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: 1N6RZ

Calculation Name: 2CVB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CVB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SKQ0

Base Structure: X-ray

Registration Date: 2023-09-22

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2150524.117187
FMO2-HF: Nuclear repulsion 2076518.546654
FMO2-HF: Total energy -74005.570533
FMO2-MP2: Total energy -74223.504758


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:LEU)


Summations of interaction energy for fragment #1(A:2: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.
-15.441-5.1817.734-6.583-11.41-0.038
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : 0.006
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].
3A4TYR00.007-0.0043.814-1.2881.350-0.029-1.325-1.2840.005
4A5PRO00.0310.0342.478-1.3690.1190.842-0.363-1.9660.001
5A6GLU-1-0.763-0.8544.421-0.179-0.0660.000-0.025-0.0880.000
6A7LEU0-0.034-0.0166.9230.0190.0190.0000.0000.0000.000
7A8PRO00.0050.0127.4290.0320.0320.0000.0000.0000.000
8A9LEU00.0480.0229.603-0.022-0.0220.0000.0000.0000.000
9A10GLU-1-0.793-0.89312.7980.0120.0120.0000.0000.0000.000
10A11SER0-0.064-0.03111.619-0.010-0.0100.0000.0000.0000.000
11A12PRO00.036-0.00313.706-0.001-0.0010.0000.0000.0000.000
12A13LEU0-0.0100.01215.858-0.023-0.0230.0000.0000.0000.000
13A14ILE0-0.0370.00013.040-0.004-0.0040.0000.0000.0000.000
14A15ASP-1-0.763-0.86817.698-0.134-0.1340.0000.0000.0000.000
15A16ALA0-0.006-0.01120.626-0.023-0.0230.0000.0000.0000.000
16A17GLU-1-0.854-0.89722.818-0.113-0.1130.0000.0000.0000.000
17A18LEU0-0.0120.00222.878-0.010-0.0100.0000.0000.0000.000
18A19PRO00.0000.00127.2340.0110.0110.0000.0000.0000.000
19A20ASP-1-0.704-0.81929.690-0.104-0.1040.0000.0000.0000.000
20A21PRO0-0.047-0.03230.9730.0040.0040.0000.0000.0000.000
21A22ARG10.7670.86633.3990.0880.0880.0000.0000.0000.000
22A23GLY0-0.028-0.00935.7240.0060.0060.0000.0000.0000.000
23A24GLY0-0.023-0.01035.7690.0000.0000.0000.0000.0000.000
24A25ARG10.7980.85928.2900.1290.1290.0000.0000.0000.000
25A26TYR00.0140.00629.4540.0080.0080.0000.0000.0000.000
26A27ARG10.9330.97126.4250.1170.1170.0000.0000.0000.000
27A28LEU0-0.007-0.00721.3340.0090.0090.0000.0000.0000.000
28A29SER0-0.038-0.05624.6670.0120.0120.0000.0000.0000.000
29A30GLN0-0.0190.00026.0430.0030.0030.0000.0000.0000.000
30A31PHE0-0.027-0.00527.1240.0070.0070.0000.0000.0000.000
31A32HIS00.0220.01528.3040.0000.0000.0000.0000.0000.000
32A33GLU-1-0.915-0.93929.843-0.056-0.0560.0000.0000.0000.000
33A34PRO00.0300.01728.764-0.004-0.0040.0000.0000.0000.000
34A35LEU00.0210.01925.226-0.001-0.0010.0000.0000.0000.000
35A36LEU0-0.0090.00523.160-0.002-0.0020.0000.0000.0000.000
36A37ALA00.0210.00922.900-0.002-0.0020.0000.0000.0000.000
37A38VAL00.0180.01120.1480.0000.0000.0000.0000.0000.000
38A39VAL0-0.008-0.01820.691-0.004-0.0040.0000.0000.0000.000
39A40PHE00.0310.03517.497-0.003-0.0030.0000.0000.0000.000
40A41MET0-0.026-0.04420.9510.0120.0120.0000.0000.0000.000
41A42CYS0-0.053-0.01423.749-0.010-0.0100.0000.0000.0000.000
42A43ASN00.0430.02826.3410.0090.0090.0000.0000.0000.000
43A44HIS0-0.053-0.05724.7010.0080.0080.0000.0000.0000.000
44A45CYS0-0.091-0.00219.9060.0070.0070.0000.0000.0000.000
45A46PRO00.0390.00127.0110.0050.0050.0000.0000.0000.000
46A47TYR00.038-0.00524.2020.0060.0060.0000.0000.0000.000
47A48VAL00.0400.03624.6830.0040.0040.0000.0000.0000.000
48A49LYS10.8270.91426.9440.0940.0940.0000.0000.0000.000
49A50GLY0-0.0180.01129.6360.0050.0050.0000.0000.0000.000
50A51SER0-0.002-0.02826.7510.0030.0030.0000.0000.0000.000
51A52ILE00.0020.00829.0310.0020.0020.0000.0000.0000.000
52A53GLY00.0190.01730.3800.0020.0020.0000.0000.0000.000
53A54GLU-1-0.794-0.87928.835-0.041-0.0410.0000.0000.0000.000
54A55LEU00.016-0.00525.3350.0020.0020.0000.0000.0000.000
55A56VAL00.0010.01129.5690.0000.0000.0000.0000.0000.000
56A57ALA00.0070.00932.8260.0030.0030.0000.0000.0000.000
57A58LEU0-0.022-0.01128.2260.0030.0030.0000.0000.0000.000
58A59ALA00.0080.00930.9840.0020.0020.0000.0000.0000.000
59A60GLU-1-0.852-0.89332.328-0.042-0.0420.0000.0000.0000.000
60A61ARG10.8930.95034.2130.0300.0300.0000.0000.0000.000
61A62TYR0-0.078-0.08631.2730.0020.0020.0000.0000.0000.000
62A63ARG10.8940.93133.3680.0460.0460.0000.0000.0000.000
63A64GLY0-0.034-0.01934.6070.0040.0040.0000.0000.0000.000
64A65LYS10.8380.92732.5950.0340.0340.0000.0000.0000.000
65A66VAL00.0220.00227.0760.0000.0000.0000.0000.0000.000
66A67ALA0-0.0140.01728.1850.0000.0000.0000.0000.0000.000
67A68PHE00.013-0.00426.705-0.004-0.0040.0000.0000.0000.000
68A69VAL00.0210.00925.0820.0010.0010.0000.0000.0000.000
69A70GLY0-0.0140.00824.923-0.006-0.0060.0000.0000.0000.000
70A71ILE0-0.008-0.00421.137-0.001-0.0010.0000.0000.0000.000
71A72ASN00.008-0.03223.114-0.016-0.0160.0000.0000.0000.000
72A73ALA00.0310.01420.2200.0000.0000.0000.0000.0000.000
73A74ASN0-0.031-0.02421.991-0.037-0.0370.0000.0000.0000.000
74A75ASP-1-0.795-0.89323.469-0.197-0.1970.0000.0000.0000.000
75A76TYR0-0.026-0.05925.0210.0150.0150.0000.0000.0000.000
76A77GLU-1-0.831-0.87828.389-0.158-0.1580.0000.0000.0000.000
77A78LYS10.9020.95823.4890.2070.2070.0000.0000.0000.000
78A79TYR0-0.041-0.03224.6630.0030.0030.0000.0000.0000.000
79A80PRO00.0860.04029.2270.0000.0000.0000.0000.0000.000
80A81GLU-1-0.869-0.94231.407-0.092-0.0920.0000.0000.0000.000
81A82ASP-1-0.754-0.84426.777-0.139-0.1390.0000.0000.0000.000
82A83ALA00.0410.02029.350-0.007-0.0070.0000.0000.0000.000
83A84PRO00.0690.01430.7530.0070.0070.0000.0000.0000.000
84A85GLU-1-0.862-0.91632.569-0.078-0.0780.0000.0000.0000.000
85A86LYS10.8610.91433.3680.0890.0890.0000.0000.0000.000
86A87MET0-0.0490.02828.5290.0000.0000.0000.0000.0000.000
87A88ALA00.0100.01532.7730.0030.0030.0000.0000.0000.000
88A89ALA00.0480.02535.9700.0040.0040.0000.0000.0000.000
89A90PHE0-0.008-0.00430.1220.0040.0040.0000.0000.0000.000
90A91ALA0-0.009-0.01933.9720.0030.0030.0000.0000.0000.000
91A92GLU-1-0.892-0.95735.164-0.067-0.0670.0000.0000.0000.000
92A93GLU-1-0.936-0.95036.656-0.063-0.0630.0000.0000.0000.000
93A94HIS10.7520.86434.1150.0710.0710.0000.0000.0000.000
94A95GLY00.0490.03835.9790.0010.0010.0000.0000.0000.000
95A96ILE0-0.033-0.01530.9450.0010.0010.0000.0000.0000.000
96A97PHE0-0.010-0.00934.368-0.003-0.0030.0000.0000.0000.000
97A98PHE0-0.043-0.00228.3050.0010.0010.0000.0000.0000.000
98A99PRO00.0280.01229.616-0.002-0.0020.0000.0000.0000.000
99A100TYR0-0.027-0.03826.992-0.008-0.0080.0000.0000.0000.000
100A101LEU00.014-0.01225.8800.0020.0020.0000.0000.0000.000
101A102LEU00.0040.00926.247-0.006-0.0060.0000.0000.0000.000
102A103ASP-1-0.817-0.93319.978-0.276-0.2760.0000.0000.0000.000
103A104GLU-1-0.807-0.88223.101-0.193-0.1930.0000.0000.0000.000
104A105THR0-0.012-0.04821.447-0.002-0.0020.0000.0000.0000.000
105A106GLN0-0.016-0.00118.662-0.068-0.0680.0000.0000.0000.000
106A107GLU-1-0.860-0.90217.075-0.324-0.3240.0000.0000.0000.000
107A108VAL00.0230.01816.421-0.030-0.0300.0000.0000.0000.000
108A109ALA00.007-0.00316.212-0.015-0.0150.0000.0000.0000.000
109A110LYS10.8260.90712.9770.5770.5770.0000.0000.0000.000
110A111ALA0-0.023-0.00311.711-0.086-0.0860.0000.0000.0000.000
111A112TYR0-0.036-0.05212.222-0.007-0.0070.0000.0000.0000.000
112A113ARG10.8010.8996.6380.5780.5780.0000.0000.0000.000
113A114ALA00.0040.03310.7370.0150.0150.0000.0000.0000.000
114A115LEU0-0.018-0.0379.728-0.050-0.0500.0000.0000.0000.000
115A116ARG10.8000.90113.8250.1850.1850.0000.0000.0000.000
116A117THR00.0060.03917.403-0.001-0.0010.0000.0000.0000.000
117A118PRO0-0.034-0.03620.8980.0070.0070.0000.0000.0000.000
118A119GLU-1-0.772-0.88213.865-0.264-0.2640.0000.0000.0000.000
119A120VAL0-0.022-0.00918.582-0.009-0.0090.0000.0000.0000.000
120A121PHE00.006-0.00613.0230.0040.0040.0000.0000.0000.000
121A122LEU0-0.0060.00418.3190.0000.0000.0000.0000.0000.000
122A123PHE00.010-0.01116.6380.0020.0020.0000.0000.0000.000
123A124ASP-1-0.718-0.84821.057-0.029-0.0290.0000.0000.0000.000
124A125GLU-1-0.830-0.92323.534-0.036-0.0360.0000.0000.0000.000
125A126ARG10.6530.80320.3260.0100.0100.0000.0000.0000.000
126A127ARG10.7450.84721.6910.0630.0630.0000.0000.0000.000
127A128LEU0-0.0180.00417.603-0.014-0.0140.0000.0000.0000.000
128A129LEU0-0.079-0.03013.0710.0040.0040.0000.0000.0000.000
129A130ARG10.8730.91116.5500.0210.0210.0000.0000.0000.000
130A131TYR0-0.019-0.02917.8770.0140.0140.0000.0000.0000.000
131A132HIS10.8110.89711.4960.1670.1670.0000.0000.0000.000
132A133GLY0-0.027-0.00915.5570.0110.0110.0000.0000.0000.000
133A134ARG10.8360.93716.7320.0210.0210.0000.0000.0000.000
134A135VAL00.0500.04119.8560.0060.0060.0000.0000.0000.000
135A136ASN00.002-0.02223.3900.0050.0050.0000.0000.0000.000
136A137ASP-1-0.763-0.89223.371-0.025-0.0250.0000.0000.0000.000
137A138ASN0-0.055-0.03024.465-0.004-0.0040.0000.0000.0000.000
138A139PRO0-0.0190.00623.082-0.001-0.0010.0000.0000.0000.000
139A140LYS10.8960.94926.4090.0670.0670.0000.0000.0000.000
140A141ASP-1-0.798-0.86628.594-0.032-0.0320.0000.0000.0000.000
141A142PRO00.0660.03131.1600.0040.0040.0000.0000.0000.000
142A143SER0-0.098-0.06632.5760.0040.0040.0000.0000.0000.000
143A144LYS10.8580.91331.3150.0310.0310.0000.0000.0000.000
144A145VAL0-0.073-0.01528.3700.0020.0020.0000.0000.0000.000
145A146GLN0-0.084-0.04228.7820.0050.0050.0000.0000.0000.000
146A147SER0-0.074-0.04424.8210.0060.0060.0000.0000.0000.000
147A148HIS10.8680.90526.7950.0250.0250.0000.0000.0000.000
148A149ASP-1-0.808-0.90721.950-0.021-0.0210.0000.0000.0000.000
149A150LEU00.0270.02422.7870.0010.0010.0000.0000.0000.000
150A151GLU-1-0.885-0.94524.406-0.026-0.0260.0000.0000.0000.000
151A152ALA0-0.007-0.00825.7060.0030.0030.0000.0000.0000.000
152A153ALA0-0.004-0.00422.6780.0040.0040.0000.0000.0000.000
153A154ILE00.0160.00524.5700.0010.0010.0000.0000.0000.000
154A155GLU-1-0.861-0.91227.052-0.014-0.0140.0000.0000.0000.000
155A156ALA0-0.031-0.00425.7900.0030.0030.0000.0000.0000.000
156A157LEU00.0070.00122.6900.0020.0020.0000.0000.0000.000
157A158LEU0-0.051-0.01726.9000.0010.0010.0000.0000.0000.000
158A159ARG10.7840.88330.2370.0040.0040.0000.0000.0000.000
159A160GLY0-0.0280.00028.5850.0030.0030.0000.0000.0000.000
160A161GLU-1-0.908-0.94127.4960.0140.0140.0000.0000.0000.000
161A162GLU-1-0.861-0.91820.9600.0110.0110.0000.0000.0000.000
162A163PRO0-0.004-0.00621.1040.0010.0010.0000.0000.0000.000
163A164PRO0-0.029-0.02321.5470.0090.0090.0000.0000.0000.000
164A165LEU00.0450.02219.185-0.001-0.0010.0000.0000.0000.000
165A166LYS10.8870.95917.409-0.044-0.0440.0000.0000.0000.000
166A167GLH0-0.009-0.04110.540-0.008-0.0080.0000.0000.0000.000
167A168ALA00.0090.00915.7780.0080.0080.0000.0000.0000.000
168A169PRO00.0560.02313.024-0.017-0.0170.0000.0000.0000.000
169A170ALA00.0490.02815.1130.0120.0120.0000.0000.0000.000
170A171ILE0-0.024-0.00116.913-0.002-0.0020.0000.0000.0000.000
171A172GLY00.037-0.00119.6800.0040.0040.0000.0000.0000.000
172A174THR00.0190.01016.5060.0040.0040.0000.0000.0000.000
173A175ILE00.0490.03316.2810.0240.0240.0000.0000.0000.000
174A176LYS10.7650.89318.8200.1720.1720.0000.0000.0000.000
175A177TRP00.0340.00014.573-0.003-0.0030.0000.0000.0000.000
176A178ARG10.7820.85919.5280.2280.2280.0000.0000.0000.000
177A179PRO0-0.018-0.01920.279-0.033-0.0330.0000.0000.0000.000
178A180GLY0-0.0120.00818.3760.0090.0090.0000.0000.0000.000
179A181ASN0-0.025-0.02416.845-0.086-0.0860.0000.0000.0000.000
180A182GLU-1-0.904-0.94215.044-0.427-0.4270.0000.0000.0000.000
181A183PRO0-0.0310.00910.232-0.092-0.0920.0000.0000.0000.000
182A184GLU-1-0.868-0.9318.475-0.989-0.9890.0000.0000.0000.000
183A185VAL0-0.037-0.0205.884-0.519-0.5190.0000.0000.0000.000
184A186ARG10.8060.8973.1241.1531.7620.077-0.183-0.5020.000
185A187ILE00.0590.0152.497-4.855-2.3172.600-2.260-2.878-0.028
186A188GLY00.0130.0232.440-7.166-4.2924.244-2.427-4.692-0.016