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: R1JN8

Calculation Name: 1B77-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B77

Chain ID: A

ChEMBL ID:

UniProt ID: O80164

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2602965.222816
FMO2-HF: Nuclear repulsion 2514816.648982
FMO2-HF: Total energy -88148.573834
FMO2-MP2: Total energy -88405.732604


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:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-357.752-359.17559.415-25.827-32.165-0.26
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.705 / q_NPA : 0.856
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].
3A3LEU 0-0.0070.0022.0922.8662.6046.247-1.692-4.293-0.004
4A4SER 00.0450.0164.1694.1904.3290.002-0.043-0.0990.000
5A5LYS 11.0090.9677.81720.14420.1440.0000.0000.0000.000
6A6ASP -1-0.899-0.93410.641-18.217-18.2170.0000.0000.0000.000
7A7THR 0-0.026-0.0384.8672.1072.1070.0000.0000.0000.000
8A8ILE 0-0.027-0.0127.1671.3991.3990.0000.0000.0000.000
9A9ALA 0-0.024-0.0148.8941.3711.3710.0000.0000.0000.000
10A10ILE 00.0230.01510.2011.1391.1390.0000.0000.0000.000
11A11LEU 00.007-0.0025.0980.9500.9500.0000.0000.0000.000
12A12LYS 10.9400.9709.78117.41717.4170.0000.0000.0000.000
13A13ASN 0-0.0130.02212.9120.8610.8610.0000.0000.0000.000
14A14PHE 00.0530.04011.0850.7720.7720.0000.0000.0000.000
15A15ALA 00.0180.02312.9400.6690.6690.0000.0000.0000.000
16A16SER 0-0.111-0.06814.4250.9090.9090.0000.0000.0000.000
17A17ILE 0-0.068-0.04816.4920.8910.8910.0000.0000.0000.000
18A18ASN 0-0.066-0.05215.5510.6490.6490.0000.0000.0000.000
19A19SER 00.0270.02615.149-0.453-0.4530.0000.0000.0000.000
20A20GLY 00.0150.01813.722-0.681-0.6810.0000.0000.0000.000
21A21ILE 0-0.050-0.0318.7230.3240.3240.0000.0000.0000.000
22A22LEU 0-0.015-0.00310.521-0.409-0.4090.0000.0000.0000.000
23A23LEU 0-0.022-0.0013.7430.1210.4050.007-0.043-0.2480.000
24A24SER 0-0.005-0.0217.2250.5940.5940.0000.0000.0000.000
25A25GLN 0-0.061-0.0466.600-2.135-2.1350.0000.0000.0000.000
26A26GLY 00.0210.0316.6903.5173.5170.0000.0000.0000.000
27A27LYS 10.9170.9706.11125.37425.3740.0000.0000.0000.000
28A28PHE 0-0.022-0.0177.8161.9791.9790.0000.0000.0000.000
29A29ILE 00.0120.0266.120-1.183-1.1830.0000.0000.0000.000
30A30MET 0-0.0010.0028.9681.8021.8020.0000.0000.0000.000
31A31THR 0-0.010-0.00211.755-0.337-0.3370.0000.0000.0000.000
32A32ARG 10.9480.97014.15412.21912.2190.0000.0000.0000.000
33A33ALA 00.0090.03617.860-0.212-0.2120.0000.0000.0000.000
34A34VAL 00.0660.02920.2510.1970.1970.0000.0000.0000.000
35A35ASN 00.0040.01922.0800.0250.0250.0000.0000.0000.000
36A36GLY 0-0.072-0.04422.9210.2990.2990.0000.0000.0000.000
37A37THR 00.017-0.01623.938-0.038-0.0380.0000.0000.0000.000
38A38THR 00.0440.02219.8010.2520.2520.0000.0000.0000.000
39A39TYR 0-0.072-0.07516.646-0.436-0.4360.0000.0000.0000.000
40A40ALA 00.0180.00515.2690.3800.3800.0000.0000.0000.000
41A41GLU -1-0.847-0.89813.245-15.119-15.1190.0000.0000.0000.000
42A42ALA 00.0240.00011.3830.7390.7390.0000.0000.0000.000
43A43ASN 00.0020.01610.741-1.536-1.5360.0000.0000.0000.000
44A44ILE 0-0.009-0.0054.8620.6910.6910.0000.0000.0000.000
45A45SER 0-0.011-0.0218.761-0.498-0.4980.0000.0000.0000.000
46A46ASP -1-0.788-0.8503.530-36.580-36.3880.007-0.036-0.1630.000
47A47GLU -1-0.880-0.9684.444-29.437-29.2190.000-0.057-0.1610.000
48A48ILE 0-0.071-0.0302.312-17.554-15.1565.660-2.865-5.193-0.015
49A49ASP -1-0.797-0.9081.960-118.011-113.5219.876-6.245-8.121-0.104
50A50PHE 0-0.029-0.0221.9374.3375.0222.689-0.999-2.374-0.003
51A51ASP -1-0.842-0.9105.468-25.501-25.3310.000-0.009-0.1610.000
52A52VAL 0-0.014-0.0105.9920.6800.6800.0000.0000.0000.000
53A53ALA 0-0.0040.0068.5310.2520.2520.0000.0000.0000.000
54A54LEU 0-0.0040.0007.298-0.058-0.0580.0000.0000.0000.000
55A55TYR 00.0120.00211.4690.8570.8570.0000.0000.0000.000
56A56ASP -1-0.844-0.91914.233-15.024-15.0240.0000.0000.0000.000
57A57LEU 00.0240.0088.474-0.824-0.8240.0000.0000.0000.000
58A58ASN 00.0480.00911.479-1.126-1.1260.0000.0000.0000.000
59A59SER 0-0.028-0.02813.933-0.131-0.1310.0000.0000.0000.000
60A60PHE 00.0230.0195.999-0.216-0.2160.0000.0000.0000.000
61A61LEU 0-0.003-0.0127.897-0.938-0.9380.0000.0000.0000.000
62A62SER 0-0.070-0.03710.5870.1120.1120.0000.0000.0000.000
63A63ILE 00.0190.04111.0440.4870.4870.0000.0000.0000.000
64A64LEU 0-0.0040.0026.416-0.368-0.3680.0000.0000.0000.000
65A65SER 0-0.144-0.08610.4570.3030.3030.0000.0000.0000.000
66A66LEU 0-0.043-0.02713.3831.1161.1160.0000.0000.0000.000
67A67VAL 0-0.047-0.00310.0380.4150.4150.0000.0000.0000.000
68A68SER 0-0.027-0.05611.8101.0931.0930.0000.0000.0000.000
69A69ASP -1-0.933-0.96810.556-24.179-24.1790.0000.0000.0000.000
70A70ASP -1-0.996-0.9988.705-31.495-31.4950.0000.0000.0000.000
71A71ALA 00.0020.0057.611-3.519-3.5190.0000.0000.0000.000
72A72GLU -1-0.870-0.9051.705-113.636-118.08713.596-5.557-3.588-0.066
73A73ILE 0-0.003-0.0101.91411.68210.2567.388-2.275-3.686-0.004
74A74SER 0-0.025-0.0041.735-37.209-41.22813.943-5.951-3.973-0.064
75A75MET 00.0180.0154.2288.2948.4530.000-0.055-0.1050.000
76A76HIS 0-0.024-0.0137.602-1.023-1.0230.0000.0000.0000.000
77A77THR 0-0.013-0.02910.5951.3291.3290.0000.0000.0000.000
78A78ASP -1-0.884-0.95113.893-19.874-19.8740.0000.0000.0000.000
79A79GLY 0-0.0090.00812.6191.0851.0850.0000.0000.0000.000
80A80ASN 0-0.0050.00111.738-0.561-0.5610.0000.0000.0000.000
81A81ILE 00.0080.0126.048-2.259-2.2590.0000.0000.0000.000
82A82LYS 10.9220.9627.41132.97632.9760.0000.0000.0000.000
83A83ILE 00.0050.0046.456-6.679-6.6790.0000.0000.0000.000
84A84ALA 0-0.035-0.0337.2154.9394.9390.0000.0000.0000.000
85A85ASP -1-0.735-0.8228.909-25.294-25.2940.0000.0000.0000.000
86A86THR 0-0.038-0.02711.6961.1041.1040.0000.0000.0000.000
87A87ARG 10.9130.94614.31216.56216.5620.0000.0000.0000.000
88A88SER 0-0.0100.00314.9490.8270.8270.0000.0000.0000.000
89A89THR 0-0.032-0.02411.184-1.760-1.7600.0000.0000.0000.000
90A90VAL 00.0210.02811.6092.0132.0130.0000.0000.0000.000
91A91TYR 00.000-0.01011.060-2.602-2.6020.0000.0000.0000.000
92A92TRP 0-0.004-0.00610.2851.6141.6140.0000.0000.0000.000
93A93PRO 0-0.015-0.00411.502-1.150-1.1500.0000.0000.0000.000
94A94ALA 00.0290.03111.038-0.783-0.7830.0000.0000.0000.000
95A95ALA 0-0.047-0.02712.4191.3001.3000.0000.0000.0000.000
96A96ASP -1-0.802-0.88814.346-15.112-15.1120.0000.0000.0000.000
97A97LYS 10.9740.96013.95317.99517.9950.0000.0000.0000.000
98A98SER 0-0.087-0.04016.6020.4480.4480.0000.0000.0000.000
99A99THR 0-0.057-0.02717.9570.4440.4440.0000.0000.0000.000
100A100ILE 00.0030.00413.7760.0080.0080.0000.0000.0000.000
101A101VAL 0-0.0030.00517.8130.2380.2380.0000.0000.0000.000
102A102PHE 0-0.020-0.02014.466-0.543-0.5430.0000.0000.0000.000
103A103PRO 00.008-0.00114.6550.6810.6810.0000.0000.0000.000
104A104ASN 00.0100.00015.810-0.721-0.7210.0000.0000.0000.000
105A105LYS 10.9280.96217.25711.80111.8010.0000.0000.0000.000
106A106PRO 00.0670.03015.9650.3060.3060.0000.0000.0000.000
107A107ILE 0-0.045-0.01017.6380.6580.6580.0000.0000.0000.000
108A108GLN 0-0.001-0.00420.750-0.329-0.3290.0000.0000.0000.000
109A109PHE 0-0.046-0.03223.2760.2650.2650.0000.0000.0000.000
110A110PRO 00.0040.01625.340-0.001-0.0010.0000.0000.0000.000
111A111VAL 0-0.0020.00128.935-0.135-0.1350.0000.0000.0000.000
112A112ALA 0-0.037-0.02730.2770.1380.1380.0000.0000.0000.000
113A113SER 00.0090.01731.8950.0580.0580.0000.0000.0000.000
114A114VAL 00.0260.00734.0060.2090.2090.0000.0000.0000.000
115A115ILE 0-0.049-0.02130.666-0.311-0.3110.0000.0000.0000.000
116A116THR 00.0320.03131.6340.2350.2350.0000.0000.0000.000
117A117GLU -1-0.960-0.98929.739-9.301-9.3010.0000.0000.0000.000
118A118ILE 00.0120.02727.7120.2630.2630.0000.0000.0000.000
119A119LYS 10.9960.99328.3448.2178.2170.0000.0000.0000.000
120A120ALA 00.0280.00626.3900.0260.0260.0000.0000.0000.000
121A121GLU -1-0.945-0.97627.647-8.734-8.7340.0000.0000.0000.000
122A122ASP -1-0.829-0.91030.659-8.275-8.2750.0000.0000.0000.000
123A123LEU 0-0.013-0.00324.4690.1100.1100.0000.0000.0000.000
124A124GLN 0-0.024-0.02127.837-0.282-0.2820.0000.0000.0000.000
125A125GLN 00.0220.03428.8800.1140.1140.0000.0000.0000.000
126A126LEU 00.0670.04330.1660.1400.1400.0000.0000.0000.000
127A127LEU 00.009-0.00225.4130.1060.1060.0000.0000.0000.000
128A128ARG 10.8270.92028.0639.4759.4750.0000.0000.0000.000
129A129VAL 00.0100.00031.6810.1110.1110.0000.0000.0000.000
130A130SER 00.017-0.00332.0270.2100.2100.0000.0000.0000.000
131A131ARG 10.9280.96926.9899.6599.6590.0000.0000.0000.000
132A132GLY 0-0.0230.00133.5540.1080.1080.0000.0000.0000.000
133A133LEU 0-0.037-0.00936.8680.2260.2260.0000.0000.0000.000
134A134GLN 0-0.047-0.02436.4630.2650.2650.0000.0000.0000.000
135A135ILE 0-0.0220.00534.8830.1000.1000.0000.0000.0000.000
136A136ASP -1-0.789-0.90033.537-7.873-7.8730.0000.0000.0000.000
137A137THR 0-0.043-0.01133.355-0.140-0.1400.0000.0000.0000.000
138A138ILE 00.0260.00330.8360.1550.1550.0000.0000.0000.000
139A139ALA 00.0070.00434.893-0.069-0.0690.0000.0000.0000.000
140A140ILE 0-0.043-0.01731.4940.0460.0460.0000.0000.0000.000
141A141THR 0-0.023-0.05636.0890.0740.0740.0000.0000.0000.000
142A142ASN 00.0100.02639.468-0.136-0.1360.0000.0000.0000.000
143A143LYS 10.9430.95341.7946.3706.3700.0000.0000.0000.000
144A144ASP -1-0.933-0.96944.360-6.088-6.0880.0000.0000.0000.000
145A145GLY 00.0380.03145.3280.0120.0120.0000.0000.0000.000
146A146LYS 10.8740.93841.2526.7016.7010.0000.0000.0000.000
147A147ILE 00.0040.02535.8220.0350.0350.0000.0000.0000.000
148A148VAL 0-0.041-0.03138.295-0.054-0.0540.0000.0000.0000.000
149A149ILE 00.0190.01032.344-0.088-0.0880.0000.0000.0000.000
150A150ASN 0-0.020-0.00236.6480.1270.1270.0000.0000.0000.000
151A151GLY 00.0240.00136.895-0.178-0.1780.0000.0000.0000.000
152A152TYR 00.011-0.01237.5830.1920.1920.0000.0000.0000.000
153A153ASN 00.0460.02637.850-0.211-0.2110.0000.0000.0000.000
154A154LYS 10.9250.95038.0487.3057.3050.0000.0000.0000.000
155A155VAL 0-0.041-0.01538.7340.1460.1460.0000.0000.0000.000
156A156GLU -1-0.959-0.97341.281-6.390-6.3900.0000.0000.0000.000
157A157ASP -1-0.834-0.94642.977-6.283-6.2830.0000.0000.0000.000
158A158SER 00.0050.00942.937-0.114-0.1140.0000.0000.0000.000
159A159GLY 0-0.001-0.00843.256-0.064-0.0640.0000.0000.0000.000
160A160LEU 0-0.039-0.00838.5870.0000.0000.0000.0000.0000.000
161A161THR 0-0.054-0.02742.9810.0950.0950.0000.0000.0000.000
162A162ARG 10.8560.93144.9756.2316.2310.0000.0000.0000.000
163A163PRO 0-0.0080.02042.145-0.104-0.1040.0000.0000.0000.000
164A164LYS 10.8780.93640.5906.9616.9610.0000.0000.0000.000
165A165TYR 0-0.049-0.07935.368-0.050-0.0500.0000.0000.0000.000
166A166SER 0-0.0090.00039.4770.0130.0130.0000.0000.0000.000
167A167LEU 00.0120.02533.4180.0310.0310.0000.0000.0000.000
168A168THR 00.002-0.00537.6830.0500.0500.0000.0000.0000.000
169A169LEU 0-0.060-0.02733.167-0.144-0.1440.0000.0000.0000.000
170A170THR 0-0.008-0.00934.8360.0750.0750.0000.0000.0000.000
171A171ASP -1-0.861-0.92137.643-6.840-6.8400.0000.0000.0000.000
172A172TYR 0-0.074-0.04339.681-0.222-0.2220.0000.0000.0000.000
173A173ASP -1-0.893-0.95241.546-6.523-6.5230.0000.0000.0000.000
174A174GLY 0-0.074-0.04742.5250.0880.0880.0000.0000.0000.000
175A175SER 0-0.047-0.01943.4760.0870.0870.0000.0000.0000.000
176A176ASN 00.0230.00841.7210.1390.1390.0000.0000.0000.000
177A177ASN 0-0.030-0.01743.4380.0070.0070.0000.0000.0000.000
178A178PHE 00.0490.00837.935-0.120-0.1200.0000.0000.0000.000
179A179ASN 0-0.0010.03739.4270.0890.0890.0000.0000.0000.000
180A180PHE 00.010-0.00834.077-0.021-0.0210.0000.0000.0000.000
181A181VAL 00.0090.01635.127-0.071-0.0710.0000.0000.0000.000
182A182ILE 00.0170.00128.954-0.225-0.2250.0000.0000.0000.000
183A183ASN 00.0890.04729.5390.2550.2550.0000.0000.0000.000
184A184MET 00.0110.00429.047-0.313-0.3130.0000.0000.0000.000
185A185ALA 0-0.031-0.00827.788-0.308-0.3080.0000.0000.0000.000
186A186ASN 0-0.033-0.03524.752-0.095-0.0950.0000.0000.0000.000
187A187MET 00.0180.01123.915-0.397-0.3970.0000.0000.0000.000
188A188LYS 10.8460.94020.17411.50811.5080.0000.0000.0000.000
189A189ILE 00.0010.02219.812-0.563-0.5630.0000.0000.0000.000
190A190GLN 0-0.0020.01015.8000.0230.0230.0000.0000.0000.000
191A191PRO 0-0.0170.00519.9910.3280.3280.0000.0000.0000.000
192A192GLY 00.0630.02021.194-0.474-0.4740.0000.0000.0000.000
193A193ASN 0-0.021-0.00823.3030.6540.6540.0000.0000.0000.000
194A194TYR 0-0.055-0.06420.510-0.569-0.5690.0000.0000.0000.000
195A195LYS 10.9951.01325.19110.81610.8160.0000.0000.0000.000
196A196VAL 0-0.041-0.04026.128-0.304-0.3040.0000.0000.0000.000
197A197MET 0-0.044-0.02124.7170.3070.3070.0000.0000.0000.000
198A198LEU 00.0360.01428.833-0.235-0.2350.0000.0000.0000.000
199A199TRP 00.0300.00130.4940.0200.0200.0000.0000.0000.000
200A200GLY 00.0630.02432.526-0.073-0.0730.0000.0000.0000.000
201A201ALA 0-0.019-0.00135.2270.1050.1050.0000.0000.0000.000
202A202GLY 00.0200.00936.900-0.053-0.0530.0000.0000.0000.000
203A203ASP -1-0.912-0.95837.503-7.648-7.6480.0000.0000.0000.000
204A204LYS 10.8940.96032.2098.2458.2450.0000.0000.0000.000
205A205VAL 00.0560.03132.9400.0630.0630.0000.0000.0000.000
206A206ALA 0-0.048-0.02627.525-0.237-0.2370.0000.0000.0000.000
207A207ALA 00.0300.01627.6500.2130.2130.0000.0000.0000.000
208A208LYS 10.9360.98421.50811.39711.3970.0000.0000.0000.000
209A209PHE 0-0.011-0.00123.1160.3240.3240.0000.0000.0000.000
210A210GLU -1-0.916-0.97220.751-12.403-12.4030.0000.0000.0000.000
211A211SER 00.0240.03219.3270.2570.2570.0000.0000.0000.000
212A212SER 0-0.051-0.03519.758-0.232-0.2320.0000.0000.0000.000
213A213GLN 00.0160.00015.200-0.816-0.8160.0000.0000.0000.000
214A214VAL 0-0.0070.00414.067-0.822-0.8220.0000.0000.0000.000
215A215SER 00.0300.01716.4421.0581.0580.0000.0000.0000.000
216A216TYR 0-0.020-0.03917.328-0.349-0.3490.0000.0000.0000.000
217A217VAL 0-0.031-0.01520.1880.4210.4210.0000.0000.0000.000
218A218ILE 0-0.043-0.02522.599-0.268-0.2680.0000.0000.0000.000
219A219ALA 0-0.0070.00025.1070.2590.2590.0000.0000.0000.000
220A220MET 0-0.025-0.00527.9240.0470.0470.0000.0000.0000.000
221A221GLU -1-0.897-0.95331.339-8.488-8.4880.0000.0000.0000.000
222A222ALA 00.0160.01634.2770.0790.0790.0000.0000.0000.000
223A223ASP -1-0.916-0.96037.206-7.274-7.2740.0000.0000.0000.000
224A224SER 0-0.033-0.03135.6300.0600.0600.0000.0000.0000.000
225A225THR 0-0.043-0.02138.2350.1200.1200.0000.0000.0000.000
226A226HIS 0-0.086-0.05638.535-0.079-0.0790.0000.0000.0000.000
227A227ASP -1-0.840-0.91240.904-6.358-6.3580.0000.0000.0000.000
228A228PHE -1-0.947-0.96138.904-7.023-7.0230.0000.0000.0000.000