FMO DATABASE

FMODB ID: 85NMY

Calculation Name: 4J2C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J2C

Chain ID: A

ChEMBL ID:

UniProt ID: O43752

Base Structure: X-ray

Registration Date: 2023-06-22

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-803747.380727
FMO2-HF: Nuclear repulsion	759812.406639
FMO2-HF: Total energy	-43934.974088
FMO2-MP2: Total energy	-44063.103413

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:1:GLY)

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

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.
-0.602	0.219	0.004	-0.365	-0.46	0.001

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.016

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	3	MET	0	-0.006	-0.004	3.814	-0.787	0.034	0.004	-0.365	-0.460	0.001
4	A	4	GLU	-1	-0.925	-0.958	6.269	0.205	0.205	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.790	-0.892	9.737	-0.374	-0.374	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.040	0.014	12.439	0.075	0.075	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.030	0.016	15.096	0.051	0.051	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.022	-0.027	15.292	0.031	0.031	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.001	0.011	16.377	0.021	0.021	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.065	0.027	18.945	0.018	0.018	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.919	0.977	21.396	0.089	0.089	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.016	0.006	22.982	0.013	0.013	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.853	-0.912	22.864	-0.082	-0.082	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.060	0.033	25.482	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.032	-0.025	27.469	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.818	0.907	25.891	0.084	0.084	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.044	0.019	29.609	0.006	0.006	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.016	-0.002	31.446	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.028	-0.013	32.666	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.032	-0.013	33.400	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.001	0.001	35.534	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.017	-0.003	37.406	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.001	0.010	39.008	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.013	-0.015	38.634	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.016	0.005	41.589	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.046	-0.018	43.447	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.846	0.913	44.866	0.026	0.026	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.016	-0.010	45.605	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.013	-0.013	47.234	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.851	-0.913	48.924	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.077	-0.026	48.583	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.028	-0.029	50.092	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.063	-0.008	53.222	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.835	-0.898	55.397	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	35	PRO	0	-0.016	-0.014	56.681	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.091	-0.058	58.267	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.050	-0.034	54.138	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.019	0.004	53.706	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.010	0.014	52.983	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.875	0.907	52.264	0.028	0.028	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.868	-0.916	50.735	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.826	-0.915	48.690	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.043	0.028	47.923	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.860	-0.925	47.647	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	45	TRP	0	-0.022	-0.010	40.795	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.014	-0.003	43.308	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.028	-0.033	42.878	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.088	-0.059	41.898	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.837	-0.907	37.564	-0.058	-0.058	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.025	0.010	37.930	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.948	0.961	38.263	0.047	0.047	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.089	-0.060	34.563	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.009	-0.011	33.488	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.009	-0.012	33.103	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.932	0.987	32.460	0.069	0.069	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.015	-0.003	28.193	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.016	-0.006	28.686	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.824	-0.892	29.512	-0.077	-0.077	0.000	0.000	0.000	0.000
59	A	59	TRP	0	-0.025	0.008	23.827	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.833	-0.929	24.982	-0.139	-0.139	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.072	-0.050	24.854	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.959	-0.970	26.538	-0.118	-0.118	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.837	-0.913	21.595	-0.201	-0.201	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.056	-0.036	21.066	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.786	-0.894	22.560	-0.122	-0.122	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.914	-0.946	22.109	-0.189	-0.189	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.107	-0.071	18.147	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.021	-0.012	19.446	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.026	0.017	21.982	0.009	0.009	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.036	-0.021	16.488	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.034	-0.020	16.681	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.844	-0.914	18.533	-0.095	-0.095	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.018	0.009	20.646	0.014	0.014	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.081	-0.046	14.631	0.015	0.015	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.089	0.051	16.149	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.913	0.949	14.087	0.041	0.041	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.916	0.964	10.043	0.746	0.746	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.024	0.003	11.212	-0.084	-0.084	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.091	-0.023	13.233	0.043	0.043	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.050	0.025	15.052	0.021	0.021	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.818	-0.906	17.627	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.030	0.008	20.709	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.001	-0.002	23.738	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.849	-0.917	19.151	-0.104	-0.104	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.012	0.014	21.104	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.004	-0.016	23.229	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.041	-0.011	25.543	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.727	0.844	16.714	0.177	0.177	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.864	0.908	24.729	0.097	0.097	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.007	0.003	27.389	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.009	0.010	25.952	0.005	0.005	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.055	0.047	24.514	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.038	-0.022	28.861	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.050	-0.049	31.982	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.007	-0.012	30.392	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.848	0.896	29.198	0.102	0.102	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.067	-0.038	34.044	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.048	0.032	35.549	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.008	-0.004	33.902	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.908	0.952	37.034	0.056	0.056	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.841	-0.909	39.313	-0.040	-0.040	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.055	-0.022	37.138	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.803	0.868	37.237	0.067	0.067	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.899	-0.941	42.199	-0.043	-0.043	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.083	-0.037	45.136	0.002	0.002	0.000	0.000	0.000	0.000
106	A	106	MET	0	-0.049	-0.013	43.331	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.044	-0.023	44.409	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.095	-0.030	47.047	0.002	0.002	0.000	0.000	0.000	0.000

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