FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: QVMVY

Calculation Name: 4OPH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OPH

Chain ID: A

ChEMBL ID:

UniProt ID: Q20NS3

Base Structure: X-ray

Registration Date: 2023-09-22

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078106.071861
FMO2-HF: Nuclear repulsion 1997639.891869
FMO2-HF: Total energy -80466.179993
FMO2-MP2: Total energy -80698.260213


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:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-32.93-38.43130.554-12.324-12.730.091
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.773 / q_NPA : -0.870
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].
3A4ASN00.005-0.0081.749-55.384-63.16925.683-9.468-8.4310.104
4A5THR00.0010.0162.166-17.153-15.4274.870-2.662-3.934-0.013
5A6VAL00.0300.0133.829-7.242-6.6840.001-0.194-0.3650.000
6A7SER0-0.033-0.0246.025-7.156-7.1560.0000.0000.0000.000
7A8SER0-0.005-0.0196.777-5.158-5.1580.0000.0000.0000.000
8A9PHE0-0.0100.0027.820-3.496-3.4960.0000.0000.0000.000
9A10GLN00.0210.0139.554-3.487-3.4870.0000.0000.0000.000
10A11VAL00.0240.01711.728-2.257-2.2570.0000.0000.0000.000
11A12ASP-1-0.796-0.87912.28720.71120.7110.0000.0000.0000.000
12A13CYS0-0.066-0.02813.036-1.777-1.7770.0000.0000.0000.000
13A14PHE00.0160.02115.729-1.506-1.5060.0000.0000.0000.000
14A15LEU00.0370.01416.420-1.171-1.1710.0000.0000.0000.000
15A16TRP0-0.050-0.03718.096-1.227-1.2270.0000.0000.0000.000
16A17HIS00.0160.00819.830-0.948-0.9480.0000.0000.0000.000
17A18VAL0-0.0030.00621.760-0.768-0.7680.0000.0000.0000.000
18A19ARG10.8220.88520.027-15.007-15.0070.0000.0000.0000.000
19A20LYS10.8190.90123.906-11.222-11.2220.0000.0000.0000.000
20A21ARG10.9610.97225.717-11.450-11.4500.0000.0000.0000.000
21A22PHE0-0.0010.00427.425-0.386-0.3860.0000.0000.0000.000
22A23ALA0-0.016-0.02028.377-0.363-0.3630.0000.0000.0000.000
23A24ASP-1-0.858-0.91729.12010.19810.1980.0000.0000.0000.000
24A25GLN0-0.080-0.02731.698-0.319-0.3190.0000.0000.0000.000
25A26GLU-1-0.952-0.98533.5327.9337.9330.0000.0000.0000.000
26A27LEU00.0020.00632.923-0.136-0.1360.0000.0000.0000.000
27A28GLY0-0.065-0.01030.7970.0730.0730.0000.0000.0000.000
28A29ASP-1-0.763-0.89930.8349.9659.9650.0000.0000.0000.000
29A30ALA00.0430.01031.1330.2500.2500.0000.0000.0000.000
30A31PRO00.0890.03229.2140.2460.2460.0000.0000.0000.000
31A32PHE0-0.0670.00026.2700.5850.5850.0000.0000.0000.000
32A33LEU00.0450.02026.2610.5060.5060.0000.0000.0000.000
33A34ASP-1-0.864-0.91126.76210.36110.3610.0000.0000.0000.000
34A35ARG10.8360.89523.102-11.044-11.0440.0000.0000.0000.000
35A36LEU00.0180.03122.1110.5770.5770.0000.0000.0000.000
36A37ARG10.8590.90822.280-10.211-10.2110.0000.0000.0000.000
37A38ALA0-0.021-0.00621.5320.2570.2570.0000.0000.0000.000
38A39ASP-1-0.780-0.87818.06915.86115.8610.0000.0000.0000.000
39A40GLN0-0.0010.03017.5670.5180.5180.0000.0000.0000.000
40A41ALA0-0.029-0.01118.7680.2660.2660.0000.0000.0000.000
41A42SER00.010-0.00515.2910.7350.7350.0000.0000.0000.000
42A43LEU0-0.006-0.00113.2171.1091.1090.0000.0000.0000.000
43A44ARG10.8940.93414.028-12.575-12.5750.0000.0000.0000.000
44A45GLY00.0030.00514.9670.1070.1070.0000.0000.0000.000
45A46ARG10.8330.9019.400-22.147-22.1470.0000.0000.0000.000
46A47GLY00.0500.02410.4311.2151.2150.0000.0000.0000.000
47A48SER0-0.021-0.02012.1730.0610.0610.0000.0000.0000.000
48A49THR0-0.090-0.0499.613-0.605-0.6050.0000.0000.0000.000
49A50LEU0-0.063-0.0335.7061.0201.0200.0000.0000.0000.000
50A51GLY0-0.0150.0098.5081.1751.1750.0000.0000.0000.000
51A52LEU0-0.024-0.0108.835-0.038-0.0380.0000.0000.0000.000
52A53ASP-1-0.761-0.86512.32915.49815.4980.0000.0000.0000.000
53A54ILE00.000-0.01014.7310.8850.8850.0000.0000.0000.000
54A55GLU-1-0.860-0.90416.64714.90514.9050.0000.0000.0000.000
55A56THR00.014-0.02416.0220.7070.7070.0000.0000.0000.000
56A57ALA00.0230.01212.8420.6980.6980.0000.0000.0000.000
57A58THR0-0.025-0.03614.2580.5250.5250.0000.0000.0000.000
58A59ARG10.7860.87517.272-15.073-15.0730.0000.0000.0000.000
59A60ALA00.0210.01213.639-0.188-0.1880.0000.0000.0000.000
60A61GLY00.011-0.00214.7990.5260.5260.0000.0000.0000.000
61A62LYS10.7680.85715.667-14.369-14.3690.0000.0000.0000.000
62A63GLN00.0500.02016.840-0.259-0.2590.0000.0000.0000.000
63A64ILE0-0.032-0.01511.2650.1100.1100.0000.0000.0000.000
64A65VAL00.003-0.01115.221-0.234-0.2340.0000.0000.0000.000
65A66GLU-1-0.817-0.87817.59313.59313.5930.0000.0000.0000.000
66A67ARG10.7910.86516.269-18.672-18.6720.0000.0000.0000.000
67A68ILE0-0.015-0.01613.969-0.182-0.1820.0000.0000.0000.000
68A69LEU0-0.002-0.00718.255-0.594-0.5940.0000.0000.0000.000
69A70GLU-1-0.916-0.92821.41111.99011.9900.0000.0000.0000.000
70A71GLU-1-0.913-0.92418.17817.00617.0060.0000.0000.0000.000
71A72GLU-1-0.855-0.91721.02313.46113.4610.0000.0000.0000.000
72A73SER0-0.094-0.05823.3980.3380.3380.0000.0000.0000.000
73A74ASP-1-0.913-0.97725.60211.58111.5810.0000.0000.0000.000
74A75GLU-1-0.868-0.92527.50110.16010.1600.0000.0000.0000.000
75A76ALA0-0.072-0.04130.637-0.211-0.2110.0000.0000.0000.000
76A77LEU0-0.043-0.00325.512-0.148-0.1480.0000.0000.0000.000
77A78LYS10.7880.88324.182-12.704-12.7040.0000.0000.0000.000
78A79MET0-0.0010.01026.155-0.326-0.3260.0000.0000.0000.000
79A80THR0-0.007-0.01728.595-0.105-0.1050.0000.0000.0000.000
80A81ILE0-0.029-0.01527.428-0.258-0.2580.0000.0000.0000.000
81A82ALA00.0350.01430.2690.2040.2040.0000.0000.0000.000
82A83SER0-0.049-0.01431.009-0.252-0.2520.0000.0000.0000.000
83A84VAL00.0320.01931.126-0.073-0.0730.0000.0000.0000.000
84A85PRO0-0.012-0.00233.754-0.275-0.2750.0000.0000.0000.000
85A86ALA0-0.061-0.05235.893-0.050-0.0500.0000.0000.0000.000
86A87SER0-0.006-0.00832.836-0.334-0.3340.0000.0000.0000.000
87A88ARG10.9330.98336.030-7.896-7.8960.0000.0000.0000.000
88A89TYR00.008-0.00632.9240.1510.1510.0000.0000.0000.000
89A90LEU0-0.031-0.01237.192-0.372-0.3720.0000.0000.0000.000
90A91THR0-0.060-0.04637.4640.2670.2670.0000.0000.0000.000
91A92ASP-1-0.689-0.77339.1568.0898.0890.0000.0000.0000.000
92A93MET0-0.083-0.01534.638-0.211-0.2110.0000.0000.0000.000
93A94THR00.032-0.00839.9300.0950.0950.0000.0000.0000.000
94A95LEU00.024-0.01338.1000.1630.1630.0000.0000.0000.000
95A96GLU-1-0.851-0.90639.1697.7077.7070.0000.0000.0000.000
96A97GLU-1-0.753-0.84540.2127.7987.7980.0000.0000.0000.000
97A98MET0-0.063-0.02134.6430.2300.2300.0000.0000.0000.000
98A99SER0-0.042-0.02235.1120.2800.2800.0000.0000.0000.000
99A100ARG10.8000.90636.794-7.751-7.7510.0000.0000.0000.000
100A101ASP-1-0.924-0.95936.5908.4458.4450.0000.0000.0000.000
101A102TRP0-0.025-0.03531.493-0.125-0.1250.0000.0000.0000.000
102A103PHE0-0.042-0.02133.9400.2520.2520.0000.0000.0000.000
103A104MET0-0.0490.00429.3900.0000.0000.0000.0000.0000.000
104A105LEU00.010-0.00134.6450.1130.1130.0000.0000.0000.000
105A106MET0-0.063-0.02934.2530.0620.0620.0000.0000.0000.000
106A107PRO00.004-0.00429.5800.1090.1090.0000.0000.0000.000
107A108LYS10.9080.97128.319-10.011-10.0110.0000.0000.0000.000
108A109GLN00.0380.01024.580-0.117-0.1170.0000.0000.0000.000
109A110LYS10.9260.96822.744-12.950-12.9500.0000.0000.0000.000
110A111VAL00.0320.02317.834-0.180-0.1800.0000.0000.0000.000
111A112ALA0-0.030-0.02119.7820.1750.1750.0000.0000.0000.000
112A113GLY00.0740.04019.779-0.268-0.2680.0000.0000.0000.000
113A114SER0-0.007-0.01517.815-0.019-0.0190.0000.0000.0000.000
114A115LEU0-0.0130.01119.613-0.518-0.5180.0000.0000.0000.000
115A116CYS0-0.024-0.02321.8620.5280.5280.0000.0000.0000.000
116A117ILE00.0030.01023.509-0.500-0.5000.0000.0000.0000.000
117A118ARG10.7970.87424.931-11.746-11.7460.0000.0000.0000.000
118A119MET00.0290.01328.899-0.217-0.2170.0000.0000.0000.000
119A120ASP-1-0.732-0.85931.8849.0339.0330.0000.0000.0000.000
120A121GLN0-0.087-0.06233.4480.1450.1450.0000.0000.0000.000
121A122ALA0-0.027-0.02435.296-0.186-0.1860.0000.0000.0000.000
122A123ILE0-0.021-0.00238.594-0.208-0.2080.0000.0000.0000.000
123A124MET0-0.0020.01240.0370.0790.0790.0000.0000.0000.000
124A125ASP-1-0.886-0.92842.8836.6996.6990.0000.0000.0000.000
125A126LYS10.7160.84443.208-6.995-6.9950.0000.0000.0000.000
126A127ASN00.0090.00544.0270.1380.1380.0000.0000.0000.000
127A128ILE0-0.015-0.01739.2870.0320.0320.0000.0000.0000.000
128A129ILE0-0.059-0.02341.839-0.058-0.0580.0000.0000.0000.000
129A130LEU0-0.005-0.00935.0980.1450.1450.0000.0000.0000.000
130A131LYS10.7910.86937.726-7.944-7.9440.0000.0000.0000.000
131A132ALA00.008-0.01634.2590.2580.2580.0000.0000.0000.000
132A133ASN00.0030.00534.591-0.393-0.3930.0000.0000.0000.000
133A134PHE0-0.004-0.02032.8250.3900.3900.0000.0000.0000.000
134A135SER00.002-0.02931.938-0.260-0.2600.0000.0000.0000.000
135A136VAL0-0.001-0.00733.6970.1490.1490.0000.0000.0000.000
136A137ILE00.0340.02032.788-0.111-0.1110.0000.0000.0000.000
137A138PHE0-0.027-0.02535.385-0.021-0.0210.0000.0000.0000.000
138A139ASP-1-0.819-0.86938.8508.2028.2020.0000.0000.0000.000
139A140ARG10.8420.88534.131-8.655-8.6550.0000.0000.0000.000
140A141LEU00.002-0.00431.8670.0180.0180.0000.0000.0000.000
141A142GLU-1-0.834-0.85529.70110.58410.5840.0000.0000.0000.000
142A143THR0-0.019-0.01827.5960.6730.6730.0000.0000.0000.000
143A144LEU0-0.034-0.01328.280-0.532-0.5320.0000.0000.0000.000
144A145ILE0-0.029-0.01728.1950.4280.4280.0000.0000.0000.000
145A146LEU0-0.016-0.02029.2460.3410.3410.0000.0000.0000.000
146A147LEU0-0.0090.00131.224-0.344-0.3440.0000.0000.0000.000
147A148ARG10.8180.89732.448-9.216-9.2160.0000.0000.0000.000
148A149ALA00.0060.00635.116-0.176-0.1760.0000.0000.0000.000
149A150PHE00.010-0.00237.3920.0660.0660.0000.0000.0000.000
150A151THR0-0.003-0.02340.897-0.034-0.0340.0000.0000.0000.000
151A152GLU-1-0.810-0.89943.6036.7296.7290.0000.0000.0000.000
152A153GLU-1-0.887-0.93046.2466.9226.9220.0000.0000.0000.000
153A154GLY00.0140.03444.3510.1650.1650.0000.0000.0000.000
154A155ALA00.0350.01741.8860.1830.1830.0000.0000.0000.000
155A156ILE0-0.026-0.01035.4780.0180.0180.0000.0000.0000.000
156A157VAL00.0290.01236.9680.0270.0270.0000.0000.0000.000
157A158GLY00.010-0.01133.1120.1600.1600.0000.0000.0000.000
158A159GLU-1-0.800-0.87529.65310.54610.5460.0000.0000.0000.000
159A160ILE0-0.010-0.00627.0860.3330.3330.0000.0000.0000.000
160A161SER00.0070.00726.054-0.163-0.1630.0000.0000.0000.000
161A162PRO00.0230.01624.0640.4520.4520.0000.0000.0000.000
162A163LEU0-0.017-0.00618.6560.1320.1320.0000.0000.0000.000
163A164PRO0-0.022-0.00917.203-0.056-0.0560.0000.0000.0000.000
164A165SER0-0.048-0.03914.7680.9370.9370.0000.0000.0000.000
165A166LEU0-0.0300.00311.537-0.770-0.7700.0000.0000.0000.000
166A167PRO00.0100.00213.9050.9640.9640.0000.0000.0000.000
167A168GLY00.0490.03316.810-0.182-0.1820.0000.0000.0000.000
168A169HIS0-0.0030.02320.095-0.537-0.5370.0000.0000.0000.000
169A170THR00.003-0.02422.793-0.354-0.3540.0000.0000.0000.000
170A171ASP-1-0.782-0.90325.75710.62510.6250.0000.0000.0000.000
171A172GLU-1-0.906-0.93426.42811.32511.3250.0000.0000.0000.000
172A173ASP-1-0.822-0.87622.50714.08614.0860.0000.0000.0000.000
173A174VAL00.013-0.00325.352-0.118-0.1180.0000.0000.0000.000
174A175LYS10.7930.89428.269-10.446-10.4460.0000.0000.0000.000
175A176ASN0-0.024-0.02325.864-0.654-0.6540.0000.0000.0000.000
176A177ALA0-0.025-0.01226.142-0.124-0.1240.0000.0000.0000.000
177A178ILE00.008-0.00327.901-0.213-0.2130.0000.0000.0000.000
178A179GLY00.0210.01731.490-0.261-0.2610.0000.0000.0000.000
179A180VAL0-0.065-0.03426.865-0.140-0.1400.0000.0000.0000.000
180A181LEU0-0.023-0.01030.164-0.135-0.1350.0000.0000.0000.000
181A182ILE00.0210.00631.927-0.214-0.2140.0000.0000.0000.000
182A183GLY00.0420.02733.962-0.202-0.2020.0000.0000.0000.000
183A184GLY0-0.030-0.02132.729-0.138-0.1380.0000.0000.0000.000
184A185LEU00.036-0.00233.588-0.139-0.1390.0000.0000.0000.000
185A186GLU-1-0.864-0.93036.6797.6977.6970.0000.0000.0000.000
186A187TRP0-0.090-0.04134.692-0.233-0.2330.0000.0000.0000.000
187A188ASN0-0.073-0.01935.621-0.118-0.1180.0000.0000.0000.000
188A189ASP-1-0.860-0.92439.6697.1737.1730.0000.0000.0000.000
189A190ASN0-0.035-0.03839.640-0.233-0.2330.0000.0000.0000.000
190A191THR0-0.048-0.02742.519-0.098-0.0980.0000.0000.0000.000
191A192VAL0-0.036-0.01737.631-0.017-0.0170.0000.0000.0000.000
192A193ARG10.8040.91340.960-7.467-7.4670.0000.0000.0000.000
193A194VAL00.0450.00737.5830.1700.1700.0000.0000.0000.000
194A195SER00.025-0.00639.549-0.218-0.2180.0000.0000.0000.000
195A196GLU-1-0.768-0.87941.4287.4527.4520.0000.0000.0000.000
196A197THR0-0.076-0.07240.3460.0250.0250.0000.0000.0000.000
197A198LEU00.0550.02735.0100.1300.1300.0000.0000.0000.000
198A199GLN0-0.046-0.01238.308-0.011-0.0110.0000.0000.0000.000
199A200ARG10.7730.87840.737-7.462-7.4620.0000.0000.0000.000
200A201PHE0-0.014-0.00837.538-0.118-0.1180.0000.0000.0000.000
201A202ALA00.0120.01434.1990.2550.2550.0000.0000.0000.000
202A203TRP00.0000.00234.5870.1790.1790.0000.0000.0000.000