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: 6N32Z

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1940722.688395
FMO2-HF: Nuclear repulsion 1869315.50116
FMO2-HF: Total energy -71407.187235
FMO2-MP2: Total energy -71613.554814


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.
-8.822-8.098.918-3.627-6.021-0.004
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 : -0.023 / q_NPA : -0.025
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].
3A3ALA00.0230.0183.812-0.9650.427-0.011-0.758-0.6230.002
4A4GLU-1-0.918-0.9605.132-0.495-0.405-0.001-0.001-0.0870.000
5A5LYS10.8720.9494.923-0.467-0.4670.0000.0000.0000.000
6A6VAL00.0240.0166.7470.4540.4540.0000.0000.0000.000
7A7TYR0-0.031-0.0319.5990.1430.1430.0000.0000.0000.000
8A8ASP-1-0.817-0.91812.414-0.468-0.4680.0000.0000.0000.000
9A9ILE0-0.054-0.05715.7890.0260.0260.0000.0000.0000.000
10A10GLU-1-0.985-0.98118.316-0.179-0.1790.0000.0000.0000.000
11A11GLY0-0.037-0.00115.9910.0520.0520.0000.0000.0000.000
12A12TYR0-0.066-0.03014.2510.0740.0740.0000.0000.0000.000
13A13PRO0-0.070-0.0428.992-0.080-0.0800.0000.0000.0000.000
14A14VAL00.0200.02710.4040.1290.1290.0000.0000.0000.000
15A15PHE0-0.024-0.0359.705-0.230-0.2300.0000.0000.0000.000
16A16LEU00.0360.0238.0700.1460.1460.0000.0000.0000.000
17A17GLY0-0.034-0.01811.8570.1600.1600.0000.0000.0000.000
18A18SER0-0.075-0.02914.8810.1320.1320.0000.0000.0000.000
19A19GLH0-0.029-0.02116.762-0.053-0.0530.0000.0000.0000.000
20A20TYR00.0090.00514.404-0.007-0.0070.0000.0000.0000.000
21A21TYR0-0.0010.02019.0650.0150.0150.0000.0000.0000.000
22A22ILE00.0190.01018.382-0.036-0.0360.0000.0000.0000.000
23A23VAL00.008-0.01020.8680.0410.0410.0000.0000.0000.000
24A24SER00.0000.00222.263-0.040-0.0400.0000.0000.0000.000
25A25ALA0-0.019-0.00521.4120.0180.0180.0000.0000.0000.000
26A26ILE00.0630.02523.2920.0210.0210.0000.0000.0000.000
27A27ILE0-0.040-0.01122.2770.0210.0210.0000.0000.0000.000
28A28GLY0-0.023-0.01326.003-0.010-0.0100.0000.0000.0000.000
29A29ALA0-0.012-0.00626.4720.0220.0220.0000.0000.0000.000
30A30GLY00.0210.01529.1230.0190.0190.0000.0000.0000.000
31A31GLY0-0.014-0.01029.442-0.018-0.0180.0000.0000.0000.000
32A32GLY00.0200.01928.217-0.003-0.0030.0000.0000.0000.000
33A33GLY0-0.024-0.02925.324-0.027-0.0270.0000.0000.0000.000
34A34VAL0-0.020-0.00223.1890.0220.0220.0000.0000.0000.000
35A35ARG10.9520.98726.2680.2490.2490.0000.0000.0000.000
36A36PRO00.0490.03927.7000.0030.0030.0000.0000.0000.000
37A37GLY00.009-0.00529.8980.0180.0180.0000.0000.0000.000
38A38ARG10.9200.94633.1210.1840.1840.0000.0000.0000.000
39A39THR00.0700.04634.878-0.011-0.0110.0000.0000.0000.000
40A40ARG10.9210.95036.5970.2140.2140.0000.0000.0000.000
41A41GLY00.0650.04639.5880.0000.0000.0000.0000.0000.000
42A42SER0-0.018-0.00138.215-0.002-0.0020.0000.0000.0000.000
43A43MET0-0.016-0.01540.2490.0000.0000.0000.0000.0000.000
44A44CYS0-0.114-0.02935.5380.0010.0010.0000.0000.0000.000
45A45PRO0-0.067-0.04234.158-0.004-0.0040.0000.0000.0000.000
46A46MET00.0510.02731.349-0.011-0.0110.0000.0000.0000.000
47A47SER0-0.002-0.00130.365-0.020-0.0200.0000.0000.0000.000
48A48ILE00.0380.03824.5670.0120.0120.0000.0000.0000.000
49A49ILE0-0.051-0.02128.4730.0050.0050.0000.0000.0000.000
50A50GLN00.0060.00127.023-0.002-0.0020.0000.0000.0000.000
51A51GLU-1-0.950-0.98629.086-0.227-0.2270.0000.0000.0000.000
52A52GLN0-0.008-0.01331.078-0.004-0.0040.0000.0000.0000.000
53A53SER0-0.0010.00133.6600.0050.0050.0000.0000.0000.000
54A54ASP-1-0.887-0.94529.954-0.226-0.2260.0000.0000.0000.000
55A55LEU0-0.013-0.00630.131-0.004-0.0040.0000.0000.0000.000
56A56GLN0-0.013-0.00331.0340.0030.0030.0000.0000.0000.000
57A57MET00.0410.01025.545-0.021-0.0210.0000.0000.0000.000
58A58GLY0-0.0120.00925.831-0.031-0.0310.0000.0000.0000.000
59A59LEU0-0.048-0.03026.1350.0180.0180.0000.0000.0000.000
60A60PRO00.008-0.00222.442-0.031-0.0310.0000.0000.0000.000
61A61VAL00.0110.00818.0000.0250.0250.0000.0000.0000.000
62A62ARG10.8750.93617.2890.4490.4490.0000.0000.0000.000
63A63PHE00.0160.00812.8330.0030.0030.0000.0000.0000.000
64A64SER0-0.008-0.01013.0720.0700.0700.0000.0000.0000.000
65A65SER00.1000.0328.1240.0410.0410.0000.0000.0000.000
66A66PRO0-0.053-0.01510.8650.2220.2220.0000.0000.0000.000
67A67GLU-1-0.970-0.9745.773-2.282-2.2820.0000.0000.0000.000
68A68GLU-1-0.895-0.9425.647-2.343-2.3430.0000.0000.0000.000
69A69LYS10.8980.9309.7550.4790.4790.0000.0000.0000.000
70A70GLN0-0.037-0.02710.7150.1100.1100.0000.0000.0000.000
71A71GLY00.1110.0647.5090.0260.0260.0000.0000.0000.000
72A72LYS10.8700.9325.362-0.332-0.3320.0000.0000.0000.000
73A73ILE00.0890.0495.455-0.830-0.8300.0000.0000.0000.000
74A74TYR0-0.018-0.0062.389-0.536-1.3518.931-2.865-5.251-0.006
75A75THR0-0.036-0.0315.1690.6290.694-0.001-0.003-0.0600.000
76A76ASP-1-0.907-0.9467.234-2.679-2.6790.0000.0000.0000.000
77A77THR0-0.0230.0024.902-0.034-0.0340.0000.0000.0000.000
78A78GLU-1-0.987-1.0088.284-0.923-0.9230.0000.0000.0000.000
79A79LEU0-0.018-0.0109.271-0.056-0.0560.0000.0000.0000.000
80A80GLU-1-0.871-0.91412.428-0.553-0.5530.0000.0000.0000.000
81A81ILE0-0.005-0.01115.462-0.057-0.0570.0000.0000.0000.000
82A82GLU-1-0.840-0.90717.993-0.431-0.4310.0000.0000.0000.000
83A83PHE0-0.007-0.00920.984-0.015-0.0150.0000.0000.0000.000
84A84VAL0-0.048-0.02122.1800.0060.0060.0000.0000.0000.000
85A85GLU-1-0.848-0.91824.482-0.225-0.2250.0000.0000.0000.000
86A86LYS10.8640.93027.7740.2170.2170.0000.0000.0000.000
87A87PRO0-0.051-0.01429.8480.0170.0170.0000.0000.0000.000
88A88ASP-1-0.861-0.95833.196-0.192-0.1920.0000.0000.0000.000
89A90ALA00.0080.01531.035-0.002-0.0020.0000.0000.0000.000
90A91GLU-1-0.843-0.92931.125-0.210-0.2100.0000.0000.0000.000
91A92SER0-0.091-0.04926.212-0.022-0.0220.0000.0000.0000.000
92A93SER0-0.009-0.03524.9380.0080.0080.0000.0000.0000.000
93A94LYS10.8630.91919.6390.5810.5810.0000.0000.0000.000
94A95TRP0-0.018-0.01820.7110.0200.0200.0000.0000.0000.000
95A96VAL0-0.041-0.02321.850-0.041-0.0410.0000.0000.0000.000
96A97ILE00.0110.01722.6700.0120.0120.0000.0000.0000.000
97A98VAL00.000-0.00125.5440.0130.0130.0000.0000.0000.000
98A99LYS10.9110.95629.3140.3080.3080.0000.0000.0000.000
99A100ASP-1-0.880-0.95031.272-0.255-0.2550.0000.0000.0000.000
100A101SER00.006-0.00334.7490.0140.0140.0000.0000.0000.000
101A102GLY0-0.0370.00235.1110.0020.0020.0000.0000.0000.000
102A103GLU-1-0.908-1.00030.121-0.351-0.3510.0000.0000.0000.000
103A104ALA0-0.0430.00427.8880.0050.0050.0000.0000.0000.000
104A105ARG11.0441.02128.4850.2860.2860.0000.0000.0000.000
105A106VAL0-0.008-0.00223.362-0.013-0.0130.0000.0000.0000.000
106A107ALA0-0.070-0.03826.1850.0330.0330.0000.0000.0000.000
107A108ILE00.0060.01425.515-0.036-0.0360.0000.0000.0000.000
108A109GLY00.0700.05626.5980.0290.0290.0000.0000.0000.000
109A110GLY00.003-0.01027.030-0.023-0.0230.0000.0000.0000.000
110A111SER0-0.011-0.03027.7130.0110.0110.0000.0000.0000.000
111A112GLU-1-0.955-0.96630.111-0.224-0.2240.0000.0000.0000.000
112A113ASP-1-0.795-0.88930.548-0.266-0.2660.0000.0000.0000.000
113A114HIS10.7820.86429.5510.3100.3100.0000.0000.0000.000
114A115PRO00.0360.03933.001-0.001-0.0010.0000.0000.0000.000
115A116GLN00.0500.00729.494-0.036-0.0360.0000.0000.0000.000
116A117GLY0-0.049-0.02831.038-0.015-0.0150.0000.0000.0000.000
117A118GLU-1-0.880-0.94532.267-0.250-0.2500.0000.0000.0000.000
118A119LEU0-0.063-0.01627.086-0.020-0.0200.0000.0000.0000.000
119A120VAL0-0.0200.00324.1460.0110.0110.0000.0000.0000.000
120A121ARG10.9210.94321.8080.4300.4300.0000.0000.0000.000
121A122GLY00.033-0.00119.2750.0210.0210.0000.0000.0000.000
122A123PHE0-0.0140.01914.2470.0250.0250.0000.0000.0000.000
123A124PHE0-0.014-0.01115.4480.0800.0800.0000.0000.0000.000
124A125LYS10.9891.00411.6321.5781.5780.0000.0000.0000.000
125A126ILE0-0.020-0.00710.9760.2950.2950.0000.0000.0000.000
126A127GLU-1-0.804-0.91411.165-1.953-1.9530.0000.0000.0000.000
127A128LYS10.8450.91411.9560.8840.8840.0000.0000.0000.000
128A129LEU0-0.033-0.01914.1000.0680.0680.0000.0000.0000.000
129A130GLY00.0430.02717.2970.0850.0850.0000.0000.0000.000
130A131SER0-0.034-0.04116.644-0.082-0.0820.0000.0000.0000.000
131A132LEU00.0080.00018.0390.0070.0070.0000.0000.0000.000
132A133ALA0-0.029-0.00718.4860.0230.0230.0000.0000.0000.000
133A134TYR00.0610.05211.832-0.092-0.0920.0000.0000.0000.000
134A135LYS10.8800.93216.0260.8520.8520.0000.0000.0000.000
135A136LEU0-0.0170.00915.872-0.125-0.1250.0000.0000.0000.000
136A137VAL00.0340.02115.3270.1090.1090.0000.0000.0000.000
137A138PHE00.009-0.00817.025-0.089-0.0890.0000.0000.0000.000
138A139CYS0-0.016-0.00516.164-0.040-0.0400.0000.0000.0000.000
139A140PRO00.0140.00718.501-0.012-0.0120.0000.0000.0000.000
140A141LYS10.9600.98219.6930.4970.4970.0000.0000.0000.000
141A142SER0-0.015-0.02520.7720.0010.0010.0000.0000.0000.000
142A143ASP-1-0.940-0.95622.378-0.441-0.4410.0000.0000.0000.000
143A144SER0-0.008-0.02319.071-0.047-0.0470.0000.0000.0000.000
144A145GLY0-0.014-0.00518.2490.0370.0370.0000.0000.0000.000
145A146SER0-0.034-0.00719.2650.0140.0140.0000.0000.0000.000
146A148SER00.0260.02919.8050.0400.0400.0000.0000.0000.000
147A149ASP-1-0.738-0.85920.570-0.703-0.7030.0000.0000.0000.000
148A150ILE0-0.0020.00319.3760.0530.0530.0000.0000.0000.000
149A151GLY00.021-0.01322.559-0.006-0.0060.0000.0000.0000.000
150A152ILE0-0.039-0.00625.5450.0030.0030.0000.0000.0000.000
151A153ASN0-0.0330.00028.5560.0180.0180.0000.0000.0000.000
152A154TYR00.026-0.00429.7600.0050.0050.0000.0000.0000.000
153A155GLU-1-0.833-0.94234.362-0.245-0.2450.0000.0000.0000.000
154A156GLY0-0.042-0.02137.1860.0080.0080.0000.0000.0000.000
155A157ARG10.8790.92835.0220.2160.2160.0000.0000.0000.000
156A158ARG10.8560.94930.7630.2620.2620.0000.0000.0000.000
157A159SER00.0430.02930.456-0.016-0.0160.0000.0000.0000.000
158A160LEU00.0280.00623.437-0.002-0.0020.0000.0000.0000.000
159A161VAL0-0.055-0.01826.9230.0110.0110.0000.0000.0000.000
160A162LEU0-0.006-0.00122.760-0.038-0.0380.0000.0000.0000.000
161A163LYS10.8480.94525.1980.3910.3910.0000.0000.0000.000
162A164SER0-0.014-0.02026.000-0.015-0.0150.0000.0000.0000.000
163A165SER0-0.045-0.01527.4060.0010.0010.0000.0000.0000.000
164A166ASP-1-0.892-0.94322.644-0.526-0.5260.0000.0000.0000.000
165A167ASP-1-0.913-0.95924.387-0.332-0.3320.0000.0000.0000.000
166A168VAL0-0.094-0.04826.1680.0230.0230.0000.0000.0000.000
167A169PRO00.0010.00821.659-0.001-0.0010.0000.0000.0000.000
168A170PHE0-0.031-0.02322.9800.0370.0370.0000.0000.0000.000
169A171ARG10.9100.95421.2260.3320.3320.0000.0000.0000.000
170A172VAL00.0050.01417.9690.0480.0480.0000.0000.0000.000
171A173VAL00.0130.00517.940-0.037-0.0370.0000.0000.0000.000
172A174PHE00.0260.00914.0860.0200.0200.0000.0000.0000.000
173A175VAL00.0400.02217.8110.0360.0360.0000.0000.0000.000
174A176LYS11.0221.02318.5360.2430.2430.0000.0000.0000.000
175A177PRO0-0.022-0.01620.2290.0370.0370.0000.0000.0000.000
176A178ARG10.9420.97723.3630.2470.2470.0000.0000.0000.000
177A179SER00.002-0.01024.1560.0020.0020.0000.0000.0000.000
178A180GLY00.019-0.00726.7720.0130.0130.0000.0000.0000.000
179A181SER0-0.038-0.01327.2770.0020.0020.0000.0000.0000.000
180A182GLU-1-0.905-0.96028.082-0.123-0.1230.0000.0000.0000.000
181A183THR0-0.090-0.04725.145-0.006-0.0060.0000.0000.0000.000
182A184GLU-1-0.935-0.95927.534-0.154-0.1540.0000.0000.0000.000
183A185SER0-0.0370.01126.274-0.010-0.0100.0000.0000.0000.000