FMO DATABASE

FMODB ID: 767NK

Calculation Name: 3MAB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MAB

Chain ID: A

ChEMBL ID:

UniProt ID:

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-579245.286756
FMO2-HF: Nuclear repulsion	546276.269613
FMO2-HF: Total energy	-32969.017143
FMO2-MP2: Total energy	-33066.169905

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-6.918	-1.872	5.768	-3.271	-7.541	0

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.009

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	5	ASN	0	-0.027	-0.038	3.152	-2.245	0.591	0.120	-1.524	-1.431	0.001
4	A	6	LEU	0	0.032	0.013	5.895	0.333	0.333	0.000	0.000	0.000	0.000
5	A	7	SER	0	-0.061	-0.053	7.422	0.177	0.177	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.895	-0.924	7.313	-2.408	-2.408	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.033	-0.002	6.279	0.189	0.189	0.000	0.000	0.000	0.000
8	A	10	PRO	0	-0.010	-0.015	9.663	0.012	0.012	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.050	-0.031	13.411	0.034	0.034	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.000	0.029	10.058	0.034	0.034	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.032	0.021	13.348	-0.074	-0.074	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.906	0.911	12.359	0.827	0.827	0.000	0.000	0.000	0.000
13	A	15	VAL	0	0.010	0.023	15.442	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.090	0.041	14.450	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.806	-0.881	9.735	-1.067	-1.067	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.009	-0.008	12.566	0.030	0.030	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.805	-0.893	15.069	-0.235	-0.235	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.007	0.004	10.368	0.039	0.039	0.000	0.000	0.000	0.000
19	A	21	ILE	0	-0.008	-0.001	10.265	0.036	0.036	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.787	0.876	12.635	0.313	0.313	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.031	0.029	14.727	0.027	0.027	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.025	-0.013	13.315	0.042	0.042	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.041	0.002	8.416	0.000	0.000	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.828	0.881	7.431	0.230	0.230	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.039	-0.038	2.285	-1.249	-0.643	2.074	-0.716	-1.963	0.000
26	A	28	PRO	0	0.016	-0.019	2.390	-1.024	0.247	0.723	-0.450	-1.544	0.001
27	A	29	VAL	0	-0.032	0.004	2.445	-0.375	-0.179	2.850	-0.556	-2.490	-0.002
28	A	30	GLU	-1	-0.723	-0.830	4.209	-0.444	-0.307	0.001	-0.025	-0.113	0.000
29	A	31	LEU	0	0.008	-0.001	6.528	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.832	0.904	6.465	-0.560	-0.560	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.920	-0.949	7.767	0.644	0.644	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.069	-0.030	10.256	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.010	0.013	11.803	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	36	SER	0	-0.037	-0.057	13.573	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.851	0.912	15.479	-0.088	-0.088	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.754	-0.849	15.586	0.023	0.023	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.004	-0.009	12.954	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.020	-0.016	14.854	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.001	0.006	18.092	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.901	0.938	14.761	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.036	-0.018	15.212	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	44	TRP	0	-0.033	-0.030	18.756	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.960	-0.987	21.128	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.141	-0.069	19.270	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.850	-0.908	22.382	-0.134	-0.134	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.007	0.006	23.487	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.126	-0.077	25.486	0.005	0.005	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.023	0.013	19.626	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	51	CYS	0	-0.030	-0.036	22.992	0.019	0.019	0.000	0.000	0.000	0.000
50	A	52	MET	0	0.032	0.019	22.782	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.025	-0.035	23.149	0.010	0.010	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.797	-0.889	19.081	-0.174	-0.174	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.022	0.032	18.268	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.084	-0.056	18.721	0.013	0.013	0.000	0.000	0.000	0.000
55	A	57	ALA	0	-0.023	-0.018	16.893	0.010	0.010	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.050	0.028	13.238	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.774	-0.856	13.974	0.114	0.114	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.011	-0.010	14.961	0.032	0.032	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.017	-0.001	10.954	0.020	0.020	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.010	0.002	10.395	0.054	0.054	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.086	-0.064	11.154	0.096	0.096	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.003	0.016	11.431	0.049	0.049	0.000	0.000	0.000	0.000
63	A	65	ILE	0	-0.038	-0.022	12.227	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.945	0.958	15.765	0.080	0.080	0.000	0.000	0.000	0.000
65	A	67	TRP	0	0.058	0.011	18.244	0.031	0.031	0.000	0.000	0.000	0.000
66	A	68	HIS	0	-0.018	-0.008	19.789	0.012	0.012	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.020	-0.003	21.457	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.034	0.003	18.178	0.015	0.015	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.816	-0.905	21.713	0.054	0.054	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.812	-0.910	24.519	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	73	ALA	0	-0.013	0.003	26.590	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.857	0.925	19.281	-0.090	-0.090	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.865	0.911	23.905	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.024	0.010	25.310	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.889	-0.924	22.127	0.072	0.072	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.028	0.004	20.100	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.945	0.980	24.029	0.011	0.011	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.911	0.948	27.304	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.026	0.019	21.656	0.002	0.002	0.000	0.000	0.000	0.000
80	A	82	HIS	0	0.037	0.009	25.314	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.061	-0.053	26.647	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.075	-0.027	27.874	0.003	0.003	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.005	0.023	24.542	0.003	0.003	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.859	-0.902	28.262	-0.057	-0.057	0.000	0.000	0.000	0.000
85	A	87	GLY	0	-0.073	-0.043	31.061	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:3:LEU)