FMO DATABASE

FMODB ID: G56L1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-819595.46437
FMO2-HF: Nuclear repulsion	777020.070005
FMO2-HF: Total energy	-42575.394366
FMO2-MP2: Total energy	-42700.464965

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.
23.654	28.844	0.621	-2.416	-3.394	-0.005

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 : -0.969 / q_NPA : -0.977

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	0.019	-0.011	3.518	-10.329	-8.025	0.033	-1.091	-1.245	0.006
4	A	5	THR	0	-0.001	0.008	2.681	-9.304	-6.760	0.589	-1.252	-1.881	-0.011
5	A	6	HIS	0	0.039	0.022	4.269	-2.916	-2.574	-0.001	-0.073	-0.268	0.000
6	A	7	TYR	0	-0.055	-0.075	6.348	-4.056	-4.056	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.914	0.969	5.323	-31.095	-31.095	0.000	0.000	0.000	0.000
8	A	9	HIS	0	-0.042	-0.022	8.261	-1.981	-1.981	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.019	0.008	10.233	-2.120	-2.120	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.011	0.002	12.177	-1.773	-1.773	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.033	-0.025	11.620	-2.832	-2.832	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.910	-0.941	14.725	15.960	15.960	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.005	-0.004	16.099	-1.038	-1.038	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.055	-0.030	17.671	-0.987	-0.987	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.947	0.959	16.631	-17.233	-17.233	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.890	0.958	20.637	-14.528	-14.528	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.061	-0.068	22.174	-0.987	-0.987	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.051	-0.023	23.766	-0.605	-0.605	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.845	-0.932	24.498	11.870	11.870	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.109	-0.051	26.742	-0.447	-0.447	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.076	-0.029	28.575	-0.480	-0.480	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.065	-0.032	28.534	-0.295	-0.295	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.029	0.004	30.058	-0.202	-0.202	0.000	0.000	0.000	0.000
24	A	38	LEU	0	0.043	0.022	40.518	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	39	PRO	0	-0.039	-0.043	37.579	0.149	0.149	0.000	0.000	0.000	0.000
26	A	40	ASP	-1	-0.915	-0.945	37.613	7.555	7.555	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.005	0.008	38.721	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	42	VAL	0	-0.054	-0.043	35.331	0.139	0.139	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.056	0.040	34.019	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	44	ASP	-1	-0.803	-0.910	28.776	9.926	9.926	0.000	0.000	0.000	0.000
31	A	45	ARG	1	0.866	0.924	27.369	-9.351	-9.351	0.000	0.000	0.000	0.000
32	A	46	LEU	0	0.043	0.032	20.791	0.131	0.131	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.043	-0.034	21.561	-0.244	-0.244	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.015	-0.005	15.694	0.329	0.329	0.000	0.000	0.000	0.000
35	A	49	ASP	-1	-0.823	-0.915	16.521	14.799	14.799	0.000	0.000	0.000	0.000
36	A	50	GLU	-1	-0.879	-0.961	10.922	21.444	21.444	0.000	0.000	0.000	0.000
37	A	51	GLN	0	-0.103	-0.043	11.517	0.643	0.643	0.000	0.000	0.000	0.000
38	A	52	ARG	1	0.865	0.916	12.990	-13.596	-13.596	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.832	-0.888	10.058	23.777	23.777	0.000	0.000	0.000	0.000
40	A	54	GLN	0	-0.011	0.005	13.163	-0.811	-0.811	0.000	0.000	0.000	0.000
41	A	55	TYR	0	-0.021	-0.027	11.162	0.007	0.007	0.000	0.000	0.000	0.000
42	A	56	LEU	0	0.021	0.006	17.850	-0.246	-0.246	0.000	0.000	0.000	0.000
43	A	57	TRP	0	0.009	0.014	21.642	0.138	0.138	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.011	0.008	24.501	-0.188	-0.188	0.000	0.000	0.000	0.000
45	A	59	CYS	0	0.035	0.031	28.013	-0.050	-0.050	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.082	-0.059	31.484	-0.165	-0.165	0.000	0.000	0.000	0.000
47	A	61	GLY	0	0.025	0.017	33.968	0.002	0.002	0.000	0.000	0.000	0.000
48	A	62	TRP	0	-0.013	-0.015	37.584	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	63	ASP	-1	-0.810	-0.873	41.153	7.164	7.164	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.023	0.004	42.974	-0.120	-0.120	0.000	0.000	0.000	0.000
51	A	65	LYS	1	0.963	0.966	45.593	-6.010	-6.010	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.810	0.898	41.708	-7.198	-7.198	0.000	0.000	0.000	0.000
53	A	67	ARG	1	0.937	0.987	36.104	-7.989	-7.989	0.000	0.000	0.000	0.000
54	A	68	VAL	0	0.002	-0.009	35.484	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	69	GLN	0	-0.041	-0.044	32.574	0.007	0.007	0.000	0.000	0.000	0.000
56	A	70	HIS	0	-0.005	0.007	31.830	-0.187	-0.187	0.000	0.000	0.000	0.000
57	A	71	ILE	0	0.035	0.021	25.714	0.099	0.099	0.000	0.000	0.000	0.000
58	A	72	ILE	0	-0.039	-0.006	27.192	-0.198	-0.198	0.000	0.000	0.000	0.000
59	A	73	LEU	0	0.013	0.014	21.862	0.117	0.117	0.000	0.000	0.000	0.000
60	A	74	TYR	0	-0.072	-0.066	19.845	-0.214	-0.214	0.000	0.000	0.000	0.000
61	A	75	LEU	0	0.023	0.014	16.593	0.132	0.132	0.000	0.000	0.000	0.000
62	A	76	GLN	0	0.003	0.014	15.519	0.109	0.109	0.000	0.000	0.000	0.000
63	A	77	ILE	0	-0.023	-0.005	9.242	0.678	0.678	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.028	0.015	12.804	-0.508	-0.508	0.000	0.000	0.000	0.000
65	A	79	ASN	0	-0.046	-0.042	12.926	-0.173	-0.173	0.000	0.000	0.000	0.000
66	A	80	GLY	0	-0.023	-0.006	9.400	0.387	0.387	0.000	0.000	0.000	0.000
67	A	81	LYS	1	0.882	0.957	10.241	-17.584	-17.584	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.050	0.026	11.854	-0.353	-0.353	0.000	0.000	0.000	0.000
69	A	83	TRP	0	-0.036	-0.014	14.428	-1.360	-1.360	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.032	0.001	17.908	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.890	-0.960	20.343	13.267	13.267	0.000	0.000	0.000	0.000
72	A	86	GLU	-1	-0.970	-0.980	22.872	10.182	10.182	0.000	0.000	0.000	0.000
73	A	87	ASP	-1	-0.778	-0.891	23.782	13.137	13.137	0.000	0.000	0.000	0.000
74	A	88	SER	0	0.019	0.022	25.474	-0.267	-0.267	0.000	0.000	0.000	0.000
75	A	89	THR	0	-0.049	-0.053	24.553	-0.188	-0.188	0.000	0.000	0.000	0.000
76	A	90	ASN	0	-0.043	-0.018	27.199	-0.132	-0.132	0.000	0.000	0.000	0.000
77	A	91	LEU	0	-0.022	-0.019	24.033	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	92	ALA	0	0.049	0.039	23.335	0.501	0.501	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.022	-0.002	20.034	0.660	0.660	0.000	0.000	0.000	0.000
80	A	94	VAL	0	-0.014	-0.011	18.892	1.009	1.009	0.000	0.000	0.000	0.000
81	A	95	ASP	-1	-0.931	-0.964	18.615	15.067	15.067	0.000	0.000	0.000	0.000
82	A	96	GLU	-1	-0.765	-0.867	18.107	15.408	15.408	0.000	0.000	0.000	0.000
83	A	97	MET	0	-0.033	-0.014	14.652	1.304	1.304	0.000	0.000	0.000	0.000
84	A	98	LEU	0	-0.038	-0.012	13.868	1.551	1.551	0.000	0.000	0.000	0.000
85	A	99	VAL	0	-0.013	0.006	14.941	1.000	1.000	0.000	0.000	0.000	0.000
86	A	100	ALA	0	-0.034	-0.004	11.811	0.608	0.608	0.000	0.000	0.000	0.000
87	A	101	GLY	0	0.004	0.000	10.516	3.093	3.093	0.000	0.000	0.000	0.000
88	A	102	ILE	0	-0.034	-0.010	10.162	2.024	2.024	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.006	0.009	10.578	-2.349	-2.349	0.000	0.000	0.000	0.000
90	A	104	GLN	0	0.084	0.011	13.696	-0.348	-0.348	0.000	0.000	0.000	0.000
91	A	105	THR	0	-0.013	-0.001	14.506	-0.633	-0.633	0.000	0.000	0.000	0.000
92	A	106	ASP	-1	-0.869	-0.914	10.497	26.863	26.863	0.000	0.000	0.000	0.000
93	A	107	ILE	0	0.027	0.027	13.983	0.501	0.501	0.000	0.000	0.000	0.000
94	A	108	ILE	0	-0.066	-0.026	16.810	-0.881	-0.881	0.000	0.000	0.000	0.000
95	A	109	LEU	0	0.024	0.013	19.587	0.049	0.049	0.000	0.000	0.000	0.000
96	A	110	GLY	0	-0.006	-0.008	22.104	-0.484	-0.484	0.000	0.000	0.000	0.000
97	A	111	PHE	0	0.063	0.028	23.440	-0.543	-0.543	0.000	0.000	0.000	0.000
98	A	112	HIS	0	-0.060	-0.009	26.312	-0.812	-0.812	0.000	0.000	0.000	0.000
99	A	113	HIS	0	0.010	0.000	27.151	0.392	0.392	0.000	0.000	0.000	0.000
100	A	114	PRO	0	0.047	0.007	26.477	0.074	0.074	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.039	-0.037	27.751	0.161	0.161	0.000	0.000	0.000	0.000
102	A	116	LYS	1	0.932	0.971	29.680	-9.735	-9.735	0.000	0.000	0.000	0.000
103	A	117	ARG	1	0.895	0.973	23.247	-12.534	-12.534	0.000	0.000	0.000	0.000
104	A	118	GLY	0	0.008	0.023	25.483	0.220	0.220	0.000	0.000	0.000	0.000

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