FMO DATABASE

FMODB ID: KG9R3

Calculation Name: 2NWV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NWV

Chain ID: A

ChEMBL ID:

UniProt ID: Q3M7V9

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-952413.518308
FMO2-HF: Nuclear repulsion	906175.621425
FMO2-HF: Total energy	-46237.896882
FMO2-MP2: Total energy	-46374.597992

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:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
26.017	18.296	18.89	-1.745	-9.421	0.091

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.852 / q_NPA : -0.928

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

Sort

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	VAL	0	0.022	0.001	2.793	7.048	2.144	0.121	5.767	-0.983	0.000
4	A	5	ALA	0	-0.017	0.001	2.435	-10.710	-10.157	4.590	-2.247	-2.896	0.026
5	A	6	GLU	-1	-0.812	-0.900	1.802	27.526	23.679	14.065	-5.191	-5.025	0.060
6	A	7	TYR	0	-0.050	-0.067	3.490	-13.524	-13.047	0.114	-0.074	-0.517	0.005
7	A	8	ARG	1	0.853	0.914	6.261	-42.789	-42.789	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.800	0.900	5.613	-48.471	-48.471	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.044	0.015	7.746	-4.134	-4.134	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.000	0.006	9.756	-3.298	-3.298	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.828	0.900	10.563	-29.243	-29.243	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.009	0.021	11.717	0.210	0.210	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.055	0.021	13.662	-1.503	-1.503	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.017	-0.012	15.643	-1.327	-1.327	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.030	-0.031	16.369	-1.180	-1.180	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.961	-0.978	17.066	16.900	16.900	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.041	-0.050	19.631	-0.656	-0.656	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.809	-0.838	21.394	12.075	12.075	0.000	0.000	0.000	0.000
19	A	20	ASN	0	0.006	-0.007	22.404	-0.938	-0.938	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.029	-0.012	22.236	-0.642	-0.642	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.026	-0.019	25.480	-0.674	-0.674	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.869	0.929	27.472	-10.980	-10.980	0.000	0.000	0.000	0.000
23	A	24	GLN	0	-0.049	-0.023	29.036	-0.034	-0.034	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.028	0.004	30.745	-0.195	-0.195	0.000	0.000	0.000	0.000
25	A	26	PRO	0	-0.034	-0.012	32.254	-0.181	-0.181	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.909	-0.938	33.551	8.402	8.402	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.030	-0.037	34.737	0.026	0.026	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.050	-0.034	30.900	0.106	0.106	0.000	0.000	0.000	0.000
29	A	30	TYR	0	-0.022	-0.019	32.116	-0.283	-0.283	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.949	-0.968	31.145	10.249	10.249	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.046	-0.072	26.001	-0.143	-0.143	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.072	-0.041	25.353	-0.186	-0.186	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.051	0.042	19.442	0.224	0.224	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.058	-0.036	20.318	-0.278	-0.278	0.000	0.000	0.000	0.000
35	A	36	PHE	0	0.025	0.010	14.901	0.739	0.739	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.793	-0.869	16.114	17.676	17.676	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.811	-0.900	10.123	29.181	29.181	0.000	0.000	0.000	0.000
38	A	39	ASN	0	-0.060	-0.018	12.445	1.831	1.831	0.000	0.000	0.000	0.000
39	A	40	HIS	1	0.750	0.834	15.107	-16.548	-16.548	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.744	-0.831	11.120	28.646	28.646	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.031	-0.011	13.885	-0.823	-0.823	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.001	-0.016	11.154	0.516	0.516	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.012	-0.008	16.697	-0.413	-0.413	0.000	0.000	0.000	0.000
44	A	45	TRP	0	0.005	0.006	20.152	0.386	0.386	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.040	-0.026	22.199	-0.448	-0.448	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.091	0.061	25.864	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.105	-0.074	28.808	-0.191	-0.191	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.735	-0.860	31.609	9.014	9.014	0.000	0.000	0.000	0.000
49	A	50	TRP	0	-0.091	-0.055	34.993	-0.119	-0.119	0.000	0.000	0.000	0.000
50	A	51	GLN	0	0.080	0.048	38.751	0.153	0.153	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.008	-0.002	41.003	-0.159	-0.159	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.001	-0.016	43.247	0.048	0.048	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.948	0.985	39.473	-7.881	-7.881	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.897	0.964	34.426	-8.940	-8.940	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.027	0.001	33.393	-0.089	-0.089	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.915	0.942	29.554	-10.418	-10.418	0.000	0.000	0.000	0.000
57	A	58	TYR	0	-0.022	-0.005	29.496	-0.167	-0.167	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.039	0.027	24.173	0.075	0.075	0.000	0.000	0.000	0.000
59	A	60	TYR	0	0.008	0.009	24.349	-0.328	-0.328	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.041	0.028	18.942	0.075	0.075	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.090	-0.049	19.082	-0.379	-0.379	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.026	0.015	13.959	-0.057	-0.057	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.960	0.973	15.551	-17.113	-17.113	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.000	0.018	8.661	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.887	0.945	12.739	-16.680	-16.680	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.102	-0.067	13.774	0.084	0.084	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.886	-0.940	7.749	32.633	32.633	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.807	0.927	9.026	-18.618	-18.618	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.032	0.015	9.616	-0.084	-0.084	0.000	0.000	0.000	0.000
70	A	71	TYR	0	-0.018	-0.033	12.897	-2.111	-2.111	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.032	0.010	16.569	0.166	0.166	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.948	-0.996	18.752	14.360	14.360	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.914	-0.966	21.592	11.201	11.201	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.772	-0.884	22.028	14.715	14.715	0.000	0.000	0.000	0.000
75	A	76	TYR	0	-0.108	-0.044	23.887	-0.553	-0.553	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.049	-0.029	22.680	-0.289	-0.289	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.945	-0.960	25.773	10.017	10.017	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.889	-0.933	22.644	13.179	13.179	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.021	0.023	22.926	0.105	0.105	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.013	-0.028	16.842	0.552	0.552	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.012	-0.017	17.114	0.855	0.855	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.035	-0.026	17.258	0.674	0.674	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.854	-0.917	16.478	17.151	17.151	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.012	-0.017	12.134	1.035	1.035	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.034	-0.003	13.258	0.952	0.952	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.865	0.937	15.186	-14.513	-14.513	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.052	-0.014	12.043	0.225	0.225	0.000	0.000	0.000	0.000
88	A	89	GLY	0	-0.017	0.003	11.177	2.061	2.061	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.050	-0.017	9.251	1.432	1.432	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.018	0.007	10.085	-2.661	-2.661	0.000	0.000	0.000	0.000
91	A	92	ASN	0	0.088	0.018	12.529	1.080	1.080	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.042	-0.026	12.240	-1.262	-1.262	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.834	-0.899	8.356	27.215	27.215	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.010	0.019	11.884	0.942	0.942	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.046	-0.024	14.865	-0.984	-0.984	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.044	0.027	17.836	0.290	0.290	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.045	-0.031	20.206	-0.692	-0.692	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.068	0.042	21.881	-0.518	-0.518	0.000	0.000	0.000	0.000
99	A	100	HIS	0	-0.030	-0.009	24.454	-0.489	-0.489	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.039	0.009	25.686	0.399	0.399	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.005	-0.020	25.006	0.104	0.104	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.944	-0.967	25.850	10.223	10.223	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.018	0.001	27.325	-0.239	-0.239	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.893	0.969	21.770	-13.309	-13.309	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.928	0.979	23.802	-9.995	-9.995	0.000	0.000	0.000	0.000
106	A	107	PHE	0	-0.074	-0.026	25.024	-0.205	-0.205	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.055	-0.030	23.170	-0.030	-0.030	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.867	-0.922	21.563	12.453	12.453	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.036	-0.026	17.692	0.695	0.695	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.001	0.018	15.972	-0.512	-0.512	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.005	-0.017	18.074	-0.509	-0.509	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.029	0.037	15.447	-0.159	-0.159	0.000	0.000	0.000	0.000

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