FMO DATABASE

FMODB ID: LZNV9

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	OptH
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	-343672.589381
FMO2-HF: Nuclear repulsion	315571.826364
FMO2-HF: Total energy	-28100.763017
FMO2-MP2: Total energy	-28182.872478

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.
-1.911	0.248	-0.021	-1.12	-1.018	0.003

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 : 0.023 / q_NPA : 0.001

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

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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	0.012	3.832	-0.008	2.151	-0.021	-1.120	-1.018	0.003
4	A	102	LYS	1	0.931	0.966	6.465	1.392	1.392	0.000	0.000	0.000	0.000
5	A	103	ARG	1	0.920	0.969	8.554	0.382	0.382	0.000	0.000	0.000	0.000
6	A	104	LYS	1	1.049	1.012	5.434	-3.177	-3.177	0.000	0.000	0.000	0.000
7	A	105	THR	0	0.018	0.012	9.686	0.092	0.092	0.000	0.000	0.000	0.000
8	A	106	THR	0	0.057	0.014	12.198	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	107	ASN	0	0.042	0.017	14.992	-0.085	-0.085	0.000	0.000	0.000	0.000
10	A	108	ALA	0	-0.024	-0.015	15.907	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	109	ASP	-1	-0.886	-0.930	14.450	0.158	0.158	0.000	0.000	0.000	0.000
12	A	110	ARG	1	0.938	0.960	17.792	-0.143	-0.143	0.000	0.000	0.000	0.000
13	A	111	ARG	1	0.976	0.992	20.588	-0.150	-0.150	0.000	0.000	0.000	0.000
14	A	112	LYS	1	1.039	1.018	18.659	-0.089	-0.089	0.000	0.000	0.000	0.000
15	A	113	ALA	0	0.021	0.012	21.773	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	114	ALA	0	0.004	-0.008	23.485	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	115	THR	0	0.002	0.003	25.392	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	116	MET	0	-0.040	-0.015	24.455	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	117	ARG	1	0.937	0.959	26.046	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	118	GLU	-1	-0.796	-0.880	29.767	0.041	0.041	0.000	0.000	0.000	0.000
21	A	119	ARG	1	0.974	0.982	27.817	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	120	ARG	1	0.914	0.953	26.657	0.006	0.006	0.000	0.000	0.000	0.000
23	A	121	ARG	1	0.925	0.966	33.587	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	122	LEU	0	0.011	0.004	35.552	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	123	SER	0	-0.009	-0.011	36.225	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	124	LYS	1	1.004	1.008	36.846	0.013	0.013	0.000	0.000	0.000	0.000
27	A	125	VAL	0	0.023	0.016	39.953	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	126	ASN	0	-0.037	-0.037	40.048	0.002	0.002	0.000	0.000	0.000	0.000
29	A	127	GLU	-1	-0.915	-0.949	41.275	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	128	ALA	0	0.008	0.009	43.917	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	129	PHE	0	-0.014	-0.021	44.669	0.001	0.001	0.000	0.000	0.000	0.000
32	A	130	GLU	-1	-0.928	-0.976	46.695	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	131	THR	0	-0.009	0.004	47.729	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	132	LEU	0	0.037	0.030	50.279	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	133	LYS	1	0.904	0.950	49.710	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	134	ARG	1	0.892	0.931	47.363	0.008	0.008	0.000	0.000	0.000	0.000
37	A	135	SER	0	-0.017	0.011	54.216	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	136	THR	0	0.000	-0.007	56.143	0.000	0.000	0.000	0.000	0.000	0.000
39	A	137	SER	0	-0.067	-0.025	56.861	0.000	0.000	0.000	0.000	0.000	0.000
40	A	138	SER	0	0.094	0.049	58.841	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	139	ASN	0	-0.031	-0.016	58.294	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	140	PRO	0	-0.017	-0.017	54.771	0.001	0.001	0.000	0.000	0.000	0.000
43	A	141	ASN	0	0.017	-0.003	53.784	0.001	0.001	0.000	0.000	0.000	0.000
44	A	142	GLN	0	0.042	0.051	53.820	0.000	0.000	0.000	0.000	0.000	0.000
45	A	143	ARG	1	0.941	0.950	45.963	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	144	LEU	0	0.017	0.026	51.698	0.002	0.002	0.000	0.000	0.000	0.000
47	A	145	PRO	0	0.013	0.007	49.917	0.000	0.000	0.000	0.000	0.000	0.000
48	A	146	LYS	1	0.991	0.983	42.488	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	147	VAL	0	0.041	0.023	49.509	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	148	GLU	-1	-0.877	-0.941	51.953	0.018	0.018	0.000	0.000	0.000	0.000
51	A	149	ILE	0	-0.053	-0.015	49.911	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	150	LEU	0	-0.014	-0.018	49.738	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	151	ARG	1	0.998	0.992	53.759	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	152	ASN	0	-0.037	-0.012	56.746	0.000	0.000	0.000	0.000	0.000	0.000
55	A	153	ALA	0	0.017	0.011	55.766	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	154	ILE	0	-0.014	0.005	56.202	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	155	ARG	1	0.943	0.971	59.448	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	156	TYR	0	0.002	-0.008	60.310	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	157	ILE	0	0.010	0.005	58.318	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	158	GLU	-1	-0.908	-0.946	62.554	0.009	0.009	0.000	0.000	0.000	0.000
61	A	159	GLY	0	-0.033	-0.009	65.355	0.000	0.000	0.000	0.000	0.000	0.000
62	A	160	LEU	0	-0.001	-0.020	63.391	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	161	GLN	0	-0.025	-0.003	64.770	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	162	ALA	0	0.019	0.000	67.521	0.000	0.000	0.000	0.000	0.000	0.000
65	A	163	LEU	0	-0.119	-0.039	68.940	0.000	0.000	0.000	0.000	0.000	0.000
66	A	164	LEU	0	0.020	0.006	68.262	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	165	ARG	1	0.920	0.987	71.813	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	166	ASP	-1	-0.979	-0.996	73.688	0.000	0.000	0.000	0.000	0.000	0.000

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