FMO DATABASE

FMODB ID: 7G1RK

Calculation Name: 4DJB-A-Xray372

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: 2023-06-20

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-979009.965194
FMO2-HF: Nuclear repulsion	931525.254735
FMO2-HF: Total energy	-47484.710459
FMO2-MP2: Total energy	-47622.47618

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:ASP)

Summations of interaction energy for fragment #1(A:-1: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.
112.017	113.458	0.002	-0.778	-0.664	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.995 / q_NPA : -1.011

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	A	1	MET	0	-0.018	0.003	3.510	-8.030	-6.589	0.002	-0.778	-0.664	0.002
4	A	2	ILE	0	-0.027	-0.015	6.149	-3.155	-3.155	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.801	0.889	7.783	-26.761	-26.761	0.000	0.000	0.000	0.000
6	A	4	CYS	0	-0.022	-0.010	11.887	-0.450	-0.450	0.000	0.000	0.000	0.000
7	A	5	LEU	0	0.002	0.013	15.525	-0.418	-0.418	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.935	0.956	18.253	-13.052	-13.052	0.000	0.000	0.000	0.000
9	A	7	LEU	0	-0.010	0.008	21.607	-0.197	-0.197	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.909	0.961	24.913	-9.835	-9.835	0.000	0.000	0.000	0.000
11	A	9	VAL	0	0.002	0.002	28.100	-0.100	-0.100	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.906	-0.969	31.370	8.854	8.854	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.078	0.025	34.436	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.046	0.021	37.147	-0.107	-0.107	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.002	0.010	33.815	-0.118	-0.118	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.788	-0.898	35.659	8.884	8.884	0.000	0.000	0.000	0.000
17	A	15	GLN	0	-0.013	-0.003	37.359	-0.066	-0.066	0.000	0.000	0.000	0.000
18	A	16	ILE	0	-0.007	-0.016	40.203	-0.167	-0.167	0.000	0.000	0.000	0.000
19	A	17	PHE	0	0.004	-0.003	36.928	-0.071	-0.071	0.000	0.000	0.000	0.000
20	A	18	THR	0	0.001	0.009	40.079	-0.102	-0.102	0.000	0.000	0.000	0.000
21	A	19	MET	0	-0.101	-0.055	42.039	-0.151	-0.151	0.000	0.000	0.000	0.000
22	A	20	ALA	0	0.010	0.024	42.730	-0.165	-0.165	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.033	-0.012	44.428	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	22	LEU	0	-0.044	-0.016	38.989	0.135	0.135	0.000	0.000	0.000	0.000
25	A	23	ASN	0	0.040	0.013	35.867	0.191	0.191	0.000	0.000	0.000	0.000
26	A	24	ILE	0	0.071	0.020	33.053	0.221	0.221	0.000	0.000	0.000	0.000
27	A	25	ARG	1	0.761	0.841	31.644	-8.930	-8.930	0.000	0.000	0.000	0.000
28	A	26	ASP	-1	-0.941	-0.973	31.171	9.704	9.704	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.015	0.010	32.047	0.278	0.278	0.000	0.000	0.000	0.000
30	A	28	LEU	0	0.004	0.000	28.261	0.346	0.346	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.844	0.920	27.457	-9.584	-9.584	0.000	0.000	0.000	0.000
32	A	30	ASP	-1	-0.860	-0.944	27.258	10.644	10.644	0.000	0.000	0.000	0.000
33	A	31	ILE	0	-0.026	-0.001	26.358	0.220	0.220	0.000	0.000	0.000	0.000
34	A	32	LEU	0	0.030	0.006	21.609	0.446	0.446	0.000	0.000	0.000	0.000
35	A	33	ARG	1	0.884	0.943	23.201	-10.814	-10.814	0.000	0.000	0.000	0.000
36	A	34	ARG	1	0.972	0.999	24.862	-10.509	-10.509	0.000	0.000	0.000	0.000
37	A	35	TRP	0	0.057	0.039	16.702	0.142	0.142	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.850	0.905	20.218	-12.829	-12.829	0.000	0.000	0.000	0.000
39	A	37	ASP	-1	-0.897	-0.943	21.226	12.912	12.912	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.966	-0.970	22.723	12.731	12.731	0.000	0.000	0.000	0.000
41	A	39	ASN	0	-0.021	-0.021	17.194	0.607	0.607	0.000	0.000	0.000	0.000
42	A	40	TYR	0	0.025	0.008	16.363	0.998	0.998	0.000	0.000	0.000	0.000
43	A	41	LEU	0	-0.003	-0.001	17.482	0.817	0.817	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.044	-0.017	15.524	0.290	0.290	0.000	0.000	0.000	0.000
45	A	43	MET	0	-0.042	-0.003	13.502	2.007	2.007	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.014	-0.011	11.421	2.425	2.425	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.821	-0.912	9.380	27.085	27.085	0.000	0.000	0.000	0.000
48	A	46	GLY	0	-0.025	-0.015	12.258	-1.830	-1.830	0.000	0.000	0.000	0.000
49	A	47	ALA	0	-0.046	-0.025	13.759	1.249	1.249	0.000	0.000	0.000	0.000
50	A	48	GLY	0	-0.029	0.007	16.209	-0.858	-0.858	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.023	-0.021	18.905	0.064	0.064	0.000	0.000	0.000	0.000
52	A	50	PHE	0	-0.036	-0.008	19.481	-0.315	-0.315	0.000	0.000	0.000	0.000
53	A	51	ILE	0	0.006	-0.007	24.168	0.165	0.165	0.000	0.000	0.000	0.000
54	A	52	GLU	-1	-0.957	-0.959	24.961	11.345	11.345	0.000	0.000	0.000	0.000
55	A	53	GLU	-1	-0.784	-0.870	27.921	9.192	9.192	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.069	-0.025	29.520	0.221	0.221	0.000	0.000	0.000	0.000
57	A	55	HIS	0	-0.016	0.023	32.351	-0.364	-0.364	0.000	0.000	0.000	0.000
58	A	56	PRO	0	-0.060	-0.058	35.634	0.063	0.063	0.000	0.000	0.000	0.000
59	A	57	GLU	-1	-0.895	-0.957	36.715	7.628	7.628	0.000	0.000	0.000	0.000
60	A	58	GLY	0	0.065	0.040	34.132	0.107	0.107	0.000	0.000	0.000	0.000
61	A	59	PHE	0	-0.047	-0.016	29.114	0.065	0.065	0.000	0.000	0.000	0.000
62	A	60	SER	0	-0.030	-0.013	25.366	0.118	0.118	0.000	0.000	0.000	0.000
63	A	61	LEU	0	0.012	0.005	23.933	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	62	TYR	0	-0.015	-0.016	20.235	0.343	0.343	0.000	0.000	0.000	0.000
65	A	63	VAL	0	0.022	0.002	17.792	-0.105	-0.105	0.000	0.000	0.000	0.000
66	A	64	HIS	0	-0.013	-0.001	14.831	-0.214	-0.214	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.019	0.000	13.045	-0.349	-0.349	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.805	-0.891	6.236	46.156	46.156	0.000	0.000	0.000	0.000
69	A	67	VAL	0	-0.010	-0.010	9.709	-0.236	-0.236	0.000	0.000	0.000	0.000
70	A	68	ARG	1	0.811	0.913	6.286	-34.672	-34.672	0.000	0.000	0.000	0.000
71	A	69	ALA	0	-0.001	-0.018	5.918	4.922	4.922	0.000	0.000	0.000	0.000
72	A	70	VAL	0	0.056	0.026	8.487	-2.342	-2.342	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.010	0.008	11.606	-0.627	-0.627	0.000	0.000	0.000	0.000
74	A	72	LEU	0	-0.005	0.005	10.496	-1.584	-1.584	0.000	0.000	0.000	0.000
75	A	73	LEU	0	0.013	0.002	12.366	-1.366	-1.366	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.925	-0.972	13.986	16.591	16.591	0.000	0.000	0.000	0.000
77	A	75	ALA	0	-0.006	-0.001	16.094	-1.163	-1.163	0.000	0.000	0.000	0.000
78	A	76	ILE	0	-0.013	-0.006	13.434	-0.928	-0.928	0.000	0.000	0.000	0.000
79	A	77	VAL	0	-0.002	-0.003	17.564	-1.034	-1.034	0.000	0.000	0.000	0.000
80	A	78	GLN	0	-0.016	0.010	19.881	-0.776	-0.776	0.000	0.000	0.000	0.000
81	A	79	HIS	0	0.065	0.031	20.644	-0.782	-0.782	0.000	0.000	0.000	0.000
82	A	80	LEU	0	-0.011	-0.012	19.621	-0.711	-0.711	0.000	0.000	0.000	0.000
83	A	81	THR	0	-0.041	-0.036	23.225	-0.671	-0.671	0.000	0.000	0.000	0.000
84	A	82	GLU	-1	-0.929	-0.960	25.612	11.592	11.592	0.000	0.000	0.000	0.000
85	A	83	ALA	0	-0.020	-0.002	25.757	-0.541	-0.541	0.000	0.000	0.000	0.000
86	A	84	ILE	0	-0.011	-0.024	25.516	-0.456	-0.456	0.000	0.000	0.000	0.000
87	A	85	ILE	0	-0.014	0.002	28.947	-0.487	-0.487	0.000	0.000	0.000	0.000
88	A	86	SER	0	-0.036	-0.022	30.462	-0.429	-0.429	0.000	0.000	0.000	0.000
89	A	87	SER	0	0.018	0.001	31.207	-0.273	-0.273	0.000	0.000	0.000	0.000
90	A	88	LEU	0	-0.019	-0.012	31.877	-0.293	-0.293	0.000	0.000	0.000	0.000
91	A	89	ALA	0	0.007	0.004	34.703	-0.318	-0.318	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.017	-0.001	36.126	-0.272	-0.272	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.924	-0.967	35.788	8.533	8.533	0.000	0.000	0.000	0.000
94	A	92	PHE	0	-0.022	-0.016	38.550	-0.229	-0.229	0.000	0.000	0.000	0.000
95	A	93	ASP	-1	-0.901	-0.940	40.699	7.277	7.277	0.000	0.000	0.000	0.000
96	A	94	HIS	0	-0.043	-0.031	40.566	-0.120	-0.120	0.000	0.000	0.000	0.000
97	A	95	ALA	0	-0.049	-0.016	42.539	-0.185	-0.185	0.000	0.000	0.000	0.000
98	A	96	THR	0	-0.015	-0.010	44.344	-0.194	-0.194	0.000	0.000	0.000	0.000
99	A	97	GLY	0	-0.063	-0.017	46.575	-0.169	-0.169	0.000	0.000	0.000	0.000
100	A	98	GLY	0	-0.034	-0.017	45.758	-0.143	-0.143	0.000	0.000	0.000	0.000
101	A	99	GLU	-1	-1.001	-0.989	46.039	6.761	6.761	0.000	0.000	0.000	0.000
102	A	100	ARG	1	0.925	0.944	42.335	-7.058	-7.058	0.000	0.000	0.000	0.000
103	A	101	VAL	0	0.029	0.013	38.356	-0.119	-0.119	0.000	0.000	0.000	0.000
104	A	102	HIS	0	-0.061	-0.027	36.235	0.029	0.029	0.000	0.000	0.000	0.000
105	A	103	LEU	0	0.036	0.007	33.726	0.093	0.093	0.000	0.000	0.000	0.000
106	A	104	ILE	0	-0.015	-0.013	32.590	0.300	0.300	0.000	0.000	0.000	0.000
107	A	105	ASP	-1	-0.853	-0.912	31.730	9.371	9.371	0.000	0.000	0.000	0.000
108	A	106	LEU	0	-0.074	-0.023	29.009	0.262	0.262	0.000	0.000	0.000	0.000
109	A	107	HIS	1	0.890	0.934	24.717	-11.241	-11.241	0.000	0.000	0.000	0.000
110	A	108	PHE	0	0.022	0.003	20.669	-0.107	-0.107	0.000	0.000	0.000	0.000
111	A	109	GLU	-1	-0.916	-0.948	21.137	12.115	12.115	0.000	0.000	0.000	0.000
112	A	110	VAL	0	0.012	-0.003	14.541	0.344	0.344	0.000	0.000	0.000	0.000
113	A	111	LEU	0	-0.050	-0.025	16.049	-0.455	-0.455	0.000	0.000	0.000	0.000
114	A	112	ASP	-1	-0.870	-0.945	12.196	20.144	20.144	0.000	0.000	0.000	0.000
115	A	113	ASN	0	-0.005	-0.008	7.055	-2.702	-2.702	0.000	0.000	0.000	0.000
116	A	114	LEU	0	-0.012	-0.020	10.009	0.513	0.513	0.000	0.000	0.000	0.000
117	A	115	LEU	0	-0.056	-0.022	9.054	-0.637	-0.637	0.000	0.000	0.000	0.000
118	A	116	GLU	-1	-0.865	-0.901	5.383	29.533	29.533	0.000	0.000	0.000	0.000

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