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: N23GQ

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1958035.302555
FMO2-HF: Nuclear repulsion 1880702.505658
FMO2-HF: Total energy -77332.796897
FMO2-MP2: Total energy -77557.954613


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.
-7.135-1.726.701-3.637-8.478-0.02
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 : -0.038 / q_NPA : -0.028
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-1-0.902-0.9423.820-0.6541.102-0.015-0.869-0.8720.001
4A6SER0-0.003-0.0086.3380.3410.3410.0000.0000.0000.000
5A7TRP0-0.016-0.0192.765-1.719-0.4380.559-0.504-1.336-0.004
6A8LEU0-0.009-0.0068.3180.0650.0650.0000.0000.0000.000
7A9ILE00.0270.0269.4220.0120.0120.0000.0000.0000.000
8A10PRO00.004-0.01912.064-0.027-0.0270.0000.0000.0000.000
9A11ALA00.0110.00915.5310.0180.0180.0000.0000.0000.000
10A12ALA0-0.035-0.02118.015-0.001-0.0010.0000.0000.0000.000
11A13PRO0-0.0130.00319.997-0.001-0.0010.0000.0000.0000.000
12A14VAL0-0.0050.00221.035-0.008-0.0080.0000.0000.0000.000
13A15THR00.0050.01523.5150.0020.0020.0000.0000.0000.000
14A16VAL00.0030.01026.254-0.004-0.0040.0000.0000.0000.000
15A17VAL00.015-0.01528.5450.0020.0020.0000.0000.0000.000
16A18GLU-1-0.917-0.95831.084-0.011-0.0110.0000.0000.0000.000
17A19GLU-1-0.858-0.92033.4560.0040.0040.0000.0000.0000.000
18A20ILE00.0190.01332.732-0.003-0.0030.0000.0000.0000.000
19A21LYS10.8860.92937.1730.0100.0100.0000.0000.0000.000
20A22LYS11.0021.00140.5680.0010.0010.0000.0000.0000.000
21A23SER0-0.0180.01636.8710.0020.0020.0000.0000.0000.000
22A24ARG10.7920.86734.670-0.009-0.0090.0000.0000.0000.000
23A25PHE00.0300.01230.3830.0020.0020.0000.0000.0000.000
24A26ILE00.0100.00228.824-0.003-0.0030.0000.0000.0000.000
25A27THR0-0.0040.01923.4850.0030.0030.0000.0000.0000.000
26A28MET0-0.0210.00323.961-0.002-0.0020.0000.0000.0000.000
27A29LEU00.021-0.00618.8210.0020.0020.0000.0000.0000.000
28A30ALA00.030-0.00518.128-0.004-0.0040.0000.0000.0000.000
29A31HIS0-0.036-0.00611.200-0.028-0.0280.0000.0000.0000.000
30A32THR0-0.028-0.01113.174-0.020-0.0200.0000.0000.0000.000
31A33ASP-1-0.878-0.9228.8170.5750.5750.0000.0000.0000.000
32A34GLY00.0860.0349.833-0.023-0.0230.0000.0000.0000.000
33A35VAL0-0.011-0.02310.699-0.052-0.0520.0000.0000.0000.000
34A36GLU-1-0.953-0.96813.3390.1510.1510.0000.0000.0000.000
35A37ALA00.0750.04813.987-0.028-0.0280.0000.0000.0000.000
36A38ALA00.0160.00414.492-0.025-0.0250.0000.0000.0000.000
37A39LYS10.8760.93116.323-0.130-0.1300.0000.0000.0000.000
38A40ALA00.0440.01918.661-0.016-0.0160.0000.0000.0000.000
39A41PHE00.0010.00118.468-0.012-0.0120.0000.0000.0000.000
40A42VAL0-0.023-0.02420.454-0.013-0.0130.0000.0000.0000.000
41A43GLU-1-0.961-0.97723.0350.0560.0560.0000.0000.0000.000
42A44SER00.0250.01624.842-0.005-0.0050.0000.0000.0000.000
43A45VAL00.0240.00724.627-0.006-0.0060.0000.0000.0000.000
44A46ARG10.8090.89224.959-0.056-0.0560.0000.0000.0000.000
45A47ALA0-0.0090.00729.114-0.004-0.0040.0000.0000.0000.000
46A48GLU-1-0.898-0.93829.6080.0400.0400.0000.0000.0000.000
47A49HIS0-0.066-0.01730.406-0.008-0.0080.0000.0000.0000.000
48A50PRO00.0410.03132.9180.0000.0000.0000.0000.0000.000
49A51ASP-1-0.935-0.97835.0400.0220.0220.0000.0000.0000.000
50A52ALA0-0.071-0.01733.018-0.003-0.0030.0000.0000.0000.000
51A53ARG10.8320.89333.986-0.008-0.0080.0000.0000.0000.000
52A54HIS0-0.025-0.00230.225-0.003-0.0030.0000.0000.0000.000
53A55HIS10.8560.93727.194-0.035-0.0350.0000.0000.0000.000
54A56CYS0-0.050-0.00525.2310.0040.0040.0000.0000.0000.000
55A57VAL00.0400.01919.1750.0030.0030.0000.0000.0000.000
56A58ALA0-0.005-0.02417.859-0.009-0.0090.0000.0000.0000.000
57A59TRP00.0000.02012.083-0.024-0.0240.0000.0000.0000.000
58A60VAL00.0850.0428.826-0.013-0.0130.0000.0000.0000.000
59A61ALA0-0.056-0.0377.816-0.031-0.0310.0000.0000.0000.000
60A62GLY0-0.102-0.0456.4830.1010.1010.0000.0000.0000.000
61A63ALA00.0230.2102.1970.219-0.7714.217-0.813-2.4130.000
62A64PRO00.005-0.1252.631-2.249-0.9010.773-0.470-1.651-0.015
63A65ASP-1-0.790-0.9505.9630.0550.0550.0000.0000.0000.000
64A66ASP-1-0.897-0.9282.582-2.924-2.2470.481-0.446-0.711-0.002
65A67SER0-0.028-0.0432.351-1.162-0.1040.684-0.477-1.2640.000
66A68GLN00.0310.0004.089-0.226-0.0290.003-0.055-0.1460.000
67A69GLN0-0.026-0.0134.957-0.161-0.1610.0000.0000.0000.000
68A70LEU0-0.021-0.0089.097-0.016-0.0160.0000.0000.0000.000
69A71GLY0-0.0040.01312.044-0.003-0.0030.0000.0000.0000.000
70A72PHE0-0.012-0.02715.571-0.016-0.0160.0000.0000.0000.000
71A73SER0-0.010-0.01019.1780.0000.0000.0000.0000.0000.000
72A74ASP-1-0.741-0.89422.8110.0030.0030.0000.0000.0000.000
73A75ASP-1-0.798-0.88226.3380.0330.0330.0000.0000.0000.000
74A76GLY00.0750.03928.233-0.002-0.0020.0000.0000.0000.000
75A77GLU-1-0.786-0.83529.3090.0020.0020.0000.0000.0000.000
76A78PRO0-0.035-0.02930.0890.0000.0000.0000.0000.0000.000
77A79ALA00.0390.01028.020-0.001-0.0010.0000.0000.0000.000
78A80GLY0-0.031-0.00824.998-0.004-0.0040.0000.0000.0000.000
79A81THR0-0.050-0.03026.056-0.006-0.0060.0000.0000.0000.000
80A82ALA00.0220.00026.326-0.001-0.0010.0000.0000.0000.000
81A83GLY00.0170.01522.5850.0040.0040.0000.0000.0000.000
82A84LYS10.9420.96919.0840.0300.0300.0000.0000.0000.000
83A85PRO0-0.020-0.00720.149-0.005-0.0050.0000.0000.0000.000
84A86MET0-0.013-0.00120.862-0.005-0.0050.0000.0000.0000.000
85A87LEU00.0380.02813.965-0.001-0.0010.0000.0000.0000.000
86A88ALA00.002-0.00816.325-0.006-0.0060.0000.0000.0000.000
87A89GLN0-0.0240.01317.620-0.019-0.0190.0000.0000.0000.000
88A90LEU0-0.0170.01814.229-0.013-0.0130.0000.0000.0000.000
89A91MET00.006-0.00510.794-0.001-0.0010.0000.0000.0000.000
90A92GLY0-0.028-0.00513.660-0.037-0.0370.0000.0000.0000.000
91A93SER0-0.141-0.08614.674-0.008-0.0080.0000.0000.0000.000
92A94GLY00.0500.04111.301-0.013-0.0130.0000.0000.0000.000
93A95VAL0-0.075-0.03711.386-0.003-0.0030.0000.0000.0000.000
94A96GLY00.0350.0037.7400.0160.0160.0000.0000.0000.000
95A97GLU-1-0.769-0.8767.3260.4720.4720.0000.0000.0000.000
96A98ILE00.0270.0169.838-0.038-0.0380.0000.0000.0000.000
97A99THR00.009-0.03213.372-0.001-0.0010.0000.0000.0000.000
98A100ALA0-0.052-0.02416.149-0.011-0.0110.0000.0000.0000.000
99A101VAL0-0.007-0.01419.5920.0020.0020.0000.0000.0000.000
100A102VAL0-0.0370.00123.047-0.005-0.0050.0000.0000.0000.000
101A103VAL00.0180.00726.1870.0030.0030.0000.0000.0000.000
102A104ARG10.7820.86529.396-0.009-0.0090.0000.0000.0000.000
103A105TYR00.0530.00832.4590.0000.0000.0000.0000.0000.000
104A106TYR0-0.075-0.04536.023-0.003-0.0030.0000.0000.0000.000
105A107GLY00.1250.05738.3030.0010.0010.0000.0000.0000.000
106A108GLY0-0.061-0.02641.048-0.001-0.0010.0000.0000.0000.000
107A109ILE0-0.069-0.03541.891-0.001-0.0010.0000.0000.0000.000
108A110LEU00.0330.02639.5570.0000.0000.0000.0000.0000.000
109A111LEU0-0.039-0.03635.258-0.002-0.0020.0000.0000.0000.000
110A112GLY00.0420.01536.9730.0010.0010.0000.0000.0000.000
111A113THR00.0370.02932.0170.0000.0000.0000.0000.0000.000
112A114GLY00.0430.01232.1790.0000.0000.0000.0000.0000.000
113A115GLY0-0.025-0.02732.1540.0000.0000.0000.0000.0000.000
114A116LEU00.0240.01831.1280.0010.0010.0000.0000.0000.000
115A117VAL00.0570.04426.8300.0010.0010.0000.0000.0000.000
116A118LYS10.8720.92027.8740.0320.0320.0000.0000.0000.000
117A119ALA00.0310.02329.7160.0000.0000.0000.0000.0000.000
118A120TYR0-0.030-0.04725.7500.0040.0040.0000.0000.0000.000
119A121GLY00.0280.01423.7640.0020.0020.0000.0000.0000.000
120A122GLY0-0.011-0.01224.270-0.001-0.0010.0000.0000.0000.000
121A123GLY00.0590.03826.5600.0000.0000.0000.0000.0000.000
122A124VAL00.0300.00219.5600.0020.0020.0000.0000.0000.000
123A125ASN0-0.035-0.02022.2170.0020.0020.0000.0000.0000.000
124A126GLN00.0240.00023.637-0.004-0.0040.0000.0000.0000.000
125A127ALA00.0200.01022.6780.0000.0000.0000.0000.0000.000
126A128LEU00.0230.02117.4530.0030.0030.0000.0000.0000.000
127A129ARG10.8210.92221.2540.0330.0330.0000.0000.0000.000
128A130GLN0-0.067-0.04523.7210.0010.0010.0000.0000.0000.000
129A131LEU0-0.0150.01616.2540.0080.0080.0000.0000.0000.000
130A132THR00.0120.01820.244-0.010-0.0100.0000.0000.0000.000
131A133THR0-0.040-0.03015.1150.0080.0080.0000.0000.0000.000
132A134GLN00.0190.00014.330-0.013-0.0130.0000.0000.0000.000
133A135ARG10.8690.93510.1500.1480.1480.0000.0000.0000.000
134A136LYS10.8440.9167.688-0.516-0.5160.0000.0000.0000.000
135A137THR0-0.007-0.0178.3970.0090.0090.0000.0000.0000.000
136A138PRO0-0.0060.0254.722-0.157-0.069-0.001-0.003-0.0850.000
137A139LEU0-0.012-0.0127.522-0.009-0.0090.0000.0000.0000.000
138A140THR0-0.0190.0037.9180.1180.1180.0000.0000.0000.000
139A141GLU-1-0.809-0.9038.7490.4690.4690.0000.0000.0000.000
140A142TYR0-0.022-0.03011.1750.0180.0180.0000.0000.0000.000
141A143THR0-0.012-0.01514.266-0.017-0.0170.0000.0000.0000.000
142A144LEU0-0.012-0.00417.197-0.011-0.0110.0000.0000.0000.000
143A145GLN00.0230.02020.858-0.002-0.0020.0000.0000.0000.000
144A146CYS0-0.027-0.00424.121-0.003-0.0030.0000.0000.0000.000
145A147GLU-1-0.861-0.93227.0370.0730.0730.0000.0000.0000.000
146A148TYR00.015-0.03029.9870.0050.0050.0000.0000.0000.000
147A149HIS0-0.075-0.03031.3690.0010.0010.0000.0000.0000.000
148A150GLN00.0120.00329.2220.0020.0020.0000.0000.0000.000
149A151LEU00.0560.03225.2850.0050.0050.0000.0000.0000.000
150A152THR00.0440.02527.1860.0040.0040.0000.0000.0000.000
151A153GLY0-0.017-0.00428.0330.0030.0030.0000.0000.0000.000
152A154ILE00.0340.00223.0500.0020.0020.0000.0000.0000.000
153A155GLU-1-0.943-0.97223.2780.1390.1390.0000.0000.0000.000
154A156ALA0-0.011-0.00723.6210.0060.0060.0000.0000.0000.000
155A157LEU0-0.019-0.01724.5130.0020.0020.0000.0000.0000.000
156A158LEU00.0090.01017.7180.0040.0040.0000.0000.0000.000
157A159GLY00.0350.03720.3050.0110.0110.0000.0000.0000.000
158A160GLN0-0.091-0.04722.070-0.005-0.0050.0000.0000.0000.000
159A161CYS0-0.109-0.05019.861-0.013-0.0130.0000.0000.0000.000
160A162ASP-1-0.862-0.92117.3400.1690.1690.0000.0000.0000.000
161A163GLY00.0390.00216.2910.0310.0310.0000.0000.0000.000
162A164LYS10.8600.92214.964-0.275-0.2750.0000.0000.0000.000
163A165ILE00.0760.03415.9490.0280.0280.0000.0000.0000.000
164A166ILE0-0.066-0.02912.491-0.018-0.0180.0000.0000.0000.000
165A167ASN0-0.015-0.01115.8900.0150.0150.0000.0000.0000.000
166A168SER0-0.020-0.01818.4100.0060.0060.0000.0000.0000.000
167A169ASP-1-0.860-0.91321.8690.1300.1300.0000.0000.0000.000
168A170TYR0-0.030-0.01623.9470.0000.0000.0000.0000.0000.000
169A171GLN00.0150.00924.199-0.011-0.0110.0000.0000.0000.000
170A172ALA0-0.038-0.01029.208-0.004-0.0040.0000.0000.0000.000
171A173PHE0-0.020-0.01128.259-0.004-0.0040.0000.0000.0000.000
172A174VAL0-0.029-0.01424.6540.0030.0030.0000.0000.0000.000
173A175LEU00.0100.00320.4650.0010.0010.0000.0000.0000.000
174A176LEU00.0270.01520.2490.0050.0050.0000.0000.0000.000
175A177ARG10.9150.96010.277-0.451-0.4510.0000.0000.0000.000
176A178VAL0-0.057-0.05015.987-0.010-0.0100.0000.0000.0000.000
177A179ALA00.0520.03311.4020.0420.0420.0000.0000.0000.000
178A180LEU00.0110.01112.953-0.045-0.0450.0000.0000.0000.000
179A181PRO00.0240.01812.6940.0480.0480.0000.0000.0000.000
180A182ALA00.0290.01711.196-0.022-0.0220.0000.0000.0000.000
181A183ALA0-0.047-0.02213.277-0.040-0.0400.0000.0000.0000.000
182A184LYS10.8750.92416.321-0.154-0.1540.0000.0000.0000.000
183A185VAL00.0720.05516.056-0.016-0.0160.0000.0000.0000.000
184A186ALA00.0120.01018.148-0.011-0.0110.0000.0000.0000.000
185A187GLU-1-0.826-0.91321.2040.1060.1060.0000.0000.0000.000
186A188PHE00.0550.01219.718-0.007-0.0070.0000.0000.0000.000
187A189SER00.001-0.00620.870-0.005-0.0050.0000.0000.0000.000
188A190ALA0-0.0170.00123.309-0.008-0.0080.0000.0000.0000.000
189A191LYS10.8560.93324.716-0.114-0.1140.0000.0000.0000.000
190A192LEU00.007-0.00322.823-0.006-0.0060.0000.0000.0000.000
191A193ALA0-0.024-0.00226.374-0.005-0.0050.0000.0000.0000.000
192A194ASP-1-0.883-0.95028.7820.0600.0600.0000.0000.0000.000
193A195PHE0-0.097-0.04028.506-0.005-0.0050.0000.0000.0000.000
194A196SER0-0.032-0.02629.165-0.002-0.0020.0000.0000.0000.000
195A197ARG10.8980.95131.697-0.059-0.0590.0000.0000.0000.000
196A198GLY00.003-0.00429.802-0.003-0.0030.0000.0000.0000.000
197A199SER0-0.078-0.02729.9170.0010.0010.0000.0000.0000.000
198A200LEU0-0.0010.00625.7670.0020.0020.0000.0000.0000.000
199A201GLN0-0.023-0.02222.961-0.001-0.0010.0000.0000.0000.000
200A202LEU0-0.028-0.00518.0400.0050.0050.0000.0000.0000.000
201A203LEU0-0.001-0.00417.987-0.005-0.0050.0000.0000.0000.000
202A204ALA00.0000.00013.0140.0260.0260.0000.0000.0000.000
203A205ILE0-0.039-0.0168.202-0.046-0.0460.0000.0000.0000.000
204A206GLU-1-0.943-0.97211.5900.2260.2260.0000.0000.0000.000
205A207GLU-1-0.989-0.98911.5470.1780.1780.0000.0000.0000.000
206A208GLU-1-0.997-0.9887.5200.4490.4490.0000.0000.0000.000