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: 4JJ1N

Calculation Name: 1RK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RK4

Chain ID: A

ChEMBL ID:

UniProt ID: O00299

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2508873.368317
FMO2-HF: Nuclear repulsion 2424808.189503
FMO2-HF: Total energy -84065.178814
FMO2-MP2: Total energy -84310.397748


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:22:GLY)


Summations of interaction energy for fragment #1(A:22:GLY)
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.
-1.0680.688-0.008-0.891-0.8570.004
Interaction energy analysis for fragmet #1(A:22:GLY)
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 : 0.015
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].
3A24CYS0-0.0540.0123.851-0.5370.942-0.005-0.833-0.6420.004
4A25PRO00.0240.0155.8320.5260.5260.0000.0000.0000.000
5A26PHE0-0.006-0.0257.8220.3110.3110.0000.0000.0000.000
6A27SER00.0530.0258.9660.1570.1570.0000.0000.0000.000
7A28GLN00.019-0.00911.6390.0770.0770.0000.0000.0000.000
8A29ARG10.7800.8638.5480.2570.2570.0000.0000.0000.000
9A30LEU00.0110.00511.8890.1080.1080.0000.0000.0000.000
10A31PHE0-0.025-0.01613.7600.0670.0670.0000.0000.0000.000
11A32MET00.0080.02716.7940.0350.0350.0000.0000.0000.000
12A33VAL00.0180.01014.8370.0460.0460.0000.0000.0000.000
13A34LEU0-0.031-0.02016.8880.0360.0360.0000.0000.0000.000
14A35TRP00.0540.00919.4620.0350.0350.0000.0000.0000.000
15A36LEU00.0060.00920.0260.0210.0210.0000.0000.0000.000
16A37LYS10.6840.83119.8870.0530.0530.0000.0000.0000.000
17A38GLY00.0020.00023.0350.0140.0140.0000.0000.0000.000
18A39VAL0-0.089-0.03921.8740.0040.0040.0000.0000.0000.000
19A40THR00.0250.01322.527-0.024-0.0240.0000.0000.0000.000
20A41PHE0-0.049-0.02118.434-0.012-0.0120.0000.0000.0000.000
21A42ASN0-0.031-0.02524.7300.0220.0220.0000.0000.0000.000
22A43VAL00.0540.03626.200-0.022-0.0220.0000.0000.0000.000
23A44THR0-0.033-0.03327.1680.0090.0090.0000.0000.0000.000
24A45THR00.0670.02126.621-0.020-0.0200.0000.0000.0000.000
25A46VAL00.0020.00526.489-0.021-0.0210.0000.0000.0000.000
26A47ASP-1-0.792-0.87825.149-0.233-0.2330.0000.0000.0000.000
27A48THR00.0260.00721.817-0.031-0.0310.0000.0000.0000.000
28A49LYS10.9561.00121.6800.2250.2250.0000.0000.0000.000
29A50ARG10.9460.97221.9450.1920.1920.0000.0000.0000.000
30A51ARG10.9040.98118.0990.3720.3720.0000.0000.0000.000
31A52THR00.0200.00017.566-0.069-0.0690.0000.0000.0000.000
32A53GLU-1-0.885-0.95217.327-0.406-0.4060.0000.0000.0000.000
33A54THR0-0.078-0.05317.076-0.017-0.0170.0000.0000.0000.000
34A55VAL00.000-0.01312.393-0.040-0.0400.0000.0000.0000.000
35A56GLN0-0.006-0.00312.982-0.121-0.1210.0000.0000.0000.000
36A57LYS10.9140.96113.9590.3300.3300.0000.0000.0000.000
37A58LEU0-0.058-0.03012.2360.0220.0220.0000.0000.0000.000
38A60PRO00.0450.0259.956-0.061-0.0610.0000.0000.0000.000
39A61GLY0-0.028-0.0078.7340.1370.1370.0000.0000.0000.000
40A62GLY00.0220.0129.638-0.006-0.0060.0000.0000.0000.000
41A63GLN0-0.030-0.0258.965-0.354-0.3540.0000.0000.0000.000
42A64LEU00.0300.02110.513-0.001-0.0010.0000.0000.0000.000
43A65PRO0-0.057-0.0187.560-0.306-0.3060.0000.0000.0000.000
44A66PHE00.0450.0304.5690.3820.564-0.001-0.046-0.1350.000
45A67LEU00.0110.0138.0300.2430.2430.0000.0000.0000.000
46A68LEU00.0220.0297.5210.0240.0240.0000.0000.0000.000
47A69TYR00.003-0.0088.5090.0750.0750.0000.0000.0000.000
48A70GLY0-0.006-0.00811.8440.0700.0700.0000.0000.0000.000
49A71THR0-0.023-0.01213.416-0.028-0.0280.0000.0000.0000.000
50A72GLU-1-0.861-0.9146.1150.0060.0060.0000.0000.0000.000
51A73VAL00.0260.0068.571-0.147-0.1470.0000.0000.0000.000
52A74HIS0-0.013-0.0158.3300.0910.0910.0000.0000.0000.000
53A75THR0-0.0200.0007.042-0.151-0.1510.0000.0000.0000.000
54A76ASP-1-0.775-0.8795.178-0.787-0.757-0.001-0.004-0.0250.000
55A77THR0-0.0090.0194.4620.0670.132-0.001-0.008-0.0550.000
56A78ASN00.019-0.0045.287-0.297-0.2970.0000.0000.0000.000
57A79LYS10.9940.9887.195-0.814-0.8140.0000.0000.0000.000
58A80ILE0-0.0140.0119.5610.0200.0200.0000.0000.0000.000
59A81GLU-1-0.767-0.85411.133-0.106-0.1060.0000.0000.0000.000
60A82GLU-1-0.863-0.9499.2630.6420.6420.0000.0000.0000.000
61A83PHE0-0.023-0.01013.4700.0050.0050.0000.0000.0000.000
62A84LEU00.023-0.00515.363-0.001-0.0010.0000.0000.0000.000
63A85GLU-1-0.744-0.85316.6080.0150.0150.0000.0000.0000.000
64A86ALA0-0.039-0.01017.9690.0050.0050.0000.0000.0000.000
65A87VAL0-0.029-0.01819.470-0.001-0.0010.0000.0000.0000.000
66A88LEU0-0.0330.00020.829-0.010-0.0100.0000.0000.0000.000
67A89CYS0-0.0130.00122.676-0.006-0.0060.0000.0000.0000.000
68A90PRO00.0070.01024.471-0.005-0.0050.0000.0000.0000.000
69A91PRO0-0.019-0.02327.9920.0080.0080.0000.0000.0000.000
70A92ARG10.8930.95428.2700.0230.0230.0000.0000.0000.000
71A93TYR00.0410.02224.875-0.007-0.0070.0000.0000.0000.000
72A94PRO00.0460.03924.4030.0150.0150.0000.0000.0000.000
73A95LYS10.9220.95722.970-0.056-0.0560.0000.0000.0000.000
74A96LEU00.0270.00419.264-0.011-0.0110.0000.0000.0000.000
75A97ALA0-0.049-0.02919.070-0.005-0.0050.0000.0000.0000.000
76A98ALA0-0.0110.00319.719-0.004-0.0040.0000.0000.0000.000
77A99LEU0-0.027-0.02421.6420.0250.0250.0000.0000.0000.000
78A100ASN0-0.007-0.01324.1460.0180.0180.0000.0000.0000.000
79A101PRO0-0.017-0.02220.9890.0020.0020.0000.0000.0000.000
80A102GLU-1-0.847-0.92819.9690.1130.1130.0000.0000.0000.000
81A103SER00.006-0.01620.397-0.010-0.0100.0000.0000.0000.000
82A104ASN0-0.087-0.03716.634-0.029-0.0290.0000.0000.0000.000
83A105THR0-0.063-0.04515.5610.0340.0340.0000.0000.0000.000
84A106ALA00.0030.01117.002-0.006-0.0060.0000.0000.0000.000
85A107GLY00.0340.00917.883-0.023-0.0230.0000.0000.0000.000
86A108LEU0-0.0170.00011.787-0.045-0.0450.0000.0000.0000.000
87A109ASP-1-0.840-0.92112.847-0.017-0.0170.0000.0000.0000.000
88A110ILE0-0.0100.01814.944-0.028-0.0280.0000.0000.0000.000
89A111PHE00.0510.0199.8910.0170.0170.0000.0000.0000.000
90A112ALA00.0250.03811.921-0.063-0.0630.0000.0000.0000.000
91A113LYS10.8090.88413.032-0.037-0.0370.0000.0000.0000.000
92A114PHE00.0470.01714.2530.0130.0130.0000.0000.0000.000
93A115SER00.017-0.00212.095-0.064-0.0640.0000.0000.0000.000
94A116ALA0-0.020-0.01714.3450.0010.0010.0000.0000.0000.000
95A117TYR0-0.102-0.09116.754-0.001-0.0010.0000.0000.0000.000
96A118ILE0-0.007-0.00216.3690.0150.0150.0000.0000.0000.000
97A119LYS10.8050.89211.3150.4550.4550.0000.0000.0000.000
98A120ASN0-0.038-0.01017.7400.0300.0300.0000.0000.0000.000
99A121SER00.0310.01721.143-0.007-0.0070.0000.0000.0000.000
100A122ASN00.0170.01324.0370.0100.0100.0000.0000.0000.000
101A123PRO00.0690.01826.7450.0020.0020.0000.0000.0000.000
102A124ALA0-0.026-0.01129.2830.0030.0030.0000.0000.0000.000
103A125LEU0-0.0030.00223.8250.0100.0100.0000.0000.0000.000
104A126ASN0-0.016-0.00525.004-0.014-0.0140.0000.0000.0000.000
105A127ASP-1-0.774-0.86825.682-0.053-0.0530.0000.0000.0000.000
106A128ASN0-0.007-0.01626.187-0.003-0.0030.0000.0000.0000.000
107A129LEU0-0.0040.00620.1680.0090.0090.0000.0000.0000.000
108A130GLU-1-0.787-0.85922.425-0.120-0.1200.0000.0000.0000.000
109A131LYS10.8090.88924.5500.0490.0490.0000.0000.0000.000
110A132GLY0-0.048-0.01522.2040.0180.0180.0000.0000.0000.000
111A133LEU00.0280.00918.8020.0110.0110.0000.0000.0000.000
112A134LEU00.0220.00221.3940.0030.0030.0000.0000.0000.000
113A135LYS10.8700.94123.8700.0120.0120.0000.0000.0000.000
114A136ALA00.0400.02419.1190.0090.0090.0000.0000.0000.000
115A137LEU00.006-0.00621.1130.0030.0030.0000.0000.0000.000
116A138LYS10.8610.92622.6920.0290.0290.0000.0000.0000.000
117A139VAL0-0.038-0.01822.0460.0080.0080.0000.0000.0000.000
118A140LEU00.0290.01619.8810.0070.0070.0000.0000.0000.000
119A141ASP-1-0.754-0.87022.914-0.046-0.0460.0000.0000.0000.000
120A142ASN00.0080.00926.461-0.003-0.0030.0000.0000.0000.000
121A143TYR00.0010.00022.9120.0060.0060.0000.0000.0000.000
122A144LEU0-0.030-0.00823.5880.0010.0010.0000.0000.0000.000
123A145THR0-0.037-0.04227.247-0.003-0.0030.0000.0000.0000.000
124A146SER0-0.022-0.00429.2080.0040.0040.0000.0000.0000.000
125A147PRO0-0.020-0.01130.101-0.001-0.0010.0000.0000.0000.000
126A148LEU0-0.0290.00026.6190.0080.0080.0000.0000.0000.000
127A149PRO0-0.010-0.02429.546-0.003-0.0030.0000.0000.0000.000
128A150GLU-1-0.916-0.95331.558-0.005-0.0050.0000.0000.0000.000
129A151GLU-1-0.721-0.85431.519-0.010-0.0100.0000.0000.0000.000
130A152VAL0-0.077-0.01834.971-0.001-0.0010.0000.0000.0000.000
131A153ASP-1-0.911-0.95037.1810.0190.0190.0000.0000.0000.000
132A154GLU-1-0.942-0.95336.309-0.017-0.0170.0000.0000.0000.000
133A155THR0-0.067-0.05539.4800.0020.0020.0000.0000.0000.000
134A156SER0-0.031-0.02137.338-0.002-0.0020.0000.0000.0000.000
135A157ALA0-0.033-0.01739.2700.0010.0010.0000.0000.0000.000
136A158GLU-1-1.007-0.99640.655-0.035-0.0350.0000.0000.0000.000
137A159ASP-1-0.933-0.96139.071-0.017-0.0170.0000.0000.0000.000
138A160GLU-1-0.963-0.99839.7340.0030.0030.0000.0000.0000.000
139A161GLY00.0090.00938.3600.0020.0020.0000.0000.0000.000
140A162VAL0-0.049-0.01634.1960.0020.0020.0000.0000.0000.000
141A163SER0-0.075-0.03630.973-0.004-0.0040.0000.0000.0000.000
142A164GLN0-0.015-0.04632.917-0.009-0.0090.0000.0000.0000.000
143A165ARG10.7430.89325.375-0.001-0.0010.0000.0000.0000.000
144A166LYS10.8640.93928.7460.0460.0460.0000.0000.0000.000
145A167PHE0-0.006-0.01923.688-0.018-0.0180.0000.0000.0000.000
146A168LEU0-0.006-0.00918.6020.0140.0140.0000.0000.0000.000
147A169ASP-1-0.717-0.82722.8450.0510.0510.0000.0000.0000.000
148A170GLY00.0840.04824.7180.0090.0090.0000.0000.0000.000
149A171ASN0-0.032-0.02727.923-0.018-0.0180.0000.0000.0000.000
150A172GLU-1-0.815-0.88126.582-0.080-0.0800.0000.0000.0000.000
151A173LEU0-0.0400.00421.7230.0020.0020.0000.0000.0000.000
152A174THR0-0.001-0.02620.3150.0160.0160.0000.0000.0000.000
153A175LEU00.007-0.01415.169-0.031-0.0310.0000.0000.0000.000
154A176ALA00.0200.02415.355-0.036-0.0360.0000.0000.0000.000
155A177ASP-1-0.714-0.82516.153-0.110-0.1100.0000.0000.0000.000
156A178CYS0-0.061-0.02715.472-0.041-0.0410.0000.0000.0000.000
157A179ASN00.003-0.00510.660-0.197-0.1970.0000.0000.0000.000
158A180LEU0-0.0070.00612.744-0.086-0.0860.0000.0000.0000.000
159A181LEU00.0210.01615.235-0.038-0.0380.0000.0000.0000.000
160A182PRO00.0110.00313.782-0.010-0.0100.0000.0000.0000.000
161A183LYS10.8170.9098.3490.5930.5930.0000.0000.0000.000
162A184LEU00.0250.00514.3090.0130.0130.0000.0000.0000.000
163A185HIS10.8940.96517.9310.3540.3540.0000.0000.0000.000
164A186ILE00.0110.00513.4290.0150.0150.0000.0000.0000.000
165A187VAL0-0.011-0.00316.0680.0220.0220.0000.0000.0000.000
166A188GLN00.0310.02418.3260.0140.0140.0000.0000.0000.000
167A189VAL0-0.041-0.00120.1450.0200.0200.0000.0000.0000.000
168A190VAL00.0430.01617.2870.0190.0190.0000.0000.0000.000
169A191CYS0-0.071-0.03420.2920.0270.0270.0000.0000.0000.000
170A192LYS10.8120.89922.6620.2800.2800.0000.0000.0000.000
171A193LYS10.8130.90723.7190.2740.2740.0000.0000.0000.000
172A194TYR0-0.029-0.03921.5230.0280.0280.0000.0000.0000.000
173A195ARG10.7840.88722.4120.2080.2080.0000.0000.0000.000
174A196GLY00.0030.02826.0990.0170.0170.0000.0000.0000.000
175A197PHE0-0.036-0.00823.4300.0140.0140.0000.0000.0000.000
176A198THR00.002-0.01525.698-0.015-0.0150.0000.0000.0000.000
177A199ILE00.0230.00722.0790.0100.0100.0000.0000.0000.000
178A200PRO00.0170.00926.1730.0030.0030.0000.0000.0000.000
179A201GLU-1-0.784-0.87329.677-0.095-0.0950.0000.0000.0000.000
180A202ALA0-0.008-0.00231.9710.0050.0050.0000.0000.0000.000
181A203PHE0-0.054-0.02026.0870.0080.0080.0000.0000.0000.000
182A204ARG10.8970.90428.8500.0670.0670.0000.0000.0000.000
183A205GLY00.0490.04328.745-0.002-0.0020.0000.0000.0000.000
184A206VAL0-0.008-0.01923.343-0.006-0.0060.0000.0000.0000.000
185A207HIS0-0.029-0.01525.747-0.015-0.0150.0000.0000.0000.000
186A208ARG10.9020.97828.2410.0360.0360.0000.0000.0000.000
187A209TYR0-0.030-0.02020.129-0.014-0.0140.0000.0000.0000.000
188A210LEU00.008-0.01121.501-0.011-0.0110.0000.0000.0000.000
189A211SER0-0.031-0.02025.071-0.010-0.0100.0000.0000.0000.000
190A212ASN0-0.043-0.04027.5800.0000.0000.0000.0000.0000.000
191A213ALA0-0.020-0.00522.719-0.002-0.0020.0000.0000.0000.000
192A214TYR0-0.046-0.04822.123-0.024-0.0240.0000.0000.0000.000
193A215ALA0-0.0240.00626.200-0.002-0.0020.0000.0000.0000.000
194A216ARG10.7430.83325.5960.1120.1120.0000.0000.0000.000
195A217GLU-1-0.828-0.90325.416-0.173-0.1730.0000.0000.0000.000
196A218GLU-1-0.786-0.88922.293-0.157-0.1570.0000.0000.0000.000
197A219PHE0-0.0120.00718.658-0.036-0.0360.0000.0000.0000.000
198A220ALA00.0320.00021.890-0.030-0.0300.0000.0000.0000.000
199A221SER0-0.073-0.05424.336-0.016-0.0160.0000.0000.0000.000
200A222THR0-0.100-0.06519.107-0.029-0.0290.0000.0000.0000.000
201A223CYS0-0.067-0.03719.229-0.057-0.0570.0000.0000.0000.000
202A224PRO0-0.0370.00016.4850.0100.0100.0000.0000.0000.000
203A225ASP-1-0.816-0.91519.709-0.355-0.3550.0000.0000.0000.000
204A226ASP-1-0.802-0.93521.261-0.321-0.3210.0000.0000.0000.000
205A227GLU-1-0.954-0.96322.340-0.278-0.2780.0000.0000.0000.000
206A228GLU-1-0.882-0.95317.855-0.610-0.6100.0000.0000.0000.000
207A229ILE0-0.070-0.04317.177-0.065-0.0650.0000.0000.0000.000
208A230GLU-1-0.808-0.90818.225-0.310-0.3100.0000.0000.0000.000
209A231LEU00.0300.03620.4860.0040.0040.0000.0000.0000.000
210A232ALA0-0.046-0.00714.898-0.024-0.0240.0000.0000.0000.000
211A233TYR0-0.074-0.06311.391-0.055-0.0550.0000.0000.0000.000
212A234GLU-1-1.030-1.00416.979-0.289-0.2890.0000.0000.0000.000