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: 3JJ2L

Calculation Name: 3L7O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7O

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DTT9

Base Structure: X-ray

Registration Date: 2023-09-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2617216.578746
FMO2-HF: Nuclear repulsion 2531736.107161
FMO2-HF: Total energy -85480.471585
FMO2-MP2: Total energy -85731.504227


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:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-71.769-75.25138.677-19.612-15.5840.201
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.764 / q_NPA : -0.856
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].
3A4LEU00.0020.0053.162-4.497-2.1150.139-1.025-1.4970.006
4A5LYS10.7970.8801.659-140.240-141.11020.836-10.994-8.9720.131
5A6LYS10.9990.9913.998-37.081-36.6940.000-0.115-0.2720.000
6A7ILE00.0020.0066.061-4.932-4.9320.0000.0000.0000.000
7A8ALA00.0080.0017.433-3.313-3.3130.0000.0000.0000.000
8A9GLY0-0.006-0.0068.053-3.008-3.0080.0000.0000.0000.000
9A10VAL00.0340.0099.832-2.484-2.4840.0000.0000.0000.000
10A11ARG10.8860.95211.608-19.994-19.9940.0000.0000.0000.000
11A12ALA0-0.017-0.01512.792-1.903-1.9030.0000.0000.0000.000
12A13ALA00.0390.02114.396-1.271-1.2710.0000.0000.0000.000
13A14GLN0-0.032-0.03316.079-1.343-1.3430.0000.0000.0000.000
14A15TYR0-0.027-0.02017.621-0.505-0.5050.0000.0000.0000.000
15A16VAL00.0050.01618.632-0.527-0.5270.0000.0000.0000.000
16A17GLU-1-0.942-0.99021.19912.16712.1670.0000.0000.0000.000
17A18ASP-1-0.811-0.92924.61511.98511.9850.0000.0000.0000.000
18A19GLY0-0.071-0.03926.811-0.304-0.3040.0000.0000.0000.000
19A20MET0-0.0620.02524.4610.0510.0510.0000.0000.0000.000
20A21ILE00.0100.01625.4770.1700.1700.0000.0000.0000.000
21A22VAL0-0.034-0.04219.3150.2610.2610.0000.0000.0000.000
22A23GLY00.0270.01020.392-0.013-0.0130.0000.0000.0000.000
23A24LEU0-0.059-0.04416.5161.0311.0310.0000.0000.0000.000
24A25GLY00.0810.03715.208-0.582-0.5820.0000.0000.0000.000
25A26THR0-0.074-0.03611.7881.0601.0600.0000.0000.0000.000
26A27GLY00.1280.0489.668-0.888-0.8880.0000.0000.0000.000
27A28SER0-0.056-0.0243.7693.9364.2580.001-0.156-0.1670.001
28A29THR00.0090.0034.42012.33012.538-0.001-0.007-0.2000.000
29A30ALA00.0450.0176.455-1.587-1.5870.0000.0000.0000.000
30A31TYR0-0.038-0.0236.476-1.815-1.8150.0000.0000.0000.000
31A32TYR0-0.027-0.0591.653-32.884-38.79517.702-7.315-4.4760.063
32A33PHE0-0.0020.0228.161-2.489-2.4890.0000.0000.0000.000
33A34VAL0-0.001-0.00411.448-2.046-2.0460.0000.0000.0000.000
34A35GLU-1-0.856-0.9079.21824.43024.4300.0000.0000.0000.000
35A36GLU-1-0.821-0.86112.12518.86418.8640.0000.0000.0000.000
36A37VAL0-0.005-0.01713.785-1.614-1.6140.0000.0000.0000.000
37A38GLY00.0160.00515.657-1.178-1.1780.0000.0000.0000.000
38A39ARG10.7560.82814.512-18.783-18.7830.0000.0000.0000.000
39A40ARG10.8500.93117.188-16.414-16.4140.0000.0000.0000.000
40A41VAL0-0.032-0.01119.782-0.818-0.8180.0000.0000.0000.000
41A42GLN0-0.106-0.03718.393-0.331-0.3310.0000.0000.0000.000
42A43GLU-1-0.981-0.99919.09213.73013.7300.0000.0000.0000.000
43A44GLU-1-0.894-0.93519.96714.95314.9530.0000.0000.0000.000
44A45GLY0-0.0050.00923.750-0.372-0.3720.0000.0000.0000.000
45A46LEU0-0.0110.02320.867-0.319-0.3190.0000.0000.0000.000
46A47GLN0-0.103-0.07224.599-0.149-0.1490.0000.0000.0000.000
47A48VAL00.0280.01021.489-0.030-0.0300.0000.0000.0000.000
48A49ILE0-0.026-0.00724.963-0.239-0.2390.0000.0000.0000.000
49A50GLY00.0050.00821.4130.2320.2320.0000.0000.0000.000
50A51VAL00.0380.01321.703-0.557-0.5570.0000.0000.0000.000
51A52THR0-0.044-0.02918.3570.5110.5110.0000.0000.0000.000
52A53THR00.0530.03717.283-0.463-0.4630.0000.0000.0000.000
53A54SER00.020-0.00716.836-0.054-0.0540.0000.0000.0000.000
54A55SER00.0400.02718.8810.4090.4090.0000.0000.0000.000
55A56ARG10.9500.95814.407-19.414-19.4140.0000.0000.0000.000
56A57THR00.0590.02614.4620.2550.2550.0000.0000.0000.000
57A58THR00.0050.01516.118-0.438-0.4380.0000.0000.0000.000
58A59ALA0-0.011-0.00117.702-0.370-0.3700.0000.0000.0000.000
59A60GLN0-0.053-0.02910.782-0.862-0.8620.0000.0000.0000.000
60A61ALA00.0520.00915.802-0.078-0.0780.0000.0000.0000.000
61A62GLN0-0.032-0.02118.037-0.438-0.4380.0000.0000.0000.000
62A63ALA0-0.054-0.01717.241-0.543-0.5430.0000.0000.0000.000
63A64LEU0-0.031-0.01714.016-0.427-0.4270.0000.0000.0000.000
64A65GLY0-0.0030.01418.618-0.442-0.4420.0000.0000.0000.000
65A66ILE0-0.019-0.01017.037-0.401-0.4010.0000.0000.0000.000
66A67PRO0-0.018-0.00121.608-0.116-0.1160.0000.0000.0000.000
67A68LEU0-0.039-0.02120.6610.4420.4420.0000.0000.0000.000
68A69LYS10.8590.93524.808-10.665-10.6650.0000.0000.0000.000
69A70SER0-0.053-0.05025.8530.4720.4720.0000.0000.0000.000
70A71ILE00.015-0.01625.734-0.109-0.1090.0000.0000.0000.000
71A72ASP-1-0.911-0.94728.21510.03210.0320.0000.0000.0000.000
72A73GLU-1-0.934-0.92830.51110.08310.0830.0000.0000.0000.000
73A74VAL0-0.009-0.00827.921-0.082-0.0820.0000.0000.0000.000
74A75ASP-1-0.888-0.94531.2819.2809.2800.0000.0000.0000.000
75A76SER0-0.085-0.05330.059-0.177-0.1770.0000.0000.0000.000
76A77VAL00.0240.02323.255-0.028-0.0280.0000.0000.0000.000
77A78ASP-1-0.818-0.88825.61011.36911.3690.0000.0000.0000.000
78A79VAL00.0220.01019.7630.1060.1060.0000.0000.0000.000
79A80THR0-0.002-0.00918.6640.1220.1220.0000.0000.0000.000
80A81VAL0-0.019-0.00413.6250.2780.2780.0000.0000.0000.000
81A82ASP-1-0.792-0.89814.27721.11521.1150.0000.0000.0000.000
82A83GLY0-0.0010.00211.8430.9990.9990.0000.0000.0000.000
83A84ALA0-0.024-0.01512.480-2.262-2.2620.0000.0000.0000.000
84A85ASP-1-0.849-0.93313.02424.35524.3550.0000.0000.0000.000
85A86GLU-1-0.806-0.90214.24917.81317.8130.0000.0000.0000.000
86A87VAL0-0.015-0.01715.828-0.698-0.6980.0000.0000.0000.000
87A88ASP-1-0.752-0.86818.13214.21114.2110.0000.0000.0000.000
88A89PRO0-0.009-0.00520.9450.1640.1640.0000.0000.0000.000
89A90ASN0-0.133-0.06722.258-0.738-0.7380.0000.0000.0000.000
90A91PHE0-0.057-0.02120.433-0.284-0.2840.0000.0000.0000.000
91A92ASN0-0.013-0.00922.659-0.517-0.5170.0000.0000.0000.000
92A93GLY00.0530.01719.7940.6880.6880.0000.0000.0000.000
93A94ILE0-0.059-0.00818.935-1.083-1.0830.0000.0000.0000.000
94A95LYS10.7870.89915.850-18.349-18.3490.0000.0000.0000.000
95A96GLY00.0990.04117.521-1.061-1.0610.0000.0000.0000.000
96A97GLY00.0170.00916.145-0.714-0.7140.0000.0000.0000.000
97A98GLY0-0.075-0.03915.4520.0200.0200.0000.0000.0000.000
98A99GLY0-0.048-0.02716.199-0.397-0.3970.0000.0000.0000.000
99A100ALA00.0090.00818.139-0.871-0.8710.0000.0000.0000.000
100A101LEU00.0330.01420.071-0.191-0.1910.0000.0000.0000.000
101A102LEU00.0220.03421.688-0.205-0.2050.0000.0000.0000.000
102A103MET00.015-0.00522.420-0.324-0.3240.0000.0000.0000.000
103A104GLU-1-0.852-0.94816.79618.92618.9260.0000.0000.0000.000
104A105LYS10.8260.91221.122-12.616-12.6160.0000.0000.0000.000
105A106ILE0-0.0100.01324.147-0.372-0.3720.0000.0000.0000.000
106A107VAL00.005-0.00621.592-0.272-0.2720.0000.0000.0000.000
107A108GLY00.0000.00722.864-0.143-0.1430.0000.0000.0000.000
108A109THR0-0.060-0.04923.508-0.330-0.3300.0000.0000.0000.000
109A110LEU0-0.0140.01126.855-0.376-0.3760.0000.0000.0000.000
110A111THR0-0.057-0.02122.4700.1570.1570.0000.0000.0000.000
111A112LYS10.8050.90825.736-10.918-10.9180.0000.0000.0000.000
112A113ASP-1-0.844-0.90322.78714.29914.2990.0000.0000.0000.000
113A114TYR00.0070.00218.8980.6770.6770.0000.0000.0000.000
114A115ILE0-0.007-0.01016.1760.0550.0550.0000.0000.0000.000
115A116TRP00.0150.01115.2200.6050.6050.0000.0000.0000.000
116A117VAL0-0.0070.00510.0120.0150.0150.0000.0000.0000.000
117A118VAL0-0.004-0.0069.6882.1152.1150.0000.0000.0000.000
118A119ASP-1-0.777-0.8576.14244.30044.3000.0000.0000.0000.000
119A120GLU-1-0.684-0.8238.14319.52319.5230.0000.0000.0000.000
120A121SER0-0.101-0.0698.657-2.494-2.4940.0000.0000.0000.000
121A122LYS10.8370.9067.991-37.907-37.9070.0000.0000.0000.000
122A123MET0-0.0490.00112.804-1.438-1.4380.0000.0000.0000.000
123A124VAL0-0.011-0.00815.0490.0360.0360.0000.0000.0000.000
124A125ASP-1-0.881-0.94318.01314.31614.3160.0000.0000.0000.000
125A126THR0-0.098-0.06421.414-0.851-0.8510.0000.0000.0000.000
126A127LEU00.0090.02420.3690.3970.3970.0000.0000.0000.000
127A128GLY0-0.012-0.03621.130-0.899-0.8990.0000.0000.0000.000
128A129ALA0-0.0350.00019.004-0.327-0.3270.0000.0000.0000.000
129A130PHE0-0.045-0.01614.5540.3970.3970.0000.0000.0000.000
130A131ARG10.8370.90418.801-14.689-14.6890.0000.0000.0000.000
131A132LEU00.0420.02020.6530.6210.6210.0000.0000.0000.000
132A133PRO00.0100.02520.341-0.680-0.6800.0000.0000.0000.000
133A134VAL00.008-0.00623.402-0.247-0.2470.0000.0000.0000.000
134A135GLU-1-0.750-0.83325.73512.40712.4070.0000.0000.0000.000
135A136VAL0-0.043-0.03227.759-0.440-0.4400.0000.0000.0000.000
136A137VAL00.0550.02031.3790.0500.0500.0000.0000.0000.000
137A138GLN0-0.007-0.01532.951-0.203-0.2030.0000.0000.0000.000
138A139TYR0-0.037-0.02134.997-0.149-0.1490.0000.0000.0000.000
139A140GLY00.0260.01438.674-0.040-0.0400.0000.0000.0000.000
140A141ALA00.0440.03133.4910.0180.0180.0000.0000.0000.000
141A142GLU-1-0.826-0.90934.9939.1969.1960.0000.0000.0000.000
142A143ARG10.7690.86736.633-8.039-8.0390.0000.0000.0000.000
143A144LEU00.0340.02934.174-0.117-0.1170.0000.0000.0000.000
144A145PHE00.0450.03330.2160.0570.0570.0000.0000.0000.000
145A146ARG10.9460.97434.335-8.316-8.3160.0000.0000.0000.000
146A147GLU-1-0.805-0.86937.3888.2238.2230.0000.0000.0000.000
147A148PHE00.0510.00431.624-0.054-0.0540.0000.0000.0000.000
148A149GLU-1-0.875-0.93934.0548.9038.9030.0000.0000.0000.000
149A150LYS10.8180.90634.968-8.313-8.3130.0000.0000.0000.000
150A151LYS10.8140.91235.633-8.923-8.9230.0000.0000.0000.000
151A152GLY00.0100.01834.4950.0560.0560.0000.0000.0000.000
152A153TYR0-0.023-0.03430.3330.2070.2070.0000.0000.0000.000
153A154LYS10.8690.93226.740-11.594-11.5940.0000.0000.0000.000
154A155PRO00.0230.02827.9380.4640.4640.0000.0000.0000.000
155A156SER0-0.010-0.00925.295-0.096-0.0960.0000.0000.0000.000
156A157PHE0-0.036-0.02926.6830.1050.1050.0000.0000.0000.000
157A158ARG10.7720.85618.866-16.215-16.2150.0000.0000.0000.000
158A159GLU-1-0.923-0.96223.65012.59112.5910.0000.0000.0000.000
159A160TYR0-0.0030.00618.0660.6820.6820.0000.0000.0000.000
160A161ASP-1-0.918-0.94922.28914.21614.2160.0000.0000.0000.000
161A162GLY0-0.0090.00024.653-0.566-0.5660.0000.0000.0000.000
162A163VAL0-0.078-0.04126.570-0.622-0.6220.0000.0000.0000.000
163A164ARG10.8070.89826.456-9.788-9.7880.0000.0000.0000.000
164A165PHE0-0.002-0.02321.824-0.086-0.0860.0000.0000.0000.000
165A166VAL0-0.034-0.01825.765-0.382-0.3820.0000.0000.0000.000
166A167THR0-0.041-0.03124.7250.2350.2350.0000.0000.0000.000
167A168ASP-1-0.810-0.91222.80213.53013.5300.0000.0000.0000.000
168A169MET0-0.071-0.03526.079-0.649-0.6490.0000.0000.0000.000
169A170LYS10.8120.91028.785-11.321-11.3210.0000.0000.0000.000
170A171ASN00.0050.00828.922-0.833-0.8330.0000.0000.0000.000
171A172PHE0-0.008-0.00828.3290.1450.1450.0000.0000.0000.000
172A173ILE00.0690.03022.748-0.006-0.0060.0000.0000.0000.000
173A174ILE0-0.076-0.03426.632-0.154-0.1540.0000.0000.0000.000
174A175ASP-1-0.771-0.86222.26315.05615.0560.0000.0000.0000.000
175A176LEU0-0.002-0.00924.884-0.503-0.5030.0000.0000.0000.000
176A177ASP-1-0.851-0.89924.20014.00114.0010.0000.0000.0000.000
177A178LEU00.041-0.00725.391-0.523-0.5230.0000.0000.0000.000
178A179GLY0-0.0280.01424.584-0.437-0.4370.0000.0000.0000.000
179A180SER0-0.044-0.03224.3340.2790.2790.0000.0000.0000.000
180A181ILE0-0.018-0.01624.522-0.521-0.5210.0000.0000.0000.000
181A182PRO00.0180.01427.1300.1830.1830.0000.0000.0000.000
182A183ASP-1-0.851-0.92829.05010.02110.0210.0000.0000.0000.000
183A184PRO00.0390.01826.290-0.204-0.2040.0000.0000.0000.000
184A185ILE00.0080.01028.511-0.023-0.0230.0000.0000.0000.000
185A186ALA00.0060.00031.075-0.208-0.2080.0000.0000.0000.000
186A187PHE00.006-0.00429.647-0.197-0.1970.0000.0000.0000.000
187A188GLY00.0120.00130.119-0.048-0.0480.0000.0000.0000.000
188A189ASN0-0.012-0.00630.651-0.371-0.3710.0000.0000.0000.000
189A190MET0-0.066-0.01633.463-0.356-0.3560.0000.0000.0000.000
190A191LEU0-0.057-0.04529.150-0.174-0.1740.0000.0000.0000.000
191A192ASP-1-0.820-0.89431.86410.33310.3330.0000.0000.0000.000
192A193HIS0-0.055-0.01934.175-0.331-0.3310.0000.0000.0000.000
193A194GLN0-0.107-0.04435.158-0.282-0.2820.0000.0000.0000.000
194A195VAL00.015-0.00736.3700.1550.1550.0000.0000.0000.000
195A196GLY00.0170.00036.572-0.021-0.0210.0000.0000.0000.000
196A197VAL0-0.034-0.01730.7830.2630.2630.0000.0000.0000.000
197A198VAL0-0.076-0.03430.272-0.251-0.2510.0000.0000.0000.000
198A199GLU-1-0.786-0.86926.30511.78711.7870.0000.0000.0000.000
199A200HIS0-0.036-0.06026.4400.5590.5590.0000.0000.0000.000
200A201GLY00.0610.03222.6100.0860.0860.0000.0000.0000.000
201A202LEU0-0.035-0.00522.2210.7010.7010.0000.0000.0000.000
202A203PHE0-0.048-0.02921.544-0.452-0.4520.0000.0000.0000.000
203A204ASN00.049-0.00523.6580.7850.7850.0000.0000.0000.000
204A205GLY00.0360.02526.221-0.345-0.3450.0000.0000.0000.000
205A206MET0-0.065-0.01823.814-0.161-0.1610.0000.0000.0000.000
206A207VAL0-0.022-0.00619.145-0.261-0.2610.0000.0000.0000.000
207A208ASN00.0340.01022.288-0.431-0.4310.0000.0000.0000.000
208A209ARG10.7680.85218.264-15.184-15.1840.0000.0000.0000.000
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