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: 8247Y

Calculation Name: 1LRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LRV

Chain ID: A

ChEMBL ID:

UniProt ID: Q44534

Base Structure: X-ray

Registration Date: 2023-06-19

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2619837.312389
FMO2-HF: Nuclear repulsion 2525339.879124
FMO2-HF: Total energy -94497.433265
FMO2-MP2: Total energy -94772.330054


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:9:THR)


Summations of interaction energy for fragment #1(A:9:THR)
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.
-7.007-2.020.469-2.478-2.978-0.002
Interaction energy analysis for fragmet #1(A:9:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.013
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].
3A11ILE00.0260.0062.871-0.7802.3600.302-1.761-1.682-0.004
4A12GLY00.0560.0265.0290.0900.125-0.001-0.003-0.0300.000
5A13ASP-1-0.788-0.9118.598-0.445-0.4450.0000.0000.0000.000
6A14CYS0-0.033-0.02310.8910.1340.1340.0000.0000.0000.000
7A15ARG10.9200.97413.5250.3110.3110.0000.0000.0000.000
8A16VAL00.0340.01816.0460.0400.0400.0000.0000.0000.000
9A17CYS0-0.0110.01613.4710.0520.0520.0000.0000.0000.000
10A18SER00.0650.02216.275-0.003-0.0030.0000.0000.0000.000
11A19PHE00.0760.01915.234-0.007-0.0070.0000.0000.0000.000
12A20ARG10.8300.90316.4130.1600.1600.0000.0000.0000.000
13A21MET0-0.0160.00117.249-0.019-0.0190.0000.0000.0000.000
14A22SER00.0010.00519.6250.0050.0050.0000.0000.0000.000
15A23LEU0-0.0160.00016.5450.0100.0100.0000.0000.0000.000
16A24LEU00.0510.01613.2960.0090.0090.0000.0000.0000.000
17A25LEU0-0.019-0.00615.901-0.007-0.0070.0000.0000.0000.000
18A26THR0-0.063-0.04318.2570.0050.0050.0000.0000.0000.000
19A27GLY00.0320.02815.2620.0160.0160.0000.0000.0000.000
20A28ARG10.8970.95814.836-0.053-0.0530.0000.0000.0000.000
21A29CYS0-0.0240.00512.3960.0460.0460.0000.0000.0000.000
22A30THR0-0.010-0.0118.758-0.117-0.1170.0000.0000.0000.000
23A31PRO00.0280.0047.2410.2330.2330.0000.0000.0000.000
24A32GLY00.0260.0243.099-0.706-0.4500.054-0.104-0.2070.000
25A33ASP-1-0.915-0.9423.7771.5291.8660.005-0.105-0.237-0.001
26A34ALA00.0320.0096.5790.2880.2880.0000.0000.0000.000
27A35CYS0-0.041-0.0327.804-0.329-0.3290.0000.0000.0000.000
28A36VAL00.0810.0519.4090.2140.2140.0000.0000.0000.000
29A37ALA0-0.035-0.01811.0870.0160.0160.0000.0000.0000.000
30A38VAL00.000-0.0025.216-0.198-0.1980.0000.0000.0000.000
31A39GLU-1-0.914-0.9468.5880.3620.3620.0000.0000.0000.000
32A40SER0-0.005-0.0133.757-0.677-0.5060.000-0.054-0.1160.000
33A41GLY00.1080.0616.8090.0360.0360.0000.0000.0000.000
34A42ARG10.9290.9555.243-1.477-1.4770.0000.0000.0000.000
35A43GLN0-0.0150.0043.047-3.489-2.4410.109-0.451-0.7060.003
36A44ILE00.0220.0217.735-0.434-0.4340.0000.0000.0000.000
37A45ASP-1-0.759-0.83010.8260.4490.4490.0000.0000.0000.000
38A46ARG10.8630.9175.638-1.640-1.6400.0000.0000.0000.000
39A47PHE0-0.015-0.00111.693-0.139-0.1390.0000.0000.0000.000
40A48PHE00.0300.00113.330-0.093-0.0930.0000.0000.0000.000
41A49ARG10.8590.91614.836-0.540-0.5400.0000.0000.0000.000
42A50ASN0-0.031-0.01013.452-0.041-0.0410.0000.0000.0000.000
43A51ASN0-0.091-0.05416.043-0.090-0.0900.0000.0000.0000.000
44A52PRO00.0590.02919.194-0.001-0.0010.0000.0000.0000.000
45A53HIS00.001-0.00621.2210.0090.0090.0000.0000.0000.000
46A54LEU00.0110.00618.855-0.012-0.0120.0000.0000.0000.000
47A55ALA0-0.0170.00119.5990.0010.0010.0000.0000.0000.000
48A56VAL00.0320.01020.5690.0000.0000.0000.0000.0000.000
49A57GLN0-0.048-0.02921.962-0.006-0.0060.0000.0000.0000.000
50A58TYR0-0.013-0.01517.366-0.002-0.0020.0000.0000.0000.000
51A59LEU00.0020.00520.3490.0170.0170.0000.0000.0000.000
52A60ALA00.0080.00222.742-0.007-0.0070.0000.0000.0000.000
53A61ASP-1-0.826-0.90316.9940.2380.2380.0000.0000.0000.000
54A62PRO00.0340.01018.9910.0130.0130.0000.0000.0000.000
55A63PHE0-0.012-0.00210.9430.0210.0210.0000.0000.0000.000
56A64TRP00.0780.03113.2120.0480.0480.0000.0000.0000.000
57A65GLU-1-0.839-0.91910.9110.7880.7880.0000.0000.0000.000
58A66ARG10.7720.87811.574-0.404-0.4040.0000.0000.0000.000
59A67ARG10.8170.88514.825-0.212-0.2120.0000.0000.0000.000
60A68ALA00.0520.03116.471-0.023-0.0230.0000.0000.0000.000
61A69ILE0-0.104-0.05712.620-0.006-0.0060.0000.0000.0000.000
62A70ALA00.0150.01116.235-0.024-0.0240.0000.0000.0000.000
63A71VAL00.0310.02118.945-0.030-0.0300.0000.0000.0000.000
64A72ARG10.8170.91014.117-0.530-0.5300.0000.0000.0000.000
65A73TYR0-0.081-0.07615.956-0.028-0.0280.0000.0000.0000.000
66A74SER00.0080.00321.371-0.026-0.0260.0000.0000.0000.000
67A75PRO00.0090.00524.0770.0040.0040.0000.0000.0000.000
68A76VAL00.0410.02427.6230.0050.0050.0000.0000.0000.000
69A77GLU-1-0.836-0.93029.0450.1240.1240.0000.0000.0000.000
70A78ALA0-0.035-0.00927.724-0.006-0.0060.0000.0000.0000.000
71A79LEU00.0080.00424.9440.0040.0040.0000.0000.0000.000
72A80THR00.0040.00028.083-0.002-0.0020.0000.0000.0000.000
73A81PRO0-0.035-0.02629.164-0.005-0.0050.0000.0000.0000.000
74A82LEU00.0050.01224.237-0.005-0.0050.0000.0000.0000.000
75A83ILE0-0.0150.00627.3470.0050.0050.0000.0000.0000.000
76A84ARG10.8640.92529.906-0.103-0.1030.0000.0000.0000.000
77A85ASP-1-0.761-0.83423.4960.1750.1750.0000.0000.0000.000
78A86SER0-0.013-0.01424.513-0.001-0.0010.0000.0000.0000.000
79A87ASP-1-0.836-0.92219.9600.2470.2470.0000.0000.0000.000
80A88GLU-1-0.752-0.87722.1100.2130.2130.0000.0000.0000.000
81A89VAL0-0.025-0.00517.1570.0090.0090.0000.0000.0000.000
82A90VAL0-0.039-0.02819.6550.0140.0140.0000.0000.0000.000
83A91ARG10.7510.84621.409-0.144-0.1440.0000.0000.0000.000
84A92ARG10.7500.84020.748-0.226-0.2260.0000.0000.0000.000
85A93ALA0-0.033-0.01620.041-0.002-0.0020.0000.0000.0000.000
86A94VAL0-0.005-0.01022.080-0.006-0.0060.0000.0000.0000.000
87A95ALA00.0160.02125.520-0.010-0.0100.0000.0000.0000.000
88A96TYR0-0.006-0.00521.995-0.004-0.0040.0000.0000.0000.000
89A97ARG10.7970.88822.941-0.225-0.2250.0000.0000.0000.000
90A98LEU0-0.0100.01327.266-0.008-0.0080.0000.0000.0000.000
91A99PRO00.0370.02130.1040.0000.0000.0000.0000.0000.000
92A100ARG10.9390.94933.701-0.111-0.1110.0000.0000.0000.000
93A101GLU-1-0.909-0.95035.6710.0950.0950.0000.0000.0000.000
94A102GLN0-0.009-0.02134.1010.0020.0020.0000.0000.0000.000
95A103LEU0-0.009-0.00131.2460.0020.0020.0000.0000.0000.000
96A104SER0-0.001-0.02134.3580.0010.0010.0000.0000.0000.000
97A105ALA0-0.062-0.02834.612-0.003-0.0030.0000.0000.0000.000
98A106LEU0-0.002-0.00129.6050.0010.0010.0000.0000.0000.000
99A107MET0-0.054-0.01033.0090.0020.0020.0000.0000.0000.000
100A108PHE00.000-0.02035.482-0.002-0.0020.0000.0000.0000.000
101A109ASP-1-0.782-0.86629.0210.1340.1340.0000.0000.0000.000
102A110GLU-1-0.812-0.88128.9450.1150.1150.0000.0000.0000.000
103A111ASP-1-0.747-0.86125.8210.1790.1790.0000.0000.0000.000
104A112ARG10.7590.84827.447-0.150-0.1500.0000.0000.0000.000
105A113GLU-1-0.808-0.88424.1980.1730.1730.0000.0000.0000.000
106A114VAL0-0.0140.00626.0940.0030.0030.0000.0000.0000.000
107A115ARG10.7740.86527.964-0.117-0.1170.0000.0000.0000.000
108A116ILE00.004-0.00128.830-0.006-0.0060.0000.0000.0000.000
109A117THR0-0.039-0.02826.4030.0010.0010.0000.0000.0000.000
110A118VAL0-0.021-0.01529.061-0.002-0.0020.0000.0000.0000.000
111A119ALA00.0250.00832.249-0.007-0.0070.0000.0000.0000.000
112A120ASP-1-0.947-0.96331.1980.1390.1390.0000.0000.0000.000
113A121ARG10.8350.91129.299-0.160-0.1600.0000.0000.0000.000
114A122LEU00.0040.01533.728-0.005-0.0050.0000.0000.0000.000
115A123PRO0-0.013-0.00336.8940.0000.0000.0000.0000.0000.000
116A124LEU00.0380.02140.5040.0000.0000.0000.0000.0000.000
117A125GLU-1-0.876-0.95242.4630.0760.0760.0000.0000.0000.000
118A126GLN00.0400.02539.9560.0020.0020.0000.0000.0000.000
119A127LEU00.0060.01437.6790.0010.0010.0000.0000.0000.000
120A128GLU-1-0.729-0.83240.7440.0680.0680.0000.0000.0000.000
121A129GLN0-0.048-0.02241.806-0.002-0.0020.0000.0000.0000.000
122A130MET0-0.0300.00234.5000.0000.0000.0000.0000.0000.000
123A131ALA0-0.055-0.02639.7580.0020.0020.0000.0000.0000.000
124A132ALA0-0.007-0.00541.812-0.002-0.0020.0000.0000.0000.000
125A133ASP-1-0.769-0.85435.5410.1010.1010.0000.0000.0000.000
126A134ARG10.9170.95133.346-0.099-0.0990.0000.0000.0000.000
127A135ASP-1-0.846-0.91833.0100.1160.1160.0000.0000.0000.000
128A136TYR00.0750.02532.0570.0030.0030.0000.0000.0000.000
129A137LEU0-0.0140.01129.863-0.001-0.0010.0000.0000.0000.000
130A138VAL00.0220.01232.9990.0020.0020.0000.0000.0000.000
131A139ARG10.7440.82634.991-0.081-0.0810.0000.0000.0000.000
132A140ALA0-0.010-0.00835.777-0.003-0.0030.0000.0000.0000.000
133A141TYR0-0.013-0.00930.2420.0000.0000.0000.0000.0000.000
134A142VAL0-0.0040.00036.128-0.002-0.0020.0000.0000.0000.000
135A143VAL0-0.012-0.00239.493-0.003-0.0030.0000.0000.0000.000
136A144GLN0-0.007-0.00336.024-0.007-0.0070.0000.0000.0000.000
137A145ARG10.8030.89335.894-0.107-0.1070.0000.0000.0000.000
138A146ILE0-0.0180.00340.242-0.003-0.0030.0000.0000.0000.000
139A147PRO00.025-0.00343.6960.0000.0000.0000.0000.0000.000
140A148PRO00.0730.03446.784-0.001-0.0010.0000.0000.0000.000
141A149GLY00.0150.00948.645-0.001-0.0010.0000.0000.0000.000
142A150ARG10.8300.88847.972-0.063-0.0630.0000.0000.0000.000
143A151LEU00.0060.01344.3780.0000.0000.0000.0000.0000.000
144A152PHE00.0390.01947.8770.0010.0010.0000.0000.0000.000
145A153ARG10.7680.87245.956-0.066-0.0660.0000.0000.0000.000
146A154PHE00.0380.01742.9330.0000.0000.0000.0000.0000.000
147A155MET0-0.024-0.00546.5200.0010.0010.0000.0000.0000.000
148A156ARG10.8110.88748.609-0.053-0.0530.0000.0000.0000.000
149A157ASP-1-0.797-0.87242.6360.0750.0750.0000.0000.0000.000
150A158GLU-1-0.769-0.84941.6460.0720.0720.0000.0000.0000.000
151A159ASP-1-0.823-0.92338.6450.0900.0900.0000.0000.0000.000
152A160ARG10.8940.93138.841-0.078-0.0780.0000.0000.0000.000
153A161GLN0-0.0050.00635.8650.0000.0000.0000.0000.0000.000
154A162VAL00.0400.01738.9440.0010.0010.0000.0000.0000.000
155A163ARG10.7640.85440.418-0.066-0.0660.0000.0000.0000.000
156A164LYS10.7890.87538.494-0.091-0.0910.0000.0000.0000.000
157A165LEU0-0.037-0.01837.033-0.001-0.0010.0000.0000.0000.000
158A166VAL0-0.011-0.01241.673-0.001-0.0010.0000.0000.0000.000
159A167ALA00.0510.02045.059-0.002-0.0020.0000.0000.0000.000
160A168LYS10.9210.97039.210-0.092-0.0920.0000.0000.0000.000
161A169ARG10.8250.91441.409-0.083-0.0830.0000.0000.0000.000
162A170LEU0-0.0170.00345.907-0.001-0.0010.0000.0000.0000.000
163A171PRO00.0130.00349.3020.0010.0010.0000.0000.0000.000
164A172GLU-1-0.762-0.86952.1380.0560.0560.0000.0000.0000.000
165A173GLU-1-0.891-0.95854.1850.0500.0500.0000.0000.0000.000
166A174SER0-0.048-0.03054.160-0.002-0.0020.0000.0000.0000.000
167A175LEU0-0.0150.00350.2440.0000.0000.0000.0000.0000.000
168A176GLY00.0780.04353.8980.0000.0000.0000.0000.0000.000
169A177LEU0-0.050-0.01654.991-0.001-0.0010.0000.0000.0000.000
170A178MET0-0.055-0.04047.4550.0010.0010.0000.0000.0000.000
171A179THR0-0.006-0.00352.0610.0020.0020.0000.0000.0000.000
172A180GLN0-0.018-0.01754.1750.0000.0000.0000.0000.0000.000
173A181ASP-1-0.782-0.85348.3790.0610.0610.0000.0000.0000.000
174A182PRO00.0270.01049.0990.0000.0000.0000.0000.0000.000
175A183GLU-1-0.847-0.89844.0040.0690.0690.0000.0000.0000.000
176A184PRO00.0520.01446.6150.0000.0000.0000.0000.0000.000
177A185GLU-1-0.895-0.94240.5040.0850.0850.0000.0000.0000.000
178A186VAL0-0.031-0.01844.7950.0010.0010.0000.0000.0000.000
179A187ARG10.7870.86046.534-0.052-0.0520.0000.0000.0000.000
180A188ARG10.9380.97642.840-0.070-0.0700.0000.0000.0000.000
181A189ILE0-0.061-0.02344.2640.0010.0010.0000.0000.0000.000
182A190VAL00.0170.00446.746-0.001-0.0010.0000.0000.0000.000
183A191ALA00.0330.01250.226-0.001-0.0010.0000.0000.0000.000
184A192SER0-0.077-0.04647.5300.0000.0000.0000.0000.0000.000
185A193ARG10.7140.83747.373-0.062-0.0620.0000.0000.0000.000
186A194LEU00.0560.03650.880-0.001-0.0010.0000.0000.0000.000
187A195ARG10.8160.88452.132-0.053-0.0530.0000.0000.0000.000
188A196GLY00.0180.02657.336-0.001-0.0010.0000.0000.0000.000
189A197ASP-1-0.838-0.94160.4260.0370.0370.0000.0000.0000.000
190A198ASP-1-0.920-0.95358.5610.0420.0420.0000.0000.0000.000
191A199LEU0-0.061-0.01954.8950.0010.0010.0000.0000.0000.000
192A200LEU0-0.010-0.00558.4610.0000.0000.0000.0000.0000.000
193A201GLU-1-0.847-0.87858.1750.0420.0420.0000.0000.0000.000
194A202LEU00.0280.00253.8670.0000.0000.0000.0000.0000.000
195A203LEU0-0.012-0.00656.3150.0010.0010.0000.0000.0000.000
196A204HIS10.7600.85458.552-0.038-0.0380.0000.0000.0000.000
197A205ASP-1-0.730-0.81553.4650.0490.0490.0000.0000.0000.000
198A206PRO00.0200.00954.3270.0000.0000.0000.0000.0000.000
199A207ASP-1-0.878-0.90948.6800.0570.0570.0000.0000.0000.000
200A208TRP00.0600.01147.7240.0000.0000.0000.0000.0000.000
201A209THR0-0.034-0.02946.5320.0010.0010.0000.0000.0000.000
202A210VAL0-0.043-0.02549.3460.0020.0020.0000.0000.0000.000
203A211ARG10.7950.89650.729-0.044-0.0440.0000.0000.0000.000
204A212LEU00.0100.00049.176-0.001-0.0010.0000.0000.0000.000
205A213ALA0-0.016-0.01749.0690.0000.0000.0000.0000.0000.000
206A214ALA00.001-0.00351.0350.0000.0000.0000.0000.0000.000
207A215VAL0-0.024-0.03054.567-0.001-0.0010.0000.0000.0000.000
208A216GLU-1-0.983-0.97950.0080.0560.0560.0000.0000.0000.000
209A217HIS0-0.0070.01350.406-0.001-0.0010.0000.0000.0000.000
210A218ALA00.0040.01755.855-0.001-0.0010.0000.0000.0000.000
211A219SER0-0.010-0.01059.2020.0000.0000.0000.0000.0000.000
212A220LEU00.003-0.02161.8740.0000.0000.0000.0000.0000.000
213A221GLU-1-0.819-0.87864.1260.0320.0320.0000.0000.0000.000
214A222ALA00.0710.04662.988-0.001-0.0010.0000.0000.0000.000
215A223LEU00.0110.00059.2670.0000.0000.0000.0000.0000.000
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