FMO DATABASE

FMODB ID: 39JML

Calculation Name: 1NLW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NLW

Chain ID: A

ChEMBL ID:

UniProt ID: Q05195

Base Structure: X-ray

Registration Date: 2023-06-22

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-419561.030778
FMO2-HF: Nuclear repulsion	387427.237741
FMO2-HF: Total energy	-32133.793037
FMO2-MP2: Total energy	-32229.157978

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-4.389	0.588	2.988	-3.427	-4.538	-0.012

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.055

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	4	SER	0	0.030	0.016	2.266	-7.260	-4.257	2.378	-2.583	-2.798	-0.007
4	A	5	THR	0	0.050	0.011	2.457	-0.932	0.896	0.611	-0.820	-1.619	-0.005
5	A	6	HIS	0	0.025	0.023	4.575	0.998	1.144	-0.001	-0.024	-0.121	0.000
6	A	7	ASN	0	-0.003	-0.016	6.977	0.459	0.459	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.799	-0.872	7.647	-0.621	-0.621	0.000	0.000	0.000	0.000
8	A	9	MET	0	0.008	0.006	7.433	0.347	0.347	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.758	-0.831	10.713	-0.187	-0.187	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.800	0.871	11.901	0.834	0.834	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.048	0.018	13.182	0.165	0.165	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.869	0.912	14.757	0.452	0.452	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.898	0.924	14.146	0.416	0.416	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.012	0.009	17.818	0.052	0.052	0.000	0.000	0.000	0.000
15	A	16	HIS	0	0.020	0.005	18.032	0.063	0.063	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.014	0.003	20.803	0.035	0.035	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.959	0.974	20.282	0.250	0.250	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.046	0.022	22.452	0.023	0.023	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.056	-0.031	24.890	0.020	0.020	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.039	-0.015	26.796	0.017	0.017	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.821	-0.909	27.529	-0.121	-0.121	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.968	0.989	29.335	0.184	0.184	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.054	-0.034	31.237	0.009	0.009	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.792	0.869	30.573	0.126	0.126	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.017	0.030	34.249	0.006	0.006	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.029	-0.007	36.012	0.006	0.006	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.019	0.005	37.827	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.052	0.048	40.339	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.028	-0.018	36.859	0.005	0.005	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.003	-0.020	40.245	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.002	0.011	42.455	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.824	-0.901	43.516	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.003	-0.003	39.091	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.067	-0.031	37.642	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.965	0.977	35.754	0.041	0.041	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.061	0.029	28.050	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.007	-0.019	31.980	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.006	0.023	27.710	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.061	0.019	30.858	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.049	0.029	33.568	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.013	0.022	31.797	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.031	0.009	30.330	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.054	-0.034	34.756	0.003	0.003	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.851	0.919	38.236	0.062	0.062	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.044	0.020	36.485	0.002	0.002	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.961	0.986	38.159	0.062	0.062	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.011	-0.010	39.682	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	HIS	0	0.037	0.018	41.382	0.004	0.004	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.026	0.008	38.017	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.852	0.905	42.374	0.064	0.064	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.868	0.937	45.354	0.050	0.050	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.021	0.011	43.130	0.002	0.002	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.739	-0.856	44.198	-0.060	-0.060	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.886	-0.920	48.017	-0.041	-0.041	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.053	-0.035	50.361	0.003	0.003	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.909	-0.949	49.582	-0.055	-0.055	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.935	0.958	48.101	0.053	0.053	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.853	0.917	53.633	0.042	0.042	0.000	0.000	0.000	0.000
59	A	60	ALA	0	0.019	0.019	54.468	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.023	0.005	53.695	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	HIS	0	0.008	0.012	56.732	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.037	0.006	59.535	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.003	0.003	57.137	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.796	-0.858	61.028	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	66	GLN	0	-0.042	-0.031	62.810	0.002	0.002	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.036	0.018	63.058	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	GLN	0	0.012	0.017	62.033	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.759	0.847	64.486	0.034	0.034	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.909	-0.948	69.007	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	71	GLN	0	0.015	0.005	67.701	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.945	0.954	65.859	0.035	0.035	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.058	-0.001	72.318	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.037	0.009	72.828	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.961	0.983	73.208	0.030	0.030	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.943	0.953	74.179	0.027	0.027	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.041	-0.013	78.483	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.012	0.001	78.620	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.958	-0.973	79.086	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.842	0.939	81.843	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)