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: 3QM7L

Calculation Name: 3D3J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3J

Chain ID: A

ChEMBL ID:

UniProt ID: Q96F86

Base Structure: X-ray

Registration Date: 2023-03-14

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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3006165.352632
FMO2-HF: Nuclear repulsion 2913091.483715
FMO2-HF: Total energy -93073.868917
FMO2-MP2: Total energy -93343.160286


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:258:TYR)


Summations of interaction energy for fragment #1(A:258:TYR)
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.
-13.13-4.3993.836-4.09-8.4770.008
Interaction energy analysis for fragmet #1(A:258:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.031
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].
3A260ARG10.8980.9512.651-10.727-5.2303.091-2.732-5.8560.010
4A261ILE00.0070.0074.845-0.1300.084-0.001-0.023-0.1910.000
5A262ILE0-0.039-0.0205.555-0.236-0.2360.0000.0000.0000.000
6A263VAL00.008-0.0019.4380.0870.0870.0000.0000.0000.000
7A264PRO00.0130.01313.066-0.017-0.0170.0000.0000.0000.000
8A265HIS0-0.075-0.03415.6740.0170.0170.0000.0000.0000.000
9A266ASN00.023-0.00414.983-0.028-0.0280.0000.0000.0000.000
10A267VAL00.0150.01416.390-0.001-0.0010.0000.0000.0000.000
11A268SER00.001-0.00116.0820.0180.0180.0000.0000.0000.000
12A269LYS10.8990.96714.8770.1600.1600.0000.0000.0000.000
13A270GLU-1-0.794-0.8559.158-0.648-0.6480.0000.0000.0000.000
14A271PHE0-0.0260.00310.7670.0650.0650.0000.0000.0000.000
15A272CYS0-0.0070.0016.347-0.145-0.1450.0000.0000.0000.000
16A273THR00.0660.0336.8030.2380.2380.0000.0000.0000.000
17A274ASP-1-0.840-0.9257.914-0.213-0.2130.0000.0000.0000.000
18A275SER0-0.066-0.0286.5790.0290.0290.0000.0000.0000.000
19A276GLY00.0220.0034.7720.3120.414-0.001-0.008-0.0930.000
20A277LEU0-0.077-0.0222.532-3.727-1.5170.702-1.161-1.750-0.002
21A278VAL0-0.003-0.0093.2070.8921.6000.045-0.166-0.5870.000
22A279VAL0-0.017-0.0095.5090.2900.2900.0000.0000.0000.000
23A280PRO00.0050.0118.9480.0710.0710.0000.0000.0000.000
24A281SER0-0.039-0.03211.3750.0700.0700.0000.0000.0000.000
25A282ILE0-0.009-0.01115.1050.0060.0060.0000.0000.0000.000
26A283SER00.0280.00317.9100.0050.0050.0000.0000.0000.000
27A284TYR0-0.007-0.03521.4910.0010.0010.0000.0000.0000.000
28A285GLU-1-0.835-0.92924.382-0.041-0.0410.0000.0000.0000.000
29A286LEU0-0.057-0.01917.8130.0090.0090.0000.0000.0000.000
30A287HIS00.0120.00020.0650.0160.0160.0000.0000.0000.000
31A288LYS10.9030.92922.5190.0320.0320.0000.0000.0000.000
32A289LYS10.9300.96122.2470.0170.0170.0000.0000.0000.000
33A290LEU0-0.0010.00018.9200.0080.0080.0000.0000.0000.000
34A291LEU00.010-0.00422.6020.0100.0100.0000.0000.0000.000
35A292SER0-0.0130.00125.3170.0060.0060.0000.0000.0000.000
36A293VAL0-0.0250.00422.8460.0020.0020.0000.0000.0000.000
37A294ALA00.0340.01323.4710.0050.0050.0000.0000.0000.000
38A295GLU-1-0.841-0.89825.092-0.002-0.0020.0000.0000.0000.000
39A296LYS10.8370.91328.381-0.007-0.0070.0000.0000.0000.000
40A297HIS0-0.090-0.04924.7370.0010.0010.0000.0000.0000.000
41A298GLY00.0130.01627.1120.0050.0050.0000.0000.0000.000
42A299LEU0-0.051-0.02124.258-0.004-0.0040.0000.0000.0000.000
43A300THR00.0680.01728.067-0.003-0.0030.0000.0000.0000.000
44A301LEU00.0710.02530.250-0.002-0.0020.0000.0000.0000.000
45A302GLU-1-0.918-0.96531.190-0.004-0.0040.0000.0000.0000.000
46A303ARG10.9460.98929.443-0.011-0.0110.0000.0000.0000.000
47A304ARG10.8200.89625.6330.0070.0070.0000.0000.0000.000
48A305LEU0-0.0180.00227.686-0.005-0.0050.0000.0000.0000.000
49A306GLU-1-0.767-0.81930.185-0.014-0.0140.0000.0000.0000.000
50A307MET0-0.039-0.01022.1380.0000.0000.0000.0000.0000.000
51A308THR0-0.019-0.04025.136-0.006-0.0060.0000.0000.0000.000
52A309GLY00.0210.02326.218-0.005-0.0050.0000.0000.0000.000
53A310VAL00.0240.01426.676-0.003-0.0030.0000.0000.0000.000
54A311CYS0-0.021-0.00322.539-0.001-0.0010.0000.0000.0000.000
55A312ALA00.0240.00424.177-0.007-0.0070.0000.0000.0000.000
56A313SER0-0.020-0.02125.640-0.001-0.0010.0000.0000.0000.000
57A314GLN00.0290.00124.800-0.003-0.0030.0000.0000.0000.000
58A315MET0-0.0390.00421.236-0.004-0.0040.0000.0000.0000.000
59A316ALA00.020-0.00524.2770.0000.0000.0000.0000.0000.000
60A317LEU00.0290.00927.5940.0010.0010.0000.0000.0000.000
61A318THR0-0.056-0.03222.9680.0010.0010.0000.0000.0000.000
62A319LEU0-0.109-0.05623.6420.0000.0000.0000.0000.0000.000
63A320LEU0-0.0200.00127.0990.0020.0020.0000.0000.0000.000
64A321GLY0-0.072-0.01129.2320.0040.0040.0000.0000.0000.000
65A333GLN0-0.010-0.00942.3240.0000.0000.0000.0000.0000.000
66A334ARG10.7810.85140.0020.0130.0130.0000.0000.0000.000
67A335PRO00.0350.03935.5760.0000.0000.0000.0000.0000.000
68A336THR0-0.024-0.02937.8850.0010.0010.0000.0000.0000.000
69A337VAL00.000-0.01233.201-0.002-0.0020.0000.0000.0000.000
70A338ALA0-0.0030.01636.0040.0020.0020.0000.0000.0000.000
71A339LEU00.007-0.00532.850-0.003-0.0030.0000.0000.0000.000
72A340LEU00.0010.00534.7170.0020.0020.0000.0000.0000.000
73A341CYS0-0.0050.02134.459-0.003-0.0030.0000.0000.0000.000
74A342GLY00.0640.02535.2400.0020.0020.0000.0000.0000.000
75A343PRO0-0.033-0.01136.9930.0000.0000.0000.0000.0000.000
76A344HIS0-0.011-0.03933.2280.0020.0020.0000.0000.0000.000
77A345VAL00.030-0.00330.9760.0000.0000.0000.0000.0000.000
78A346LYS10.8560.92825.9830.0520.0520.0000.0000.0000.000
79A347GLY00.0100.01931.014-0.002-0.0020.0000.0000.0000.000
80A348ALA0-0.017-0.01833.7600.0000.0000.0000.0000.0000.000
81A349GLN0-0.024-0.01926.683-0.001-0.0010.0000.0000.0000.000
82A350GLY00.0600.02430.7770.0000.0000.0000.0000.0000.000
83A351ILE0-0.0170.00031.9430.0010.0010.0000.0000.0000.000
84A352SER00.0000.00731.5250.0010.0010.0000.0000.0000.000
85A353CYS0-0.056-0.02529.0030.0000.0000.0000.0000.0000.000
86A354GLY00.011-0.00431.3000.0000.0000.0000.0000.0000.000
87A355ARG10.8100.84734.4110.0140.0140.0000.0000.0000.000
88A356HIS0-0.021-0.01931.8700.0010.0010.0000.0000.0000.000
89A357LEU0-0.023-0.00430.6290.0000.0000.0000.0000.0000.000
90A358ALA0-0.0040.00434.1210.0010.0010.0000.0000.0000.000
91A359ASN0-0.028-0.01635.6350.0020.0020.0000.0000.0000.000
92A360HIS0-0.132-0.06632.7690.0010.0010.0000.0000.0000.000
93A361ASP-1-0.809-0.87336.296-0.015-0.0150.0000.0000.0000.000
94A362VAL0-0.0170.00934.204-0.001-0.0010.0000.0000.0000.000
95A363GLN0-0.023-0.02537.6890.0020.0020.0000.0000.0000.000
96A364VAL00.0000.01536.276-0.001-0.0010.0000.0000.0000.000
97A365ILE00.0020.01238.8900.0020.0020.0000.0000.0000.000
98A366LEU0-0.031-0.02637.169-0.002-0.0020.0000.0000.0000.000
99A367PHE0-0.008-0.00739.1680.0010.0010.0000.0000.0000.000
100A368LEU0-0.018-0.02138.714-0.001-0.0010.0000.0000.0000.000
101A369PRO0-0.0080.01840.6240.0010.0010.0000.0000.0000.000
102A370ASN00.027-0.00843.6290.0000.0000.0000.0000.0000.000
103A371PHE0-0.024-0.02142.063-0.001-0.0010.0000.0000.0000.000
104A372VAL00.0240.01646.2040.0010.0010.0000.0000.0000.000
105A373LYS10.9180.95445.2560.0090.0090.0000.0000.0000.000
106A374MET00.0620.03044.332-0.001-0.0010.0000.0000.0000.000
107A375LEU00.0040.01537.4330.0000.0000.0000.0000.0000.000
108A376GLU-1-0.918-0.94139.766-0.006-0.0060.0000.0000.0000.000
109A377SER00.0310.00735.4760.0000.0000.0000.0000.0000.000
110A378ILE00.0170.01036.8210.0000.0000.0000.0000.0000.000
111A379THR0-0.031-0.02639.0050.0000.0000.0000.0000.0000.000
112A380ASN00.014-0.00438.8960.0000.0000.0000.0000.0000.000
113A381GLU-1-0.774-0.89134.541-0.015-0.0150.0000.0000.0000.000
114A382LEU00.0050.01138.2670.0000.0000.0000.0000.0000.000
115A383SER0-0.0190.01141.2000.0000.0000.0000.0000.0000.000
116A384LEU00.0140.00637.5880.0010.0010.0000.0000.0000.000
117A385PHE00.0220.01237.9160.0000.0000.0000.0000.0000.000
118A386SER0-0.070-0.04740.6370.0000.0000.0000.0000.0000.000
119A387LYS10.8190.91343.2370.0090.0090.0000.0000.0000.000
120A388THR0-0.0350.00339.1810.0000.0000.0000.0000.0000.000
121A389GLN00.0370.01142.1320.0010.0010.0000.0000.0000.000
122A390GLY0-0.0180.00140.9420.0000.0000.0000.0000.0000.000
123A391GLN00.003-0.00541.8570.0010.0010.0000.0000.0000.000
124A392GLN0-0.0050.00042.405-0.001-0.0010.0000.0000.0000.000
125A393VAL0-0.016-0.01043.2250.0010.0010.0000.0000.0000.000
126A394SER00.0150.00943.789-0.001-0.0010.0000.0000.0000.000
127A395SER0-0.070-0.06345.8690.0000.0000.0000.0000.0000.000
128A396LEU00.0140.00141.4070.0000.0000.0000.0000.0000.000
129A397LYS10.8880.93444.8270.0140.0140.0000.0000.0000.000
130A398ASP-1-0.807-0.86846.534-0.013-0.0130.0000.0000.0000.000
131A399LEU0-0.053-0.00840.8230.0000.0000.0000.0000.0000.000
132A400PRO00.008-0.00242.3120.0010.0010.0000.0000.0000.000
133A401THR0-0.013-0.01243.649-0.001-0.0010.0000.0000.0000.000
134A402SER0-0.041-0.01043.9820.0000.0000.0000.0000.0000.000
135A403PRO0-0.023-0.01739.1090.0000.0000.0000.0000.0000.000
136A404VAL0-0.030-0.00136.5900.0010.0010.0000.0000.0000.000
137A405ASP-1-0.830-0.90734.659-0.024-0.0240.0000.0000.0000.000
138A406LEU0-0.060-0.03229.145-0.003-0.0030.0000.0000.0000.000
139A407VAL00.0180.02232.4500.0020.0020.0000.0000.0000.000
140A408ILE0-0.008-0.01029.258-0.004-0.0040.0000.0000.0000.000
141A409ASN0-0.001-0.01829.9120.0060.0060.0000.0000.0000.000
142A410CYS0-0.029-0.01829.228-0.004-0.0040.0000.0000.0000.000
143A411LEU00.0790.02331.5320.0030.0030.0000.0000.0000.000
144A412ASP-1-0.778-0.86431.364-0.035-0.0350.0000.0000.0000.000
145A413CYS0-0.058-0.00530.887-0.003-0.0030.0000.0000.0000.000
146A414PRO00.0400.00928.2930.0020.0020.0000.0000.0000.000
147A415GLU-1-0.786-0.85931.360-0.025-0.0250.0000.0000.0000.000
148A416ASN0-0.079-0.03434.0020.0020.0020.0000.0000.0000.000
149A417VAL00.0650.03035.9950.0000.0000.0000.0000.0000.000
150A418PHE00.0430.00236.923-0.001-0.0010.0000.0000.0000.000
151A419LEU0-0.063-0.02337.9850.0010.0010.0000.0000.0000.000
152A420ARG10.9110.94331.4690.0380.0380.0000.0000.0000.000
153A421ASP-1-0.828-0.90838.735-0.023-0.0230.0000.0000.0000.000
154A422GLN0-0.041-0.01642.0050.0020.0020.0000.0000.0000.000
155A423PRO00.0340.00943.252-0.001-0.0010.0000.0000.0000.000
156A424TRP00.0350.00639.0430.0000.0000.0000.0000.0000.000
157A425TYR0-0.030-0.02434.3510.0000.0000.0000.0000.0000.000
158A426LYS10.8680.91839.7970.0220.0220.0000.0000.0000.000
159A427ALA0-0.0230.00141.5840.0000.0000.0000.0000.0000.000
160A428ALA00.0190.00139.0140.0000.0000.0000.0000.0000.000
161A429VAL00.0100.00836.0250.0000.0000.0000.0000.0000.000
162A430ALA0-0.012-0.00437.994-0.001-0.0010.0000.0000.0000.000
163A431TRP0-0.0080.00337.5670.0000.0000.0000.0000.0000.000
164A432ALA00.032-0.00335.0250.0000.0000.0000.0000.0000.000
165A433ASN0-0.0010.00135.204-0.002-0.0020.0000.0000.0000.000
166A434GLN0-0.098-0.04037.3770.0020.0020.0000.0000.0000.000
167A435ASN00.0170.01438.0050.0000.0000.0000.0000.0000.000
168A436ARG10.9030.93836.9370.0220.0220.0000.0000.0000.000
169A437ALA00.0220.03335.076-0.001-0.0010.0000.0000.0000.000
170A438PRO0-0.031-0.00729.505-0.002-0.0020.0000.0000.0000.000
171A439VAL00.0760.03029.3700.0010.0010.0000.0000.0000.000
172A440LEU0-0.024-0.00124.459-0.006-0.0060.0000.0000.0000.000
173A441SER00.0460.02026.0030.0070.0070.0000.0000.0000.000
174A442ILE0-0.003-0.00124.873-0.010-0.0100.0000.0000.0000.000
175A443ASP-1-0.815-0.89923.904-0.055-0.0550.0000.0000.0000.000
176A444PRO00.0310.02223.3110.0060.0060.0000.0000.0000.000
177A445PRO0-0.031-0.02525.027-0.006-0.0060.0000.0000.0000.000
178A446VAL0-0.038-0.02122.741-0.004-0.0040.0000.0000.0000.000
179A447HIS00.010-0.00925.057-0.001-0.0010.0000.0000.0000.000
180A448GLU-1-0.909-0.95028.036-0.040-0.0400.0000.0000.0000.000
181A449VAL00.0750.04726.7540.0030.0030.0000.0000.0000.000
182A450GLU-1-0.883-0.91730.160-0.039-0.0390.0000.0000.0000.000
183A451GLN0-0.109-0.05032.9730.0040.0040.0000.0000.0000.000
184A452GLY00.0820.05432.3310.0020.0020.0000.0000.0000.000
185A453ILE0-0.110-0.06331.7010.0030.0030.0000.0000.0000.000
186A454ASP-1-0.876-0.93329.449-0.047-0.0470.0000.0000.0000.000
187A455ALA0-0.050-0.02025.9210.0030.0030.0000.0000.0000.000
188A456LYS10.9280.97725.4810.0440.0440.0000.0000.0000.000
189A457TRP00.011-0.02322.122-0.007-0.0070.0000.0000.0000.000
190A458SER00.0340.01321.6340.0110.0110.0000.0000.0000.000
191A459LEU0-0.054-0.02719.553-0.015-0.0150.0000.0000.0000.000
192A460ALA00.0220.01317.6720.0090.0090.0000.0000.0000.000
193A461LEU00.0430.00919.381-0.001-0.0010.0000.0000.0000.000
194A462GLY00.0160.02217.9090.0060.0060.0000.0000.0000.000
195A463LEU0-0.040-0.04413.505-0.019-0.0190.0000.0000.0000.000
196A464PRO00.0080.01713.9620.0240.0240.0000.0000.0000.000
197A465LEU00.0770.04717.106-0.005-0.0050.0000.0000.0000.000
198A466PRO0-0.024-0.03317.716-0.020-0.0200.0000.0000.0000.000
199A467LEU0-0.0020.01118.6570.0150.0150.0000.0000.0000.000
200A468GLY00.0490.01119.322-0.016-0.0160.0000.0000.0000.000
201A469GLU-1-0.943-0.98421.675-0.070-0.0700.0000.0000.0000.000
202A470HIS00.016-0.01122.585-0.002-0.0020.0000.0000.0000.000
203A471ALA0-0.0250.00521.4750.0030.0030.0000.0000.0000.000
204A472GLY00.0480.05722.7350.0020.0020.0000.0000.0000.000
205A473ARG10.8720.91618.9560.0710.0710.0000.0000.0000.000
206A474ILE00.0350.02116.2820.0040.0040.0000.0000.0000.000
207A475TYR00.015-0.00516.237-0.024-0.0240.0000.0000.0000.000
208A476LEU0-0.050-0.01613.049-0.002-0.0020.0000.0000.0000.000
209A477CYS00.0280.01216.3810.0040.0040.0000.0000.0000.000
210A478ASP-1-0.844-0.92317.432-0.005-0.0050.0000.0000.0000.000
211A479ILE0-0.030-0.02618.8250.0030.0030.0000.0000.0000.000
212A480GLY00.0390.01720.5740.0050.0050.0000.0000.0000.000
213A481ILE0-0.035-0.01818.9660.0050.0050.0000.0000.0000.000
214A482PRO00.0340.01118.3920.0170.0170.0000.0000.0000.000
215A483GLN0-0.019-0.03311.009-0.071-0.0710.0000.0000.0000.000
216A484GLN00.0300.00215.595-0.007-0.0070.0000.0000.0000.000
217A485VAL00.0270.02717.855-0.010-0.0100.0000.0000.0000.000
218A486PHE0-0.014-0.02014.826-0.015-0.0150.0000.0000.0000.000
219A487GLN0-0.0010.00112.730-0.043-0.0430.0000.0000.0000.000
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