FMO DATABASE

FMODB ID: 8958Y

Calculation Name: 2NVM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NVM

Chain ID: A

ChEMBL ID:

UniProt ID: Q3MD55

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	OptHSide
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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-820248.497137
FMO2-HF: Nuclear repulsion	777672.668254
FMO2-HF: Total energy	-42575.828883
FMO2-MP2: Total energy	-42700.920267

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.
25.39	30.629	1.263	-2.705	-3.796	-0.007

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 : -0.970 / q_NPA : -0.984

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	LEU	0	0.012	-0.012	3.528	-12.663	-10.036	0.041	-1.233	-1.435	0.007
4	A	5	THR	0	0.010	0.011	2.499	-8.900	-6.623	1.222	-1.388	-2.111	-0.014
5	A	6	HIS	0	0.034	0.016	4.170	-3.590	-3.255	0.000	-0.084	-0.250	0.000
6	A	7	TYR	0	-0.036	-0.056	6.367	-3.695	-3.695	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.867	0.906	6.655	-29.174	-29.174	0.000	0.000	0.000	0.000
8	A	9	HIS	0	-0.045	-0.027	8.329	-1.286	-1.286	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.015	0.008	10.266	-2.238	-2.238	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.006	-0.002	12.043	-1.818	-1.818	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.036	-0.021	11.936	-2.603	-2.603	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.908	-0.947	14.616	16.032	16.032	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.008	-0.003	16.158	-1.088	-1.088	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.044	-0.028	17.536	-0.963	-0.963	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.901	0.938	16.027	-17.666	-17.666	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.859	0.943	20.554	-14.739	-14.739	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.039	-0.059	22.050	-0.946	-0.946	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.056	-0.026	23.644	-0.565	-0.565	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.851	-0.940	24.440	11.892	11.892	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.110	-0.048	26.634	-0.447	-0.447	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.082	-0.034	28.454	-0.487	-0.487	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.097	-0.059	28.323	-0.338	-0.338	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.021	0.012	29.971	-0.195	-0.195	0.000	0.000	0.000	0.000
24	A	38	LEU	0	0.044	0.020	40.436	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	39	PRO	0	-0.035	-0.041	37.464	0.142	0.142	0.000	0.000	0.000	0.000
26	A	40	ASP	-1	-0.905	-0.947	37.519	7.599	7.599	0.000	0.000	0.000	0.000
27	A	41	THR	0	0.012	0.021	38.790	-0.104	-0.104	0.000	0.000	0.000	0.000
28	A	42	VAL	0	-0.053	-0.042	35.174	0.141	0.141	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.053	0.038	33.908	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	44	ASP	-1	-0.750	-0.859	28.652	10.074	10.074	0.000	0.000	0.000	0.000
31	A	45	ARG	1	0.818	0.898	27.418	-9.322	-9.322	0.000	0.000	0.000	0.000
32	A	46	LEU	0	0.051	0.035	20.571	0.141	0.141	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.042	-0.031	21.307	-0.237	-0.237	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.004	0.000	15.547	0.380	0.380	0.000	0.000	0.000	0.000
35	A	49	ASP	-1	-0.807	-0.885	16.317	14.895	14.895	0.000	0.000	0.000	0.000
36	A	50	GLU	-1	-0.824	-0.930	10.530	21.863	21.863	0.000	0.000	0.000	0.000
37	A	51	GLN	0	-0.082	-0.031	11.441	0.547	0.547	0.000	0.000	0.000	0.000
38	A	52	ARG	1	0.812	0.869	12.919	-14.092	-14.092	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.782	-0.822	9.761	24.180	24.180	0.000	0.000	0.000	0.000
40	A	54	GLN	0	-0.024	-0.015	13.038	-0.831	-0.831	0.000	0.000	0.000	0.000
41	A	55	TYR	0	-0.019	-0.033	11.082	-0.078	-0.078	0.000	0.000	0.000	0.000
42	A	56	LEU	0	0.020	0.005	17.716	-0.236	-0.236	0.000	0.000	0.000	0.000
43	A	57	TRP	0	0.024	0.008	21.506	0.144	0.144	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.015	0.005	24.369	-0.183	-0.183	0.000	0.000	0.000	0.000
45	A	59	CYS	0	0.029	0.029	27.880	-0.061	-0.061	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.080	-0.057	31.356	-0.151	-0.151	0.000	0.000	0.000	0.000
47	A	61	GLY	0	0.040	0.026	33.847	0.013	0.013	0.000	0.000	0.000	0.000
48	A	62	TRP	0	-0.032	-0.023	37.468	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	63	ASP	-1	-0.808	-0.871	41.032	7.158	7.158	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.016	0.001	42.846	-0.120	-0.120	0.000	0.000	0.000	0.000
51	A	65	LYS	1	0.957	0.963	45.471	-6.051	-6.051	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.811	0.898	41.830	-7.167	-7.167	0.000	0.000	0.000	0.000
53	A	67	ARG	1	0.931	0.980	35.744	-8.004	-8.004	0.000	0.000	0.000	0.000
54	A	68	VAL	0	-0.004	-0.009	35.508	0.001	0.001	0.000	0.000	0.000	0.000
55	A	69	GLN	0	-0.006	-0.023	32.617	-0.089	-0.089	0.000	0.000	0.000	0.000
56	A	70	HIS	0	0.006	0.011	31.218	-0.220	-0.220	0.000	0.000	0.000	0.000
57	A	71	ILE	0	0.032	0.020	25.605	0.101	0.101	0.000	0.000	0.000	0.000
58	A	72	ILE	0	-0.052	-0.017	27.006	-0.206	-0.206	0.000	0.000	0.000	0.000
59	A	73	LEU	0	0.024	0.022	21.651	0.119	0.119	0.000	0.000	0.000	0.000
60	A	74	TYR	0	-0.069	-0.049	19.567	-0.252	-0.252	0.000	0.000	0.000	0.000
61	A	75	LEU	0	0.010	0.010	16.781	0.141	0.141	0.000	0.000	0.000	0.000
62	A	76	GLN	0	0.000	0.001	15.355	0.205	0.205	0.000	0.000	0.000	0.000
63	A	77	ILE	0	-0.025	-0.007	9.260	0.668	0.668	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.019	0.014	12.637	-0.586	-0.586	0.000	0.000	0.000	0.000
65	A	79	ASN	0	-0.034	-0.035	12.916	0.171	0.171	0.000	0.000	0.000	0.000
66	A	80	GLY	0	0.001	0.008	9.383	0.415	0.415	0.000	0.000	0.000	0.000
67	A	81	LYS	1	0.830	0.926	10.241	-18.473	-18.473	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.045	0.022	11.469	-0.400	-0.400	0.000	0.000	0.000	0.000
69	A	83	TRP	0	-0.027	-0.012	14.244	-1.322	-1.322	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.027	0.003	17.728	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.850	-0.944	20.163	13.586	13.586	0.000	0.000	0.000	0.000
72	A	86	GLU	-1	-0.952	-0.977	22.698	10.352	10.352	0.000	0.000	0.000	0.000
73	A	87	ASP	-1	-0.769	-0.877	23.613	13.206	13.206	0.000	0.000	0.000	0.000
74	A	88	SER	0	-0.005	0.013	25.303	-0.287	-0.287	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.054	-0.056	24.452	-0.193	-0.193	0.000	0.000	0.000	0.000
76	A	90	ASN	0	-0.052	-0.023	27.037	-0.180	-0.180	0.000	0.000	0.000	0.000
77	A	91	LEU	0	-0.017	-0.019	23.992	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	92	ALA	0	0.052	0.041	23.310	0.516	0.516	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.020	0.001	19.859	0.672	0.672	0.000	0.000	0.000	0.000
80	A	94	VAL	0	-0.018	-0.012	18.908	1.022	1.022	0.000	0.000	0.000	0.000
81	A	95	ASP	-1	-0.934	-0.964	18.564	15.174	15.174	0.000	0.000	0.000	0.000
82	A	96	GLU	-1	-0.771	-0.866	18.428	15.429	15.429	0.000	0.000	0.000	0.000
83	A	97	MET	0	-0.025	-0.010	14.731	1.332	1.332	0.000	0.000	0.000	0.000
84	A	98	LEU	0	-0.038	-0.010	13.889	1.601	1.601	0.000	0.000	0.000	0.000
85	A	99	VAL	0	-0.011	0.004	14.945	1.013	1.013	0.000	0.000	0.000	0.000
86	A	100	ALA	0	-0.028	0.001	12.188	0.562	0.562	0.000	0.000	0.000	0.000
87	A	101	GLY	0	-0.004	0.001	10.728	3.136	3.136	0.000	0.000	0.000	0.000
88	A	102	ILE	0	-0.036	-0.009	10.057	2.178	2.178	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.006	0.006	10.153	-2.466	-2.466	0.000	0.000	0.000	0.000
90	A	104	GLN	0	0.083	0.013	13.213	-0.360	-0.360	0.000	0.000	0.000	0.000
91	A	105	THR	0	0.003	0.006	14.055	-0.620	-0.620	0.000	0.000	0.000	0.000
92	A	106	ASP	-1	-0.823	-0.874	10.371	28.324	28.324	0.000	0.000	0.000	0.000
93	A	107	ILE	0	0.031	0.031	13.815	0.516	0.516	0.000	0.000	0.000	0.000
94	A	108	ILE	0	-0.057	-0.024	16.570	-0.901	-0.901	0.000	0.000	0.000	0.000
95	A	109	LEU	0	0.032	0.018	19.512	0.034	0.034	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.001	-0.007	21.903	-0.501	-0.501	0.000	0.000	0.000	0.000
97	A	111	PHE	0	0.057	0.021	23.259	-0.555	-0.555	0.000	0.000	0.000	0.000
98	A	112	HIS	0	-0.052	0.000	26.129	-0.789	-0.789	0.000	0.000	0.000	0.000
99	A	113	HIS	0	0.032	0.030	27.023	0.449	0.449	0.000	0.000	0.000	0.000
100	A	114	PRO	0	0.063	0.014	26.286	0.072	0.072	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.029	-0.045	27.734	0.118	0.118	0.000	0.000	0.000	0.000
102	A	116	LYS	1	0.887	0.949	29.620	-9.798	-9.798	0.000	0.000	0.000	0.000
103	A	117	ARG	1	0.853	0.953	23.109	-12.695	-12.695	0.000	0.000	0.000	0.000
104	A	118	GLY	0	0.013	0.025	25.414	0.235	0.235	0.000	0.000	0.000	0.000

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