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: 76ZVK

Calculation Name: 2BDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BDV

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646703.872142
FMO2-HF: Nuclear repulsion 2562495.458032
FMO2-HF: Total energy -84208.41411
FMO2-MP2: Total energy -84457.884381


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-35.129-30.41534.972-17.771-21.916-0.109
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.019
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].
3A4ARG10.7730.8753.344-4.779-0.602-0.027-2.258-1.8930.008
4A5ILE00.0580.0293.4790.4871.2760.412-0.219-0.9820.000
5A6ALA0-0.029-0.0175.843-0.624-0.637-0.001-0.0060.0200.000
6A7GLN0-0.028-0.0199.244-0.056-0.0560.0000.0000.0000.000
7A8LYS10.8120.87411.740-0.355-0.3550.0000.0000.0000.000
8A9SER0-0.006-0.02514.678-0.078-0.0780.0000.0000.0000.000
9A10ALA00.0110.02616.7380.0400.0400.0000.0000.0000.000
10A11PRO00.016-0.00617.6010.0200.0200.0000.0000.0000.000
11A12GLU-1-0.890-0.96218.6780.2400.2400.0000.0000.0000.000
12A13ASP-1-0.868-0.93318.3860.2110.2110.0000.0000.0000.000
13A14TYR0-0.077-0.06712.9310.0410.0410.0000.0000.0000.000
14A15VAL00.0400.00316.819-0.003-0.0030.0000.0000.0000.000
15A16GLU-1-0.892-0.92819.6760.1320.1320.0000.0000.0000.000
16A17ILE0-0.001-0.00316.377-0.021-0.0210.0000.0000.0000.000
17A18LEU0-0.015-0.01116.342-0.017-0.0170.0000.0000.0000.000
18A19TRP0-0.045-0.02418.743-0.016-0.0160.0000.0000.0000.000
19A20PRO00.0130.01321.931-0.005-0.0050.0000.0000.0000.000
20A21ASN0-0.095-0.04024.390-0.008-0.0080.0000.0000.0000.000
21A22ALA00.0560.01325.679-0.007-0.0070.0000.0000.0000.000
22A23ARG10.9160.97025.358-0.125-0.1250.0000.0000.0000.000
23A24LEU00.0080.00921.601-0.001-0.0010.0000.0000.0000.000
24A25ILE0-0.012-0.00125.610-0.003-0.0030.0000.0000.0000.000
25A26PHE0-0.018-0.01023.268-0.005-0.0050.0000.0000.0000.000
26A27ASP-1-0.910-0.96021.7570.2440.2440.0000.0000.0000.000
27A28ASP-1-0.815-0.89219.3430.4090.4090.0000.0000.0000.000
28A29VAL00.0350.03421.716-0.008-0.0080.0000.0000.0000.000
29A30ALA00.0180.00619.677-0.006-0.0060.0000.0000.0000.000
30A31GLY0-0.0080.01120.3790.0010.0010.0000.0000.0000.000
31A32PRO00.0180.02816.6420.0460.0460.0000.0000.0000.000
32A33ARG10.8630.91713.267-0.422-0.4220.0000.0000.0000.000
33A34TYR00.1000.06412.3310.1000.1000.0000.0000.0000.000
34A35ASN00.0520.04910.8250.0630.0630.0000.0000.0000.000
35A36ILE00.0030.0128.734-0.123-0.1230.0000.0000.0000.000
36A37PRO0-0.0110.0087.9240.4490.4490.0000.0000.0000.000
37A38PRO00.006-0.0156.538-0.043-0.0430.0000.0000.0000.000
38A39GLY00.0070.0029.093-0.113-0.1130.0000.0000.0000.000
39A40THR0-0.022-0.00211.370-0.076-0.0760.0000.0000.0000.000
40A41ARG10.9350.97112.880-0.380-0.3800.0000.0000.0000.000
41A42PRO0-0.0030.0119.483-0.068-0.0680.0000.0000.0000.000
42A43LEU00.0350.01412.207-0.067-0.0670.0000.0000.0000.000
43A44THR0-0.047-0.02311.8970.1350.1350.0000.0000.0000.000
44A45MET00.0060.01013.724-0.087-0.0870.0000.0000.0000.000
45A46HIS0-0.027-0.02615.5600.0000.0000.0000.0000.0000.000
46A47ARG11.0091.00618.130-0.191-0.1910.0000.0000.0000.000
47A48LEU0-0.069-0.03416.869-0.021-0.0210.0000.0000.0000.000
48A49VAL0-0.048-0.03521.264-0.016-0.0160.0000.0000.0000.000
49A50ASP-1-0.890-0.94324.6390.1430.1430.0000.0000.0000.000
50A51GLN0-0.045-0.02724.994-0.007-0.0070.0000.0000.0000.000
51A52ALA00.0290.03325.757-0.002-0.0020.0000.0000.0000.000
52A53GLU-1-0.918-0.95522.3600.1950.1950.0000.0000.0000.000
53A54ALA0-0.023-0.01421.023-0.009-0.0090.0000.0000.0000.000
54A55LEU00.0220.00516.7720.0420.0420.0000.0000.0000.000
55A56ALA00.0050.00617.694-0.030-0.0300.0000.0000.0000.000
56A57ARG10.7880.85514.849-0.452-0.4520.0000.0000.0000.000
57A58LEU0-0.018-0.00114.044-0.061-0.0610.0000.0000.0000.000
58A59PRO00.006-0.01113.3580.0890.0890.0000.0000.0000.000
59A60TRP0-0.0390.0183.475-0.3350.1060.008-0.090-0.3580.000
60A61GLY00.014-0.0179.647-0.019-0.0190.0000.0000.0000.000
61A62TYR0-0.054-0.01810.451-0.108-0.1080.0000.0000.0000.000
62A63LYS10.9460.97312.653-0.267-0.2670.0000.0000.0000.000
63A64PRO0-0.078-0.01915.374-0.026-0.0260.0000.0000.0000.000
64A65HIS00.0580.00318.0900.0000.0000.0000.0000.0000.000
65A66GLY00.0260.02421.672-0.008-0.0080.0000.0000.0000.000
66A67SER0-0.053-0.03818.997-0.019-0.0190.0000.0000.0000.000
67A68SER00.0230.02519.1030.0080.0080.0000.0000.0000.000
68A69PHE0-0.016-0.00714.4460.0140.0140.0000.0000.0000.000
69A70PHE00.0210.01410.5320.0040.0040.0000.0000.0000.000
70A71MET0-0.038-0.0169.9700.0850.0850.0000.0000.0000.000
71A72ILE00.0900.0415.044-0.072-0.0720.0000.0000.0000.000
72A73ASN0-0.047-0.0212.1233.2654.2371.822-0.989-1.805-0.001
73A74ALA00.0050.0015.485-0.126-0.1260.0000.0000.0000.000
74A75LYS10.9090.9578.5310.2700.2700.0000.0000.0000.000
75A76LEU00.1060.0549.4020.0910.0910.0000.0000.0000.000
76A77GLU-1-0.814-0.89711.219-0.188-0.1880.0000.0000.0000.000
77A78THR0-0.022-0.00513.3770.0270.0270.0000.0000.0000.000
78A79ILE00.0050.00710.9840.0430.0430.0000.0000.0000.000
79A80GLU-1-0.837-0.91015.188-0.083-0.0830.0000.0000.0000.000
80A81ARG10.7730.87317.3630.1810.1810.0000.0000.0000.000
81A82HIS00.0260.02318.6760.0130.0130.0000.0000.0000.000
82A83GLY00.0200.00217.9830.0040.0040.0000.0000.0000.000
83A84TRP0-0.0490.00017.5820.0230.0230.0000.0000.0000.000
84A85PRO00.051-0.00514.293-0.019-0.0190.0000.0000.0000.000
85A86TRP00.1420.02910.5610.0160.0160.0000.0000.0000.000
86A87LYS10.9240.97615.350-0.057-0.0570.0000.0000.0000.000
87A88LEU0-0.038-0.02818.402-0.010-0.0100.0000.0000.0000.000
88A89MET0-0.054-0.01114.5780.0210.0210.0000.0000.0000.000
89A90ILE0-0.0020.01415.4180.0140.0140.0000.0000.0000.000
90A91GLY0-0.014-0.00617.310-0.007-0.0070.0000.0000.0000.000
91A92THR00.0360.00620.2230.0070.0070.0000.0000.0000.000
92A93GLY00.0280.01116.8490.0060.0060.0000.0000.0000.000
93A94ARG10.8050.89814.669-0.113-0.1130.0000.0000.0000.000
94A95ILE0-0.0080.00211.068-0.022-0.0220.0000.0000.0000.000
95A96LEU00.0230.01311.5740.0210.0210.0000.0000.0000.000
96A97VAL0-0.032-0.0197.635-0.028-0.0280.0000.0000.0000.000
97A98PRO0-0.0100.0158.6250.2260.2260.0000.0000.0000.000
98A99ALA00.0350.0137.1530.2220.2220.0000.0000.0000.000
99A100ASP-1-0.727-0.8038.9950.3300.3300.0000.0000.0000.000
100A101GLY00.000-0.0117.363-0.252-0.2520.0000.0000.0000.000
101A102TRP0-0.074-0.0522.813-2.106-0.3982.065-1.214-2.560-0.014
102A103TYR0-0.078-0.0704.733-0.810-0.695-0.001-0.021-0.0920.000
103A104GLU-1-0.714-0.8003.997-4.220-3.8580.001-0.074-0.2900.000
104A105TRP0-0.030-0.0235.4040.4100.4100.0000.0000.0000.000
105A106LYS10.9610.9888.8680.5300.5300.0000.0000.0000.000
106A107ALA0-0.031-0.02811.3730.1170.1170.0000.0000.0000.000
107A108LEU0-0.012-0.00613.407-0.015-0.0150.0000.0000.0000.000
108A109ASP-1-0.846-0.91716.924-0.214-0.2140.0000.0000.0000.000
109A110SER0-0.032-0.02317.152-0.028-0.0280.0000.0000.0000.000
110A111GLY00.0350.02519.0570.0140.0140.0000.0000.0000.000
111A112PRO0-0.008-0.02018.460-0.019-0.0190.0000.0000.0000.000
112A113LYS10.9140.95216.9040.0500.0500.0000.0000.0000.000
113A114PRO00.0290.04714.7530.0130.0130.0000.0000.0000.000
114A115ALA00.0300.01815.904-0.003-0.0030.0000.0000.0000.000
115A116LYS10.8960.9439.6590.5810.5810.0000.0000.0000.000
116A117GLN0-0.005-0.00513.7440.0830.0830.0000.0000.0000.000
117A118PRO0-0.0120.00610.419-0.144-0.1440.0000.0000.0000.000
118A119TYR00.0480.0189.5130.1200.1200.0000.0000.0000.000
119A120TYR00.0030.0008.710-0.082-0.0820.0000.0000.0000.000
120A121ILE00.0020.0015.9700.0420.0420.0000.0000.0000.000
121A122HIS10.8620.9117.8100.2700.2700.0000.0000.0000.000
122A123GLY00.0830.0449.952-0.105-0.1050.0000.0000.0000.000
123A124ASP-1-0.898-0.92912.485-0.045-0.0450.0000.0000.0000.000
124A125ALA0-0.020-0.01514.3460.0140.0140.0000.0000.0000.000
125A126PRO0-0.036-0.00612.6710.0170.0170.0000.0000.0000.000
126A127LEU0-0.020-0.0097.408-0.088-0.0880.0000.0000.0000.000
127A128LEU00.0230.00610.4690.1630.1630.0000.0000.0000.000
128A129PHE0-0.019-0.0084.052-0.3430.2500.075-0.202-0.466-0.002
129A130ALA00.0870.0558.113-0.056-0.0560.0000.0000.0000.000
130A131GLY0-0.001-0.0038.1640.1770.1770.0000.0000.0000.000
131A132LEU0-0.034-0.0119.715-0.136-0.1360.0000.0000.0000.000
132A133SER00.0540.02011.4530.0540.0540.0000.0000.0000.000
133A134ALA00.0290.02313.893-0.056-0.0560.0000.0000.0000.000
134A135TRP0-0.029-0.01616.542-0.029-0.0290.0000.0000.0000.000
135A136ARG10.8430.90817.727-0.264-0.2640.0000.0000.0000.000
136A137ARG11.0551.01821.798-0.153-0.1530.0000.0000.0000.000
137A138GLY0-0.054-0.02024.779-0.013-0.0130.0000.0000.0000.000
138A139ALA0-0.0280.00522.020-0.008-0.0080.0000.0000.0000.000
139A140GLU-1-0.876-0.93322.8550.2160.2160.0000.0000.0000.000
140A141LEU0-0.050-0.03118.6180.0230.0230.0000.0000.0000.000
141A142ASP-1-0.759-0.87918.7480.2950.2950.0000.0000.0000.000
142A143GLU-1-0.842-0.94715.4460.3450.3450.0000.0000.0000.000
143A144ALA0-0.049-0.00515.8860.0170.0170.0000.0000.0000.000
144A145HIS10.7670.86017.404-0.283-0.2830.0000.0000.0000.000
145A146GLY00.0560.04213.3770.0160.0160.0000.0000.0000.000
146A147PHE0-0.049-0.0387.470-0.059-0.0590.0000.0000.0000.000
147A148ALA0-0.008-0.0017.2100.0830.0830.0000.0000.0000.000
148A149ILE0-0.021-0.0103.211-0.948-0.1980.081-0.175-0.6550.000
149A150VAL00.0170.0015.273-0.304-0.3040.0000.0000.0000.000
150A151THR00.0010.0052.819-0.3640.3740.231-0.242-0.7280.000
151A152ASN00.000-0.0125.5250.5810.5810.0000.0000.0000.000
152A153ASP-1-0.827-0.9476.986-0.980-0.9800.0000.0000.0000.000
153A154ALA0-0.0130.0168.007-0.034-0.0340.0000.0000.0000.000
154A155LEU0-0.020-0.0119.8200.1030.1030.0000.0000.0000.000
155A156GLY00.0240.0257.3840.0260.0260.0000.0000.0000.000
156A157GLY0-0.009-0.0055.395-0.637-0.6370.0000.0000.0000.000
157A158MET0-0.063-0.0406.2690.7210.7210.0000.0000.0000.000
158A159VAL0-0.066-0.0378.2300.4170.4170.0000.0000.0000.000
159A160ASP-1-0.883-0.9536.703-1.373-1.3730.0000.0000.0000.000
160A161VAL00.0240.0087.379-0.468-0.4680.0000.0000.0000.000
161A162HIS0-0.088-0.0408.3240.1950.1950.0000.0000.0000.000
162A163ASP-1-0.864-0.9171.771-13.141-20.02716.351-5.831-3.634-0.061
163A164ARG10.8380.9142.659-0.3961.2930.285-0.840-1.1340.004
164A165ARG10.9090.9661.966-10.367-10.0666.540-3.560-3.282-0.041
165A166PRO0-0.019-0.0122.1500.273-1.4647.061-1.794-3.530-0.004
166A167VAL00.008-0.0054.098-0.277-0.1040.010-0.055-0.1270.000
167A168ALA00.0040.0097.8010.3670.3670.0000.0000.0000.000
168A169LEU0-0.0040.0029.487-0.167-0.1670.0000.0000.0000.000
169A170PRO00.0550.02913.0840.0490.0490.0000.0000.0000.000
170A171PRO00.0730.02116.2310.0240.0240.0000.0000.0000.000
171A172GLU-1-0.927-0.96617.9100.0760.0760.0000.0000.0000.000
172A173LEU00.0180.00317.1210.0020.0020.0000.0000.0000.000
173A174ALA0-0.0190.00315.1210.0150.0150.0000.0000.0000.000
174A175ARG10.8820.92016.424-0.121-0.1210.0000.0000.0000.000
175A176GLU-1-0.800-0.89419.7670.0600.0600.0000.0000.0000.000
176A177TRP0-0.045-0.03312.859-0.039-0.0390.0000.0000.0000.000
177A178VAL0-0.0320.00217.2450.0080.0080.0000.0000.0000.000
178A179ASP-1-0.870-0.92718.6120.1270.1270.0000.0000.0000.000
179A180PRO0-0.037-0.01922.351-0.010-0.0100.0000.0000.0000.000
180A181ALA0-0.0100.00223.532-0.011-0.0110.0000.0000.0000.000
181A182THR0-0.053-0.01421.407-0.017-0.0170.0000.0000.0000.000
182A183PRO00.0300.01823.0930.0080.0080.0000.0000.0000.000
183A184VAL00.0500.00520.083-0.001-0.0010.0000.0000.0000.000
184A185ALA0-0.039-0.01820.719-0.007-0.0070.0000.0000.0000.000
185A186ARG10.8880.93621.821-0.032-0.0320.0000.0000.0000.000
186A187ALA00.0050.00317.728-0.006-0.0060.0000.0000.0000.000
187A188LYS10.8640.92316.931-0.018-0.0180.0000.0000.0000.000
188A189GLU-1-0.908-0.94217.001-0.054-0.0540.0000.0000.0000.000
189A190ILE0-0.013-0.00215.609-0.031-0.0310.0000.0000.0000.000
190A191LEU0-0.0070.00611.830-0.011-0.0110.0000.0000.0000.000
191A192ARG10.8120.89712.5680.1070.1070.0000.0000.0000.000
192A193ALA0-0.046-0.01614.742-0.042-0.0420.0000.0000.0000.000
193A194GLY0-0.019-0.01511.6340.0440.0440.0000.0000.0000.000
194A195LEU0-0.026-0.02411.339-0.045-0.0450.0000.0000.0000.000
195A196PRO00.0150.01611.640-0.123-0.1230.0000.0000.0000.000
196A197GLU-1-0.861-0.97211.513-0.745-0.7450.0000.0000.0000.000
197A198THR0-0.017-0.00812.5190.0190.0190.0000.0000.0000.000
198A199ALA0-0.0330.00213.2490.0530.0530.0000.0000.0000.000
199A200PHE0-0.049-0.0289.3020.0210.0210.0000.0000.0000.000
200A201SER0-0.0080.01612.174-0.009-0.0090.0000.0000.0000.000
201A202TRP00.026-0.01610.511-0.057-0.0570.0000.0000.0000.000
202A203TYR0-0.035-0.00812.4120.0430.0430.0000.0000.0000.000
203A204PRO0-0.0050.01113.052-0.027-0.0270.0000.0000.0000.000
204A205VAL0-0.027-0.02312.3510.0570.0570.0000.0000.0000.000
205A206ARG10.9740.95814.9200.0880.0880.0000.0000.0000.000
206A207GLN00.0050.02416.0020.0390.0390.0000.0000.0000.000
207A208GLU-1-0.846-0.92416.587-0.024-0.0240.0000.0000.0000.000
208A209VAL00.008-0.00511.4300.0380.0380.0000.0000.0000.000
209A210GLY00.0400.01912.0990.0800.0800.0000.0000.0000.000
210A211SER00.0250.02113.134-0.045-0.0450.0000.0000.0000.000
211A212SER00.004-0.02210.221-0.112-0.1120.0000.0000.0000.000
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