FMO DATABASE

FMODB ID: MVNLZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-344623.420103
FMO2-HF: Nuclear repulsion	316521.53717
FMO2-HF: Total energy	-28101.882933
FMO2-MP2: Total energy	-28183.843608

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.
0.416	2.74	-0.016	-1.219	-1.089	0.006

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 : 0.030 / 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 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	0.005	0.016	3.879	-0.281	2.043	-0.016	-1.219	-1.089	0.006
4	A	102	LYS	1	0.840	0.897	6.499	2.106	2.106	0.000	0.000	0.000	0.000
5	A	103	ARG	1	0.917	0.965	8.118	0.757	0.757	0.000	0.000	0.000	0.000
6	A	104	LYS	1	1.045	1.009	5.516	-2.171	-2.171	0.000	0.000	0.000	0.000
7	A	105	THR	0	0.040	0.018	9.458	0.075	0.075	0.000	0.000	0.000	0.000
8	A	106	THR	0	0.038	0.015	11.928	0.003	0.003	0.000	0.000	0.000	0.000
9	A	107	ASN	0	0.039	0.022	14.800	-0.048	-0.048	0.000	0.000	0.000	0.000
10	A	108	ALA	0	0.051	0.025	15.754	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	109	ASP	-1	-0.849	-0.923	14.482	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	110	ARG	1	0.954	0.977	17.802	0.037	0.037	0.000	0.000	0.000	0.000
13	A	111	ARG	1	0.981	0.995	20.607	-0.067	-0.067	0.000	0.000	0.000	0.000
14	A	112	LYS	1	0.923	0.957	16.775	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	113	ALA	0	0.015	-0.003	21.583	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	114	ALA	0	-0.029	-0.021	23.281	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	115	THR	0	0.006	-0.005	25.444	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	116	MET	0	-0.007	0.006	24.386	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	117	ARG	1	0.941	0.979	25.224	0.025	0.025	0.000	0.000	0.000	0.000
20	A	118	GLU	-1	-0.754	-0.831	29.531	0.003	0.003	0.000	0.000	0.000	0.000
21	A	119	ARG	1	0.938	0.959	27.393	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	120	ARG	1	0.949	0.977	26.662	0.057	0.057	0.000	0.000	0.000	0.000
23	A	121	ARG	1	0.880	0.904	33.552	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	122	LEU	0	0.004	0.002	35.407	0.000	0.000	0.000	0.000	0.000	0.000
25	A	123	SER	0	-0.032	-0.016	36.161	0.001	0.001	0.000	0.000	0.000	0.000
26	A	124	LYS	1	0.887	0.921	37.605	0.033	0.033	0.000	0.000	0.000	0.000
27	A	125	VAL	0	0.016	0.015	39.835	0.001	0.001	0.000	0.000	0.000	0.000
28	A	126	ASN	0	0.000	-0.004	39.617	0.003	0.003	0.000	0.000	0.000	0.000
29	A	127	GLU	-1	-0.769	-0.865	39.744	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	128	ALA	0	0.024	0.036	43.853	0.000	0.000	0.000	0.000	0.000	0.000
31	A	129	PHE	0	0.015	-0.009	44.975	0.001	0.001	0.000	0.000	0.000	0.000
32	A	130	GLU	-1	-0.789	-0.880	46.239	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	131	THR	0	-0.008	-0.012	47.416	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	132	LEU	0	0.028	0.026	49.905	0.000	0.000	0.000	0.000	0.000	0.000
35	A	133	LYS	1	0.778	0.879	50.847	0.005	0.005	0.000	0.000	0.000	0.000
36	A	134	ARG	1	0.830	0.883	47.066	0.016	0.016	0.000	0.000	0.000	0.000
37	A	135	SER	0	-0.006	0.009	53.700	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	136	THR	0	-0.048	-0.011	55.526	0.000	0.000	0.000	0.000	0.000	0.000
39	A	137	SER	0	-0.085	-0.047	56.712	0.001	0.001	0.000	0.000	0.000	0.000
40	A	138	SER	0	0.060	0.031	58.437	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	139	ASN	0	0.011	0.005	58.351	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	140	PRO	0	0.042	0.019	54.815	0.001	0.001	0.000	0.000	0.000	0.000
43	A	141	ASN	0	0.027	0.009	53.749	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	142	GLN	0	0.043	0.043	53.850	0.001	0.001	0.000	0.000	0.000	0.000
45	A	143	ARG	1	0.934	0.952	46.512	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	144	LEU	0	0.033	0.028	51.113	0.002	0.002	0.000	0.000	0.000	0.000
47	A	145	PRO	0	0.027	0.020	49.729	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	146	LYS	1	0.920	0.942	42.618	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	147	VAL	0	0.030	0.015	49.367	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	148	GLU	-1	-0.786	-0.891	51.812	0.009	0.009	0.000	0.000	0.000	0.000
51	A	149	ILE	0	-0.073	-0.026	49.549	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	150	LEU	0	0.012	0.009	49.699	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	151	ARG	1	0.909	0.943	53.796	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	152	ASN	0	-0.002	-0.008	56.855	0.000	0.000	0.000	0.000	0.000	0.000
55	A	153	ALA	0	0.037	0.017	55.384	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	154	ILE	0	-0.001	-0.002	56.049	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	155	ARG	1	0.915	0.954	59.265	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	156	TYR	0	-0.021	-0.006	59.761	0.000	0.000	0.000	0.000	0.000	0.000
59	A	157	ILE	0	0.003	0.001	57.602	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	158	GLU	-1	-0.902	-0.949	62.074	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	159	GLY	0	-0.036	-0.015	65.085	0.000	0.000	0.000	0.000	0.000	0.000
62	A	160	LEU	0	-0.014	-0.026	62.772	0.000	0.000	0.000	0.000	0.000	0.000
63	A	161	GLN	0	-0.015	0.004	65.091	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	162	ALA	0	-0.019	-0.016	67.229	0.000	0.000	0.000	0.000	0.000	0.000
65	A	163	LEU	0	-0.086	-0.040	68.658	0.000	0.000	0.000	0.000	0.000	0.000
66	A	164	LEU	0	0.026	0.022	67.494	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	165	ARG	1	0.899	0.963	71.371	0.005	0.005	0.000	0.000	0.000	0.000
68	A	166	ASP	-1	-0.967	-0.978	73.538	-0.008	-0.008	0.000	0.000	0.000	0.000

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