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: 9GL12

Calculation Name: 1FLK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FLK

Chain ID: A

ChEMBL ID:

UniProt ID: Q13114

Base Structure: X-ray

Registration Date: 2023-03-13

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 OptAll
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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2107393.022457
FMO2-HF: Nuclear repulsion 2025111.692941
FMO2-HF: Total energy -82281.329516
FMO2-MP2: Total energy -82517.123585


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:300:LEU)


Summations of interaction energy for fragment #1(A:300: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.
-3.4050.3166.82-1.95-8.593-0.006
Interaction energy analysis for fragmet #1(A:300:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.010
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].
3A302SER0-0.039-0.0213.890-1.881-0.502-0.007-0.579-0.7940.000
4A303VAL0-0.022-0.0312.304-0.707-0.1043.792-0.997-3.3990.001
5A304ASP-1-0.739-0.8552.543-3.873-2.0082.935-1.443-3.357-0.005
6A305LYS10.7980.8843.1742.8451.8550.0871.362-0.459-0.001
7A306SER0-0.0210.0015.1750.3480.3480.0000.0000.0000.000
8A307ALA0-0.017-0.0083.5890.0630.2910.003-0.041-0.1910.000
9A308GLY00.0460.0123.697-1.147-0.5490.011-0.250-0.359-0.001
10A309GLN0-0.062-0.0244.7300.2540.292-0.001-0.002-0.0340.000
11A310VAL00.0130.0037.8290.1210.1210.0000.0000.0000.000
12A311ALA00.0380.0209.0150.0700.0700.0000.0000.0000.000
13A312ARG10.9330.95810.8210.3490.3490.0000.0000.0000.000
14A313ASN0-0.0160.00212.6470.0650.0650.0000.0000.0000.000
15A314THR0-0.011-0.01913.4230.0360.0360.0000.0000.0000.000
16A315GLY00.0910.05115.4330.0260.0260.0000.0000.0000.000
17A316LEU0-0.073-0.03217.0560.0240.0240.0000.0000.0000.000
18A317LEU00.0030.00117.5980.0220.0220.0000.0000.0000.000
19A318GLU-1-0.819-0.89617.396-0.223-0.2230.0000.0000.0000.000
20A319SER0-0.029-0.02421.1970.0170.0170.0000.0000.0000.000
21A320GLN0-0.031-0.01123.3930.0230.0230.0000.0000.0000.000
22A321LEU00.0110.00822.5910.0110.0110.0000.0000.0000.000
23A322SER00.0140.01825.5820.0090.0090.0000.0000.0000.000
24A323ARG10.9050.93426.9730.1190.1190.0000.0000.0000.000
25A324HIS00.005-0.00428.0980.0110.0110.0000.0000.0000.000
26A325ASP-1-0.888-0.93629.921-0.089-0.0890.0000.0000.0000.000
27A326GLN0-0.0010.01431.3410.0050.0050.0000.0000.0000.000
28A327MET0-0.032-0.00933.3780.0060.0060.0000.0000.0000.000
29A328LEU00.001-0.00132.9500.0050.0050.0000.0000.0000.000
30A329SER00.022-0.00235.0870.0050.0050.0000.0000.0000.000
31A330VAL0-0.012-0.00837.5600.0040.0040.0000.0000.0000.000
32A331HIS0-0.065-0.05138.7370.0060.0060.0000.0000.0000.000
33A332ASP-1-0.924-0.95140.206-0.055-0.0550.0000.0000.0000.000
34A333ILE00.0190.00941.0970.0030.0030.0000.0000.0000.000
35A334ARG10.8780.92943.1470.0560.0560.0000.0000.0000.000
36A335LEU0-0.022-0.00443.5090.0020.0020.0000.0000.0000.000
37A336ALA00.0650.04446.5990.0020.0020.0000.0000.0000.000
38A337ASP-1-0.919-0.96847.868-0.043-0.0430.0000.0000.0000.000
39A338MET0-0.110-0.05548.9570.0030.0030.0000.0000.0000.000
40A339ASP-1-0.865-0.92450.396-0.039-0.0390.0000.0000.0000.000
41A340LEU0-0.051-0.02452.8940.0020.0020.0000.0000.0000.000
42A341ARG10.9110.95352.2380.0390.0390.0000.0000.0000.000
43A342PHE00.0060.00753.1690.0010.0010.0000.0000.0000.000
44A343GLN00.0510.03457.1500.0010.0010.0000.0000.0000.000
45A344VAL0-0.043-0.01958.9010.0010.0010.0000.0000.0000.000
46A345LEU0-0.023-0.01560.1410.0010.0010.0000.0000.0000.000
47A346GLU-1-0.930-0.97159.509-0.030-0.0300.0000.0000.0000.000
48A347THR0-0.104-0.06763.0040.0010.0010.0000.0000.0000.000
49A348ALA0-0.0050.02364.8100.0010.0010.0000.0000.0000.000
50A349SER0-0.049-0.05166.5500.0000.0000.0000.0000.0000.000
51A350TYR00.019-0.01165.4710.0000.0000.0000.0000.0000.000
52A351ASN00.0840.03872.2040.0000.0000.0000.0000.0000.000
53A352GLY00.0300.03374.7030.0010.0010.0000.0000.0000.000
54A353VAL0-0.042-0.01275.9810.0000.0000.0000.0000.0000.000
55A354LEU00.0130.04368.7640.0000.0000.0000.0000.0000.000
56A355ILE0-0.003-0.01571.0520.0010.0010.0000.0000.0000.000
57A356TRP00.0740.04264.3730.0000.0000.0000.0000.0000.000
58A357LYS10.8410.91966.2380.0240.0240.0000.0000.0000.000
59A358ILE0-0.0160.01564.623-0.001-0.0010.0000.0000.0000.000
60A359ARG11.0020.97961.4090.0290.0290.0000.0000.0000.000
61A360ASP-1-0.762-0.86159.008-0.031-0.0310.0000.0000.0000.000
62A361TYR0-0.038-0.05062.6310.0000.0000.0000.0000.0000.000
63A362LYS10.9240.93864.4180.0240.0240.0000.0000.0000.000
64A363ARG10.7920.85156.8890.0320.0320.0000.0000.0000.000
65A364ARG10.8850.92958.0980.0300.0300.0000.0000.0000.000
66A365LYS10.8350.90862.2790.0210.0210.0000.0000.0000.000
67A366GLN00.031-0.00362.3490.0010.0010.0000.0000.0000.000
68A367GLU-1-0.828-0.88957.523-0.031-0.0310.0000.0000.0000.000
69A368ALA00.0060.01560.7500.0000.0000.0000.0000.0000.000
70A369VAL0-0.053-0.02863.6530.0000.0000.0000.0000.0000.000
71A370MET0-0.051-0.02858.5140.0000.0000.0000.0000.0000.000
72A371GLY00.0160.00859.707-0.001-0.0010.0000.0000.0000.000
73A372LYS10.9190.97155.8150.0300.0300.0000.0000.0000.000
74A373THR0-0.024-0.02857.127-0.001-0.0010.0000.0000.0000.000
75A374LEU0-0.0090.01759.6790.0010.0010.0000.0000.0000.000
76A375SER0-0.033-0.01162.2930.0010.0010.0000.0000.0000.000
77A376LEU0-0.023-0.00861.142-0.001-0.0010.0000.0000.0000.000
78A377TYR00.0520.00161.7240.0010.0010.0000.0000.0000.000
79A378SER0-0.041-0.02563.3810.0000.0000.0000.0000.0000.000
80A379GLN00.0170.00163.066-0.001-0.0010.0000.0000.0000.000
81A380PRO00.001-0.01162.3200.0010.0010.0000.0000.0000.000
82A381PHE0-0.046-0.01065.3960.0000.0000.0000.0000.0000.000
83A382TYR00.0300.01064.7200.0000.0000.0000.0000.0000.000
84A383THR0-0.017-0.02271.3020.0000.0000.0000.0000.0000.000
85A384GLY00.1110.05773.6710.0010.0010.0000.0000.0000.000
86A385TYR0-0.034-0.02969.5990.0000.0000.0000.0000.0000.000
87A386PHE0-0.0220.00768.401-0.001-0.0010.0000.0000.0000.000
88A387GLY00.0090.01571.6890.0000.0000.0000.0000.0000.000
89A388TYR0-0.022-0.05471.443-0.001-0.0010.0000.0000.0000.000
90A389LYS10.8880.95562.2670.0280.0280.0000.0000.0000.000
91A390MET0-0.083-0.02068.9180.0010.0010.0000.0000.0000.000
92A391CYS00.0080.01866.203-0.001-0.0010.0000.0000.0000.000
93A392ALA00.0250.01567.9670.0010.0010.0000.0000.0000.000
94A393ARG10.8910.94664.2550.0240.0240.0000.0000.0000.000
95A394VAL00.0090.00366.3160.0010.0010.0000.0000.0000.000
96A395TYR00.006-0.01966.295-0.001-0.0010.0000.0000.0000.000
97A396LEU0-0.011-0.00964.7060.0010.0010.0000.0000.0000.000
98A397ASN00.0310.01667.1500.0010.0010.0000.0000.0000.000
99A398GLY00.0470.03268.9140.0000.0000.0000.0000.0000.000
100A399ASP-1-0.793-0.90568.749-0.023-0.0230.0000.0000.0000.000
101A400GLY00.002-0.00171.0620.0010.0010.0000.0000.0000.000
102A401MET0-0.005-0.01873.6280.0000.0000.0000.0000.0000.000
103A402GLY00.0410.02475.2160.0000.0000.0000.0000.0000.000
104A403LYS10.8290.92867.4610.0220.0220.0000.0000.0000.000
105A404GLY0-0.019-0.00571.2210.0010.0010.0000.0000.0000.000
106A405THR0-0.019-0.00972.2260.0000.0000.0000.0000.0000.000
107A406HIS0-0.014-0.00574.5620.0000.0000.0000.0000.0000.000
108A407LEU0-0.0010.02170.625-0.001-0.0010.0000.0000.0000.000
109A408SER0-0.034-0.03571.2150.0000.0000.0000.0000.0000.000
110A409LEU0-0.042-0.02570.915-0.001-0.0010.0000.0000.0000.000
111A410PHE0-0.022-0.00970.5740.0010.0010.0000.0000.0000.000
112A411PHE00.0290.00871.4090.0000.0000.0000.0000.0000.000
113A412VAL0-0.002-0.02066.8380.0000.0000.0000.0000.0000.000
114A413ILE00.0380.03169.2600.0000.0000.0000.0000.0000.000
115A414MET0-0.017-0.03162.6940.0000.0000.0000.0000.0000.000
116A415ARG10.8560.91859.6160.0290.0290.0000.0000.0000.000
117A416GLY00.018-0.00164.619-0.001-0.0010.0000.0000.0000.000
118A417GLU-1-0.868-0.93662.224-0.028-0.0280.0000.0000.0000.000
119A418TYR00.0570.02765.3810.0000.0000.0000.0000.0000.000
120A419ASP-1-0.808-0.88868.617-0.023-0.0230.0000.0000.0000.000
121A420ALA0-0.062-0.05670.3720.0000.0000.0000.0000.0000.000
122A421LEU0-0.0130.00372.2220.0010.0010.0000.0000.0000.000
123A422LEU0-0.0040.01972.3980.0000.0000.0000.0000.0000.000
124A423PRO00.0180.00876.1460.0000.0000.0000.0000.0000.000
125A424TRP00.0650.05572.4670.0000.0000.0000.0000.0000.000
126A425PRO00.001-0.00778.1000.0010.0010.0000.0000.0000.000
127A426PHE00.0060.00276.0150.0000.0000.0000.0000.0000.000
128A427LYS10.9100.93978.1460.0170.0170.0000.0000.0000.000
129A428GLN00.0060.00979.3510.0010.0010.0000.0000.0000.000
130A429LYS10.9390.97380.9230.0160.0160.0000.0000.0000.000
131A430VAL00.0260.01876.8380.0000.0000.0000.0000.0000.000
132A431THR0-0.023-0.01179.5500.0010.0010.0000.0000.0000.000
133A432LEU0-0.0260.00075.517-0.001-0.0010.0000.0000.0000.000
134A433MET00.028-0.00676.7790.0010.0010.0000.0000.0000.000
135A434LEU00.0080.02474.023-0.001-0.0010.0000.0000.0000.000
136A435MET0-0.020-0.02075.1020.0010.0010.0000.0000.0000.000
137A436ASP-1-0.723-0.84576.305-0.017-0.0170.0000.0000.0000.000
138A437GLN0-0.012-0.01572.6810.0000.0000.0000.0000.0000.000
139A438GLY00.0180.00077.6500.0000.0000.0000.0000.0000.000
140A439SER0-0.030-0.03480.8010.0000.0000.0000.0000.0000.000
141A440SER00.0250.02283.2630.0000.0000.0000.0000.0000.000
142A441ARG10.8060.92580.7130.0170.0170.0000.0000.0000.000
143A442ARG10.9070.95383.7530.0150.0150.0000.0000.0000.000
144A443HIS00.0960.04880.2220.0000.0000.0000.0000.0000.000
145A444LEU0-0.0230.00679.6800.0000.0000.0000.0000.0000.000
146A445GLY0-0.005-0.02379.679-0.001-0.0010.0000.0000.0000.000
147A446ASP-1-0.861-0.89981.155-0.016-0.0160.0000.0000.0000.000
148A447ALA0-0.061-0.05381.6240.0000.0000.0000.0000.0000.000
149A448PHE00.0090.01977.0160.0000.0000.0000.0000.0000.000
150A449LYS10.9160.94082.6690.0160.0160.0000.0000.0000.000
151A450PRO0-0.0270.00379.0060.0000.0000.0000.0000.0000.000
152A451ASP-1-0.753-0.85280.929-0.016-0.0160.0000.0000.0000.000
153A452PRO0-0.004-0.00480.7240.0000.0000.0000.0000.0000.000
154A453ASN0-0.022-0.01681.2120.0000.0000.0000.0000.0000.000
155A454SER00.0260.01577.270-0.001-0.0010.0000.0000.0000.000
156A455SER0-0.018-0.01873.3360.0000.0000.0000.0000.0000.000
157A456SER0-0.058-0.01773.1330.0000.0000.0000.0000.0000.000
158A457PHE00.0650.03073.9320.0000.0000.0000.0000.0000.000
159A458LYS10.8130.88073.9330.0180.0180.0000.0000.0000.000
160A459LYS10.8450.92467.5110.0230.0230.0000.0000.0000.000
161A460PRO0-0.0060.01067.3000.0000.0000.0000.0000.0000.000
162A461THR00.0110.02865.4000.0000.0000.0000.0000.0000.000
163A462GLY00.027-0.00163.215-0.001-0.0010.0000.0000.0000.000
164A463GLU-1-0.858-0.92358.212-0.031-0.0310.0000.0000.0000.000
165A464MET0-0.0060.00361.3890.0000.0000.0000.0000.0000.000
166A465ASN0-0.026-0.01065.3940.0000.0000.0000.0000.0000.000
167A466ILE00.018-0.00168.4300.0000.0000.0000.0000.0000.000
168A467ALA00.0110.02468.7130.0000.0000.0000.0000.0000.000
169A468SER0-0.017-0.01870.6980.0000.0000.0000.0000.0000.000
170A469GLY00.0290.00774.3550.0000.0000.0000.0000.0000.000
171A470CYS00.0050.01675.6940.0000.0000.0000.0000.0000.000
172A471PRO00.033-0.00174.4200.0000.0000.0000.0000.0000.000
173A472VAL0-0.0030.02075.2680.0000.0000.0000.0000.0000.000
174A473PHE0-0.0390.00075.8280.0000.0000.0000.0000.0000.000
175A474VAL00.0390.01276.7100.0000.0000.0000.0000.0000.000
176A475ALA00.0610.04676.6080.0000.0000.0000.0000.0000.000
177A476GLN00.0350.01171.3880.0000.0000.0000.0000.0000.000
178A477THR00.0090.00075.4660.0000.0000.0000.0000.0000.000
179A478VAL0-0.019-0.00178.1460.0000.0000.0000.0000.0000.000
180A479LEU0-0.026-0.00572.5280.0000.0000.0000.0000.0000.000
181A480GLU-1-0.798-0.88871.207-0.021-0.0210.0000.0000.0000.000
182A481ASN0-0.074-0.02675.0680.0000.0000.0000.0000.0000.000
183A482GLY0-0.023-0.02777.3300.0010.0010.0000.0000.0000.000
184A483THR0-0.016-0.04176.7250.0000.0000.0000.0000.0000.000
185A484TYR0-0.034-0.01675.5670.0000.0000.0000.0000.0000.000
186A485ILE0-0.0220.01070.497-0.001-0.0010.0000.0000.0000.000
187A486LYS10.8610.91571.6510.0210.0210.0000.0000.0000.000
188A487ASP-1-0.840-0.90068.420-0.022-0.0220.0000.0000.0000.000
189A488ASP-1-0.794-0.87364.852-0.025-0.0250.0000.0000.0000.000
190A489THR0-0.094-0.03665.439-0.001-0.0010.0000.0000.0000.000
191A490ILE00.0760.03767.7980.0010.0010.0000.0000.0000.000
192A491PHE00.019-0.00369.291-0.001-0.0010.0000.0000.0000.000
193A492ILE0-0.015-0.00170.1520.0010.0010.0000.0000.0000.000
194A493LYS10.9350.97072.1060.0180.0180.0000.0000.0000.000
195A494VAL0-0.008-0.00373.0570.0000.0000.0000.0000.0000.000
196A495ILE0-0.019-0.01975.6960.0000.0000.0000.0000.0000.000
197A496VAL0-0.006-0.00475.1200.0000.0000.0000.0000.0000.000
198A497ASP-1-0.907-0.96878.257-0.016-0.0160.0000.0000.0000.000
199A498THR0-0.021-0.02577.7290.0000.0000.0000.0000.0000.000
200A499SER0-0.0300.00281.0680.0000.0000.0000.0000.0000.000
201A500ASP-1-0.910-0.94084.631-0.015-0.0150.0000.0000.0000.000
202A501LEU0-0.105-0.06680.8720.0000.0000.0000.0000.0000.000
203A502PRO0-0.013-0.00682.2640.0000.0000.0000.0000.0000.000
204A503ASP-1-0.856-0.89877.660-0.019-0.0190.0000.0000.0000.000
205A504PRO0-0.102-0.05979.1650.0000.0000.0000.0000.0000.000