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: 8NJVY

Calculation Name: 1VI7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VI7

Chain ID: A

ChEMBL ID:

UniProt ID: P27862

Base Structure: X-ray

Registration Date: 2023-09-26

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1957978.494793
FMO2-HF: Nuclear repulsion 1880647.246034
FMO2-HF: Total energy -77331.248759
FMO2-MP2: Total energy -77556.518293


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-1.553-5.06416.441-2.783-10.146-0.018
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.023
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].
3A5GLU-1-0.900-0.9443.811-0.5041.196-0.016-0.833-0.8510.001
4A6SER0-0.024-0.0066.3810.4150.4150.0000.0000.0000.000
5A7TRP00.0270.0083.309-1.297-0.2870.160-0.321-0.848-0.002
6A8LEU0-0.009-0.0058.2440.0570.0570.0000.0000.0000.000
7A9ILE00.0130.0209.2390.0290.0290.0000.0000.0000.000
8A10PRO00.005-0.01511.802-0.038-0.0380.0000.0000.0000.000
9A11ALA00.0200.01715.2760.0210.0210.0000.0000.0000.000
10A12ALA0-0.037-0.02317.812-0.004-0.0040.0000.0000.0000.000
11A13PRO0-0.0130.00919.7450.0000.0000.0000.0000.0000.000
12A14VAL0-0.0030.00421.023-0.009-0.0090.0000.0000.0000.000
13A15THR0-0.0110.00823.2290.0030.0030.0000.0000.0000.000
14A16VAL00.0340.01925.769-0.005-0.0050.0000.0000.0000.000
15A17VAL00.007-0.00728.2210.0020.0020.0000.0000.0000.000
16A18GLU-1-0.937-0.96830.870-0.005-0.0050.0000.0000.0000.000
17A19GLU-1-0.904-0.96933.1060.0080.0080.0000.0000.0000.000
18A20ILE00.0210.02532.508-0.003-0.0030.0000.0000.0000.000
19A21LYS10.9100.93536.8120.0090.0090.0000.0000.0000.000
20A22LYS11.0051.01240.211-0.002-0.0020.0000.0000.0000.000
21A23SER0-0.0220.00936.6020.0020.0020.0000.0000.0000.000
22A24ARG10.8330.90334.279-0.015-0.0150.0000.0000.0000.000
23A25PHE00.0330.00630.0130.0020.0020.0000.0000.0000.000
24A26ILE00.0080.00328.594-0.003-0.0030.0000.0000.0000.000
25A27THR00.0150.02523.1030.0030.0030.0000.0000.0000.000
26A28MET0-0.020-0.00423.676-0.003-0.0030.0000.0000.0000.000
27A29LEU00.0240.00018.5400.0030.0030.0000.0000.0000.000
28A30ALA00.013-0.01417.861-0.006-0.0060.0000.0000.0000.000
29A31HIS0-0.0170.00511.570-0.030-0.0300.0000.0000.0000.000
30A32THR0-0.020-0.02512.745-0.027-0.0270.0000.0000.0000.000
31A33ASP-1-0.908-0.9158.8070.6620.6620.0000.0000.0000.000
32A34GLY00.0910.0359.592-0.038-0.0380.0000.0000.0000.000
33A35VAL0-0.013-0.02510.557-0.056-0.0560.0000.0000.0000.000
34A36GLU-1-0.956-0.97513.1580.1680.1680.0000.0000.0000.000
35A37ALA00.0750.05413.761-0.031-0.0310.0000.0000.0000.000
36A38ALA00.0170.00014.246-0.028-0.0280.0000.0000.0000.000
37A39LYS10.8580.92116.065-0.147-0.1470.0000.0000.0000.000
38A40ALA00.0470.02018.476-0.018-0.0180.0000.0000.0000.000
39A41PHE0-0.016-0.00817.795-0.015-0.0150.0000.0000.0000.000
40A42VAL0-0.017-0.02320.015-0.014-0.0140.0000.0000.0000.000
41A43GLU-1-0.960-0.97222.7530.0670.0670.0000.0000.0000.000
42A44SER00.0330.02724.441-0.005-0.0050.0000.0000.0000.000
43A45VAL00.0040.00424.492-0.007-0.0070.0000.0000.0000.000
44A46ARG10.8480.92324.998-0.066-0.0660.0000.0000.0000.000
45A47ALA0-0.0130.00528.819-0.005-0.0050.0000.0000.0000.000
46A48GLU-1-0.946-0.97929.7950.0490.0490.0000.0000.0000.000
47A49HIS0-0.0130.03230.000-0.009-0.0090.0000.0000.0000.000
48A50PRO00.0660.02632.5940.0000.0000.0000.0000.0000.000
49A51ASP-1-0.940-0.97034.7340.0260.0260.0000.0000.0000.000
50A52ALA0-0.093-0.03332.757-0.003-0.0030.0000.0000.0000.000
51A53ARG10.8480.90333.631-0.012-0.0120.0000.0000.0000.000
52A54HIS0-0.0150.00429.853-0.003-0.0030.0000.0000.0000.000
53A55HIS10.8310.92426.667-0.043-0.0430.0000.0000.0000.000
54A56CYS0-0.0460.00024.8310.0050.0050.0000.0000.0000.000
55A57VAL00.0490.03318.6640.0040.0040.0000.0000.0000.000
56A58ALA0-0.027-0.03417.523-0.011-0.0110.0000.0000.0000.000
57A59TRP0-0.0070.01411.721-0.026-0.0260.0000.0000.0000.000
58A60VAL00.0770.0398.561-0.019-0.0190.0000.0000.0000.000
59A61ALA0-0.048-0.0337.788-0.030-0.0300.0000.0000.0000.000
60A62GLY0-0.106-0.0396.1640.0980.0980.0000.0000.0000.000
61A63ALA00.0350.2282.0364.064-3.65114.038-2.547-3.7760.005
62A64PRO0-0.008-0.1442.569-0.350-1.3591.0522.053-2.096-0.021
63A65ASP-1-0.800-0.9505.5470.0800.0800.0000.0000.0000.000
64A66ASP-1-0.922-0.9432.579-3.435-2.6170.511-0.493-0.836-0.002
65A67SER0-0.008-0.0302.520-1.490-0.0690.692-0.606-1.5070.001
66A68GLN00.0470.0013.967-0.1870.0090.005-0.035-0.1660.000
67A69GLN0-0.036-0.0264.713-0.228-0.160-0.001-0.001-0.0660.000
68A70LEU0-0.031-0.0078.753-0.011-0.0110.0000.0000.0000.000
69A71GLY0-0.0040.01611.720-0.008-0.0080.0000.0000.0000.000
70A72PHE0-0.028-0.03315.184-0.015-0.0150.0000.0000.0000.000
71A73SER0-0.024-0.02118.772-0.002-0.0020.0000.0000.0000.000
72A74ASP-1-0.758-0.88522.4230.0070.0070.0000.0000.0000.000
73A75ASP-1-0.828-0.91925.9310.0370.0370.0000.0000.0000.000
74A76GLY00.0480.03227.862-0.001-0.0010.0000.0000.0000.000
75A77GLU-1-0.815-0.87829.0470.0060.0060.0000.0000.0000.000
76A78PRO0-0.046-0.02829.8180.0000.0000.0000.0000.0000.000
77A79ALA00.0640.01327.898-0.002-0.0020.0000.0000.0000.000
78A80GLY0-0.056-0.01824.824-0.005-0.0050.0000.0000.0000.000
79A81THR0-0.036-0.02525.881-0.006-0.0060.0000.0000.0000.000
80A82ALA00.0170.00226.115-0.001-0.0010.0000.0000.0000.000
81A83GLY00.0250.01522.2840.0050.0050.0000.0000.0000.000
82A84LYS10.9560.98018.7810.0390.0390.0000.0000.0000.000
83A85PRO0-0.027-0.01719.931-0.004-0.0040.0000.0000.0000.000
84A86MET00.0050.00320.297-0.004-0.0040.0000.0000.0000.000
85A87LEU00.0380.03213.8070.0000.0000.0000.0000.0000.000
86A88ALA0-0.002-0.01216.089-0.004-0.0040.0000.0000.0000.000
87A89GLN0-0.0160.03117.335-0.020-0.0200.0000.0000.0000.000
88A90LEU00.0070.02014.030-0.012-0.0120.0000.0000.0000.000
89A91MET0-0.009-0.00710.8940.0060.0060.0000.0000.0000.000
90A92GLY0-0.0030.01013.576-0.038-0.0380.0000.0000.0000.000
91A93SER0-0.127-0.08114.421-0.007-0.0070.0000.0000.0000.000
92A94GLY00.0330.02911.210-0.015-0.0150.0000.0000.0000.000
93A95VAL0-0.066-0.03411.0190.0000.0000.0000.0000.0000.000
94A96GLY00.028-0.0077.4050.0170.0170.0000.0000.0000.000
95A97GLU-1-0.824-0.9447.3830.5790.5790.0000.0000.0000.000
96A98ILE00.0120.0099.597-0.055-0.0550.0000.0000.0000.000
97A99THR00.003-0.02513.094-0.004-0.0040.0000.0000.0000.000
98A100ALA0-0.049-0.02615.885-0.012-0.0120.0000.0000.0000.000
99A101VAL00.005-0.01019.2980.0010.0010.0000.0000.0000.000
100A102VAL0-0.040-0.00822.770-0.006-0.0060.0000.0000.0000.000
101A103VAL00.0220.00925.8850.0030.0030.0000.0000.0000.000
102A104ARG10.7880.87129.108-0.014-0.0140.0000.0000.0000.000
103A105TYR00.0460.00132.132-0.001-0.0010.0000.0000.0000.000
104A106TYR0-0.066-0.05135.716-0.003-0.0030.0000.0000.0000.000
105A107GLY00.1230.05437.9480.0010.0010.0000.0000.0000.000
106A108GLY0-0.062-0.01740.734-0.001-0.0010.0000.0000.0000.000
107A109ILE0-0.029-0.01641.086-0.002-0.0020.0000.0000.0000.000
108A110LEU0-0.0160.00539.2610.0010.0010.0000.0000.0000.000
109A111LEU0-0.029-0.03035.084-0.002-0.0020.0000.0000.0000.000
110A112GLY00.0280.01136.7770.0010.0010.0000.0000.0000.000
111A113THR00.0660.03632.2150.0010.0010.0000.0000.0000.000
112A114GLY00.0360.01331.9580.0000.0000.0000.0000.0000.000
113A115GLY0-0.038-0.03531.9150.0000.0000.0000.0000.0000.000
114A116LEU00.0430.03030.8140.0020.0020.0000.0000.0000.000
115A117VAL00.0570.04526.7050.0020.0020.0000.0000.0000.000
116A118LYS10.8750.91527.6400.0300.0300.0000.0000.0000.000
117A119ALA00.0350.02829.3320.0000.0000.0000.0000.0000.000
118A120TYR0-0.019-0.01225.3940.0060.0060.0000.0000.0000.000
119A121GLY00.0280.01423.4110.0030.0030.0000.0000.0000.000
120A122GLY0-0.015-0.01423.8830.0000.0000.0000.0000.0000.000
121A123GLY00.0650.03926.1910.0000.0000.0000.0000.0000.000
122A124VAL00.026-0.00319.2420.0020.0020.0000.0000.0000.000
123A125ASN0-0.088-0.06421.8380.0040.0040.0000.0000.0000.000
124A126GLN00.016-0.00523.241-0.001-0.0010.0000.0000.0000.000
125A127ALA00.0250.00622.2910.0000.0000.0000.0000.0000.000
126A128LEU00.0110.01517.4010.0040.0040.0000.0000.0000.000
127A129ARG10.8510.94320.8790.0270.0270.0000.0000.0000.000
128A130GLN0-0.042-0.03023.3600.0020.0020.0000.0000.0000.000
129A131LEU0-0.0140.01715.9370.0080.0080.0000.0000.0000.000
130A132THR0-0.0070.00820.059-0.008-0.0080.0000.0000.0000.000
131A133THR00.001-0.01214.9950.0090.0090.0000.0000.0000.000
132A134GLN00.025-0.00214.394-0.021-0.0210.0000.0000.0000.000
133A135ARG10.8760.92810.4160.0890.0890.0000.0000.0000.000
134A136LYS10.9130.9706.728-0.740-0.7400.0000.0000.0000.000
135A137THR0-0.016-0.0268.3380.0340.0340.0000.0000.0000.000
136A138PRO0-0.0320.0144.943-0.091-0.0910.0000.0000.0000.000
137A139LEU00.0130.0027.656-0.013-0.0130.0000.0000.0000.000
138A140THR00.0010.0088.2620.1710.1710.0000.0000.0000.000
139A141GLU-1-0.897-0.9669.2080.5510.5510.0000.0000.0000.000
140A142TYR0-0.031-0.03111.4870.0280.0280.0000.0000.0000.000
141A143THR0-0.013-0.02014.525-0.007-0.0070.0000.0000.0000.000
142A144LEU0-0.0160.00117.457-0.013-0.0130.0000.0000.0000.000
143A145GLN00.0200.01321.113-0.002-0.0020.0000.0000.0000.000
144A146CYS0-0.0410.00124.375-0.003-0.0030.0000.0000.0000.000
145A147GLU-1-0.863-0.92827.2740.0820.0820.0000.0000.0000.000
146A148TYR00.031-0.01230.3140.0050.0050.0000.0000.0000.000
147A149HIS0-0.070-0.02431.7230.0000.0000.0000.0000.0000.000
148A150GLN00.003-0.01129.6460.0000.0000.0000.0000.0000.000
149A151LEU00.0440.03325.8370.0050.0050.0000.0000.0000.000
150A152THR00.0390.01727.5350.0050.0050.0000.0000.0000.000
151A153GLY00.0010.00528.3570.0040.0040.0000.0000.0000.000
152A154ILE00.035-0.00223.3960.0030.0030.0000.0000.0000.000
153A155GLU-1-0.954-0.97023.6000.1570.1570.0000.0000.0000.000
154A156ALA0-0.002-0.00623.9250.0080.0080.0000.0000.0000.000
155A157LEU0-0.031-0.02724.9120.0020.0020.0000.0000.0000.000
156A158LEU00.0220.01518.6100.0050.0050.0000.0000.0000.000
157A159GLY00.0330.03420.5990.0140.0140.0000.0000.0000.000
158A160GLN0-0.072-0.03422.331-0.008-0.0080.0000.0000.0000.000
159A161CYS0-0.092-0.03120.169-0.014-0.0140.0000.0000.0000.000
160A162ASP-1-0.885-0.92817.5600.2010.2010.0000.0000.0000.000
161A163GLY00.025-0.00816.5800.0360.0360.0000.0000.0000.000
162A164LYS10.8890.93515.330-0.323-0.3230.0000.0000.0000.000
163A165ILE00.0540.02116.2650.0310.0310.0000.0000.0000.000
164A166ILE0-0.054-0.02212.859-0.019-0.0190.0000.0000.0000.000
165A167ASN0-0.012-0.01416.1590.0260.0260.0000.0000.0000.000
166A168SER0-0.041-0.02718.7130.0070.0070.0000.0000.0000.000
167A169ASP-1-0.904-0.93622.1980.1450.1450.0000.0000.0000.000
168A170TYR0-0.014-0.01324.110-0.002-0.0020.0000.0000.0000.000
169A171GLN00.0870.04325.355-0.003-0.0030.0000.0000.0000.000
170A172ALA0-0.046-0.02229.404-0.004-0.0040.0000.0000.0000.000
171A173PHE0-0.036-0.01528.355-0.004-0.0040.0000.0000.0000.000
172A174VAL0-0.013-0.01224.7030.0020.0020.0000.0000.0000.000
173A175LEU00.0140.00819.8330.0010.0010.0000.0000.0000.000
174A176LEU0-0.0040.00020.6610.0060.0060.0000.0000.0000.000
175A177ARG10.9821.01310.814-0.511-0.5110.0000.0000.0000.000
176A178VAL0-0.044-0.04416.372-0.012-0.0120.0000.0000.0000.000
177A179ALA00.0710.03711.7520.0480.0480.0000.0000.0000.000
178A180LEU0-0.0200.00013.315-0.054-0.0540.0000.0000.0000.000
179A181PRO00.0240.02112.9980.0540.0540.0000.0000.0000.000
180A182ALA00.0450.02011.355-0.027-0.0270.0000.0000.0000.000
181A183ALA0-0.055-0.02313.361-0.048-0.0480.0000.0000.0000.000
182A184LYS10.9150.93516.401-0.181-0.1810.0000.0000.0000.000
183A185VAL00.0660.05716.185-0.017-0.0170.0000.0000.0000.000
184A186ALA00.007-0.00518.236-0.012-0.0120.0000.0000.0000.000
185A187GLU-1-0.907-0.95721.2950.1140.1140.0000.0000.0000.000
186A188PHE00.0370.01120.268-0.008-0.0080.0000.0000.0000.000
187A189SER00.0030.00320.937-0.007-0.0070.0000.0000.0000.000
188A190ALA0-0.0010.01123.398-0.009-0.0090.0000.0000.0000.000
189A191LYS10.8990.95125.240-0.120-0.1200.0000.0000.0000.000
190A192LEU0-0.012-0.01323.035-0.007-0.0070.0000.0000.0000.000
191A193ALA0-0.026-0.01026.781-0.006-0.0060.0000.0000.0000.000
192A194ASP-1-0.880-0.95128.9720.0650.0650.0000.0000.0000.000
193A195PHE0-0.089-0.03229.107-0.005-0.0050.0000.0000.0000.000
194A196SER0-0.044-0.02529.519-0.003-0.0030.0000.0000.0000.000
195A197ARG10.9180.95131.984-0.065-0.0650.0000.0000.0000.000
196A198GLY00.000-0.00530.079-0.004-0.0040.0000.0000.0000.000
197A199SER0-0.086-0.02030.2120.0020.0020.0000.0000.0000.000
198A200LEU00.0190.01126.1700.0020.0020.0000.0000.0000.000
199A201GLN0-0.024-0.02123.4560.0000.0000.0000.0000.0000.000
200A202LEU0-0.020-0.00418.4150.0050.0050.0000.0000.0000.000
201A203LEU0-0.001-0.00418.291-0.007-0.0070.0000.0000.0000.000
202A204ALA00.0040.00313.3310.0320.0320.0000.0000.0000.000
203A205ILE0-0.044-0.0188.866-0.048-0.0480.0000.0000.0000.000
204A206GLU-1-0.942-0.96911.9280.2350.2350.0000.0000.0000.000
205A207GLU-1-0.986-0.99111.8680.1820.1820.0000.0000.0000.000
206A208GLU-1-0.997-0.9877.4550.4190.4190.0000.0000.0000.000