FMO DATABASE

FMODB ID: 6N3GZ

Calculation Name: 5LM7-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LM7

Chain ID: N

ChEMBL ID:

UniProt ID: P03045

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	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	-379693.400817
FMO2-HF: Nuclear repulsion	345705.384115
FMO2-HF: Total energy	-33988.016703
FMO2-MP2: Total energy	-34088.844483

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(N:-2:LEU)

Summations of interaction energy for fragment #1(N:-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.
-3.007	-1.37	-0.018	-0.704	-0.915	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.010

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	N	0	SER	0	0.027	0.011	3.790	-2.364	-0.727	-0.018	-0.704	-0.915	0.002
4	N	1	MET	0	-0.001	-0.013	5.576	-0.338	-0.338	0.000	0.000	0.000	0.000
5	N	2	ASP	-1	-0.859	-0.919	8.662	0.670	0.670	0.000	0.000	0.000	0.000
6	N	3	ALA	0	-0.030	-0.025	11.418	-0.115	-0.115	0.000	0.000	0.000	0.000
7	N	4	GLN	0	0.043	0.006	14.129	-0.065	-0.065	0.000	0.000	0.000	0.000
8	N	5	THR	0	0.040	0.012	10.841	-0.050	-0.050	0.000	0.000	0.000	0.000
9	N	6	ARG	1	1.009	1.026	9.373	-0.029	-0.029	0.000	0.000	0.000	0.000
10	N	7	ARG	1	0.884	0.946	12.697	-0.055	-0.055	0.000	0.000	0.000	0.000
11	N	8	ARG	1	0.943	0.977	15.200	-0.150	-0.150	0.000	0.000	0.000	0.000
12	N	9	GLU	-1	-0.863	-0.941	9.904	-0.263	-0.263	0.000	0.000	0.000	0.000
13	N	10	ARG	1	0.939	0.982	14.368	0.113	0.113	0.000	0.000	0.000	0.000
14	N	11	ARG	1	0.875	0.928	16.805	0.007	0.007	0.000	0.000	0.000	0.000
15	N	12	ALA	0	0.055	0.029	17.221	0.018	0.018	0.000	0.000	0.000	0.000
16	N	13	GLU	-1	-0.864	-0.928	19.323	-0.071	-0.071	0.000	0.000	0.000	0.000
17	N	14	LYS	1	0.940	0.959	22.512	0.050	0.050	0.000	0.000	0.000	0.000
18	N	15	GLN	0	-0.041	-0.026	18.235	0.014	0.014	0.000	0.000	0.000	0.000
19	N	16	ALA	0	0.007	-0.010	22.921	0.008	0.008	0.000	0.000	0.000	0.000
20	N	17	GLN	0	-0.008	0.004	24.511	0.001	0.001	0.000	0.000	0.000	0.000
21	N	18	TRP	0	-0.039	-0.025	26.839	0.004	0.004	0.000	0.000	0.000	0.000
22	N	19	LYS	1	0.917	0.981	20.698	0.052	0.052	0.000	0.000	0.000	0.000
23	N	20	ALA	0	-0.026	0.004	26.862	0.004	0.004	0.000	0.000	0.000	0.000
24	N	21	ALA	0	0.010	0.004	30.265	0.002	0.002	0.000	0.000	0.000	0.000
25	N	22	ASN	0	0.005	0.003	30.485	0.005	0.005	0.000	0.000	0.000	0.000
26	N	23	PRO	0	0.001	0.000	29.946	0.000	0.000	0.000	0.000	0.000	0.000
27	N	24	LEU	0	0.031	0.017	24.467	0.001	0.001	0.000	0.000	0.000	0.000
28	N	25	LEU	0	-0.038	-0.024	21.554	0.005	0.005	0.000	0.000	0.000	0.000
29	N	26	VAL	0	0.009	0.004	25.613	-0.004	-0.004	0.000	0.000	0.000	0.000
30	N	27	GLY	0	0.032	0.004	26.453	0.010	0.010	0.000	0.000	0.000	0.000
31	N	28	VAL	0	-0.024	0.012	27.430	-0.002	-0.002	0.000	0.000	0.000	0.000
32	N	29	SER	0	-0.015	-0.018	28.643	0.010	0.010	0.000	0.000	0.000	0.000
33	N	30	ALA	0	0.013	0.019	30.800	-0.006	-0.006	0.000	0.000	0.000	0.000
34	N	31	LYS	1	0.986	0.961	33.511	-0.095	-0.095	0.000	0.000	0.000	0.000
35	N	32	PRO	0	0.056	0.043	37.290	0.004	0.004	0.000	0.000	0.000	0.000
36	N	33	VAL	0	0.078	0.030	40.340	0.002	0.002	0.000	0.000	0.000	0.000
37	N	34	ASN	0	-0.063	-0.032	33.909	0.003	0.003	0.000	0.000	0.000	0.000
38	N	35	ARG	1	0.932	0.971	31.015	-0.124	-0.124	0.000	0.000	0.000	0.000
39	N	36	PRO	0	-0.001	0.027	37.095	-0.001	-0.001	0.000	0.000	0.000	0.000
40	N	37	ILE	0	0.025	-0.007	35.176	0.004	0.004	0.000	0.000	0.000	0.000
41	N	38	LEU	0	-0.001	0.001	39.006	0.001	0.001	0.000	0.000	0.000	0.000
42	N	39	SER	0	0.017	0.001	39.197	0.002	0.002	0.000	0.000	0.000	0.000
43	N	40	LEU	0	0.011	0.018	41.235	0.001	0.001	0.000	0.000	0.000	0.000
44	N	41	ASN	0	0.039	-0.006	44.099	0.002	0.002	0.000	0.000	0.000	0.000
45	N	42	ARG	1	0.932	0.953	41.134	-0.092	-0.092	0.000	0.000	0.000	0.000
46	N	43	LYS	1	1.015	1.032	45.170	-0.067	-0.067	0.000	0.000	0.000	0.000
47	N	44	PRO	0	-0.040	-0.021	46.399	-0.001	-0.001	0.000	0.000	0.000	0.000
48	N	45	LYS	1	0.902	0.959	47.536	-0.066	-0.066	0.000	0.000	0.000	0.000
49	N	46	SER	0	0.054	0.027	46.971	0.005	0.005	0.000	0.000	0.000	0.000
50	N	47	ARG	1	0.998	0.996	40.241	-0.098	-0.098	0.000	0.000	0.000	0.000
51	N	48	VAL	0	0.044	0.028	46.426	0.000	0.000	0.000	0.000	0.000	0.000
52	N	49	GLU	-1	-0.785	-0.887	49.693	0.059	0.059	0.000	0.000	0.000	0.000
53	N	50	SER	0	-0.055	-0.048	47.479	-0.001	-0.001	0.000	0.000	0.000	0.000
54	N	51	ALA	0	-0.024	-0.008	47.931	0.000	0.000	0.000	0.000	0.000	0.000
55	N	52	LEU	0	-0.038	-0.013	49.690	-0.001	-0.001	0.000	0.000	0.000	0.000
56	N	53	ASN	0	-0.104	-0.051	52.824	-0.004	-0.004	0.000	0.000	0.000	0.000
57	N	54	PRO	0	0.009	0.017	50.943	0.002	0.002	0.000	0.000	0.000	0.000
58	N	55	ILE	0	-0.034	-0.031	47.959	-0.002	-0.002	0.000	0.000	0.000	0.000
59	N	56	ASP	-1	-0.858	-0.909	51.964	0.059	0.059	0.000	0.000	0.000	0.000
60	N	57	LEU	0	-0.038	-0.042	53.052	-0.001	-0.001	0.000	0.000	0.000	0.000
61	N	58	THR	0	0.014	0.012	56.745	-0.001	-0.001	0.000	0.000	0.000	0.000
62	N	59	VAL	0	0.061	0.014	59.417	-0.001	-0.001	0.000	0.000	0.000	0.000
63	N	60	LEU	0	-0.011	0.008	57.060	-0.001	-0.001	0.000	0.000	0.000	0.000
64	N	61	ALA	0	0.021	0.006	58.791	-0.001	-0.001	0.000	0.000	0.000	0.000
65	N	62	GLU	-1	-0.863	-0.909	60.799	0.040	0.040	0.000	0.000	0.000	0.000
66	N	63	TYR	0	0.012	0.000	64.171	-0.002	-0.002	0.000	0.000	0.000	0.000
67	N	64	HIS	0	-0.047	-0.025	62.213	0.000	0.000	0.000	0.000	0.000	0.000
68	N	65	LYS	1	1.014	1.004	64.247	-0.041	-0.041	0.000	0.000	0.000	0.000
69	N	66	GLN	0	-0.038	-0.042	65.939	-0.001	-0.001	0.000	0.000	0.000	0.000
70	N	67	ILE	0	-0.003	0.025	65.695	-0.002	-0.002	0.000	0.000	0.000	0.000
71	N	68	GLU	-1	-0.866	-0.927	65.103	0.038	0.038	0.000	0.000	0.000	0.000
72	N	69	SER	0	-0.094	-0.054	68.411	-0.002	-0.002	0.000	0.000	0.000	0.000
73	N	70	ASN	0	-0.012	-0.040	71.288	-0.002	-0.002	0.000	0.000	0.000	0.000
74	N	71	LEU	0	0.032	0.027	69.163	-0.001	-0.001	0.000	0.000	0.000	0.000
75	N	72	GLN	0	0.013	-0.006	70.866	-0.001	-0.001	0.000	0.000	0.000	0.000
76	N	73	ARG	1	0.879	0.942	73.610	-0.032	-0.032	0.000	0.000	0.000	0.000
77	N	74	ILE	0	-0.017	0.003	74.990	-0.001	-0.001	0.000	0.000	0.000	0.000
78	N	75	GLU	-1	-0.898	-0.953	73.238	0.030	0.030	0.000	0.000	0.000	0.000
79	N	76	ARG	1	0.946	0.959	76.094	-0.029	-0.029	0.000	0.000	0.000	0.000
80	N	77	LYS	1	0.936	0.983	79.636	-0.025	-0.025	0.000	0.000	0.000	0.000
81	N	78	ASN	0	-0.038	-0.020	78.308	-0.001	-0.001	0.000	0.000	0.000	0.000
82	N	79	GLN	0	-0.016	0.010	80.170	0.000	0.000	0.000	0.000	0.000	0.000
83	N	80	ARG	1	0.896	0.953	81.992	-0.023	-0.023	0.000	0.000	0.000	0.000
84	N	81	THR	0	-0.016	-0.014	85.009	0.000	0.000	0.000	0.000	0.000	0.000
85	N	82	TRP	0	0.028	0.024	86.018	-0.001	-0.001	0.000	0.000	0.000	0.000

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