FMO DATABASE

FMODB ID: 2JKLR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-380401.101107
FMO2-HF: Nuclear repulsion	346413.802871
FMO2-HF: Total energy	-33987.298236
FMO2-MP2: Total energy	-34088.264778

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.
-3.091	-1.485	-0.019	-0.688	-0.899	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 : 0.019 / q_NPA : -0.007

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	0.024	0.003	3.790	-2.468	-0.862	-0.019	-0.688	-0.899	0.002
4	N	1	MET	0	-0.054	-0.032	5.571	-0.392	-0.392	0.000	0.000	0.000	0.000
5	N	2	ASP	-1	-0.822	-0.892	8.666	0.678	0.678	0.000	0.000	0.000	0.000
6	N	3	ALA	0	-0.030	-0.027	11.417	-0.121	-0.121	0.000	0.000	0.000	0.000
7	N	4	GLN	0	0.026	0.000	14.122	-0.060	-0.060	0.000	0.000	0.000	0.000
8	N	5	THR	0	0.036	0.010	10.746	-0.046	-0.046	0.000	0.000	0.000	0.000
9	N	6	ARG	1	1.048	1.032	9.613	0.009	0.009	0.000	0.000	0.000	0.000
10	N	7	ARG	1	0.893	0.942	12.626	-0.034	-0.034	0.000	0.000	0.000	0.000
11	N	8	ARG	1	0.931	0.965	15.257	-0.129	-0.129	0.000	0.000	0.000	0.000
12	N	9	GLU	-1	-0.875	-0.935	10.002	-0.314	-0.314	0.000	0.000	0.000	0.000
13	N	10	ARG	1	0.933	0.988	14.571	0.133	0.133	0.000	0.000	0.000	0.000
14	N	11	ARG	1	0.861	0.924	16.743	0.019	0.019	0.000	0.000	0.000	0.000
15	N	12	ALA	0	0.080	0.039	17.213	0.020	0.020	0.000	0.000	0.000	0.000
16	N	13	GLU	-1	-0.870	-0.935	19.291	-0.074	-0.074	0.000	0.000	0.000	0.000
17	N	14	LYS	1	0.937	0.962	22.480	0.058	0.058	0.000	0.000	0.000	0.000
18	N	15	GLN	0	-0.024	-0.024	18.314	0.007	0.007	0.000	0.000	0.000	0.000
19	N	16	ALA	0	0.011	-0.013	22.834	0.009	0.009	0.000	0.000	0.000	0.000
20	N	17	GLN	0	0.019	0.021	24.390	0.000	0.000	0.000	0.000	0.000	0.000
21	N	18	TRP	0	-0.059	-0.036	26.807	0.004	0.004	0.000	0.000	0.000	0.000
22	N	19	LYS	1	0.899	0.973	20.256	0.056	0.056	0.000	0.000	0.000	0.000
23	N	20	ALA	0	-0.013	0.011	26.779	0.005	0.005	0.000	0.000	0.000	0.000
24	N	21	ALA	0	0.008	0.006	30.187	0.002	0.002	0.000	0.000	0.000	0.000
25	N	22	ASN	0	-0.001	-0.001	30.371	0.005	0.005	0.000	0.000	0.000	0.000
26	N	23	PRO	0	-0.003	-0.006	29.932	0.000	0.000	0.000	0.000	0.000	0.000
27	N	24	LEU	0	0.038	0.021	24.723	0.001	0.001	0.000	0.000	0.000	0.000
28	N	25	LEU	0	-0.033	-0.019	21.566	0.004	0.004	0.000	0.000	0.000	0.000
29	N	26	VAL	0	0.005	0.004	25.605	-0.004	-0.004	0.000	0.000	0.000	0.000
30	N	27	GLY	0	0.029	0.001	26.448	0.009	0.009	0.000	0.000	0.000	0.000
31	N	28	VAL	0	-0.023	0.014	27.429	-0.002	-0.002	0.000	0.000	0.000	0.000
32	N	29	SER	0	-0.030	-0.024	28.658	0.010	0.010	0.000	0.000	0.000	0.000
33	N	30	ALA	0	0.013	0.015	30.807	-0.006	-0.006	0.000	0.000	0.000	0.000
34	N	31	LYS	1	1.016	0.976	33.522	-0.088	-0.088	0.000	0.000	0.000	0.000
35	N	32	PRO	0	0.055	0.040	37.300	0.004	0.004	0.000	0.000	0.000	0.000
36	N	33	VAL	0	0.079	0.028	40.352	0.002	0.002	0.000	0.000	0.000	0.000
37	N	34	ASN	0	-0.071	-0.037	34.037	0.004	0.004	0.000	0.000	0.000	0.000
38	N	35	ARG	1	0.927	0.977	31.103	-0.125	-0.125	0.000	0.000	0.000	0.000
39	N	36	PRO	0	-0.004	0.026	37.112	-0.001	-0.001	0.000	0.000	0.000	0.000
40	N	37	ILE	0	0.033	-0.004	34.754	0.004	0.004	0.000	0.000	0.000	0.000
41	N	38	LEU	0	-0.015	-0.008	39.028	0.000	0.000	0.000	0.000	0.000	0.000
42	N	39	SER	0	0.010	-0.011	39.203	0.002	0.002	0.000	0.000	0.000	0.000
43	N	40	LEU	0	0.013	0.022	41.260	0.002	0.002	0.000	0.000	0.000	0.000
44	N	41	ASN	0	0.036	-0.004	44.123	0.002	0.002	0.000	0.000	0.000	0.000
45	N	42	ARG	1	0.950	0.971	41.676	-0.093	-0.093	0.000	0.000	0.000	0.000
46	N	43	LYS	1	1.019	1.027	45.385	-0.069	-0.069	0.000	0.000	0.000	0.000
47	N	44	PRO	0	-0.041	-0.016	46.498	-0.001	-0.001	0.000	0.000	0.000	0.000
48	N	45	LYS	1	0.994	1.007	47.319	-0.068	-0.068	0.000	0.000	0.000	0.000
49	N	46	SER	0	0.050	0.031	47.005	0.005	0.005	0.000	0.000	0.000	0.000
50	N	47	ARG	1	0.986	0.990	40.607	-0.099	-0.099	0.000	0.000	0.000	0.000
51	N	48	VAL	0	0.038	0.030	46.451	0.000	0.000	0.000	0.000	0.000	0.000
52	N	49	GLU	-1	-0.855	-0.941	49.705	0.060	0.060	0.000	0.000	0.000	0.000
53	N	50	SER	0	-0.090	-0.067	47.505	-0.001	-0.001	0.000	0.000	0.000	0.000
54	N	51	ALA	0	-0.023	-0.009	47.958	0.000	0.000	0.000	0.000	0.000	0.000
55	N	52	LEU	0	-0.048	-0.019	49.690	-0.001	-0.001	0.000	0.000	0.000	0.000
56	N	53	ASN	0	-0.058	-0.022	52.872	-0.004	-0.004	0.000	0.000	0.000	0.000
57	N	54	PRO	0	-0.022	0.004	50.976	0.003	0.003	0.000	0.000	0.000	0.000
58	N	55	ILE	0	-0.033	-0.025	48.376	-0.002	-0.002	0.000	0.000	0.000	0.000
59	N	56	ASP	-1	-0.842	-0.909	51.999	0.061	0.061	0.000	0.000	0.000	0.000
60	N	57	LEU	0	-0.030	-0.038	53.389	-0.001	-0.001	0.000	0.000	0.000	0.000
61	N	58	THR	0	-0.010	0.002	56.780	-0.002	-0.002	0.000	0.000	0.000	0.000
62	N	59	VAL	0	0.079	0.024	59.453	-0.001	-0.001	0.000	0.000	0.000	0.000
63	N	60	LEU	0	0.008	0.014	57.151	-0.001	-0.001	0.000	0.000	0.000	0.000
64	N	61	ALA	0	0.010	0.002	58.847	-0.001	-0.001	0.000	0.000	0.000	0.000
65	N	62	GLU	-1	-0.866	-0.915	60.834	0.040	0.040	0.000	0.000	0.000	0.000
66	N	63	TYR	0	0.030	0.001	64.089	-0.001	-0.001	0.000	0.000	0.000	0.000
67	N	64	HIS	0	0.000	0.002	61.363	-0.002	-0.002	0.000	0.000	0.000	0.000
68	N	65	LYS	1	1.012	1.006	64.279	-0.042	-0.042	0.000	0.000	0.000	0.000
69	N	66	GLN	0	-0.042	-0.030	65.973	-0.001	-0.001	0.000	0.000	0.000	0.000
70	N	67	ILE	0	-0.004	0.053	66.190	-0.002	-0.002	0.000	0.000	0.000	0.000
71	N	68	GLU	-1	-0.889	-0.949	65.138	0.038	0.038	0.000	0.000	0.000	0.000
72	N	69	SER	0	-0.120	-0.079	68.442	-0.002	-0.002	0.000	0.000	0.000	0.000
73	N	70	ASN	0	-0.032	-0.072	71.321	-0.002	-0.002	0.000	0.000	0.000	0.000
74	N	71	LEU	0	0.038	0.033	69.455	-0.001	-0.001	0.000	0.000	0.000	0.000
75	N	72	GLN	0	0.052	0.013	69.389	-0.002	-0.002	0.000	0.000	0.000	0.000
76	N	73	ARG	1	0.884	0.948	73.641	-0.032	-0.032	0.000	0.000	0.000	0.000
77	N	74	ILE	0	-0.011	0.003	75.020	-0.001	-0.001	0.000	0.000	0.000	0.000
78	N	75	GLU	-1	-0.930	-0.967	73.513	0.029	0.029	0.000	0.000	0.000	0.000
79	N	76	ARG	1	0.917	0.946	76.034	-0.029	-0.029	0.000	0.000	0.000	0.000
80	N	77	LYS	1	0.931	0.979	79.667	-0.026	-0.026	0.000	0.000	0.000	0.000
81	N	78	ASN	0	-0.049	-0.024	78.884	-0.001	-0.001	0.000	0.000	0.000	0.000
82	N	79	GLN	0	-0.034	0.009	80.211	0.000	0.000	0.000	0.000	0.000	0.000
83	N	80	ARG	1	0.950	0.978	82.022	-0.023	-0.023	0.000	0.000	0.000	0.000
84	N	81	THR	0	-0.029	-0.030	85.040	0.000	0.000	0.000	0.000	0.000	0.000
85	N	82	TRP	0	0.033	0.033	86.000	-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)