FMO DATABASE

FMODB ID: 17K4Z

Calculation Name: 4M6A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M6A

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-524084.770213
FMO2-HF: Nuclear repulsion	490830.294644
FMO2-HF: Total energy	-33254.475568
FMO2-MP2: Total energy	-33353.637332

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:2:LEU)

Summations of interaction energy for fragment #1(A:2: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.
-1.216	-0.021	-0.014	-0.45	-0.731	0.002

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.021

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	4	ALA	0	0.041	0.019	3.837	-1.215	-0.020	-0.014	-0.450	-0.731	0.002
4	A	5	PRO	0	0.027	0.007	5.855	0.503	0.503	0.000	0.000	0.000	0.000
5	A	6	LYS	1	0.939	0.963	8.486	0.058	0.058	0.000	0.000	0.000	0.000
6	A	7	ASN	0	-0.044	-0.025	11.784	0.014	0.014	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.048	0.035	14.589	0.005	0.005	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.001	-0.004	16.086	0.026	0.026	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.004	0.003	19.705	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.033	-0.027	22.035	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.934	-0.957	25.518	-0.116	-0.116	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.013	-0.008	26.325	0.006	0.006	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.052	-0.024	29.192	0.001	0.001	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.920	-0.968	27.217	-0.119	-0.119	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.934	-0.959	31.881	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.020	-0.013	30.698	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.007	0.004	30.159	0.007	0.007	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.882	0.953	30.438	0.096	0.096	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.011	0.006	27.986	0.006	0.006	0.000	0.000	0.000	0.000
20	A	21	SER	0	0.007	-0.016	31.915	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	22	TRP	0	-0.030	-0.001	28.322	0.004	0.004	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.006	-0.006	34.722	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.019	-0.003	33.719	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.006	0.001	35.579	0.001	0.001	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.874	-0.936	35.375	-0.097	-0.097	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.055	-0.027	33.544	0.001	0.001	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.007	0.015	33.668	0.000	0.000	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.039	-0.021	28.505	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.796	-0.905	25.608	-0.156	-0.156	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.056	-0.030	23.485	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.008	0.006	25.048	0.012	0.012	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.049	-0.013	20.068	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.019	0.012	22.600	0.017	0.017	0.000	0.000	0.000	0.000
34	A	35	GLN	0	0.010	-0.003	20.885	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.030	0.014	22.166	0.011	0.011	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.010	-0.010	22.073	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.858	-0.922	23.813	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.017	-0.019	26.077	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.992	-0.976	27.797	-0.065	-0.065	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.829	0.908	22.885	0.099	0.099	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.026	0.008	21.525	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.023	-0.016	18.338	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.893	-0.935	16.859	-0.134	-0.134	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.035	-0.008	18.464	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.016	0.016	17.360	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.030	-0.024	16.650	0.026	0.026	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.023	0.032	17.066	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.043	-0.047	19.236	0.013	0.013	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.009	0.031	20.871	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.074	0.016	23.953	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.042	0.020	25.887	0.008	0.008	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.027	-0.017	28.658	0.007	0.007	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.944	-0.961	27.532	-0.137	-0.137	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.820	0.897	30.535	0.116	0.116	0.000	0.000	0.000	0.000
55	A	56	SER	0	0.001	-0.010	31.176	0.009	0.009	0.000	0.000	0.000	0.000
56	A	57	TYR	0	-0.012	-0.005	22.732	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.801	-0.899	28.158	-0.113	-0.113	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.050	-0.038	25.035	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.024	0.001	25.500	0.006	0.006	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.015	0.027	24.243	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.073	-0.031	24.825	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.914	0.949	26.233	0.086	0.086	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.048	0.041	28.919	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	GLY	0	-0.029	-0.009	32.715	0.003	0.003	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.051	-0.029	30.363	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.915	-0.957	31.575	-0.071	-0.071	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.021	0.038	25.190	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.055	0.029	27.659	0.005	0.005	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.045	-0.032	26.745	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.016	-0.010	26.016	0.008	0.008	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.008	-0.005	25.958	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.033	-0.020	24.312	0.011	0.011	0.000	0.000	0.000	0.000
73	A	74	GLY	0	0.066	0.031	26.918	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.013	0.002	22.910	0.004	0.004	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.891	0.958	26.270	0.131	0.131	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.004	-0.002	24.873	0.005	0.005	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.009	0.004	22.296	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	79	HIS	0	-0.116	-0.062	22.965	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.960	0.989	20.505	0.178	0.178	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.012	-0.009	26.235	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	ASN	0	-0.036	-0.030	28.982	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	83	PRO	0	-0.012	0.002	28.510	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.013	0.009	30.088	0.008	0.008	0.000	0.000	0.000	0.000
84	A	85	SER	0	-0.001	-0.018	30.650	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.012	0.005	31.329	0.006	0.006	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.870	-0.935	31.429	-0.090	-0.090	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.067	-0.017	29.050	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.023	0.004	33.136	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.043	-0.034	30.509	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)