FMO DATABASE

FMODB ID: LZZK9

Calculation Name: 5FMN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FMN

Chain ID: A

ChEMBL ID:

UniProt ID: Q55554

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-505055.54974
FMO2-HF: Nuclear repulsion	470660.112415
FMO2-HF: Total energy	-34395.437325
FMO2-MP2: Total energy	-34494.196137

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:22:SER)

Summations of interaction energy for fragment #1(A:22:SER)

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.
-5.887	-2.924	0.038	-1.143	-1.86	0.002

Interaction energy analysis for fragmet #1(A:22:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.019

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	24	GLU	-1	-0.876	-0.934	3.246	-2.456	-0.614	0.020	-0.779	-1.084	0.001
4	A	25	SER	0	-0.079	-0.069	3.086	0.281	0.860	0.017	-0.163	-0.434	0.000
5	A	26	LEU	0	0.075	0.034	3.985	0.098	0.640	0.001	-0.201	-0.342	0.001
6	A	27	GLN	0	0.029	0.011	5.684	-0.014	-0.014	0.000	0.000	0.000	0.000
7	A	28	LYS	1	0.881	0.957	7.179	1.367	1.367	0.000	0.000	0.000	0.000
8	A	29	LEU	0	0.006	-0.002	8.198	0.078	0.078	0.000	0.000	0.000	0.000
9	A	30	VAL	0	0.041	0.023	9.732	0.058	0.058	0.000	0.000	0.000	0.000
10	A	31	ASN	0	0.047	0.028	11.967	-0.049	-0.049	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.899	0.956	12.880	0.393	0.393	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.034	0.023	12.912	0.020	0.020	0.000	0.000	0.000	0.000
13	A	34	SER	0	0.058	0.023	16.095	0.020	0.020	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.846	0.922	15.648	0.093	0.093	0.000	0.000	0.000	0.000
15	A	36	ILE	0	0.010	0.013	17.616	0.007	0.007	0.000	0.000	0.000	0.000
16	A	37	GLU	-1	-0.812	-0.880	19.924	0.068	0.068	0.000	0.000	0.000	0.000
17	A	38	GLY	0	-0.041	-0.027	22.105	0.010	0.010	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.045	-0.033	23.558	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.031	0.009	23.408	0.002	0.002	0.000	0.000	0.000	0.000
20	A	41	ARG	1	0.823	0.886	22.799	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	42	GLY	0	0.034	0.026	28.078	0.004	0.004	0.000	0.000	0.000	0.000
22	A	43	VAL	0	0.007	-0.004	28.976	0.001	0.001	0.000	0.000	0.000	0.000
23	A	44	LYS	1	0.875	0.943	30.808	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	45	THR	0	-0.040	-0.027	32.521	0.003	0.003	0.000	0.000	0.000	0.000
25	A	46	MET	0	0.006	0.024	33.753	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.007	0.005	35.184	0.000	0.000	0.000	0.000	0.000	0.000
27	A	48	GLN	0	-0.007	-0.007	35.868	0.002	0.002	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.878	-0.925	37.624	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	50	ASN	0	-0.074	-0.032	40.451	0.000	0.000	0.000	0.000	0.000	0.000
30	A	51	ARG	1	0.820	0.897	36.454	0.020	0.020	0.000	0.000	0.000	0.000
31	A	52	PRO	0	0.022	0.008	40.566	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	53	CYS	0	0.019	0.016	38.976	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	54	PRO	0	0.053	0.006	37.916	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	55	GLU	-1	-0.794	-0.883	36.472	-0.036	-0.036	0.000	0.000	0.000	0.000
35	A	56	VAL	0	0.006	0.006	34.488	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	57	LEU	0	0.000	-0.007	33.178	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	58	ILE	0	0.005	0.005	32.451	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	59	GLN	0	0.018	0.008	29.471	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	60	VAL	0	0.015	-0.003	28.599	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	61	ALA	0	-0.037	-0.011	28.056	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	62	ALA	0	-0.008	0.001	26.603	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	63	VAL	0	-0.024	-0.011	24.131	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.949	0.981	23.080	0.124	0.124	0.000	0.000	0.000	0.000
44	A	65	GLY	0	0.071	0.042	22.803	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	66	ALA	0	-0.089	-0.063	20.244	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	67	LEU	0	0.031	0.012	18.371	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	68	ASP	-1	-0.835	-0.920	18.331	-0.274	-0.274	0.000	0.000	0.000	0.000
48	A	69	ARG	1	0.893	0.946	17.679	0.176	0.176	0.000	0.000	0.000	0.000
49	A	70	VAL	0	-0.060	-0.031	13.228	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	71	ALA	0	0.039	0.012	13.857	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	72	ARG	1	0.834	0.885	15.285	0.499	0.499	0.000	0.000	0.000	0.000
52	A	73	LEU	0	-0.015	-0.013	10.887	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	74	ILE	0	-0.010	-0.004	10.550	-0.177	-0.177	0.000	0.000	0.000	0.000
54	A	75	LEU	0	0.013	0.025	11.542	-0.110	-0.110	0.000	0.000	0.000	0.000
55	A	76	ASP	-1	-0.815	-0.878	12.047	-0.741	-0.741	0.000	0.000	0.000	0.000
56	A	77	ASP	-1	-0.841	-0.926	6.275	-2.777	-2.777	0.000	0.000	0.000	0.000
57	A	78	HIS	0	-0.059	-0.023	8.984	-0.258	-0.258	0.000	0.000	0.000	0.000
58	A	79	MET	0	-0.028	-0.028	11.208	0.065	0.065	0.000	0.000	0.000	0.000
59	A	80	ASN	0	-0.047	-0.017	7.718	0.286	0.286	0.000	0.000	0.000	0.000
60	A	81	GLU	-1	-0.907	-0.931	8.289	-1.778	-1.778	0.000	0.000	0.000	0.000
61	A	82	CYS	0	0.003	0.009	10.759	0.136	0.136	0.000	0.000	0.000	0.000
62	A	83	ILE	0	-0.036	-0.018	14.447	0.109	0.109	0.000	0.000	0.000	0.000
63	A	84	THR	0	-0.043	-0.027	10.328	0.115	0.115	0.000	0.000	0.000	0.000
64	A	85	ARG	1	0.780	0.857	12.240	0.950	0.950	0.000	0.000	0.000	0.000
65	A	86	ALA	0	-0.026	-0.009	14.701	0.096	0.096	0.000	0.000	0.000	0.000
66	A	87	ALA	0	-0.071	-0.040	16.167	0.068	0.068	0.000	0.000	0.000	0.000
67	A	88	ALA	0	-0.053	-0.017	15.005	0.056	0.056	0.000	0.000	0.000	0.000
68	A	89	GLU	-1	-0.948	-0.982	15.037	-0.477	-0.477	0.000	0.000	0.000	0.000
69	A	90	GLY	0	-0.030	0.003	18.836	0.043	0.043	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.017	-0.025	20.012	0.000	0.000	0.000	0.000	0.000	0.000
71	A	92	ILE	0	0.065	0.030	21.799	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	93	GLU	-1	-0.865	-0.932	22.784	-0.296	-0.296	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.007	-0.003	21.662	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	95	GLU	-1	-0.744	-0.850	16.669	-0.656	-0.656	0.000	0.000	0.000	0.000
75	A	96	LEU	0	-0.054	-0.025	19.488	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	97	ALA	0	-0.027	-0.018	22.057	0.007	0.007	0.000	0.000	0.000	0.000
77	A	98	GLU	-1	-0.763	-0.867	14.894	-0.716	-0.716	0.000	0.000	0.000	0.000
78	A	99	LEU	0	-0.019	-0.017	16.518	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	100	LYS	1	0.830	0.916	19.362	0.303	0.303	0.000	0.000	0.000	0.000
80	A	101	GLU	-1	-0.779	-0.873	20.851	-0.315	-0.315	0.000	0.000	0.000	0.000
81	A	102	ALA	0	-0.033	-0.008	17.229	0.009	0.009	0.000	0.000	0.000	0.000
82	A	103	LEU	0	-0.023	-0.025	19.064	0.015	0.015	0.000	0.000	0.000	0.000
83	A	104	ASP	-1	-0.925	-0.962	21.621	-0.263	-0.263	0.000	0.000	0.000	0.000
84	A	105	ARG	1	0.736	0.848	20.061	0.362	0.362	0.000	0.000	0.000	0.000
85	A	106	PHE	0	-0.052	-0.013	18.334	0.001	0.001	0.000	0.000	0.000	0.000
86	A	107	LEU	0	-0.056	-0.015	20.962	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:SER)