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: JL619

Calculation Name: 4R9P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R9P

Chain ID: A

ChEMBL ID:

UniProt ID: A1Z8R1

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655686.085082
FMO2-HF: Nuclear repulsion 2569884.456035
FMO2-HF: Total energy -85801.629047
FMO2-MP2: Total energy -86049.316737


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:27:GLU)


Summations of interaction energy for fragment #1(A:27:GLU)
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.
-162.941-161.04321.657-11.739-11.8160.123
Interaction energy analysis for fragmet #1(A:27:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.940
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].
3A29ASP-1-0.853-0.9202.53826.51629.5641.105-1.861-2.2920.011
4A30ILE0-0.0210.0032.394-2.771-1.4751.895-1.119-2.0720.003
5A31TRP0-0.024-0.0264.811-4.193-4.180-0.001-0.0190.0060.000
6A32PHE00.0480.0095.303-0.786-0.7860.0000.0000.0000.000
7A33GLN00.0160.00010.095-2.279-2.2790.0000.0000.0000.000
8A34LYS10.8740.92912.394-14.193-14.1930.0000.0000.0000.000
9A35ASP-1-0.816-0.90014.75816.03516.0350.0000.0000.0000.000
10A36LYS10.8330.9038.535-26.286-26.2860.0000.0000.0000.000
11A37LEU00.0190.03910.620-0.455-0.4550.0000.0000.0000.000
12A38TYR00.013-0.00712.200-0.053-0.0530.0000.0000.0000.000
13A39LYS10.9520.97314.643-17.788-17.7880.0000.0000.0000.000
14A40GLU-1-0.791-0.8679.21525.01725.0170.0000.0000.0000.000
15A41HIS00.0230.00510.3000.4120.4120.0000.0000.0000.000
16A42ILE0-0.0070.00114.704-0.708-0.7080.0000.0000.0000.000
17A43GLN00.0270.00115.628-0.122-0.1220.0000.0000.0000.000
18A44GLU-1-0.814-0.87611.72421.41721.4170.0000.0000.0000.000
19A45VAL00.0160.00515.722-0.196-0.1960.0000.0000.0000.000
20A46LEU0-0.022-0.01919.055-0.615-0.6150.0000.0000.0000.000
21A47ASP-1-0.881-0.91717.49815.36415.3640.0000.0000.0000.000
22A48LYS10.8200.89015.061-17.473-17.4730.0000.0000.0000.000
23A49TRP00.0460.01821.008-0.189-0.1890.0000.0000.0000.000
24A50THR0-0.019-0.02524.028-0.052-0.0520.0000.0000.0000.000
25A51GLN0-0.022-0.00221.693-0.043-0.0430.0000.0000.0000.000
26A52ILE0-0.097-0.03620.8150.3310.3310.0000.0000.0000.000
27A53ASP-1-0.783-0.88224.29310.28710.2870.0000.0000.0000.000
28A54ASP-1-0.872-0.93727.1199.7879.7870.0000.0000.0000.000
29A55GLU-1-0.840-0.88529.2959.8109.8100.0000.0000.0000.000
30A56ILE0-0.097-0.05323.0980.2310.2310.0000.0000.0000.000
31A57TRP0-0.001-0.02226.3520.2570.2570.0000.0000.0000.000
32A58ALA0-0.038-0.03223.4770.0450.0450.0000.0000.0000.000
33A59LYS10.8780.95015.074-17.736-17.7360.0000.0000.0000.000
34A60VAL0-0.032-0.02418.554-0.169-0.1690.0000.0000.0000.000
35A61ILE0-0.031-0.01012.2520.4380.4380.0000.0000.0000.000
36A62VAL00.0020.01014.003-0.887-0.8870.0000.0000.0000.000
37A63PHE00.021-0.00510.0882.0022.0020.0000.0000.0000.000
38A64GLU-1-0.724-0.83011.17721.71521.7150.0000.0000.0000.000
39A65ARG10.7790.87310.725-17.331-17.3310.0000.0000.0000.000
40A66ASN00.0060.0028.121-0.629-0.6290.0000.0000.0000.000
41A67ARG10.8940.9291.783-120.509-122.96818.658-8.740-7.4580.109
42A68ARG10.7420.8536.784-37.738-37.7380.0000.0000.0000.000
43A69VAL0-0.018-0.0087.7732.9092.9090.0000.0000.0000.000
44A70ALA00.0160.01710.459-1.190-1.1900.0000.0000.0000.000
45A71LYS10.8100.88810.565-23.533-23.5330.0000.0000.0000.000
46A72ALA00.0140.01914.866-0.386-0.3860.0000.0000.0000.000
47A73TYR00.014-0.01117.6130.3570.3570.0000.0000.0000.000
48A74ALA0-0.0120.00821.662-0.279-0.2790.0000.0000.0000.000
49A75ARG10.7740.84824.932-11.002-11.0020.0000.0000.0000.000
50A76ALA00.0870.04628.112-0.392-0.3920.0000.0000.0000.000
51A77PRO00.0090.00729.5480.2690.2690.0000.0000.0000.000
52A78VAL0-0.046-0.02431.0020.0090.0090.0000.0000.0000.000
53A79LEU00.0110.01723.1960.1010.1010.0000.0000.0000.000
54A80THR0-0.055-0.02327.497-0.294-0.2940.0000.0000.0000.000
55A81ILE00.0160.01221.6160.3920.3920.0000.0000.0000.000
56A82ASN0-0.009-0.01724.0240.0390.0390.0000.0000.0000.000
57A83GLY00.0470.01623.1460.6310.6310.0000.0000.0000.000
58A84SER0-0.046-0.03024.4200.1330.1330.0000.0000.0000.000
59A85ASP-1-0.871-0.96422.16813.56113.5610.0000.0000.0000.000
60A86ASP-1-0.789-0.86922.39612.48112.4810.0000.0000.0000.000
61A87GLY00.0420.03619.7870.1490.1490.0000.0000.0000.000
62A88PHE0-0.069-0.05820.399-0.005-0.0050.0000.0000.0000.000
63A89ASP-1-0.758-0.85322.13711.61311.6130.0000.0000.0000.000
64A90GLY00.0220.02324.698-0.412-0.4120.0000.0000.0000.000
65A91MET0-0.041-0.03726.222-0.272-0.2720.0000.0000.0000.000
66A92ARG10.7500.85324.824-12.236-12.2360.0000.0000.0000.000
67A93ILE00.0070.01819.6690.2270.2270.0000.0000.0000.000
68A94GLY00.0150.01121.988-0.423-0.4230.0000.0000.0000.000
69A95LEU0-0.016-0.02118.2540.6990.6990.0000.0000.0000.000
70A96CYS0-0.058-0.04318.1411.3521.3520.0000.0000.0000.000
71A97GLY00.0160.03419.2030.3880.3880.0000.0000.0000.000
72A98PHE0-0.062-0.03114.1090.1090.1090.0000.0000.0000.000
73A99ASP-1-0.871-0.92212.76921.72121.7210.0000.0000.0000.000
74A100ASN0-0.018-0.0479.2054.9214.9210.0000.0000.0000.000
75A101PRO0-0.0170.0037.262-2.116-2.1160.0000.0000.0000.000
76A102MET0-0.026-0.0135.5330.5940.5940.0000.0000.0000.000
77A103ARG10.8030.8839.007-23.352-23.3520.0000.0000.0000.000
78A104ASP-1-0.743-0.82012.42119.90819.9080.0000.0000.0000.000
79A105GLN00.013-0.02214.666-0.304-0.3040.0000.0000.0000.000
80A106LYS10.8540.89918.238-14.801-14.8010.0000.0000.0000.000
81A107THR0-0.003-0.02714.667-1.018-1.0180.0000.0000.0000.000
82A108ASP-1-0.822-0.89117.61116.57316.5730.0000.0000.0000.000
83A109GLU-1-0.828-0.88519.00113.31513.3150.0000.0000.0000.000
84A110MET0-0.050-0.02920.562-0.905-0.9050.0000.0000.0000.000
85A111LYS10.8620.91415.924-20.287-20.2870.0000.0000.0000.000
86A112ARG10.8580.91721.192-15.513-15.5130.0000.0000.0000.000
87A113VAL0-0.035-0.00624.442-0.696-0.6960.0000.0000.0000.000
88A114ILE00.0100.03320.967-0.472-0.4720.0000.0000.0000.000
89A115GLY00.0040.00425.640-0.468-0.4680.0000.0000.0000.000
90A116GLN0-0.008-0.02827.6870.1710.1710.0000.0000.0000.000
91A117GLY0-0.0030.01026.5520.0410.0410.0000.0000.0000.000
92A118VAL00.002-0.01225.673-0.445-0.4450.0000.0000.0000.000
93A119LYS10.9050.95428.040-9.933-9.9330.0000.0000.0000.000
94A120ILE00.0020.00125.146-0.146-0.1460.0000.0000.0000.000
95A121LYS10.8970.95129.371-8.690-8.6900.0000.0000.0000.000
96A122MET0-0.0110.03928.931-0.047-0.0470.0000.0000.0000.000
97A123ASP-1-0.829-0.92431.6158.4318.4310.0000.0000.0000.000
98A124ASP-1-0.810-0.92135.0088.3538.3530.0000.0000.0000.000
99A125ALA0-0.034-0.00837.176-0.154-0.1540.0000.0000.0000.000
100A126GLY00.0350.01133.1810.0350.0350.0000.0000.0000.000
101A127ASN0-0.084-0.06431.9010.3370.3370.0000.0000.0000.000
102A128ILE00.0060.01126.6360.0620.0620.0000.0000.0000.000
103A129LEU0-0.017-0.01730.658-0.054-0.0540.0000.0000.0000.000
104A130ILE00.005-0.00326.7860.3580.3580.0000.0000.0000.000
105A131ARG10.8580.92330.809-8.958-8.9580.0000.0000.0000.000
106A132ARG10.8020.90130.536-9.817-9.8170.0000.0000.0000.000
107A133TYR00.0350.00830.938-0.297-0.2970.0000.0000.0000.000
108A134ALA0-0.0220.01528.713-0.166-0.1660.0000.0000.0000.000
109A135LYS11.0051.00330.831-9.471-9.4710.0000.0000.0000.000
110A136SER0-0.012-0.01527.977-0.251-0.2510.0000.0000.0000.000
111A137ASN00.010-0.00528.456-0.405-0.4050.0000.0000.0000.000
112A138VAL00.0310.01224.8390.4400.4400.0000.0000.0000.000
113A139TYR0-0.031-0.00524.537-0.570-0.5700.0000.0000.0000.000
114A140VAL00.0290.03024.1070.5840.5840.0000.0000.0000.000
115A141LYS10.8840.94621.544-13.152-13.1520.0000.0000.0000.000
116A142SER00.0200.00623.2080.0710.0710.0000.0000.0000.000
117A143THR00.012-0.01520.0390.4290.4290.0000.0000.0000.000
118A144ALA0-0.0310.00421.3030.2270.2270.0000.0000.0000.000
119A145SER0-0.018-0.01120.3990.8200.8200.0000.0000.0000.000
120A146SER0-0.038-0.04521.422-0.053-0.0530.0000.0000.0000.000
121A147PRO00.021-0.01824.513-0.127-0.1270.0000.0000.0000.000
122A148ASN0-0.0090.00426.899-0.021-0.0210.0000.0000.0000.000
123A149GLU-1-0.736-0.81524.17012.14512.1450.0000.0000.0000.000
124A150GLU-1-0.798-0.86528.3888.8488.8480.0000.0000.0000.000
125A151THR00.0390.00427.4340.3110.3110.0000.0000.0000.000
126A152SER00.029-0.00827.525-0.409-0.4090.0000.0000.0000.000
127A153ILE00.0300.03625.942-0.236-0.2360.0000.0000.0000.000
128A154GLY00.0500.03430.060-0.340-0.3400.0000.0000.0000.000
129A155ALA0-0.018-0.03133.5060.0900.0900.0000.0000.0000.000
130A156GLU-1-0.865-0.93735.5498.5228.5220.0000.0000.0000.000
131A157ILE00.0470.02529.494-0.012-0.0120.0000.0000.0000.000
132A158LEU0-0.033-0.01530.7310.0810.0810.0000.0000.0000.000
133A159LYS10.9080.95933.335-8.091-8.0910.0000.0000.0000.000
134A160LEU0-0.0030.02732.897-0.197-0.1970.0000.0000.0000.000
135A161PRO00.0420.00732.9710.2870.2870.0000.0000.0000.000
136A162ASN0-0.018-0.01626.8310.3560.3560.0000.0000.0000.000
137A163GLN0-0.035-0.02026.8390.2230.2230.0000.0000.0000.000
138A164ALA0-0.012-0.00128.8820.3490.3490.0000.0000.0000.000
139A165LEU00.0210.00828.290-0.399-0.3990.0000.0000.0000.000
140A166GLU-1-0.797-0.88631.5108.3408.3400.0000.0000.0000.000
141A167SER00.001-0.01134.3760.2190.2190.0000.0000.0000.000
142A168GLU-1-0.850-0.91735.1828.6098.6090.0000.0000.0000.000
143A169LYS10.8110.89936.617-8.241-8.2410.0000.0000.0000.000
144A170ILE0-0.027-0.01435.1670.2880.2880.0000.0000.0000.000
145A171VAL00.0050.01132.465-0.186-0.1860.0000.0000.0000.000
146A172LYS10.8530.93333.056-8.382-8.3820.0000.0000.0000.000
147A173LEU00.002-0.00325.1330.0290.0290.0000.0000.0000.000
148A174PHE0-0.0050.00027.5620.1780.1780.0000.0000.0000.000
149A175ASP-1-0.855-0.93129.9478.3548.3540.0000.0000.0000.000
150A176MET00.0530.02731.1580.1080.1080.0000.0000.0000.000
151A177LYS10.9700.99234.081-7.864-7.8640.0000.0000.0000.000
152A178LYS10.7990.90332.903-9.520-9.5200.0000.0000.0000.000
153A179PHE00.0300.01828.120-0.090-0.0900.0000.0000.0000.000
154A180GLN00.0400.01332.9150.0520.0520.0000.0000.0000.000
155A181SER0-0.057-0.03835.843-0.223-0.2230.0000.0000.0000.000
156A182ASN0-0.050-0.03631.614-0.418-0.4180.0000.0000.0000.000
157A183VAL00.0300.01631.575-0.030-0.0300.0000.0000.0000.000
158A184ASN0-0.045-0.02733.951-0.255-0.2550.0000.0000.0000.000
159A185ARG10.8660.93235.850-8.582-8.5820.0000.0000.0000.000
160A186GLU-1-0.754-0.86631.2129.3929.3920.0000.0000.0000.000
161A187LEU0-0.046-0.01734.609-0.060-0.0600.0000.0000.0000.000
162A188ARG10.8340.89836.319-7.775-7.7750.0000.0000.0000.000
163A189ARG10.7770.86933.086-9.069-9.0690.0000.0000.0000.000
164A190ALA00.0180.00237.428-0.013-0.0130.0000.0000.0000.000
165A191TYR0-0.024-0.01533.139-0.053-0.0530.0000.0000.0000.000
166A192PRO0-0.0180.01332.5520.2790.2790.0000.0000.0000.000
167A193ASP-1-0.787-0.86226.54111.44011.4400.0000.0000.0000.000
168A194ARG10.8830.91425.189-10.999-10.9990.0000.0000.0000.000
169A195ARG10.9070.92522.218-11.679-11.6790.0000.0000.0000.000
170A196ARG10.8530.93023.829-10.528-10.5280.0000.0000.0000.000
171A197LEU0-0.0100.00726.011-0.247-0.2470.0000.0000.0000.000
172A198GLU-1-0.782-0.90122.57312.41512.4150.0000.0000.0000.000
173A199THR0-0.010-0.02020.7820.2000.2000.0000.0000.0000.000
174A200GLN0-0.0180.00522.785-0.087-0.0870.0000.0000.0000.000
175A201CYS0-0.0360.01123.748-0.466-0.4660.0000.0000.0000.000
176A202LEU0-0.0290.00918.4850.2440.2440.0000.0000.0000.000
177A203SER0-0.028-0.02821.545-0.840-0.8400.0000.0000.0000.000
178A204ALA00.0250.03019.2600.5150.5150.0000.0000.0000.000
179A205VAL0-0.025-0.01720.252-0.815-0.8150.0000.0000.0000.000
180A206ALA00.0470.02520.1570.8390.8390.0000.0000.0000.000
181A207PHE00.010-0.01320.638-1.064-1.0640.0000.0000.0000.000
182A208VAL0-0.0060.01322.3140.4070.4070.0000.0000.0000.000
183A209LYS10.7830.85722.405-14.602-14.6020.0000.0000.0000.000
184A210SER0-0.029-0.00821.9940.5010.5010.0000.0000.0000.000
185A211GLU-1-0.814-0.89219.03014.77914.7790.0000.0000.0000.000
186A212ASN0-0.021-0.01621.663-0.801-0.8010.0000.0000.0000.000
187A213ASP-1-0.844-0.91416.40418.06618.0660.0000.0000.0000.000
188A214ILE0-0.004-0.02015.5060.0010.0010.0000.0000.0000.000
189A215LEU0-0.037-0.01811.2410.8420.8420.0000.0000.0000.000
190A216GLU-1-0.832-0.91713.46217.97917.9790.0000.0000.0000.000
191A217CYS0-0.101-0.03116.131-0.686-0.6860.0000.0000.0000.000
192A218PRO00.0230.01515.6601.1841.1840.0000.0000.0000.000
193A219ILE00.0200.00615.5451.2061.2060.0000.0000.0000.000
194A220TRP0-0.068-0.04412.909-2.247-2.2470.0000.0000.0000.000
195A221VAL00.0160.01216.1870.8680.8680.0000.0000.0000.000
196A222LEU0-0.0120.00015.440-0.713-0.7130.0000.0000.0000.000
197A223ILE00.0050.00117.7230.1990.1990.0000.0000.0000.000
198A224VAL0-0.008-0.01318.163-0.059-0.0590.0000.0000.0000.000
199A225ASN00.0570.02621.356-0.257-0.2570.0000.0000.0000.000
200A226VAL00.0570.03223.291-0.028-0.0280.0000.0000.0000.000
201A227VAL00.0770.03025.507-0.229-0.2290.0000.0000.0000.000
202A228ALA0-0.029-0.01527.185-0.256-0.2560.0000.0000.0000.000
203A229MET00.004-0.01121.181-0.017-0.0170.0000.0000.0000.000
204A230ASP-1-0.844-0.92926.6269.8699.8690.0000.0000.0000.000
205A231MET0-0.037-0.00929.348-0.337-0.3370.0000.0000.0000.000
206A232LEU0-0.045-0.02226.593-0.260-0.2600.0000.0000.0000.000
207A233LYS10.8210.93226.204-10.916-10.9160.0000.0000.0000.000
208A234SER0-0.0020.01329.867-0.291-0.2910.0000.0000.0000.000
209A235LYS10.8430.91632.672-8.756-8.7560.0000.0000.0000.000
210A236LEU0-0.0120.01131.621-0.090-0.0900.0000.0000.0000.000