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: M3MRZ

Calculation Name: 4ML1-A-Xray322

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2071743.655662
FMO2-HF: Nuclear repulsion 1991853.415376
FMO2-HF: Total energy -79890.240287
FMO2-MP2: Total energy -80117.501368


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:10:ACE )


Summations of interaction energy for fragment #1(A:10:ACE )
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.
1.0191.9-0.006-0.37-0.505-0.001
Interaction energy analysis for fragmet #1(A:10:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.009
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].
3A12ALA 0-0.0230.0153.8231.0461.927-0.006-0.370-0.505-0.001
4A13LYS 10.9390.9766.2560.3110.3110.0000.0000.0000.000
5A14ILE 00.001-0.0099.7280.0850.0850.0000.0000.0000.000
6A15GLU -1-0.942-0.98612.456-0.244-0.2440.0000.0000.0000.000
7A16ASP -1-0.876-0.93715.232-0.145-0.1450.0000.0000.0000.000
8A17ILE 0-0.080-0.04016.520-0.019-0.0190.0000.0000.0000.000
9A18VAL 0-0.0010.00419.2670.0150.0150.0000.0000.0000.000
10A19GLU -1-0.962-0.96622.663-0.118-0.1180.0000.0000.0000.000
11A20LEU 00.009-0.00523.7230.0120.0120.0000.0000.0000.000
12A21PRO 0-0.034-0.00626.6960.0010.0010.0000.0000.0000.000
13A22ILE 0-0.041-0.03326.4070.0090.0090.0000.0000.0000.000
14A23LYS 10.9490.97629.0990.0610.0610.0000.0000.0000.000
15A24GLY 00.0100.00730.3380.0000.0000.0000.0000.0000.000
16A25VAL 0-0.003-0.01126.3950.0010.0010.0000.0000.0000.000
17A26ARG 10.9030.96129.6050.0360.0360.0000.0000.0000.000
18A27ALA 00.0380.02928.7470.0000.0000.0000.0000.0000.000
19A28VAL 0-0.030-0.02730.2690.0020.0020.0000.0000.0000.000
20A29GLN 00.008-0.00832.1390.0000.0000.0000.0000.0000.000
21A30SER 0-0.040-0.02633.8660.0010.0010.0000.0000.0000.000
22A31ASP -1-0.902-0.94134.5020.0050.0050.0000.0000.0000.000
23A32GLY 00.0070.00333.7420.0020.0020.0000.0000.0000.000
24A33GLN 0-0.041-0.01029.9040.0020.0020.0000.0000.0000.000
25A34ILE 0-0.026-0.02628.012-0.002-0.0020.0000.0000.0000.000
26A35MET 0-0.0180.00327.650-0.001-0.0010.0000.0000.0000.000
27A36PHE 00.0100.00124.398-0.002-0.0020.0000.0000.0000.000
28A37LEU 00.0060.01328.218-0.001-0.0010.0000.0000.0000.000
29A38SER 00.0550.02330.136-0.001-0.0010.0000.0000.0000.000
30A39GLU -1-0.834-0.93031.465-0.052-0.0520.0000.0000.0000.000
31A40ASN 0-0.009-0.00834.3760.0030.0030.0000.0000.0000.000
32A41GLY 0-0.026-0.01434.9690.0030.0030.0000.0000.0000.000
33A42ARG 10.9180.98132.7610.0510.0510.0000.0000.0000.000
34A43PHE 00.012-0.00628.8130.0010.0010.0000.0000.0000.000
35A44VAL 00.0200.00729.5530.0000.0000.0000.0000.0000.000
36A45ILE 0-0.0080.00022.9180.0000.0000.0000.0000.0000.000
37A46SER 00.0240.00525.5790.0040.0040.0000.0000.0000.000
38A47GLY 00.012-0.00522.128-0.002-0.0020.0000.0000.0000.000
39A48GLN 0-0.022-0.01118.740-0.002-0.0020.0000.0000.0000.000
40A49ILE 00.0170.02419.677-0.012-0.0120.0000.0000.0000.000
41A50TYR 00.002-0.01514.7660.0090.0090.0000.0000.0000.000
42A51ASP -1-0.823-0.90318.502-0.104-0.1040.0000.0000.0000.000
43A52LEU 00.004-0.03113.1680.0090.0090.0000.0000.0000.000
44A53TRP 0-0.0170.00216.314-0.003-0.0030.0000.0000.0000.000
45A54SER 0-0.024-0.00618.7960.0070.0070.0000.0000.0000.000
46A55LYS 10.8880.95714.0050.1230.1230.0000.0000.0000.000
47A56LYS 10.9580.97616.9980.0500.0500.0000.0000.0000.000
48A57PRO 00.0110.01518.048-0.014-0.0140.0000.0000.0000.000
49A58LEU 0-0.048-0.02019.9090.0050.0050.0000.0000.0000.000
50A59ASN 00.0700.02422.278-0.002-0.0020.0000.0000.0000.000
51A60THR 00.0160.00225.3490.0010.0010.0000.0000.0000.000
52A61MET 00.0410.01528.813-0.005-0.0050.0000.0000.0000.000
53A62SER 0-0.024-0.00131.356-0.003-0.0030.0000.0000.0000.000
54A63GLN 00.0600.02624.3220.0000.0000.0000.0000.0000.000
55A64MET 00.0080.01625.194-0.008-0.0080.0000.0000.0000.000
56A65ARG 10.9170.96228.9280.0150.0150.0000.0000.0000.000
57A66ASP -1-0.863-0.92528.337-0.032-0.0320.0000.0000.0000.000
58A67VAL 00.0340.01124.935-0.002-0.0020.0000.0000.0000.000
59A68ALA 0-0.065-0.01828.241-0.004-0.0040.0000.0000.0000.000
60A69GLU -1-0.979-0.99331.238-0.025-0.0250.0000.0000.0000.000
61A70ARG 10.8240.91331.1280.0240.0240.0000.0000.0000.000
62A71ILE 00.0260.02727.982-0.004-0.0040.0000.0000.0000.000
63A72HIS 0-0.066-0.05126.5400.0030.0030.0000.0000.0000.000
64A73PHE 00.0530.00025.900-0.003-0.0030.0000.0000.0000.000
65A74LYS 10.9860.99624.9710.0260.0260.0000.0000.0000.000
66A75SER 0-0.031-0.01123.4620.0000.0000.0000.0000.0000.000
67A76MET 0-0.0270.00421.2230.0010.0010.0000.0000.0000.000
68A77GLY 0-0.036-0.01520.401-0.015-0.0150.0000.0000.0000.000
69A78MET 0-0.052-0.01621.473-0.007-0.0070.0000.0000.0000.000
70A79ASP -1-0.828-0.92424.273-0.043-0.0430.0000.0000.0000.000
71A80VAL 00.0310.00526.870-0.004-0.0040.0000.0000.0000.000
72A81ASP -1-0.839-0.88630.030-0.039-0.0390.0000.0000.0000.000
73A82THR 0-0.115-0.05426.332-0.002-0.0020.0000.0000.0000.000
74A83LEU 0-0.031-0.00827.960-0.004-0.0040.0000.0000.0000.000
75A84ASN 0-0.034-0.02231.2050.0060.0060.0000.0000.0000.000
76A85THR 0-0.026-0.03433.1590.0020.0020.0000.0000.0000.000
77A86VAL 0-0.0230.00036.1790.0020.0020.0000.0000.0000.000
78A87SER 00.017-0.00338.4280.0000.0000.0000.0000.0000.000
79A88MET 0-0.039-0.00540.2310.0010.0010.0000.0000.0000.000
80A89GLY 00.0280.01142.9050.0000.0000.0000.0000.0000.000
81A90ARG 10.8800.92840.0000.0150.0150.0000.0000.0000.000
82A91GLY 00.0790.06743.0460.0010.0010.0000.0000.0000.000
83A92ASP -1-0.887-0.92540.056-0.011-0.0110.0000.0000.0000.000
84A93LYS 10.8830.95638.1700.0120.0120.0000.0000.0000.000
85A94GLU -1-0.858-0.92733.117-0.035-0.0350.0000.0000.0000.000
86A95VAL 0-0.0150.00336.5060.0000.0000.0000.0000.0000.000
87A96VAL 00.0080.02132.807-0.001-0.0010.0000.0000.0000.000
88A97VAL 0-0.016-0.02336.1900.0010.0010.0000.0000.0000.000
89A98PHE 00.0200.03631.410-0.001-0.0010.0000.0000.0000.000
90A99VAL 00.019-0.02437.3280.0030.0030.0000.0000.0000.000
91A100ASP -1-0.687-0.81239.776-0.048-0.0480.0000.0000.0000.000
92A101PRO 00.019-0.00341.2640.0030.0030.0000.0000.0000.000
93A102ARG 10.9150.96844.3910.0410.0410.0000.0000.0000.000
94A106CYS 0-0.0430.00443.7130.0020.0020.0000.0000.0000.000
95A104ALA 00.0570.03046.5760.0010.0010.0000.0000.0000.000
96A105VAL 00.0060.00646.5270.0010.0010.0000.0000.0000.000
97A107HIS 00.0240.00045.7060.0020.0020.0000.0000.0000.000
98A108GLN 0-0.021-0.01948.5140.0010.0010.0000.0000.0000.000
99A109LEU 0-0.0450.00243.1040.0010.0010.0000.0000.0000.000
100A110MET 00.0040.00044.4000.0010.0010.0000.0000.0000.000
101A111GLY 0-0.006-0.00546.7980.0010.0010.0000.0000.0000.000
102A112ASP -1-0.830-0.89248.798-0.020-0.0200.0000.0000.0000.000
103A113ALA 00.006-0.00545.4050.0010.0010.0000.0000.0000.000
104A114LYS 10.9560.98447.3490.0210.0210.0000.0000.0000.000
105A115SER 0-0.089-0.02949.6020.0010.0010.0000.0000.0000.000
106A116LEU 0-0.040-0.03346.5170.0010.0010.0000.0000.0000.000
107A117VAL 0-0.010-0.00845.9240.0000.0000.0000.0000.0000.000
108A118ASP -1-0.903-0.93946.169-0.012-0.0120.0000.0000.0000.000
109A119ASP -1-0.927-0.94645.233-0.010-0.0100.0000.0000.0000.000
110A120TYR 0-0.123-0.08640.9810.0000.0000.0000.0000.0000.000
111A121THR 0-0.053-0.03739.0810.0000.0000.0000.0000.0000.000
112A122PHE 0-0.013-0.01839.220-0.001-0.0010.0000.0000.0000.000
113A123LYS 10.8170.87834.1030.0340.0340.0000.0000.0000.000
114A124PHE 00.024-0.00337.414-0.001-0.0010.0000.0000.0000.000
115A125ILE 00.001-0.00532.255-0.001-0.0010.0000.0000.0000.000
116A126VAL 0-0.004-0.00136.3250.0000.0000.0000.0000.0000.000
117A127ILE 00.018-0.00534.119-0.004-0.0040.0000.0000.0000.000
118A128PRO 0-0.056-0.02636.1530.0040.0040.0000.0000.0000.000
119A129ALA 00.0240.00338.189-0.002-0.0020.0000.0000.0000.000
120A130LEU 0-0.064-0.02739.1060.0000.0000.0000.0000.0000.000
121A131GLY 0-0.0010.01341.2980.0020.0020.0000.0000.0000.000
122A132ALA 00.0380.00342.2690.0030.0030.0000.0000.0000.000
123A133GLU -1-0.805-0.87844.057-0.039-0.0390.0000.0000.0000.000
124A134SER 0-0.058-0.07042.1750.0010.0010.0000.0000.0000.000
125A135ASN 00.0310.00138.4130.0010.0010.0000.0000.0000.000
126A136ARG 10.8500.91341.1870.0360.0360.0000.0000.0000.000
127A137LEU 00.0220.00843.8340.0010.0010.0000.0000.0000.000
128A138ALA 00.0480.02138.6970.0010.0010.0000.0000.0000.000
129A139LYS 10.9530.97838.2520.0580.0580.0000.0000.0000.000
130A140ASN 00.0110.00840.3210.0010.0010.0000.0000.0000.000
131A141LEU 00.0410.02739.5610.0020.0020.0000.0000.0000.000
132A142TYR 00.0140.00932.3830.0010.0010.0000.0000.0000.000
133A168CYS 0-0.116-0.07038.123-0.003-0.0030.0000.0000.0000.000
134A144ALA 00.0140.01540.5750.0020.0020.0000.0000.0000.000
135A145LYS 10.9540.96642.1760.0260.0260.0000.0000.0000.000
136A146ASP -1-0.865-0.93243.235-0.025-0.0250.0000.0000.0000.000
137A147LYS 10.7970.88838.9860.0410.0410.0000.0000.0000.000
138A148THR 0-0.040-0.02243.3640.0000.0000.0000.0000.0000.000
139A149HIS 00.0620.03645.9860.0010.0010.0000.0000.0000.000
140A150ALA 0-0.041-0.02643.103-0.001-0.0010.0000.0000.0000.000
141A151LEU 0-0.0010.00443.800-0.001-0.0010.0000.0000.0000.000
142A152ASP -1-0.831-0.92245.412-0.023-0.0230.0000.0000.0000.000
143A153ALA 0-0.019-0.01047.1940.0000.0000.0000.0000.0000.000
144A154LEU 0-0.052-0.03442.062-0.001-0.0010.0000.0000.0000.000
145A155MET 0-0.049-0.03846.0650.0000.0000.0000.0000.0000.000
146A156ASN 0-0.0250.00148.3990.0010.0010.0000.0000.0000.000
147A157ASN 0-0.040-0.00549.049-0.001-0.0010.0000.0000.0000.000
148A158THR 00.0360.00749.9440.0000.0000.0000.0000.0000.000
149A159LEU 00.017-0.00343.7730.0000.0000.0000.0000.0000.000
150A160GLY 0-0.036-0.01347.506-0.001-0.0010.0000.0000.0000.000
151A161SER 0-0.054-0.01249.1560.0000.0000.0000.0000.0000.000
152A162LEU 00.0030.00445.0870.0010.0010.0000.0000.0000.000
153A163PRO 00.0100.00247.632-0.001-0.0010.0000.0000.0000.000
154A164SER 0-0.0060.00643.988-0.001-0.0010.0000.0000.0000.000
155A165LYS 10.9090.95037.4340.0470.0470.0000.0000.0000.000
156A166GLU -1-0.928-0.95843.039-0.033-0.0330.0000.0000.0000.000
157A167THR 0-0.025-0.01038.539-0.001-0.0010.0000.0000.0000.000
158A169ASP -1-0.905-0.94337.667-0.054-0.0540.0000.0000.0000.000
159A170PRO 0-0.0010.00734.738-0.004-0.0040.0000.0000.0000.000
160A171GLY 00.0620.03434.2060.0020.0020.0000.0000.0000.000
161A172GLN 0-0.051-0.04535.3640.0030.0030.0000.0000.0000.000
162A173TYR 0-0.023-0.00931.8540.0020.0020.0000.0000.0000.000
163A174ASP -1-0.799-0.89732.100-0.074-0.0740.0000.0000.0000.000
164A175GLN 00.0760.02627.148-0.005-0.0050.0000.0000.0000.000
165A176THR 00.0500.04829.367-0.005-0.0050.0000.0000.0000.000
166A177LEU 0-0.023-0.02831.2170.0000.0000.0000.0000.0000.000
167A178LEU 0-0.033-0.01727.770-0.001-0.0010.0000.0000.0000.000
168A179THR 0-0.007-0.01125.840-0.008-0.0080.0000.0000.0000.000
169A180ALA 00.008-0.00127.637-0.001-0.0010.0000.0000.0000.000
170A181HIS 0-0.011-0.00929.5320.0040.0040.0000.0000.0000.000
171A182PHE 0-0.049-0.01720.680-0.002-0.0020.0000.0000.0000.000
172A183ILE 0-0.059-0.03924.557-0.003-0.0030.0000.0000.0000.000
173A184GLY 00.0390.03026.5830.0060.0060.0000.0000.0000.000
174A185ILE 0-0.057-0.01729.6930.0070.0070.0000.0000.0000.000
175A186GLU -1-0.878-0.91732.606-0.058-0.0580.0000.0000.0000.000
176A187GLY 0-0.044-0.02635.6970.0040.0040.0000.0000.0000.000
177A188VAL 0-0.0280.01438.298-0.001-0.0010.0000.0000.0000.000
178A189PRO 0-0.003-0.05040.7320.0020.0020.0000.0000.0000.000
179A190PHE 0-0.0030.01033.6970.0010.0010.0000.0000.0000.000
180A191VAL 0-0.029-0.01637.7010.0000.0000.0000.0000.0000.000
181A192VAL 00.0200.00832.5230.0000.0000.0000.0000.0000.000
182A193ALA 0-0.010-0.01235.8940.0010.0010.0000.0000.0000.000
183A194PRO 00.0410.01835.375-0.001-0.0010.0000.0000.0000.000
184A195ASP -1-0.828-0.90334.475-0.020-0.0200.0000.0000.0000.000
185A196GLY 00.0530.00832.4350.0000.0000.0000.0000.0000.000
186A197ARG 10.7840.90833.2520.0170.0170.0000.0000.0000.000
187A198VAL 00.0550.04333.2130.0000.0000.0000.0000.0000.000
188A199SER 0-0.074-0.05836.3010.0030.0030.0000.0000.0000.000
189A200LYS 10.8620.92637.2960.0460.0460.0000.0000.0000.000
190A201GLY 00.0630.02739.7570.0010.0010.0000.0000.0000.000
191A202ARG 10.8350.89342.7170.0240.0240.0000.0000.0000.000
192A203PRO 0-0.0020.01243.3260.0010.0010.0000.0000.0000.000
193A204LYS 10.9520.97345.9490.0230.0230.0000.0000.0000.000
194A205ASN 00.0570.03248.8930.0010.0010.0000.0000.0000.000
195A206LEU 00.0470.02743.7070.0000.0000.0000.0000.0000.000
196A207LYS 11.0171.01145.9070.0120.0120.0000.0000.0000.000
197A208SER 0-0.008-0.02446.8740.0000.0000.0000.0000.0000.000
198A209TRP 0-0.0080.00038.6730.0010.0010.0000.0000.0000.000
199A210LEU 00.0200.00941.165-0.001-0.0010.0000.0000.0000.000
200A211GLU -1-0.928-0.93841.800-0.012-0.0120.0000.0000.0000.000
201A212SER 0-0.043-0.04040.8580.0010.0010.0000.0000.0000.000
202A213NME 0-0.039-0.01341.6790.0000.0000.0000.0000.0000.000