FMO DATABASE

FMODB ID: 17ZNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-217572.389115
FMO2-HF: Nuclear repulsion	195494.89184
FMO2-HF: Total energy	-22077.497276
FMO2-MP2: Total energy	-22140.95167

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.
-8.635	-4.411	0.597	-1.607	-3.214	0.007

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 : 0.054 / q_NPA : 0.005

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	1.018	1.010	3.892	-3.294	-2.218	0.000	-0.409	-0.667	0.001
4	A	31	ARG	1	0.928	0.958	2.726	-5.872	-3.379	0.570	-1.022	-2.041	0.006
5	A	32	ILE	0	0.039	0.023	3.237	-0.219	0.436	0.027	-0.176	-0.506	0.000
6	A	33	LEU	0	0.016	0.010	5.509	0.489	0.489	0.000	0.000	0.000	0.000
7	A	34	GLY	0	0.011	0.009	7.929	0.132	0.132	0.000	0.000	0.000	0.000
8	A	35	LEU	0	0.037	0.010	5.914	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	36	ALA	0	-0.010	0.003	9.462	0.053	0.053	0.000	0.000	0.000	0.000
10	A	37	ILE	0	0.006	0.004	11.412	0.076	0.076	0.000	0.000	0.000	0.000
11	A	38	GLU	-1	-0.935	-0.973	11.729	0.039	0.039	0.000	0.000	0.000	0.000
12	A	39	SER	0	-0.005	-0.011	13.211	0.007	0.007	0.000	0.000	0.000	0.000
13	A	40	GLN	0	-0.043	-0.010	14.926	0.021	0.021	0.000	0.000	0.000	0.000
14	A	41	ASP	-1	-0.806	-0.892	17.326	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	42	ALA	0	0.004	0.003	17.546	0.011	0.011	0.000	0.000	0.000	0.000
16	A	43	GLY	0	0.023	0.026	18.980	0.005	0.005	0.000	0.000	0.000	0.000
17	A	44	ILE	0	0.017	0.007	20.794	0.012	0.012	0.000	0.000	0.000	0.000
18	A	45	LYS	1	0.823	0.904	21.039	0.050	0.050	0.000	0.000	0.000	0.000
19	A	46	THR	0	-0.012	-0.018	22.145	0.006	0.006	0.000	0.000	0.000	0.000
20	A	47	ILE	0	-0.008	-0.009	24.384	0.004	0.004	0.000	0.000	0.000	0.000
21	A	48	THR	0	-0.003	-0.006	26.931	0.010	0.010	0.000	0.000	0.000	0.000
22	A	49	MET	0	-0.031	-0.019	26.871	0.005	0.005	0.000	0.000	0.000	0.000
23	A	50	LEU	0	-0.045	-0.024	28.081	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.943	-0.961	30.967	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	52	GLU	-1	-0.935	-0.968	32.772	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	53	GLN	0	-0.060	-0.028	31.411	0.002	0.002	0.000	0.000	0.000	0.000
27	A	54	LYS	1	0.882	0.938	35.040	0.063	0.063	0.000	0.000	0.000	0.000
28	A	55	GLU	-1	-0.800	-0.882	37.115	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	56	GLN	0	-0.031	-0.011	37.980	0.006	0.006	0.000	0.000	0.000	0.000
30	A	57	LEU	0	-0.022	-0.025	37.284	0.002	0.002	0.000	0.000	0.000	0.000
31	A	58	ASN	0	-0.016	-0.003	40.730	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	59	ARG	1	0.927	0.948	39.545	0.038	0.038	0.000	0.000	0.000	0.000
33	A	60	ILE	0	-0.045	-0.012	41.493	0.002	0.002	0.000	0.000	0.000	0.000
34	A	61	GLU	-1	-0.940	-0.970	43.619	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	62	GLU	-1	-0.894	-0.962	46.250	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	63	GLY	0	0.012	0.022	48.196	0.002	0.002	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.039	-0.039	47.654	0.002	0.002	0.000	0.000	0.000	0.000
38	A	65	ASP	-1	-0.852	-0.910	50.679	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	66	GLN	0	0.002	0.019	51.219	0.003	0.003	0.000	0.000	0.000	0.000
40	A	67	ILE	0	0.024	0.010	51.995	0.001	0.001	0.000	0.000	0.000	0.000
41	A	68	ASN	0	-0.076	-0.063	54.149	0.002	0.002	0.000	0.000	0.000	0.000
42	A	69	LYS	1	0.801	0.903	55.529	0.034	0.034	0.000	0.000	0.000	0.000
43	A	70	ASP	-1	-0.768	-0.878	59.305	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	71	MET	0	-0.079	-0.020	58.569	0.001	0.001	0.000	0.000	0.000	0.000
45	A	72	ARG	1	0.760	0.850	59.731	0.030	0.030	0.000	0.000	0.000	0.000
46	A	73	GLU	-1	-0.904	-0.949	62.471	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	74	THR	0	0.000	-0.004	63.596	0.001	0.001	0.000	0.000	0.000	0.000
48	A	75	GLU	-1	-0.828	-0.893	64.242	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	76	LYS	1	0.851	0.928	65.626	0.028	0.028	0.000	0.000	0.000	0.000
50	A	77	THR	0	0.076	0.025	68.674	0.001	0.001	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.041	-0.028	67.553	0.001	0.001	0.000	0.000	0.000	0.000
52	A	79	THR	0	-0.067	-0.036	70.554	0.000	0.000	0.000	0.000	0.000	0.000
53	A	80	GLU	-1	-0.990	-0.993	72.987	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	81	LEU	0	-0.127	-0.041	72.855	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)