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: ZN2YN

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 OptAll
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 -2099831.713172
FMO2-HF: Nuclear repulsion 2019028.04467
FMO2-HF: Total energy -80803.668502
FMO2-MP2: Total energy -81039.879109


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.
14.38720.692.63-3.594-5.3370.023
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 : -0.912 / q_NPA : -0.961
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].
3A3GLN0-0.020-0.0102.8082.6455.3660.607-1.419-1.908-0.003
4A4MET0-0.0140.0135.353-3.100-3.046-0.001-0.003-0.0490.000
5A5THR00.0240.0168.385-0.869-0.8690.0000.0000.0000.000
6A6GLN00.019-0.03011.5060.6450.6450.0000.0000.0000.000
7A7SER0-0.0530.00314.442-0.452-0.4520.0000.0000.0000.000
8A8PRO00.0580.02918.154-0.179-0.1790.0000.0000.0000.000
9A9SER00.0710.02417.8030.1770.1770.0000.0000.0000.000
10A10SER0-0.058-0.03019.4940.0890.0890.0000.0000.0000.000
11A11LEU00.0120.01422.964-0.136-0.1360.0000.0000.0000.000
12A12SER0-0.008-0.00926.2120.0000.0000.0000.0000.0000.000
13A13ALA0-0.019-0.00229.869-0.192-0.1920.0000.0000.0000.000
14A14SER0-0.038-0.05531.890-0.052-0.0520.0000.0000.0000.000
15A15VAL0-0.027-0.00234.0510.1970.1970.0000.0000.0000.000
16A16GLY00.001-0.00435.098-0.266-0.2660.0000.0000.0000.000
17A17ASP-1-0.786-0.85732.6958.7718.7710.0000.0000.0000.000
18A18ARG10.9400.97829.634-9.213-9.2130.0000.0000.0000.000
19A19VAL0-0.032-0.01025.5150.0330.0330.0000.0000.0000.000
20A20THR0-0.024-0.02623.796-0.072-0.0720.0000.0000.0000.000
21A21ILE0-0.050-0.01318.679-0.038-0.0380.0000.0000.0000.000
22A22THR00.011-0.00618.493-0.033-0.0330.0000.0000.0000.000
23A23CYS0-0.018-0.00112.7300.1310.1310.0000.0000.0000.000
24A24GLN0-0.047-0.02412.983-0.581-0.5810.0000.0000.0000.000
25A25ALA00.0310.0179.1891.3721.3720.0000.0000.0000.000
26A26SER0-0.040-0.0246.013-0.493-0.4930.0000.0000.0000.000
27A27GLN0-0.048-0.0266.6302.3042.3040.0000.0000.0000.000
28A28ASP-1-0.876-0.9399.57218.40018.4000.0000.0000.0000.000
29A29ILE00.0070.0128.7361.9691.9690.0000.0000.0000.000
30A30SER00.0210.01311.501-1.050-1.0500.0000.0000.0000.000
31A31SER00.0300.00115.276-0.030-0.0300.0000.0000.0000.000
32A32TYR0-0.0230.00312.370-1.094-1.0940.0000.0000.0000.000
33A33LEU00.0200.00211.9591.9471.9470.0000.0000.0000.000
34A34ASN0-0.015-0.00413.984-2.485-2.4850.0000.0000.0000.000
35A35TRP00.0400.00815.1650.9040.9040.0000.0000.0000.000
36A36TYR0-0.021-0.02814.772-1.201-1.2010.0000.0000.0000.000
37A37GLN00.0120.00918.957-0.272-0.2720.0000.0000.0000.000
38A38GLN0-0.0140.00419.3820.3740.3740.0000.0000.0000.000
39A39LYS10.8480.92221.993-11.188-11.1880.0000.0000.0000.000
40A40PRO00.0470.00524.9570.3600.3600.0000.0000.0000.000
41A41GLY00.0170.01725.496-0.339-0.3390.0000.0000.0000.000
42A42LYS10.8770.94824.998-11.207-11.2070.0000.0000.0000.000
43A43ALA00.0610.03221.2100.4940.4940.0000.0000.0000.000
44A44PRO00.005-0.00917.272-0.659-0.6590.0000.0000.0000.000
45A45LYS10.8950.96420.309-12.124-12.1240.0000.0000.0000.000
46A46LEU00.0320.02418.0690.1800.1800.0000.0000.0000.000
47A47LEU0-0.078-0.04920.749-0.869-0.8690.0000.0000.0000.000
48A48ILE00.0100.01120.624-0.629-0.6290.0000.0000.0000.000
49A49HIS00.0390.02817.6070.6660.6660.0000.0000.0000.000
50A50ALA00.0490.01518.178-0.686-0.6860.0000.0000.0000.000
51A51ALA00.017-0.00117.698-0.679-0.6790.0000.0000.0000.000
52A52SER0-0.089-0.03819.016-0.577-0.5770.0000.0000.0000.000
53A53SER0-0.0160.00222.503-0.762-0.7620.0000.0000.0000.000
54A54LEU0-0.042-0.01723.5860.4270.4270.0000.0000.0000.000
55A55GLU-1-0.914-0.95623.31412.70012.7000.0000.0000.0000.000
56A56THR00.004-0.01226.116-0.363-0.3630.0000.0000.0000.000
57A57GLY0-0.017-0.01229.6940.0770.0770.0000.0000.0000.000
58A58VAL0-0.056-0.01525.799-0.064-0.0640.0000.0000.0000.000
59A59PRO00.001-0.00529.179-0.195-0.1950.0000.0000.0000.000
60A60SER00.0600.01230.0080.2840.2840.0000.0000.0000.000
61A61ARG10.7700.87829.656-9.519-9.5190.0000.0000.0000.000
62A62PHE0-0.025-0.00925.5070.1410.1410.0000.0000.0000.000
63A63SER0-0.010-0.00425.862-0.155-0.1550.0000.0000.0000.000
64A64GLY00.036-0.00121.9450.3190.3190.0000.0000.0000.000
65A65SER0-0.029-0.00121.535-0.491-0.4910.0000.0000.0000.000
66A66GLY00.0430.01319.3110.3090.3090.0000.0000.0000.000
67A67SER0-0.016-0.01517.480-0.355-0.3550.0000.0000.0000.000
68A68GLY00.0160.02715.196-0.498-0.4980.0000.0000.0000.000
69A69THR0-0.001-0.02812.6491.1661.1660.0000.0000.0000.000
70A70ASP-1-0.841-0.87713.88717.41417.4140.0000.0000.0000.000
71A71PHE0-0.007-0.00813.638-0.820-0.8200.0000.0000.0000.000
72A72SER0-0.045-0.02617.604-0.238-0.2380.0000.0000.0000.000
73A73PHE00.0410.01919.949-0.042-0.0420.0000.0000.0000.000
74A74THR0-0.037-0.02621.690-0.375-0.3750.0000.0000.0000.000
75A75ILE00.0050.02425.361-0.070-0.0700.0000.0000.0000.000
76A76SER00.010-0.02028.079-0.107-0.1070.0000.0000.0000.000
77A77SER0-0.040-0.03031.472-0.245-0.2450.0000.0000.0000.000
78A78LEU0-0.0220.01228.6000.0590.0590.0000.0000.0000.000
79A79GLN00.0110.00031.765-0.490-0.4900.0000.0000.0000.000
80A80PRO00.0370.01932.1780.3110.3110.0000.0000.0000.000
81A81GLU-1-0.790-0.88632.3499.2469.2460.0000.0000.0000.000
82A82ASP-1-0.809-0.89228.34510.46910.4690.0000.0000.0000.000
83A83LEU0-0.0260.01427.2430.5210.5210.0000.0000.0000.000
84A84ALA0-0.046-0.03423.6510.0030.0030.0000.0000.0000.000
85A85THR0-0.0040.01218.737-0.222-0.2220.0000.0000.0000.000
86A86TYR0-0.003-0.01919.613-0.002-0.0020.0000.0000.0000.000
87A87TYR0-0.013-0.01314.1140.1920.1920.0000.0000.0000.000
88A89GLN00.0390.03010.533-0.674-0.6740.0000.0000.0000.000
89A90GLN00.0370.0215.581-6.041-6.0410.0000.0000.0000.000
90A91TYR0-0.075-0.0619.6741.0571.0570.0000.0000.0000.000
91A92ASP-1-0.846-0.9008.15427.29727.2970.0000.0000.0000.000
92A93SER0-0.052-0.0386.0560.9230.9230.0000.0000.0000.000
93A94LEU0-0.067-0.0156.7890.5630.5630.0000.0000.0000.000
94A95PRO00.0380.0212.721-7.055-4.0431.976-2.040-2.9490.026
95A96LEU00.017-0.0015.2480.6790.718-0.001-0.001-0.0360.000
96A97THR0-0.045-0.0333.052-4.182-3.7050.049-0.131-0.3950.000
97A98PHE0-0.004-0.0146.312-4.142-4.1420.0000.0000.0000.000
98A99GLY00.0460.0248.4702.0412.0410.0000.0000.0000.000
99A100GLY0-0.049-0.03310.879-0.511-0.5110.0000.0000.0000.000
100A101GLY0-0.010-0.00112.828-0.743-0.7430.0000.0000.0000.000
101A102THR0-0.045-0.03116.028-0.086-0.0860.0000.0000.0000.000
102A103LYS10.8430.92919.586-12.107-12.1070.0000.0000.0000.000
103A104VAL0-0.001-0.00422.704-0.187-0.1870.0000.0000.0000.000
104A105GLU-1-0.850-0.91125.94810.32410.3240.0000.0000.0000.000
105A106ILE00.006-0.00529.461-0.075-0.0750.0000.0000.0000.000
106A107LYS10.8920.95332.814-8.850-8.8500.0000.0000.0000.000
107A108ARG10.8250.89734.983-7.893-7.8930.0000.0000.0000.000
108A109THR00.0110.00238.4590.0340.0340.0000.0000.0000.000
109A110VAL00.0090.01241.5490.0960.0960.0000.0000.0000.000
110A111ALA0-0.018-0.00242.580-0.146-0.1460.0000.0000.0000.000
111A112ALA00.0430.01743.6800.1300.1300.0000.0000.0000.000
112A113PRO0-0.0200.00343.8750.0030.0030.0000.0000.0000.000
113A114SER0-0.027-0.01445.504-0.177-0.1770.0000.0000.0000.000
114A115VAL0-0.007-0.00546.9970.0900.0900.0000.0000.0000.000
115A116PHE0-0.032-0.01847.668-0.207-0.2070.0000.0000.0000.000
116A117ILE0-0.012-0.01248.8010.1240.1240.0000.0000.0000.000
117A118PHE00.000-0.00547.993-0.115-0.1150.0000.0000.0000.000
118A119PRO0-0.0070.00450.4560.0900.0900.0000.0000.0000.000
119A120PRO00.0130.00350.4710.0510.0510.0000.0000.0000.000
120A121SER00.0080.00150.585-0.112-0.1120.0000.0000.0000.000
121A122ASP-1-0.882-0.96052.7795.6815.6810.0000.0000.0000.000
122A123GLU-1-0.911-0.95248.9576.5106.5100.0000.0000.0000.000
123A124GLN00.0740.05446.796-0.030-0.0300.0000.0000.0000.000
124A125LEU00.0090.01550.1270.0300.0300.0000.0000.0000.000
125A126LYS10.8980.96152.899-6.022-6.0220.0000.0000.0000.000
126A127SER0-0.059-0.04747.9900.0190.0190.0000.0000.0000.000
127A128GLY00.0000.00349.6500.0520.0520.0000.0000.0000.000
128A129THR0-0.045-0.01745.8010.0130.0130.0000.0000.0000.000
129A130ALA0-0.026-0.01249.223-0.091-0.0910.0000.0000.0000.000
130A131SER00.005-0.01545.0970.0470.0470.0000.0000.0000.000
131A132VAL0-0.022-0.00247.361-0.060-0.0600.0000.0000.0000.000
132A133VAL00.0190.01944.2560.1380.1380.0000.0000.0000.000
133A134CYS0-0.037-0.01545.451-0.067-0.0670.0000.0000.0000.000
134A135LEU0-0.0210.00942.9090.1940.1940.0000.0000.0000.000
135A136LEU00.0130.00342.403-0.200-0.2000.0000.0000.0000.000
136A137ASN00.026-0.01042.1740.3330.3330.0000.0000.0000.000
137A138ASN00.0140.00541.359-0.078-0.0780.0000.0000.0000.000
138A139PHE0-0.0020.01138.681-0.129-0.1290.0000.0000.0000.000
139A140TYR00.0490.01634.4060.1970.1970.0000.0000.0000.000
140A141PRO00.0630.02936.888-0.210-0.2100.0000.0000.0000.000
141A142ARG10.8550.88529.808-10.167-10.1670.0000.0000.0000.000
142A143GLU-1-0.857-0.89036.3097.9577.9570.0000.0000.0000.000
143A144ALA0-0.0200.00138.091-0.231-0.2310.0000.0000.0000.000
144A145LYS10.8010.87840.064-7.578-7.5780.0000.0000.0000.000
145A146VAL00.0330.00342.654-0.165-0.1650.0000.0000.0000.000
146A147GLN0-0.049-0.02344.4370.1560.1560.0000.0000.0000.000
147A148TRP00.020-0.00144.814-0.283-0.2830.0000.0000.0000.000
148A149LYS10.8260.89248.984-6.141-6.1410.0000.0000.0000.000
149A150VAL0-0.0040.00252.300-0.019-0.0190.0000.0000.0000.000
150A151ASP-1-0.788-0.87754.9855.4025.4020.0000.0000.0000.000
151A152ASN0-0.023-0.01956.903-0.022-0.0220.0000.0000.0000.000
152A153ALA0-0.0010.02055.0490.0500.0500.0000.0000.0000.000
153A154LEU00.0290.01049.4600.0580.0580.0000.0000.0000.000
154A155GLN0-0.0170.00748.169-0.004-0.0040.0000.0000.0000.000
155A156SER00.012-0.01444.8500.1160.1160.0000.0000.0000.000
156A157GLY0-0.025-0.00142.015-0.085-0.0850.0000.0000.0000.000
157A158ASN0-0.008-0.00842.7670.1530.1530.0000.0000.0000.000
158A159SER0-0.026-0.03242.469-0.198-0.1980.0000.0000.0000.000
159A160GLN0-0.0060.01538.3200.0100.0100.0000.0000.0000.000
160A161GLU-1-0.748-0.83137.1817.6047.6040.0000.0000.0000.000
161A162SER0-0.059-0.03935.1520.3260.3260.0000.0000.0000.000
162A163VAL0-0.0200.00332.961-0.232-0.2320.0000.0000.0000.000
163A164THR0-0.013-0.01133.5190.1710.1710.0000.0000.0000.000
164A165GLU-1-0.771-0.87027.58611.01411.0140.0000.0000.0000.000
165A166GLN0-0.018-0.02131.149-0.053-0.0530.0000.0000.0000.000
166A167ASP-1-0.737-0.85332.5128.6178.6170.0000.0000.0000.000
167A168SER0-0.029-0.01532.625-0.064-0.0640.0000.0000.0000.000
168A169LYS10.8050.87934.224-8.300-8.3000.0000.0000.0000.000
169A170ASP-1-0.792-0.87537.9177.5987.5980.0000.0000.0000.000
170A171SER0-0.047-0.01734.934-0.064-0.0640.0000.0000.0000.000
171A172THR0-0.068-0.04036.5600.0580.0580.0000.0000.0000.000
172A173TYR0-0.053-0.04332.2330.1560.1560.0000.0000.0000.000
173A174SER00.0340.02237.172-0.371-0.3710.0000.0000.0000.000
174A175LEU0-0.043-0.01337.5690.2770.2770.0000.0000.0000.000
175A176SER00.0110.01839.037-0.319-0.3190.0000.0000.0000.000
176A177SER00.023-0.02439.8340.1360.1360.0000.0000.0000.000
177A178THR0-0.043-0.04042.165-0.143-0.1430.0000.0000.0000.000
178A179LEU00.0240.04343.4580.1040.1040.0000.0000.0000.000
179A180THR00.008-0.01243.366-0.150-0.1500.0000.0000.0000.000
180A181LEU0-0.035-0.01246.192-0.008-0.0080.0000.0000.0000.000
181A182SER00.041-0.00749.112-0.010-0.0100.0000.0000.0000.000
182A183LYS10.9120.92950.793-5.735-5.7350.0000.0000.0000.000
183A184ALA00.0140.00353.774-0.115-0.1150.0000.0000.0000.000
184A185ASP-1-0.831-0.89052.5865.9515.9510.0000.0000.0000.000
185A186TYR00.0550.02653.193-0.051-0.0510.0000.0000.0000.000
186A187GLU-1-0.797-0.90054.9555.4195.4190.0000.0000.0000.000
187A188LYS10.7860.89055.714-5.858-5.8580.0000.0000.0000.000
188A189HIS10.8530.92755.581-5.737-5.7370.0000.0000.0000.000
189A190LYS10.9260.96558.617-5.024-5.0240.0000.0000.0000.000
190A191VAL0-0.022-0.01057.9960.0260.0260.0000.0000.0000.000
191A192TYR00.0010.01052.8610.1160.1160.0000.0000.0000.000
192A193ALA0-0.002-0.01953.499-0.057-0.0570.0000.0000.0000.000
193A195GLU-1-0.814-0.88749.4506.1246.1240.0000.0000.0000.000
194A196VAL00.0460.02545.0470.1490.1490.0000.0000.0000.000
195A197THR0-0.009-0.01345.844-0.208-0.2080.0000.0000.0000.000
196A198HIS00.011-0.01640.7590.0000.0000.0000.0000.0000.000
197A199GLN00.0570.02741.775-0.035-0.0350.0000.0000.0000.000
198A200GLY0-0.006-0.00544.797-0.100-0.1000.0000.0000.0000.000
199A201LEU0-0.069-0.03646.911-0.119-0.1190.0000.0000.0000.000
200A202SER00.0130.01149.5580.0360.0360.0000.0000.0000.000
201A203SER0-0.008-0.00952.291-0.102-0.1020.0000.0000.0000.000
202A204PRO0-0.005-0.00350.4050.0350.0350.0000.0000.0000.000
203A205VAL0-0.0140.00850.560-0.145-0.1450.0000.0000.0000.000
204A206THR00.004-0.00251.0560.1240.1240.0000.0000.0000.000
205A207LYS10.8830.95751.553-6.060-6.0600.0000.0000.0000.000
206A208SER00.019-0.00753.2230.0730.0730.0000.0000.0000.000
207A209PHE00.0360.02253.473-0.057-0.0570.0000.0000.0000.000
208A210ASN0-0.035-0.02557.740-0.115-0.1150.0000.0000.0000.000
209A211ARG10.8240.91857.639-5.425-5.4250.0000.0000.0000.000
210A212GLY00.0120.01559.796-0.123-0.1230.0000.0000.0000.000