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: Z628N

Calculation Name: 1R8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8N

Chain ID: A

ChEMBL ID:

UniProt ID: P83667

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1939342.87862
FMO2-HF: Nuclear repulsion 1867934.70639
FMO2-HF: Total energy -71408.172231
FMO2-MP2: Total energy -71614.444558


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-9.075-8.0388.546-3.496-6.089-0.004
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.030
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].
3A3ALA00.0240.0143.812-0.9780.327-0.013-0.705-0.5880.002
4A4GLU-1-0.852-0.8975.127-0.642-0.548-0.001-0.001-0.0920.000
5A5LYS10.8900.9584.946-0.219-0.2190.0000.0000.0000.000
6A6VAL00.0070.0106.7380.4860.4860.0000.0000.0000.000
7A7TYR0-0.030-0.0289.6010.1400.1400.0000.0000.0000.000
8A8ASP-1-0.808-0.92212.407-0.490-0.4900.0000.0000.0000.000
9A9ILE0-0.051-0.05015.7860.0210.0210.0000.0000.0000.000
10A10GLU-1-0.972-0.97118.348-0.201-0.2010.0000.0000.0000.000
11A11GLY0-0.037-0.00415.9740.0540.0540.0000.0000.0000.000
12A12TYR0-0.058-0.02814.2220.0700.0700.0000.0000.0000.000
13A13PRO0-0.051-0.0318.941-0.082-0.0820.0000.0000.0000.000
14A14VAL00.0090.01910.3950.1410.1410.0000.0000.0000.000
15A15PHE0-0.023-0.0319.711-0.233-0.2330.0000.0000.0000.000
16A16LEU00.0400.0268.0330.1340.1340.0000.0000.0000.000
17A17GLY0-0.035-0.01911.8440.1640.1640.0000.0000.0000.000
18A18SER0-0.076-0.02914.8910.1290.1290.0000.0000.0000.000
19A19GLH0-0.037-0.02916.772-0.053-0.0530.0000.0000.0000.000
20A20TYR0-0.010-0.00914.432-0.006-0.0060.0000.0000.0000.000
21A21TYR00.0140.02419.0770.0150.0150.0000.0000.0000.000
22A22ILE00.0060.00618.043-0.039-0.0390.0000.0000.0000.000
23A23VAL00.005-0.01220.8850.0440.0440.0000.0000.0000.000
24A24SER00.0100.01022.276-0.042-0.0420.0000.0000.0000.000
25A25ALA0-0.025-0.00721.4180.0190.0190.0000.0000.0000.000
26A26ILE00.0570.02123.3000.0230.0230.0000.0000.0000.000
27A27ILE0-0.022-0.00322.2420.0230.0230.0000.0000.0000.000
28A28GLY0-0.014-0.00326.012-0.010-0.0100.0000.0000.0000.000
29A29ALA0-0.009-0.00726.4840.0230.0230.0000.0000.0000.000
30A30GLY00.0240.01829.1300.0200.0200.0000.0000.0000.000
31A31GLY0-0.007-0.00929.457-0.019-0.0190.0000.0000.0000.000
32A32GLY00.0180.01728.228-0.004-0.0040.0000.0000.0000.000
33A33GLY0-0.016-0.01925.340-0.029-0.0290.0000.0000.0000.000
34A34VAL0-0.031-0.00823.2580.0230.0230.0000.0000.0000.000
35A35ARG10.8870.94326.2910.2550.2550.0000.0000.0000.000
36A36PRO00.0570.04127.8000.0010.0010.0000.0000.0000.000
37A37GLY00.000-0.00729.9270.0190.0190.0000.0000.0000.000
38A38ARG10.9010.93933.1500.1840.1840.0000.0000.0000.000
39A39THR00.0680.04434.895-0.011-0.0110.0000.0000.0000.000
40A40ARG10.9110.94636.6310.2210.2210.0000.0000.0000.000
41A41GLY00.0670.04739.6220.0000.0000.0000.0000.0000.000
42A42SER00.0010.00238.099-0.002-0.0020.0000.0000.0000.000
43A43MET0-0.027-0.02140.2190.0000.0000.0000.0000.0000.000
44A44CYS0-0.111-0.03335.5440.0010.0010.0000.0000.0000.000
45A45PRO0-0.063-0.04034.157-0.004-0.0040.0000.0000.0000.000
46A46MET00.0380.02331.296-0.010-0.0100.0000.0000.0000.000
47A47SER00.0100.01030.335-0.020-0.0200.0000.0000.0000.000
48A48ILE00.0310.03124.5870.0120.0120.0000.0000.0000.000
49A49ILE0-0.047-0.02028.5040.0040.0040.0000.0000.0000.000
50A50GLN00.0100.01226.866-0.002-0.0020.0000.0000.0000.000
51A51GLU-1-0.879-0.93829.108-0.232-0.2320.0000.0000.0000.000
52A52GLN0-0.005-0.01331.096-0.006-0.0060.0000.0000.0000.000
53A53SER0-0.021-0.01633.6810.0040.0040.0000.0000.0000.000
54A54ASP-1-0.885-0.94429.980-0.236-0.2360.0000.0000.0000.000
55A55LEU00.000-0.00330.138-0.003-0.0030.0000.0000.0000.000
56A56GLN0-0.0200.00231.0460.0060.0060.0000.0000.0000.000
57A57MET00.0470.01625.585-0.020-0.0200.0000.0000.0000.000
58A58GLY0-0.0060.01025.845-0.031-0.0310.0000.0000.0000.000
59A59LEU0-0.042-0.02826.1920.0180.0180.0000.0000.0000.000
60A60PRO00.009-0.00122.365-0.032-0.0320.0000.0000.0000.000
61A61VAL00.0030.00218.3030.0230.0230.0000.0000.0000.000
62A62ARG10.8930.94117.3000.4270.4270.0000.0000.0000.000
63A63PHE00.0210.01212.860-0.001-0.0010.0000.0000.0000.000
64A64SER0-0.009-0.01513.0220.0760.0760.0000.0000.0000.000
65A65SER00.1010.0418.0320.0340.0340.0000.0000.0000.000
66A66PRO0-0.043-0.01610.6960.2290.2290.0000.0000.0000.000
67A67GLU-1-0.955-0.9706.146-2.017-2.0170.0000.0000.0000.000
68A68GLU-1-0.916-0.9575.991-1.701-1.7010.0000.0000.0000.000
69A69LYS10.8990.9349.7650.4430.4430.0000.0000.0000.000
70A70GLN0-0.038-0.02610.7430.0960.0960.0000.0000.0000.000
71A71GLY00.1030.0627.5160.0650.0650.0000.0000.0000.000
72A72LYS10.8720.9365.455-0.363-0.3630.0000.0000.0000.000
73A73ILE00.0910.0485.468-0.865-0.8650.0000.0000.0000.000
74A74TYR0-0.027-0.0122.447-1.893-2.3368.562-2.780-5.340-0.006
75A75THR0-0.040-0.0265.1900.6710.736-0.001-0.003-0.0610.000
76A76ASP-1-0.791-0.8907.264-2.824-2.8240.0000.0000.0000.000
77A77THR0-0.0160.0104.766-0.075-0.059-0.001-0.007-0.0080.000
78A78GLU-1-0.969-0.9918.249-1.001-1.0010.0000.0000.0000.000
79A79LEU0-0.019-0.0099.268-0.057-0.0570.0000.0000.0000.000
80A80GLU-1-0.842-0.89812.400-0.519-0.5190.0000.0000.0000.000
81A81ILE0-0.010-0.01315.437-0.055-0.0550.0000.0000.0000.000
82A82GLU-1-0.846-0.90517.966-0.415-0.4150.0000.0000.0000.000
83A83PHE00.004-0.00620.966-0.018-0.0180.0000.0000.0000.000
84A84VAL0-0.050-0.03022.1650.0070.0070.0000.0000.0000.000
85A85GLU-1-0.825-0.90124.488-0.217-0.2170.0000.0000.0000.000
86A86LYS10.8560.92727.7510.2080.2080.0000.0000.0000.000
87A87PRO0-0.039-0.01529.8260.0170.0170.0000.0000.0000.000
88A88ASP-1-0.867-0.95233.175-0.190-0.1900.0000.0000.0000.000
89A90ALA00.0290.02030.996-0.001-0.0010.0000.0000.0000.000
90A91GLU-1-0.857-0.93531.204-0.202-0.2020.0000.0000.0000.000
91A92SER0-0.094-0.04725.923-0.020-0.0200.0000.0000.0000.000
92A93SER00.006-0.01325.0270.0090.0090.0000.0000.0000.000
93A94LYS10.8230.89119.5190.5790.5790.0000.0000.0000.000
94A95TRP0-0.015-0.01720.6880.0170.0170.0000.0000.0000.000
95A96VAL0-0.037-0.01821.823-0.041-0.0410.0000.0000.0000.000
96A97ILE00.0130.01622.5280.0130.0130.0000.0000.0000.000
97A98VAL00.0090.00425.5120.0170.0170.0000.0000.0000.000
98A99LYS10.8900.93629.2830.3310.3310.0000.0000.0000.000
99A100ASP-1-0.755-0.85331.240-0.262-0.2620.0000.0000.0000.000
100A101SER0-0.007-0.01934.7270.0120.0120.0000.0000.0000.000
101A102GLY0-0.0280.01235.0660.0020.0020.0000.0000.0000.000
102A103GLU-1-0.939-1.00130.980-0.354-0.3540.0000.0000.0000.000
103A104ALA0-0.0220.00027.8670.0060.0060.0000.0000.0000.000
104A105ARG10.9070.93428.5250.2790.2790.0000.0000.0000.000
105A106VAL0-0.0020.00123.255-0.012-0.0120.0000.0000.0000.000
106A107ALA0-0.054-0.02526.1930.0320.0320.0000.0000.0000.000
107A108ILE00.0030.00725.364-0.037-0.0370.0000.0000.0000.000
108A109GLY00.0600.05126.5810.0290.0290.0000.0000.0000.000
109A110GLY00.005-0.01027.007-0.024-0.0240.0000.0000.0000.000
110A111SER0-0.023-0.03427.6920.0090.0090.0000.0000.0000.000
111A112GLU-1-0.966-0.97230.092-0.224-0.2240.0000.0000.0000.000
112A113ASP-1-0.788-0.87430.187-0.270-0.2700.0000.0000.0000.000
113A114HIS10.8020.87429.6450.3100.3100.0000.0000.0000.000
114A115PRO00.0120.02532.9790.0000.0000.0000.0000.0000.000
115A116GLN00.0600.01529.541-0.031-0.0310.0000.0000.0000.000
116A117GLY0-0.047-0.02631.015-0.016-0.0160.0000.0000.0000.000
117A118GLU-1-0.882-0.94632.240-0.254-0.2540.0000.0000.0000.000
118A119LEU0-0.065-0.01527.039-0.020-0.0200.0000.0000.0000.000
119A120VAL0-0.024-0.00324.2890.0120.0120.0000.0000.0000.000
120A121ARG10.9240.94921.5830.4230.4230.0000.0000.0000.000
121A122GLY00.036-0.00219.2510.0200.0200.0000.0000.0000.000
122A123PHE0-0.0400.00614.2310.0260.0260.0000.0000.0000.000
123A124PHE00.003-0.00615.4200.0760.0760.0000.0000.0000.000
124A125LYS10.8300.91510.3472.0252.0250.0000.0000.0000.000
125A126ILE0-0.017-0.00511.0170.2970.2970.0000.0000.0000.000
126A127GLU-1-0.773-0.90711.191-2.146-2.1460.0000.0000.0000.000
127A128LYS10.8250.88311.8521.0471.0470.0000.0000.0000.000
128A129LEU0-0.031-0.02014.1110.0670.0670.0000.0000.0000.000
129A130GLY00.0200.01417.2920.0880.0880.0000.0000.0000.000
130A131SER0-0.030-0.03716.643-0.075-0.0750.0000.0000.0000.000
131A132LEU0-0.013-0.01618.0330.0110.0110.0000.0000.0000.000
132A133ALA0-0.025-0.00718.4740.0270.0270.0000.0000.0000.000
133A134TYR00.0430.04111.977-0.100-0.1000.0000.0000.0000.000
134A135LYS10.8360.90616.0450.8910.8910.0000.0000.0000.000
135A136LEU0-0.0120.00415.897-0.130-0.1300.0000.0000.0000.000
136A137VAL00.0240.01815.3730.1090.1090.0000.0000.0000.000
137A138PHE00.004-0.00817.062-0.088-0.0880.0000.0000.0000.000
138A139CYS00.0090.00616.086-0.027-0.0270.0000.0000.0000.000
139A140PRO00.0160.00518.469-0.006-0.0060.0000.0000.0000.000
140A141LYS10.9610.98219.2710.5120.5120.0000.0000.0000.000
141A142SER0-0.019-0.02320.7640.0000.0000.0000.0000.0000.000
142A143ASP-1-0.908-0.92422.539-0.463-0.4630.0000.0000.0000.000
143A144SER0-0.019-0.03219.089-0.058-0.0580.0000.0000.0000.000
144A145GLY0-0.011-0.00318.3770.0390.0390.0000.0000.0000.000
145A146SER0-0.073-0.03619.3550.0200.0200.0000.0000.0000.000
146A148SER00.0250.02719.7700.0420.0420.0000.0000.0000.000
147A149ASP-1-0.703-0.84120.315-0.763-0.7630.0000.0000.0000.000
148A150ILE0-0.025-0.00119.3610.0580.0580.0000.0000.0000.000
149A151GLY00.044-0.00422.591-0.008-0.0080.0000.0000.0000.000
150A152ILE0-0.042-0.01225.5740.0050.0050.0000.0000.0000.000
151A153ASN0-0.037-0.01428.5830.0160.0160.0000.0000.0000.000
152A154TYR00.015-0.00629.5390.0070.0070.0000.0000.0000.000
153A155GLU-1-0.778-0.88534.388-0.251-0.2510.0000.0000.0000.000
154A156GLY0-0.051-0.02737.1740.0100.0100.0000.0000.0000.000
155A157ARG10.8800.92335.2170.2170.2170.0000.0000.0000.000
156A158ARG10.8300.93230.3110.2770.2770.0000.0000.0000.000
157A159SER00.0340.01330.491-0.017-0.0170.0000.0000.0000.000
158A160LEU00.0180.00623.489-0.003-0.0030.0000.0000.0000.000
159A161VAL0-0.026-0.01426.9500.0120.0120.0000.0000.0000.000
160A162LEU00.0050.00623.029-0.036-0.0360.0000.0000.0000.000
161A163LYS10.8340.93625.2340.4070.4070.0000.0000.0000.000
162A164SER0-0.009-0.01726.034-0.016-0.0160.0000.0000.0000.000
163A165SER0-0.057-0.04027.4220.0000.0000.0000.0000.0000.000
164A166ASP-1-0.893-0.93922.737-0.574-0.5740.0000.0000.0000.000
165A167ASP-1-0.904-0.94024.410-0.352-0.3520.0000.0000.0000.000
166A168VAL0-0.082-0.04526.1830.0250.0250.0000.0000.0000.000
167A169PRO00.0060.01521.7150.0010.0010.0000.0000.0000.000
168A170PHE0-0.047-0.02922.9950.0390.0390.0000.0000.0000.000
169A171ARG10.8980.94121.2470.3480.3480.0000.0000.0000.000
170A172VAL0-0.0010.01118.0230.0500.0500.0000.0000.0000.000
171A173VAL00.0200.00517.939-0.042-0.0420.0000.0000.0000.000
172A174PHE00.0260.01414.0560.0220.0220.0000.0000.0000.000
173A175VAL00.0320.01417.8190.0350.0350.0000.0000.0000.000
174A176LYS11.0241.02718.3180.2540.2540.0000.0000.0000.000
175A177PRO0-0.003-0.00820.2310.0350.0350.0000.0000.0000.000
176A178ARG10.9100.96223.3630.2530.2530.0000.0000.0000.000
177A179SER00.010-0.01023.9680.0010.0010.0000.0000.0000.000
178A180GLY00.019-0.00126.7970.0120.0120.0000.0000.0000.000
179A181SER0-0.041-0.01427.2710.0020.0020.0000.0000.0000.000
180A182GLU-1-0.904-0.95828.084-0.118-0.1180.0000.0000.0000.000
181A183THR0-0.085-0.04225.114-0.007-0.0070.0000.0000.0000.000
182A184GLU-1-0.912-0.94927.543-0.151-0.1510.0000.0000.0000.000
183A185SER0-0.082-0.02326.426-0.022-0.0220.0000.0000.0000.000