FMO DATABASE

FMODB ID: MN4MZ

Calculation Name: 4M78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: A

ChEMBL ID:

UniProt ID: P38203

Base Structure: X-ray

Registration Date: 2023-09-23

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-381253.604016
FMO2-HF: Nuclear repulsion	355714.365087
FMO2-HF: Total energy	-25539.23893
FMO2-MP2: Total energy	-25615.125658

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.
-2.055	1.99	1.014	-2.46	-2.599	-0.002

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 : 0.042 / q_NPA : 0.027

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	ALA	0	0.048	0.023	2.623	-3.912	0.080	1.015	-2.449	-2.558	-0.002
4	A	4	THR	0	-0.003	-0.004	4.779	0.394	0.447	-0.001	-0.011	-0.041	0.000
5	A	5	LEU	0	0.045	0.027	8.339	0.107	0.107	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.983	0.976	10.738	0.528	0.528	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.873	-0.936	9.549	-0.477	-0.477	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.017	0.007	10.629	0.084	0.084	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.062	-0.011	15.110	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.019	-0.012	17.183	0.028	0.028	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.856	0.930	16.200	0.274	0.274	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.829	0.911	20.902	0.144	0.144	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.010	-0.006	17.734	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.009	-0.007	19.417	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.010	-0.007	19.066	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.019	-0.005	19.761	0.037	0.037	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.042	0.018	20.417	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.015	-0.018	20.812	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.877	-0.935	23.091	-0.196	-0.196	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.013	-0.001	24.795	0.018	0.018	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.809	-0.883	25.781	-0.143	-0.143	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.068	-0.031	24.623	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.006	-0.001	24.178	0.016	0.016	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.036	-0.025	23.899	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.010	0.012	23.238	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.006	0.001	22.762	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.030	0.044	16.015	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.015	-0.015	20.503	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.043	0.018	19.120	0.012	0.012	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.023	-0.006	12.561	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.752	-0.848	16.695	-0.609	-0.609	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.953	0.966	11.321	1.347	1.347	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.065	-0.036	13.213	-0.151	-0.151	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.038	-0.019	12.672	0.038	0.038	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.005	-0.003	15.458	0.089	0.089	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.017	-0.013	16.431	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.002	-0.005	20.009	0.036	0.036	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.002	-0.002	20.683	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.016	-0.020	24.191	0.020	0.020	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.033	-0.039	26.744	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.025	0.023	26.515	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.005	-0.008	28.105	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.047	0.019	28.212	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.921	0.935	23.973	0.168	0.168	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.014	0.025	29.498	0.013	0.013	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.007	-0.053	32.183	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.811	0.903	32.407	0.102	0.102	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.838	-0.868	33.842	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.054	-0.032	32.605	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.028	0.018	29.521	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.012	-0.014	30.373	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.947	0.989	30.933	0.110	0.110	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.022	0.005	28.864	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.003	0.004	27.121	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.001	0.001	23.596	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.018	0.022	21.952	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.949	0.960	21.644	0.326	0.326	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.065	0.030	18.148	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.079	-0.072	18.898	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.836	-0.880	21.065	-0.290	-0.290	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.068	-0.028	17.345	0.028	0.028	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.011	0.014	17.981	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.025	-0.023	14.438	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.004	0.007	14.482	0.028	0.028	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.008	0.009	14.335	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.020	-0.013	14.525	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.009	0.004	17.282	0.027	0.027	0.000	0.000	0.000	0.000

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