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: 85MMY

Calculation Name: 1DOV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DOV

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1602506.648044
FMO2-HF: Nuclear repulsion 1532542.287427
FMO2-HF: Total energy -69964.360617
FMO2-MP2: Total energy -70167.368041


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:82:GLU)


Summations of interaction energy for fragment #1(A:82: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.
-111.623-113.62715.81-5.522-8.2840.036
Interaction energy analysis for fragmet #1(A:82:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.918 / 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].
3A84GLN00.0240.0081.815-17.494-20.84015.445-5.043-7.0570.034
4A85PHE00.1000.0564.436-3.933-3.7430.000-0.028-0.1610.000
5A86LEU00.0500.0287.051-2.654-2.6540.0000.0000.0000.000
6A87LYS10.9140.9675.986-48.888-48.8880.0000.0000.0000.000
7A88GLU-1-0.933-0.9778.56227.69827.6980.0000.0000.0000.000
8A89GLU-1-0.866-0.92810.52618.40818.4080.0000.0000.0000.000
9A90LEU0-0.024-0.01911.354-1.770-1.7700.0000.0000.0000.000
10A91VAL00.0120.01012.387-1.464-1.4640.0000.0000.0000.000
11A92VAL00.0190.00914.941-1.509-1.5090.0000.0000.0000.000
12A93ALA0-0.014-0.00516.345-1.202-1.2020.0000.0000.0000.000
13A94VAL0-0.005-0.01216.512-1.063-1.0630.0000.0000.0000.000
14A95GLU-1-0.850-0.91819.22313.73113.7310.0000.0000.0000.000
15A96ASP-1-0.928-0.94321.32713.33913.3390.0000.0000.0000.000
16A97VAL0-0.030-0.02821.690-0.790-0.7900.0000.0000.0000.000
17A98ARG10.8560.93522.913-13.622-13.6220.0000.0000.0000.000
18A99LYS10.9230.95524.007-13.486-13.4860.0000.0000.0000.000
19A100GLN0-0.031-0.02326.734-0.839-0.8390.0000.0000.0000.000
20A101GLY00.0380.01927.727-0.428-0.4280.0000.0000.0000.000
21A102ASP-1-0.914-0.95029.28510.55110.5510.0000.0000.0000.000
22A103LEU0-0.027-0.02831.200-0.388-0.3880.0000.0000.0000.000
23A104MET0-0.054-0.00532.234-0.372-0.3720.0000.0000.0000.000
24A105LYS10.9670.98233.526-9.801-9.8010.0000.0000.0000.000
25A106SER00.0250.01035.256-0.170-0.1700.0000.0000.0000.000
26A107ALA00.0100.01137.409-0.257-0.2570.0000.0000.0000.000
27A108ALA0-0.047-0.03037.314-0.236-0.2360.0000.0000.0000.000
28A109GLY0-0.009-0.00339.249-0.188-0.1880.0000.0000.0000.000
29A110GLU-1-0.892-0.96141.2907.3577.3570.0000.0000.0000.000
30A111PHE0-0.065-0.02942.490-0.217-0.2170.0000.0000.0000.000
31A112ALA0-0.017-0.01743.180-0.166-0.1660.0000.0000.0000.000
32A113ASP-1-0.908-0.94245.0377.0017.0010.0000.0000.0000.000
33A114ASP-1-0.915-0.95147.3446.1996.1990.0000.0000.0000.000
34A115PRO00.0410.02747.460-0.001-0.0010.0000.0000.0000.000
35A116CYS0-0.060-0.03048.485-0.027-0.0270.0000.0000.0000.000
36A117SER0-0.0140.00748.425-0.046-0.0460.0000.0000.0000.000
37A118SER0-0.013-0.01748.1900.1880.1880.0000.0000.0000.000
38A119VAL00.027-0.00846.0120.1470.1470.0000.0000.0000.000
39A120LYS10.9310.95944.648-6.584-6.5840.0000.0000.0000.000
40A121ARG11.0091.03143.257-6.752-6.7520.0000.0000.0000.000
41A122GLY00.0160.00442.2710.1980.1980.0000.0000.0000.000
42A123ASN0-0.055-0.04440.4300.0670.0670.0000.0000.0000.000
43A124MET00.0930.05638.5290.2370.2370.0000.0000.0000.000
44A125VAL0-0.030-0.00837.5630.2490.2490.0000.0000.0000.000
45A126ARG10.8660.90636.577-7.626-7.6260.0000.0000.0000.000
46A127ALA00.0370.04934.4980.2540.2540.0000.0000.0000.000
47A128ALA00.0690.01332.9180.3470.3470.0000.0000.0000.000
48A129ARG10.8920.95032.160-8.171-8.1710.0000.0000.0000.000
49A130ALA00.0320.01930.3450.3150.3150.0000.0000.0000.000
50A131LEU00.0200.01127.4550.4200.4200.0000.0000.0000.000
51A132LEU00.0130.00827.3200.4750.4750.0000.0000.0000.000
52A133SER0-0.026-0.01426.6340.3230.3230.0000.0000.0000.000
53A134ALA00.0150.01323.9440.5010.5010.0000.0000.0000.000
54A135VAL00.0220.00922.5230.7050.7050.0000.0000.0000.000
55A136THR0-0.032-0.01822.2360.5780.5780.0000.0000.0000.000
56A137ARG10.8890.94116.538-16.369-16.3690.0000.0000.0000.000
57A138LEU00.0050.00316.9990.8700.8700.0000.0000.0000.000
58A139LEU00.000-0.01017.3600.9230.9230.0000.0000.0000.000
59A140ILE00.0050.01317.7310.5310.5310.0000.0000.0000.000
60A141LEU0-0.018-0.00812.6170.6240.6240.0000.0000.0000.000
61A142ALA0-0.015-0.02013.2601.6871.6870.0000.0000.0000.000
62A143ASP-1-0.816-0.89313.04918.85118.8510.0000.0000.0000.000
63A144MET0-0.014-0.00511.6810.5250.5250.0000.0000.0000.000
64A145ALA0-0.0110.0069.0351.8301.8300.0000.0000.0000.000
65A146ASP-1-0.919-0.9618.63826.89426.8940.0000.0000.0000.000
66A147VAL00.0140.00110.0661.4771.4770.0000.0000.0000.000
67A148TYR0-0.007-0.0153.679-1.119-0.9120.003-0.034-0.1760.000
68A149LYS10.9430.9745.496-27.330-27.3300.0000.0000.0000.000
69A150LEU0-0.061-0.0606.5811.1821.1820.0000.0000.0000.000
70A151LEU00.012-0.0048.497-0.417-0.4170.0000.0000.0000.000
71A152VAL0-0.0200.0022.795-1.894-0.9490.362-0.417-0.8900.002
72A153GLN0-0.045-0.0095.9342.0642.0640.0000.0000.0000.000
73A154LEU0-0.026-0.0238.078-2.142-2.1420.0000.0000.0000.000
74A155LYS10.9990.9917.915-25.061-25.0610.0000.0000.0000.000
75A156VAL00.0120.0316.237-1.289-1.2890.0000.0000.0000.000
76A157VAL0-0.020-0.0248.936-1.997-1.9970.0000.0000.0000.000
77A158GLU-1-0.904-0.93512.07216.52316.5230.0000.0000.0000.000
78A159ASP-1-0.874-0.94410.75819.05319.0530.0000.0000.0000.000
79A160GLY0-0.045-0.01613.155-0.927-0.9270.0000.0000.0000.000
80A161ILE00.0270.00214.697-1.198-1.1980.0000.0000.0000.000
81A162LEU0-0.025-0.01417.011-0.934-0.9340.0000.0000.0000.000
82A163LYS10.9330.96311.787-19.854-19.8540.0000.0000.0000.000
83A164LEU0-0.057-0.01618.314-0.530-0.5300.0000.0000.0000.000
84A165ARG10.8310.89320.469-11.558-11.5580.0000.0000.0000.000
85A166ASN0-0.066-0.03420.557-0.918-0.9180.0000.0000.0000.000
86A167ALA00.0090.03122.752-0.098-0.0980.0000.0000.0000.000
87A168GLY00.0390.01423.862-0.327-0.3270.0000.0000.0000.000
88A169ASN0-0.028-0.01626.286-0.681-0.6810.0000.0000.0000.000
89A170GLU-1-0.862-0.95026.7449.5979.5970.0000.0000.0000.000
90A171GLN00.003-0.00926.9480.4650.4650.0000.0000.0000.000
91A172ASP-1-0.797-0.91422.26112.30412.3040.0000.0000.0000.000
92A173LEU0-0.0120.02522.0290.6660.6660.0000.0000.0000.000
93A174GLY00.0240.00722.6630.3960.3960.0000.0000.0000.000
94A175ILE0-0.052-0.02219.2540.4380.4380.0000.0000.0000.000
95A176GLN0-0.001-0.01416.9671.3181.3180.0000.0000.0000.000
96A177TYR00.0150.01118.0080.7940.7940.0000.0000.0000.000
97A178LYS10.9000.95619.473-12.216-12.2160.0000.0000.0000.000
98A179ALA00.0190.01114.6000.5770.5770.0000.0000.0000.000
99A180LEU00.000-0.00114.3721.2011.2010.0000.0000.0000.000
100A181LYS10.9220.96815.431-14.037-14.0370.0000.0000.0000.000
101A182PRO00.0390.02414.3160.1650.1650.0000.0000.0000.000
102A183GLU-1-0.845-0.9339.84627.98227.9820.0000.0000.0000.000
103A184VAL0-0.018-0.01112.6470.7100.7100.0000.0000.0000.000
104A185ASP-1-0.864-0.93515.38716.10516.1050.0000.0000.0000.000
105A186LYS10.8690.9318.273-31.247-31.2470.0000.0000.0000.000
106A187LEU00.0420.00911.5740.3110.3110.0000.0000.0000.000
107A188ASN00.0510.04813.131-0.894-0.8940.0000.0000.0000.000
108A189ILE0-0.0080.00114.564-0.602-0.6020.0000.0000.0000.000
109A190MET0-0.092-0.0348.335-0.191-0.1910.0000.0000.0000.000
110A191ALA00.0230.01113.815-0.579-0.5790.0000.0000.0000.000
111A192ALA00.000-0.00816.018-0.713-0.7130.0000.0000.0000.000
112A193LYS10.9510.97813.062-22.895-22.8950.0000.0000.0000.000
113A194ARG10.9160.95314.742-18.666-18.6660.0000.0000.0000.000
114A195GLN0-0.0060.00717.472-0.389-0.3890.0000.0000.0000.000
115A196GLN0-0.090-0.05920.635-0.308-0.3080.0000.0000.0000.000
116A197GLU-1-0.908-0.95717.13616.91716.9170.0000.0000.0000.000
117A198LEU0-0.065-0.01818.978-0.397-0.3970.0000.0000.0000.000
118A199LYS10.9800.97422.191-12.392-12.3920.0000.0000.0000.000
119A200ASP-1-0.882-0.94125.66610.07710.0770.0000.0000.0000.000
120A201VAL00.026-0.02726.4850.4240.4240.0000.0000.0000.000
121A202GLY00.0920.07327.8040.1360.1360.0000.0000.0000.000
122A203ASN0-0.005-0.01022.9530.1890.1890.0000.0000.0000.000
123A204ARG10.8620.94823.614-11.450-11.4500.0000.0000.0000.000
124A205ASP-1-0.877-0.92824.67810.70010.7000.0000.0000.0000.000
125A206GLN0-0.021-0.01123.619-0.014-0.0140.0000.0000.0000.000
126A207MET0-0.0110.01317.5140.4070.4070.0000.0000.0000.000
127A208ALA0-0.0090.00821.7410.3640.3640.0000.0000.0000.000
128A209ALA00.015-0.00124.0830.0390.0390.0000.0000.0000.000
129A210ALA0-0.040-0.02021.097-0.052-0.0520.0000.0000.0000.000
130A211ARG10.8630.90318.949-14.647-14.6470.0000.0000.0000.000
131A212GLY00.0170.02521.2560.0830.0830.0000.0000.0000.000
132A213ILE0-0.037-0.02124.265-0.139-0.1390.0000.0000.0000.000
133A214LEU0-0.0110.00216.859-0.130-0.1300.0000.0000.0000.000
134A215GLN0-0.006-0.00721.4090.4330.4330.0000.0000.0000.000
135A216LYS10.9320.95922.587-10.346-10.3460.0000.0000.0000.000
136A217ASN00.026-0.02124.280-0.512-0.5120.0000.0000.0000.000
137A218VAL00.0360.04719.144-0.189-0.1890.0000.0000.0000.000
138A219PRO0-0.037-0.01522.169-0.022-0.0220.0000.0000.0000.000
139A220ILE00.0490.03024.952-0.228-0.2280.0000.0000.0000.000
140A221LEU00.0130.00621.646-0.314-0.3140.0000.0000.0000.000
141A222TYR00.0050.01024.010-0.102-0.1020.0000.0000.0000.000
142A223THR0-0.002-0.00325.418-0.335-0.3350.0000.0000.0000.000
143A224ALA00.0020.00228.229-0.311-0.3110.0000.0000.0000.000
144A225SER0-0.062-0.07825.698-0.173-0.1730.0000.0000.0000.000
145A226GLN00.0070.01627.9260.0890.0890.0000.0000.0000.000
146A227ALA00.0510.03629.607-0.208-0.2080.0000.0000.0000.000
147A228CYS0-0.103-0.03830.578-0.229-0.2290.0000.0000.0000.000
148A229LEU0-0.026-0.00827.503-0.170-0.1700.0000.0000.0000.000
149A230GLN0-0.0270.00232.056-0.232-0.2320.0000.0000.0000.000
150A231HIS0-0.048-0.01935.351-0.182-0.1820.0000.0000.0000.000
151A232PRO00.0320.00534.8430.0010.0010.0000.0000.0000.000
152A233ASP-1-0.907-0.95536.1367.5067.5060.0000.0000.0000.000
153A234VAL0-0.0190.00437.731-0.173-0.1730.0000.0000.0000.000
154A235ALA0-0.010-0.01336.4740.2280.2280.0000.0000.0000.000
155A236ALA00.0240.00435.8840.1980.1980.0000.0000.0000.000
156A237TYR00.0410.01433.9530.1560.1560.0000.0000.0000.000
157A238LYS10.9540.97231.553-8.220-8.2200.0000.0000.0000.000
158A239ALA00.0200.01731.1020.2750.2750.0000.0000.0000.000
159A240ASN00.0070.00631.7610.1700.1700.0000.0000.0000.000
160A241ARG10.9210.95926.701-9.901-9.9010.0000.0000.0000.000
161A242ASP-1-0.818-0.90626.89910.51410.5140.0000.0000.0000.000
162A243LEU00.0190.01227.1750.3060.3060.0000.0000.0000.000
163A244ILE00.0080.01225.4510.2360.2360.0000.0000.0000.000
164A245TYR00.0000.00219.1440.1480.1480.0000.0000.0000.000
165A246LYS10.9440.96222.917-10.077-10.0770.0000.0000.0000.000
166A247GLN0-0.016-0.00523.9790.1210.1210.0000.0000.0000.000
167A248LEU0-0.0130.00520.2220.2620.2620.0000.0000.0000.000
168A249GLN0-0.026-0.02316.9560.6180.6180.0000.0000.0000.000
169A250GLN0-0.007-0.00919.7390.3270.3270.0000.0000.0000.000
170A251ALA0-0.023-0.00621.3080.1620.1620.0000.0000.0000.000
171A252VAL00.0300.01915.1280.3800.3800.0000.0000.0000.000
172A253THR00.016-0.00416.8480.5880.5880.0000.0000.0000.000
173A254GLY00.0000.00718.2990.0450.0450.0000.0000.0000.000
174A255ILE0-0.003-0.01215.314-0.032-0.0320.0000.0000.0000.000
175A256SER0-0.027-0.02214.7820.4690.4690.0000.0000.0000.000
176A257ASN0-0.025-0.01415.7510.1840.1840.0000.0000.0000.000
177A258ALA0-0.0190.00218.935-0.204-0.2040.0000.0000.0000.000
178A259ALA00.0270.00114.844-0.073-0.0730.0000.0000.0000.000
179A260GLN0-0.079-0.03215.1460.3900.3900.0000.0000.0000.000
180A261ALA0-0.0180.00717.531-0.469-0.4690.0000.0000.0000.000
181A262THR0-0.0170.01020.022-0.669-0.6690.0000.0000.0000.000