FMO DATABASE

FMODB ID: 948R2

Calculation Name: 1MDY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MDY

Chain ID: A

ChEMBL ID:

UniProt ID: P10085

Base Structure: X-ray

Registration Date: 2023-06-22

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343624.632051
FMO2-HF: Nuclear repulsion	315523.207278
FMO2-HF: Total energy	-28101.424773
FMO2-MP2: Total energy	-28183.436463

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-0.23	2.637	-0.021	-1.534	-1.311	0.007

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.017

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 ES EX CT+mix DI(MP2)

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].
3	A	3	LEU	0	-0.016	0.010	3.832	-0.965	1.902	-0.021	-1.534	-1.311	0.007
4	A	102	LYS	1	0.907	0.937	6.629	1.752	1.752	0.000	0.000	0.000	0.000
5	A	103	ARG	1	0.921	0.969	8.573	0.653	0.653	0.000	0.000	0.000	0.000
6	A	104	LYS	1	1.043	1.010	5.523	-1.758	-1.758	0.000	0.000	0.000	0.000
7	A	105	THR	0	0.026	0.011	9.694	0.077	0.077	0.000	0.000	0.000	0.000
8	A	106	THR	0	0.062	0.022	12.205	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	107	ASN	0	0.019	0.010	15.002	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	108	ALA	0	-0.004	-0.004	15.767	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	109	ASP	-1	-0.888	-0.941	14.482	-0.036	-0.036	0.000	0.000	0.000	0.000
12	A	110	ARG	1	0.935	0.961	17.803	0.042	0.042	0.000	0.000	0.000	0.000
13	A	111	ARG	1	0.972	0.986	20.596	-0.040	-0.040	0.000	0.000	0.000	0.000
14	A	112	LYS	1	1.035	1.018	18.029	0.001	0.001	0.000	0.000	0.000	0.000
15	A	113	ALA	0	0.026	0.014	21.791	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	114	ALA	0	0.000	-0.010	23.498	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	115	THR	0	-0.008	-0.004	25.401	0.001	0.001	0.000	0.000	0.000	0.000
18	A	116	MET	0	-0.036	-0.014	24.411	0.000	0.000	0.000	0.000	0.000	0.000
19	A	117	ARG	1	0.956	0.977	25.811	0.034	0.034	0.000	0.000	0.000	0.000
20	A	118	GLU	-1	-0.755	-0.822	29.781	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	119	ARG	1	0.970	0.988	27.705	0.002	0.002	0.000	0.000	0.000	0.000
22	A	120	ARG	1	0.937	0.962	26.592	0.055	0.055	0.000	0.000	0.000	0.000
23	A	121	ARG	1	0.866	0.894	33.602	0.006	0.006	0.000	0.000	0.000	0.000
24	A	122	LEU	0	0.012	0.006	35.563	0.000	0.000	0.000	0.000	0.000	0.000
25	A	123	SER	0	0.013	-0.003	36.254	0.000	0.000	0.000	0.000	0.000	0.000
26	A	124	LYS	1	0.869	0.924	37.786	0.034	0.034	0.000	0.000	0.000	0.000
27	A	125	VAL	0	0.024	0.017	39.963	0.001	0.001	0.000	0.000	0.000	0.000
28	A	126	ASN	0	-0.016	-0.015	40.129	0.003	0.003	0.000	0.000	0.000	0.000
29	A	127	GLU	-1	-0.808	-0.885	41.181	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	128	ALA	0	0.021	0.022	43.955	0.000	0.000	0.000	0.000	0.000	0.000
31	A	129	PHE	0	0.003	-0.018	44.958	0.001	0.001	0.000	0.000	0.000	0.000
32	A	130	GLU	-1	-0.793	-0.888	46.647	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	131	THR	0	-0.010	0.004	47.760	0.000	0.000	0.000	0.000	0.000	0.000
34	A	132	LEU	0	0.039	0.036	50.320	0.000	0.000	0.000	0.000	0.000	0.000
35	A	133	LYS	1	0.836	0.915	50.749	0.009	0.009	0.000	0.000	0.000	0.000
36	A	134	ARG	1	0.799	0.866	47.114	0.018	0.018	0.000	0.000	0.000	0.000
37	A	135	SER	0	-0.019	0.003	54.250	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	136	THR	0	0.002	-0.007	56.315	0.001	0.001	0.000	0.000	0.000	0.000
39	A	137	SER	0	-0.050	-0.020	56.987	0.001	0.001	0.000	0.000	0.000	0.000
40	A	138	SER	0	0.086	0.049	58.864	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	139	ASN	0	-0.013	0.003	58.645	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	140	PRO	0	0.006	-0.006	54.686	0.001	0.001	0.000	0.000	0.000	0.000
43	A	141	ASN	0	0.018	-0.006	53.799	0.000	0.000	0.000	0.000	0.000	0.000
44	A	142	GLN	0	0.030	0.037	53.823	0.000	0.000	0.000	0.000	0.000	0.000
45	A	143	ARG	1	0.938	0.951	46.118	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	144	LEU	0	0.014	0.022	51.691	0.002	0.002	0.000	0.000	0.000	0.000
47	A	145	PRO	0	0.026	0.012	49.932	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	146	LYS	1	0.928	0.951	42.728	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	147	VAL	0	0.039	0.021	49.520	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	148	GLU	-1	-0.804	-0.894	51.962	0.004	0.004	0.000	0.000	0.000	0.000
51	A	149	ILE	0	-0.049	-0.011	49.993	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	150	LEU	0	-0.013	-0.017	49.593	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	151	ARG	1	0.937	0.956	53.770	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	152	ASN	0	-0.028	-0.024	56.828	0.000	0.000	0.000	0.000	0.000	0.000
55	A	153	ALA	0	0.029	0.020	55.743	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	154	ILE	0	-0.011	0.001	56.171	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	155	ARG	1	0.911	0.961	59.460	0.001	0.001	0.000	0.000	0.000	0.000
58	A	156	TYR	0	-0.012	-0.015	60.275	0.000	0.000	0.000	0.000	0.000	0.000
59	A	157	ILE	0	0.007	0.003	58.210	0.000	0.000	0.000	0.000	0.000	0.000
60	A	158	GLU	-1	-0.894	-0.938	62.567	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	159	GLY	0	-0.036	-0.012	65.367	0.000	0.000	0.000	0.000	0.000	0.000
62	A	160	LEU	0	0.000	-0.018	63.478	0.000	0.000	0.000	0.000	0.000	0.000
63	A	161	GLN	0	-0.035	-0.003	65.020	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	162	ALA	0	0.031	0.004	67.535	0.000	0.000	0.000	0.000	0.000	0.000
65	A	163	LEU	0	-0.108	-0.034	69.035	0.000	0.000	0.000	0.000	0.000	0.000
66	A	164	LEU	0	0.020	0.008	68.009	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	165	ARG	1	0.869	0.948	71.828	0.006	0.006	0.000	0.000	0.000	0.000
68	A	166	ASP	-1	-0.949	-0.970	73.702	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)