FMO DATABASE

FMODB ID: MNY8Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-579806.714784
FMO2-HF: Nuclear repulsion	546837.933
FMO2-HF: Total energy	-32968.781784
FMO2-MP2: Total energy	-33065.977457

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.
-6.816	-1.579	4.263	-2.824	-6.675	0.004

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 : -0.003 / q_NPA : -0.006

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	-0.013	-0.030	3.194	-2.446	0.579	0.110	-1.594	-1.541	0.003
4	A	6	LEU	0	0.023	0.000	5.907	0.389	0.389	0.000	0.000	0.000	0.000
5	A	7	SER	0	-0.074	-0.045	7.476	0.150	0.150	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.910	-0.938	7.186	-2.511	-2.511	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.050	-0.005	6.065	0.183	0.183	0.000	0.000	0.000	0.000
8	A	10	PRO	0	0.015	-0.003	9.671	0.028	0.028	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.060	-0.042	13.238	0.035	0.035	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.015	0.031	10.430	0.044	0.044	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.039	0.034	12.970	-0.082	-0.082	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.931	0.927	12.589	0.818	0.818	0.000	0.000	0.000	0.000
13	A	15	VAL	0	0.026	0.020	15.536	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.078	0.044	14.490	0.006	0.006	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.811	-0.890	9.897	-1.061	-1.061	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.044	-0.033	12.687	0.045	0.045	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.789	-0.884	15.317	-0.215	-0.215	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.002	0.000	10.555	0.034	0.034	0.000	0.000	0.000	0.000
19	A	21	ILE	0	-0.009	0.000	10.276	0.044	0.044	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.814	0.891	12.656	0.297	0.297	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.029	0.035	14.870	0.029	0.029	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.083	-0.050	13.101	0.034	0.034	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.048	-0.010	8.956	0.045	0.045	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.889	0.924	7.597	0.169	0.169	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.017	-0.028	2.372	-0.970	-0.377	1.198	-0.394	-1.397	0.001
26	A	28	PRO	0	0.029	-0.007	2.446	-0.904	0.166	0.756	-0.380	-1.446	0.001
27	A	29	VAL	0	-0.020	-0.006	2.402	-0.564	-0.144	2.199	-0.436	-2.182	-0.001
28	A	30	GLU	-1	-0.755	-0.832	4.350	-0.278	-0.149	0.000	-0.020	-0.109	0.000
29	A	31	LEU	0	0.003	0.002	6.634	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.832	0.897	6.834	-0.532	-0.532	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.938	-0.949	8.403	0.608	0.608	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.072	-0.030	10.356	-0.046	-0.046	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.022	0.018	11.998	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	36	SER	0	-0.040	-0.060	13.849	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.850	0.909	15.624	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.755	-0.851	15.976	0.036	0.036	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.023	-0.018	13.273	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.022	-0.021	15.238	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.015	0.011	18.402	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.874	0.927	14.514	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.021	-0.019	15.307	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	44	TRP	0	-0.037	-0.035	18.952	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.958	-0.968	21.506	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.147	-0.073	19.665	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.861	-0.909	22.597	-0.133	-0.133	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.017	0.007	23.640	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.131	-0.080	25.529	0.003	0.003	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.037	0.009	19.862	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	CYS	0	-0.017	-0.029	23.180	0.017	0.017	0.000	0.000	0.000	0.000
50	A	52	MET	0	0.028	0.027	23.009	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.039	-0.047	23.283	0.008	0.008	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.768	-0.871	19.370	-0.169	-0.169	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.008	0.022	18.497	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.077	-0.041	18.810	0.013	0.013	0.000	0.000	0.000	0.000
55	A	57	ALA	0	-0.027	-0.015	16.860	0.009	0.009	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.045	0.018	13.430	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.787	-0.867	14.099	0.106	0.106	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.017	-0.017	15.285	0.029	0.029	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.004	0.008	10.982	0.015	0.015	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.019	-0.004	10.669	0.053	0.053	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.083	-0.067	11.301	0.090	0.090	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.014	0.016	11.745	0.029	0.029	0.000	0.000	0.000	0.000
63	A	65	ILE	0	-0.036	-0.014	12.398	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.940	0.958	15.965	0.103	0.103	0.000	0.000	0.000	0.000
65	A	67	TRP	0	0.051	0.004	18.131	0.032	0.032	0.000	0.000	0.000	0.000
66	A	68	HIS	0	-0.006	0.001	19.810	0.014	0.014	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.045	-0.024	21.709	0.008	0.008	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.021	0.013	18.284	0.015	0.015	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.828	-0.913	21.906	0.048	0.048	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.821	-0.916	24.518	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	73	ALA	0	-0.021	-0.007	26.465	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.886	0.951	19.909	-0.083	-0.083	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.879	0.913	23.960	0.011	0.011	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.019	0.004	25.424	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.860	-0.907	22.669	0.066	0.066	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.035	0.005	20.322	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.951	0.971	24.307	0.015	0.015	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.928	0.966	27.574	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.023	0.013	21.772	0.002	0.002	0.000	0.000	0.000	0.000
80	A	82	HIS	0	0.019	0.012	25.368	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.060	-0.057	26.693	0.000	0.000	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.104	-0.051	28.016	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.022	0.020	24.801	0.002	0.002	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.869	-0.914	28.258	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	87	GLY	0	-0.057	-0.016	31.089	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)