FMO DATABASE

FMODB ID: YZLV2

Calculation Name: 1NHL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NHL

Chain ID: A

ChEMBL ID:

UniProt ID: O00161

Base Structure: X-ray

Registration Date: 2023-09-20

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-217642.653265
FMO2-HF: Nuclear repulsion	195566.080029
FMO2-HF: Total energy	-22076.573236
FMO2-MP2: Total energy	-22140.120623

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:28:SER)

Summations of interaction energy for fragment #1(A:28: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.
-4.053	-0.195	0.497	-1.404	-2.951	0.001

Interaction energy analysis for fragmet #1(A:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.009

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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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	30	ARG	1	1.028	1.023	3.605	-2.987	-1.581	0.019	-0.543	-0.882	0.001
4	A	31	ARG	1	0.918	0.948	2.788	-1.149	0.041	0.421	-0.331	-1.280	0.000
5	A	32	ILE	0	0.027	0.009	3.080	-0.599	0.663	0.057	-0.530	-0.789	0.000
6	A	33	LEU	0	0.008	0.005	5.432	0.517	0.517	0.000	0.000	0.000	0.000
7	A	34	GLY	0	0.007	0.003	7.362	0.155	0.155	0.000	0.000	0.000	0.000
8	A	35	LEU	0	0.028	0.000	6.531	0.043	0.043	0.000	0.000	0.000	0.000
9	A	36	ALA	0	-0.020	0.004	9.559	0.101	0.101	0.000	0.000	0.000	0.000
10	A	37	ILE	0	-0.002	-0.004	11.489	0.087	0.087	0.000	0.000	0.000	0.000
11	A	38	GLU	-1	-0.926	-0.964	12.818	-0.235	-0.235	0.000	0.000	0.000	0.000
12	A	39	SER	0	-0.040	-0.023	13.439	0.055	0.055	0.000	0.000	0.000	0.000
13	A	40	GLN	0	0.008	0.005	15.116	0.032	0.032	0.000	0.000	0.000	0.000
14	A	41	ASP	-1	-0.899	-0.949	17.581	-0.112	-0.112	0.000	0.000	0.000	0.000
15	A	42	ALA	0	0.009	0.002	17.940	0.020	0.020	0.000	0.000	0.000	0.000
16	A	43	GLY	0	0.020	0.027	19.309	0.015	0.015	0.000	0.000	0.000	0.000
17	A	44	ILE	0	0.012	0.006	21.118	0.018	0.018	0.000	0.000	0.000	0.000
18	A	45	LYS	1	0.929	0.971	22.537	0.130	0.130	0.000	0.000	0.000	0.000
19	A	46	THR	0	-0.021	-0.025	22.484	0.007	0.007	0.000	0.000	0.000	0.000
20	A	47	ILE	0	0.004	-0.008	24.791	0.009	0.009	0.000	0.000	0.000	0.000
21	A	48	THR	0	-0.027	-0.014	27.166	0.012	0.012	0.000	0.000	0.000	0.000
22	A	49	MET	0	-0.014	-0.015	27.347	0.004	0.004	0.000	0.000	0.000	0.000
23	A	50	LEU	0	-0.039	-0.014	27.945	0.003	0.003	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.933	-0.956	31.327	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	52	GLU	-1	-0.947	-0.975	32.907	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	53	GLN	0	-0.071	-0.044	32.542	0.001	0.001	0.000	0.000	0.000	0.000
27	A	54	LYS	1	0.945	0.973	35.333	0.077	0.077	0.000	0.000	0.000	0.000
28	A	55	GLU	-1	-0.823	-0.906	37.291	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	56	GLN	0	-0.081	-0.029	37.651	0.007	0.007	0.000	0.000	0.000	0.000
30	A	57	LEU	0	-0.022	-0.020	37.609	0.002	0.002	0.000	0.000	0.000	0.000
31	A	58	ASN	0	-0.005	-0.006	41.142	0.001	0.001	0.000	0.000	0.000	0.000
32	A	59	ARG	1	0.952	0.977	40.710	0.056	0.056	0.000	0.000	0.000	0.000
33	A	60	ILE	0	-0.058	-0.024	42.041	0.002	0.002	0.000	0.000	0.000	0.000
34	A	61	GLU	-1	-0.961	-0.975	44.966	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	62	GLU	-1	-0.854	-0.926	46.800	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	63	GLY	0	-0.003	-0.009	48.577	0.002	0.002	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.069	-0.052	47.855	0.002	0.002	0.000	0.000	0.000	0.000
38	A	65	ASP	-1	-0.956	-0.976	50.550	-0.043	-0.043	0.000	0.000	0.000	0.000
39	A	66	GLN	0	-0.077	-0.045	52.511	0.003	0.003	0.000	0.000	0.000	0.000
40	A	67	ILE	0	0.048	0.038	52.967	0.001	0.001	0.000	0.000	0.000	0.000
41	A	68	ASN	0	-0.024	-0.017	55.357	0.002	0.002	0.000	0.000	0.000	0.000
42	A	69	LYS	1	0.909	0.966	57.196	0.034	0.034	0.000	0.000	0.000	0.000
43	A	70	ASP	-1	-0.720	-0.850	59.496	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	71	MET	0	-0.095	-0.029	59.093	0.001	0.001	0.000	0.000	0.000	0.000
45	A	72	ARG	1	0.823	0.918	59.176	0.034	0.034	0.000	0.000	0.000	0.000
46	A	73	GLU	-1	-0.888	-0.973	62.646	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	74	THR	0	0.016	0.005	63.894	0.001	0.001	0.000	0.000	0.000	0.000
48	A	75	GLU	-1	-0.964	-0.995	64.724	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	76	LYS	1	0.899	0.945	65.673	0.029	0.029	0.000	0.000	0.000	0.000
50	A	77	THR	0	0.027	0.013	69.054	0.001	0.001	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.057	-0.028	67.598	0.001	0.001	0.000	0.000	0.000	0.000
52	A	79	THR	0	-0.028	-0.018	71.078	0.001	0.001	0.000	0.000	0.000	0.000
53	A	80	GLU	-1	-1.039	-1.000	73.438	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	81	LEU	0	-0.084	-0.020	72.751	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:SER)