FMO DATABASE

FMODB ID: 22V1R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-979769.521021
FMO2-HF: Nuclear repulsion	932284.451172
FMO2-HF: Total energy	-47485.06985
FMO2-MP2: Total energy	-47622.872766

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.
112.373	113.884	-0.002	-0.844	-0.666	0.003

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 : -1.004 / q_NPA : -1.016

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

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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	-0.024	0.001	3.538	-7.747	-6.236	-0.002	-0.844	-0.666	0.003
4	A	2	ILE	0	-0.024	-0.015	6.166	-3.161	-3.161	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.747	0.844	7.653	-26.187	-26.187	0.000	0.000	0.000	0.000
6	A	4	CYS	0	-0.045	-0.014	11.912	-0.446	-0.446	0.000	0.000	0.000	0.000
7	A	5	LEU	0	0.008	0.018	15.552	-0.416	-0.416	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.915	0.940	18.278	-12.854	-12.854	0.000	0.000	0.000	0.000
9	A	7	LEU	0	-0.014	0.005	21.631	-0.193	-0.193	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.864	0.924	24.938	-9.755	-9.755	0.000	0.000	0.000	0.000
11	A	9	VAL	0	0.005	0.005	28.124	-0.107	-0.107	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.836	-0.922	31.395	8.988	8.988	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.062	0.017	34.459	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.039	0.017	37.172	-0.107	-0.107	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.002	0.010	33.807	-0.117	-0.117	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.756	-0.864	35.617	8.882	8.882	0.000	0.000	0.000	0.000
17	A	15	GLN	0	-0.020	0.002	37.386	-0.146	-0.146	0.000	0.000	0.000	0.000
18	A	16	ILE	0	0.008	-0.008	40.298	-0.160	-0.160	0.000	0.000	0.000	0.000
19	A	17	PHE	0	0.011	0.000	37.156	-0.073	-0.073	0.000	0.000	0.000	0.000
20	A	18	THR	0	-0.013	-0.008	40.155	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	19	MET	0	-0.090	-0.046	42.069	-0.147	-0.147	0.000	0.000	0.000	0.000
22	A	20	ALA	0	0.001	0.021	42.746	-0.164	-0.164	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.028	-0.010	44.446	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	22	LEU	0	-0.049	-0.018	38.989	0.134	0.134	0.000	0.000	0.000	0.000
25	A	23	ASN	0	0.008	-0.003	36.022	0.097	0.097	0.000	0.000	0.000	0.000
26	A	24	ILE	0	0.076	0.021	33.034	0.219	0.219	0.000	0.000	0.000	0.000
27	A	25	ARG	1	0.775	0.843	31.676	-8.867	-8.867	0.000	0.000	0.000	0.000
28	A	26	ASP	-1	-0.855	-0.925	31.203	9.654	9.654	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.020	0.015	32.061	0.267	0.267	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.004	-0.002	28.231	0.329	0.329	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.741	0.841	27.462	-9.445	-9.445	0.000	0.000	0.000	0.000
32	A	30	ASP	-1	-0.794	-0.889	27.282	10.664	10.664	0.000	0.000	0.000	0.000
33	A	31	ILE	0	-0.014	0.008	26.399	0.200	0.200	0.000	0.000	0.000	0.000
34	A	32	LEU	0	0.031	0.006	21.727	0.432	0.432	0.000	0.000	0.000	0.000
35	A	33	ARG	1	0.833	0.917	23.237	-10.500	-10.500	0.000	0.000	0.000	0.000
36	A	34	ARG	1	0.958	0.984	24.924	-10.434	-10.434	0.000	0.000	0.000	0.000
37	A	35	TRP	0	0.060	0.043	16.647	0.197	0.197	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.822	0.872	20.285	-12.647	-12.647	0.000	0.000	0.000	0.000
39	A	37	ASP	-1	-0.877	-0.914	21.311	12.870	12.870	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.941	-0.960	22.764	12.671	12.671	0.000	0.000	0.000	0.000
41	A	39	ASN	0	-0.040	-0.034	16.808	0.037	0.037	0.000	0.000	0.000	0.000
42	A	40	TYR	0	0.025	0.010	16.427	1.067	1.067	0.000	0.000	0.000	0.000
43	A	41	LEU	0	0.001	0.001	17.537	0.796	0.796	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.039	-0.013	15.622	0.295	0.295	0.000	0.000	0.000	0.000
45	A	43	MET	0	-0.039	-0.003	13.582	2.010	2.010	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.012	-0.006	11.473	2.191	2.191	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.810	-0.884	9.581	26.424	26.424	0.000	0.000	0.000	0.000
48	A	46	GLY	0	-0.019	-0.013	12.353	-1.762	-1.762	0.000	0.000	0.000	0.000
49	A	47	ALA	0	-0.050	-0.024	13.793	1.207	1.207	0.000	0.000	0.000	0.000
50	A	48	GLY	0	-0.022	0.007	16.230	-0.830	-0.830	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.021	-0.019	18.909	0.075	0.075	0.000	0.000	0.000	0.000
52	A	50	PHE	0	-0.044	-0.012	19.534	-0.260	-0.260	0.000	0.000	0.000	0.000
53	A	51	ILE	0	0.004	-0.009	24.202	0.163	0.163	0.000	0.000	0.000	0.000
54	A	52	GLU	-1	-0.937	-0.947	25.208	11.243	11.243	0.000	0.000	0.000	0.000
55	A	53	GLU	-1	-0.821	-0.900	27.950	9.226	9.226	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.088	-0.030	29.589	0.215	0.215	0.000	0.000	0.000	0.000
57	A	55	HIS	0	-0.016	0.022	32.376	-0.422	-0.422	0.000	0.000	0.000	0.000
58	A	56	PRO	0	-0.060	-0.060	35.658	0.061	0.061	0.000	0.000	0.000	0.000
59	A	57	GLU	-1	-0.892	-0.958	36.730	7.623	7.623	0.000	0.000	0.000	0.000
60	A	58	GLY	0	0.070	0.043	34.156	0.103	0.103	0.000	0.000	0.000	0.000
61	A	59	PHE	0	-0.043	-0.015	29.160	0.052	0.052	0.000	0.000	0.000	0.000
62	A	60	SER	0	-0.028	-0.012	25.405	0.105	0.105	0.000	0.000	0.000	0.000
63	A	61	LEU	0	0.008	0.004	24.088	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	62	TYR	0	-0.003	-0.015	20.169	0.348	0.348	0.000	0.000	0.000	0.000
65	A	63	VAL	0	0.018	-0.001	17.983	-0.095	-0.095	0.000	0.000	0.000	0.000
66	A	64	HIS	0	0.002	0.002	14.900	-0.271	-0.271	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.017	-0.004	13.139	-0.379	-0.379	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.808	-0.893	6.289	44.822	44.822	0.000	0.000	0.000	0.000
69	A	67	VAL	0	0.000	-0.005	9.692	-0.273	-0.273	0.000	0.000	0.000	0.000
70	A	68	ARG	1	0.778	0.872	6.477	-33.260	-33.260	0.000	0.000	0.000	0.000
71	A	69	ALA	0	-0.008	-0.019	6.328	4.542	4.542	0.000	0.000	0.000	0.000
72	A	70	VAL	0	0.052	0.022	8.715	-2.288	-2.288	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.019	0.017	11.571	-0.566	-0.566	0.000	0.000	0.000	0.000
74	A	72	LEU	0	-0.018	-0.003	10.574	-1.530	-1.530	0.000	0.000	0.000	0.000
75	A	73	LEU	0	0.014	0.002	12.314	-1.352	-1.352	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.915	-0.967	13.968	16.554	16.554	0.000	0.000	0.000	0.000
77	A	75	ALA	0	-0.003	0.001	16.531	-1.128	-1.128	0.000	0.000	0.000	0.000
78	A	76	ILE	0	-0.017	-0.007	13.490	-0.941	-0.941	0.000	0.000	0.000	0.000
79	A	77	VAL	0	-0.002	-0.004	17.579	-1.011	-1.011	0.000	0.000	0.000	0.000
80	A	78	GLN	0	-0.057	-0.015	19.870	-0.414	-0.414	0.000	0.000	0.000	0.000
81	A	79	HIS	0	0.029	0.013	20.682	-0.816	-0.816	0.000	0.000	0.000	0.000
82	A	80	LEU	0	-0.005	-0.008	19.610	-0.707	-0.707	0.000	0.000	0.000	0.000
83	A	81	THR	0	-0.032	-0.034	23.249	-0.671	-0.671	0.000	0.000	0.000	0.000
84	A	82	GLU	-1	-0.872	-0.925	25.732	11.513	11.513	0.000	0.000	0.000	0.000
85	A	83	ALA	0	-0.012	0.015	25.728	-0.542	-0.542	0.000	0.000	0.000	0.000
86	A	84	ILE	0	-0.014	-0.023	25.539	-0.453	-0.453	0.000	0.000	0.000	0.000
87	A	85	ILE	0	-0.014	0.003	28.929	-0.485	-0.485	0.000	0.000	0.000	0.000
88	A	86	SER	0	-0.039	-0.037	30.424	-0.395	-0.395	0.000	0.000	0.000	0.000
89	A	87	SER	0	0.019	0.008	31.111	-0.271	-0.271	0.000	0.000	0.000	0.000
90	A	88	LEU	0	-0.012	-0.011	31.953	-0.289	-0.289	0.000	0.000	0.000	0.000
91	A	89	ALA	0	0.003	0.005	34.691	-0.317	-0.317	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.016	-0.004	36.276	-0.270	-0.270	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.921	-0.963	35.576	8.593	8.593	0.000	0.000	0.000	0.000
94	A	92	PHE	0	-0.007	-0.014	38.556	-0.225	-0.225	0.000	0.000	0.000	0.000
95	A	93	ASP	-1	-0.872	-0.908	40.689	7.257	7.257	0.000	0.000	0.000	0.000
96	A	94	HIS	0	-0.078	-0.060	41.197	-0.132	-0.132	0.000	0.000	0.000	0.000
97	A	95	ALA	0	-0.054	-0.016	42.504	-0.185	-0.185	0.000	0.000	0.000	0.000
98	A	96	THR	0	-0.015	-0.022	44.348	-0.191	-0.191	0.000	0.000	0.000	0.000
99	A	97	GLY	0	-0.064	-0.020	46.587	-0.170	-0.170	0.000	0.000	0.000	0.000
100	A	98	GLY	0	-0.034	-0.014	45.739	-0.138	-0.138	0.000	0.000	0.000	0.000
101	A	99	GLU	-1	-0.999	-0.986	45.918	6.739	6.739	0.000	0.000	0.000	0.000
102	A	100	ARG	1	0.917	0.939	42.367	-7.024	-7.024	0.000	0.000	0.000	0.000
103	A	101	VAL	0	0.025	0.015	38.483	-0.112	-0.112	0.000	0.000	0.000	0.000
104	A	102	HIS	0	-0.093	-0.055	36.368	0.033	0.033	0.000	0.000	0.000	0.000
105	A	103	LEU	0	0.044	0.010	33.792	0.090	0.090	0.000	0.000	0.000	0.000
106	A	104	ILE	0	-0.019	-0.013	32.610	0.303	0.303	0.000	0.000	0.000	0.000
107	A	105	ASP	-1	-0.830	-0.890	31.746	9.240	9.240	0.000	0.000	0.000	0.000
108	A	106	LEU	0	-0.062	-0.014	29.067	0.256	0.256	0.000	0.000	0.000	0.000
109	A	107	HIS	1	0.834	0.890	24.604	-11.148	-11.148	0.000	0.000	0.000	0.000
110	A	108	PHE	0	0.030	0.005	20.687	-0.099	-0.099	0.000	0.000	0.000	0.000
111	A	109	GLU	-1	-0.851	-0.895	21.162	11.936	11.936	0.000	0.000	0.000	0.000
112	A	110	VAL	0	0.014	-0.003	14.532	0.295	0.295	0.000	0.000	0.000	0.000
113	A	111	LEU	0	-0.045	-0.022	16.135	-0.436	-0.436	0.000	0.000	0.000	0.000
114	A	112	ASP	-1	-0.817	-0.922	12.185	20.762	20.762	0.000	0.000	0.000	0.000
115	A	113	ASN	0	-0.039	-0.031	6.903	-2.771	-2.771	0.000	0.000	0.000	0.000
116	A	114	LEU	0	-0.023	-0.024	10.018	0.510	0.510	0.000	0.000	0.000	0.000
117	A	115	LEU	0	-0.050	-0.017	9.044	-0.692	-0.692	0.000	0.000	0.000	0.000
118	A	116	GLU	-1	-0.824	-0.854	5.263	29.230	29.230	0.000	0.000	0.000	0.000

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