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: 6NM7Z

Calculation Name: 4MYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MYB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2822007.585388
FMO2-HF: Nuclear repulsion 2732262.240536
FMO2-HF: Total energy -89745.344852
FMO2-MP2: Total energy -90009.030926


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-15.319-5.5888.336-7.804-10.264-0.027
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / 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].
3A4LYS10.8320.9133.2394.0967.2630.015-1.638-1.5440.004
4A5TYR00.0150.0055.963-0.275-0.2750.0000.0000.0000.000
5A6VAL0-0.012-0.0058.7000.2690.2690.0000.0000.0000.000
6A7ILE00.0150.02812.099-0.071-0.0710.0000.0000.0000.000
7A8ILE0-0.006-0.01014.6730.0570.0570.0000.0000.0000.000
8A9PRO0-0.055-0.01918.169-0.020-0.0200.0000.0000.0000.000
9A10ALA00.0530.04720.7980.0020.0020.0000.0000.0000.000
10A11ALA0-0.037-0.04124.4400.0120.0120.0000.0000.0000.000
11A12GLY00.0490.01226.769-0.003-0.0030.0000.0000.0000.000
12A13ILE0-0.0190.04726.571-0.001-0.0010.0000.0000.0000.000
13A14GLY00.020-0.02030.6300.0030.0030.0000.0000.0000.000
14A15THR0-0.004-0.03832.2340.0060.0060.0000.0000.0000.000
15A16ARG10.7940.92432.668-0.028-0.0280.0000.0000.0000.000
16A17MET00.1050.07931.5360.0050.0050.0000.0000.0000.000
17A18GLN0-0.049-0.06132.1000.0030.0030.0000.0000.0000.000
18A19LEU00.0140.00633.5690.0000.0000.0000.0000.0000.000
19A20ASP-1-0.885-0.93235.332-0.028-0.0280.0000.0000.0000.000
20A21ILE00.0180.01234.324-0.006-0.0060.0000.0000.0000.000
21A22PRO0-0.034-0.00929.9330.0050.0050.0000.0000.0000.000
22A23LYS10.9710.96930.941-0.008-0.0080.0000.0000.0000.000
23A24GLN0-0.036-0.02026.3670.0110.0110.0000.0000.0000.000
24A25TYR00.0670.01727.289-0.005-0.0050.0000.0000.0000.000
25A26TYR00.0060.00031.0950.0010.0010.0000.0000.0000.000
26A27LYS10.9490.97831.9280.0660.0660.0000.0000.0000.000
27A28LEU0-0.0160.00330.6020.0030.0030.0000.0000.0000.000
28A29ASN00.0330.00533.201-0.001-0.0010.0000.0000.0000.000
29A30ASN00.002-0.00433.087-0.005-0.0050.0000.0000.0000.000
30A31GLY00.0080.01034.014-0.006-0.0060.0000.0000.0000.000
31A32LYS10.9490.98427.9050.0810.0810.0000.0000.0000.000
32A33THR0-0.045-0.04028.5050.0130.0130.0000.0000.0000.000
33A34ILE0-0.074-0.00927.504-0.004-0.0040.0000.0000.0000.000
34A35LEU00.0370.02423.0340.0050.0050.0000.0000.0000.000
35A36ASP-1-0.780-0.89223.675-0.108-0.1080.0000.0000.0000.000
36A37ASN0-0.016-0.01824.066-0.016-0.0160.0000.0000.0000.000
37A38THR0-0.082-0.04120.3550.0090.0090.0000.0000.0000.000
38A39LEU00.002-0.00419.1120.0010.0010.0000.0000.0000.000
39A40VAL00.0090.01419.444-0.026-0.0260.0000.0000.0000.000
40A41LYS10.8150.89719.121-0.029-0.0290.0000.0000.0000.000
41A42PHE0-0.005-0.00614.0580.0110.0110.0000.0000.0000.000
42A43ILE0-0.0070.00715.285-0.084-0.0840.0000.0000.0000.000
43A44ASP-1-0.914-0.96016.834-0.271-0.2710.0000.0000.0000.000
44A45ASN0-0.023-0.02413.289-0.036-0.0360.0000.0000.0000.000
45A46PRO00.012-0.00211.834-0.038-0.0380.0000.0000.0000.000
46A47LEU0-0.0370.0107.600-0.245-0.2450.0000.0000.0000.000
47A48PHE0-0.028-0.0258.173-0.083-0.0830.0000.0000.0000.000
48A49ASP-1-0.801-0.8936.365-2.976-2.9760.0000.0000.0000.000
49A50LYS10.8580.9239.6860.7910.7910.0000.0000.0000.000
50A51ILE0-0.032-0.01511.3820.0820.0820.0000.0000.0000.000
51A52PHE00.0390.00910.8230.0070.0070.0000.0000.0000.000
52A53VAL00.0030.00115.7060.0570.0570.0000.0000.0000.000
53A54ALA00.0090.00119.295-0.011-0.0110.0000.0000.0000.000
54A55ILE0-0.020-0.02821.1740.0220.0220.0000.0000.0000.000
55A56ALA00.0270.03425.001-0.006-0.0060.0000.0000.0000.000
56A57ALA00.0460.01227.586-0.005-0.0050.0000.0000.0000.000
57A58SER0-0.068-0.04829.410-0.002-0.0020.0000.0000.0000.000
58A59ASP-1-0.851-0.92229.750-0.032-0.0320.0000.0000.0000.000
59A60ASN0-0.059-0.02424.532-0.008-0.0080.0000.0000.0000.000
60A61PHE00.0000.00428.668-0.011-0.0110.0000.0000.0000.000
61A62TRP00.031-0.00523.5930.0150.0150.0000.0000.0000.000
62A63ASN0-0.005-0.00228.041-0.010-0.0100.0000.0000.0000.000
63A64ASN0-0.039-0.04729.764-0.010-0.0100.0000.0000.0000.000
64A65SER00.0060.05126.7800.0130.0130.0000.0000.0000.000
65A66LEU00.002-0.02229.2340.0100.0100.0000.0000.0000.000
66A67TYR0-0.075-0.03725.929-0.006-0.0060.0000.0000.0000.000
67A68TYR00.0240.01322.490-0.004-0.0040.0000.0000.0000.000
68A69ASN0-0.0270.00123.6900.0040.0040.0000.0000.0000.000
69A70HIS00.0560.01918.351-0.015-0.0150.0000.0000.0000.000
70A71ASP-1-0.811-0.89217.776-0.399-0.3990.0000.0000.0000.000
71A72LYS10.7970.90313.0560.5170.5170.0000.0000.0000.000
72A73ILE0-0.060-0.02115.226-0.014-0.0140.0000.0000.0000.000
73A74VAL00.0290.02615.249-0.006-0.0060.0000.0000.0000.000
74A75VAL00.0040.01117.8190.0270.0270.0000.0000.0000.000
75A76CYS0-0.026-0.00818.691-0.003-0.0030.0000.0000.0000.000
76A77ASN00.0260.01220.9130.0200.0200.0000.0000.0000.000
77A78GLY00.0390.02022.6920.0080.0080.0000.0000.0000.000
78A79GLY00.002-0.02123.960-0.003-0.0030.0000.0000.0000.000
79A80GLU-1-0.964-0.97225.7250.0140.0140.0000.0000.0000.000
80A81THR00.002-0.02325.6910.0080.0080.0000.0000.0000.000
81A82ARG10.9160.94119.543-0.112-0.1120.0000.0000.0000.000
82A83PHE00.0350.02320.338-0.008-0.0080.0000.0000.0000.000
83A84ASN00.0580.03020.5620.0060.0060.0000.0000.0000.000
84A85SER00.0380.02420.785-0.017-0.0170.0000.0000.0000.000
85A86VAL0-0.028-0.01515.626-0.023-0.0230.0000.0000.0000.000
86A87TYR0-0.043-0.03916.475-0.018-0.0180.0000.0000.0000.000
87A88ASN0-0.043-0.04017.355-0.011-0.0110.0000.0000.0000.000
88A89ALA00.0210.00015.581-0.028-0.0280.0000.0000.0000.000
89A90LEU0-0.010-0.00511.602-0.050-0.0500.0000.0000.0000.000
90A91ASN0-0.025-0.02113.489-0.061-0.0610.0000.0000.0000.000
91A92VAL0-0.062-0.02215.477-0.015-0.0150.0000.0000.0000.000
92A93ILE0-0.066-0.0199.105-0.039-0.0390.0000.0000.0000.000
93A94ASP-1-0.893-0.94611.882-0.526-0.5260.0000.0000.0000.000
94A95GLU-1-0.967-0.9939.578-0.951-0.9510.0000.0000.0000.000
95A96ARG10.7560.8997.775-0.062-0.0620.0000.0000.0000.000
96A97LYS10.8280.8882.4891.5832.3790.528-0.506-0.8180.000
97A98ASN00.028-0.0146.0050.1190.1190.0000.0000.0000.000
98A99ASP-1-0.822-0.9012.390-3.600-1.3411.760-1.699-2.321-0.024
99A100ASP-1-0.712-0.8311.894-4.401-2.1445.418-4.305-3.371-0.017
100A101TRP0-0.017-0.0052.782-1.389-1.0490.5440.722-1.6050.008
101A102VAL00.0200.0155.248-0.769-0.763-0.001-0.001-0.0040.000
102A103PHE00.0110.0068.1650.1720.1720.0000.0000.0000.000
103A104VAL00.0580.03911.632-0.147-0.1470.0000.0000.0000.000
104A105HIS00.0790.01014.8730.0650.0650.0000.0000.0000.000
105A106ASP-1-0.808-0.89517.6160.0620.0620.0000.0000.0000.000
106A107ALA00.0560.01421.389-0.008-0.0080.0000.0000.0000.000
107A108ALA0-0.025-0.01122.800-0.011-0.0110.0000.0000.0000.000
108A109ARG10.8460.91721.921-0.109-0.1090.0000.0000.0000.000
109A110PRO00.0650.04622.6720.0080.0080.0000.0000.0000.000
110A111CYS0-0.0040.00224.229-0.011-0.0110.0000.0000.0000.000
111A112VAL0-0.0070.01919.1060.0090.0090.0000.0000.0000.000
112A113SER0-0.0020.00121.503-0.024-0.0240.0000.0000.0000.000
113A114ILE00.0750.02015.3810.0250.0250.0000.0000.0000.000
114A115ASP-1-0.854-0.92817.1470.1320.1320.0000.0000.0000.000
115A116SER0-0.019-0.01017.9150.0310.0310.0000.0000.0000.000
116A117ILE00.0010.00813.0610.0570.0570.0000.0000.0000.000
117A118ILE00.005-0.00313.1080.1080.1080.0000.0000.0000.000
118A119ASP-1-0.839-0.90213.2570.4900.4900.0000.0000.0000.000
119A120LEU0-0.022-0.00712.9220.0770.0770.0000.0000.0000.000
120A121TYR0-0.0030.0004.110-1.099-0.993-0.001-0.039-0.0670.000
121A122GLU-1-0.798-0.8899.6621.1661.1660.0000.0000.0000.000
122A123GLN0-0.020-0.02811.4230.1240.1240.0000.0000.0000.000
123A124THR0-0.040-0.02910.050-0.021-0.0210.0000.0000.0000.000
124A125LYS10.8210.9046.326-1.126-1.1260.0000.0000.0000.000
125A126SER0-0.066-0.0208.9000.0020.0020.0000.0000.0000.000
126A127SER0-0.054-0.02411.943-0.189-0.1890.0000.0000.0000.000
127A128HIS00.021-0.00112.7820.1240.1240.0000.0000.0000.000
128A129SER0-0.042-0.04314.1600.0370.0370.0000.0000.0000.000
129A130GLN0-0.0170.0078.0000.6590.6590.0000.0000.0000.000
130A131ALA00.0420.00210.4440.1150.1150.0000.0000.0000.000
131A132GLY00.0300.01312.884-0.044-0.0440.0000.0000.0000.000
132A133ILE0-0.022-0.00314.824-0.011-0.0110.0000.0000.0000.000
133A134LEU00.0050.01617.318-0.010-0.0100.0000.0000.0000.000
134A135ALA00.012-0.00419.276-0.021-0.0210.0000.0000.0000.000
135A136VAL0-0.012-0.00822.890-0.006-0.0060.0000.0000.0000.000
136A137ARG10.9730.99826.385-0.175-0.1750.0000.0000.0000.000
137A138ALA0-0.052-0.03328.940-0.011-0.0110.0000.0000.0000.000
138A139TYR0-0.001-0.01131.0860.0010.0010.0000.0000.0000.000
139A140GLU-1-0.865-0.91934.2140.0920.0920.0000.0000.0000.000
140A141THR0-0.048-0.03836.1180.0030.0030.0000.0000.0000.000
141A142VAL00.0600.04033.300-0.005-0.0050.0000.0000.0000.000
142A143LYS10.8910.93636.737-0.074-0.0740.0000.0000.0000.000
143A144GLN00.0120.00435.1900.0010.0010.0000.0000.0000.000
144A145VAL00.0210.01939.368-0.003-0.0030.0000.0000.0000.000
145A146THR0-0.0020.00241.3410.0000.0000.0000.0000.0000.000
146A147LYS10.9550.96943.864-0.036-0.0360.0000.0000.0000.000
147A148ASN00.011-0.00344.7010.0000.0000.0000.0000.0000.000
148A149ILE00.0660.04845.9110.0000.0000.0000.0000.0000.000
149A150VAL0-0.013-0.01343.2650.0020.0020.0000.0000.0000.000
150A151VAL0-0.005-0.00542.953-0.001-0.0010.0000.0000.0000.000
151A152LYS10.9520.97440.022-0.074-0.0740.0000.0000.0000.000
152A153THR00.033-0.00140.449-0.002-0.0020.0000.0000.0000.000
153A154LEU00.0000.01534.1860.0010.0010.0000.0000.0000.000
154A155ALA0-0.027-0.00538.087-0.003-0.0030.0000.0000.0000.000
155A156ARG10.9710.99736.227-0.089-0.0890.0000.0000.0000.000
156A157ASP-1-0.842-0.95534.0360.1310.1310.0000.0000.0000.000
157A158ASN0-0.048-0.00429.6520.0100.0100.0000.0000.0000.000
158A159ILE0-0.011-0.01029.9110.0060.0060.0000.0000.0000.000
159A160TRP00.0320.01725.099-0.003-0.0030.0000.0000.0000.000
160A161LEU0-0.032-0.00727.355-0.004-0.0040.0000.0000.0000.000
161A162ALA00.0580.03822.2510.0070.0070.0000.0000.0000.000
162A163GLN0-0.064-0.04122.033-0.043-0.0430.0000.0000.0000.000
163A164THR00.0000.00818.3240.0210.0210.0000.0000.0000.000
164A165PRO0-0.019-0.04314.537-0.032-0.0320.0000.0000.0000.000
165A166GLN0-0.083-0.04115.4800.0100.0100.0000.0000.0000.000
166A167LEU00.0100.0238.198-0.021-0.0210.0000.0000.0000.000
167A168SER00.0630.02510.1750.0260.0260.0000.0000.0000.000
168A169ARG10.8380.9273.354-6.274-5.4740.073-0.338-0.5340.002
169A170LEU00.0320.0126.242-0.311-0.3110.0000.0000.0000.000
170A171GLY00.0500.0217.935-0.117-0.1170.0000.0000.0000.000
171A172GLN0-0.067-0.03410.017-0.092-0.0920.0000.0000.0000.000
172A173LEU00.0220.02111.113-0.072-0.0720.0000.0000.0000.000
173A174GLU-1-0.805-0.89911.710-0.096-0.0960.0000.0000.0000.000
174A175LYS10.8290.91912.241-0.291-0.2910.0000.0000.0000.000
175A176ALA00.0250.02515.722-0.030-0.0300.0000.0000.0000.000
176A177PHE00.001-0.01616.639-0.033-0.0330.0000.0000.0000.000
177A178ASP-1-0.817-0.87418.0590.0510.0510.0000.0000.0000.000
178A179PHE0-0.0360.00519.852-0.015-0.0150.0000.0000.0000.000
179A180CYS0-0.009-0.00921.032-0.011-0.0110.0000.0000.0000.000
180A181TYR0-0.019-0.00822.413-0.015-0.0150.0000.0000.0000.000
181A182SER0-0.064-0.05023.614-0.007-0.0070.0000.0000.0000.000
182A183ASN0-0.065-0.03625.154-0.010-0.0100.0000.0000.0000.000
183A184ASN0-0.063-0.03027.564-0.001-0.0010.0000.0000.0000.000
184A185LEU00.013-0.00325.2110.0000.0000.0000.0000.0000.000
185A186VAL00.0310.01224.5200.0080.0080.0000.0000.0000.000
186A187ALA0-0.0040.00426.3070.0030.0030.0000.0000.0000.000
187A188LYS10.8790.94926.735-0.153-0.1530.0000.0000.0000.000
188A189VAL0-0.027-0.00521.8330.0110.0110.0000.0000.0000.000
189A190THR0-0.068-0.03124.145-0.011-0.0110.0000.0000.0000.000
190A191ASP-1-0.853-0.91720.8050.2180.2180.0000.0000.0000.000
191A192GLU-1-0.838-0.93613.7210.4500.4500.0000.0000.0000.000
192A193ALA00.0280.01318.0020.0250.0250.0000.0000.0000.000
193A194SER0-0.007-0.00818.925-0.007-0.0070.0000.0000.0000.000
194A195ALA00.009-0.00318.656-0.012-0.0120.0000.0000.0000.000
195A196LEU00.014-0.00514.1630.0010.0010.0000.0000.0000.000
196A197GLU-1-0.913-0.94818.3170.2630.2630.0000.0000.0000.000
197A198MET0-0.107-0.04721.571-0.019-0.0190.0000.0000.0000.000
198A199PHE0-0.021-0.00416.312-0.018-0.0180.0000.0000.0000.000
199A200GLY0-0.0130.00320.8460.0040.0040.0000.0000.0000.000
200A201ILE0-0.071-0.04014.8900.0270.0270.0000.0000.0000.000
201A202ASN00.0190.00218.668-0.027-0.0270.0000.0000.0000.000
202A203PRO0-0.0100.01316.1500.0500.0500.0000.0000.0000.000
203A204ILE00.0000.01614.697-0.068-0.0680.0000.0000.0000.000
204A205VAL0-0.013-0.01517.7530.0010.0010.0000.0000.0000.000
205A206VAL00.0070.01216.1030.0050.0050.0000.0000.0000.000
206A207GLU-1-0.926-0.96319.3700.1650.1650.0000.0000.0000.000
207A208CYS0-0.0110.01421.024-0.003-0.0030.0000.0000.0000.000
208A209SER00.0310.01522.677-0.014-0.0140.0000.0000.0000.000
209A210LYS10.9280.95026.008-0.105-0.1050.0000.0000.0000.000
210A211LYS10.9100.95427.447-0.059-0.0590.0000.0000.0000.000
211A212ASN0-0.035-0.02321.589-0.031-0.0310.0000.0000.0000.000
212A213ILE00.0380.01725.5840.0120.0120.0000.0000.0000.000
213A214LYS10.8600.93224.862-0.069-0.0690.0000.0000.0000.000
214A215ILE00.008-0.00627.443-0.002-0.0020.0000.0000.0000.000
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