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: N9NJQ

Calculation Name: 1V5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V5X

Chain ID: A

ChEMBL ID:

UniProt ID: P83825

Base Structure: X-ray

Registration Date: 2023-06-22

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 200
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2188348.839399
FMO2-HF: Nuclear repulsion 2113923.387917
FMO2-HF: Total energy -74425.451482
FMO2-MP2: Total energy -74647.287161


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.807-3.34612.451-5.068-15.843-0.042
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.009
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].
3A3VAL00.0200.0152.848-3.4590.0270.385-1.657-2.214-0.007
4A4LYS10.7770.8474.7970.3150.402-0.001-0.010-0.0760.000
5A5ILE00.0080.0068.261-0.126-0.1260.0000.0000.0000.000
6A6CYM-1-0.779-0.79810.9400.1010.1010.0000.0000.0000.000
7A7GLY0-0.020-0.03813.687-0.052-0.0520.0000.0000.0000.000
8A8ILE0-0.029-0.01414.883-0.027-0.0270.0000.0000.0000.000
9A9THR0-0.021-0.01518.2920.0240.0240.0000.0000.0000.000
10A10ARG10.7990.84821.0730.1610.1610.0000.0000.0000.000
11A11LEU00.0450.02320.936-0.012-0.0120.0000.0000.0000.000
12A12GLU-1-0.848-0.90820.985-0.149-0.1490.0000.0000.0000.000
13A13ASP-1-0.775-0.87217.558-0.203-0.2030.0000.0000.0000.000
14A14ALA0-0.012-0.00316.657-0.037-0.0370.0000.0000.0000.000
15A15LEU00.0530.02016.481-0.011-0.0110.0000.0000.0000.000
16A16LEU0-0.045-0.00215.177-0.012-0.0120.0000.0000.0000.000
17A17ALA00.0210.00212.455-0.057-0.0570.0000.0000.0000.000
18A18GLU-1-0.837-0.92512.030-0.019-0.0190.0000.0000.0000.000
19A19ALA0-0.027-0.01412.6770.0150.0150.0000.0000.0000.000
20A20LEU0-0.093-0.05310.6420.0230.0230.0000.0000.0000.000
21A21GLY00.0020.0168.296-0.172-0.1720.0000.0000.0000.000
22A22ALA0-0.056-0.0197.484-0.116-0.1160.0000.0000.0000.000
23A23PHE00.014-0.0044.8920.4630.4630.0000.0000.0000.000
24A24ALA0-0.035-0.0199.4100.1360.1360.0000.0000.0000.000
25A25LEU00.0190.01510.939-0.151-0.1510.0000.0000.0000.000
26A26GLY00.011-0.00413.5900.0650.0650.0000.0000.0000.000
27A27PHE00.0110.00215.338-0.048-0.0480.0000.0000.0000.000
28A28VAL0-0.030-0.01818.7560.0190.0190.0000.0000.0000.000
29A29LEU00.0070.00020.823-0.012-0.0120.0000.0000.0000.000
30A30ALA00.0370.02823.4320.0020.0020.0000.0000.0000.000
31A31PRO0-0.050-0.03725.093-0.015-0.0150.0000.0000.0000.000
32A32GLY00.0470.02728.1990.0010.0010.0000.0000.0000.000
33A33SER0-0.021-0.00321.731-0.014-0.0140.0000.0000.0000.000
34A34ARG10.8900.92421.5140.1190.1190.0000.0000.0000.000
35A35ARG10.7680.85118.2140.1510.1510.0000.0000.0000.000
36A36ARG10.9210.98521.924-0.001-0.0010.0000.0000.0000.000
37A37ILE00.0220.01822.102-0.011-0.0110.0000.0000.0000.000
38A38ALA0-0.029-0.00425.2050.0090.0090.0000.0000.0000.000
39A39PRO00.0600.03126.224-0.001-0.0010.0000.0000.0000.000
40A40GLU-1-0.800-0.92726.8860.0310.0310.0000.0000.0000.000
41A41ALA0-0.028-0.01226.8600.0000.0000.0000.0000.0000.000
42A42ALA0-0.018-0.01922.504-0.002-0.0020.0000.0000.0000.000
43A43ARG10.8670.94623.328-0.061-0.0610.0000.0000.0000.000
44A44ALA0-0.032-0.01325.7150.0040.0040.0000.0000.0000.000
45A45ILE0-0.022-0.02720.977-0.002-0.0020.0000.0000.0000.000
46A46GLY00.0300.02421.5740.0010.0010.0000.0000.0000.000
47A47GLU-1-0.889-0.93322.6280.0730.0730.0000.0000.0000.000
48A48ALA0-0.045-0.01823.6700.0010.0010.0000.0000.0000.000
49A49LEU0-0.066-0.01417.676-0.009-0.0090.0000.0000.0000.000
50A50GLY00.0290.01618.7700.0130.0130.0000.0000.0000.000
51A51PRO0-0.019-0.03918.8820.0070.0070.0000.0000.0000.000
52A52PHE0-0.096-0.04914.6550.0360.0360.0000.0000.0000.000
53A53VAL00.0670.04812.6990.0370.0370.0000.0000.0000.000
54A54VAL0-0.056-0.02512.993-0.009-0.0090.0000.0000.0000.000
55A55ARG10.8650.94214.351-0.206-0.2060.0000.0000.0000.000
56A56VAL0-0.007-0.01713.1480.0320.0320.0000.0000.0000.000
57A57GLY00.0680.02716.497-0.045-0.0450.0000.0000.0000.000
58A58VAL0-0.053-0.02616.8260.0210.0210.0000.0000.0000.000
59A59PHE00.0330.00919.607-0.020-0.0200.0000.0000.0000.000
60A60ARG10.8380.88522.071-0.020-0.0200.0000.0000.0000.000
61A61ASP-1-0.861-0.92724.6490.0380.0380.0000.0000.0000.000
62A62GLN0-0.034-0.02426.215-0.004-0.0040.0000.0000.0000.000
63A63PRO00.0420.02628.2770.0090.0090.0000.0000.0000.000
64A64PRO00.0440.01428.4450.0020.0020.0000.0000.0000.000
65A65GLU-1-0.923-0.96129.5060.0720.0720.0000.0000.0000.000
66A66GLU-1-0.881-0.93229.3560.0480.0480.0000.0000.0000.000
67A67VAL00.0130.00224.3840.0030.0030.0000.0000.0000.000
68A68LEU0-0.0160.00226.5270.0050.0050.0000.0000.0000.000
69A69ARG10.8900.95128.142-0.061-0.0610.0000.0000.0000.000
70A70LEU0-0.013-0.00926.713-0.004-0.0040.0000.0000.0000.000
71A71MET0-0.077-0.02020.762-0.006-0.0060.0000.0000.0000.000
72A72GLU-1-0.860-0.90425.2550.1000.1000.0000.0000.0000.000
73A73GLU-1-0.870-0.92427.9950.0550.0550.0000.0000.0000.000
74A74ALA0-0.036-0.02724.297-0.006-0.0060.0000.0000.0000.000
75A75ARG10.7500.85224.466-0.102-0.1020.0000.0000.0000.000
76A76LEU0-0.020-0.00220.0230.0080.0080.0000.0000.0000.000
77A77GLN00.0360.00418.2940.0090.0090.0000.0000.0000.000
78A78VAL0-0.016-0.01015.0810.0310.0310.0000.0000.0000.000
79A79ALA00.0480.03518.182-0.036-0.0360.0000.0000.0000.000
80A80GLN0-0.032-0.03814.1800.0660.0660.0000.0000.0000.000
81A81LEU00.0030.00918.006-0.034-0.0340.0000.0000.0000.000
82A82HIS00.049-0.00515.6910.0270.0270.0000.0000.0000.000
83A83GLY0-0.069-0.01120.332-0.021-0.0210.0000.0000.0000.000
84A84GLU-1-0.930-0.95423.2010.0710.0710.0000.0000.0000.000
85A85GLU-1-0.751-0.88223.4300.0930.0930.0000.0000.0000.000
86A86PRO00.0270.03125.4060.0070.0070.0000.0000.0000.000
87A87PRO00.0490.02325.0850.0110.0110.0000.0000.0000.000
88A88GLU-1-0.844-0.93526.1030.1100.1100.0000.0000.0000.000
89A89TRP00.002-0.01627.3640.0040.0040.0000.0000.0000.000
90A90ALA00.0040.00522.4570.0070.0070.0000.0000.0000.000
91A91GLU-1-0.847-0.91824.0130.2040.2040.0000.0000.0000.000
92A92ALA0-0.042-0.01626.0920.0060.0060.0000.0000.0000.000
93A93VAL00.017-0.00923.1370.0020.0020.0000.0000.0000.000
94A94GLY00.005-0.00522.5830.0120.0120.0000.0000.0000.000
95A95ARG10.8040.90023.451-0.140-0.1400.0000.0000.0000.000
96A96PHE0-0.087-0.04425.305-0.006-0.0060.0000.0000.0000.000
97A97TYR0-0.003-0.00421.1560.0080.0080.0000.0000.0000.000
98A98PRO0-0.0190.00616.9500.0030.0030.0000.0000.0000.000
99A99VAL00.0420.03518.295-0.015-0.0150.0000.0000.0000.000
100A100ILE0-0.042-0.02212.3120.0580.0580.0000.0000.0000.000
101A101LYS10.8480.92615.751-0.157-0.1570.0000.0000.0000.000
102A102ALA0-0.0200.00115.9040.0320.0320.0000.0000.0000.000
103A103PHE00.0330.00616.524-0.010-0.0100.0000.0000.0000.000
104A104PRO00.0070.02017.101-0.007-0.0070.0000.0000.0000.000
105A105LEU0-0.006-0.00914.4500.0060.0060.0000.0000.0000.000
106A106GLU-1-0.936-0.95918.632-0.066-0.0660.0000.0000.0000.000
107A107GLY00.040-0.00419.874-0.004-0.0040.0000.0000.0000.000
108A108PRO0-0.061-0.01718.400-0.006-0.0060.0000.0000.0000.000
109A109ALA00.0330.01016.1900.0130.0130.0000.0000.0000.000
110A110ARG10.9550.97818.188-0.011-0.0110.0000.0000.0000.000
111A111PRO00.0240.00217.9950.0170.0170.0000.0000.0000.000
112A112GLU-1-0.888-0.93519.0710.0820.0820.0000.0000.0000.000
113A113TRP00.0530.01717.7370.0030.0030.0000.0000.0000.000
114A114ALA0-0.091-0.03416.5110.0310.0310.0000.0000.0000.000
115A115ASP-1-0.839-0.93017.5340.1570.1570.0000.0000.0000.000
116A116TYR0-0.080-0.05719.5750.0050.0050.0000.0000.0000.000
117A117PRO00.0120.01019.5760.0350.0350.0000.0000.0000.000
118A118ALA00.0040.00917.194-0.004-0.0040.0000.0000.0000.000
119A119GLN0-0.019-0.01714.9770.0760.0760.0000.0000.0000.000
120A120ALA0-0.059-0.03411.1050.1140.1140.0000.0000.0000.000
121A121LEU00.0250.03812.243-0.080-0.0800.0000.0000.0000.000
122A122LEU0-0.014-0.01311.3390.0880.0880.0000.0000.0000.000
123A123LEU00.0170.01411.139-0.078-0.0780.0000.0000.0000.000
124A124ASP-1-0.819-0.93012.736-0.106-0.1060.0000.0000.0000.000
125A125GLY00.0560.02115.099-0.006-0.0060.0000.0000.0000.000
126A126LYS10.8550.92417.2680.0700.0700.0000.0000.0000.000
127A127ARG10.8750.91221.0310.1360.1360.0000.0000.0000.000
128A128PRO00.0650.05618.727-0.015-0.0150.0000.0000.0000.000
129A129GLY00.0250.01517.637-0.004-0.0040.0000.0000.0000.000
130A130SER0-0.055-0.04518.625-0.009-0.0090.0000.0000.0000.000
131A131GLY0-0.003-0.01216.955-0.006-0.0060.0000.0000.0000.000
132A132GLU-1-0.868-0.89817.786-0.201-0.2010.0000.0000.0000.000
133A133ALA0-0.013-0.00214.6040.0100.0100.0000.0000.0000.000
134A134TYR0-0.045-0.03311.8470.0210.0210.0000.0000.0000.000
135A135PRO0-0.0070.00714.664-0.052-0.0520.0000.0000.0000.000
136A136ARG10.9390.9389.6710.6010.6010.0000.0000.0000.000
137A137ALA00.000-0.00711.6970.0090.0090.0000.0000.0000.000
138A138TRP00.0040.01114.1230.0240.0240.0000.0000.0000.000
139A139ALA00.1050.05310.6840.0380.0380.0000.0000.0000.000
140A140LYS10.8930.95211.8990.3480.3480.0000.0000.0000.000
141A141PRO0-0.0030.00613.4090.0230.0230.0000.0000.0000.000
142A142LEU00.0640.03813.0620.0180.0180.0000.0000.0000.000
143A143LEU00.0020.0057.3330.0400.0400.0000.0000.0000.000
144A144ALA0-0.038-0.01711.0280.0240.0240.0000.0000.0000.000
145A145THR0-0.043-0.03713.8380.0330.0330.0000.0000.0000.000
146A146GLY00.0000.01111.9870.0200.0200.0000.0000.0000.000
147A147ARG10.7790.90012.072-0.240-0.2400.0000.0000.0000.000
148A148ARG10.9280.9649.289-0.871-0.8710.0000.0000.0000.000
149A149VAL00.0320.0148.247-0.056-0.0560.0000.0000.0000.000
150A150ILE0-0.035-0.0206.9030.4600.4600.0000.0000.0000.000
151A151LEU00.0040.0065.896-0.399-0.3990.0000.0000.0000.000
152A152ALA00.0680.0227.7970.0000.0000.0000.0000.0000.000
153A153GLY00.0300.01810.450-0.073-0.0730.0000.0000.0000.000
154A154GLY0-0.039-0.01812.635-0.044-0.0440.0000.0000.0000.000
155A155ILE0-0.0310.0096.709-0.064-0.0640.0000.0000.0000.000
156A156ALA00.014-0.01010.0150.0420.0420.0000.0000.0000.000
157A157PRO00.0490.0209.407-0.168-0.1680.0000.0000.0000.000
158A158GLU-1-0.875-0.93210.423-0.708-0.7080.0000.0000.0000.000
159A159ASN00.0260.01811.118-0.057-0.0570.0000.0000.0000.000
160A160LEU00.0310.0215.108-0.054-0.0540.0000.0000.0000.000
161A161GLU-1-0.835-0.9186.988-1.092-1.0920.0000.0000.0000.000
162A162GLU-1-0.885-0.9238.143-0.625-0.6250.0000.0000.0000.000
163A163VAL00.022-0.0045.263-0.021-0.0210.0000.0000.0000.000
164A164LEU0-0.024-0.0112.390-1.589-0.6651.654-0.395-2.184-0.002
165A165ALA00.0140.0173.944-0.317-0.1290.000-0.018-0.1700.000
166A166LEU0-0.096-0.0576.0510.1490.1490.0000.0000.0000.000
167A167ARG10.8960.9662.7350.5991.0980.275-0.201-0.5720.000
168A168PRO00.0220.0302.319-1.119-0.3161.888-0.478-2.2130.000
169A169TYR0-0.010-0.0132.444-4.112-2.0161.598-1.637-2.056-0.024
170A170ALA0-0.004-0.0172.9351.4682.0882.329-1.244-1.705-0.003
171A171LEU00.0040.0012.326-1.028-2.0523.7660.857-3.599-0.005
172A172ASP-1-0.781-0.9004.469-0.511-0.4780.000-0.015-0.0190.000
173A173LEU0-0.006-0.0076.279-0.126-0.1260.0000.0000.0000.000
174A174ALA00.0550.0059.6580.0790.0790.0000.0000.0000.000
175A175SER00.0240.00513.392-0.017-0.0170.0000.0000.0000.000
176A176GLY0-0.0180.00212.5430.0090.0090.0000.0000.0000.000
177A177VAL0-0.030-0.02511.098-0.064-0.0640.0000.0000.0000.000
178A178GLU-1-0.711-0.80914.048-0.180-0.1800.0000.0000.0000.000
179A179GLU-1-0.888-0.91917.498-0.250-0.2500.0000.0000.0000.000
180A180ALA0-0.003-0.01320.7850.0180.0180.0000.0000.0000.000
181A181PRO0-0.066-0.03020.258-0.012-0.0120.0000.0000.0000.000
182A182GLY00.0200.01119.5890.0210.0210.0000.0000.0000.000
183A183VAL0-0.0040.00920.6690.0120.0120.0000.0000.0000.000
184A184LYS10.7860.87415.1090.1940.1940.0000.0000.0000.000
185A185SER0-0.0020.00017.0630.0150.0150.0000.0000.0000.000
186A186ALA00.0190.00216.600-0.057-0.0570.0000.0000.0000.000
187A187GLU-1-0.941-0.96916.267-0.504-0.5040.0000.0000.0000.000
188A188LYS10.9650.98314.6280.3370.3370.0000.0000.0000.000
189A189LEU0-0.009-0.00411.559-0.133-0.1330.0000.0000.0000.000
190A190ARG10.9840.98311.3170.1850.1850.0000.0000.0000.000
191A191ALA00.0610.03211.929-0.097-0.0970.0000.0000.0000.000
192A192LEU0-0.0080.0117.300-0.127-0.1270.0000.0000.0000.000
193A193PHE00.020-0.0196.621-0.442-0.4420.0000.0000.0000.000
194A194ALA0-0.0250.0048.086-0.003-0.0030.0000.0000.0000.000
195A195ARG10.7180.8278.5631.0351.0350.0000.0000.0000.000
196A196LEU00.0230.0032.419-0.922-0.1730.557-0.270-1.035-0.001
197A197ALA00.0210.0285.6220.1270.1270.0000.0000.0000.000
198A198SER0-0.018-0.0136.9090.3430.3430.0000.0000.0000.000
199A199LEU0-0.145-0.0556.7310.2430.2430.0000.0000.0000.000
200A200ARG10.9450.9805.7900.2720.2720.0000.0000.0000.000