FMO DATABASE

FMODB ID: NN9VQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-822611.459845
FMO2-HF: Nuclear repulsion	780035.43122
FMO2-HF: Total energy	-42576.028626
FMO2-MP2: Total energy	-42701.128297

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.
22.98	27.172	5.072	-4.396	-4.868	-0.011

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 : -0.896 / q_NPA : -0.956

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	0.000	0.002	3.456	-15.342	-12.009	0.086	-1.768	-1.652	0.011
4	A	5	THR	0	0.037	0.020	2.112	-9.574	-9.220	4.982	-2.435	-2.901	-0.022
5	A	6	HIS	0	0.020	0.013	3.741	-3.793	-3.288	0.004	-0.193	-0.315	0.000
6	A	7	TYR	0	-0.026	-0.049	6.249	-3.645	-3.645	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.854	0.905	6.877	-28.618	-28.618	0.000	0.000	0.000	0.000
8	A	9	HIS	0	-0.024	-0.015	7.887	-1.381	-1.381	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.008	0.005	9.855	-2.288	-2.288	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.010	-0.011	11.542	-1.831	-1.831	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.054	-0.033	11.334	-2.562	-2.562	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.856	-0.920	13.988	16.206	16.206	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.014	-0.001	15.731	-1.123	-1.123	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.036	-0.028	16.884	-0.955	-0.955	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.831	0.919	14.873	-18.053	-18.053	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.844	0.925	19.962	-14.648	-14.648	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.034	-0.055	21.711	-0.934	-0.934	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.043	-0.015	23.215	-0.575	-0.575	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.861	-0.954	23.200	12.015	12.015	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.115	-0.050	26.025	-0.417	-0.417	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.089	-0.053	27.775	-0.481	-0.481	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.095	-0.060	27.599	-0.382	-0.382	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.038	0.000	29.222	-0.251	-0.251	0.000	0.000	0.000	0.000
24	A	38	LEU	0	0.072	0.040	39.623	-0.070	-0.070	0.000	0.000	0.000	0.000
25	A	39	PRO	0	-0.015	-0.021	36.540	0.115	0.115	0.000	0.000	0.000	0.000
26	A	40	ASP	-1	-0.868	-0.930	36.558	7.685	7.685	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.039	-0.035	38.702	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	42	VAL	0	-0.037	-0.027	35.065	0.159	0.159	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.061	0.039	33.461	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	44	ASP	-1	-0.736	-0.832	28.070	10.145	10.145	0.000	0.000	0.000	0.000
31	A	45	ARG	1	0.796	0.899	27.200	-9.217	-9.217	0.000	0.000	0.000	0.000
32	A	46	LEU	0	0.046	0.023	20.003	0.114	0.114	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.035	-0.017	20.531	-0.217	-0.217	0.000	0.000	0.000	0.000
34	A	48	ILE	0	0.013	0.007	14.907	0.436	0.436	0.000	0.000	0.000	0.000
35	A	49	ASP	-1	-0.793	-0.878	15.815	15.198	15.198	0.000	0.000	0.000	0.000
36	A	50	GLU	-1	-0.830	-0.935	9.925	22.498	22.498	0.000	0.000	0.000	0.000
37	A	51	GLN	0	-0.068	-0.029	10.860	0.616	0.616	0.000	0.000	0.000	0.000
38	A	52	ARG	1	0.783	0.861	13.265	-14.606	-14.606	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.776	-0.822	9.798	24.451	24.451	0.000	0.000	0.000	0.000
40	A	54	GLN	0	-0.017	-0.012	12.928	-0.835	-0.835	0.000	0.000	0.000	0.000
41	A	55	TYR	0	-0.010	-0.034	10.684	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	56	LEU	0	0.027	0.010	17.282	-0.208	-0.208	0.000	0.000	0.000	0.000
43	A	57	TRP	0	-0.003	-0.012	21.106	0.100	0.100	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.014	0.002	23.913	-0.160	-0.160	0.000	0.000	0.000	0.000
45	A	59	CYS	0	0.028	0.033	27.575	-0.068	-0.068	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.086	-0.063	31.012	-0.142	-0.142	0.000	0.000	0.000	0.000
47	A	61	GLY	0	0.047	0.035	33.452	0.017	0.017	0.000	0.000	0.000	0.000
48	A	62	TRP	0	-0.067	-0.040	37.022	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	63	ASP	-1	-0.798	-0.873	40.528	7.207	7.207	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.034	0.024	42.524	-0.114	-0.114	0.000	0.000	0.000	0.000
51	A	65	LYS	1	0.927	0.959	44.924	-6.002	-6.002	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.803	0.876	41.700	-7.196	-7.196	0.000	0.000	0.000	0.000
53	A	67	ARG	1	0.908	0.967	35.369	-8.044	-8.044	0.000	0.000	0.000	0.000
54	A	68	VAL	0	0.019	0.001	35.130	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	69	GLN	0	0.028	-0.004	32.462	-0.141	-0.141	0.000	0.000	0.000	0.000
56	A	70	HIS	0	0.022	0.028	31.052	-0.161	-0.161	0.000	0.000	0.000	0.000
57	A	71	ILE	0	0.018	0.011	25.300	0.093	0.093	0.000	0.000	0.000	0.000
58	A	72	ILE	0	-0.012	-0.003	26.859	-0.207	-0.207	0.000	0.000	0.000	0.000
59	A	73	LEU	0	0.017	0.024	21.225	0.130	0.130	0.000	0.000	0.000	0.000
60	A	74	TYR	0	-0.076	-0.049	19.382	-0.234	-0.234	0.000	0.000	0.000	0.000
61	A	75	LEU	0	0.012	0.012	16.593	0.118	0.118	0.000	0.000	0.000	0.000
62	A	76	GLN	0	-0.011	-0.011	15.238	0.193	0.193	0.000	0.000	0.000	0.000
63	A	77	ILE	0	-0.028	-0.014	9.351	0.801	0.801	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.027	0.024	12.736	-0.343	-0.343	0.000	0.000	0.000	0.000
65	A	79	ASN	0	-0.032	-0.032	13.458	0.559	0.559	0.000	0.000	0.000	0.000
66	A	80	GLY	0	0.010	0.015	9.611	0.598	0.598	0.000	0.000	0.000	0.000
67	A	81	LYS	1	0.792	0.885	10.119	-19.913	-19.913	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.058	0.031	11.498	-0.642	-0.642	0.000	0.000	0.000	0.000
69	A	83	TRP	0	-0.047	-0.021	14.059	-1.400	-1.400	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.019	0.010	17.611	0.124	0.124	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.825	-0.918	20.159	13.828	13.828	0.000	0.000	0.000	0.000
72	A	86	GLU	-1	-0.940	-0.966	22.766	10.375	10.375	0.000	0.000	0.000	0.000
73	A	87	ASP	-1	-0.779	-0.881	23.380	13.478	13.478	0.000	0.000	0.000	0.000
74	A	88	SER	0	-0.018	-0.007	25.140	-0.297	-0.297	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.071	-0.062	23.708	-0.198	-0.198	0.000	0.000	0.000	0.000
76	A	90	ASN	0	-0.060	-0.032	26.509	-0.229	-0.229	0.000	0.000	0.000	0.000
77	A	91	LEU	0	-0.002	-0.007	23.746	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	92	ALA	0	0.034	0.032	23.243	0.582	0.582	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.021	-0.001	19.352	0.677	0.677	0.000	0.000	0.000	0.000
80	A	94	VAL	0	-0.020	-0.017	18.795	1.077	1.077	0.000	0.000	0.000	0.000
81	A	95	ASP	-1	-0.924	-0.948	18.592	15.285	15.285	0.000	0.000	0.000	0.000
82	A	96	GLU	-1	-0.749	-0.854	18.456	15.525	15.525	0.000	0.000	0.000	0.000
83	A	97	MET	0	-0.025	-0.009	14.717	1.451	1.451	0.000	0.000	0.000	0.000
84	A	98	LEU	0	-0.035	-0.012	14.152	1.624	1.624	0.000	0.000	0.000	0.000
85	A	99	VAL	0	-0.022	-0.005	15.447	0.872	0.872	0.000	0.000	0.000	0.000
86	A	100	ALA	0	-0.041	-0.008	12.534	0.559	0.559	0.000	0.000	0.000	0.000
87	A	101	GLY	0	-0.001	0.001	11.305	2.986	2.986	0.000	0.000	0.000	0.000
88	A	102	ILE	0	-0.042	-0.016	10.132	2.209	2.209	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.012	0.011	10.496	-2.521	-2.521	0.000	0.000	0.000	0.000
90	A	104	GLN	0	0.108	0.025	13.429	-0.172	-0.172	0.000	0.000	0.000	0.000
91	A	105	THR	0	-0.019	-0.006	13.657	-0.634	-0.634	0.000	0.000	0.000	0.000
92	A	106	ASP	-1	-0.834	-0.868	10.245	28.910	28.910	0.000	0.000	0.000	0.000
93	A	107	ILE	0	0.021	0.019	13.793	0.493	0.493	0.000	0.000	0.000	0.000
94	A	108	ILE	0	-0.036	-0.011	16.520	-1.202	-1.202	0.000	0.000	0.000	0.000
95	A	109	LEU	0	0.067	0.021	19.413	-0.081	-0.081	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.021	0.004	21.629	-0.553	-0.553	0.000	0.000	0.000	0.000
97	A	111	PHE	0	0.018	0.006	23.069	-0.565	-0.565	0.000	0.000	0.000	0.000
98	A	112	HIS	0	-0.046	-0.014	25.954	-0.708	-0.708	0.000	0.000	0.000	0.000
99	A	113	HIS	0	0.050	0.053	26.884	0.487	0.487	0.000	0.000	0.000	0.000
100	A	114	PRO	0	0.074	0.014	26.203	0.016	0.016	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.029	-0.037	27.693	0.052	0.052	0.000	0.000	0.000	0.000
102	A	116	LYS	1	0.889	0.942	29.435	-9.948	-9.948	0.000	0.000	0.000	0.000
103	A	117	ARG	1	0.849	0.956	22.899	-13.017	-13.017	0.000	0.000	0.000	0.000
104	A	118	GLY	0	-0.042	-0.010	24.988	-0.006	-0.006	0.000	0.000	0.000	0.000

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