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: 6G36Z

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 OptHSide
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 -2100493.001801
FMO2-HF: Nuclear repulsion 2019689.836673
FMO2-HF: Total energy -80803.165128
FMO2-MP2: Total energy -81039.333838


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.
17.46824.4891.813-3.474-5.3590.014
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 : -0.927 / q_NPA : -0.966
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].
3A3GLN0-0.021-0.0202.9831.3814.5180.287-1.566-1.857-0.005
4A4MET0-0.0140.0235.477-2.917-2.9170.0000.0000.0000.000
5A5THR0-0.017-0.0178.609-0.307-0.3070.0000.0000.0000.000
6A6GLN0-0.029-0.05511.606-0.003-0.0030.0000.0000.0000.000
7A7SER0-0.0340.00814.610-0.384-0.3840.0000.0000.0000.000
8A8PRO00.0450.02318.148-0.227-0.2270.0000.0000.0000.000
9A9SER00.0640.02118.3460.2710.2710.0000.0000.0000.000
10A10SER0-0.038-0.02219.8750.2080.2080.0000.0000.0000.000
11A11LEU00.0080.01423.226-0.094-0.0940.0000.0000.0000.000
12A12SER0-0.0010.00126.394-0.041-0.0410.0000.0000.0000.000
13A13ALA0-0.018-0.00529.964-0.097-0.0970.0000.0000.0000.000
14A14SER0-0.045-0.04132.074-0.087-0.0870.0000.0000.0000.000
15A15VAL0-0.015-0.00634.4010.1610.1610.0000.0000.0000.000
16A16GLY00.0070.00234.882-0.244-0.2440.0000.0000.0000.000
17A17ASP-1-0.847-0.90233.0278.7178.7170.0000.0000.0000.000
18A18ARG10.9720.99329.423-9.279-9.2790.0000.0000.0000.000
19A19VAL0-0.041-0.02025.3310.0440.0440.0000.0000.0000.000
20A20THR0-0.019-0.01923.608-0.078-0.0780.0000.0000.0000.000
21A21ILE0-0.054-0.00718.6920.0000.0000.0000.0000.0000.000
22A22THR00.016-0.00218.563-0.005-0.0050.0000.0000.0000.000
23A23CYS0-0.0200.00412.9750.1660.1660.0000.0000.0000.000
24A24GLN0-0.014-0.00413.080-0.727-0.7270.0000.0000.0000.000
25A25ALA00.0420.0209.0141.4301.4300.0000.0000.0000.000
26A26SER0-0.035-0.0165.936-0.354-0.3540.0000.0000.0000.000
27A27GLN0-0.024-0.0166.2600.6890.6890.0000.0000.0000.000
28A28ASP-1-0.890-0.9509.41518.77218.7720.0000.0000.0000.000
29A29ILE00.0120.0128.5151.2601.2600.0000.0000.0000.000
30A30SER00.0220.01311.338-1.047-1.0470.0000.0000.0000.000
31A31SER00.023-0.00315.0380.1080.1080.0000.0000.0000.000
32A32TYR0-0.0160.00312.272-1.203-1.2030.0000.0000.0000.000
33A33LEU00.0220.01411.6871.7631.7630.0000.0000.0000.000
34A34ASN0-0.0080.01213.597-2.302-2.3020.0000.0000.0000.000
35A35TRP00.0720.02214.9860.8610.8610.0000.0000.0000.000
36A36TYR0-0.032-0.04214.298-1.131-1.1310.0000.0000.0000.000
37A37GLN00.0130.00818.638-0.262-0.2620.0000.0000.0000.000
38A38GLN0-0.011-0.01319.4190.4320.4320.0000.0000.0000.000
39A39LYS10.8310.92421.928-11.121-11.1210.0000.0000.0000.000
40A40PRO00.0520.00124.7580.3880.3880.0000.0000.0000.000
41A41GLY00.0210.02025.051-0.398-0.3980.0000.0000.0000.000
42A42LYS10.8880.95824.916-11.053-11.0530.0000.0000.0000.000
43A43ALA00.0400.02321.6030.4940.4940.0000.0000.0000.000
44A44PRO00.020-0.00117.367-0.585-0.5850.0000.0000.0000.000
45A45LYS10.9070.96620.265-12.107-12.1070.0000.0000.0000.000
46A46LEU00.0110.01717.8420.1930.1930.0000.0000.0000.000
47A47LEU0-0.071-0.04320.569-0.810-0.8100.0000.0000.0000.000
48A48ILE00.0090.00419.883-0.557-0.5570.0000.0000.0000.000
49A49HIS00.0220.01117.1460.6160.6160.0000.0000.0000.000
50A50ALA00.0280.01717.373-0.652-0.6520.0000.0000.0000.000
51A51ALA00.0170.01317.418-0.723-0.7230.0000.0000.0000.000
52A52SER0-0.084-0.06418.613-0.513-0.5130.0000.0000.0000.000
53A53SER0-0.0040.01421.884-0.750-0.7500.0000.0000.0000.000
54A54LEU0-0.049-0.01723.1140.4050.4050.0000.0000.0000.000
55A55GLU-1-0.902-0.95223.00512.44812.4480.0000.0000.0000.000
56A56THR00.021-0.00125.791-0.370-0.3700.0000.0000.0000.000
57A57GLY0-0.032-0.02128.9410.1440.1440.0000.0000.0000.000
58A58VAL0-0.065-0.01925.343-0.081-0.0810.0000.0000.0000.000
59A59PRO00.001-0.00428.647-0.190-0.1900.0000.0000.0000.000
60A60SER00.0720.01429.4010.2940.2940.0000.0000.0000.000
61A61ARG10.7740.88829.511-9.479-9.4790.0000.0000.0000.000
62A62PHE0-0.015-0.00625.2210.1410.1410.0000.0000.0000.000
63A63SER0-0.0030.00125.360-0.163-0.1630.0000.0000.0000.000
64A64GLY00.0400.01421.4080.2310.2310.0000.0000.0000.000
65A65SER0-0.053-0.01920.952-0.504-0.5040.0000.0000.0000.000
66A66GLY00.0380.01819.6080.5050.5050.0000.0000.0000.000
67A67SER0-0.007-0.02217.231-0.298-0.2980.0000.0000.0000.000
68A68GLY0-0.0010.01515.107-0.516-0.5160.0000.0000.0000.000
69A69THR0-0.004-0.01412.6211.2481.2480.0000.0000.0000.000
70A70ASP-1-0.845-0.90114.10617.10517.1050.0000.0000.0000.000
71A71PHE0-0.0040.00213.299-0.694-0.6940.0000.0000.0000.000
72A72SER0-0.057-0.03317.598-0.169-0.1690.0000.0000.0000.000
73A73PHE00.0260.01819.935-0.214-0.2140.0000.0000.0000.000
74A74THR0-0.005-0.02421.659-0.331-0.3310.0000.0000.0000.000
75A75ILE0-0.0220.01125.369-0.034-0.0340.0000.0000.0000.000
76A76SER0-0.003-0.02528.009-0.124-0.1240.0000.0000.0000.000
77A77SER0-0.031-0.01431.379-0.188-0.1880.0000.0000.0000.000
78A78LEU0-0.039-0.00829.0830.0200.0200.0000.0000.0000.000
79A79GLN00.0360.01631.984-0.432-0.4320.0000.0000.0000.000
80A80PRO00.0350.01632.3510.3090.3090.0000.0000.0000.000
81A81GLU-1-0.805-0.90031.9549.2679.2670.0000.0000.0000.000
82A82ASP-1-0.844-0.90128.34510.46710.4670.0000.0000.0000.000
83A83LEU00.0060.02327.3990.4800.4800.0000.0000.0000.000
84A84ALA0-0.060-0.04624.068-0.006-0.0060.0000.0000.0000.000
85A85THR00.0060.01919.084-0.184-0.1840.0000.0000.0000.000
86A86TYR0-0.014-0.01819.7510.0010.0010.0000.0000.0000.000
87A87TYR0-0.0100.01114.2970.1930.1930.0000.0000.0000.000
88A89GLN00.0370.02310.278-0.278-0.2780.0000.0000.0000.000
89A90GLN00.0640.0184.700-5.695-5.622-0.001-0.001-0.0710.000
90A91TYR0-0.069-0.0608.5101.4871.4870.0000.0000.0000.000
91A92ASP-1-0.860-0.9078.22327.02527.0250.0000.0000.0000.000
92A93SER0-0.049-0.0446.2600.8620.8620.0000.0000.0000.000
93A94LEU0-0.084-0.0136.2510.6680.6680.0000.0000.0000.000
94A95PRO00.0330.0192.613-5.920-2.6081.498-1.809-3.0010.019
95A96LEU00.031-0.0054.4690.6390.703-0.001-0.009-0.0540.000
96A97THR0-0.0150.0063.412-1.748-1.3130.030-0.089-0.3760.000
97A98PHE0-0.029-0.0296.247-3.996-3.9960.0000.0000.0000.000
98A99GLY00.0490.0358.9871.7011.7010.0000.0000.0000.000
99A100GLY0-0.038-0.03211.253-0.471-0.4710.0000.0000.0000.000
100A101GLY00.0260.01313.431-0.472-0.4720.0000.0000.0000.000
101A102THR0-0.045-0.03116.511-0.067-0.0670.0000.0000.0000.000
102A103LYS10.8310.92020.019-12.051-12.0510.0000.0000.0000.000
103A104VAL00.0050.00623.180-0.208-0.2080.0000.0000.0000.000
104A105GLU-1-0.916-0.97626.14510.51110.5110.0000.0000.0000.000
105A106ILE00.0260.01129.504-0.080-0.0800.0000.0000.0000.000
106A107LYS10.9160.97132.828-8.589-8.5890.0000.0000.0000.000
107A108ARG10.8220.89135.334-7.798-7.7980.0000.0000.0000.000
108A109THR00.0110.00238.8800.0440.0440.0000.0000.0000.000
109A110VAL0-0.0020.00441.8270.1010.1010.0000.0000.0000.000
110A111ALA0-0.0210.00642.756-0.152-0.1520.0000.0000.0000.000
111A112ALA00.0310.00344.0400.1100.1100.0000.0000.0000.000
112A113PRO0-0.0060.01244.025-0.010-0.0100.0000.0000.0000.000
113A114SER0-0.0230.00145.788-0.159-0.1590.0000.0000.0000.000
114A115VAL00.000-0.01347.1930.1000.1000.0000.0000.0000.000
115A116PHE0-0.037-0.01548.001-0.192-0.1920.0000.0000.0000.000
116A117ILE0-0.0030.00048.8810.1240.1240.0000.0000.0000.000
117A118PHE0-0.020-0.01148.015-0.123-0.1230.0000.0000.0000.000
118A119PRO00.0060.01250.3300.1050.1050.0000.0000.0000.000
119A120PRO00.0330.01650.6270.0430.0430.0000.0000.0000.000
120A121SER00.0490.03350.467-0.100-0.1000.0000.0000.0000.000
121A122ASP-1-0.892-0.95652.6665.6525.6520.0000.0000.0000.000
122A123GLU-1-0.995-1.01049.4966.4956.4950.0000.0000.0000.000
123A124GLN00.1040.05846.453-0.034-0.0340.0000.0000.0000.000
124A125LEU00.0120.01650.3820.0360.0360.0000.0000.0000.000
125A126LYS10.8950.95752.987-6.018-6.0180.0000.0000.0000.000
126A127SER0-0.069-0.04448.2510.0160.0160.0000.0000.0000.000
127A128GLY00.0150.00949.5040.0650.0650.0000.0000.0000.000
128A129THR0-0.072-0.05045.8260.0700.0700.0000.0000.0000.000
129A130ALA0-0.0180.00349.255-0.072-0.0720.0000.0000.0000.000
130A131SER00.000-0.01045.3330.0790.0790.0000.0000.0000.000
131A132VAL0-0.0300.00147.542-0.098-0.0980.0000.0000.0000.000
132A133VAL00.001-0.00144.1540.1330.1330.0000.0000.0000.000
133A134CYS0-0.056-0.02045.458-0.058-0.0580.0000.0000.0000.000
134A135LEU0-0.0220.00343.0160.1920.1920.0000.0000.0000.000
135A136LEU00.0000.00742.331-0.190-0.1900.0000.0000.0000.000
136A137ASN00.025-0.02242.4400.2960.2960.0000.0000.0000.000
137A138ASN0-0.008-0.00441.448-0.016-0.0160.0000.0000.0000.000
138A139PHE00.0090.01439.195-0.133-0.1330.0000.0000.0000.000
139A140TYR00.0430.02534.6250.2020.2020.0000.0000.0000.000
140A141PRO00.0370.01237.099-0.207-0.2070.0000.0000.0000.000
141A142ARG10.8850.91230.051-10.099-10.0990.0000.0000.0000.000
142A143GLU-1-0.888-0.91836.6657.8987.8980.0000.0000.0000.000
143A144ALA00.0040.00638.208-0.229-0.2290.0000.0000.0000.000
144A145LYS10.8330.91140.407-7.542-7.5420.0000.0000.0000.000
145A146VAL00.0580.01242.733-0.173-0.1730.0000.0000.0000.000
146A147GLN0-0.041-0.00844.4110.1630.1630.0000.0000.0000.000
147A148TRP00.0260.00444.699-0.287-0.2870.0000.0000.0000.000
148A149LYS10.8510.90449.087-6.120-6.1200.0000.0000.0000.000
149A150VAL00.0170.01751.913-0.044-0.0440.0000.0000.0000.000
150A151ASP-1-0.786-0.88854.6215.3925.3920.0000.0000.0000.000
151A152ASN0-0.040-0.03456.917-0.004-0.0040.0000.0000.0000.000
152A153ALA00.0070.02754.9540.0280.0280.0000.0000.0000.000
153A154LEU00.002-0.00949.3560.0570.0570.0000.0000.0000.000
154A155GLN0-0.0270.00347.9790.0290.0290.0000.0000.0000.000
155A156SER0-0.009-0.02944.9410.1030.1030.0000.0000.0000.000
156A157GLY0-0.0090.01141.726-0.057-0.0570.0000.0000.0000.000
157A158ASN0-0.005-0.00542.7870.0900.0900.0000.0000.0000.000
158A159SER0-0.015-0.01742.101-0.210-0.2100.0000.0000.0000.000
159A160GLN00.0010.01437.9940.0240.0240.0000.0000.0000.000
160A161GLU-1-0.765-0.86937.8667.6267.6260.0000.0000.0000.000
161A162SER0-0.059-0.00835.0510.3440.3440.0000.0000.0000.000
162A163VAL0-0.009-0.01233.204-0.253-0.2530.0000.0000.0000.000
163A164THR0-0.010-0.00433.5570.2070.2070.0000.0000.0000.000
164A165GLU-1-0.796-0.88327.92710.88510.8850.0000.0000.0000.000
165A166GLN0-0.051-0.04931.575-0.018-0.0180.0000.0000.0000.000
166A167ASP-1-0.753-0.86832.8708.6318.6310.0000.0000.0000.000
167A168SER0-0.027-0.01932.626-0.087-0.0870.0000.0000.0000.000
168A169LYS10.8260.89934.489-8.278-8.2780.0000.0000.0000.000
169A170ASP-1-0.810-0.89038.1967.6207.6200.0000.0000.0000.000
170A171SER0-0.0120.00035.263-0.099-0.0990.0000.0000.0000.000
171A172THR0-0.053-0.03136.6660.0450.0450.0000.0000.0000.000
172A173TYR0-0.029-0.01732.2790.1370.1370.0000.0000.0000.000
173A174SER00.0540.03037.437-0.361-0.3610.0000.0000.0000.000
174A175LEU0-0.012-0.00137.7500.2890.2890.0000.0000.0000.000
175A176SER0-0.0130.00339.277-0.297-0.2970.0000.0000.0000.000
176A177SER00.017-0.01440.0560.1430.1430.0000.0000.0000.000
177A178THR0-0.017-0.02041.801-0.191-0.1910.0000.0000.0000.000
178A179LEU00.0090.03043.2230.0870.0870.0000.0000.0000.000
179A180THR00.015-0.02043.220-0.119-0.1190.0000.0000.0000.000
180A181LEU0-0.032-0.00846.086-0.020-0.0200.0000.0000.0000.000
181A182SER00.0550.01249.224-0.029-0.0290.0000.0000.0000.000
182A183LYS10.9010.92150.571-5.721-5.7210.0000.0000.0000.000
183A184ALA00.0070.00453.612-0.119-0.1190.0000.0000.0000.000
184A185ASP-1-0.815-0.89552.4775.9475.9470.0000.0000.0000.000
185A186TYR00.0470.02453.025-0.078-0.0780.0000.0000.0000.000
186A187GLU-1-0.786-0.89254.8135.3955.3950.0000.0000.0000.000
187A188LYS10.7950.90255.713-5.838-5.8380.0000.0000.0000.000
188A189HIS10.8390.92255.684-5.712-5.7120.0000.0000.0000.000
189A190LYS10.9430.97558.914-4.994-4.9940.0000.0000.0000.000
190A191VAL0-0.014-0.00257.8650.0410.0410.0000.0000.0000.000
191A192TYR0-0.0010.01952.5980.1070.1070.0000.0000.0000.000
192A193ALA00.008-0.02153.709-0.041-0.0410.0000.0000.0000.000
193A195GLU-1-0.824-0.90649.5986.1186.1180.0000.0000.0000.000
194A196VAL00.0490.01545.3490.1510.1510.0000.0000.0000.000
195A197THR0-0.020-0.00946.222-0.181-0.1810.0000.0000.0000.000
196A198HIS00.012-0.01041.090-0.002-0.0020.0000.0000.0000.000
197A199GLN00.0610.02741.878-0.009-0.0090.0000.0000.0000.000
198A200GLY0-0.022-0.01445.093-0.100-0.1000.0000.0000.0000.000
199A201LEU0-0.061-0.03147.126-0.112-0.1120.0000.0000.0000.000
200A202SER00.0070.01449.6750.0290.0290.0000.0000.0000.000
201A203SER0-0.006-0.01052.506-0.048-0.0480.0000.0000.0000.000
202A204PRO0-0.023-0.01950.6540.0350.0350.0000.0000.0000.000
203A205VAL00.0060.02450.749-0.141-0.1410.0000.0000.0000.000
204A206THR00.018-0.00151.3150.1460.1460.0000.0000.0000.000
205A207LYS10.8840.97151.880-6.046-6.0460.0000.0000.0000.000
206A208SER00.018-0.01253.5180.0590.0590.0000.0000.0000.000
207A209PHE00.0210.01853.261-0.068-0.0680.0000.0000.0000.000
208A210ASN0-0.016-0.01057.662-0.072-0.0720.0000.0000.0000.000
209A211ARG10.8270.89957.413-5.423-5.4230.0000.0000.0000.000
210A212GLY00.0040.01559.590-0.134-0.1340.0000.0000.0000.000