FMO DATABASE

FMODB ID: J3MM9

Calculation Name: 4DJB-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DJB

Chain ID: A

ChEMBL ID:

UniProt ID: P04489

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	119
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-982443.203062
FMO2-HF: Nuclear repulsion	934808.395358
FMO2-HF: Total energy	-47634.807703
FMO2-MP2: Total energy	-47773.000971

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:ACE )

Summations of interaction energy for fragment #1(A:-2:ACE )

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.
1.234	2.72	0.031	-0.714	-0.802	-0.003

Interaction energy analysis for fragmet #1(A:-2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.028

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	0	PRO	0	-0.002	0.019	3.349	0.247	1.733	0.031	-0.714	-0.802	-0.003
4	A	1	MET	0	-0.003	0.011	5.215	0.153	0.153	0.000	0.000	0.000	0.000
5	A	2	ILE	0	-0.030	-0.017	7.778	0.096	0.096	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.795	0.887	8.489	0.105	0.105	0.000	0.000	0.000	0.000
7	A	4	CYS	0	-0.030	-0.015	12.990	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	5	LEU	0	0.004	0.015	16.510	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	6	ARG	1	0.916	0.945	19.447	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	7	LEU	0	0.005	0.017	22.598	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	8	LYS	1	0.919	0.965	26.043	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	9	VAL	0	0.001	0.001	29.056	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	10	GLU	-1	-0.905	-0.970	32.422	0.009	0.009	0.000	0.000	0.000	0.000
14	A	11	GLY	0	0.073	0.022	35.360	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	12	ALA	0	0.044	0.019	38.027	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	13	LEU	0	0.002	0.013	35.047	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	14	GLU	-1	-0.790	-0.898	36.668	0.004	0.004	0.000	0.000	0.000	0.000
18	A	15	GLN	0	-0.011	-0.003	38.510	0.000	0.000	0.000	0.000	0.000	0.000
19	A	16	ILE	0	-0.011	-0.018	41.461	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	17	PHE	0	0.007	-0.002	38.471	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	18	THR	0	0.002	0.010	41.271	0.000	0.000	0.000	0.000	0.000	0.000
22	A	19	MET	0	-0.108	-0.057	43.314	0.000	0.000	0.000	0.000	0.000	0.000
23	A	20	ALA	0	0.011	0.024	44.206	0.000	0.000	0.000	0.000	0.000	0.000
24	A	21	GLY	0	-0.037	-0.015	45.832	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.046	-0.018	40.583	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	ASN	0	0.038	0.011	37.176	0.001	0.001	0.000	0.000	0.000	0.000
27	A	24	ILE	0	0.075	0.022	34.449	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	25	ARG	1	0.764	0.844	32.954	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.945	-0.975	32.573	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	27	LEU	0	0.012	0.008	34.057	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	28	LEU	0	0.013	0.005	29.747	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	29	ARG	1	0.847	0.921	29.254	0.007	0.007	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.865	-0.947	29.612	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	31	ILE	0	-0.026	-0.001	29.009	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	32	LEU	0	0.036	0.010	23.818	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	33	ARG	1	0.882	0.941	26.301	0.012	0.012	0.000	0.000	0.000	0.000
37	A	34	ARG	1	0.967	0.997	28.317	0.034	0.034	0.000	0.000	0.000	0.000
38	A	35	TRP	0	0.058	0.041	19.711	0.000	0.000	0.000	0.000	0.000	0.000
39	A	36	ARG	1	0.854	0.907	23.866	0.035	0.035	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.901	-0.945	25.135	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	38	GLU	-1	-0.968	-0.972	27.370	-0.074	-0.074	0.000	0.000	0.000	0.000
42	A	39	ASN	0	-0.027	-0.024	22.837	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	40	TYR	0	0.028	0.010	20.947	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	41	LEU	0	-0.006	-0.002	22.222	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	42	GLY	0	-0.045	-0.018	21.158	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	43	MET	0	-0.043	-0.003	19.007	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	44	VAL	0	-0.007	-0.007	15.873	-0.040	-0.040	0.000	0.000	0.000	0.000
48	A	45	GLU	-1	-0.826	-0.915	14.442	-0.239	-0.239	0.000	0.000	0.000	0.000
49	A	46	GLY	0	-0.030	-0.017	16.413	0.029	0.029	0.000	0.000	0.000	0.000
50	A	47	ALA	0	-0.042	-0.023	16.579	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	48	GLY	0	-0.034	0.004	18.262	0.009	0.009	0.000	0.000	0.000	0.000
52	A	49	MET	0	-0.021	-0.019	19.940	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	50	PHE	0	-0.042	-0.011	20.242	0.004	0.004	0.000	0.000	0.000	0.000
54	A	51	ILE	0	0.005	-0.006	25.102	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	52	GLU	-1	-0.959	-0.961	25.495	0.056	0.056	0.000	0.000	0.000	0.000
56	A	53	GLU	-1	-0.791	-0.873	28.576	0.014	0.014	0.000	0.000	0.000	0.000
57	A	54	ILE	0	-0.062	-0.021	30.204	0.004	0.004	0.000	0.000	0.000	0.000
58	A	55	HIS	0	-0.018	0.021	32.872	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	56	PRO	0	-0.065	-0.061	36.008	0.001	0.001	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.898	-0.959	37.252	0.008	0.008	0.000	0.000	0.000	0.000
61	A	58	GLY	0	0.065	0.039	34.927	0.000	0.000	0.000	0.000	0.000	0.000
62	A	59	PHE	0	-0.049	-0.018	30.137	0.002	0.002	0.000	0.000	0.000	0.000
63	A	60	SER	0	-0.023	-0.008	26.186	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	61	LEU	0	0.007	0.001	25.242	0.003	0.003	0.000	0.000	0.000	0.000
65	A	62	TYR	0	-0.006	-0.011	20.983	0.001	0.001	0.000	0.000	0.000	0.000
66	A	63	VAL	0	0.014	-0.002	19.377	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	64	HIS	0	-0.006	0.003	15.859	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.011	-0.005	14.573	0.002	0.002	0.000	0.000	0.000	0.000
69	A	66	ASP	-1	-0.807	-0.891	9.476	-0.578	-0.578	0.000	0.000	0.000	0.000
70	A	67	VAL	0	-0.009	-0.009	11.732	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	68	ARG	1	0.806	0.911	10.050	0.367	0.367	0.000	0.000	0.000	0.000
72	A	69	ALA	0	0.001	-0.017	9.722	-0.167	-0.167	0.000	0.000	0.000	0.000
73	A	70	VAL	0	0.061	0.029	11.795	0.074	0.074	0.000	0.000	0.000	0.000
74	A	71	SER	0	0.004	0.006	13.914	0.023	0.023	0.000	0.000	0.000	0.000
75	A	72	LEU	0	-0.012	0.002	14.800	0.032	0.032	0.000	0.000	0.000	0.000
76	A	73	LEU	0	0.020	0.006	13.969	0.034	0.034	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.923	-0.970	16.244	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.008	-0.002	19.361	0.020	0.020	0.000	0.000	0.000	0.000
79	A	76	ILE	0	-0.018	-0.009	16.523	0.017	0.017	0.000	0.000	0.000	0.000
80	A	77	VAL	0	0.007	0.002	19.286	0.018	0.018	0.000	0.000	0.000	0.000
81	A	78	GLN	0	-0.015	0.011	21.812	0.009	0.009	0.000	0.000	0.000	0.000
82	A	79	HIS	0	0.059	0.027	23.934	0.008	0.008	0.000	0.000	0.000	0.000
83	A	80	LEU	0	-0.017	-0.015	21.877	0.010	0.010	0.000	0.000	0.000	0.000
84	A	81	THR	0	-0.024	-0.027	25.247	0.011	0.011	0.000	0.000	0.000	0.000
85	A	82	GLU	-1	-0.933	-0.962	27.565	-0.062	-0.062	0.000	0.000	0.000	0.000
86	A	83	ALA	0	-0.023	-0.004	28.571	0.005	0.005	0.000	0.000	0.000	0.000
87	A	84	ILE	0	-0.012	-0.024	27.157	0.005	0.005	0.000	0.000	0.000	0.000
88	A	85	ILE	0	-0.010	0.005	31.011	0.004	0.004	0.000	0.000	0.000	0.000
89	A	86	SER	0	-0.038	-0.023	33.340	0.003	0.003	0.000	0.000	0.000	0.000
90	A	87	SER	0	0.015	-0.001	33.816	0.002	0.002	0.000	0.000	0.000	0.000
91	A	88	LEU	0	-0.015	-0.010	33.406	0.003	0.003	0.000	0.000	0.000	0.000
92	A	89	ALA	0	0.009	0.005	36.715	0.003	0.003	0.000	0.000	0.000	0.000
93	A	90	VAL	0	-0.021	-0.003	38.887	0.001	0.001	0.000	0.000	0.000	0.000
94	A	91	GLU	-1	-0.926	-0.968	38.209	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	92	PHE	0	-0.021	-0.016	40.844	0.002	0.002	0.000	0.000	0.000	0.000
96	A	93	ASP	-1	-0.900	-0.939	42.623	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	94	HIS	0	-0.043	-0.031	43.682	0.000	0.000	0.000	0.000	0.000	0.000
98	A	95	ALA	0	-0.052	-0.017	44.687	0.001	0.001	0.000	0.000	0.000	0.000
99	A	96	THR	0	-0.024	-0.014	46.092	0.001	0.001	0.000	0.000	0.000	0.000
100	A	97	GLY	0	-0.057	-0.015	48.621	0.001	0.001	0.000	0.000	0.000	0.000
101	A	98	GLY	0	-0.037	-0.019	48.072	0.000	0.000	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-1.004	-0.991	47.613	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	100	ARG	1	0.925	0.944	43.989	0.017	0.017	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.029	0.013	39.874	0.002	0.002	0.000	0.000	0.000	0.000
105	A	102	HIS	0	-0.067	-0.030	37.439	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	103	LEU	0	0.029	0.003	35.251	0.001	0.001	0.000	0.000	0.000	0.000
107	A	104	ILE	0	-0.022	-0.018	34.042	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	105	ASP	-1	-0.859	-0.918	32.970	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	106	LEU	0	-0.082	-0.027	30.402	0.002	0.002	0.000	0.000	0.000	0.000
110	A	107	HIS	0	-0.017	-0.017	25.781	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	108	PHE	0	-0.006	-0.012	21.949	0.005	0.005	0.000	0.000	0.000	0.000
112	A	109	GLU	-1	-0.881	-0.927	21.934	0.009	0.009	0.000	0.000	0.000	0.000
113	A	110	VAL	0	-0.007	-0.015	15.554	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	111	LEU	0	-0.060	-0.031	16.586	0.014	0.014	0.000	0.000	0.000	0.000
115	A	112	ASP	-1	-0.867	-0.946	12.175	0.019	0.019	0.000	0.000	0.000	0.000
116	A	113	ASN	0	-0.020	-0.017	7.252	0.017	0.017	0.000	0.000	0.000	0.000
117	A	114	LEU	0	-0.026	-0.027	9.584	0.053	0.053	0.000	0.000	0.000	0.000
118	A	115	LEU	0	-0.097	-0.047	8.218	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	116	GLU	-2	-1.769	-1.847	4.929	1.249	1.249	0.000	0.000	0.000	0.000

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