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: 2LK2R

Calculation Name: 1B6D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B6D

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098881.168273
FMO2-HF: Nuclear repulsion 2018079.489448
FMO2-HF: Total energy -80801.678825
FMO2-MP2: Total energy -81037.847664


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
18.34324.7361.22-3.059-4.5530.01
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.936 / q_NPA : -0.975
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].
3A3GLN0-0.023-0.0212.7912.7045.0320.222-1.173-1.377-0.005
4A4MET0-0.0070.0185.396-2.987-2.919-0.001-0.003-0.0640.000
5A5THR0-0.015-0.0148.519-0.276-0.2760.0000.0000.0000.000
6A6GLN00.007-0.02611.5270.2850.2850.0000.0000.0000.000
7A7SER0-0.0400.00214.529-0.371-0.3710.0000.0000.0000.000
8A8PRO00.0510.02818.071-0.215-0.2150.0000.0000.0000.000
9A9SER00.0590.01918.1550.2600.2600.0000.0000.0000.000
10A10SER0-0.067-0.03119.814-0.014-0.0140.0000.0000.0000.000
11A11LEU00.0170.01423.162-0.067-0.0670.0000.0000.0000.000
12A12SER00.0080.00926.324-0.039-0.0390.0000.0000.0000.000
13A13ALA0-0.002-0.00129.893-0.097-0.0970.0000.0000.0000.000
14A14SER0-0.0140.00031.997-0.056-0.0560.0000.0000.0000.000
15A15VAL0-0.001-0.00234.3190.1670.1670.0000.0000.0000.000
16A16GLY00.002-0.00534.899-0.243-0.2430.0000.0000.0000.000
17A17ASP-1-0.895-0.95132.7848.7058.7050.0000.0000.0000.000
18A18ARG10.9590.98829.418-9.264-9.2640.0000.0000.0000.000
19A19VAL0-0.037-0.01825.2860.0480.0480.0000.0000.0000.000
20A20THR0-0.011-0.01123.516-0.078-0.0780.0000.0000.0000.000
21A21ILE0-0.049-0.00118.6370.0320.0320.0000.0000.0000.000
22A22THR00.009-0.00418.532-0.014-0.0140.0000.0000.0000.000
23A23CYS0-0.0090.00112.8720.1860.1860.0000.0000.0000.000
24A24GLN00.0140.02512.995-1.144-1.1440.0000.0000.0000.000
25A25ALA00.0360.0258.9271.3991.3990.0000.0000.0000.000
26A26SER0-0.047-0.0155.322-1.139-1.1390.0000.0000.0000.000
27A27GLN0-0.003-0.0095.8501.8461.8460.0000.0000.0000.000
28A28ASP-1-0.905-0.9679.41518.46518.4650.0000.0000.0000.000
29A29ILE00.0030.0148.5511.2461.2460.0000.0000.0000.000
30A30SER00.0320.02411.326-1.038-1.0380.0000.0000.0000.000
31A31SER00.022-0.00515.0270.1100.1100.0000.0000.0000.000
32A32TYR0-0.0220.00112.277-0.930-0.9300.0000.0000.0000.000
33A33LEU00.0210.01011.7011.7601.7600.0000.0000.0000.000
34A34ASN00.0270.03813.587-2.354-2.3540.0000.0000.0000.000
35A35TRP00.0600.02314.9810.8350.8350.0000.0000.0000.000
36A36TYR0-0.032-0.03614.043-1.202-1.2020.0000.0000.0000.000
37A37GLN0-0.021-0.02118.639-0.143-0.1430.0000.0000.0000.000
38A38GLN0-0.019-0.02219.1980.4820.4820.0000.0000.0000.000
39A39LYS10.8940.95621.940-10.916-10.9160.0000.0000.0000.000
40A40PRO00.0550.00724.7730.3910.3910.0000.0000.0000.000
41A41GLY00.0240.02325.215-0.396-0.3960.0000.0000.0000.000
42A42LYS10.8900.95824.962-11.031-11.0310.0000.0000.0000.000
43A43ALA00.0390.02621.6700.4860.4860.0000.0000.0000.000
44A44PRO00.009-0.00517.459-0.602-0.6020.0000.0000.0000.000
45A45LYS10.9420.98120.269-11.814-11.8140.0000.0000.0000.000
46A46LEU0-0.0010.00817.8870.1950.1950.0000.0000.0000.000
47A47LEU0-0.082-0.04420.565-0.756-0.7560.0000.0000.0000.000
48A48ILE0-0.0030.00419.444-0.576-0.5760.0000.0000.0000.000
49A49HIS00.0990.02217.2500.7060.7060.0000.0000.0000.000
50A50ALA0-0.0280.00117.354-0.673-0.6730.0000.0000.0000.000
51A51ALA00.0190.01617.401-0.713-0.7130.0000.0000.0000.000
52A52SER0-0.087-0.07018.598-0.501-0.5010.0000.0000.0000.000
53A53SER0-0.0220.00921.860-0.751-0.7510.0000.0000.0000.000
54A54LEU0-0.041-0.01523.0980.4010.4010.0000.0000.0000.000
55A55GLU-1-0.904-0.95023.04012.28412.2840.0000.0000.0000.000
56A56THR00.014-0.00125.775-0.375-0.3750.0000.0000.0000.000
57A57GLY0-0.028-0.02128.9270.1370.1370.0000.0000.0000.000
58A58VAL0-0.078-0.02325.325-0.103-0.1030.0000.0000.0000.000
59A59PRO0-0.019-0.01028.640-0.218-0.2180.0000.0000.0000.000
60A60SER00.0700.01329.3970.2870.2870.0000.0000.0000.000
61A61ARG10.8280.91329.848-9.558-9.5580.0000.0000.0000.000
62A62PHE0-0.0190.00125.1650.1320.1320.0000.0000.0000.000
63A63SER0-0.005-0.00525.352-0.145-0.1450.0000.0000.0000.000
64A64GLY00.0550.01621.4000.2340.2340.0000.0000.0000.000
65A65SER0-0.042-0.01920.954-0.522-0.5220.0000.0000.0000.000
66A66GLY00.0340.02019.6010.4910.4910.0000.0000.0000.000
67A67SER0-0.011-0.02617.202-0.279-0.2790.0000.0000.0000.000
68A68GLY00.0040.02315.102-0.504-0.5040.0000.0000.0000.000
69A69THR0-0.001-0.00312.1991.2411.2410.0000.0000.0000.000
70A70ASP-1-0.865-0.92914.10816.76416.7640.0000.0000.0000.000
71A71PHE0-0.015-0.01113.164-0.644-0.6440.0000.0000.0000.000
72A72SER0-0.060-0.03417.598-0.170-0.1700.0000.0000.0000.000
73A73PHE00.0250.01719.968-0.209-0.2090.0000.0000.0000.000
74A74THR0-0.005-0.02421.663-0.296-0.2960.0000.0000.0000.000
75A75ILE0-0.0330.00325.375-0.039-0.0390.0000.0000.0000.000
76A76SER0-0.017-0.03028.016-0.094-0.0940.0000.0000.0000.000
77A77SER0-0.016-0.00431.385-0.182-0.1820.0000.0000.0000.000
78A78LEU0-0.053-0.00929.2420.0270.0270.0000.0000.0000.000
79A79GLN00.0400.01031.991-0.395-0.3950.0000.0000.0000.000
80A80PRO00.0400.02532.3650.3120.3120.0000.0000.0000.000
81A81GLU-1-0.912-0.96832.0959.0979.0970.0000.0000.0000.000
82A82ASP-1-0.825-0.89328.34310.40110.4010.0000.0000.0000.000
83A83LEU00.0100.03027.4130.4840.4840.0000.0000.0000.000
84A84ALA0-0.053-0.05124.4230.0130.0130.0000.0000.0000.000
85A85THR0-0.0090.02118.956-0.149-0.1490.0000.0000.0000.000
86A86TYR0-0.020-0.01919.7650.0210.0210.0000.0000.0000.000
87A87TYR0-0.0120.01314.3570.2300.2300.0000.0000.0000.000
88A89GLN00.0320.01310.030-0.705-0.7050.0000.0000.0000.000
89A90GLN00.0590.0204.732-5.608-5.539-0.001-0.001-0.0670.000
90A91TYR0-0.070-0.0588.4891.4611.4610.0000.0000.0000.000
91A92ASP-1-0.888-0.9358.40025.03425.0340.0000.0000.0000.000
92A93SER0-0.029-0.0225.8471.4771.4770.0000.0000.0000.000
93A94LEU0-0.064-0.0066.2120.3940.3940.0000.0000.0000.000
94A95PRO00.0300.0202.580-4.980-1.5020.946-1.779-2.6450.015
95A96LEU00.035-0.0104.4480.4270.488-0.001-0.010-0.0500.000
96A97THR0-0.0150.0103.215-1.923-1.5340.055-0.093-0.3500.000
97A98PHE0-0.010-0.0226.252-3.732-3.7320.0000.0000.0000.000
98A99GLY00.0390.0308.9161.7591.7590.0000.0000.0000.000
99A100GLY0-0.035-0.03211.176-0.444-0.4440.0000.0000.0000.000
100A101GLY00.0250.01613.371-0.478-0.4780.0000.0000.0000.000
101A102THR0-0.056-0.04416.443-0.085-0.0850.0000.0000.0000.000
102A103LYS10.8950.95819.948-12.651-12.6510.0000.0000.0000.000
103A104VAL00.0090.01123.115-0.185-0.1850.0000.0000.0000.000
104A105GLU-1-0.955-0.98826.07410.66310.6630.0000.0000.0000.000
105A106ILE00.0340.02029.437-0.088-0.0880.0000.0000.0000.000
106A107LYS10.9600.98632.757-8.436-8.4360.0000.0000.0000.000
107A108ARG10.8240.89235.264-7.796-7.7960.0000.0000.0000.000
108A109THR00.005-0.00538.8100.0430.0430.0000.0000.0000.000
109A110VAL00.0020.00441.7630.1030.1030.0000.0000.0000.000
110A111ALA0-0.0270.00342.741-0.150-0.1500.0000.0000.0000.000
111A112ALA00.0340.00243.9860.1080.1080.0000.0000.0000.000
112A113PRO0-0.0140.01243.964-0.006-0.0060.0000.0000.0000.000
113A114SER0-0.007-0.00145.740-0.177-0.1770.0000.0000.0000.000
114A115VAL00.019-0.00247.1500.1020.1020.0000.0000.0000.000
115A116PHE0-0.058-0.02248.354-0.181-0.1810.0000.0000.0000.000
116A117ILE00.0080.00248.8960.1240.1240.0000.0000.0000.000
117A118PHE0-0.036-0.01748.336-0.121-0.1210.0000.0000.0000.000
118A119PRO0-0.0020.00550.4210.1040.1040.0000.0000.0000.000
119A120PRO00.0260.01750.7190.0390.0390.0000.0000.0000.000
120A121SER00.0570.03749.954-0.109-0.1090.0000.0000.0000.000
121A122ASP-1-0.887-0.95252.7955.6445.6440.0000.0000.0000.000
122A123GLU-1-1.006-1.01749.7246.5006.5000.0000.0000.0000.000
123A124GLN00.0910.05446.299-0.048-0.0480.0000.0000.0000.000
124A125LEU00.0290.02050.4950.0370.0370.0000.0000.0000.000
125A126LYS10.8980.96153.068-6.003-6.0030.0000.0000.0000.000
126A127SER0-0.066-0.05048.3130.0220.0220.0000.0000.0000.000
127A128GLY00.0040.00549.5580.0680.0680.0000.0000.0000.000
128A129THR0-0.062-0.04945.9560.0720.0720.0000.0000.0000.000
129A130ALA00.0060.00849.292-0.069-0.0690.0000.0000.0000.000
130A131SER0-0.025-0.00745.3940.0830.0830.0000.0000.0000.000
131A132VAL0-0.0210.00447.600-0.098-0.0980.0000.0000.0000.000
132A133VAL00.0130.00544.2850.1380.1380.0000.0000.0000.000
133A134CYS0-0.069-0.03345.521-0.073-0.0730.0000.0000.0000.000
134A135LEU0-0.0150.00243.2240.1940.1940.0000.0000.0000.000
135A136LEU00.0050.00542.516-0.193-0.1930.0000.0000.0000.000
136A137ASN00.034-0.00842.3990.3640.3640.0000.0000.0000.000
137A138ASN0-0.013-0.00341.410-0.012-0.0120.0000.0000.0000.000
138A139PHE0-0.0100.01238.956-0.134-0.1340.0000.0000.0000.000
139A140TYR00.0420.02334.6850.2010.2010.0000.0000.0000.000
140A141PRO00.0450.01537.123-0.210-0.2100.0000.0000.0000.000
141A142ARG11.0070.99429.961-10.032-10.0320.0000.0000.0000.000
142A143GLU-1-0.940-0.96336.6197.9127.9120.0000.0000.0000.000
143A144ALA00.0050.00438.167-0.228-0.2280.0000.0000.0000.000
144A145LYS10.8920.95940.008-7.597-7.5970.0000.0000.0000.000
145A146VAL00.0640.01642.966-0.177-0.1770.0000.0000.0000.000
146A147GLN0-0.0100.00844.3900.1480.1480.0000.0000.0000.000
147A148TRP00.0180.00444.884-0.257-0.2570.0000.0000.0000.000
148A149LYS10.9350.94949.059-5.960-5.9600.0000.0000.0000.000
149A150VAL00.0150.01552.009-0.042-0.0420.0000.0000.0000.000
150A151ASP-1-0.807-0.92054.5765.3775.3770.0000.0000.0000.000
151A152ASN0-0.031-0.02656.960-0.005-0.0050.0000.0000.0000.000
152A153ALA00.0020.01454.8080.0320.0320.0000.0000.0000.000
153A154LEU0-0.008-0.01049.4410.0390.0390.0000.0000.0000.000
154A155GLN0-0.0220.00647.8420.0410.0410.0000.0000.0000.000
155A156SER00.012-0.02244.8270.1120.1120.0000.0000.0000.000
156A157GLY0-0.0200.00941.612-0.058-0.0580.0000.0000.0000.000
157A158ASN0-0.0010.00042.6720.1100.1100.0000.0000.0000.000
158A159SER00.0080.00142.285-0.122-0.1220.0000.0000.0000.000
159A160GLN00.0350.02337.9380.0160.0160.0000.0000.0000.000
160A161GLU-1-0.901-0.96437.7177.8427.8420.0000.0000.0000.000
161A162SER0-0.041-0.00635.1110.3370.3370.0000.0000.0000.000
162A163VAL0-0.010-0.01333.139-0.248-0.2480.0000.0000.0000.000
163A164THR0-0.021-0.01233.5230.2040.2040.0000.0000.0000.000
164A165GLU-1-0.920-0.96927.91410.92110.9210.0000.0000.0000.000
165A166GLN0-0.077-0.05831.508-0.036-0.0360.0000.0000.0000.000
166A167ASP-1-0.808-0.90732.8118.5848.5840.0000.0000.0000.000
167A168SER0-0.061-0.04132.684-0.057-0.0570.0000.0000.0000.000
168A169LYS10.9280.96834.505-8.171-8.1710.0000.0000.0000.000
169A170ASP-1-0.854-0.91638.2107.6327.6320.0000.0000.0000.000
170A171SER0-0.013-0.00835.580-0.107-0.1070.0000.0000.0000.000
171A172THR0-0.029-0.01436.6010.0370.0370.0000.0000.0000.000
172A173TYR0-0.016-0.01432.0650.1480.1480.0000.0000.0000.000
173A174SER00.0470.02537.393-0.362-0.3620.0000.0000.0000.000
174A175LEU00.0010.00337.7110.2860.2860.0000.0000.0000.000
175A176SER0-0.0210.00039.296-0.288-0.2880.0000.0000.0000.000
176A177SER00.0650.03640.1200.1280.1280.0000.0000.0000.000
177A178THR0-0.015-0.01441.857-0.198-0.1980.0000.0000.0000.000
178A179LEU0-0.0130.02043.2300.0810.0810.0000.0000.0000.000
179A180THR00.002-0.02343.396-0.093-0.0930.0000.0000.0000.000
180A181LEU0-0.024-0.00446.086-0.014-0.0140.0000.0000.0000.000
181A182SER00.0840.04549.2060.0020.0020.0000.0000.0000.000
182A183LYS10.9280.95250.555-5.726-5.7260.0000.0000.0000.000
183A184ALA0-0.009-0.00553.624-0.114-0.1140.0000.0000.0000.000
184A185ASP-1-0.893-0.95952.4425.9935.9930.0000.0000.0000.000
185A186TYR00.0390.01553.060-0.074-0.0740.0000.0000.0000.000
186A187GLU-1-0.863-0.95154.8075.4425.4420.0000.0000.0000.000
187A188LYS10.8860.96356.505-5.759-5.7590.0000.0000.0000.000
188A189HIS10.8480.94555.664-5.740-5.7400.0000.0000.0000.000
189A190LYS10.9781.00858.886-4.949-4.9490.0000.0000.0000.000
190A191VAL00.0130.01657.7610.0430.0430.0000.0000.0000.000
191A192TYR0-0.0090.01152.5360.1090.1090.0000.0000.0000.000
192A193ALA00.018-0.01453.700-0.041-0.0410.0000.0000.0000.000
193A195GLU-1-0.953-0.97749.6016.0766.0760.0000.0000.0000.000
194A196VAL00.0500.01345.6140.1570.1570.0000.0000.0000.000
195A197THR0-0.022-0.00846.001-0.172-0.1720.0000.0000.0000.000
196A198HIS0-0.010-0.02940.810-0.006-0.0060.0000.0000.0000.000
197A199GLN00.0660.03041.854-0.005-0.0050.0000.0000.0000.000
198A200GLY0-0.029-0.01045.044-0.103-0.1030.0000.0000.0000.000
199A201LEU0-0.062-0.03147.074-0.108-0.1080.0000.0000.0000.000
200A202SER0-0.0040.00649.6270.0330.0330.0000.0000.0000.000
201A203SER0-0.010-0.01252.457-0.044-0.0440.0000.0000.0000.000
202A204PRO00.001-0.00750.5010.0400.0400.0000.0000.0000.000
203A205VAL00.0340.03850.651-0.142-0.1420.0000.0000.0000.000
204A206THR00.0110.00251.2810.1160.1160.0000.0000.0000.000
205A207LYS10.8870.96451.918-6.027-6.0270.0000.0000.0000.000
206A208SER00.005-0.01953.4910.0340.0340.0000.0000.0000.000
207A209PHE00.0040.01553.112-0.065-0.0650.0000.0000.0000.000
208A210ASN0-0.009-0.01357.716-0.057-0.0570.0000.0000.0000.000
209A211ARG10.8510.90157.265-5.422-5.4220.0000.0000.0000.000
210A212GLY00.0000.01759.635-0.131-0.1310.0000.0000.0000.000