Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K9QG3

Calculation Name: 1R0D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R0D

Chain ID: A

ChEMBL ID:

UniProt ID: O75146

Base Structure: X-ray

Registration Date: 2023-06-26

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1961934.270792
FMO2-HF: Nuclear repulsion 1886780.881912
FMO2-HF: Total energy -75153.38888
FMO2-MP2: Total energy -75369.705424


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:773:ASP)


Summations of interaction energy for fragment #1(A:773: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.
17.90819.668-0.025-0.718-1.0160.004
Interaction energy analysis for fragmet #1(A:773:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.966 / q_NPA : -0.987
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].
3A775ARG10.9861.0043.807-29.278-27.613-0.024-0.717-0.9240.004
4A776GLN00.0450.0056.263-0.983-0.9830.0000.0000.0000.000
5A777GLU-1-0.941-0.9757.77119.60219.6020.0000.0000.0000.000
6A778GLU-1-0.882-0.9439.41824.35124.3510.0000.0000.0000.000
7A779LEU0-0.0030.0046.903-1.077-1.0770.0000.0000.0000.000
8A780GLY00.010-0.0029.996-1.098-1.0980.0000.0000.0000.000
9A781ALA00.0290.01812.622-0.843-0.8430.0000.0000.0000.000
10A782VAL00.001-0.0057.592-1.061-1.0610.0000.0000.0000.000
11A783VAL00.0430.02110.876-0.328-0.3280.0000.0000.0000.000
12A784ASP-1-0.934-0.95812.53416.37916.3790.0000.0000.0000.000
13A785LYS10.8830.93313.192-18.224-18.2240.0000.0000.0000.000
14A786GLU-1-0.886-0.95211.17623.23123.2310.0000.0000.0000.000
15A787MET0-0.0210.00613.773-0.677-0.6770.0000.0000.0000.000
16A788ALA0-0.037-0.01616.931-1.136-1.1360.0000.0000.0000.000
17A789ALA0-0.016-0.01115.704-0.879-0.8790.0000.0000.0000.000
18A790THR0-0.014-0.03216.193-0.671-0.6710.0000.0000.0000.000
19A791SER00.002-0.00318.483-0.925-0.9250.0000.0000.0000.000
20A792ALA0-0.027-0.01021.013-0.682-0.6820.0000.0000.0000.000
21A793ALA00.0220.01119.777-0.534-0.5340.0000.0000.0000.000
22A794ILE00.0000.00321.867-0.472-0.4720.0000.0000.0000.000
23A795GLU-1-0.886-0.95624.24110.37310.3730.0000.0000.0000.000
24A796ASP-1-0.985-0.99024.63011.24311.2430.0000.0000.0000.000
25A797ALA00.0220.00625.335-0.364-0.3640.0000.0000.0000.000
26A798VAL0-0.055-0.02527.150-0.409-0.4090.0000.0000.0000.000
27A799ARG10.9760.98128.782-10.724-10.7240.0000.0000.0000.000
28A800ARG10.8670.95129.204-9.952-9.9520.0000.0000.0000.000
29A801ILE00.006-0.01129.281-0.249-0.2490.0000.0000.0000.000
30A802GLU-1-0.913-0.98132.7138.6298.6290.0000.0000.0000.000
31A803ASP-1-0.953-0.97634.4178.3248.3240.0000.0000.0000.000
32A804MET0-0.055-0.01431.137-0.275-0.2750.0000.0000.0000.000
33A805MET0-0.0290.01336.482-0.233-0.2330.0000.0000.0000.000
34A806ASN0-0.027-0.00839.484-0.405-0.4050.0000.0000.0000.000
35A807GLN00.024-0.00135.506-0.054-0.0540.0000.0000.0000.000
36A808ALA00.0920.05640.014-0.139-0.1390.0000.0000.0000.000
37A809ARG10.8730.93941.424-6.745-6.7450.0000.0000.0000.000
38A810HIS0-0.033-0.02042.928-0.260-0.2600.0000.0000.0000.000
39A811ALA0-0.0130.01441.284-0.057-0.0570.0000.0000.0000.000
40A812SER0-0.103-0.05343.377-0.055-0.0550.0000.0000.0000.000
41A813SER00.042-0.00345.587-0.048-0.0480.0000.0000.0000.000
42A814GLY00.0030.00048.5040.0120.0120.0000.0000.0000.000
43A815VAL00.0540.01948.1030.0690.0690.0000.0000.0000.000
44A816LYS11.0281.02242.075-7.295-7.2950.0000.0000.0000.000
45A817LEU0-0.0340.01143.7110.1240.1240.0000.0000.0000.000
46A818GLU-1-0.921-0.96344.0926.8656.8650.0000.0000.0000.000
47A819VAL00.010-0.00442.5410.1180.1180.0000.0000.0000.000
48A820ASN00.0340.02240.1780.2530.2530.0000.0000.0000.000
49A821GLU-1-0.833-0.92139.5077.8417.8410.0000.0000.0000.000
50A822ARG10.9360.98240.326-6.770-6.7700.0000.0000.0000.000
51A823ILE00.0110.02335.9200.1830.1830.0000.0000.0000.000
52A824LEU00.0380.02935.0400.3120.3120.0000.0000.0000.000
53A825ASN0-0.007-0.03035.4640.2790.2790.0000.0000.0000.000
54A826SER0-0.032-0.01036.3060.1660.1660.0000.0000.0000.000
55A827CYS0-0.013-0.02431.7650.3160.3160.0000.0000.0000.000
56A828THR00.0060.01131.3920.4290.4290.0000.0000.0000.000
57A829ASP-1-0.914-0.95932.4608.7998.7990.0000.0000.0000.000
58A830LEU0-0.064-0.02928.3580.1720.1720.0000.0000.0000.000
59A831MET00.0140.01324.6480.4280.4280.0000.0000.0000.000
60A832LYS10.9340.96928.130-8.697-8.6970.0000.0000.0000.000
61A833ALA0-0.027-0.00830.0210.0970.0970.0000.0000.0000.000
62A834ILE00.018-0.00623.8580.2610.2610.0000.0000.0000.000
63A835ARG10.9080.97325.144-9.826-9.8260.0000.0000.0000.000
64A836LEU0-0.034-0.02626.0110.2470.2470.0000.0000.0000.000
65A837LEU00.0260.02322.9300.1430.1430.0000.0000.0000.000
66A838VAL00.0530.02620.2240.3670.3670.0000.0000.0000.000
67A839THR00.0220.02422.3750.4210.4210.0000.0000.0000.000
68A840THR0-0.047-0.04024.754-0.104-0.1040.0000.0000.0000.000
69A841SER0-0.043-0.01620.4090.3210.3210.0000.0000.0000.000
70A842THR00.015-0.00520.1230.5840.5840.0000.0000.0000.000
71A843SER0-0.049-0.02621.449-0.017-0.0170.0000.0000.0000.000
72A844LEU0-0.019-0.01323.122-0.116-0.1160.0000.0000.0000.000
73A845GLN00.014-0.01117.3880.5700.5700.0000.0000.0000.000
74A846LYS10.9960.98520.796-13.948-13.9480.0000.0000.0000.000
75A847GLU-1-0.925-0.94822.46611.88911.8890.0000.0000.0000.000
76A848ILE00.0140.01220.802-0.074-0.0740.0000.0000.0000.000
77A849VAL0-0.037-0.01918.6690.1030.1030.0000.0000.0000.000
78A850GLU-1-0.926-0.96821.70612.57512.5750.0000.0000.0000.000
79A851SER0-0.053-0.01525.147-0.378-0.3780.0000.0000.0000.000
80A852GLY0-0.015-0.00423.101-0.289-0.2890.0000.0000.0000.000
81A853ARG10.7780.87721.639-12.853-12.8530.0000.0000.0000.000
82A854GLY00.0120.01322.701-0.008-0.0080.0000.0000.0000.000
83A855ALA0-0.041-0.02825.867-0.168-0.1680.0000.0000.0000.000
84A856ALA00.0050.02520.5060.0060.0060.0000.0000.0000.000
85A857THR00.0070.01019.607-0.068-0.0680.0000.0000.0000.000
86A858GLN00.034-0.00718.9640.3710.3710.0000.0000.0000.000
87A859GLN0-0.041-0.01614.350-0.261-0.2610.0000.0000.0000.000
88A860GLU-1-0.787-0.89114.84616.83316.8330.0000.0000.0000.000
89A861PHE0-0.0090.00815.9510.8250.8250.0000.0000.0000.000
90A862TYR00.008-0.00413.2110.4990.4990.0000.0000.0000.000
91A863ALA00.0050.01211.2231.9161.9160.0000.0000.0000.000
92A864LYS10.9680.97511.634-14.990-14.9900.0000.0000.0000.000
93A865ASN0-0.108-0.04613.985-0.734-0.7340.0000.0000.0000.000
94A866SER00.0920.0408.239-1.046-1.0460.0000.0000.0000.000
95A867ARG11.0121.0149.580-22.293-22.2930.0000.0000.0000.000
96A868TRP0-0.036-0.02610.7920.4910.4910.0000.0000.0000.000
97A869THR00.0380.00310.602-1.253-1.2530.0000.0000.0000.000
98A870GLU-1-0.910-0.9505.01355.60555.700-0.001-0.001-0.0920.000
99A871GLY0-0.037-0.0128.940-0.335-0.3350.0000.0000.0000.000
100A872LEU0-0.038-0.01911.672-1.334-1.3340.0000.0000.0000.000
101A873ILE00.0230.0157.754-1.303-1.3030.0000.0000.0000.000
102A874SER0-0.016-0.0049.197-1.495-1.4950.0000.0000.0000.000
103A875ALA00.0090.00110.544-1.646-1.6460.0000.0000.0000.000
104A876SER00.0090.01713.613-1.823-1.8230.0000.0000.0000.000
105A877LYS10.9430.98710.720-23.777-23.7770.0000.0000.0000.000
106A878ALA0-0.017-0.01013.304-1.148-1.1480.0000.0000.0000.000
107A879VAL00.0030.01815.504-1.152-1.1520.0000.0000.0000.000
108A880GLY00.0120.01117.093-0.929-0.9290.0000.0000.0000.000
109A881TRP0-0.006-0.01711.317-0.263-0.2630.0000.0000.0000.000
110A882GLY00.0530.02718.057-0.717-0.7170.0000.0000.0000.000
111A883ALA0-0.005-0.02120.902-0.793-0.7930.0000.0000.0000.000
112A884THR0-0.033-0.01620.669-0.544-0.5440.0000.0000.0000.000
113A885GLN0-0.036-0.01920.761-0.029-0.0290.0000.0000.0000.000
114A886LEU00.0070.00423.622-0.516-0.5160.0000.0000.0000.000
115A887VAL00.0050.00426.090-0.514-0.5140.0000.0000.0000.000
116A888GLU-1-0.875-0.93625.87410.58810.5880.0000.0000.0000.000
117A889ALA0-0.0060.00027.787-0.406-0.4060.0000.0000.0000.000
118A890ALA0-0.015-0.01329.731-0.416-0.4160.0000.0000.0000.000
119A891ASP-1-0.817-0.92430.7909.1569.1560.0000.0000.0000.000
120A892LYS10.9460.96330.193-10.184-10.1840.0000.0000.0000.000
121A893VAL0-0.049-0.00933.163-0.278-0.2780.0000.0000.0000.000
122A894VAL0-0.051-0.02035.609-0.310-0.3100.0000.0000.0000.000
123A895LEU0-0.068-0.03635.203-0.305-0.3050.0000.0000.0000.000
124A896HIS0-0.095-0.03134.352-0.226-0.2260.0000.0000.0000.000
125A897THR0-0.038-0.02636.574-0.077-0.0770.0000.0000.0000.000
126A898GLY0-0.0150.00233.9900.0310.0310.0000.0000.0000.000
127A899LYS10.9550.97533.903-9.057-9.0570.0000.0000.0000.000
128A900TYR00.0650.01034.0690.2490.2490.0000.0000.0000.000
129A901GLU-1-0.900-0.97134.1528.8068.8060.0000.0000.0000.000
130A902GLU-1-0.915-0.95227.47011.40911.4090.0000.0000.0000.000
131A903LEU00.0390.01829.6220.3710.3710.0000.0000.0000.000
132A904ILE0-0.035-0.01730.5080.1970.1970.0000.0000.0000.000
133A905VAL00.0130.00726.6440.1350.1350.0000.0000.0000.000
134A906CYS00.0240.02425.7800.5390.5390.0000.0000.0000.000
135A907SER0-0.032-0.01926.0190.3000.3000.0000.0000.0000.000
136A908HIS0-0.030-0.02427.5800.2910.2910.0000.0000.0000.000
137A909GLU-1-0.913-0.96622.35414.16714.1670.0000.0000.0000.000
138A910ILE0-0.0130.01922.4630.6860.6860.0000.0000.0000.000
139A911ALA00.0440.02323.1930.3550.3550.0000.0000.0000.000
140A912ALA0-0.0160.00122.6280.2090.2090.0000.0000.0000.000
141A913SER0-0.042-0.02818.5900.6240.6240.0000.0000.0000.000
142A914THR00.004-0.00719.5260.3800.3800.0000.0000.0000.000
143A915ALA00.0130.00521.8710.1530.1530.0000.0000.0000.000
144A916GLN0-0.028-0.01716.5590.8680.8680.0000.0000.0000.000
145A917LEU00.0700.03616.7550.6380.6380.0000.0000.0000.000
146A918VAL0-0.020-0.00718.7160.0540.0540.0000.0000.0000.000
147A919ALA0-0.053-0.03319.756-0.160-0.1600.0000.0000.0000.000
148A920ALA00.0300.01715.3760.0030.0030.0000.0000.0000.000
149A921SER0-0.014-0.03117.3090.3790.3790.0000.0000.0000.000
150A922LYS10.9440.96319.509-13.184-13.1840.0000.0000.0000.000
151A923VAL0-0.055-0.00517.312-0.470-0.4700.0000.0000.0000.000
152A924LYS10.8630.93316.510-19.112-19.1120.0000.0000.0000.000
153A925ALA00.0120.02220.680-0.436-0.4360.0000.0000.0000.000
154A926ASN00.0270.00823.896-0.524-0.5240.0000.0000.0000.000
155A927LYS10.9400.97527.514-9.368-9.3680.0000.0000.0000.000
156A928HIS0-0.001-0.01728.167-0.283-0.2830.0000.0000.0000.000
157A929SER0-0.039-0.05329.4840.1260.1260.0000.0000.0000.000
158A930PRO00.038-0.00126.5820.1880.1880.0000.0000.0000.000
159A931HIS00.0790.08529.1720.2590.2590.0000.0000.0000.000
160A932LEU00.0330.04025.4510.1980.1980.0000.0000.0000.000
161A933SER0-0.002-0.02428.2580.1050.1050.0000.0000.0000.000
162A934ARG10.9701.00130.357-9.976-9.9760.0000.0000.0000.000
163A935LEU00.0470.02722.994-0.040-0.0400.0000.0000.0000.000
164A936GLN0-0.019-0.02727.644-0.179-0.1790.0000.0000.0000.000
165A937GLU-1-0.950-0.97328.8999.3249.3240.0000.0000.0000.000
166A938CYS0-0.039-0.01728.134-0.259-0.2590.0000.0000.0000.000
167A939SER00.0500.02326.1440.0480.0480.0000.0000.0000.000
168A940ARG10.9290.97428.129-9.896-9.8960.0000.0000.0000.000
169A941THR00.0080.00331.603-0.223-0.2230.0000.0000.0000.000
170A942VAL00.0380.02026.490-0.220-0.2200.0000.0000.0000.000
171A943ASN00.003-0.00828.3050.1290.1290.0000.0000.0000.000
172A944GLU-1-0.971-0.98330.6848.7598.7590.0000.0000.0000.000
173A945ARG10.9030.95131.825-9.243-9.2430.0000.0000.0000.000
174A946ALA00.0600.04029.525-0.124-0.1240.0000.0000.0000.000
175A947ALA0-0.004-0.00431.602-0.147-0.1470.0000.0000.0000.000
176A948ASN0-0.052-0.02434.581-0.160-0.1600.0000.0000.0000.000
177A949VAL00.0920.05532.222-0.227-0.2270.0000.0000.0000.000
178A950VAL0-0.021-0.00933.198-0.213-0.2130.0000.0000.0000.000
179A951ALA0-0.050-0.03535.692-0.204-0.2040.0000.0000.0000.000
180A952SER0-0.018-0.00838.157-0.300-0.3000.0000.0000.0000.000
181A953THR00.0270.00536.223-0.118-0.1180.0000.0000.0000.000
182A954LYS10.8950.95137.609-8.528-8.5280.0000.0000.0000.000
183A955SER0-0.0010.01840.873-0.178-0.1780.0000.0000.0000.000
184A956GLY00.027-0.00542.404-0.168-0.1680.0000.0000.0000.000
185A957GLN00.0350.00739.618-0.140-0.1400.0000.0000.0000.000
186A958GLU-1-0.916-0.96343.2286.8856.8850.0000.0000.0000.000
187A959GLN0-0.038-0.01046.116-0.255-0.2550.0000.0000.0000.000
188A960ILE0-0.102-0.05943.362-0.159-0.1590.0000.0000.0000.000
189A961GLU-1-0.954-0.98344.6247.0397.0390.0000.0000.0000.000
190A962ASP-1-0.889-0.93148.6286.2546.2540.0000.0000.0000.000
191A963ARG10.8140.90851.237-6.235-6.2350.0000.0000.0000.000
192A964ASP-1-0.986-1.00851.5735.9965.9960.0000.0000.0000.000
193A965THR00.0060.02252.525-0.130-0.1300.0000.0000.0000.000
194A966MET0-0.062-0.01355.129-0.151-0.1510.0000.0000.0000.000