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: 49GJN

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 OptHSide
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 -1962775.314745
FMO2-HF: Nuclear repulsion 1887620.558291
FMO2-HF: Total energy -75154.756453
FMO2-MP2: Total energy -75371.016979


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.
9.3110.954-0.024-0.701-0.920.004
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 : -0.968 / q_NPA : -0.989
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].
3A775ARG10.8650.9173.807-27.428-25.784-0.024-0.701-0.9200.004
4A776GLN00.0600.0166.494-1.284-1.2840.0000.0000.0000.000
5A777GLU-1-0.952-0.9788.14520.22420.2240.0000.0000.0000.000
6A778GLU-1-0.770-0.8659.39525.32025.3200.0000.0000.0000.000
7A779LEU00.0200.0176.750-1.293-1.2930.0000.0000.0000.000
8A780GLY00.021-0.00510.002-1.145-1.1450.0000.0000.0000.000
9A781ALA00.0070.00412.682-0.882-0.8820.0000.0000.0000.000
10A782VAL0-0.002-0.0047.569-1.156-1.1560.0000.0000.0000.000
11A783VAL00.0430.02510.860-0.432-0.4320.0000.0000.0000.000
12A784ASP-1-0.844-0.91212.52415.80915.8090.0000.0000.0000.000
13A785LYS10.9160.95613.180-18.263-18.2630.0000.0000.0000.000
14A786GLU-1-0.807-0.88910.69923.90323.9030.0000.0000.0000.000
15A787MET0-0.0050.01813.748-0.594-0.5940.0000.0000.0000.000
16A788ALA0-0.024-0.00216.916-1.127-1.1270.0000.0000.0000.000
17A789ALA0-0.023-0.01015.621-0.897-0.8970.0000.0000.0000.000
18A790THR00.010-0.01016.116-0.749-0.7490.0000.0000.0000.000
19A791SER0-0.021-0.02018.455-0.910-0.9100.0000.0000.0000.000
20A792ALA0-0.036-0.01520.941-0.699-0.6990.0000.0000.0000.000
21A793ALA00.0320.01719.750-0.550-0.5500.0000.0000.0000.000
22A794ILE00.0000.00421.832-0.501-0.5010.0000.0000.0000.000
23A795GLU-1-0.846-0.91124.21010.01310.0130.0000.0000.0000.000
24A796ASP-1-0.962-0.98224.64911.13311.1330.0000.0000.0000.000
25A797ALA00.0220.00725.284-0.366-0.3660.0000.0000.0000.000
26A798VAL0-0.059-0.02827.115-0.408-0.4080.0000.0000.0000.000
27A799ARG10.8980.93728.914-10.886-10.8860.0000.0000.0000.000
28A800ARG10.8360.91029.160-9.797-9.7970.0000.0000.0000.000
29A801ILE00.007-0.01029.250-0.253-0.2530.0000.0000.0000.000
30A802GLU-1-0.825-0.92832.6788.6508.6500.0000.0000.0000.000
31A803ASP-1-0.876-0.93834.1548.4738.4730.0000.0000.0000.000
32A804MET0-0.046-0.00731.029-0.283-0.2830.0000.0000.0000.000
33A805MET0-0.0110.01736.415-0.247-0.2470.0000.0000.0000.000
34A806ASN0-0.035-0.01739.422-0.393-0.3930.0000.0000.0000.000
35A807GLN0-0.0050.00435.447-0.079-0.0790.0000.0000.0000.000
36A808ALA00.0960.05239.895-0.141-0.1410.0000.0000.0000.000
37A809ARG10.8740.93941.385-6.758-6.7580.0000.0000.0000.000
38A810HIS0-0.038-0.02242.879-0.273-0.2730.0000.0000.0000.000
39A811ALA0-0.0170.01441.255-0.056-0.0560.0000.0000.0000.000
40A812SER0-0.083-0.04543.347-0.049-0.0490.0000.0000.0000.000
41A813SER00.033-0.00645.557-0.052-0.0520.0000.0000.0000.000
42A814GLY00.0120.00548.4670.0120.0120.0000.0000.0000.000
43A815VAL00.0410.01348.1890.0760.0760.0000.0000.0000.000
44A816LYS11.0181.02041.122-7.424-7.4240.0000.0000.0000.000
45A817LEU0-0.0420.00943.6010.1320.1320.0000.0000.0000.000
46A818GLU-1-0.809-0.88844.0586.8576.8570.0000.0000.0000.000
47A819VAL0-0.002-0.00642.7660.1200.1200.0000.0000.0000.000
48A820ASN00.0340.02640.1910.2310.2310.0000.0000.0000.000
49A821GLU-1-0.852-0.92439.4757.7637.7630.0000.0000.0000.000
50A822ARG10.8230.90540.295-6.714-6.7140.0000.0000.0000.000
51A823ILE00.0170.02435.9790.1900.1900.0000.0000.0000.000
52A824LEU00.0480.04034.9380.3140.3140.0000.0000.0000.000
53A825ASN0-0.022-0.02735.4340.2730.2730.0000.0000.0000.000
54A826SER0-0.027-0.00836.2300.1370.1370.0000.0000.0000.000
55A827CYS0-0.031-0.03331.6610.2960.2960.0000.0000.0000.000
56A828THR0-0.008-0.01031.3650.4060.4060.0000.0000.0000.000
57A829ASP-1-0.908-0.96032.4348.8068.8060.0000.0000.0000.000
58A830LEU0-0.060-0.02428.6040.1820.1820.0000.0000.0000.000
59A831MET00.0170.01324.6170.4250.4250.0000.0000.0000.000
60A832LYS10.8440.91728.106-8.687-8.6870.0000.0000.0000.000
61A833ALA0-0.023-0.00630.0010.1110.1110.0000.0000.0000.000
62A834ILE00.018-0.01023.8950.2720.2720.0000.0000.0000.000
63A835ARG10.9020.95525.126-9.839-9.8390.0000.0000.0000.000
64A836LEU0-0.017-0.00525.9930.2610.2610.0000.0000.0000.000
65A837LEU00.0200.02923.0120.1550.1550.0000.0000.0000.000
66A838VAL00.0660.02920.1760.3600.3600.0000.0000.0000.000
67A839THR00.0070.01222.3630.4210.4210.0000.0000.0000.000
68A840THR0-0.045-0.03524.740-0.083-0.0830.0000.0000.0000.000
69A841SER0-0.049-0.02220.3340.3160.3160.0000.0000.0000.000
70A842THR00.004-0.01019.9520.5820.5820.0000.0000.0000.000
71A843SER0-0.050-0.04221.442-0.024-0.0240.0000.0000.0000.000
72A844LEU0-0.023-0.01023.206-0.099-0.0990.0000.0000.0000.000
73A845GLN00.016-0.00917.6880.4030.4030.0000.0000.0000.000
74A846LYS10.9200.93720.183-14.961-14.9610.0000.0000.0000.000
75A847GLU-1-0.938-0.95922.46911.75911.7590.0000.0000.0000.000
76A848ILE00.0230.01420.396-0.098-0.0980.0000.0000.0000.000
77A849VAL0-0.049-0.02318.6550.1070.1070.0000.0000.0000.000
78A850GLU-1-0.845-0.89521.51512.78212.7820.0000.0000.0000.000
79A851SER0-0.048-0.01225.038-0.406-0.4060.0000.0000.0000.000
80A852GLY0-0.015-0.00323.172-0.288-0.2880.0000.0000.0000.000
81A853ARG10.7050.81221.766-12.789-12.7890.0000.0000.0000.000
82A854GLY00.0150.01423.007-0.007-0.0070.0000.0000.0000.000
83A855ALA0-0.044-0.03026.284-0.164-0.1640.0000.0000.0000.000
84A856ALA0-0.0120.01620.9160.0210.0210.0000.0000.0000.000
85A857THR00.000-0.03120.184-0.069-0.0690.0000.0000.0000.000
86A858GLN00.029-0.00918.9820.6750.6750.0000.0000.0000.000
87A859GLN0-0.052-0.02014.513-0.331-0.3310.0000.0000.0000.000
88A860GLU-1-0.747-0.84515.27316.90616.9060.0000.0000.0000.000
89A861PHE0-0.0090.01016.3660.8180.8180.0000.0000.0000.000
90A862TYR0-0.028-0.01213.2090.4460.4460.0000.0000.0000.000
91A863ALA00.0040.01211.6531.8591.8590.0000.0000.0000.000
92A864LYS10.9640.97412.039-15.018-15.0180.0000.0000.0000.000
93A865ASN0-0.112-0.05114.179-0.910-0.9100.0000.0000.0000.000
94A866SER00.0780.0398.539-1.277-1.2770.0000.0000.0000.000
95A867ARG10.9941.0099.273-22.351-22.3510.0000.0000.0000.000
96A868TRP0-0.044-0.03010.5240.4530.4530.0000.0000.0000.000
97A869THR00.0340.00210.547-1.236-1.2360.0000.0000.0000.000
98A870GLU-1-0.870-0.9425.70746.74946.7490.0000.0000.0000.000
99A871GLY0-0.040-0.0148.611-0.369-0.3690.0000.0000.0000.000
100A872LEU0-0.034-0.01511.462-1.364-1.3640.0000.0000.0000.000
101A873ILE00.0070.0047.644-1.304-1.3040.0000.0000.0000.000
102A874SER0-0.006-0.0019.177-1.418-1.4180.0000.0000.0000.000
103A875ALA0-0.001-0.00310.536-1.643-1.6430.0000.0000.0000.000
104A876SER00.0200.00613.626-1.692-1.6920.0000.0000.0000.000
105A877LYS10.8300.90810.708-25.532-25.5320.0000.0000.0000.000
106A878ALA0-0.0040.00313.278-1.116-1.1160.0000.0000.0000.000
107A879VAL00.0030.01415.482-1.139-1.1390.0000.0000.0000.000
108A880GLY00.0170.01817.063-0.930-0.9300.0000.0000.0000.000
109A881TRP0-0.004-0.01910.933-0.253-0.2530.0000.0000.0000.000
110A882GLY00.0720.03818.025-0.721-0.7210.0000.0000.0000.000
111A883ALA0-0.013-0.02520.875-0.812-0.8120.0000.0000.0000.000
112A884THR0-0.046-0.02920.285-0.558-0.5580.0000.0000.0000.000
113A885GLN0-0.047-0.02620.0090.1670.1670.0000.0000.0000.000
114A886LEU00.0020.00323.589-0.540-0.5400.0000.0000.0000.000
115A887VAL0-0.0030.00126.056-0.515-0.5150.0000.0000.0000.000
116A888GLU-1-0.808-0.89325.87310.35910.3590.0000.0000.0000.000
117A889ALA00.0110.01027.757-0.396-0.3960.0000.0000.0000.000
118A890ALA0-0.010-0.01029.697-0.415-0.4150.0000.0000.0000.000
119A891ASP-1-0.772-0.88830.7089.1919.1910.0000.0000.0000.000
120A892LYS10.8080.87629.644-10.510-10.5100.0000.0000.0000.000
121A893VAL0-0.045-0.00133.133-0.280-0.2800.0000.0000.0000.000
122A894VAL0-0.056-0.02935.578-0.323-0.3230.0000.0000.0000.000
123A895LEU0-0.076-0.03835.183-0.299-0.2990.0000.0000.0000.000
124A896HIS0-0.073-0.02434.098-0.209-0.2090.0000.0000.0000.000
125A897THR0-0.040-0.02636.532-0.087-0.0870.0000.0000.0000.000
126A898GLY0-0.0070.00733.9530.0270.0270.0000.0000.0000.000
127A899LYS10.8870.92933.877-8.795-8.7950.0000.0000.0000.000
128A900TYR00.0710.01134.0410.2400.2400.0000.0000.0000.000
129A901GLU-1-0.840-0.92934.3338.8008.8000.0000.0000.0000.000
130A902GLU-1-0.909-0.94627.69411.20111.2010.0000.0000.0000.000
131A903LEU00.0410.01929.5960.3780.3780.0000.0000.0000.000
132A904ILE0-0.024-0.00930.4830.2110.2110.0000.0000.0000.000
133A905VAL00.0150.00926.6260.1430.1430.0000.0000.0000.000
134A906CYS00.0240.02425.7480.5260.5260.0000.0000.0000.000
135A907SER0-0.039-0.03225.9970.3020.3020.0000.0000.0000.000
136A908HIS0-0.031-0.02327.5620.2820.2820.0000.0000.0000.000
137A909GLU-1-0.901-0.95322.46614.04614.0460.0000.0000.0000.000
138A910ILE0-0.0040.02022.3760.6630.6630.0000.0000.0000.000
139A911ALA00.0240.01723.1780.3630.3630.0000.0000.0000.000
140A912ALA0-0.020-0.00122.7430.2060.2060.0000.0000.0000.000
141A913SER0-0.037-0.02918.6380.6010.6010.0000.0000.0000.000
142A914THR00.019-0.00619.5170.4070.4070.0000.0000.0000.000
143A915ALA00.0080.00821.8660.1730.1730.0000.0000.0000.000
144A916GLN0-0.028-0.01416.5240.6290.6290.0000.0000.0000.000
145A917LEU00.0570.02916.7300.6720.6720.0000.0000.0000.000
146A918VAL0-0.012-0.01018.7130.0730.0730.0000.0000.0000.000
147A919ALA0-0.046-0.02319.659-0.148-0.1480.0000.0000.0000.000
148A920ALA00.0280.01215.1590.0450.0450.0000.0000.0000.000
149A921SER0-0.003-0.01917.1040.4100.4100.0000.0000.0000.000
150A922LYS10.9490.96619.228-13.038-13.0380.0000.0000.0000.000
151A923VAL0-0.062-0.00617.007-0.470-0.4700.0000.0000.0000.000
152A924LYS10.8770.94016.656-18.500-18.5000.0000.0000.0000.000
153A925ALA00.0150.02120.377-0.436-0.4360.0000.0000.0000.000
154A926ASN00.018-0.00223.585-0.568-0.5680.0000.0000.0000.000
155A927LYS10.9410.98227.220-9.329-9.3290.0000.0000.0000.000
156A928HIS0-0.013-0.02828.096-0.303-0.3030.0000.0000.0000.000
157A929SER0-0.035-0.07529.1510.0870.0870.0000.0000.0000.000
158A930PRO00.0700.01326.7620.1770.1770.0000.0000.0000.000
159A931HIS00.0390.08929.1740.2350.2350.0000.0000.0000.000
160A932LEU00.0450.05224.9810.2090.2090.0000.0000.0000.000
161A933SER0-0.006-0.02227.9630.1160.1160.0000.0000.0000.000
162A934ARG10.9730.98230.511-9.854-9.8540.0000.0000.0000.000
163A935LEU00.0470.03822.939-0.042-0.0420.0000.0000.0000.000
164A936GLN0-0.015-0.02327.448-0.106-0.1060.0000.0000.0000.000
165A937GLU-1-0.942-0.95728.7039.3589.3580.0000.0000.0000.000
166A938CYS0-0.033-0.01728.085-0.177-0.1770.0000.0000.0000.000
167A939SER00.0220.01526.2900.0620.0620.0000.0000.0000.000
168A940ARG10.9270.96628.124-9.871-9.8710.0000.0000.0000.000
169A941THR00.0270.01131.598-0.115-0.1150.0000.0000.0000.000
170A942VAL00.0460.02326.409-0.204-0.2040.0000.0000.0000.000
171A943ASN0-0.001-0.00728.1680.1210.1210.0000.0000.0000.000
172A944GLU-1-0.907-0.94230.6748.8528.8520.0000.0000.0000.000
173A945ARG10.8350.90731.869-9.210-9.2100.0000.0000.0000.000
174A946ALA00.0600.03929.524-0.120-0.1200.0000.0000.0000.000
175A947ALA0-0.011-0.00631.585-0.144-0.1440.0000.0000.0000.000
176A948ASN0-0.040-0.02134.566-0.171-0.1710.0000.0000.0000.000
177A949VAL00.0930.05232.220-0.217-0.2170.0000.0000.0000.000
178A950VAL0-0.017-0.00533.048-0.209-0.2090.0000.0000.0000.000
179A951ALA0-0.046-0.03035.672-0.202-0.2020.0000.0000.0000.000
180A952SER0-0.008-0.00238.098-0.311-0.3110.0000.0000.0000.000
181A953THR00.006-0.00836.120-0.118-0.1180.0000.0000.0000.000
182A954LYS10.9130.96037.624-8.445-8.4450.0000.0000.0000.000
183A955SER0-0.0080.01340.851-0.184-0.1840.0000.0000.0000.000
184A956GLY00.034-0.00342.375-0.168-0.1680.0000.0000.0000.000
185A957GLN0-0.054-0.05040.2550.0820.0820.0000.0000.0000.000
186A958GLU-1-0.915-0.95743.2016.8996.8990.0000.0000.0000.000
187A959GLN0-0.039-0.01746.088-0.230-0.2300.0000.0000.0000.000
188A960ILE0-0.086-0.04843.495-0.158-0.1580.0000.0000.0000.000
189A961GLU-1-0.898-0.94945.0147.0567.0560.0000.0000.0000.000
190A962ASP-1-0.884-0.92848.6016.1976.1970.0000.0000.0000.000
191A963ARG10.8230.90951.211-6.193-6.1930.0000.0000.0000.000
192A964ASP-1-0.983-0.99851.4856.0026.0020.0000.0000.0000.000
193A965THR00.0040.01352.520-0.125-0.1250.0000.0000.0000.000
194A966MET0-0.057-0.00955.101-0.147-0.1470.0000.0000.0000.000