FMO DATABASE

FMODB ID: 2NM2R

Calculation Name: 2FNJ-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FNJ

Chain ID: C

ChEMBL ID:

UniProt ID: P62869

Base Structure: X-ray

Registration Date: 2023-09-23

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601420.239513
FMO2-HF: Nuclear repulsion	565677.952478
FMO2-HF: Total energy	-35742.287034
FMO2-MP2: Total energy	-35843.534606

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(C:17:MET)

Summations of interaction energy for fragment #1(C:17:MET)

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.
-6.584	-0.754	0.076	-2.639	-3.268	0.005

Interaction energy analysis for fragmet #1(C:17:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.011

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	C	19	VAL	0	0.011	0.018	3.674	-1.178	1.385	-0.013	-1.354	-1.197	0.002
4	C	20	LYS	1	0.864	0.942	6.597	-0.121	-0.121	0.000	0.000	0.000	0.000
5	C	21	LEU	0	-0.017	-0.015	10.052	0.087	0.087	0.000	0.000	0.000	0.000
6	C	22	ILE	0	0.020	0.003	13.172	-0.050	-0.050	0.000	0.000	0.000	0.000
7	C	23	SER	0	-0.018	-0.022	16.373	0.020	0.020	0.000	0.000	0.000	0.000
8	C	24	SER	0	0.045	0.016	19.599	-0.010	-0.010	0.000	0.000	0.000	0.000
9	C	25	ASP	-1	-0.827	-0.883	22.762	0.071	0.071	0.000	0.000	0.000	0.000
10	C	26	GLY	0	0.002	0.004	20.785	-0.013	-0.013	0.000	0.000	0.000	0.000
11	C	27	HIS	0	-0.047	-0.004	17.847	-0.026	-0.026	0.000	0.000	0.000	0.000
12	C	28	GLU	-1	-0.858	-0.929	13.700	-0.020	-0.020	0.000	0.000	0.000	0.000
13	C	29	PHE	0	-0.018	-0.021	12.522	-0.037	-0.037	0.000	0.000	0.000	0.000
14	C	30	ILE	0	0.000	0.007	6.436	0.037	0.037	0.000	0.000	0.000	0.000
15	C	31	VAL	0	0.009	0.000	7.298	0.013	0.013	0.000	0.000	0.000	0.000
16	C	32	LYS	1	0.972	0.984	3.794	-2.650	-1.848	0.068	-0.236	-0.634	0.001
17	C	33	ARG	1	1.042	1.000	3.730	-4.830	-3.100	0.016	-0.900	-0.846	0.003
18	C	34	GLU	-1	-0.926	-0.979	4.167	2.719	3.454	0.005	-0.149	-0.591	-0.001
19	C	35	HIS	0	-0.046	-0.028	6.935	-0.353	-0.353	0.000	0.000	0.000	0.000
20	C	36	ALA	0	0.070	0.044	8.387	-0.179	-0.179	0.000	0.000	0.000	0.000
21	C	37	LEU	0	-0.081	-0.035	8.433	-0.125	-0.125	0.000	0.000	0.000	0.000
22	C	38	THR	0	-0.063	-0.032	11.151	-0.115	-0.115	0.000	0.000	0.000	0.000
23	C	39	SER	0	-0.066	-0.031	13.737	-0.072	-0.072	0.000	0.000	0.000	0.000
24	C	40	GLY	0	0.053	0.028	15.032	0.078	0.078	0.000	0.000	0.000	0.000
25	C	41	THR	0	-0.017	-0.049	17.191	0.030	0.030	0.000	0.000	0.000	0.000
26	C	42	ILE	0	0.027	0.008	11.655	0.021	0.021	0.000	0.000	0.000	0.000
27	C	43	LYS	1	0.923	0.964	12.391	-0.703	-0.703	0.000	0.000	0.000	0.000
28	C	44	ALA	0	-0.015	-0.010	13.530	0.056	0.056	0.000	0.000	0.000	0.000
29	C	45	MET	0	-0.029	-0.015	14.641	-0.014	-0.014	0.000	0.000	0.000	0.000
30	C	46	LEU	0	-0.053	-0.027	8.482	0.056	0.056	0.000	0.000	0.000	0.000
31	C	47	SER	0	-0.122	-0.035	11.267	0.125	0.125	0.000	0.000	0.000	0.000
32	C	48	GLY	0	0.009	0.015	13.629	-0.032	-0.032	0.000	0.000	0.000	0.000
33	C	49	PRO	0	-0.021	-0.011	16.612	-0.021	-0.021	0.000	0.000	0.000	0.000
34	C	58	ASN	0	-0.025	-0.027	6.729	0.100	0.100	0.000	0.000	0.000	0.000
35	C	59	GLU	-1	-0.915	-0.969	8.417	0.150	0.150	0.000	0.000	0.000	0.000
36	C	60	VAL	0	0.001	0.006	11.212	0.059	0.059	0.000	0.000	0.000	0.000
37	C	61	ASN	0	-0.026	-0.011	13.812	-0.045	-0.045	0.000	0.000	0.000	0.000
38	C	62	PHE	0	0.008	-0.001	15.506	0.022	0.022	0.000	0.000	0.000	0.000
39	C	63	ARG	1	0.962	0.962	20.022	-0.148	-0.148	0.000	0.000	0.000	0.000
40	C	64	GLU	-1	-0.909	-0.959	23.620	0.102	0.102	0.000	0.000	0.000	0.000
41	C	65	ILE	0	-0.007	0.020	20.126	0.001	0.001	0.000	0.000	0.000	0.000
42	C	66	PRO	0	0.057	0.052	21.770	0.002	0.002	0.000	0.000	0.000	0.000
43	C	67	SER	0	-0.012	-0.052	20.045	0.016	0.016	0.000	0.000	0.000	0.000
44	C	68	HIS	0	-0.044	-0.037	20.331	0.009	0.009	0.000	0.000	0.000	0.000
45	C	69	VAL	0	0.024	0.017	21.817	0.007	0.007	0.000	0.000	0.000	0.000
46	C	70	LEU	0	-0.010	-0.017	15.806	0.021	0.021	0.000	0.000	0.000	0.000
47	C	71	SER	0	-0.013	0.000	16.607	0.029	0.029	0.000	0.000	0.000	0.000
48	C	72	LYS	1	0.914	0.938	16.987	-0.113	-0.113	0.000	0.000	0.000	0.000
49	C	73	VAL	0	0.034	0.022	16.100	0.017	0.017	0.000	0.000	0.000	0.000
50	C	74	CYS	0	-0.036	-0.006	12.834	0.050	0.050	0.000	0.000	0.000	0.000
51	C	75	MET	0	-0.034	-0.017	13.777	0.043	0.043	0.000	0.000	0.000	0.000
52	C	76	TYR	0	0.044	0.020	16.023	0.007	0.007	0.000	0.000	0.000	0.000
53	C	77	PHE	0	0.023	0.005	12.169	0.028	0.028	0.000	0.000	0.000	0.000
54	C	78	THR	0	-0.056	-0.032	11.731	0.063	0.063	0.000	0.000	0.000	0.000
55	C	79	TYR	0	-0.057	-0.040	13.083	0.004	0.004	0.000	0.000	0.000	0.000
56	C	80	LYS	1	0.974	0.995	15.674	-0.360	-0.360	0.000	0.000	0.000	0.000
57	C	81	VAL	0	0.015	0.025	10.179	-0.019	-0.019	0.000	0.000	0.000	0.000
58	C	82	ARG	1	0.908	0.956	13.511	-0.198	-0.198	0.000	0.000	0.000	0.000
59	C	83	TYR	0	0.004	-0.021	14.404	-0.047	-0.047	0.000	0.000	0.000	0.000
60	C	84	THR	0	-0.036	-0.015	16.314	-0.025	-0.025	0.000	0.000	0.000	0.000
61	C	85	ASN	0	-0.093	-0.041	13.354	-0.036	-0.036	0.000	0.000	0.000	0.000
62	C	86	SER	0	-0.004	-0.015	15.931	-0.027	-0.027	0.000	0.000	0.000	0.000
63	C	87	SER	0	0.021	0.017	18.674	0.007	0.007	0.000	0.000	0.000	0.000
64	C	88	THR	0	-0.076	-0.030	20.932	-0.012	-0.012	0.000	0.000	0.000	0.000
65	C	89	GLU	-1	-0.909	-0.964	22.820	0.083	0.083	0.000	0.000	0.000	0.000
66	C	90	ILE	0	-0.029	-0.006	21.823	0.003	0.003	0.000	0.000	0.000	0.000
67	C	91	PRO	0	-0.016	0.012	21.818	-0.007	-0.007	0.000	0.000	0.000	0.000
68	C	92	GLU	-1	-0.871	-0.935	24.275	0.110	0.110	0.000	0.000	0.000	0.000
69	C	93	PHE	0	-0.053	-0.017	19.186	0.004	0.004	0.000	0.000	0.000	0.000
70	C	94	PRO	0	0.021	0.013	22.880	-0.004	-0.004	0.000	0.000	0.000	0.000
71	C	95	ILE	0	0.003	-0.005	24.524	0.011	0.011	0.000	0.000	0.000	0.000
72	C	96	ALA	0	0.010	0.020	26.871	-0.006	-0.006	0.000	0.000	0.000	0.000
73	C	97	PRO	0	0.047	0.002	29.417	0.007	0.007	0.000	0.000	0.000	0.000
74	C	98	GLU	-1	-0.905	-0.960	30.832	0.070	0.070	0.000	0.000	0.000	0.000
75	C	99	ILE	0	0.009	0.011	24.245	0.002	0.002	0.000	0.000	0.000	0.000
76	C	100	ALA	0	0.006	0.007	27.871	0.011	0.011	0.000	0.000	0.000	0.000
77	C	101	LEU	0	0.013	0.013	28.940	0.009	0.009	0.000	0.000	0.000	0.000
78	C	102	GLU	-1	-0.810	-0.905	26.797	0.107	0.107	0.000	0.000	0.000	0.000
79	C	103	LEU	0	-0.012	-0.024	21.962	0.015	0.015	0.000	0.000	0.000	0.000
80	C	104	LEU	0	-0.013	0.012	24.691	0.019	0.019	0.000	0.000	0.000	0.000
81	C	105	MET	0	-0.018	-0.012	26.477	0.009	0.009	0.000	0.000	0.000	0.000
82	C	106	ALA	0	0.016	0.014	21.940	0.011	0.011	0.000	0.000	0.000	0.000
83	C	107	ALA	0	-0.002	-0.011	21.770	0.026	0.026	0.000	0.000	0.000	0.000
84	C	108	ASN	0	-0.001	-0.007	22.553	0.027	0.027	0.000	0.000	0.000	0.000
85	C	109	PHE	0	-0.048	-0.006	20.709	0.013	0.013	0.000	0.000	0.000	0.000
86	C	110	LEU	0	-0.033	-0.001	17.483	0.024	0.024	0.000	0.000	0.000	0.000
87	C	111	ASP	-1	-0.864	-0.901	18.825	0.369	0.369	0.000	0.000	0.000	0.000
88	C	112	CYS	0	-0.004	0.001	17.993	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:17:MET)