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: 53K3Z

Calculation Name: 4OK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZKK2

Base Structure: X-ray

Registration Date: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842424.541323
FMO2-HF: Nuclear repulsion 2751143.760023
FMO2-HF: Total energy -91280.7813
FMO2-MP2: Total energy -91546.003223


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:12:LEU)


Summations of interaction energy for fragment #1(A:12:LEU)
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.
-7.726-1.6526.872-3.648-9.299-0.013
Interaction energy analysis for fragmet #1(A:12:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.005
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].
3A14GLU-1-0.866-0.9483.079-3.272-0.9460.126-1.185-1.267-0.002
4A15GLN0-0.048-0.0255.5680.1080.1080.0000.0000.0000.000
5A16ALA00.0730.0382.371-0.137-0.5942.512-0.603-1.4530.000
6A17LEU0-0.0030.0092.297-2.780-1.1042.130-0.851-2.955-0.002
7A18ASN0-0.050-0.0493.6220.0740.2140.0250.123-0.2890.000
8A19HIS0-0.0020.0205.5000.0880.0880.0000.0000.0000.000
9A20GLU-1-0.780-0.8643.530-2.834-2.1010.027-0.235-0.524-0.001
10A21LYS10.8530.9255.8700.7020.7020.0000.0000.0000.000
11A22LEU00.0000.0007.9840.1020.1020.0000.0000.0000.000
12A23MET0-0.0120.0056.6160.0980.0980.0000.0000.0000.000
13A24ARG10.8950.9296.8180.9690.9690.0000.0000.0000.000
14A25ALA0-0.0300.00110.8290.0570.0570.0000.0000.0000.000
15A26ILE00.004-0.00613.3870.0490.0490.0000.0000.0000.000
16A27VAL00.007-0.00413.4300.0340.0340.0000.0000.0000.000
17A28LYS10.8790.92213.1010.3960.3960.0000.0000.0000.000
18A29ASN0-0.0410.00216.3940.0370.0370.0000.0000.0000.000
19A30LEU00.012-0.00818.3390.0230.0230.0000.0000.0000.000
20A31ALA00.0260.03918.9960.0160.0160.0000.0000.0000.000
21A32ASP-1-0.829-0.87720.899-0.134-0.1340.0000.0000.0000.000
22A33THR0-0.081-0.04723.0700.0180.0180.0000.0000.0000.000
23A34PRO0-0.002-0.03624.705-0.004-0.0040.0000.0000.0000.000
24A35MET0-0.0350.01821.1110.0060.0060.0000.0000.0000.000
25A36VAL0-0.0010.00621.118-0.010-0.0100.0000.0000.0000.000
26A37LEU00.0000.01213.2960.0130.0130.0000.0000.0000.000
27A38LYS10.8880.91817.4430.0650.0650.0000.0000.0000.000
28A39GLY00.0740.03016.014-0.014-0.0140.0000.0000.0000.000
29A40GLU-1-0.790-0.87512.101-0.031-0.0310.0000.0000.0000.000
30A41THR00.001-0.0259.669-0.040-0.0400.0000.0000.0000.000
31A42ALA0-0.0130.01611.531-0.080-0.0800.0000.0000.0000.000
32A43LEU0-0.0030.00212.946-0.039-0.0390.0000.0000.0000.000
33A44TYR0-0.053-0.0413.418-0.982-0.1660.047-0.283-0.580-0.002
34A45LEU0-0.045-0.0367.805-0.088-0.0880.0000.0000.0000.000
35A46GLY0-0.041-0.02210.274-0.012-0.0120.0000.0000.0000.000
36A47TYR0-0.021-0.03212.8180.0340.0340.0000.0000.0000.000
37A48GLY00.0440.04210.1450.0420.0420.0000.0000.0000.000
38A49LEU0-0.018-0.0039.8750.0140.0140.0000.0000.0000.000
39A50ASN0-0.010-0.0068.440-0.166-0.1660.0000.0000.0000.000
40A51ARG10.8200.8886.9760.0380.0380.0000.0000.0000.000
41A52PHE00.0000.0122.546-1.144-0.3112.006-0.613-2.225-0.006
42A53SER00.002-0.0325.2920.1800.187-0.001-0.001-0.0060.000
43A54GLU-1-0.799-0.8906.9830.2490.2490.0000.0000.0000.000
44A55ASP-1-0.767-0.8489.2430.0220.0220.0000.0000.0000.000
45A56LEU0-0.009-0.00212.179-0.054-0.0540.0000.0000.0000.000
46A57ASP-1-0.861-0.91714.538-0.036-0.0360.0000.0000.0000.000
47A58PHE0-0.008-0.02916.860-0.027-0.0270.0000.0000.0000.000
48A59ASP-1-0.797-0.87720.084-0.053-0.0530.0000.0000.0000.000
49A60CYS0-0.041-0.03423.551-0.014-0.0140.0000.0000.0000.000
50A61HIS00.0800.04926.0630.0100.0100.0000.0000.0000.000
51A62LYS10.8790.93429.0140.0800.0800.0000.0000.0000.000
52A63LYS10.8590.92028.5990.0380.0380.0000.0000.0000.000
53A64ILE00.0240.00924.095-0.001-0.0010.0000.0000.0000.000
54A65ASN00.0120.00827.7730.0040.0040.0000.0000.0000.000
55A66LEU00.0490.03020.787-0.008-0.0080.0000.0000.0000.000
56A67LEU00.0400.01022.752-0.010-0.0100.0000.0000.0000.000
57A68GLY0-0.0030.00323.667-0.004-0.0040.0000.0000.0000.000
58A69ARG10.7890.86721.9360.1340.1340.0000.0000.0000.000
59A70VAL00.0410.01517.598-0.014-0.0140.0000.0000.0000.000
60A71LYS10.9460.96819.1450.0600.0600.0000.0000.0000.000
61A72SER0-0.068-0.03721.393-0.001-0.0010.0000.0000.0000.000
62A73ALA0-0.035-0.01116.924-0.008-0.0080.0000.0000.0000.000
63A74ILE00.0020.00915.849-0.033-0.0330.0000.0000.0000.000
64A75PRO0-0.0170.01611.9300.0110.0110.0000.0000.0000.000
65A76ASN00.042-0.00114.6690.0150.0150.0000.0000.0000.000
66A77GLY0-0.008-0.00913.653-0.051-0.0510.0000.0000.0000.000
67A78ILE0-0.0180.01410.3600.0070.0070.0000.0000.0000.000
68A79ILE0-0.0100.00014.4450.0150.0150.0000.0000.0000.000
69A80LEU0-0.015-0.00417.0830.0070.0070.0000.0000.0000.000
70A81ASN0-0.057-0.04718.657-0.007-0.0070.0000.0000.0000.000
71A82ASP-1-0.841-0.94520.059-0.015-0.0150.0000.0000.0000.000
72A83ILE0-0.075-0.03519.915-0.012-0.0120.0000.0000.0000.000
73A84HIS00.0510.04021.7980.0040.0040.0000.0000.0000.000
74A85ILE00.016-0.00123.030-0.002-0.0020.0000.0000.0000.000
75A86LYS10.8600.93422.005-0.032-0.0320.0000.0000.0000.000
76A87LYS10.9330.96125.5770.0100.0100.0000.0000.0000.000
77A88ASP-1-0.813-0.86926.452-0.052-0.0520.0000.0000.0000.000
78A89THR0-0.004-0.01428.9070.0060.0060.0000.0000.0000.000
79A90ASP-1-0.891-0.94330.644-0.032-0.0320.0000.0000.0000.000
80A91SER0-0.025-0.01530.966-0.001-0.0010.0000.0000.0000.000
81A92VAL00.0040.01225.276-0.001-0.0010.0000.0000.0000.000
82A93GLY00.0090.02125.4300.0040.0040.0000.0000.0000.000
83A94ARG10.8110.85821.750-0.006-0.0060.0000.0000.0000.000
84A95TYR0-0.029-0.05420.3860.0060.0060.0000.0000.0000.000
85A96MET0-0.0100.00418.4780.0100.0100.0000.0000.0000.000
86A97VAL00.0160.01515.6520.0040.0040.0000.0000.0000.000
87A98ARG10.8840.94815.918-0.016-0.0160.0000.0000.0000.000
88A99TYR0-0.016-0.0469.183-0.030-0.0300.0000.0000.0000.000
89A100ALA00.0840.06314.9960.0280.0280.0000.0000.0000.000
90A101THR0-0.041-0.04510.433-0.059-0.0590.0000.0000.0000.000
91A102LYS10.8210.88211.2060.3970.3970.0000.0000.0000.000
92A103ASP-1-0.768-0.85010.671-0.327-0.3270.0000.0000.0000.000
93A104ASN00.005-0.00812.4650.0340.0340.0000.0000.0000.000
94A105LYS10.9830.99114.347-0.089-0.0890.0000.0000.0000.000
95A106GLU-1-0.947-0.95913.7620.2360.2360.0000.0000.0000.000
96A107GLU-1-0.853-0.90215.1670.0010.0010.0000.0000.0000.000
97A108GLN0-0.0050.00510.9930.0820.0820.0000.0000.0000.000
98A109THR0-0.036-0.03913.031-0.020-0.0200.0000.0000.0000.000
99A110LEU0-0.0020.01110.9050.0200.0200.0000.0000.0000.000
100A111LYS10.7970.88113.356-0.086-0.0860.0000.0000.0000.000
101A112LEU0-0.0020.00814.972-0.026-0.0260.0000.0000.0000.000
102A113GLU-1-0.801-0.86717.5370.0080.0080.0000.0000.0000.000
103A114ILE0-0.002-0.00520.033-0.014-0.0140.0000.0000.0000.000
104A115SER00.0160.01522.7500.0130.0130.0000.0000.0000.000
105A116TYR0-0.021-0.03025.660-0.011-0.0110.0000.0000.0000.000
106A117ARG10.9420.96728.7390.0240.0240.0000.0000.0000.000
107A118ASP-1-0.861-0.93228.756-0.036-0.0360.0000.0000.0000.000
108A119ALA0-0.0180.01027.235-0.003-0.0030.0000.0000.0000.000
109A120PRO0-0.014-0.00624.3870.0030.0030.0000.0000.0000.000
110A121LYS10.9740.98627.7110.0730.0730.0000.0000.0000.000
111A122GLU-1-0.775-0.89628.084-0.109-0.1090.0000.0000.0000.000
112A123SER0-0.091-0.04129.5000.0000.0000.0000.0000.0000.000
113A124GLU-1-0.780-0.87526.983-0.074-0.0740.0000.0000.0000.000
114A125VAL0-0.043-0.00123.327-0.007-0.0070.0000.0000.0000.000
115A126ASN00.0010.00721.0450.0180.0180.0000.0000.0000.000
116A127VAL0-0.012-0.01820.292-0.004-0.0040.0000.0000.0000.000
117A128ILE00.0220.01715.2080.0060.0060.0000.0000.0000.000
118A129GLU-1-0.883-0.94613.214-0.389-0.3890.0000.0000.0000.000
119A130GLY0-0.0330.00115.389-0.017-0.0170.0000.0000.0000.000
120A131MET0-0.022-0.00611.954-0.005-0.0050.0000.0000.0000.000
121A132ARG10.8150.88317.1930.1400.1400.0000.0000.0000.000
122A133ILE0-0.016-0.00515.147-0.006-0.0060.0000.0000.0000.000
123A134ALA00.0420.02119.2860.0140.0140.0000.0000.0000.000
124A135LYS10.8220.92120.1920.1010.1010.0000.0000.0000.000
125A136ILE00.0410.02618.0910.0070.0070.0000.0000.0000.000
126A137GLU-1-0.795-0.88121.277-0.085-0.0850.0000.0000.0000.000
127A138ARG10.8100.88723.6360.0790.0790.0000.0000.0000.000
128A139ILE0-0.029-0.01017.3940.0080.0080.0000.0000.0000.000
129A140ILE00.0310.01721.0350.0120.0120.0000.0000.0000.000
130A141ASP-1-0.822-0.90622.675-0.014-0.0140.0000.0000.0000.000
131A142ASN0-0.051-0.03221.8850.0090.0090.0000.0000.0000.000
132A143LYS10.7410.85115.7540.0000.0000.0000.0000.0000.000
133A144LEU00.0020.00721.8620.0130.0130.0000.0000.0000.000
134A145CYS00.0120.01025.3940.0080.0080.0000.0000.0000.000
135A146ALA0-0.043-0.01822.1180.0070.0070.0000.0000.0000.000
136A147CYS0-0.055-0.03522.3410.0090.0090.0000.0000.0000.000
137A148PHE0-0.088-0.03424.4730.0080.0080.0000.0000.0000.000
138A149ASP-1-0.771-0.88127.9390.0080.0080.0000.0000.0000.000
139A150GLY00.0600.04629.039-0.005-0.0050.0000.0000.0000.000
140A151GLU-1-0.985-1.00330.0870.0130.0130.0000.0000.0000.000
141A152HIS0-0.089-0.04526.1230.0030.0030.0000.0000.0000.000
142A153THR0-0.0150.01826.6020.0040.0040.0000.0000.0000.000
143A154ARG10.7350.82117.685-0.049-0.0490.0000.0000.0000.000
144A155THR00.0120.00323.855-0.005-0.0050.0000.0000.0000.000
145A156LYS10.7920.89515.518-0.241-0.2410.0000.0000.0000.000
146A157ALA00.0640.02717.827-0.018-0.0180.0000.0000.0000.000
147A158ARG10.7440.82711.169-0.338-0.3380.0000.0000.0000.000
148A159ASP-1-0.770-0.83815.7860.0340.0340.0000.0000.0000.000
149A160LEU00.0430.03118.567-0.020-0.0200.0000.0000.0000.000
150A161PHE00.034-0.00111.438-0.010-0.0100.0000.0000.0000.000
151A162ASP-1-0.740-0.86113.591-0.003-0.0030.0000.0000.0000.000
152A163LEU0-0.001-0.00615.987-0.032-0.0320.0000.0000.0000.000
153A164HIS0-0.047-0.01618.112-0.019-0.0190.0000.0000.0000.000
154A165PHE00.0300.01013.525-0.017-0.0170.0000.0000.0000.000
155A166LEU0-0.046-0.03716.834-0.024-0.0240.0000.0000.0000.000
156A167ALA0-0.018-0.01419.124-0.009-0.0090.0000.0000.0000.000
157A168LYS10.8140.88018.766-0.039-0.0390.0000.0000.0000.000
158A169HIS0-0.053-0.02016.219-0.019-0.0190.0000.0000.0000.000
159A170TYR0-0.067-0.04215.544-0.017-0.0170.0000.0000.0000.000
160A171GLU-1-0.882-0.94921.479-0.035-0.0350.0000.0000.0000.000
161A172GLU-1-0.843-0.91323.978-0.099-0.0990.0000.0000.0000.000
162A173HIS10.7090.82922.9740.1040.1040.0000.0000.0000.000
163A174PHE0-0.002-0.00122.4970.0050.0050.0000.0000.0000.000
164A175ASN00.0290.01227.3550.0060.0060.0000.0000.0000.000
165A176LEU00.023-0.00730.8600.0030.0030.0000.0000.0000.000
166A177ASP-1-0.832-0.90731.620-0.010-0.0100.0000.0000.0000.000
167A178LEU00.0210.01426.3340.0040.0040.0000.0000.0000.000
168A179ALA00.0270.01128.4120.0050.0050.0000.0000.0000.000
169A180SER0-0.035-0.01029.7880.0060.0060.0000.0000.0000.000
170A181ARG10.6890.80128.6990.0140.0140.0000.0000.0000.000
171A182LEU00.0250.02223.9120.0070.0070.0000.0000.0000.000
172A183LYS10.8330.93327.8410.0010.0010.0000.0000.0000.000
173A184ASP-1-0.853-0.92630.7160.0350.0350.0000.0000.0000.000
174A185PHE00.0020.00823.2850.0050.0050.0000.0000.0000.000
175A186SER0-0.019-0.04026.3920.0080.0080.0000.0000.0000.000
176A187LYS10.7440.86328.329-0.035-0.0350.0000.0000.0000.000
177A188ASP-1-0.891-0.94330.5430.0720.0720.0000.0000.0000.000
178A189PRO00.0310.01027.5400.0070.0070.0000.0000.0000.000
179A190ASP-1-0.844-0.91927.5910.1060.1060.0000.0000.0000.000
180A191LYS10.8120.90329.336-0.073-0.0730.0000.0000.0000.000
181A192LEU00.0080.00724.7560.0090.0090.0000.0000.0000.000
182A193VAL0-0.001-0.00624.3250.0150.0150.0000.0000.0000.000
183A194SER0-0.062-0.05525.3710.0160.0160.0000.0000.0000.000
184A195ASP-1-0.867-0.90826.3110.1020.1020.0000.0000.0000.000
185A196TYR0-0.013-0.01521.3560.0060.0060.0000.0000.0000.000
186A197LEU00.0010.01521.5650.0350.0350.0000.0000.0000.000
187A198VAL0-0.020-0.02321.6830.0290.0290.0000.0000.0000.000
188A199ASP-1-0.781-0.90118.8480.2760.2760.0000.0000.0000.000
189A200VAL00.0240.00316.4380.0450.0450.0000.0000.0000.000
190A201LYS10.9260.96516.234-0.265-0.2650.0000.0000.0000.000
191A202LEU0-0.017-0.00516.9970.0510.0510.0000.0000.0000.000
192A203ASP-1-0.767-0.84612.4380.4990.4990.0000.0000.0000.000
193A204ALA00.0160.00610.3430.0370.0370.0000.0000.0000.000
194A205LEU0-0.078-0.0266.4350.3340.3340.0000.0000.0000.000
195A206LEU0-0.020-0.0229.538-0.107-0.1070.0000.0000.0000.000
196A207ASN0-0.014-0.01012.3260.1560.1560.0000.0000.0000.000
197A208GLN0-0.043-0.0219.336-0.211-0.2110.0000.0000.0000.000
198A209ILE0-0.068-0.0367.7480.0300.0300.0000.0000.0000.000
199A210MET0-0.0320.00811.132-0.114-0.1140.0000.0000.0000.000
200A211ASP-1-0.821-0.89014.5760.2440.2440.0000.0000.0000.000
201A212LEU0-0.056-0.00317.812-0.030-0.0300.0000.0000.0000.000
202A213GLU-1-0.844-0.94420.0060.2080.2080.0000.0000.0000.000
203A214GLU-1-0.954-0.97719.0770.1200.1200.0000.0000.0000.000
204A215THR0-0.057-0.05118.386-0.022-0.0220.0000.0000.0000.000
205A216ALA0-0.017-0.01220.660-0.024-0.0240.0000.0000.0000.000
206A217LEU0-0.0120.00424.090-0.017-0.0170.0000.0000.0000.000
207A218GLU-1-0.774-0.87120.8950.0450.0450.0000.0000.0000.000
208A219LEU00.0080.00522.139-0.015-0.0150.0000.0000.0000.000
209A220GLY00.0780.05424.621-0.011-0.0110.0000.0000.0000.000
210A221VAL0-0.068-0.03527.741-0.009-0.0090.0000.0000.0000.000
211A222MET0-0.012-0.00421.495-0.012-0.0120.0000.0000.0000.000
212A223ALA00.0410.02727.184-0.009-0.0090.0000.0000.0000.000
213A224GLN00.0100.00228.534-0.009-0.0090.0000.0000.0000.000
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