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

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FMODB ID: G66L1

Calculation Name: 4ABY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ABY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXF2

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 358
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5068168.352471
FMO2-HF: Nuclear repulsion 4935157.341316
FMO2-HF: Total energy -133011.011155
FMO2-MP2: Total energy -133405.215449


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:32:PRO)


Summations of interaction energy for fragment #1(A:32:PRO)
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.
-2.9531.181.35-2.039-3.4410.001
Interaction energy analysis for fragmet #1(A:32:PRO)
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 : 0.000
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].
3A34LEU00.0090.0133.718-1.6160.606-0.018-1.136-1.0680.004
4A35SER0-0.075-0.0605.4660.5300.5300.0000.0000.0000.000
5A36ARG10.9180.9757.7720.2440.2440.0000.0000.0000.000
6A37LEU0-0.020-0.00711.175-0.117-0.1170.0000.0000.0000.000
7A38GLU-1-0.877-0.94013.834-0.098-0.0980.0000.0000.0000.000
8A39ILE0-0.027-0.00917.115-0.019-0.0190.0000.0000.0000.000
9A40ARG10.9340.97320.0400.1450.1450.0000.0000.0000.000
10A41ASN0-0.021-0.03723.445-0.004-0.0040.0000.0000.0000.000
11A42LEU00.0340.02421.112-0.001-0.0010.0000.0000.0000.000
12A43ALA00.0400.02225.0620.0020.0020.0000.0000.0000.000
13A44THR0-0.020-0.01727.2840.0100.0100.0000.0000.0000.000
14A45ILE00.0310.01022.2620.0090.0090.0000.0000.0000.000
15A46THR0-0.031-0.01326.194-0.010-0.0100.0000.0000.0000.000
16A47GLN00.0610.01422.030-0.005-0.0050.0000.0000.0000.000
17A48LEU0-0.0090.00718.4950.0080.0080.0000.0000.0000.000
18A49GLU-1-0.924-0.96617.883-0.103-0.1030.0000.0000.0000.000
19A50LEU0-0.016-0.01215.0340.0260.0260.0000.0000.0000.000
20A51GLU-1-0.912-0.95912.221-0.045-0.0450.0000.0000.0000.000
21A52LEU0-0.021-0.01810.9870.0480.0480.0000.0000.0000.000
22A53GLY00.004-0.0408.701-0.105-0.1050.0000.0000.0000.000
23A54GLY0-0.040-0.0277.5680.0860.0860.0000.0000.0000.000
24A55GLY00.0720.0477.470-0.127-0.1270.0000.0000.0000.000
25A56PHE00.020-0.0029.832-0.139-0.1390.0000.0000.0000.000
26A57CYS0-0.082-0.01611.3490.0550.0550.0000.0000.0000.000
27A58ALA00.0370.02314.163-0.029-0.0290.0000.0000.0000.000
28A59PHE0-0.018-0.00914.8620.0180.0180.0000.0000.0000.000
29A60THR00.0310.01619.9190.0060.0060.0000.0000.0000.000
30A61GLY00.0200.01323.616-0.001-0.0010.0000.0000.0000.000
31A62GLU-1-0.876-0.93826.536-0.085-0.0850.0000.0000.0000.000
32A63THR00.0570.01124.698-0.010-0.0100.0000.0000.0000.000
33A64GLY00.0150.01424.611-0.016-0.0160.0000.0000.0000.000
34A65ALA0-0.001-0.00125.494-0.011-0.0110.0000.0000.0000.000
35A66GLY00.0470.01721.618-0.014-0.0140.0000.0000.0000.000
36A67LYS10.9460.98420.4890.1830.1830.0000.0000.0000.000
37A68SER0-0.019-0.00720.958-0.022-0.0220.0000.0000.0000.000
38A69ILE00.000-0.00317.308-0.019-0.0190.0000.0000.0000.000
39A70ILE00.003-0.00214.943-0.044-0.0440.0000.0000.0000.000
40A71VAL0-0.009-0.00516.349-0.049-0.0490.0000.0000.0000.000
41A72ASP-1-0.924-0.96318.596-0.237-0.2370.0000.0000.0000.000
42A73ALA0-0.037-0.02917.460-0.003-0.0030.0000.0000.0000.000
43A74LEU00.0100.00712.023-0.020-0.0200.0000.0000.0000.000
44A75GLY00.0570.04014.747-0.037-0.0370.0000.0000.0000.000
45A76LEU0-0.071-0.04517.2700.0090.0090.0000.0000.0000.000
46A77LEU0-0.031-0.01511.9680.0190.0190.0000.0000.0000.000
47A78LEU00.0390.02712.220-0.026-0.0260.0000.0000.0000.000
48A79GLY0-0.007-0.01214.5170.0280.0280.0000.0000.0000.000
49A80GLY00.0390.03017.5630.0340.0340.0000.0000.0000.000
50A81ARG10.9840.98819.9880.2050.2050.0000.0000.0000.000
51A82ALA00.0130.00622.898-0.010-0.0100.0000.0000.0000.000
52A83ASN00.0170.00624.6400.0250.0250.0000.0000.0000.000
53A84HIS10.8840.92526.3800.1340.1340.0000.0000.0000.000
54A85ASP-1-0.845-0.90328.830-0.124-0.1240.0000.0000.0000.000
55A86LEU0-0.025-0.01822.6990.0030.0030.0000.0000.0000.000
56A87ILE0-0.054-0.02726.492-0.004-0.0040.0000.0000.0000.000
57A88ARG10.9010.97228.0410.1040.1040.0000.0000.0000.000
58A89SER0-0.032-0.01729.7390.0070.0070.0000.0000.0000.000
59A90GLY00.0100.00833.4570.0020.0020.0000.0000.0000.000
60A91GLU-1-0.926-0.95030.206-0.081-0.0810.0000.0000.0000.000
61A92LYS10.9900.99731.0850.0740.0740.0000.0000.0000.000
62A93GLU-1-0.916-0.98627.115-0.114-0.1140.0000.0000.0000.000
63A94LEU00.0050.03922.2460.0060.0060.0000.0000.0000.000
64A95LEU0-0.042-0.04619.7550.0030.0030.0000.0000.0000.000
65A96VAL00.0090.01415.7470.0080.0080.0000.0000.0000.000
66A97THR00.0220.00814.205-0.020-0.0200.0000.0000.0000.000
67A98GLY00.0140.02411.3810.0130.0130.0000.0000.0000.000
68A99PHE00.017-0.0039.3310.0120.0120.0000.0000.0000.000
69A100TRP00.0110.0123.682-0.4140.4720.014-0.264-0.6340.000
70A109ASP-1-0.934-0.9666.117-0.283-0.2830.0000.0000.0000.000
71A110SER0-0.005-0.0068.150-0.095-0.0950.0000.0000.0000.000
72A111ALA00.0350.03310.6870.0130.0130.0000.0000.0000.000
73A112SER0-0.017-0.01512.4390.0100.0100.0000.0000.0000.000
74A113ARG10.8630.93815.8600.2860.2860.0000.0000.0000.000
75A114ARG10.8990.96618.7340.1390.1390.0000.0000.0000.000
76A115LEU0-0.024-0.00322.2970.0050.0050.0000.0000.0000.000
77A116SER00.0240.00625.2290.0100.0100.0000.0000.0000.000
78A117SER00.039-0.00328.730-0.001-0.0010.0000.0000.0000.000
79A118ALA0-0.060-0.01831.8620.0040.0040.0000.0000.0000.000
80A119GLY00.0320.01531.4240.0040.0040.0000.0000.0000.000
81A120ARG10.8990.95328.5110.0950.0950.0000.0000.0000.000
82A121GLY00.012-0.01325.281-0.006-0.0060.0000.0000.0000.000
83A122ALA0-0.068-0.03822.7730.0120.0120.0000.0000.0000.000
84A123ALA00.0440.03817.868-0.010-0.0100.0000.0000.0000.000
85A124ARG10.8850.94317.1270.1760.1760.0000.0000.0000.000
86A125LEU00.0540.03611.898-0.057-0.0570.0000.0000.0000.000
87A126SER00.0480.00911.2930.0230.0230.0000.0000.0000.000
88A127GLY0-0.051-0.01913.6390.0400.0400.0000.0000.0000.000
89A128GLU-1-0.913-0.95016.787-0.122-0.1220.0000.0000.0000.000
90A129VAL0-0.079-0.04718.288-0.027-0.0270.0000.0000.0000.000
91A130VAL00.0710.04816.8320.0110.0110.0000.0000.0000.000
92A131SER0-0.090-0.05719.888-0.001-0.0010.0000.0000.0000.000
93A132VAL00.013-0.02118.971-0.021-0.0210.0000.0000.0000.000
94A133ARG10.8970.94618.3910.1890.1890.0000.0000.0000.000
95A134GLU-1-0.802-0.89616.849-0.225-0.2250.0000.0000.0000.000
96A135LEU0-0.031-0.00913.433-0.032-0.0320.0000.0000.0000.000
97A136GLN0-0.051-0.02113.504-0.065-0.0650.0000.0000.0000.000
98A137GLU-1-0.891-0.93513.759-0.332-0.3320.0000.0000.0000.000
99A138TRP0-0.0140.0087.247-0.118-0.1180.0000.0000.0000.000
100A139ALA00.029-0.0019.240-0.168-0.1680.0000.0000.0000.000
101A140GLN0-0.0010.0029.686-0.109-0.1090.0000.0000.0000.000
102A141GLY00.0230.0338.5130.0340.0340.0000.0000.0000.000
103A142ARG10.8380.9093.7260.9271.1910.001-0.031-0.2340.000
104A143LEU0-0.005-0.0276.395-0.199-0.1990.0000.0000.0000.000
105A144THR00.0630.0329.4640.1270.1270.0000.0000.0000.000
106A145ILE0-0.024-0.01112.4130.0050.0050.0000.0000.0000.000
107A146HIS00.027-0.00514.6840.0540.0540.0000.0000.0000.000
108A147TRP0-0.0090.01817.9990.0110.0110.0000.0000.0000.000
109A148GLN0-0.056-0.05220.271-0.011-0.0110.0000.0000.0000.000
110A149HIS0-0.045-0.03317.0560.0110.0110.0000.0000.0000.000
111A150SER00.0760.03217.850-0.024-0.0240.0000.0000.0000.000
112A151ALA0-0.026-0.00119.3780.0050.0050.0000.0000.0000.000
113A152VAL0-0.033-0.01716.4760.0210.0210.0000.0000.0000.000
114A153SER00.0040.01514.262-0.025-0.0250.0000.0000.0000.000
115A154LEU00.037-0.00815.2000.0200.0200.0000.0000.0000.000
116A155LEU0-0.017-0.01118.7370.0280.0280.0000.0000.0000.000
117A156SER0-0.0140.01819.7860.0220.0220.0000.0000.0000.000
118A157PRO00.0670.01222.2770.0030.0030.0000.0000.0000.000
119A158ALA0-0.051-0.02821.0930.0100.0100.0000.0000.0000.000
120A159ASN00.0050.00017.3850.0110.0110.0000.0000.0000.000
121A160GLN00.0420.02820.3520.0120.0120.0000.0000.0000.000
122A161ARG11.0141.00823.1320.1510.1510.0000.0000.0000.000
123A162GLY0-0.0120.00120.4800.0100.0100.0000.0000.0000.000
124A163LEU0-0.062-0.04018.6660.0050.0050.0000.0000.0000.000
125A164LEU00.0180.02821.2560.0080.0080.0000.0000.0000.000
126A165ASP-1-0.739-0.86523.617-0.100-0.1000.0000.0000.0000.000
127A166ARG10.8180.92316.1560.2250.2250.0000.0000.0000.000
128A167ARG10.9330.96521.4830.1010.1010.0000.0000.0000.000
129A168VAL00.0060.01724.1790.0110.0110.0000.0000.0000.000
130A169THR00.0380.01821.6610.0030.0030.0000.0000.0000.000
131A170LYS10.9380.98224.8930.0380.0380.0000.0000.0000.000
132A171GLU-1-0.813-0.93128.049-0.048-0.0480.0000.0000.0000.000
133A172ALA00.0470.02825.6760.0010.0010.0000.0000.0000.000
134A173GLN0-0.046-0.03722.8740.0050.0050.0000.0000.0000.000
135A174ALA0-0.015-0.00127.2710.0030.0030.0000.0000.0000.000
136A175TYR00.001-0.00430.0240.0040.0040.0000.0000.0000.000
137A176ALA00.0050.00627.0970.0020.0020.0000.0000.0000.000
138A177ALA0-0.013-0.00129.0930.0010.0010.0000.0000.0000.000
139A178ALA00.0380.02131.0500.0020.0020.0000.0000.0000.000
140A179HIS0-0.017-0.02031.3660.0000.0000.0000.0000.0000.000
141A180ALA0-0.009-0.01230.2850.0000.0000.0000.0000.0000.000
142A181ALA00.0420.01832.3620.0020.0020.0000.0000.0000.000
143A182TRP00.0320.00535.5760.0010.0010.0000.0000.0000.000
144A183ARG10.9230.96733.3820.0590.0590.0000.0000.0000.000
145A184GLU-1-0.937-0.95935.122-0.034-0.0340.0000.0000.0000.000
146A185ALA0-0.050-0.01937.4990.0020.0020.0000.0000.0000.000
147A186VAL00.0160.00039.1370.0020.0020.0000.0000.0000.000
148A187SER0-0.0100.01337.8500.0010.0010.0000.0000.0000.000
149A188ARG10.9060.91439.0820.0310.0310.0000.0000.0000.000
150A189LEU0-0.012-0.00442.6610.0020.0020.0000.0000.0000.000
151A190GLU-1-0.935-0.96641.467-0.046-0.0460.0000.0000.0000.000
152A191ARG10.8390.94938.8600.0350.0350.0000.0000.0000.000
153A192LEU0-0.0410.00045.2270.0020.0020.0000.0000.0000.000
154A360LEU0-0.002-0.00756.3490.0000.0000.0000.0000.0000.000
155A361VAL00.0200.00850.9790.0010.0010.0000.0000.0000.000
156A362PRO0-0.019-0.01151.574-0.001-0.0010.0000.0000.0000.000
157A363ARG10.9480.97046.4310.0330.0330.0000.0000.0000.000
158A364GLY00.0160.00347.889-0.001-0.0010.0000.0000.0000.000
159A365SER0-0.002-0.00344.098-0.001-0.0010.0000.0000.0000.000
160A366VAL00.0420.00541.934-0.001-0.0010.0000.0000.0000.000
161A367ASP-1-0.820-0.90343.297-0.034-0.0340.0000.0000.0000.000
162A368ALA0-0.019-0.00245.016-0.001-0.0010.0000.0000.0000.000
163A369LEU0-0.008-0.01838.900-0.001-0.0010.0000.0000.0000.000
164A370HIS00.0020.00939.940-0.002-0.0020.0000.0000.0000.000
165A371ALA00.0290.01741.265-0.002-0.0020.0000.0000.0000.000
166A372GLU-1-0.903-0.96438.781-0.033-0.0330.0000.0000.0000.000
167A373LEU0-0.0250.00834.591-0.002-0.0020.0000.0000.0000.000
168A374LEU00.0170.01037.018-0.003-0.0030.0000.0000.0000.000
169A375LYS10.9330.98239.1480.0300.0300.0000.0000.0000.000
170A376VAL0-0.042-0.03333.857-0.001-0.0010.0000.0000.0000.000
171A377GLY00.032-0.00834.389-0.003-0.0030.0000.0000.0000.000
172A378GLN0-0.011-0.01035.089-0.003-0.0030.0000.0000.0000.000
173A379ALA0-0.045-0.01635.3060.0000.0000.0000.0000.0000.000
174A380LEU0-0.027-0.01328.8770.0000.0000.0000.0000.0000.000
175A381ASP-1-0.817-0.91332.281-0.073-0.0730.0000.0000.0000.000
176A382ALA00.0230.01634.277-0.001-0.0010.0000.0000.0000.000
177A383ALA0-0.048-0.02331.0790.0010.0010.0000.0000.0000.000
178A384ARG10.7360.84827.7110.0920.0920.0000.0000.0000.000
179A385GLU-1-0.892-0.96330.839-0.062-0.0620.0000.0000.0000.000
180A386ARG10.7790.91630.3680.0500.0500.0000.0000.0000.000
181A387GLU-1-0.925-0.98027.929-0.054-0.0540.0000.0000.0000.000
182A388ALA0-0.0040.00128.477-0.006-0.0060.0000.0000.0000.000
183A389GLU-1-0.893-0.94229.267-0.066-0.0660.0000.0000.0000.000
184A390PRO00.0340.01728.797-0.002-0.0020.0000.0000.0000.000
185A391LEU0-0.072-0.02522.703-0.003-0.0030.0000.0000.0000.000
186A392VAL00.0380.00625.853-0.009-0.0090.0000.0000.0000.000
187A393ASP-1-0.882-0.93928.092-0.067-0.0670.0000.0000.0000.000
188A394SER0-0.154-0.07524.494-0.002-0.0020.0000.0000.0000.000
189A395LEU00.004-0.00321.356-0.006-0.0060.0000.0000.0000.000
190A396LEU0-0.011-0.01124.809-0.003-0.0030.0000.0000.0000.000
191A397ALA0-0.0220.00126.7510.0020.0020.0000.0000.0000.000
192A398VAL00.0090.01322.1050.0030.0030.0000.0000.0000.000
193A399ILE00.021-0.00824.6220.0000.0000.0000.0000.0000.000
194A400ARG10.8360.92726.3730.0740.0740.0000.0000.0000.000
195A401GLU-1-0.909-0.94727.230-0.061-0.0610.0000.0000.0000.000
196A402LEU0-0.111-0.06622.719-0.001-0.0010.0000.0000.0000.000
197A403GLY0-0.007-0.01527.305-0.006-0.0060.0000.0000.0000.000
198A404MET0-0.0130.00826.174-0.003-0.0030.0000.0000.0000.000
199A405PRO00.0190.01031.4900.0000.0000.0000.0000.0000.000
200A406HIS0-0.031-0.02733.8030.0030.0030.0000.0000.0000.000
201A407ALA00.0280.03930.4960.0000.0000.0000.0000.0000.000
202A408ARG10.9280.97132.5110.0700.0700.0000.0000.0000.000
203A409MET0-0.013-0.00725.172-0.007-0.0070.0000.0000.0000.000
204A410GLU-1-0.845-0.91430.646-0.072-0.0720.0000.0000.0000.000
205A411PHE0-0.003-0.01024.241-0.009-0.0090.0000.0000.0000.000
206A412ALA00.0040.00830.2520.0070.0070.0000.0000.0000.000
207A413LEU0-0.003-0.00531.371-0.008-0.0080.0000.0000.0000.000
208A414SER0-0.016-0.00233.6520.0060.0060.0000.0000.0000.000
209A415ALA00.0360.01935.148-0.003-0.0030.0000.0000.0000.000
210A416LEU0-0.034-0.00632.5850.0000.0000.0000.0000.0000.000
211A417ALA0-0.026-0.00337.1830.0040.0040.0000.0000.0000.000
212A418GLU-1-0.946-0.98138.037-0.059-0.0590.0000.0000.0000.000
213A419PRO0-0.048-0.02835.823-0.004-0.0040.0000.0000.0000.000
214A420ALA00.0680.05730.727-0.001-0.0010.0000.0000.0000.000
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