FMO DATABASE

FMODB ID: 3QR5L

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	OptAll
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	-763356.050183
FMO2-HF: Nuclear repulsion	724859.172629
FMO2-HF: Total energy	-38496.877554
FMO2-MP2: Total energy	-38612.708813

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.
-26.105	-20.119	19.553	-11.081	-14.458	-0.07

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 : 0.063 / q_NPA : 0.032

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	0.032	0.022	3.888	-1.533	0.456	-0.016	-1.096	-0.877	0.001
4	A	40	LYS	1	0.891	0.938	6.444	0.186	0.186	0.000	0.000	0.000	0.000
5	A	41	LEU	0	0.017	0.011	9.732	-0.013	-0.013	0.000	0.000	0.000	0.000
6	A	42	ALA	0	0.020	0.021	12.356	-0.063	-0.063	0.000	0.000	0.000	0.000
7	A	66	SER	0	0.009	-0.014	21.787	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	67	LYS	1	0.724	0.886	16.953	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	68	ASP	-1	-0.758	-0.862	22.401	0.150	0.150	0.000	0.000	0.000	0.000
10	A	69	ASN	0	-0.015	-0.014	17.841	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	70	THR	0	-0.030	-0.036	20.541	0.026	0.026	0.000	0.000	0.000	0.000
12	A	71	LEU	0	0.003	-0.004	22.877	0.015	0.015	0.000	0.000	0.000	0.000
13	A	72	THR	0	-0.059	-0.016	18.899	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	73	ILE	0	-0.022	-0.007	14.861	0.040	0.040	0.000	0.000	0.000	0.000
15	A	74	PRO	0	0.065	0.052	18.412	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	75	ASN	0	-0.010	-0.005	19.023	0.030	0.030	0.000	0.000	0.000	0.000
17	A	76	ALA	0	0.022	-0.009	17.837	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	77	TYR	0	0.012	0.012	18.657	0.028	0.028	0.000	0.000	0.000	0.000
19	A	78	ASN	0	-0.017	-0.025	15.881	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	79	LEU	0	-0.023	-0.016	12.640	0.071	0.071	0.000	0.000	0.000	0.000
21	A	80	GLN	0	-0.002	-0.001	15.234	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	81	ALA	0	-0.013	0.002	14.034	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	82	ARG	1	0.811	0.870	14.103	-0.204	-0.204	0.000	0.000	0.000	0.000
24	A	83	ALA	0	-0.008	-0.013	10.219	0.039	0.039	0.000	0.000	0.000	0.000
25	A	84	SER	0	-0.043	-0.010	11.052	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	85	VAL	0	-0.019	-0.038	5.216	0.162	0.162	0.000	0.000	0.000	0.000
27	A	86	ASP	-1	-0.771	-0.849	6.953	-0.129	-0.129	0.000	0.000	0.000	0.000
28	A	87	TRP	0	-0.039	-0.013	2.859	-3.538	-0.434	2.505	-1.767	-3.843	-0.020
29	A	88	SER	0	0.006	0.010	5.585	0.243	0.243	0.000	0.000	0.000	0.000
30	A	89	GLY	0	0.054	0.026	5.842	-0.309	-0.309	0.000	0.000	0.000	0.000
31	A	90	PRO	0	0.000	-0.012	5.675	0.389	0.389	0.000	0.000	0.000	0.000
32	A	91	ILE	0	0.049	0.024	5.342	-0.166	-0.166	0.000	0.000	0.000	0.000
33	A	92	GLU	-1	-0.804	-0.852	6.811	0.321	0.321	0.000	0.000	0.000	0.000
34	A	93	GLU	-1	-0.864	-0.913	1.808	-14.456	-15.722	13.465	-6.678	-5.521	-0.059
35	A	94	LEU	0	0.032	0.013	2.353	2.454	3.743	1.569	-1.068	-1.790	-0.002
36	A	95	THR	0	-0.007	-0.021	3.310	0.863	0.292	0.037	0.589	-0.054	0.000
37	A	96	ALA	0	-0.009	0.001	6.034	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	97	ARG	1	0.862	0.926	2.253	-6.858	-5.470	1.994	-1.055	-2.327	0.010
39	A	98	ILE	0	0.033	0.019	4.816	-1.010	-0.957	-0.001	-0.006	-0.046	0.000
40	A	99	ALA	0	0.001	0.003	7.180	-0.336	-0.336	0.000	0.000	0.000	0.000
41	A	100	LYS	1	0.961	0.976	8.062	-1.493	-1.493	0.000	0.000	0.000	0.000
42	A	101	ALA	0	-0.048	-0.017	8.174	-0.259	-0.259	0.000	0.000	0.000	0.000
43	A	102	ALA	0	0.015	0.019	9.991	-0.219	-0.219	0.000	0.000	0.000	0.000
44	A	103	HIS	0	-0.035	-0.021	12.569	-0.129	-0.129	0.000	0.000	0.000	0.000
45	A	104	PHE	0	-0.013	0.008	13.283	-0.122	-0.122	0.000	0.000	0.000	0.000
46	A	105	ARG	1	0.872	0.925	13.061	-0.267	-0.267	0.000	0.000	0.000	0.000
47	A	106	PHE	0	0.044	0.007	9.866	0.070	0.070	0.000	0.000	0.000	0.000
48	A	107	ARG	1	0.834	0.904	12.934	-0.367	-0.367	0.000	0.000	0.000	0.000
49	A	108	VAL	0	0.026	0.020	12.184	0.036	0.036	0.000	0.000	0.000	0.000
50	A	109	LEU	0	-0.029	-0.008	15.011	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	110	GLY	0	0.028	0.025	17.657	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	111	LYS	1	0.899	0.928	17.780	0.094	0.094	0.000	0.000	0.000	0.000
53	A	112	SER	0	0.038	-0.005	12.784	0.011	0.011	0.000	0.000	0.000	0.000
54	A	113	PRO	0	-0.054	-0.019	14.361	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	114	SER	0	-0.009	-0.006	16.137	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	115	VAL	0	0.011	0.018	16.222	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	116	PRO	0	0.019	0.004	10.988	0.041	0.041	0.000	0.000	0.000	0.000
58	A	117	VAL	0	0.017	0.000	11.668	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	118	LEU	0	-0.028	-0.002	9.451	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	119	ILE	0	-0.028	-0.001	6.087	0.127	0.127	0.000	0.000	0.000	0.000
61	A	120	SER	0	0.026	-0.015	8.209	-0.211	-0.211	0.000	0.000	0.000	0.000
62	A	121	ILE	0	-0.043	0.002	7.223	0.104	0.104	0.000	0.000	0.000	0.000
63	A	122	SER	0	0.022	-0.019	8.242	-0.072	-0.072	0.000	0.000	0.000	0.000
64	A	123	THR	0	-0.014	-0.003	10.799	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	124	LYS	1	0.872	0.912	11.819	0.063	0.063	0.000	0.000	0.000	0.000
66	A	125	ASP	-1	-0.783	-0.868	14.487	0.242	0.242	0.000	0.000	0.000	0.000
67	A	126	GLU	-1	-0.790	-0.850	13.241	0.242	0.242	0.000	0.000	0.000	0.000
68	A	127	SER	0	-0.044	-0.033	13.367	0.066	0.066	0.000	0.000	0.000	0.000
69	A	128	LEU	0	-0.015	-0.013	9.094	0.042	0.042	0.000	0.000	0.000	0.000
70	A	129	ALA	0	-0.009	-0.002	11.913	0.033	0.033	0.000	0.000	0.000	0.000
71	A	130	GLU	-1	-0.801	-0.888	14.632	0.250	0.250	0.000	0.000	0.000	0.000
72	A	131	ILE	0	-0.007	0.003	8.404	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	132	LEU	0	-0.024	-0.022	9.424	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	133	ARG	1	0.803	0.884	11.765	-0.322	-0.322	0.000	0.000	0.000	0.000
75	A	134	ASP	-1	-0.826	-0.897	12.600	0.101	0.101	0.000	0.000	0.000	0.000
76	A	135	ILE	0	0.015	0.002	7.419	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	136	ASP	-1	-0.769	-0.877	11.612	0.134	0.134	0.000	0.000	0.000	0.000
78	A	137	TYR	0	-0.017	-0.030	14.599	-0.051	-0.051	0.000	0.000	0.000	0.000
79	A	138	GLN	0	-0.019	-0.023	11.460	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	139	ALA	0	-0.020	-0.006	13.301	-0.054	-0.054	0.000	0.000	0.000	0.000
81	A	140	GLY	0	0.033	0.020	14.789	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	141	LYS	1	0.961	0.959	18.574	0.000	0.000	0.000	0.000	0.000	0.000
83	A	142	LYS	1	0.823	0.926	15.253	0.060	0.060	0.000	0.000	0.000	0.000
84	A	143	ALA	0	-0.034	-0.020	14.383	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	144	SER	0	-0.001	0.000	16.376	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	145	ILE	0	-0.019	0.002	10.946	0.018	0.018	0.000	0.000	0.000	0.000
87	A	146	HIS	0	0.028	0.016	15.204	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	147	VAL	0	-0.003	-0.010	14.677	0.073	0.073	0.000	0.000	0.000	0.000
89	A	148	TYR	0	-0.039	-0.040	17.310	-0.059	-0.059	0.000	0.000	0.000	0.000
90	A	149	PRO	0	0.037	0.011	19.817	0.023	0.023	0.000	0.000	0.000	0.000
91	A	150	ASN	0	0.009	-0.005	20.805	0.019	0.019	0.000	0.000	0.000	0.000
92	A	151	SER	0	-0.004	0.002	22.065	0.000	0.000	0.000	0.000	0.000	0.000
93	A	152	GLN	0	0.061	0.043	17.974	0.046	0.046	0.000	0.000	0.000	0.000
94	A	153	VAL	0	-0.045	-0.007	16.185	0.038	0.038	0.000	0.000	0.000	0.000
95	A	154	VAL	0	0.032	0.022	11.167	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	155	GLU	-1	-0.758	-0.847	14.087	0.288	0.288	0.000	0.000	0.000	0.000
97	A	156	LEU	0	0.016	0.025	10.900	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	157	ARG	1	0.910	0.935	13.660	-0.235	-0.235	0.000	0.000	0.000	0.000
99	A	158	TYR	0	-0.010	-0.054	11.304	-0.034	-0.034	0.000	0.000	0.000	0.000
100	A	159	ALA	0	0.037	0.029	17.037	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	160	LYS	1	0.765	0.869	17.752	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	161	ILE	0	0.044	0.031	21.624	0.007	0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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