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: JQJG9

Calculation Name: 4OXP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OXP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9A749

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2320075.806493
FMO2-HF: Nuclear repulsion 2239719.069868
FMO2-HF: Total energy -80356.736626
FMO2-MP2: Total energy -80593.854267


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:36:LYS)


Summations of interaction energy for fragment #1(A:36:LYS)
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.
25.77428.7850.739-1.074-2.675-0.001
Interaction energy analysis for fragmet #1(A:36:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 0.970
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].
3A38LEU00.0480.0012.492-8.129-5.5100.741-0.988-2.371-0.001
4A39ARG10.8490.9225.59427.03627.0360.0000.0000.0000.000
5A40GLY00.0510.0318.962-0.164-0.1640.0000.0000.0000.000
6A41ASN00.0950.0684.7184.5014.595-0.001-0.001-0.0920.000
7A42ILE0-0.083-0.0499.0842.4632.4630.0000.0000.0000.000
8A43TYR00.0430.0305.351-0.686-0.6860.0000.0000.0000.000
9A44LEU0-0.0070.00611.5871.9531.9530.0000.0000.0000.000
10A45ALA00.0240.00113.564-1.132-1.1320.0000.0000.0000.000
11A46LYS10.9760.98615.04019.88119.8810.0000.0000.0000.000
12A47VAL0-0.039-0.01217.837-0.586-0.5860.0000.0000.0000.000
13A48THR0-0.0080.00317.6020.7580.7580.0000.0000.0000.000
14A49ARG10.8910.93220.35114.91914.9190.0000.0000.0000.000
15A50VAL00.0170.01722.900-0.478-0.4780.0000.0000.0000.000
16A51GLU-1-0.908-0.97224.666-11.503-11.5030.0000.0000.0000.000
17A52PRO00.0150.00526.8950.0050.0050.0000.0000.0000.000
18A53SER00.0340.01929.6300.3030.3030.0000.0000.0000.000
19A54LEU0-0.027-0.01823.7980.0560.0560.0000.0000.0000.000
20A55GLN0-0.031-0.00926.964-0.161-0.1610.0000.0000.0000.000
21A56ALA00.0170.01322.701-0.247-0.2470.0000.0000.0000.000
22A57ALA00.0190.02121.7790.4020.4020.0000.0000.0000.000
23A58PHE0-0.014-0.00718.014-0.486-0.4860.0000.0000.0000.000
24A59ILE00.002-0.00114.5550.6670.6670.0000.0000.0000.000
25A60GLU-1-0.867-0.94311.956-25.710-25.7100.0000.0000.0000.000
26A61TYR0-0.010-0.0307.5240.9760.9760.0000.0000.0000.000
27A62GLY00.0370.0188.589-1.781-1.7810.0000.0000.0000.000
28A63GLY0-0.0240.0116.661-4.824-4.8240.0000.0000.0000.000
29A64ASN0-0.030-0.0146.5482.8312.8310.0000.0000.0000.000
30A65ARG10.8740.9509.42924.24324.2430.0000.0000.0000.000
31A66HIS0-0.010-0.00211.732-0.387-0.3870.0000.0000.0000.000
32A67GLY00.0090.00513.871-0.169-0.1690.0000.0000.0000.000
33A68PHE0-0.062-0.04614.2991.2311.2310.0000.0000.0000.000
34A69LEU00.0190.00317.555-0.386-0.3860.0000.0000.0000.000
35A70ALA00.0540.04019.7470.6610.6610.0000.0000.0000.000
36A71PHE00.0700.01822.964-0.244-0.2440.0000.0000.0000.000
37A72ASN0-0.003-0.01625.228-0.237-0.2370.0000.0000.0000.000
38A73GLU-1-0.900-0.92120.824-14.034-14.0340.0000.0000.0000.000
39A74ILE0-0.035-0.00121.957-0.625-0.6250.0000.0000.0000.000
40A75HIS00.0230.04023.5820.6340.6340.0000.0000.0000.000
41A76PRO00.0860.00925.515-0.040-0.0400.0000.0000.0000.000
42A77ASP-1-0.859-0.94326.324-11.114-11.1140.0000.0000.0000.000
43A78TYR0-0.016-0.00720.628-0.186-0.1860.0000.0000.0000.000
44A79TYR0-0.025-0.00326.3940.1490.1490.0000.0000.0000.000
45A80GLN0-0.100-0.07027.4820.4620.4620.0000.0000.0000.000
46A81ILE0-0.039-0.01531.4250.2030.2030.0000.0000.0000.000
47A82PRO00.0690.03834.727-0.168-0.1680.0000.0000.0000.000
48A83VAL00.0710.02334.913-0.119-0.1190.0000.0000.0000.000
49A84ALA0-0.002-0.00236.692-0.062-0.0620.0000.0000.0000.000
50A85ASP-1-0.915-0.94837.178-8.053-8.0530.0000.0000.0000.000
51A86ARG10.8340.90730.81710.19310.1930.0000.0000.0000.000
52A87GLU-1-0.902-0.95234.888-8.589-8.5890.0000.0000.0000.000
53A88ALA0-0.045-0.01137.3170.0440.0440.0000.0000.0000.000
54A89LEU0-0.016-0.01333.7650.0540.0540.0000.0000.0000.000
55A90MET0-0.076-0.02130.091-0.181-0.1810.0000.0000.0000.000
56A91ARG10.9620.97334.6458.0288.0280.0000.0000.0000.000
57A92ASP-1-0.801-0.88435.916-8.872-8.8720.0000.0000.0000.000
58A93ASP-1-0.965-0.95837.853-7.422-7.4220.0000.0000.0000.000
59A129ASP-1-0.819-0.90433.135-9.379-9.3790.0000.0000.0000.000
60A130VAL00.0210.00334.671-0.003-0.0030.0000.0000.0000.000
61A131GLU-1-0.827-0.90428.399-10.934-10.9340.0000.0000.0000.000
62A132GLU-1-0.821-0.90632.587-8.870-8.8700.0000.0000.0000.000
63A133GLU-1-0.785-0.85635.163-8.105-8.1050.0000.0000.0000.000
64A134LEU0-0.019-0.02029.209-0.096-0.0960.0000.0000.0000.000
65A135ALA0-0.061-0.01931.528-0.214-0.2140.0000.0000.0000.000
66A136ARG10.8330.86432.5298.0148.0140.0000.0000.0000.000
67A137ARG10.8480.92431.1989.6959.6950.0000.0000.0000.000
68A138LYS10.9180.95824.82912.27212.2720.0000.0000.0000.000
69A139ARG10.8750.91931.4428.9578.9570.0000.0000.0000.000
70A140ARG10.8320.91734.0578.7108.7100.0000.0000.0000.000
71A141LEU0-0.001-0.00230.3020.1720.1720.0000.0000.0000.000
72A142MET0-0.039-0.01028.360-0.042-0.0420.0000.0000.0000.000
73A143ARG10.9370.97833.0618.0868.0860.0000.0000.0000.000
74A144LYS10.9170.96836.4588.2468.2460.0000.0000.0000.000
75A145TYR00.0390.02533.2420.1110.1110.0000.0000.0000.000
76A146LYS10.9370.97332.9438.6198.6190.0000.0000.0000.000
77A147ILE00.0170.01925.1560.0120.0120.0000.0000.0000.000
78A148GLN00.0700.02229.727-0.405-0.4050.0000.0000.0000.000
79A149GLU-1-0.894-0.96131.039-8.684-8.6840.0000.0000.0000.000
80A150VAL0-0.0260.01329.7470.1160.1160.0000.0000.0000.000
81A151ILE00.0450.04324.650-0.302-0.3020.0000.0000.0000.000
82A152ARG10.8930.93926.74410.35710.3570.0000.0000.0000.000
83A153ARG10.9380.94424.02311.48411.4840.0000.0000.0000.000
84A154ARG10.9220.95022.13612.91012.9100.0000.0000.0000.000
85A155GLN00.0330.04822.4710.0680.0680.0000.0000.0000.000
86A156ILE00.0270.00718.327-0.576-0.5760.0000.0000.0000.000
87A157MET0-0.050-0.01318.5801.0681.0680.0000.0000.0000.000
88A158LEU00.0240.01715.441-1.032-1.0320.0000.0000.0000.000
89A159VAL0-0.077-0.03613.2831.0671.0670.0000.0000.0000.000
90A160GLN00.0590.02212.7320.0070.0070.0000.0000.0000.000
91A161VAL0-0.027-0.0118.5431.6891.6890.0000.0000.0000.000
92A162VAL00.0110.01911.4770.4120.4120.0000.0000.0000.000
93A163LYS10.8160.89612.61620.93620.9360.0000.0000.0000.000
94A164GLU-1-0.750-0.8776.558-34.816-34.8160.0000.0000.0000.000
95A165GLU-1-0.861-0.9268.243-29.205-29.2050.0000.0000.0000.000
96A166ARG10.9340.9578.58918.60618.6060.0000.0000.0000.000
97A167GLY00.0530.0269.9581.7271.7270.0000.0000.0000.000
98A168ASN00.0450.00311.788-1.974-1.9740.0000.0000.0000.000
99A169LYS10.9070.96613.92117.14917.1490.0000.0000.0000.000
100A170GLY00.0980.05012.438-1.235-1.2350.0000.0000.0000.000
101A171ALA0-0.0070.0029.9151.3471.3470.0000.0000.0000.000
102A172VAL0-0.037-0.02611.9441.4331.4330.0000.0000.0000.000
103A173LEU00.0470.03212.401-1.170-1.1700.0000.0000.0000.000
104A174THR0-0.007-0.04315.4921.3911.3910.0000.0000.0000.000
105A175THR00.016-0.00617.004-0.686-0.6860.0000.0000.0000.000
106A176TYR0-0.041-0.00219.5660.5650.5650.0000.0000.0000.000
107A177LEU00.0150.01216.208-0.279-0.2790.0000.0000.0000.000
108A178SER0-0.081-0.06617.2351.1021.1020.0000.0000.0000.000
109A179LEU00.0530.03815.835-1.008-1.0080.0000.0000.0000.000
110A180ALA0-0.022-0.00716.1511.3801.3800.0000.0000.0000.000
111A181GLY00.0880.06617.109-0.576-0.5760.0000.0000.0000.000
112A182ARG10.9530.96019.50912.00612.0060.0000.0000.0000.000
113A183TYR0-0.023-0.01521.2240.2800.2800.0000.0000.0000.000
114A184GLY00.0020.00222.7710.5130.5130.0000.0000.0000.000
115A185VAL00.0020.02719.549-0.558-0.5580.0000.0000.0000.000
116A186LEU00.0420.01921.1620.7630.7630.0000.0000.0000.000
117A187MET0-0.044-0.02321.040-0.877-0.8770.0000.0000.0000.000
118A188PRO00.0160.00920.6440.7580.7580.0000.0000.0000.000
119A189ASN00.0680.02321.7150.6790.6790.0000.0000.0000.000
120A190THR0-0.039-0.02123.8710.2180.2180.0000.0000.0000.000
121A191ALA00.0260.01826.4950.0760.0760.0000.0000.0000.000
122A192ARG10.8400.92326.67011.47911.4790.0000.0000.0000.000
123A193GLY00.0340.02330.4950.2000.2000.0000.0000.0000.000
124A194GLY0-0.087-0.01529.3540.0340.0340.0000.0000.0000.000
125A195GLY0-0.011-0.02129.6190.4460.4460.0000.0000.0000.000
126A196ILE0-0.025-0.00129.425-0.279-0.2790.0000.0000.0000.000
127A197SER00.0110.01225.6370.0450.0450.0000.0000.0000.000
128A198ARG10.9200.90527.55810.53510.5350.0000.0000.0000.000
129A199LYS10.9380.99825.66911.11111.1110.0000.0000.0000.000
130A200ILE0-0.042-0.02629.6640.0950.0950.0000.0000.0000.000
131A201THR0-0.013-0.02032.4430.2480.2480.0000.0000.0000.000
132A202ALA00.0680.03434.9300.2270.2270.0000.0000.0000.000
133A203VAL00.0480.00937.116-0.103-0.1030.0000.0000.0000.000
134A204THR00.0250.01439.269-0.018-0.0180.0000.0000.0000.000
135A205ASP-1-0.779-0.88634.459-8.479-8.4790.0000.0000.0000.000
136A206ARG10.9781.01235.2468.0978.0970.0000.0000.0000.000
137A207LYS10.9760.99036.2687.0437.0430.0000.0000.0000.000
138A208ARG10.9370.98734.0548.5708.5700.0000.0000.0000.000
139A209LEU0-0.017-0.02031.312-0.043-0.0430.0000.0000.0000.000
140A210LYS10.9240.98134.6828.5018.5010.0000.0000.0000.000
141A211SER0-0.004-0.00336.208-0.038-0.0380.0000.0000.0000.000
142A212VAL00.011-0.00732.8330.0000.0000.0000.0000.0000.000
143A213VAL0-0.017-0.02230.872-0.057-0.0570.0000.0000.0000.000
144A214GLN00.0010.01733.392-0.136-0.1360.0000.0000.0000.000
145A215SER0-0.014-0.03836.5170.0100.0100.0000.0000.0000.000
146A216LEU0-0.111-0.05230.1530.0350.0350.0000.0000.0000.000
147A217ASP-1-0.867-0.90333.401-8.563-8.5630.0000.0000.0000.000
148A218VAL0-0.089-0.04529.133-0.187-0.1870.0000.0000.0000.000
149A219PRO00.0510.01929.5100.2210.2210.0000.0000.0000.000
150A220GLN0-0.037-0.01729.118-0.544-0.5440.0000.0000.0000.000
151A221GLY00.0470.01630.2510.1610.1610.0000.0000.0000.000
152A222MET0-0.0190.01725.827-0.440-0.4400.0000.0000.0000.000
153A223GLY00.0260.01426.4460.4900.4900.0000.0000.0000.000
154A224LEU00.0440.01124.782-0.393-0.3930.0000.0000.0000.000
155A225ILE0-0.006-0.00224.8070.5060.5060.0000.0000.0000.000
156A226VAL0-0.024-0.00324.838-0.421-0.4210.0000.0000.0000.000
157A227ARG10.8640.85218.79614.53014.5300.0000.0000.0000.000
158A228THR0-0.002-0.02125.0100.1720.1720.0000.0000.0000.000
159A229ALA00.0260.02623.3630.3470.3470.0000.0000.0000.000
160A230GLY00.034-0.00525.4490.1850.1850.0000.0000.0000.000
161A231ALA0-0.0080.00027.9450.3290.3290.0000.0000.0000.000
162A232LYS10.8300.90430.6348.8658.8650.0000.0000.0000.000
163A233ARG10.8720.96428.15310.22610.2260.0000.0000.0000.000
164A234THR00.054-0.00731.2590.1620.1620.0000.0000.0000.000
165A235LYS10.9791.00032.7767.7567.7560.0000.0000.0000.000
166A236ALA00.0280.00333.210-0.082-0.0820.0000.0000.0000.000
167A237GLU-1-0.819-0.87128.021-10.580-10.5800.0000.0000.0000.000
168A238ILE00.011-0.01927.918-0.420-0.4200.0000.0000.0000.000
169A239LYS10.9060.95928.2468.7918.7910.0000.0000.0000.000
170A240ARG10.8440.89427.6569.8259.8250.0000.0000.0000.000
171A241ASP-1-0.821-0.89922.733-13.385-13.3850.0000.0000.0000.000
172A242TYR00.0830.02923.858-0.576-0.5760.0000.0000.0000.000
173A243GLU-1-0.782-0.87025.135-10.470-10.4700.0000.0000.0000.000
174A244TYR0-0.045-0.01616.9440.1020.1020.0000.0000.0000.000
175A245LEU00.009-0.00519.510-0.463-0.4630.0000.0000.0000.000
176A246LEU0-0.026-0.01421.578-0.382-0.3820.0000.0000.0000.000
177A247ARG10.9830.99422.98412.23012.2300.0000.0000.0000.000
178A248LEU00.0190.03315.528-0.181-0.1810.0000.0000.0000.000
179A249TRP00.019-0.01018.759-0.940-0.9400.0000.0000.0000.000
180A250GLU-1-0.905-0.95720.638-12.687-12.6870.0000.0000.0000.000
181A251ASN00.0390.01718.2830.4060.4060.0000.0000.0000.000
182A252ILE0-0.038-0.00315.429-0.469-0.4690.0000.0000.0000.000
183A253ARG10.8880.93017.78212.54612.5460.0000.0000.0000.000
184A254GLU-1-0.911-0.94820.605-13.653-13.6530.0000.0000.0000.000
185A255ASN00.006-0.00314.6200.7670.7670.0000.0000.0000.000
186A256THR0-0.114-0.04616.705-0.250-0.2500.0000.0000.0000.000
187A257LEU0-0.0110.00017.8800.1290.1290.0000.0000.0000.000
188A258HIS0-0.0240.00218.9120.3580.3580.0000.0000.0000.000
189A259SER0-0.030-0.02814.675-1.211-1.2110.0000.0000.0000.000
190A260ILE0-0.001-0.01415.6090.9980.9980.0000.0000.0000.000
191A261ALA0-0.096-0.01414.710-1.183-1.1830.0000.0000.0000.000
192A262PRO0-0.048-0.04110.9870.0480.0480.0000.0000.0000.000
193A263ALA00.0950.04110.366-0.768-0.7680.0000.0000.0000.000
194A264LEU0-0.026-0.0135.0930.4980.4980.0000.0000.0000.000
195A265ILE0-0.046-0.0228.7731.3611.3610.0000.0000.0000.000
196A266TYR00.009-0.02110.6941.9701.9700.0000.0000.0000.000
197A267GLU-1-0.920-0.9624.104-53.446-53.148-0.001-0.085-0.2120.000
198A268GLU-1-0.941-0.9708.047-20.038-20.0380.0000.0000.0000.000
199A269GLU-1-0.979-0.9838.166-29.333-29.3330.0000.0000.0000.000
200A270ASP-1-1.032-1.0048.929-22.516-22.5160.0000.0000.0000.000