640.03928.4110.3280.3280.0000.0000.0000.000
90A92ASN00.0160.00531.008-0.268-0.2680.0000.0000.0000.000
91A93ILE0-0.009-0.02131.6840.2670.2670.0000.0000.0000.000
92A94ASP-1-0.933-0.97234.237-7.733-7.7330.0000.0000.0000.000
93A95GLY00.0310.02835.9250.0310.0310.0000.0000.0000.000
94A96THR0-0.050-0.02729.683-0.184-0.1840.0000.0000.0000.000
95A97LEU0-0.020-0.00928.1540.0300.0300.0000.0000.0000.000
96A98LYS10.8830.93926.9289.6909.6900.0000.0000.0000.000
97A99TYR00.0110.00823.2910.1090.1090.0000.0000.0000.000
98A100GLU-2-1.499-1.78525.736-19.682-19.6820.0000.0000.0000.000
99A221NA+10.7500.92620.21713.39513.3950.0000.0000.0000.000
100A222NA+10.7320.94134.4008.6108.6100.0000.0000.0000.000
101A223PO4-2-1.687-1.8061.705-226.148-225.66419.606-13.576-6.514-0.153
102A224PO4-2-2.011-2.02220.839-25.719-25.7190.0000.0000.0000.000
103A225PO4-2-1.789-1.8814.794-70.636-70.5170.000-0.006-0.1120.000
104A101HOH00.0260.01915.392-0.052-0.0520.0000.0000.0000.000
105A102HOH0-0.034-0.01823.343-0.032-0.0320.0000.0000.0000.000
106A103HOH0-0.049-0.03434.2060.0620.0620.0000.0000.0000.000
107A104HOH0-0.007-0.0086.2071.7861.7860.0000.0000.0000.000
108A105HOH0-0.007-0.01128.5110.0580.0580.0000.0000.0000.000
109A106HOH0-0.048-0.04119.4310.3130.3130.0000.0000.0000.000
110A107HOH0-0.013-0.0068.8381.3821.3820.0000.0000.0000.000
111A108HOH00.0150.01021.896-0.086-0.0860.0000.0000.0000.000
112A109HOH00.0020.00228.6490.0020.0020.0000.0000.0000.000
113A110HOH00.0560.0359.6790.7030.7030.0000.0000.0000.000
114A111HOH00.033-0.01717.0120.3420.3420.0000.0000.0000.000
115A112HOH00.0510.03321.667-0.223-0.2230.0000.0000.0000.000
116A113HOH0-0.012-0.01126.3000.1730.1730.0000.0000.0000.000
117A114HOH0-0.027-0.01810.948-0.936-0.9360.0000.0000.0000.000
118A115HOH0-0.040-0.02236.7890.0250.0250.0000.0000.0000.000
119A116HOH0-0.024-0.02014.5860.0230.0230.0000.0000.0000.000
120A117HOH0-0.037-0.03226.607-0.038-0.0380.0000.0000.0000.000
121A118HOH0-0.051-0.02914.9690.1630.1630.0000.0000.0000.000
122A119HOH0-0.042-0.0203.0247.5327.8990.004-0.164-0.208-0.001
123A120HOH0-0.054-0.02812.6420.2180.2180.0000.0000.0000.000
124A121HOH0-0.032-0.03316.0700.2420.2420.0000.0000.0000.000
125A122HOH0-0.024-0.01217.247-0.309-0.3090.0000.0000.0000.000
126A123HOH00.0230.01922.368-0.217-0.2170.0000.0000.0000.000
127A124HOH0-0.024-0.02225.488-0.090-0.0900.0000.0000.0000.000
128A125HOH0-0.014-0.00827.5670.1130.1130.0000.0000.0000.000
129A126HOH0-0.024-0.02326.1990.0670.0670.0000.0000.0000.000
130A127HOH0-0.042-0.03813.225-0.404-0.4040.0000.0000.0000.000
131A129HOH0-0.017-0.01314.039-0.121-0.1210.0000.0000.0000.000
132A131HOH00.0220.02313.765-0.501-0.5010.0000.0000.0000.000
133A132HOH0-0.034-0.02514.8650.5180.5180.0000.0000.0000.000
134A133HOH00.0230.02827.164-0.059-0.0590.0000.0000.0000.000
135A134HOH00.0160.01622.3870.1330.1330.0000.0000.0000.000
136A135HOH00.000-0.00715.860-0.107-0.1070.0000.0000.0000.000
137A136HOH00.0210.01033.7270.0200.0200.0000.0000.0000.000
138A137HOH0-0.075-0.05828.3410.1150.1150.0000.0000.0000.000
139A138HOH00.0010.00321.270-0.244-0.2440.0000.0000.0000.000
140A139HOH0-0.063-0.04426.801-0.075-0.0750.0000.0000.0000.000
141A140HOH0-0.023-0.01934.8330.0210.0210.0000.0000.0000.000
142A141HOH0-0.063-0.04815.3980.3010.3010.0000.0000.0000.000
143A142HOH00.0220.01723.957-0.228-0.2280.0000.0000.0000.000
144A143HOH0-0.038-0.04125.9330.0140.0140.0000.0000.0000.000
145A144HOH0-0.055-0.04411.736-0.570-0.5700.0000.0000.0000.000
146A145HOH00.001-0.00223.689-0.144-0.1440.0000.0000.0000.000
147A146HOH0-0.038-0.03511.570-0.076-0.0760.0000.0000.0000.000
148A147HOH0-0.015-0.01325.171-0.054-0.0540.0000.0000.0000.000
149A149HOH00.0270.01426.948-0.073-0.0730.0000.0000.0000.000
150A151HOH00.0270.01618.051-0.067-0.0670.0000.0000.0000.000
151A152HOH0-0.017-0.01621.108-0.083-0.0830.0000.0000.0000.000
152A153HOH0-0.034-0.02532.3110.1140.1140.0000.0000.0000.000
153A154HOH00.0010.00626.312-0.067-0.0670.0000.0000.0000.000
154A155HOH0-0.040-0.02630.652-0.023-0.0230.0000.0000.0000.000
155A157HOH0-0.043-0.03425.121-0.105-0.1050.0000.0000.0000.000
156A158HOH0-0.024-0.02019.382-0.293-0.2930.0000.0000.0000.000
157A159HOH00.0240.01620.569-0.284-0.2840.0000.0000.0000.000
158A161HOH0-0.052-0.03821.2750.1790.1790.0000.0000.0000.000
159A164HOH00.0570.03725.396-0.198-0.1980.0000.0000.0000.000
160A166HOH0-0.025-0.02021.7850.2230.2230.0000.0000.0000.000
161A167HOH00.0250.02713.9740.3310.3310.0000.0000.0000.000
162A168HOH0-0.015-0.00431.2790.1230.1230.0000.0000.0000.000
163A178HOH00.0160.01819.561-0.286-0.2860.0000.0000.0000.000
164A179HOH0-0.017-0.03324.0000.2410.2410.0000.0000.0000.000
165A180HOH0-0.064-0.04927.9880.0500.0500.0000.0000.0000.000
166A183HOH00.0310.02222.706-0.181-0.1810.0000.0000.0000.000
167A186HOH0-0.045-0.02316.168-0.039-0.0390.0000.0000.0000.000
168A187HOH0-0.044-0.03613.6000.1800.1800.0000.0000.0000.000
169A192HOH0-0.005-0.00518.715-0.277-0.2770.0000.0000.0000.000
170A193HOH0-0.003-0.00330.293-0.023-0.0230.0000.0000.0000.000
171A194HOH0-0.025-0.03313.5840.2170.2170.0000.0000.0000.000
172A195HOH0-0.097-0.0666.7340.8820.8820.0000.0000.0000.000
173A197HOH0-0.038-0.02627.8230.1370.1370.0000.0000.0000.000
174A198HOH00.0320.02436.7960.0510.0510.0000.0000.0000.000
175A199HOH0-0.007-0.00234.7960.0580.0580.0000.0000.0000.000
176A200HOH0-0.004-0.00212.5260.4710.4710.0000.0000.0000.000
177A201HOH0-0.036-0.03211.9910.3740.3740.0000.0000.0000.000
178A202HOH00.0020.01015.848-0.321-0.3210.0000.0000.0000.000
179A203HOH0-0.026-0.02820.2860.0460.0460.0000.0000.0000.000
180A207HOH0-0.046-0.04821.1540.0340.0340.0000.0000.0000.000
181A210HOH0-0.020-0.00633.006-0.023-0.0230.0000.0000.0000.000
182A211HOH0-0.017-0.01326.2890.1440.1440.0000.0000.0000.000
183A212HOH0-0.037-0.02328.718-0.090-0.0900.0000.0000.0000.000
184A213HOH00.0610.03823.6370.1740.1740.0000.0000.0000.000
185A215HOH0-0.026-0.0323.9854.0354.068-0.001-0.005-0.0270.000
186A216HOH0-0.010-0.01426.7720.0780.0780.0000.0000.0000.000
187A217HOH0-0.004-0.01310.9840.3700.3700.0000.0000.0000.000
188A218HOH0-0.031-0.01835.257-0.098-0.0980.0000.0000.0000.000