FMO DATABASE

FMODB ID: N9NLQ

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:

Apendix: None

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-419643.073178
FMO2-HF: Nuclear repulsion	387510.328949
FMO2-HF: Total energy	-32132.744229
FMO2-MP2: Total energy	-32228.231304

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.
-9.961	-3.516	0.829	-3.192	-4.083	-0.005

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 : 0.054 / q_NPA : 0.014

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	-0.003	2.929	-5.995	-2.473	0.122	-1.668	-1.977	0.009
4	A	5	THR	0	0.058	0.027	2.491	-6.547	-3.817	0.708	-1.486	-1.952	-0.014
5	A	6	HIS	0	0.036	0.013	4.066	1.100	1.293	-0.001	-0.038	-0.154	0.000
6	A	7	ASN	0	-0.003	-0.026	6.676	0.093	0.093	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.907	-0.943	7.190	-0.118	-0.118	0.000	0.000	0.000	0.000
8	A	9	MET	0	-0.025	-0.012	7.132	0.250	0.250	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.793	-0.878	10.169	-0.127	-0.127	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.923	0.960	11.910	0.071	0.071	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.046	0.021	12.879	0.153	0.153	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.868	0.930	14.289	0.419	0.419	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.935	0.945	14.912	0.118	0.118	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.024	0.000	17.564	0.048	0.048	0.000	0.000	0.000	0.000
15	A	16	HIS	0	0.066	0.029	17.583	0.054	0.054	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.019	-0.001	20.493	0.025	0.025	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.934	0.954	19.493	0.106	0.106	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.033	0.022	22.730	0.019	0.019	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.043	-0.016	24.911	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.045	-0.023	26.586	0.015	0.015	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.894	-0.959	27.759	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.996	1.007	29.627	0.165	0.165	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.053	-0.028	31.312	0.007	0.007	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.863	0.932	31.440	0.059	0.059	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.005	0.027	34.060	0.007	0.007	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.027	-0.005	35.976	0.004	0.004	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.020	0.004	37.760	0.004	0.004	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.018	0.007	39.956	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.010	-0.027	36.414	0.004	0.004	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.014	0.016	40.226	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.012	0.016	42.355	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.787	-0.883	43.828	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.046	-0.042	39.480	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.016	0.006	37.347	0.000	0.000	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.970	0.973	35.855	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.134	0.067	27.507	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.038	0.004	32.134	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.009	0.008	27.589	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.059	-0.012	30.612	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.015	-0.017	33.242	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.040	0.025	31.403	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.024	-0.002	29.935	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.036	-0.011	34.215	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.810	0.914	37.679	0.031	0.031	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.038	0.020	35.970	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.969	0.996	37.759	0.042	0.042	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.011	-0.022	39.169	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	49	HIS	0	0.034	0.024	40.948	0.004	0.004	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.029	0.011	37.627	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.968	0.976	41.578	0.061	0.061	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.933	0.981	44.823	0.038	0.038	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.013	-0.017	42.653	0.001	0.001	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.872	-0.939	43.548	-0.068	-0.068	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.911	-0.968	47.436	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.042	-0.033	49.999	0.003	0.003	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.899	-0.933	49.148	-0.060	-0.060	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.912	0.960	48.606	0.050	0.050	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.874	0.937	53.274	0.036	0.036	0.000	0.000	0.000	0.000
59	A	60	ALA	0	0.008	0.018	54.076	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.030	0.006	53.454	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	HIS	0	0.004	0.005	56.377	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.032	0.012	59.163	0.002	0.002	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.014	0.013	56.983	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.790	-0.858	60.685	-0.039	-0.039	0.000	0.000	0.000	0.000
65	A	66	GLN	0	-0.012	-0.016	62.460	0.003	0.003	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.025	0.017	62.673	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.020	-0.008	61.673	0.001	0.001	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.736	0.835	64.109	0.039	0.039	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.930	-0.958	68.542	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.005	-0.011	67.620	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.958	0.961	66.306	0.039	0.039	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.047	-0.009	72.168	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.029	0.011	72.655	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.937	0.973	72.424	0.034	0.034	0.000	0.000	0.000	0.000
75	A	76	ARG	1	1.014	0.999	73.617	0.031	0.031	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.074	-0.033	78.274	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.035	-0.024	78.037	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.944	-0.948	79.422	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.909	0.967	82.233	0.025	0.025	0.000	0.000	0.000	0.000

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