FMO DATABASE

FMODB ID: J3GZ9

Calculation Name: 3ADY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ADY

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZS45

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-764394.530331
FMO2-HF: Nuclear repulsion	725897.915058
FMO2-HF: Total energy	-38496.615272
FMO2-MP2: Total energy	-38612.48335

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:37:ALA)

Summations of interaction energy for fragment #1(A:37:ALA)

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.
-20.61	-21.095	27.558	-11.94	-15.131	-0.074

Interaction energy analysis for fragmet #1(A:37:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.022

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	39	ILE	0	0.020	0.016	3.822	-1.794	0.576	-0.026	-1.318	-1.025	0.001
4	A	40	LYS	1	0.899	0.936	6.469	0.459	0.459	0.000	0.000	0.000	0.000
5	A	41	LEU	0	0.002	0.008	9.476	0.021	0.021	0.000	0.000	0.000	0.000
6	A	42	ALA	0	0.029	0.024	12.142	-0.049	-0.049	0.000	0.000	0.000	0.000
7	A	66	SER	0	0.016	-0.010	21.350	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	67	LYS	1	0.715	0.876	16.253	-0.182	-0.182	0.000	0.000	0.000	0.000
9	A	68	ASP	-1	-0.774	-0.874	21.558	0.151	0.151	0.000	0.000	0.000	0.000
10	A	69	ASN	0	-0.008	-0.016	17.582	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	70	THR	0	-0.014	-0.025	20.427	0.024	0.024	0.000	0.000	0.000	0.000
12	A	71	LEU	0	-0.004	-0.007	22.797	0.012	0.012	0.000	0.000	0.000	0.000
13	A	72	THR	0	-0.016	0.000	18.897	0.004	0.004	0.000	0.000	0.000	0.000
14	A	73	ILE	0	-0.037	-0.003	14.708	0.041	0.041	0.000	0.000	0.000	0.000
15	A	74	PRO	0	0.054	0.055	18.289	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	75	ASN	0	-0.010	-0.011	18.688	0.029	0.029	0.000	0.000	0.000	0.000
17	A	76	ALA	0	0.030	-0.006	17.268	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	77	TYR	0	0.010	0.011	18.146	0.024	0.024	0.000	0.000	0.000	0.000
19	A	78	ASN	0	0.026	-0.002	15.465	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	79	LEU	0	-0.045	-0.020	12.128	0.046	0.046	0.000	0.000	0.000	0.000
21	A	80	GLN	0	-0.003	0.003	14.774	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	81	ALA	0	-0.011	0.005	13.702	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	82	ARG	1	0.820	0.881	13.944	-0.158	-0.158	0.000	0.000	0.000	0.000
24	A	83	ALA	0	-0.021	-0.020	9.760	0.027	0.027	0.000	0.000	0.000	0.000
25	A	84	SER	0	-0.022	0.016	10.924	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	85	VAL	0	-0.032	-0.042	5.045	0.063	0.063	0.000	0.000	0.000	0.000
27	A	86	ASP	-1	-0.786	-0.883	7.006	-0.194	-0.194	0.000	0.000	0.000	0.000
28	A	87	TRP	0	-0.063	-0.024	3.011	-3.195	0.026	0.921	-1.426	-2.717	-0.015
29	A	88	SER	0	0.010	0.021	5.958	0.268	0.268	0.000	0.000	0.000	0.000
30	A	89	GLY	0	0.059	0.024	6.330	-0.323	-0.323	0.000	0.000	0.000	0.000
31	A	90	PRO	0	-0.005	-0.016	5.847	0.386	0.386	0.000	0.000	0.000	0.000
32	A	91	ILE	0	0.060	0.029	5.029	-0.247	-0.142	-0.001	-0.002	-0.101	0.000
33	A	92	GLU	-1	-0.827	-0.883	6.287	0.611	0.611	0.000	0.000	0.000	0.000
34	A	93	GLU	-1	-0.851	-0.915	1.884	-15.226	-17.559	14.577	-7.171	-5.073	-0.061
35	A	94	LEU	0	0.024	0.003	1.985	3.556	2.703	9.783	-5.305	-3.625	-0.002
36	A	95	THR	0	-0.022	-0.026	2.904	4.783	0.243	0.136	4.559	-0.154	-0.002
37	A	96	ALA	0	-0.002	0.008	5.810	-0.122	-0.122	0.000	0.000	0.000	0.000
38	A	97	ARG	1	0.908	0.949	2.206	-5.796	-4.378	2.169	-1.244	-2.343	0.005
39	A	98	ILE	0	0.011	0.009	4.291	-1.210	-1.083	-0.001	-0.033	-0.093	0.000
40	A	99	ALA	0	0.019	0.009	6.513	-0.356	-0.356	0.000	0.000	0.000	0.000
41	A	100	LYS	1	0.946	0.976	7.638	-1.349	-1.349	0.000	0.000	0.000	0.000
42	A	101	ALA	0	-0.052	-0.022	7.775	-0.267	-0.267	0.000	0.000	0.000	0.000
43	A	102	ALA	0	0.006	0.016	9.533	-0.191	-0.191	0.000	0.000	0.000	0.000
44	A	103	HIS	0	-0.024	-0.009	12.192	-0.098	-0.098	0.000	0.000	0.000	0.000
45	A	104	PHE	0	-0.001	0.005	12.569	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	105	ARG	1	0.886	0.946	12.587	-0.274	-0.274	0.000	0.000	0.000	0.000
47	A	106	PHE	0	0.040	0.010	9.631	0.066	0.066	0.000	0.000	0.000	0.000
48	A	107	ARG	1	0.845	0.908	12.494	-0.379	-0.379	0.000	0.000	0.000	0.000
49	A	108	VAL	0	0.026	0.018	11.847	0.014	0.014	0.000	0.000	0.000	0.000
50	A	109	LEU	0	-0.048	-0.014	14.571	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	110	GLY	0	0.038	0.021	17.370	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	111	LYS	1	0.903	0.936	17.977	0.021	0.021	0.000	0.000	0.000	0.000
53	A	112	SER	0	0.050	0.014	12.835	0.000	0.000	0.000	0.000	0.000	0.000
54	A	113	PRO	0	-0.051	-0.022	14.212	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	114	SER	0	-0.041	-0.003	16.153	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	115	VAL	0	0.049	0.027	16.550	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	116	PRO	0	0.019	-0.001	11.162	0.039	0.039	0.000	0.000	0.000	0.000
58	A	117	VAL	0	-0.002	-0.005	11.763	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	118	LEU	0	-0.038	-0.012	9.456	-0.024	-0.024	0.000	0.000	0.000	0.000
60	A	119	ILE	0	-0.014	0.006	5.995	0.105	0.105	0.000	0.000	0.000	0.000
61	A	120	SER	0	0.031	-0.013	8.338	-0.194	-0.194	0.000	0.000	0.000	0.000
62	A	121	ILE	0	-0.038	-0.001	6.864	0.103	0.103	0.000	0.000	0.000	0.000
63	A	122	SER	0	0.034	0.001	8.359	-0.079	-0.079	0.000	0.000	0.000	0.000
64	A	123	THR	0	0.000	0.002	10.314	0.010	0.010	0.000	0.000	0.000	0.000
65	A	124	LYS	1	0.885	0.922	11.553	0.118	0.118	0.000	0.000	0.000	0.000
66	A	125	ASP	-1	-0.809	-0.890	14.167	0.170	0.170	0.000	0.000	0.000	0.000
67	A	126	GLU	-1	-0.800	-0.871	12.534	0.198	0.198	0.000	0.000	0.000	0.000
68	A	127	SER	0	-0.024	-0.009	13.195	0.048	0.048	0.000	0.000	0.000	0.000
69	A	128	LEU	0	0.007	-0.011	8.773	0.043	0.043	0.000	0.000	0.000	0.000
70	A	129	ALA	0	-0.010	-0.008	11.442	0.051	0.051	0.000	0.000	0.000	0.000
71	A	130	GLU	-1	-0.833	-0.907	14.172	0.232	0.232	0.000	0.000	0.000	0.000
72	A	131	ILE	0	-0.003	0.005	7.839	0.001	0.001	0.000	0.000	0.000	0.000
73	A	132	LEU	0	-0.031	-0.024	8.914	0.005	0.005	0.000	0.000	0.000	0.000
74	A	133	ARG	1	0.837	0.906	11.288	-0.304	-0.304	0.000	0.000	0.000	0.000
75	A	134	ASP	-1	-0.849	-0.897	11.856	0.105	0.105	0.000	0.000	0.000	0.000
76	A	135	ILE	0	0.006	-0.015	7.018	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	136	ASP	-1	-0.785	-0.890	11.104	0.181	0.181	0.000	0.000	0.000	0.000
78	A	137	TYR	0	-0.027	-0.026	13.995	-0.049	-0.049	0.000	0.000	0.000	0.000
79	A	138	GLN	0	-0.014	-0.016	11.240	-0.082	-0.082	0.000	0.000	0.000	0.000
80	A	139	ALA	0	-0.035	-0.004	12.840	-0.046	-0.046	0.000	0.000	0.000	0.000
81	A	140	GLY	0	0.017	0.001	14.472	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	141	LYS	1	0.957	0.954	18.184	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	142	LYS	1	0.870	0.954	15.458	0.028	0.028	0.000	0.000	0.000	0.000
84	A	143	ALA	0	0.007	-0.005	13.980	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	144	SER	0	0.008	0.009	16.042	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	145	ILE	0	0.000	0.017	10.519	0.030	0.030	0.000	0.000	0.000	0.000
87	A	146	HIS	0	0.007	-0.006	14.787	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	147	VAL	0	0.005	0.002	14.277	0.073	0.073	0.000	0.000	0.000	0.000
89	A	148	TYR	0	-0.041	-0.033	16.885	-0.061	-0.061	0.000	0.000	0.000	0.000
90	A	149	PRO	0	0.050	0.012	19.146	0.028	0.028	0.000	0.000	0.000	0.000
91	A	150	ASN	0	0.009	0.006	20.476	0.009	0.009	0.000	0.000	0.000	0.000
92	A	151	SER	0	-0.018	-0.011	21.435	0.006	0.006	0.000	0.000	0.000	0.000
93	A	152	GLN	0	0.050	0.028	17.450	0.041	0.041	0.000	0.000	0.000	0.000
94	A	153	VAL	0	-0.048	-0.019	15.909	0.039	0.039	0.000	0.000	0.000	0.000
95	A	154	VAL	0	0.026	0.018	10.704	-0.035	-0.035	0.000	0.000	0.000	0.000
96	A	155	GLU	-1	-0.783	-0.888	13.480	0.332	0.332	0.000	0.000	0.000	0.000
97	A	156	LEU	0	0.023	0.045	10.367	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	157	ARG	1	0.902	0.925	13.401	-0.252	-0.252	0.000	0.000	0.000	0.000
99	A	158	TYR	0	-0.002	-0.032	11.087	-0.049	-0.049	0.000	0.000	0.000	0.000
100	A	159	ALA	0	-0.010	0.008	16.760	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	160	LYS	1	0.785	0.870	17.115	-0.060	-0.060	0.000	0.000	0.000	0.000
102	A	161	ILE	0	0.022	0.026	20.887	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:ALA)