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

tag_button

FMODB ID: 6NQ4Z

Calculation Name: 3D7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7L

Chain ID: A

ChEMBL ID:

UniProt ID: Q92AH8

Base Structure: X-ray

Registration Date: 2023-09-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101964.992035
FMO2-HF: Nuclear repulsion 2027369.716316
FMO2-HF: Total energy -74595.275719
FMO2-MP2: Total energy -74812.810399


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:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-4.1010.298-0.114-1.622-2.663-0.006
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.033
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].
3A0ALA00.0060.0333.600-3.0311.019-0.121-1.545-2.384-0.006
4A1MET00.0230.0145.545-0.967-0.9670.0000.0000.0000.000
5A2LYS10.8670.9213.3321.0951.4440.007-0.077-0.2790.000
6A3ILE0-0.009-0.0117.9440.0930.0930.0000.0000.0000.000
7A4LEU00.0360.02711.6740.0770.0770.0000.0000.0000.000
8A5LEU0-0.042-0.02313.5860.0010.0010.0000.0000.0000.000
9A6ILE00.0510.01417.0350.0340.0340.0000.0000.0000.000
10A7GLY0-0.008-0.02219.830-0.005-0.0050.0000.0000.0000.000
11A8ALA0-0.010-0.00719.3940.0010.0010.0000.0000.0000.000
12A9SER00.0030.00621.5250.0030.0030.0000.0000.0000.000
13A10GLY0-0.0120.00724.4030.0050.0050.0000.0000.0000.000
14A11THR00.025-0.00326.349-0.003-0.0030.0000.0000.0000.000
15A12LEU00.0320.01825.758-0.001-0.0010.0000.0000.0000.000
16A13GLY00.0410.01623.035-0.008-0.0080.0000.0000.0000.000
17A14SER00.0290.02222.206-0.005-0.0050.0000.0000.0000.000
18A15ALA0-0.019-0.01023.0070.0000.0000.0000.0000.0000.000
19A16VAL0-0.013-0.01919.692-0.007-0.0070.0000.0000.0000.000
20A17LYS10.8530.90917.236-0.024-0.0240.0000.0000.0000.000
21A18GLU-1-0.842-0.89518.522-0.030-0.0300.0000.0000.0000.000
22A19ARG10.7880.87320.1830.0940.0940.0000.0000.0000.000
23A20LEU00.006-0.00515.766-0.006-0.0060.0000.0000.0000.000
24A21GLU-1-0.800-0.87714.660-0.019-0.0190.0000.0000.0000.000
25A22LYS10.7360.85414.6460.0590.0590.0000.0000.0000.000
26A23LYS10.7920.88213.6630.2070.2070.0000.0000.0000.000
27A24ALA0-0.0050.01510.410-0.082-0.0820.0000.0000.0000.000
28A25GLU-1-0.810-0.8765.835-0.175-0.1750.0000.0000.0000.000
29A26VAL0-0.059-0.0399.636-0.125-0.1250.0000.0000.0000.000
30A27ILE00.0240.0268.5980.0690.0690.0000.0000.0000.000
31A28THR0-0.061-0.07312.994-0.029-0.0290.0000.0000.0000.000
32A29ALA00.0590.02516.7560.0240.0240.0000.0000.0000.000
33A30GLY00.0310.01118.883-0.016-0.0160.0000.0000.0000.000
34A31ARG10.8140.91222.683-0.013-0.0130.0000.0000.0000.000
35A32HIS00.003-0.01425.6330.0080.0080.0000.0000.0000.000
36A33SER0-0.010-0.00123.5240.0060.0060.0000.0000.0000.000
37A34GLY00.0160.00919.680-0.013-0.0130.0000.0000.0000.000
38A35ASP-1-0.840-0.87314.6470.0890.0890.0000.0000.0000.000
39A36VAL0-0.010-0.00415.2530.0210.0210.0000.0000.0000.000
40A37THR0-0.021-0.01118.026-0.018-0.0180.0000.0000.0000.000
41A38VAL0-0.012-0.01520.6180.0030.0030.0000.0000.0000.000
42A39ASP-1-0.816-0.89222.6560.0020.0020.0000.0000.0000.000
43A40ILE00.016-0.00923.2840.0000.0000.0000.0000.0000.000
44A41THR0-0.033-0.01525.671-0.004-0.0040.0000.0000.0000.000
45A42ASN0-0.021-0.01127.4510.0030.0030.0000.0000.0000.000
46A43ILE00.0700.02025.3530.0020.0020.0000.0000.0000.000
47A44ASP-1-0.837-0.91124.1480.0460.0460.0000.0000.0000.000
48A45SER0-0.0100.00223.3180.0090.0090.0000.0000.0000.000
49A46ILE0-0.037-0.01020.3720.0050.0050.0000.0000.0000.000
50A47LYS10.9580.97519.554-0.016-0.0160.0000.0000.0000.000
51A48LYS10.9070.95218.841-0.045-0.0450.0000.0000.0000.000
52A49MET00.0040.02716.6830.0160.0160.0000.0000.0000.000
53A50TYR0-0.043-0.06514.4650.0010.0010.0000.0000.0000.000
54A51GLU-1-0.969-0.96913.7740.1590.1590.0000.0000.0000.000
55A52GLN0-0.068-0.04014.1200.0380.0380.0000.0000.0000.000
56A53VAL0-0.046-0.01310.6560.0550.0550.0000.0000.0000.000
57A54GLY00.0090.0249.4900.1010.1010.0000.0000.0000.000
58A55LYS10.8450.9077.303-0.057-0.0570.0000.0000.0000.000
59A56VAL0-0.023-0.0076.915-0.119-0.1190.0000.0000.0000.000
60A57ASP-1-0.781-0.8776.926-2.276-2.2760.0000.0000.0000.000
61A58ALA0-0.025-0.0159.6340.1500.1500.0000.0000.0000.000
62A59ILE00.0010.02412.8580.0150.0150.0000.0000.0000.000
63A60VAL0-0.025-0.02615.3820.0120.0120.0000.0000.0000.000
64A61SER0-0.010-0.01118.2790.0240.0240.0000.0000.0000.000
65A62ALA0-0.0010.01221.545-0.001-0.0010.0000.0000.0000.000
66A63THR0-0.045-0.03423.4520.0130.0130.0000.0000.0000.000
67A64GLY00.0300.02025.912-0.005-0.0050.0000.0000.0000.000
68A65SER0-0.054-0.03128.6670.0010.0010.0000.0000.0000.000
69A66ALA00.029-0.01532.293-0.001-0.0010.0000.0000.0000.000
70A67THR0-0.014-0.00935.5950.0020.0020.0000.0000.0000.000
71A68PHE0-0.0110.00737.307-0.002-0.0020.0000.0000.0000.000
72A69SER00.0400.00741.5240.0030.0030.0000.0000.0000.000
73A70PRO00.0200.03344.987-0.002-0.0020.0000.0000.0000.000
74A71LEU00.0480.01346.6250.0000.0000.0000.0000.0000.000
75A72THR00.003-0.00848.2410.0000.0000.0000.0000.0000.000
76A73GLU-1-0.922-0.96448.702-0.008-0.0080.0000.0000.0000.000
77A74LEU0-0.085-0.03342.3840.0010.0010.0000.0000.0000.000
78A75THR00.007-0.01646.356-0.001-0.0010.0000.0000.0000.000
79A76PRO00.0410.00544.154-0.001-0.0010.0000.0000.0000.000
80A77GLU-1-0.829-0.89942.532-0.008-0.0080.0000.0000.0000.000
81A78LYS10.8740.94541.4520.0090.0090.0000.0000.0000.000
82A79ASN00.0370.01340.186-0.002-0.0020.0000.0000.0000.000
83A80ALA00.0190.01038.404-0.003-0.0030.0000.0000.0000.000
84A81VAL00.0130.02136.036-0.001-0.0010.0000.0000.0000.000
85A82THR00.024-0.00334.756-0.001-0.0010.0000.0000.0000.000
86A83ILE0-0.027-0.00533.534-0.004-0.0040.0000.0000.0000.000
87A84SER0-0.025-0.00532.423-0.003-0.0030.0000.0000.0000.000
88A85SER00.0170.01429.889-0.001-0.0010.0000.0000.0000.000
89A86LYS10.7960.90429.1840.0460.0460.0000.0000.0000.000
90A87LEU00.0000.01629.398-0.007-0.0070.0000.0000.0000.000
91A88GLY00.0360.00429.084-0.006-0.0060.0000.0000.0000.000
92A89GLY00.0340.02227.051-0.002-0.0020.0000.0000.0000.000
93A90GLN0-0.019-0.01824.544-0.012-0.0120.0000.0000.0000.000
94A91ILE00.0170.01323.996-0.010-0.0100.0000.0000.0000.000
95A92ASN00.000-0.01224.523-0.007-0.0070.0000.0000.0000.000
96A93LEU0-0.0160.00719.8400.0020.0020.0000.0000.0000.000
97A94VAL00.0070.02219.708-0.011-0.0110.0000.0000.0000.000
98A95LEU0-0.022-0.02020.538-0.006-0.0060.0000.0000.0000.000
99A96LEU0-0.053-0.03320.8050.0080.0080.0000.0000.0000.000
100A97GLY00.0420.02716.9110.0140.0140.0000.0000.0000.000
101A98ILE00.0030.00315.622-0.030-0.0300.0000.0000.0000.000
102A99ASP-1-0.899-0.94615.315-0.106-0.1060.0000.0000.0000.000
103A100SER0-0.051-0.01812.4460.0400.0400.0000.0000.0000.000
104A101LEU0-0.0140.01411.144-0.066-0.0660.0000.0000.0000.000
105A102ASN0-0.033-0.0345.8110.5210.5210.0000.0000.0000.000
106A103ASP-1-0.835-0.92910.084-0.326-0.3260.0000.0000.0000.000
107A104LYS10.8340.91511.8110.2650.2650.0000.0000.0000.000
108A105GLY00.0620.05612.696-0.026-0.0260.0000.0000.0000.000
109A106SER0-0.062-0.03813.3220.0950.0950.0000.0000.0000.000
110A107PHE00.0910.04215.570-0.015-0.0150.0000.0000.0000.000
111A108THR0-0.036-0.00818.3920.0060.0060.0000.0000.0000.000
112A109LEU00.0200.01920.7710.0070.0070.0000.0000.0000.000
113A110THR00.026-0.01323.697-0.001-0.0010.0000.0000.0000.000
114A111THR0-0.019-0.01526.6760.0060.0060.0000.0000.0000.000
115A112GLY00.0260.00030.2980.0040.0040.0000.0000.0000.000
116A113ILE00.0570.02533.2740.0000.0000.0000.0000.0000.000
117A114MET0-0.0040.02436.4150.0020.0020.0000.0000.0000.000
118A115MET0-0.092-0.04233.1380.0020.0020.0000.0000.0000.000
119A116GLU-1-0.935-0.96237.968-0.053-0.0530.0000.0000.0000.000
120A117ASP-1-0.908-0.94939.900-0.031-0.0310.0000.0000.0000.000
121A118PRO0-0.058-0.02742.0160.0010.0010.0000.0000.0000.000
122A119ILE00.0650.04141.3890.0010.0010.0000.0000.0000.000
123A120VAL00.024-0.00944.8290.0000.0000.0000.0000.0000.000
124A121GLN0-0.017-0.01944.4360.0000.0000.0000.0000.0000.000
125A122GLY00.0620.03641.3310.0000.0000.0000.0000.0000.000
126A123ALA0-0.006-0.00540.677-0.002-0.0020.0000.0000.0000.000
127A124SER00.0190.00939.385-0.002-0.0020.0000.0000.0000.000
128A125ALA00.0360.00136.413-0.002-0.0020.0000.0000.0000.000
129A126ALA00.0140.02236.016-0.004-0.0040.0000.0000.0000.000
130A127MET0-0.0120.00337.072-0.003-0.0030.0000.0000.0000.000
131A128ALA0-0.003-0.01132.904-0.003-0.0030.0000.0000.0000.000
132A129ASN0-0.0070.00732.340-0.006-0.0060.0000.0000.0000.000
133A130GLY00.0890.05032.789-0.006-0.0060.0000.0000.0000.000
134A131ALA0-0.021-0.01133.241-0.004-0.0040.0000.0000.0000.000
135A132VAL00.0030.00327.346-0.004-0.0040.0000.0000.0000.000
136A133THR0-0.014-0.02628.874-0.010-0.0100.0000.0000.0000.000
137A134ALA0-0.024-0.01130.327-0.006-0.0060.0000.0000.0000.000
138A135PHE00.008-0.00324.659-0.003-0.0030.0000.0000.0000.000
139A136ALA00.0340.01725.799-0.005-0.0050.0000.0000.0000.000
140A137LYS10.8670.92626.6030.0850.0850.0000.0000.0000.000
141A138SER00.0170.00728.991-0.002-0.0020.0000.0000.0000.000
142A139ALA00.0320.01024.715-0.002-0.0020.0000.0000.0000.000
143A140ALA0-0.027-0.00924.024-0.010-0.0100.0000.0000.0000.000
144A141ILE0-0.083-0.03624.650-0.011-0.0110.0000.0000.0000.000
145A142GLU-1-0.948-0.97125.692-0.082-0.0820.0000.0000.0000.000
146A143MET0-0.0530.00320.182-0.003-0.0030.0000.0000.0000.000
147A144PRO00.0160.01518.577-0.009-0.0090.0000.0000.0000.000
148A145ARG10.8340.87712.7850.2700.2700.0000.0000.0000.000
149A146GLY0-0.041-0.01816.051-0.057-0.0570.0000.0000.0000.000
150A147ILE0-0.0150.01114.862-0.029-0.0290.0000.0000.0000.000
151A148ARG10.8120.91116.6210.3590.3590.0000.0000.0000.000
152A149ILE00.0180.00518.955-0.014-0.0140.0000.0000.0000.000
153A150ASN0-0.044-0.01221.5320.0260.0260.0000.0000.0000.000
154A151THR00.0130.00923.5150.0030.0030.0000.0000.0000.000
155A152VAL0-0.0020.00624.493-0.002-0.0020.0000.0000.0000.000
156A153SER00.0140.00427.2090.0060.0060.0000.0000.0000.000
157A154PRO0-0.015-0.00329.4130.0010.0010.0000.0000.0000.000
158A155ASN00.1020.03731.9480.0040.0040.0000.0000.0000.000
159A156VAL00.0050.00534.248-0.002-0.0020.0000.0000.0000.000
160A157LEU0-0.026-0.02530.602-0.002-0.0020.0000.0000.0000.000
161A158GLU-1-0.846-0.94434.854-0.025-0.0250.0000.0000.0000.000
162A159GLU-1-0.809-0.91332.049-0.028-0.0280.0000.0000.0000.000
163A160SER0-0.087-0.05834.3780.0030.0030.0000.0000.0000.000
164A161TRP00.0420.02536.7330.0000.0000.0000.0000.0000.000
165A162ASP-1-0.862-0.93340.038-0.009-0.0090.0000.0000.0000.000
166A163LYS10.8300.92636.1950.0160.0160.0000.0000.0000.000
167A164LEU0-0.060-0.05036.7130.0000.0000.0000.0000.0000.000
168A165GLU-1-0.872-0.91541.237-0.015-0.0150.0000.0000.0000.000
169A166PRO00.0430.02243.966-0.001-0.0010.0000.0000.0000.000
170A167PHE0-0.086-0.04042.5850.0000.0000.0000.0000.0000.000
171A168PHE0-0.094-0.05938.729-0.002-0.0020.0000.0000.0000.000
172A169GLU-1-0.874-0.93043.948-0.015-0.0150.0000.0000.0000.000
173A170GLY0-0.013-0.00847.217-0.001-0.0010.0000.0000.0000.000
174A171PHE0-0.045-0.01940.849-0.002-0.0020.0000.0000.0000.000
175A172LEU0-0.023-0.01441.0440.0020.0020.0000.0000.0000.000
176A173PRO0-0.0300.00138.012-0.003-0.0030.0000.0000.0000.000
177A174VAL0-0.042-0.02333.291-0.001-0.0010.0000.0000.0000.000
178A175PRO00.0430.03632.2740.0000.0000.0000.0000.0000.000
179A176ALA00.035-0.00228.850-0.007-0.0070.0000.0000.0000.000
180A177ALA00.0200.00427.348-0.009-0.0090.0000.0000.0000.000
181A178LYS10.9030.95527.5970.0420.0420.0000.0000.0000.000
182A179VAL00.0360.01127.328-0.008-0.0080.0000.0000.0000.000
183A180ALA00.0210.01423.871-0.012-0.0120.0000.0000.0000.000
184A181ARG10.9330.96923.3400.0530.0530.0000.0000.0000.000
185A182ALA0-0.0090.00924.078-0.015-0.0150.0000.0000.0000.000
186A183PHE00.0540.01220.876-0.013-0.0130.0000.0000.0000.000
187A184GLU-1-0.777-0.85019.474-0.157-0.1570.0000.0000.0000.000
188A185LYS10.8400.92319.7920.1130.1130.0000.0000.0000.000
189A186SER0-0.039-0.01920.398-0.014-0.0140.0000.0000.0000.000
190A187VAL00.0410.02014.639-0.018-0.0180.0000.0000.0000.000
191A188PHE00.003-0.01913.771-0.040-0.0400.0000.0000.0000.000
192A189GLY0-0.0210.01717.4890.0060.0060.0000.0000.0000.000
193A190ALA00.011-0.01118.875-0.031-0.0310.0000.0000.0000.000
194A191GLN0-0.038-0.02320.8990.0080.0080.0000.0000.0000.000
195A192THR00.0600.02022.232-0.021-0.0210.0000.0000.0000.000
196A193GLY00.0750.04524.0310.0120.0120.0000.0000.0000.000
197A194GLU-1-0.921-0.93926.076-0.103-0.1030.0000.0000.0000.000
198A195SER0-0.008-0.01027.098-0.002-0.0020.0000.0000.0000.000
199A196TYR0-0.018-0.03023.7190.0010.0010.0000.0000.0000.000
200A197GLN0-0.0050.00429.1110.0020.0020.0000.0000.0000.000
201A198VAL0-0.068-0.03429.356-0.001-0.0010.0000.0000.0000.000
202A199TYR00.0540.03632.5810.0020.0020.0000.0000.0000.000