Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: J3G69

Calculation Name: 1VAJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAJ

Chain ID: A

ChEMBL ID:

UniProt ID: O57770

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2411892.44313
FMO2-HF: Nuclear repulsion 2331187.922867
FMO2-HF: Total energy -80704.520263
FMO2-MP2: Total energy -80943.183614


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:PHE)


Summations of interaction energy for fragment #1(A:3:PHE)
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.
-16.048-4.5176.517-5.632-12.415-0.021
Interaction energy analysis for fragmet #1(A:3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.044
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].
3A5ILE0-0.037-0.0183.296-0.3311.6540.000-0.814-1.1710.002
4A6LYS10.8520.9133.115-0.2821.0590.111-0.669-0.784-0.006
5A7ASP-1-0.751-0.8703.873-0.571-0.0640.006-0.086-0.4270.000
6A8GLU-1-0.776-0.8716.525-1.156-1.1560.0000.0000.0000.000
7A9TRP00.002-0.0167.1500.0330.0330.0000.0000.0000.000
8A10GLY00.0690.0437.7240.1330.1330.0000.0000.0000.000
9A11GLU-1-0.860-0.9298.873-0.320-0.3200.0000.0000.0000.000
10A12PHE0-0.074-0.04011.7330.0720.0720.0000.0000.0000.000
11A13LEU00.0270.00710.1260.0680.0680.0000.0000.0000.000
12A14VAL00.0230.01912.3800.0550.0550.0000.0000.0000.000
13A15ARG10.8650.92014.1020.3890.3890.0000.0000.0000.000
14A16LEU0-0.062-0.02316.5880.0300.0300.0000.0000.0000.000
15A17ALA00.0460.02017.1910.0250.0250.0000.0000.0000.000
16A18ARG10.7410.83518.9000.1200.1200.0000.0000.0000.000
17A19ARG10.9310.96520.9810.2050.2050.0000.0000.0000.000
18A20ALA0-0.007-0.01121.8940.0120.0120.0000.0000.0000.000
19A21ILE00.0310.02322.0490.0120.0120.0000.0000.0000.000
20A22GLU-1-0.794-0.89825.138-0.096-0.0960.0000.0000.0000.000
21A23GLU-1-0.879-0.93926.595-0.095-0.0950.0000.0000.0000.000
22A24TYR00.0370.02927.6050.0070.0070.0000.0000.0000.000
23A25LEU0-0.026-0.01428.6750.0070.0070.0000.0000.0000.000
24A26LYS10.8020.92729.5030.1050.1050.0000.0000.0000.000
25A27THR0-0.077-0.07531.9730.0040.0040.0000.0000.0000.000
26A28GLY0-0.0040.01532.7010.0030.0030.0000.0000.0000.000
27A29LYS10.8730.93631.0980.0820.0820.0000.0000.0000.000
28A30GLU-1-0.790-0.88025.041-0.123-0.1230.0000.0000.0000.000
29A31ILE0-0.082-0.03722.108-0.002-0.0020.0000.0000.0000.000
30A32GLU-1-0.879-0.93724.673-0.137-0.1370.0000.0000.0000.000
31A33PRO0-0.004-0.00819.789-0.010-0.0100.0000.0000.0000.000
32A34PRO0-0.040-0.00319.1600.0160.0160.0000.0000.0000.000
33A35LYS10.9300.96020.7040.2000.2000.0000.0000.0000.000
34A36ASP-1-0.916-0.95219.340-0.287-0.2870.0000.0000.0000.000
35A37THR00.003-0.02615.956-0.040-0.0400.0000.0000.0000.000
36A38PRO0-0.0030.01112.4600.0210.0210.0000.0000.0000.000
37A39PRO00.0390.01414.6430.0060.0060.0000.0000.0000.000
38A40GLU-1-0.868-0.94810.931-0.699-0.6990.0000.0000.0000.000
39A41LEU0-0.029-0.0149.625-0.008-0.0080.0000.0000.0000.000
40A42TRP0-0.017-0.00813.2170.0800.0800.0000.0000.0000.000
41A43GLU-1-0.882-0.90211.813-0.416-0.4160.0000.0000.0000.000
42A44LYS10.8180.90815.0310.1060.1060.0000.0000.0000.000
43A45MET0-0.006-0.0018.441-0.072-0.0720.0000.0000.0000.000
44A46GLY00.0260.03613.5410.0130.0130.0000.0000.0000.000
45A47VAL0-0.026-0.02513.014-0.050-0.0500.0000.0000.0000.000
46A48PHE00.0310.01214.5540.0330.0330.0000.0000.0000.000
47A49VAL0-0.0250.00115.460-0.023-0.0230.0000.0000.0000.000
48A50THR0-0.001-0.01916.5260.0110.0110.0000.0000.0000.000
49A51LEU0-0.0080.01318.926-0.010-0.0100.0000.0000.0000.000
50A52ASN00.0110.00117.7020.0110.0110.0000.0000.0000.000
51A53ARG10.8940.91921.739-0.005-0.0050.0000.0000.0000.000
52A54TYR00.029-0.00319.9440.0040.0040.0000.0000.0000.000
53A55ASN0-0.067-0.03422.9980.0030.0030.0000.0000.0000.000
54A56VAL0-0.0140.00824.1560.0000.0000.0000.0000.0000.000
55A57PRO00.0140.00423.7120.0030.0030.0000.0000.0000.000
56A58PRO00.0880.03719.708-0.004-0.0040.0000.0000.0000.000
57A59GLN00.0080.02121.665-0.009-0.0090.0000.0000.0000.000
58A60THR0-0.104-0.06523.451-0.005-0.0050.0000.0000.0000.000
59A61ALA0-0.0050.00221.742-0.007-0.0070.0000.0000.0000.000
60A62LEU00.0190.03520.629-0.009-0.0090.0000.0000.0000.000
61A63ARG10.7260.82623.2270.0290.0290.0000.0000.0000.000
62A64GLY00.0300.02123.564-0.003-0.0030.0000.0000.0000.000
63A65CYS0-0.102-0.05418.9340.0010.0010.0000.0000.0000.000
64A66ILE00.0220.02121.1400.0090.0090.0000.0000.0000.000
65A67GLY00.0560.00318.902-0.015-0.0150.0000.0000.0000.000
66A68PHE0-0.076-0.01518.3350.0140.0140.0000.0000.0000.000
67A69PRO00.0430.02117.328-0.015-0.0150.0000.0000.0000.000
68A70THR00.0160.00616.9350.0040.0040.0000.0000.0000.000
69A71PRO00.0310.02815.691-0.019-0.0190.0000.0000.0000.000
70A72ILE0-0.008-0.01617.612-0.003-0.0030.0000.0000.0000.000
71A73TYR00.0020.00819.3980.0040.0040.0000.0000.0000.000
72A74PRO00.0100.01417.684-0.014-0.0140.0000.0000.0000.000
73A75LEU00.0400.01210.5100.0150.0150.0000.0000.0000.000
74A76VAL00.0210.00615.0730.0240.0240.0000.0000.0000.000
75A77GLU-1-0.889-0.96216.521-0.145-0.1450.0000.0000.0000.000
76A78ALA0-0.017-0.00916.9630.0250.0250.0000.0000.0000.000
77A79THR00.001-0.01515.0380.0170.0170.0000.0000.0000.000
78A80ILE0-0.031-0.00817.3550.0210.0210.0000.0000.0000.000
79A81LYS10.8530.90720.5950.1380.1380.0000.0000.0000.000
80A82ALA00.0070.01418.9840.0150.0150.0000.0000.0000.000
81A83ALA0-0.0020.01019.5570.0150.0150.0000.0000.0000.000
82A84ILE00.0100.01021.1950.0140.0140.0000.0000.0000.000
83A85TYR00.020-0.00224.1520.0080.0080.0000.0000.0000.000
84A86SER0-0.085-0.03822.1170.0100.0100.0000.0000.0000.000
85A87ALA00.0130.00024.2260.0080.0080.0000.0000.0000.000
86A88VAL0-0.061-0.04126.4910.0070.0070.0000.0000.0000.000
87A89ASP-1-0.906-0.94328.118-0.048-0.0480.0000.0000.0000.000
88A90ASP-1-0.703-0.82025.669-0.010-0.0100.0000.0000.0000.000
89A91PRO0-0.021-0.02828.3010.0020.0020.0000.0000.0000.000
90A92ARG10.7760.86923.5720.0020.0020.0000.0000.0000.000
91A93PHE0-0.031-0.01525.8010.0030.0030.0000.0000.0000.000
92A94PRO0-0.0180.00931.137-0.002-0.0020.0000.0000.0000.000
93A95PRO00.0450.01431.152-0.001-0.0010.0000.0000.0000.000
94A96VAL0-0.025-0.01127.1140.0020.0020.0000.0000.0000.000
95A97LYS10.9320.97730.4440.0300.0300.0000.0000.0000.000
96A98LEU00.0240.00129.525-0.001-0.0010.0000.0000.0000.000
97A99GLU-1-0.877-0.95530.375-0.049-0.0490.0000.0000.0000.000
98A100GLU-1-0.771-0.85829.024-0.032-0.0320.0000.0000.0000.000
99A101MET0-0.0040.01223.3980.0030.0030.0000.0000.0000.000
100A102ASP-1-0.853-0.89626.030-0.073-0.0730.0000.0000.0000.000
101A103ASN0-0.125-0.07626.9310.0030.0030.0000.0000.0000.000
102A104LEU00.0240.02523.7690.0080.0080.0000.0000.0000.000
103A105VAL0-0.0150.00118.606-0.010-0.0100.0000.0000.0000.000
104A106VAL0-0.019-0.02417.1470.0070.0070.0000.0000.0000.000
105A107GLU-1-0.790-0.88113.3650.0330.0330.0000.0000.0000.000
106A108VAL0-0.019-0.00611.942-0.008-0.0080.0000.0000.0000.000
107A109SER00.0080.00010.8530.0290.0290.0000.0000.0000.000
108A110VAL00.013-0.0018.2490.0080.0080.0000.0000.0000.000
109A111LEU0-0.015-0.0038.8720.0160.0160.0000.0000.0000.000
110A112THR00.0150.0147.795-0.055-0.0550.0000.0000.0000.000
111A113PRO0-0.033-0.03710.436-0.007-0.0070.0000.0000.0000.000
112A114PRO0-0.0050.00113.9510.0560.0560.0000.0000.0000.000
113A115GLU-1-0.923-0.95814.7620.4200.4200.0000.0000.0000.000
114A116LEU0-0.033-0.02617.6030.0000.0000.0000.0000.0000.000
115A117ILE0-0.028-0.00919.8910.0210.0210.0000.0000.0000.000
116A118GLU-1-0.942-0.96822.0070.1740.1740.0000.0000.0000.000
117A119GLY0-0.034-0.03324.8020.0080.0080.0000.0000.0000.000
118A120PRO0-0.006-0.00527.829-0.004-0.0040.0000.0000.0000.000
119A121PRO00.0630.04028.5210.0110.0110.0000.0000.0000.000
120A122GLU-1-0.851-0.94328.3060.1140.1140.0000.0000.0000.000
121A123GLU-1-0.899-0.94826.7080.1690.1690.0000.0000.0000.000
122A124ARG10.7990.88724.039-0.102-0.1020.0000.0000.0000.000
123A125PRO00.0860.03822.3800.0200.0200.0000.0000.0000.000
124A126ARG10.8460.91521.276-0.142-0.1420.0000.0000.0000.000
125A127LYS10.8090.92019.855-0.167-0.1670.0000.0000.0000.000
126A128ILE0-0.0140.00717.0980.0340.0340.0000.0000.0000.000
127A129LYS10.9160.95312.259-0.423-0.4230.0000.0000.0000.000
128A130VAL00.0520.03113.9080.0250.0250.0000.0000.0000.000
129A131GLY0-0.016-0.01011.8680.0130.0130.0000.0000.0000.000
130A132ARG10.6870.7948.985-0.471-0.4710.0000.0000.0000.000
131A133ASP-1-0.773-0.85610.4320.4260.4260.0000.0000.0000.000
132A134GLY00.0400.03713.189-0.030-0.0300.0000.0000.0000.000
133A135LEU00.001-0.01415.0590.0250.0250.0000.0000.0000.000
134A136ILE0-0.012-0.02018.075-0.023-0.0230.0000.0000.0000.000
135A137VAL00.0220.01421.2030.0130.0130.0000.0000.0000.000
136A138GLU-1-0.850-0.92724.7380.0470.0470.0000.0000.0000.000
137A139LYS10.8760.93127.374-0.054-0.0540.0000.0000.0000.000
138A140GLY0-0.0050.01331.061-0.005-0.0050.0000.0000.0000.000
139A141ILE0-0.035-0.03031.9200.0000.0000.0000.0000.0000.000
140A142TYR0-0.046-0.00431.063-0.004-0.0040.0000.0000.0000.000
141A143SER00.025-0.00325.2880.0060.0060.0000.0000.0000.000
142A144GLY00.0150.01725.089-0.008-0.0080.0000.0000.0000.000
143A145LEU0-0.036-0.00817.7390.0080.0080.0000.0000.0000.000
144A146LEU0-0.025-0.00519.520-0.014-0.0140.0000.0000.0000.000
145A147LEU00.009-0.00214.4280.0170.0170.0000.0000.0000.000
146A148PRO00.0410.01311.082-0.001-0.0010.0000.0000.0000.000
147A149GLN0-0.007-0.02312.5780.0330.0330.0000.0000.0000.000
148A150VAL0-0.0100.01013.899-0.006-0.0060.0000.0000.0000.000
149A151PRO00.0400.02515.906-0.006-0.0060.0000.0000.0000.000
150A152VAL0-0.035-0.01512.8360.0020.0020.0000.0000.0000.000
151A153GLU-1-0.943-0.96716.2450.0510.0510.0000.0000.0000.000
152A154TRP0-0.070-0.05018.279-0.013-0.0130.0000.0000.0000.000
153A155GLY0-0.061-0.00419.800-0.005-0.0050.0000.0000.0000.000
154A156TRP00.0060.00620.3160.0000.0000.0000.0000.0000.000
155A157ASP-1-0.844-0.91919.9270.1450.1450.0000.0000.0000.000
156A158GLU-1-0.846-0.94717.9420.2140.2140.0000.0000.0000.000
157A159GLU-1-0.937-0.97521.0410.1060.1060.0000.0000.0000.000
158A160GLU-1-0.872-0.93523.8470.0940.0940.0000.0000.0000.000
159A161PHE0-0.006-0.00816.545-0.008-0.0080.0000.0000.0000.000
160A162LEU0-0.0030.00721.914-0.006-0.0060.0000.0000.0000.000
161A163ALA00.0150.02023.788-0.009-0.0090.0000.0000.0000.000
162A164GLU-1-0.871-0.94523.7550.0580.0580.0000.0000.0000.000
163A165THR0-0.091-0.06221.882-0.008-0.0080.0000.0000.0000.000
164A166CYS0-0.093-0.03324.140-0.006-0.0060.0000.0000.0000.000
165A167TRP00.0260.01827.593-0.009-0.0090.0000.0000.0000.000
166A168LYS10.8950.96123.684-0.035-0.0350.0000.0000.0000.000
167A169ALA0-0.018-0.01226.990-0.007-0.0070.0000.0000.0000.000
168A170GLY0-0.059-0.01828.400-0.005-0.0050.0000.0000.0000.000
169A171LEU0-0.050-0.02830.028-0.002-0.0020.0000.0000.0000.000
170A172PRO00.004-0.00331.9590.0000.0000.0000.0000.0000.000
171A173PRO00.0390.00130.2140.0040.0040.0000.0000.0000.000
172A174ASP-1-0.873-0.93329.7660.0710.0710.0000.0000.0000.000
173A175CYS0-0.013-0.00630.7270.0000.0000.0000.0000.0000.000
174A176TRP00.0490.01326.8970.0040.0040.0000.0000.0000.000
175A177LEU0-0.0130.01128.8360.0080.0080.0000.0000.0000.000
176A178ASP-1-0.851-0.91831.5160.0650.0650.0000.0000.0000.000
177A179GLU-1-0.916-0.96631.2680.0800.0800.0000.0000.0000.000
178A180ASP-1-0.940-0.97431.3990.0640.0640.0000.0000.0000.000
179A181THR0-0.100-0.03727.927-0.007-0.0070.0000.0000.0000.000
180A182LYS10.8450.93525.631-0.063-0.0630.0000.0000.0000.000
181A183VAL00.0370.00921.821-0.006-0.0060.0000.0000.0000.000
182A184TYR0-0.044-0.03919.1400.0140.0140.0000.0000.0000.000
183A185LYS10.9000.98215.734-0.391-0.3910.0000.0000.0000.000
184A186PHE0-0.034-0.01112.6850.0030.0030.0000.0000.0000.000
185A187THR00.0360.0158.3930.0820.0820.0000.0000.0000.000
186A188ALA00.032-0.0078.479-0.077-0.0770.0000.0000.0000.000
187A189GLU-1-0.812-0.8742.768-8.481-4.8361.194-2.223-2.615-0.022
188A190ILE0-0.0040.0016.147-0.124-0.1240.0000.0000.0000.000
189A191PHE0-0.0210.0014.6340.1620.307-0.001-0.002-0.1410.000
190A192GLU-1-0.782-0.88410.477-0.019-0.0190.0000.0000.0000.000
191A193GLU-1-0.748-0.83513.534-0.109-0.1090.0000.0000.0000.000
192A194GLU-1-0.805-0.89714.302-0.059-0.0590.0000.0000.0000.000
193A195TYR0-0.023-0.01916.5030.0090.0090.0000.0000.0000.000
194A196PRO0-0.0150.00020.104-0.014-0.0140.0000.0000.0000.000
195A197ARG10.7410.84721.2580.0910.0910.0000.0000.0000.000
196A198GLY00.0160.01819.561-0.008-0.0080.0000.0000.0000.000
197A199PRO0-0.084-0.04114.969-0.019-0.0190.0000.0000.0000.000
198A200ILE0-0.0220.00411.7200.0210.0210.0000.0000.0000.000
199A201LYS10.8090.8899.5100.0540.0540.0000.0000.0000.000
200A202ARG10.7710.8532.567-5.070-1.1625.207-1.838-7.2770.005
201A203LYS10.7900.8617.309-0.157-0.1570.0000.0000.0000.000
202A204PRO0-0.031-0.0105.0520.0220.0220.0000.0000.0000.000
203A205LEU00.0090.0126.752-0.051-0.0510.0000.0000.0000.000