FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9G1V2

Calculation Name: 3VX6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX6

Chain ID: A

ChEMBL ID:

UniProt ID: L7MTK3

Base Structure: X-ray

Registration Date: 2023-06-20

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 273
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3916186.028283
FMO2-HF: Nuclear repulsion 3807922.878592
FMO2-HF: Total energy -108263.14969
FMO2-MP2: Total energy -108582.138629


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:4:ASP)


Summations of interaction energy for fragment #1(A:4: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.
-131.251-131.437.863-19.418-18.2970.166
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.792 / q_NPA : -0.886
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].
3A6LYS10.8160.8961.668-107.496-111.58619.331-8.947-6.2930.094
4A7PHE00.0320.0035.526-3.547-3.5470.0000.0000.0000.000
5A8ALA00.0340.0319.112-0.378-0.3780.0000.0000.0000.000
6A9PRO0-0.041-0.02112.6220.5700.5700.0000.0000.0000.000
7A10SER00.008-0.02614.768-0.162-0.1620.0000.0000.0000.000
8A11PHE00.0080.00416.597-0.899-0.8990.0000.0000.0000.000
9A12GLN00.0350.04219.2770.9000.9000.0000.0000.0000.000
10A13SER0-0.070-0.07622.001-0.628-0.6280.0000.0000.0000.000
11A14PHE0-0.036-0.02925.199-0.104-0.1040.0000.0000.0000.000
12A15VAL0-0.0130.00228.621-0.219-0.2190.0000.0000.0000.000
13A16ASP-1-0.802-0.88131.0158.6798.6790.0000.0000.0000.000
14A17SER0-0.059-0.04934.442-0.072-0.0720.0000.0000.0000.000
15A18SER0-0.015-0.05437.2250.0070.0070.0000.0000.0000.000
16A19PHE00.0390.02632.123-0.062-0.0620.0000.0000.0000.000
17A20PHE00.034-0.00631.544-0.013-0.0130.0000.0000.0000.000
18A21HIS0-0.0350.01037.072-0.249-0.2490.0000.0000.0000.000
19A22GLU-1-0.805-0.88538.1787.6927.6920.0000.0000.0000.000
20A23LEU0-0.043-0.01734.617-0.066-0.0660.0000.0000.0000.000
21A24SER0-0.068-0.07538.335-0.121-0.1210.0000.0000.0000.000
22A25ARG10.7820.86841.490-7.788-7.7880.0000.0000.0000.000
23A26LEU00.0880.05338.624-0.080-0.0800.0000.0000.0000.000
24A27LYS10.7510.90238.330-8.249-8.2490.0000.0000.0000.000
25A28LEU0-0.074-0.05141.959-0.114-0.1140.0000.0000.0000.000
26A29ASP-1-0.886-0.93744.7487.0107.0100.0000.0000.0000.000
27A30ILE0-0.024-0.02445.171-0.157-0.1570.0000.0000.0000.000
28A31PHE0-0.0120.00244.7380.1780.1780.0000.0000.0000.000
29A32LYS10.8180.89538.663-8.373-8.3730.0000.0000.0000.000
30A33LEU0-0.0190.00642.0790.1180.1180.0000.0000.0000.000
31A34ASP-1-0.823-0.90239.2368.4488.4480.0000.0000.0000.000
32A35SER0-0.004-0.01435.2410.0370.0370.0000.0000.0000.000
33A36ASP-1-0.813-0.90236.3268.3438.3430.0000.0000.0000.000
34A37GLU-1-0.950-0.96731.81010.40810.4080.0000.0000.0000.000
35A38LYS10.8140.89033.521-8.653-8.6530.0000.0000.0000.000
36A39ALA0-0.031-0.00932.3430.3740.3740.0000.0000.0000.000
37A40LEU0-0.032-0.01429.201-0.193-0.1930.0000.0000.0000.000
38A41TYR00.009-0.01330.8680.2920.2920.0000.0000.0000.000
39A42THR0-0.007-0.01327.668-0.151-0.1510.0000.0000.0000.000
40A43GLN00.0050.01029.8360.1530.1530.0000.0000.0000.000
41A44LEU0-0.028-0.02224.4010.1760.1760.0000.0000.0000.000
42A45ASP-1-0.782-0.87727.99810.60310.6030.0000.0000.0000.000
43A46LEU0-0.025-0.02823.6310.3890.3890.0000.0000.0000.000
44A47ASN0-0.0520.00225.5290.3170.3170.0000.0000.0000.000
45A48GLN0-0.028-0.01226.7790.2780.2780.0000.0000.0000.000
46A49PHE0-0.0110.00720.555-0.021-0.0210.0000.0000.0000.000
47A50THR0-0.025-0.00523.641-0.425-0.4250.0000.0000.0000.000
48A51SER0-0.034-0.04121.0480.4070.4070.0000.0000.0000.000
49A52ASN0-0.015-0.00118.9140.3150.3150.0000.0000.0000.000
50A53VAL00.0130.01016.8700.9990.9990.0000.0000.0000.000
51A54LEU00.0290.02419.683-0.802-0.8020.0000.0000.0000.000
52A55ALA00.0390.00722.0090.1550.1550.0000.0000.0000.000
53A56ILE0-0.0060.01123.293-0.351-0.3510.0000.0000.0000.000
54A57SER0-0.016-0.01525.840-0.285-0.2850.0000.0000.0000.000
55A58LEU0-0.038-0.00528.052-0.016-0.0160.0000.0000.0000.000
56A59ARG10.9790.97731.486-9.647-9.6470.0000.0000.0000.000
57A60ASP-1-0.742-0.84735.3148.1278.1270.0000.0000.0000.000
58A61ASP-1-0.849-0.90635.0129.1559.1550.0000.0000.0000.000
59A62SER00.002-0.00632.3730.0620.0620.0000.0000.0000.000
60A63PHE00.001-0.01333.5370.3560.3560.0000.0000.0000.000
61A64GLN0-0.0230.01136.1110.0270.0270.0000.0000.0000.000
62A65LYS10.9090.95735.175-8.730-8.7300.0000.0000.0000.000
63A66PRO00.000-0.00734.493-0.215-0.2150.0000.0000.0000.000
64A67ASP-1-0.850-0.92937.4878.2088.2080.0000.0000.0000.000
65A68ASN0-0.121-0.08133.3190.0460.0460.0000.0000.0000.000
66A69ASP-1-0.898-0.93636.0208.2218.2210.0000.0000.0000.000
67A70GLU-1-0.870-0.94833.8789.5559.5550.0000.0000.0000.000
68A71HIS0-0.0410.00735.3140.3250.3250.0000.0000.0000.000
69A72ASN0-0.012-0.03633.2700.3280.3280.0000.0000.0000.000
70A73ILE00.0250.03927.009-0.007-0.0070.0000.0000.0000.000
71A74ILE0-0.028-0.00830.2780.0130.0130.0000.0000.0000.000
72A75LEU0-0.0130.01023.4860.2170.2170.0000.0000.0000.000
73A76LYS10.9140.95227.744-10.620-10.6200.0000.0000.0000.000
74A77GLY00.0270.01626.7940.6440.6440.0000.0000.0000.000
75A78TYR00.0020.00026.965-0.790-0.7900.0000.0000.0000.000
76A79LEU0-0.014-0.00628.3960.3780.3780.0000.0000.0000.000
77A80LEU00.0590.02830.171-0.219-0.2190.0000.0000.0000.000
78A81ASN0-0.0110.01031.4580.2560.2560.0000.0000.0000.000
79A82PHE00.0590.00329.872-0.220-0.2200.0000.0000.0000.000
80A83ASN00.0350.00734.8760.0990.0990.0000.0000.0000.000
81A84THR0-0.032-0.03637.250-0.145-0.1450.0000.0000.0000.000
82A85ILE00.0180.01133.8500.3250.3250.0000.0000.0000.000
83A86GLU-1-0.857-0.92034.3508.6648.6640.0000.0000.0000.000
84A87LEU00.0260.01734.0880.3330.3330.0000.0000.0000.000
85A88PHE0-0.0050.01828.7050.3340.3340.0000.0000.0000.000
86A89LYS10.9090.95829.956-8.911-8.9110.0000.0000.0000.000
87A90ASN00.0160.00029.3090.5760.5760.0000.0000.0000.000
88A91CYS0-0.0360.01928.2740.3320.3320.0000.0000.0000.000
89A92ASN00.0420.02224.6420.8840.8840.0000.0000.0000.000
90A93LYS10.8860.91822.532-11.699-11.6990.0000.0000.0000.000
91A94ILE0-0.0030.01217.9790.5480.5480.0000.0000.0000.000
92A95GLN00.010-0.01020.8150.9370.9370.0000.0000.0000.000
93A96PHE00.0450.02223.4760.1230.1230.0000.0000.0000.000
94A97ILE00.015-0.00617.5440.1050.1050.0000.0000.0000.000
95A98LYS10.8790.93719.175-13.843-13.8430.0000.0000.0000.000
96A99GLU-1-0.822-0.88920.17312.29812.2980.0000.0000.0000.000
97A100LYS10.8510.92122.539-12.197-12.1970.0000.0000.0000.000
98A101GLY0-0.007-0.00618.7140.2080.2080.0000.0000.0000.000
99A102GLN0-0.025-0.02919.5630.1860.1860.0000.0000.0000.000
100A103GLU-1-0.827-0.89521.60512.26212.2620.0000.0000.0000.000
101A104LEU0-0.033-0.00420.332-0.218-0.2180.0000.0000.0000.000
102A105LEU0-0.025-0.01817.3440.1700.1700.0000.0000.0000.000
103A106GLN0-0.033-0.03220.2820.2530.2530.0000.0000.0000.000
104A107ARG10.9140.92923.809-11.565-11.5650.0000.0000.0000.000
105A108GLY0-0.004-0.01521.285-0.280-0.2800.0000.0000.0000.000
106A109LEU0-0.070-0.03720.8660.0370.0370.0000.0000.0000.000
107A110GLU-1-0.874-0.91823.09411.17311.1730.0000.0000.0000.000
108A111ASN0-0.080-0.04526.270-0.768-0.7680.0000.0000.0000.000
109A112ASP-1-0.784-0.91825.41112.29612.2960.0000.0000.0000.000
110A113LEU00.0200.01418.9110.2910.2910.0000.0000.0000.000
111A114ASN0-0.057-0.06321.6960.4970.4970.0000.0000.0000.000
112A115GLU-1-0.845-0.89324.06911.62411.6240.0000.0000.0000.000
113A116ILE0-0.046-0.00117.8290.1330.1330.0000.0000.0000.000
114A117ILE0-0.016-0.00518.6291.0041.0040.0000.0000.0000.000
115A118SER00.004-0.01321.314-0.864-0.8640.0000.0000.0000.000
116A119PHE0-0.0010.00021.8720.8090.8090.0000.0000.0000.000
117A120TYR00.015-0.01323.077-0.549-0.5490.0000.0000.0000.000
118A121MET0-0.037-0.00224.3330.4830.4830.0000.0000.0000.000
119A122ILE0-0.0010.00926.026-0.306-0.3060.0000.0000.0000.000
120A123SER0-0.012-0.05228.7030.2000.2000.0000.0000.0000.000
121A124PHE0-0.049-0.01231.452-0.130-0.1300.0000.0000.0000.000
122A125ALA00.0650.03334.821-0.012-0.0120.0000.0000.0000.000
123A126ASP-1-0.778-0.88037.4337.7917.7910.0000.0000.0000.000
124A127LEU00.0520.00639.766-0.118-0.1180.0000.0000.0000.000
125A128LYS10.9420.98342.760-6.965-6.9650.0000.0000.0000.000
126A129LYS10.7840.87140.590-7.997-7.9970.0000.0000.0000.000
127A130TYR00.0460.03142.0970.0860.0860.0000.0000.0000.000
128A131LYS10.7970.89837.442-7.770-7.7700.0000.0000.0000.000
129A132PHE00.0170.01834.911-0.001-0.0010.0000.0000.0000.000
130A133TYR0-0.020-0.01231.7440.3030.3030.0000.0000.0000.000
131A134TYR00.0240.00027.2680.0260.0260.0000.0000.0000.000
132A135TRP0-0.029-0.03220.846-0.017-0.0170.0000.0000.0000.000
133A136ILE00.0560.04223.218-0.239-0.2390.0000.0000.0000.000
134A137CYS0-0.052-0.02219.5130.6720.6720.0000.0000.0000.000
135A138MET00.0430.02818.508-0.503-0.5030.0000.0000.0000.000
136A139PRO0-0.044-0.00517.1611.2431.2430.0000.0000.0000.000
137A140SER0-0.005-0.00111.8210.7740.7740.0000.0000.0000.000
138A141PHE00.008-0.00613.3011.0501.0500.0000.0000.0000.000
139A142GLN00.0160.0207.7922.0502.0500.0000.0000.0000.000
140A143SER00.0050.00811.562-1.404-1.4040.0000.0000.0000.000
141A144ASP-1-0.886-0.97310.79627.58827.5880.0000.0000.0000.000
142A145GLY00.0040.0079.714-1.032-1.0320.0000.0000.0000.000
143A146ALA0-0.054-0.0117.7792.7022.7020.0000.0000.0000.000
144A147THR0-0.041-0.0212.545-5.273-2.2011.964-2.103-2.9330.028
145A148TYR00.0380.0162.073-23.706-22.5093.900-2.457-2.6410.036
146A149GLN00.0150.0251.993-5.303-5.96112.664-5.856-6.1510.008
147A150ILE00.0140.0103.850-4.938-4.7520.005-0.053-0.1380.000
148A151ILE0-0.0260.0006.4610.6540.6540.0000.0000.0000.000
149A152SER00.0050.0019.003-1.756-1.7560.0000.0000.0000.000
150A153SER0-0.012-0.01410.8070.6770.6770.0000.0000.0000.000
151A154LYS10.8760.94312.508-16.606-16.6060.0000.0000.0000.000
152A155VAL00.0480.02115.8800.4940.4940.0000.0000.0000.000
153A156ILE0-0.069-0.02418.219-0.259-0.2590.0000.0000.0000.000
154A157ALA00.0330.03420.855-0.014-0.0140.0000.0000.0000.000
155A158SER00.012-0.02624.4510.1140.1140.0000.0000.0000.000
156A159ASP-1-0.886-0.95225.63110.27410.2740.0000.0000.0000.000
157A160SER0-0.042-0.00826.565-0.253-0.2530.0000.0000.0000.000
158A161ASP-1-0.858-0.93428.5409.5449.5440.0000.0000.0000.000
159A162ILE0-0.030-0.01925.477-0.040-0.0400.0000.0000.0000.000
160A163SER0-0.009-0.02025.0500.3200.3200.0000.0000.0000.000
161A164VAL00.0450.02526.6360.0450.0450.0000.0000.0000.000
162A165SER0-0.044-0.02029.800-0.248-0.2480.0000.0000.0000.000
163A166PHE00.0380.01822.180-0.156-0.1560.0000.0000.0000.000
164A167ILE0-0.012-0.00726.5410.0340.0340.0000.0000.0000.000
165A168LYS10.8280.92428.917-9.757-9.7570.0000.0000.0000.000
166A169GLN0-0.030-0.01028.8180.0440.0440.0000.0000.0000.000
167A170ASN00.003-0.01629.7950.5240.5240.0000.0000.0000.000
168A171VAL0-0.044-0.00426.7400.2020.2020.0000.0000.0000.000
169A172ILE00.0400.02022.0110.0710.0710.0000.0000.0000.000
170A173ILE0-0.020-0.01119.2770.7250.7250.0000.0000.0000.000
171A174ALA00.0110.01122.540-0.755-0.7550.0000.0000.0000.000
172A175CYS0-0.046-0.01322.1610.7480.7480.0000.0000.0000.000
173A176VAL0-0.014-0.00222.926-0.555-0.5550.0000.0000.0000.000
174A177ILE00.0320.01624.5590.3410.3410.0000.0000.0000.000
175A178SER0-0.041-0.03327.395-0.522-0.5220.0000.0000.0000.000
176A179GLY0-0.023-0.00827.345-0.360-0.3600.0000.0000.0000.000
177A180VAL0-0.028-0.01628.325-0.063-0.0630.0000.0000.0000.000
178A181ILE0-0.018-0.00625.9300.2480.2480.0000.0000.0000.000
179A182GLN0-0.012-0.00627.195-0.457-0.4570.0000.0000.0000.000
180A183LYS11.0031.00126.828-9.525-9.5250.0000.0000.0000.000
181A184ALA00.0420.04322.690-0.015-0.0150.0000.0000.0000.000
182A185THR00.0540.01524.2400.4140.4140.0000.0000.0000.000
183A186PRO00.0540.01824.5170.2220.2220.0000.0000.0000.000
184A187ASP-1-0.842-0.91725.04111.43711.4370.0000.0000.0000.000
185A188ASN0-0.003-0.00826.827-0.214-0.2140.0000.0000.0000.000
186A189LEU00.016-0.01620.4110.2620.2620.0000.0000.0000.000
187A190LYS10.8000.90322.181-11.264-11.2640.0000.0000.0000.000
188A191VAL0-0.0090.00023.9290.1980.1980.0000.0000.0000.000
189A192CYS0-0.0990.00021.8910.1920.1920.0000.0000.0000.000
190A193GLU-1-0.752-0.86922.08912.51112.5110.0000.0000.0000.000
191A194LYS10.8160.89218.488-13.383-13.3830.0000.0000.0000.000
192A195VAL00.0430.02617.502-0.823-0.8230.0000.0000.0000.000
193A196VAL0-0.044-0.02318.8070.3920.3920.0000.0000.0000.000
194A197PHE00.007-0.01515.727-0.196-0.1960.0000.0000.0000.000
195A198LYS10.8090.91419.565-11.731-11.7310.0000.0000.0000.000
196A199ASP-1-0.688-0.82015.62820.40920.4090.0000.0000.0000.000
197A200PHE00.007-0.01717.889-0.764-0.7640.0000.0000.0000.000
198A201SER0-0.079-0.06214.589-0.182-0.1820.0000.0000.0000.000
199A202HIS00.0900.04417.4910.4510.4510.0000.0000.0000.000
200A203LEU0-0.030-0.00614.239-0.127-0.1270.0000.0000.0000.000
201A204LYS10.8550.91813.919-17.260-17.2600.0000.0000.0000.000
202A205ASP-1-0.853-0.91110.08620.67820.6780.0000.0000.0000.000
203A206ILE0-0.0230.0089.1542.6372.6370.0000.0000.0000.000
204A207PRO00.0180.0339.557-1.811-1.8110.0000.0000.0000.000
205A208SER0-0.023-0.03111.7121.6961.6960.0000.0000.0000.000
206A209ALA00.0040.00310.9190.9910.9910.0000.0000.0000.000
207A210VAL0-0.0160.00811.9161.3051.3050.0000.0000.0000.000
208A211THR00.028-0.00511.050-0.932-0.9320.0000.0000.0000.000
209A212LYS10.8370.9327.475-36.189-36.1890.0000.0000.0000.000
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