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: 52GJZ

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1968520.963948
FMO2-HF: Nuclear repulsion 1893365.480744
FMO2-HF: Total energy -75155.483204
FMO2-MP2: Total energy -75371.696936


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.
-1.749-0.11999999999998-0.016-0.657-0.9560.003
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 : -0.915 / q_NPA : -0.971
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].
3A775ARG10.8440.8793.858-31.828-30.199-0.016-0.657-0.9560.003
4A776GLN00.0480.0276.467-2.390-2.3900.0000.0000.0000.000
5A777GLU-1-0.907-0.9598.33921.66921.6690.0000.0000.0000.000
6A778GLU-1-0.780-0.8569.10126.28226.2820.0000.0000.0000.000
7A779LEU0-0.0130.0086.195-1.921-1.9210.0000.0000.0000.000
8A780GLY00.023-0.0069.677-1.264-1.2640.0000.0000.0000.000
9A781ALA00.0080.00512.867-1.230-1.2300.0000.0000.0000.000
10A782VAL0-0.021-0.0117.760-1.125-1.1250.0000.0000.0000.000
11A783VAL00.0430.01511.046-0.746-0.7460.0000.0000.0000.000
12A784ASP-1-0.800-0.85712.92616.03516.0350.0000.0000.0000.000
13A785LYS10.9320.96913.287-18.585-18.5850.0000.0000.0000.000
14A786GLU-1-0.784-0.87410.72524.45124.4510.0000.0000.0000.000
15A787MET0-0.0160.02013.967-0.709-0.7090.0000.0000.0000.000
16A788ALA0-0.0070.01317.201-1.130-1.1300.0000.0000.0000.000
17A789ALA0-0.034-0.01515.657-0.898-0.8980.0000.0000.0000.000
18A790THR00.011-0.00816.313-0.735-0.7350.0000.0000.0000.000
19A791SER0-0.023-0.02618.614-0.961-0.9610.0000.0000.0000.000
20A792ALA0-0.044-0.02020.972-0.734-0.7340.0000.0000.0000.000
21A793ALA00.0230.01219.997-0.565-0.5650.0000.0000.0000.000
22A794ILE0-0.006-0.00122.039-0.516-0.5160.0000.0000.0000.000
23A795GLU-1-0.829-0.90224.41210.00010.0000.0000.0000.0000.000
24A796ASP-1-0.947-0.97525.02611.01511.0150.0000.0000.0000.000
25A797ALA00.0200.00925.374-0.395-0.3950.0000.0000.0000.000
26A798VAL0-0.054-0.02627.257-0.408-0.4080.0000.0000.0000.000
27A799ARG10.8780.93228.139-11.050-11.0500.0000.0000.0000.000
28A800ARG10.8280.89329.314-9.815-9.8150.0000.0000.0000.000
29A801ILE00.002-0.01129.363-0.250-0.2500.0000.0000.0000.000
30A802GLU-1-0.825-0.92632.8988.6478.6470.0000.0000.0000.000
31A803ASP-1-0.852-0.92034.2238.5058.5050.0000.0000.0000.000
32A804MET0-0.048-0.01230.906-0.275-0.2750.0000.0000.0000.000
33A805MET0-0.0210.01836.315-0.252-0.2520.0000.0000.0000.000
34A806ASN0-0.009-0.00639.548-0.405-0.4050.0000.0000.0000.000
35A807GLN0-0.026-0.01635.559-0.081-0.0810.0000.0000.0000.000
36A808ALA00.0500.02039.757-0.119-0.1190.0000.0000.0000.000
37A809ARG10.8750.93941.181-6.925-6.9250.0000.0000.0000.000
38A810HIS0-0.052-0.01842.533-0.283-0.2830.0000.0000.0000.000
39A811ALA0-0.0030.01241.423-0.049-0.0490.0000.0000.0000.000
40A812SER0-0.097-0.05143.3640.0200.0200.0000.0000.0000.000
41A813SER00.0250.00245.392-0.043-0.0430.0000.0000.0000.000
42A814GLY00.0240.00548.2710.0390.0390.0000.0000.0000.000
43A815VAL00.0310.01547.8700.0910.0910.0000.0000.0000.000
44A816LYS10.9560.98940.612-7.541-7.5410.0000.0000.0000.000
45A817LEU0-0.0310.00943.7150.1510.1510.0000.0000.0000.000
46A818GLU-1-0.817-0.89544.0026.8516.8510.0000.0000.0000.000
47A819VAL0-0.017-0.00742.6670.1130.1130.0000.0000.0000.000
48A820ASN00.0540.04039.9930.2940.2940.0000.0000.0000.000
49A821GLU-1-0.828-0.91239.6037.5917.5910.0000.0000.0000.000
50A822ARG10.7740.87740.539-6.684-6.6840.0000.0000.0000.000
51A823ILE00.0070.01936.3050.1990.1990.0000.0000.0000.000
52A824LEU00.0530.04334.9560.3160.3160.0000.0000.0000.000
53A825ASN0-0.020-0.00735.5650.2840.2840.0000.0000.0000.000
54A826SER0-0.004-0.00336.3840.1300.1300.0000.0000.0000.000
55A827CYS0-0.039-0.03331.9290.3080.3080.0000.0000.0000.000
56A828THR0-0.020-0.02731.5100.3940.3940.0000.0000.0000.000
57A829ASP-1-0.895-0.95832.3858.8938.8930.0000.0000.0000.000
58A830LEU0-0.051-0.02428.8820.2040.2040.0000.0000.0000.000
59A831MET00.0090.01524.7250.4300.4300.0000.0000.0000.000
60A832LYS10.8520.92328.283-8.608-8.6080.0000.0000.0000.000
61A833ALA0-0.033-0.01230.4180.0890.0890.0000.0000.0000.000
62A834ILE00.020-0.00724.1610.2700.2700.0000.0000.0000.000
63A835ARG10.9150.95825.439-9.843-9.8430.0000.0000.0000.000
64A836LEU00.0000.01426.3960.2230.2230.0000.0000.0000.000
65A837LEU0-0.0020.01523.4030.1700.1700.0000.0000.0000.000
66A838VAL00.0580.02220.3530.3490.3490.0000.0000.0000.000
67A839THR00.0070.01322.6740.4410.4410.0000.0000.0000.000
68A840THR0-0.041-0.03025.180-0.056-0.0560.0000.0000.0000.000
69A841SER0-0.049-0.02520.4830.3240.3240.0000.0000.0000.000
70A842THR00.008-0.01420.4480.5710.5710.0000.0000.0000.000
71A843SER0-0.042-0.03621.715-0.030-0.0300.0000.0000.0000.000
72A844LEU0-0.030-0.01223.100-0.087-0.0870.0000.0000.0000.000
73A845GLN0-0.008-0.03417.6100.5400.5400.0000.0000.0000.000
74A846LYS10.8740.90419.549-15.749-15.7490.0000.0000.0000.000
75A847GLU-1-0.870-0.91622.30111.50911.5090.0000.0000.0000.000
76A848ILE00.0180.00420.119-0.073-0.0730.0000.0000.0000.000
77A849VAL0-0.025-0.00818.2360.1320.1320.0000.0000.0000.000
78A850GLU-1-0.817-0.87721.06613.00513.0050.0000.0000.0000.000
79A851SER0-0.040-0.01924.567-0.406-0.4060.0000.0000.0000.000
80A852GLY0-0.0060.00122.596-0.275-0.2750.0000.0000.0000.000
81A853ARG10.7310.83221.412-12.751-12.7510.0000.0000.0000.000
82A854GLY00.0060.00522.667-0.098-0.0980.0000.0000.0000.000
83A855ALA0-0.041-0.03026.378-0.137-0.1370.0000.0000.0000.000
84A856ALA00.0000.02821.114-0.036-0.0360.0000.0000.0000.000
85A857THR0-0.003-0.04519.8840.0120.0120.0000.0000.0000.000
86A858GLN0-0.004-0.03718.9401.0211.0210.0000.0000.0000.000
87A859GLN0-0.061-0.01914.611-0.310-0.3100.0000.0000.0000.000
88A860GLU-1-0.737-0.83915.07416.88916.8890.0000.0000.0000.000
89A861PHE0-0.0150.01316.3400.7590.7590.0000.0000.0000.000
90A862TYR0-0.023-0.02412.9950.3410.3410.0000.0000.0000.000
91A863ALA00.0250.03011.4792.1022.1020.0000.0000.0000.000
92A864LYS10.9470.96412.165-14.918-14.9180.0000.0000.0000.000
93A865ASN0-0.081-0.04114.060-1.295-1.2950.0000.0000.0000.000
94A866SER00.0430.0348.358-1.066-1.0660.0000.0000.0000.000
95A867ARG11.0071.0029.323-23.276-23.2760.0000.0000.0000.000
96A868TRP0-0.092-0.04810.292-0.461-0.4610.0000.0000.0000.000
97A869THR00.016-0.01210.199-1.316-1.3160.0000.0000.0000.000
98A870GLU-1-0.856-0.9425.56143.72443.7240.0000.0000.0000.000
99A871GLY0-0.016-0.0018.363-0.541-0.5410.0000.0000.0000.000
100A872LEU0-0.040-0.02211.477-1.378-1.3780.0000.0000.0000.000
101A873ILE0-0.011-0.0018.001-1.282-1.2820.0000.0000.0000.000
102A874SER0-0.005-0.0019.411-1.884-1.8840.0000.0000.0000.000
103A875ALA00.007-0.00211.035-1.607-1.6070.0000.0000.0000.000
104A876SER00.0320.01714.097-1.737-1.7370.0000.0000.0000.000
105A877LYS10.8200.89610.774-25.976-25.9760.0000.0000.0000.000
106A878ALA0-0.0100.00113.800-1.029-1.0290.0000.0000.0000.000
107A879VAL00.0000.00915.828-1.106-1.1060.0000.0000.0000.000
108A880GLY00.0110.01217.286-0.901-0.9010.0000.0000.0000.000
109A881TRP0-0.017-0.01410.754-0.205-0.2050.0000.0000.0000.000
110A882GLY00.0880.04318.172-0.749-0.7490.0000.0000.0000.000
111A883ALA0-0.014-0.02821.152-0.783-0.7830.0000.0000.0000.000
112A884THR0-0.045-0.02720.244-0.590-0.5900.0000.0000.0000.000
113A885GLN0-0.058-0.04020.2690.0800.0800.0000.0000.0000.000
114A886LEU00.0090.00023.791-0.534-0.5340.0000.0000.0000.000
115A887VAL00.0060.00525.985-0.520-0.5200.0000.0000.0000.000
116A888GLU-1-0.813-0.89325.98010.40710.4070.0000.0000.0000.000
117A889ALA0-0.002-0.00727.817-0.415-0.4150.0000.0000.0000.000
118A890ALA0-0.006-0.00429.814-0.408-0.4080.0000.0000.0000.000
119A891ASP-1-0.776-0.88030.6869.3079.3070.0000.0000.0000.000
120A892LYS10.8180.88129.738-10.573-10.5730.0000.0000.0000.000
121A893VAL0-0.046-0.00833.460-0.278-0.2780.0000.0000.0000.000
122A894VAL0-0.031-0.00735.690-0.318-0.3180.0000.0000.0000.000
123A895LEU0-0.052-0.02235.104-0.293-0.2930.0000.0000.0000.000
124A896HIS0-0.080-0.03234.275-0.186-0.1860.0000.0000.0000.000
125A897THR0-0.047-0.02437.053-0.119-0.1190.0000.0000.0000.000
126A898GLY00.0210.01334.3170.0560.0560.0000.0000.0000.000
127A899LYS10.8680.91333.802-8.802-8.8020.0000.0000.0000.000
128A900TYR00.0610.00633.9760.2220.2220.0000.0000.0000.000
129A901GLU-1-0.821-0.91234.3158.8128.8120.0000.0000.0000.000
130A902GLU-1-0.908-0.94628.27911.01111.0110.0000.0000.0000.000
131A903LEU00.0500.02729.5330.4130.4130.0000.0000.0000.000
132A904ILE0-0.027-0.00230.6400.2000.2000.0000.0000.0000.000
133A905VAL0-0.001-0.00226.6370.1600.1600.0000.0000.0000.000
134A906CYS00.0030.00725.8640.5070.5070.0000.0000.0000.000
135A907SER0-0.025-0.03326.2200.3010.3010.0000.0000.0000.000
136A908HIS0-0.032-0.01927.9090.2170.2170.0000.0000.0000.000
137A909GLU-1-0.883-0.93322.15314.10614.1060.0000.0000.0000.000
138A910ILE0-0.0070.01622.7430.6430.6430.0000.0000.0000.000
139A911ALA00.0310.03523.4360.3840.3840.0000.0000.0000.000
140A912ALA00.0040.00922.9800.3010.3010.0000.0000.0000.000
141A913SER0-0.033-0.02318.9280.6510.6510.0000.0000.0000.000
142A914THR0-0.004-0.02619.8030.4070.4070.0000.0000.0000.000
143A915ALA0-0.011-0.01022.1260.0990.0990.0000.0000.0000.000
144A916GLN0-0.011-0.00416.6370.3810.3810.0000.0000.0000.000
145A917LEU00.0540.03017.0900.5770.5770.0000.0000.0000.000
146A918VAL0-0.017-0.00218.8720.0150.0150.0000.0000.0000.000
147A919ALA0-0.037-0.01919.806-0.167-0.1670.0000.0000.0000.000
148A920ALA00.0280.00815.3810.0000.0000.0000.0000.0000.000
149A921SER00.005-0.01817.3140.1970.1970.0000.0000.0000.000
150A922LYS10.9440.96519.459-12.706-12.7060.0000.0000.0000.000
151A923VAL0-0.060-0.01416.875-0.482-0.4820.0000.0000.0000.000
152A924LYS10.8880.94716.687-18.130-18.1300.0000.0000.0000.000
153A925ALA00.0160.03120.448-0.432-0.4320.0000.0000.0000.000
154A926ASN00.013-0.00523.660-0.595-0.5950.0000.0000.0000.000
155A927LYS10.9330.97227.336-9.306-9.3060.0000.0000.0000.000
156A928HIS0-0.066-0.04627.814-0.265-0.2650.0000.0000.0000.000
157A929SER00.0470.00829.610-0.187-0.1870.0000.0000.0000.000
158A930PRO0-0.015-0.00227.0380.2540.2540.0000.0000.0000.000
159A931HIS00.0100.01529.4490.1690.1690.0000.0000.0000.000
160A932LEU00.0350.02724.9720.1440.1440.0000.0000.0000.000
161A933SER0-0.013-0.01427.9250.1230.1230.0000.0000.0000.000
162A934ARG10.9950.98630.618-9.772-9.7720.0000.0000.0000.000
163A935LEU00.0440.03722.889-0.020-0.0200.0000.0000.0000.000
164A936GLN0-0.008-0.01927.5280.0030.0030.0000.0000.0000.000
165A937GLU-1-0.945-0.96128.9239.2649.2640.0000.0000.0000.000
166A938CYS0-0.031-0.00928.248-0.208-0.2080.0000.0000.0000.000
167A939SER00.0120.00726.525-0.010-0.0100.0000.0000.0000.000
168A940ARG10.9010.95728.313-9.830-9.8300.0000.0000.0000.000
169A941THR00.0340.01831.919-0.089-0.0890.0000.0000.0000.000
170A942VAL00.0460.02526.704-0.217-0.2170.0000.0000.0000.000
171A943ASN00.0090.00128.3900.1000.1000.0000.0000.0000.000
172A944GLU-1-0.886-0.93231.0838.8468.8460.0000.0000.0000.000
173A945ARG10.8280.90432.194-9.208-9.2080.0000.0000.0000.000
174A946ALA00.0550.03729.889-0.117-0.1170.0000.0000.0000.000
175A947ALA0-0.014-0.01031.936-0.170-0.1700.0000.0000.0000.000
176A948ASN0-0.046-0.02735.168-0.155-0.1550.0000.0000.0000.000
177A949VAL00.0940.04932.601-0.233-0.2330.0000.0000.0000.000
178A950VAL0-0.0110.00333.390-0.186-0.1860.0000.0000.0000.000
179A951ALA0-0.048-0.02635.975-0.198-0.1980.0000.0000.0000.000
180A952SER0-0.018-0.01138.199-0.281-0.2810.0000.0000.0000.000
181A953THR00.002-0.01636.111-0.117-0.1170.0000.0000.0000.000
182A954LYS10.8990.95438.070-8.371-8.3710.0000.0000.0000.000
183A955SER0-0.007-0.01341.009-0.165-0.1650.0000.0000.0000.000
184A956GLY00.002-0.00142.316-0.188-0.1880.0000.0000.0000.000
185A957GLN0-0.068-0.06140.5460.0690.0690.0000.0000.0000.000
186A958GLU-1-0.826-0.90643.3856.9006.9000.0000.0000.0000.000
187A959GLN00.0080.01046.425-0.251-0.2510.0000.0000.0000.000
188A960ILE0-0.053-0.03643.662-0.145-0.1450.0000.0000.0000.000
189A961GLU-1-0.872-0.92945.2736.9686.9680.0000.0000.0000.000
190A962ASP-1-0.881-0.93648.9706.1336.1330.0000.0000.0000.000
191A963ARG10.7190.85551.300-6.220-6.2200.0000.0000.0000.000
192A964ASP-1-0.884-0.93351.2246.0506.0500.0000.0000.0000.000
193A965THR0-0.055-0.02752.163-0.124-0.1240.0000.0000.0000.000
194A966MET0-0.044-0.00654.783-0.147-0.1470.0000.0000.0000.000