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: 98JV2

Calculation Name: 4ML1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ML1

Chain ID: A

ChEMBL ID:

UniProt ID: A6GV51

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2072239.956787
FMO2-HF: Nuclear repulsion 1992518.835795
FMO2-HF: Total energy -79721.120992
FMO2-MP2: Total energy -79947.915198


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:11:ALA)


Summations of interaction energy for fragment #1(A:11:ALA)
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.
0.1931.342-0.008-0.466-0.6760.001
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.018
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].
3A13LYS10.7990.8863.8590.3161.465-0.008-0.466-0.6760.001
4A14ILE0-0.012-0.0086.0160.3880.3880.0000.0000.0000.000
5A15GLU-1-0.795-0.8808.943-0.566-0.5660.0000.0000.0000.000
6A16ASP-1-0.900-0.94912.254-0.027-0.0270.0000.0000.0000.000
7A17ILE0-0.066-0.03811.8990.0460.0460.0000.0000.0000.000
8A18VAL0-0.0050.01215.797-0.014-0.0140.0000.0000.0000.000
9A19GLU-1-0.946-0.96419.4910.0700.0700.0000.0000.0000.000
10A20LEU00.010-0.00221.358-0.007-0.0070.0000.0000.0000.000
11A21PRO0-0.036-0.01324.1590.0020.0020.0000.0000.0000.000
12A22ILE0-0.043-0.03324.6290.0000.0000.0000.0000.0000.000
13A23LYS10.9250.94926.775-0.054-0.0540.0000.0000.0000.000
14A24GLY00.0130.01428.1890.0000.0000.0000.0000.0000.000
15A25VAL0-0.014-0.01124.695-0.001-0.0010.0000.0000.0000.000
16A26ARG10.8630.93628.031-0.079-0.0790.0000.0000.0000.000
17A27ALA00.0580.03128.0950.0030.0030.0000.0000.0000.000
18A28VAL0-0.029-0.02029.601-0.009-0.0090.0000.0000.0000.000
19A29GLN00.0200.00331.8070.0060.0060.0000.0000.0000.000
20A30SER0-0.013-0.01733.837-0.009-0.0090.0000.0000.0000.000
21A31ASP-1-0.914-0.95034.7900.0880.0880.0000.0000.0000.000
22A32GLY00.0080.01534.8660.0030.0030.0000.0000.0000.000
23A33GLN0-0.067-0.02530.7720.0130.0130.0000.0000.0000.000
24A34ILE0-0.023-0.03528.445-0.008-0.0080.0000.0000.0000.000
25A35MET0-0.0190.00527.6380.0100.0100.0000.0000.0000.000
26A36PHE00.015-0.00724.393-0.003-0.0030.0000.0000.0000.000
27A37LEU00.0070.01127.423-0.002-0.0020.0000.0000.0000.000
28A38SER00.0370.01228.6570.0020.0020.0000.0000.0000.000
29A39GLU-1-0.759-0.87729.7430.0710.0710.0000.0000.0000.000
30A40ASN0-0.045-0.03030.697-0.003-0.0030.0000.0000.0000.000
31A41GLY0-0.016-0.00532.976-0.004-0.0040.0000.0000.0000.000
32A42ARG10.9180.97631.311-0.046-0.0460.0000.0000.0000.000
33A43PHE00.004-0.00627.236-0.002-0.0020.0000.0000.0000.000
34A44VAL00.0180.00928.5710.0020.0020.0000.0000.0000.000
35A45ILE00.0020.01122.1970.0000.0000.0000.0000.0000.000
36A46SER00.0340.00525.0870.0020.0020.0000.0000.0000.000
37A47GLY00.0240.01122.3040.0080.0080.0000.0000.0000.000
38A48GLN0-0.021-0.00519.667-0.020-0.0200.0000.0000.0000.000
39A49ILE00.0000.00419.6680.0170.0170.0000.0000.0000.000
40A50TYR0-0.013-0.03014.9600.0330.0330.0000.0000.0000.000
41A51ASP-1-0.757-0.84617.9210.2580.2580.0000.0000.0000.000
42A52LEU00.025-0.01212.5650.0130.0130.0000.0000.0000.000
43A53TRP0-0.0120.01215.9350.0160.0160.0000.0000.0000.000
44A54SER0-0.040-0.04818.345-0.013-0.0130.0000.0000.0000.000
45A55LYS10.8330.93615.110-0.321-0.3210.0000.0000.0000.000
46A56LYS10.8710.95517.314-0.199-0.1990.0000.0000.0000.000
47A57PRO00.0250.01219.1490.0040.0040.0000.0000.0000.000
48A58LEU0-0.036-0.02120.756-0.027-0.0270.0000.0000.0000.000
49A59ASN00.0300.00423.5460.0070.0070.0000.0000.0000.000
50A60THR00.0380.01026.312-0.010-0.0100.0000.0000.0000.000
51A61MET00.0590.02729.4590.0080.0080.0000.0000.0000.000
52A62SER0-0.0120.00631.8720.0000.0000.0000.0000.0000.000
53A63GLN00.0230.01224.485-0.002-0.0020.0000.0000.0000.000
54A64MET0-0.014-0.00225.4160.0070.0070.0000.0000.0000.000
55A65ARG10.8230.89328.702-0.096-0.0960.0000.0000.0000.000
56A66ASP-1-0.845-0.91827.5020.1480.1480.0000.0000.0000.000
57A67VAL00.005-0.00824.121-0.003-0.0030.0000.0000.0000.000
58A68ALA0-0.0310.00627.320-0.002-0.0020.0000.0000.0000.000
59A69GLU-1-0.869-0.91430.2130.0820.0820.0000.0000.0000.000
60A70ARG10.7920.87730.396-0.108-0.1080.0000.0000.0000.000
61A71ILE00.0030.01326.9200.0080.0080.0000.0000.0000.000
62A72HIS0-0.038-0.03326.317-0.010-0.0100.0000.0000.0000.000
63A73PHE00.0570.00925.8140.0120.0120.0000.0000.0000.000
64A74LYS10.8680.92324.964-0.081-0.0810.0000.0000.0000.000
65A75SER00.0120.00424.0520.0050.0050.0000.0000.0000.000
66A76MET0-0.032-0.00821.1430.0180.0180.0000.0000.0000.000
67A77GLY0-0.049-0.01620.0450.0220.0220.0000.0000.0000.000
68A78MET0-0.040-0.01421.560-0.010-0.0100.0000.0000.0000.000
69A79ASP-1-0.832-0.92623.8600.0800.0800.0000.0000.0000.000
70A80VAL00.0400.01326.988-0.006-0.0060.0000.0000.0000.000
71A81ASP-1-0.805-0.87429.5500.0570.0570.0000.0000.0000.000
72A82THR0-0.092-0.05125.948-0.005-0.0050.0000.0000.0000.000
73A83LEU0-0.034-0.00126.387-0.003-0.0030.0000.0000.0000.000
74A84ASN0-0.059-0.03430.024-0.005-0.0050.0000.0000.0000.000
75A85THR0-0.016-0.02032.3040.0000.0000.0000.0000.0000.000
76A86VAL0-0.029-0.00435.137-0.003-0.0030.0000.0000.0000.000
77A87SER00.0330.00338.0710.0040.0040.0000.0000.0000.000
78A88MET0-0.048-0.00739.732-0.004-0.0040.0000.0000.0000.000
79A89GLY00.0090.00942.6170.0020.0020.0000.0000.0000.000
80A90ARG10.8690.92240.062-0.044-0.0440.0000.0000.0000.000
81A91GLY00.0910.07243.8320.0000.0000.0000.0000.0000.000
82A92ASP-1-0.945-0.96340.2700.0530.0530.0000.0000.0000.000
83A93LYS10.7750.89838.711-0.049-0.0490.0000.0000.0000.000
84A94GLU-1-0.765-0.87032.6240.0780.0780.0000.0000.0000.000
85A95VAL0-0.020-0.00537.0390.0020.0020.0000.0000.0000.000
86A96VAL0-0.0050.00832.140-0.002-0.0020.0000.0000.0000.000
87A97VAL0-0.008-0.01835.4350.0000.0000.0000.0000.0000.000
88A98PHE00.0410.03429.763-0.002-0.0020.0000.0000.0000.000
89A99VAL00.015-0.02435.613-0.002-0.0020.0000.0000.0000.000
90A100ASP-1-0.683-0.82537.6490.0310.0310.0000.0000.0000.000
91A101PRO0-0.008-0.01139.268-0.001-0.0010.0000.0000.0000.000
92A102ARG10.8880.93342.330-0.024-0.0240.0000.0000.0000.000
93A103CYS0-0.0150.01441.7030.0020.0020.0000.0000.0000.000
94A104ALA00.0530.03444.2160.0010.0010.0000.0000.0000.000
95A105VAL0-0.011-0.01044.8660.0000.0000.0000.0000.0000.000
96A107HIS00.0230.02243.9950.0010.0010.0000.0000.0000.000
97A108GLN0-0.029-0.01646.9620.0010.0010.0000.0000.0000.000
98A109LEU0-0.0120.00741.4690.0000.0000.0000.0000.0000.000
99A110MET0-0.010-0.00643.0550.0010.0010.0000.0000.0000.000
100A111GLY00.0220.00845.547-0.001-0.0010.0000.0000.0000.000
101A112ASP-1-0.815-0.88847.3100.0360.0360.0000.0000.0000.000
102A113ALA00.0160.01444.6260.0000.0000.0000.0000.0000.000
103A114LYS10.8960.94346.555-0.028-0.0280.0000.0000.0000.000
104A115SER0-0.099-0.04649.177-0.001-0.0010.0000.0000.0000.000
105A116LEU0-0.037-0.02746.4040.0000.0000.0000.0000.0000.000
106A117VAL00.013-0.00246.2510.0020.0020.0000.0000.0000.000
107A118ASP-1-0.866-0.93246.3840.0350.0350.0000.0000.0000.000
108A119ASP-1-0.795-0.87545.6290.0460.0460.0000.0000.0000.000
109A120TYR0-0.108-0.08141.2780.0040.0040.0000.0000.0000.000
110A121THR0-0.034-0.02039.012-0.004-0.0040.0000.0000.0000.000
111A122PHE00.000-0.01238.8750.0040.0040.0000.0000.0000.000
112A123LYS10.7820.86534.014-0.067-0.0670.0000.0000.0000.000
113A124PHE0-0.005-0.01636.6080.0020.0020.0000.0000.0000.000
114A125ILE00.0240.01631.378-0.002-0.0020.0000.0000.0000.000
115A126VAL0-0.026-0.02035.072-0.001-0.0010.0000.0000.0000.000
116A127ILE00.0180.00231.9880.0000.0000.0000.0000.0000.000
117A128PRO0-0.026-0.00233.898-0.001-0.0010.0000.0000.0000.000
118A129ALA0-0.013-0.01335.419-0.001-0.0010.0000.0000.0000.000
119A130LEU0-0.044-0.01836.4650.0000.0000.0000.0000.0000.000
120A131GLY00.0050.01038.335-0.003-0.0030.0000.0000.0000.000
121A132ALA00.033-0.00939.290-0.001-0.0010.0000.0000.0000.000
122A133GLU-1-0.756-0.84441.0820.0150.0150.0000.0000.0000.000
123A134SER0-0.055-0.03639.924-0.001-0.0010.0000.0000.0000.000
124A135ASN00.019-0.00635.5020.0020.0020.0000.0000.0000.000
125A136ARG10.7790.88338.538-0.014-0.0140.0000.0000.0000.000
126A137LEU00.0120.00841.3330.0000.0000.0000.0000.0000.000
127A138ALA00.0460.02036.5340.0010.0010.0000.0000.0000.000
128A139LYS10.8540.91435.797-0.008-0.0080.0000.0000.0000.000
129A140ASN0-0.016-0.01438.2550.0000.0000.0000.0000.0000.000
130A141LEU00.0430.02838.231-0.001-0.0010.0000.0000.0000.000
131A142TYR00.0330.01930.806-0.002-0.0020.0000.0000.0000.000
132A143CYS0-0.087-0.05636.3690.0010.0010.0000.0000.0000.000
133A144ALA00.0060.03038.880-0.002-0.0020.0000.0000.0000.000
134A145LYS10.8510.89340.760-0.006-0.0060.0000.0000.0000.000
135A146ASP-1-0.815-0.87842.8160.0200.0200.0000.0000.0000.000
136A147LYS10.8000.87637.967-0.025-0.0250.0000.0000.0000.000
137A148THR0-0.044-0.03742.6910.0010.0010.0000.0000.0000.000
138A149HIS00.0180.00245.7450.0010.0010.0000.0000.0000.000
139A150ALA0-0.020-0.01342.4460.0000.0000.0000.0000.0000.000
140A151LEU00.0300.02643.0910.0010.0010.0000.0000.0000.000
141A152ASP-1-0.799-0.91644.5660.0270.0270.0000.0000.0000.000
142A153ALA0-0.0010.01346.027-0.001-0.0010.0000.0000.0000.000
143A154LEU0-0.020-0.01040.789-0.001-0.0010.0000.0000.0000.000
144A155MET0-0.045-0.02744.6660.0000.0000.0000.0000.0000.000
145A156ASN0-0.076-0.04447.0440.0000.0000.0000.0000.0000.000
146A157ASN0-0.040-0.01346.888-0.001-0.0010.0000.0000.0000.000
147A158THR00.0460.02048.034-0.001-0.0010.0000.0000.0000.000
148A159LEU00.0060.00541.962-0.001-0.0010.0000.0000.0000.000
149A160GLY0-0.031-0.01145.569-0.001-0.0010.0000.0000.0000.000
150A161SER0-0.036-0.02046.854-0.002-0.0020.0000.0000.0000.000
151A162LEU00.0030.01243.539-0.001-0.0010.0000.0000.0000.000
152A163PRO00.0350.00745.625-0.001-0.0010.0000.0000.0000.000
153A164SER0-0.012-0.00342.1980.0020.0020.0000.0000.0000.000
154A165LYS10.8580.92936.258-0.020-0.0200.0000.0000.0000.000
155A166GLU-1-0.790-0.87741.5780.0050.0050.0000.0000.0000.000
156A167THR0-0.055-0.03336.742-0.002-0.0020.0000.0000.0000.000
157A169ASP-1-0.817-0.88635.8210.0050.0050.0000.0000.0000.000
158A170PRO00.0120.01132.384-0.001-0.0010.0000.0000.0000.000
159A171GLY00.0500.02631.226-0.003-0.0030.0000.0000.0000.000
160A172GLN0-0.008-0.01732.2410.0040.0040.0000.0000.0000.000
161A173TYR0-0.025-0.01429.0880.0020.0020.0000.0000.0000.000
162A174ASP-1-0.783-0.89129.6390.0390.0390.0000.0000.0000.000
163A175GLN00.0600.02025.2190.0070.0070.0000.0000.0000.000
164A176THR00.0560.03726.7970.0090.0090.0000.0000.0000.000
165A177LEU0-0.017-0.01229.0300.0060.0060.0000.0000.0000.000
166A178LEU0-0.016-0.01125.0220.0030.0030.0000.0000.0000.000
167A179THR0-0.011-0.01323.9950.0100.0100.0000.0000.0000.000
168A180ALA00.003-0.00925.3210.0100.0100.0000.0000.0000.000
169A181HIS0-0.012-0.00725.9180.0040.0040.0000.0000.0000.000
170A182PHE0-0.045-0.01817.7450.0050.0050.0000.0000.0000.000
171A183ILE0-0.038-0.02322.5230.0140.0140.0000.0000.0000.000
172A184GLY00.0130.01824.7170.0030.0030.0000.0000.0000.000
173A185ILE0-0.050-0.01627.693-0.004-0.0040.0000.0000.0000.000
174A186GLU-1-0.832-0.89430.7430.0640.0640.0000.0000.0000.000
175A187GLY0-0.011-0.00933.387-0.002-0.0020.0000.0000.0000.000
176A188VAL0-0.030-0.00835.9520.0020.0020.0000.0000.0000.000
177A189PRO0-0.009-0.03538.659-0.003-0.0030.0000.0000.0000.000
178A190PHE0-0.018-0.00332.3650.0000.0000.0000.0000.0000.000
179A191VAL0-0.038-0.01736.2690.0000.0000.0000.0000.0000.000
180A192VAL0-0.019-0.01432.0440.0030.0030.0000.0000.0000.000
181A193ALA00.0210.01735.308-0.003-0.0030.0000.0000.0000.000
182A194PRO00.0540.02235.3580.0050.0050.0000.0000.0000.000
183A195ASP-1-0.797-0.87334.9140.0870.0870.0000.0000.0000.000
184A196GLY00.0420.01632.1170.0070.0070.0000.0000.0000.000
185A197ARG10.7760.88632.637-0.068-0.0680.0000.0000.0000.000
186A198VAL00.0410.02631.840-0.004-0.0040.0000.0000.0000.000
187A199SER0-0.052-0.03935.065-0.003-0.0030.0000.0000.0000.000
188A200LYS10.8100.90835.044-0.066-0.0660.0000.0000.0000.000
189A201GLY00.0500.01337.908-0.003-0.0030.0000.0000.0000.000
190A202ARG10.8150.89041.181-0.034-0.0340.0000.0000.0000.000
191A203PRO00.0020.01042.085-0.001-0.0010.0000.0000.0000.000
192A204LYS10.9340.95944.684-0.043-0.0430.0000.0000.0000.000
193A205ASN00.0490.03647.693-0.001-0.0010.0000.0000.0000.000
194A206LEU00.0310.02942.9980.0020.0020.0000.0000.0000.000
195A207LYS10.8700.91245.222-0.041-0.0410.0000.0000.0000.000
196A208SER0-0.014-0.03046.1690.0020.0020.0000.0000.0000.000
197A209TRP0-0.007-0.00337.7480.0010.0010.0000.0000.0000.000
198A210LEU00.0090.00840.5580.0040.0040.0000.0000.0000.000
199A211GLU-1-0.793-0.84941.7400.0530.0530.0000.0000.0000.000
200A212SER0-0.060-0.02441.3030.0030.0030.0000.0000.0000.000