FMO DATABASE

FMODB ID: 2J79R

Calculation Name: 4HDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2,6-diaminopurine nucleotide

ligand 3-letter code: 1AP

PDB ID: 4HDV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UTN9

Base Structure: X-ray

Registration Date: 2023-06-21

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	-908009.15514
FMO2-HF: Nuclear repulsion	862876.003437
FMO2-HF: Total energy	-45133.151703
FMO2-MP2: Total energy	-45262.59387

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-17.798	-18.939	27.335	-11.162	-15.033	0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.019

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	3	MET	0	0.053	0.010	2.604	-4.011	-1.566	0.942	-1.397	-1.990	-0.005
4	A	4	ASP	-1	-0.822	-0.903	4.924	0.157	0.358	-0.001	-0.011	-0.188	0.000
5	A	5	GLU	-1	-0.796	-0.893	2.343	-0.584	2.554	1.689	-1.795	-3.032	-0.018
6	A	6	PHE	0	-0.028	-0.019	2.383	0.421	2.334	1.146	-0.665	-2.394	0.000
7	A	7	TYR	0	-0.009	-0.025	3.867	-0.230	-0.058	0.014	0.066	-0.253	0.000
8	A	8	THR	0	-0.006	-0.005	7.174	-0.074	-0.074	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.912	0.942	2.103	-12.856	-21.596	19.313	-6.315	-4.258	0.040
10	A	10	VAL	0	-0.023	-0.006	6.041	-0.497	-0.497	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.063	-0.062	8.169	-0.124	-0.124	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.856	-0.918	9.697	1.111	1.111	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.002	-0.003	9.356	-0.117	-0.117	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.041	-0.043	11.300	-0.082	-0.082	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.071	-0.043	13.816	-0.050	-0.050	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.846	-0.884	13.133	0.362	0.362	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.087	-0.026	15.073	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.001	0.015	17.964	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.014	-0.005	21.633	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.057	0.036	24.349	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.787	0.898	21.632	0.015	0.015	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.022	0.005	20.204	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.058	0.008	15.415	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.027	-0.016	15.389	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.016	-0.006	13.025	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.003	-0.011	11.442	-0.096	-0.096	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.825	-0.892	11.427	-0.374	-0.374	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.050	0.024	8.987	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.006	0.000	7.194	-0.032	-0.032	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.816	0.880	6.641	0.133	0.133	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.102	-0.064	8.416	-0.054	-0.054	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.013	-0.001	3.790	0.018	0.190	0.000	-0.020	-0.153	0.000
33	A	33	GLY	0	-0.003	0.011	3.613	-1.098	-0.651	0.007	-0.202	-0.252	-0.001
34	A	34	MET	0	-0.060	-0.035	2.461	-1.919	-2.826	4.226	-0.823	-2.495	-0.005
35	A	35	PRO	0	0.056	0.011	5.358	0.301	0.319	-0.001	0.000	-0.018	0.000
36	A	36	SER	0	-0.023	-0.004	8.701	0.132	0.132	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.037	-0.013	5.661	0.146	0.146	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.055	0.021	8.401	0.103	0.103	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.958	0.963	11.399	0.705	0.705	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.055	0.030	7.829	0.177	0.177	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.044	0.037	8.423	0.081	0.081	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.000	0.001	10.071	0.151	0.151	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.042	-0.031	11.253	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.055	0.041	9.374	0.091	0.091	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.009	0.023	11.495	0.127	0.127	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.855	0.926	14.765	0.330	0.330	0.000	0.000	0.000	0.000
47	A	47	HIS	0	-0.086	-0.051	13.671	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.029	0.019	14.824	0.038	0.038	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.045	0.026	16.884	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.037	-0.031	20.271	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.904	-0.956	23.126	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.042	-0.008	17.691	0.034	0.034	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.002	-0.004	20.294	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.013	0.007	14.778	0.013	0.013	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.005	0.017	17.196	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	56	TRP	0	0.065	-0.005	17.039	-0.032	-0.032	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.065	-0.035	18.055	-0.044	-0.044	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.861	0.918	19.126	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.012	0.018	14.275	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.006	0.022	17.517	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.003	-0.022	17.831	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.023	-0.010	17.469	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.764	0.858	19.772	0.229	0.229	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.017	0.014	22.335	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.050	-0.036	23.712	0.012	0.012	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.006	-0.002	23.015	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.015	-0.011	19.576	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.887	0.935	22.656	0.166	0.166	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.763	0.876	20.400	0.184	0.184	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.827	-0.903	23.452	-0.221	-0.221	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.001	0.005	25.932	0.014	0.014	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.034	0.002	27.658	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.039	0.017	28.368	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.001	-0.005	24.509	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.808	-0.905	25.249	-0.148	-0.148	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.012	0.003	26.128	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.945	0.975	22.856	0.096	0.096	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.040	-0.021	20.355	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.818	0.899	25.355	0.075	0.075	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.780	-0.870	28.291	-0.061	-0.061	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.932	0.966	22.739	0.037	0.037	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.038	-0.022	23.241	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.802	-0.899	27.080	-0.056	-0.056	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.967	-0.970	29.885	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.875	-0.910	24.887	0.008	0.008	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.015	-0.004	29.183	0.004	0.004	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.079	-0.037	26.069	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.901	-0.947	29.473	-0.047	-0.047	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.088	-0.033	27.639	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.015	0.005	31.197	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.011	-0.012	32.297	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.038	-0.028	32.116	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.055	0.028	34.741	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.016	-0.013	33.316	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.018	0.015	33.769	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.813	-0.868	26.833	-0.193	-0.193	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.024	0.011	28.335	0.008	0.008	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.941	0.977	27.714	0.117	0.117	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.071	0.055	24.440	0.010	0.010	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.020	-0.024	27.898	-0.019	-0.019	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.064	0.017	21.031	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.008	-0.013	24.496	0.006	0.006	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.853	-0.897	26.085	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.010	-0.019	24.844	0.011	0.011	0.000	0.000	0.000	0.000
105	A	105	MET	0	-0.070	-0.004	16.920	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.006	-0.006	13.844	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.874	0.937	18.312	0.039	0.039	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.035	0.035	15.050	0.016	0.016	0.000	0.000	0.000	0.000

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