FMO DATABASE

FMODB ID: N9V3Q

Calculation Name: 3H9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H9W

Chain ID: A

ChEMBL ID:

UniProt ID: A1U4R9

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	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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-928755.695057
FMO2-HF: Nuclear repulsion	883427.83807
FMO2-HF: Total energy	-45327.856987
FMO2-MP2: Total energy	-45459.368129

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:23:LYS)

Summations of interaction energy for fragment #1(A:23:LYS)

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.
-173.091	-165.377	3.933	-4.306	-7.342	-0.044

Interaction energy analysis for fragmet #1(A:23:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.939 / q_NPA : 0.960

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	25	ILE	0	-0.011	-0.002	3.386	3.858	5.135	0.018	-0.400	-0.895	0.001
4	A	26	PRO	0	-0.012	0.010	6.495	1.117	1.117	0.000	0.000	0.000	0.000
5	A	27	TRP	0	-0.022	-0.041	9.356	2.068	2.068	0.000	0.000	0.000	0.000
6	A	28	LYS	1	0.806	0.899	12.835	14.023	14.023	0.000	0.000	0.000	0.000
7	A	29	ILE	0	-0.016	0.001	16.475	0.340	0.340	0.000	0.000	0.000	0.000
8	A	30	ASN	0	0.015	0.006	19.051	0.529	0.529	0.000	0.000	0.000	0.000
9	A	31	TRP	0	0.031	0.001	22.652	-0.181	-0.181	0.000	0.000	0.000	0.000
10	A	32	GLN	0	-0.027	-0.013	24.356	0.418	0.418	0.000	0.000	0.000	0.000
11	A	33	THR	0	-0.055	-0.049	25.834	0.268	0.268	0.000	0.000	0.000	0.000
12	A	34	MET	0	0.002	0.018	23.084	-0.261	-0.261	0.000	0.000	0.000	0.000
13	A	35	ALA	0	0.036	0.022	22.209	-0.488	-0.488	0.000	0.000	0.000	0.000
14	A	36	PHE	0	-0.032	-0.028	14.655	-0.347	-0.347	0.000	0.000	0.000	0.000
15	A	37	GLU	-1	-0.819	-0.890	19.179	-13.205	-13.205	0.000	0.000	0.000	0.000
16	A	38	TYR	0	-0.062	-0.030	12.745	0.512	0.512	0.000	0.000	0.000	0.000
17	A	39	ILE	0	0.049	0.027	11.017	-0.617	-0.617	0.000	0.000	0.000	0.000
18	A	40	GLY	0	-0.003	0.021	8.724	1.073	1.073	0.000	0.000	0.000	0.000
19	A	41	PRO	0	0.023	0.001	8.856	-0.710	-0.710	0.000	0.000	0.000	0.000
20	A	42	GLN	0	-0.013	-0.029	3.612	3.576	3.851	0.005	-0.044	-0.236	0.000
21	A	43	ILE	0	0.043	0.028	6.066	-1.798	-1.798	0.000	0.000	0.000	0.000
22	A	44	GLU	-1	-0.895	-0.921	8.750	-17.090	-17.090	0.000	0.000	0.000	0.000
23	A	45	ALA	0	-0.052	-0.031	6.405	0.707	0.707	0.000	0.000	0.000	0.000
24	A	46	LEU	0	-0.023	0.000	4.870	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	47	LEU	0	0.016	-0.006	7.771	0.966	0.966	0.000	0.000	0.000	0.000
26	A	48	GLY	0	0.005	0.011	11.454	1.789	1.789	0.000	0.000	0.000	0.000
27	A	49	TRP	0	-0.049	-0.052	13.583	1.834	1.834	0.000	0.000	0.000	0.000
28	A	50	PRO	0	0.026	0.012	13.945	-0.832	-0.832	0.000	0.000	0.000	0.000
29	A	51	GLN	0	0.016	0.017	12.175	0.644	0.644	0.000	0.000	0.000	0.000
30	A	52	GLY	0	0.002	-0.001	14.052	0.150	0.150	0.000	0.000	0.000	0.000
31	A	53	SER	0	-0.079	-0.063	16.693	0.734	0.734	0.000	0.000	0.000	0.000
32	A	54	TRP	0	0.016	0.020	13.449	0.290	0.290	0.000	0.000	0.000	0.000
33	A	55	LYS	1	0.871	0.925	17.578	13.398	13.398	0.000	0.000	0.000	0.000
34	A	56	SER	0	0.016	0.017	20.632	0.269	0.269	0.000	0.000	0.000	0.000
35	A	57	VAL	0	0.079	0.022	19.254	-0.678	-0.678	0.000	0.000	0.000	0.000
36	A	58	GLU	-1	-0.905	-0.942	20.338	-12.045	-12.045	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.822	-0.886	18.636	-14.446	-14.446	0.000	0.000	0.000	0.000
38	A	60	TRP	0	-0.057	-0.043	13.864	0.455	0.455	0.000	0.000	0.000	0.000
39	A	61	ALA	0	0.027	0.025	17.006	-0.495	-0.495	0.000	0.000	0.000	0.000
40	A	62	THR	0	-0.015	-0.022	19.705	0.205	0.205	0.000	0.000	0.000	0.000
41	A	63	ARG	1	0.721	0.854	16.035	16.388	16.388	0.000	0.000	0.000	0.000
42	A	64	MET	0	0.000	0.008	15.186	-1.323	-1.323	0.000	0.000	0.000	0.000
43	A	65	HIS	0	0.008	0.000	16.909	0.871	0.871	0.000	0.000	0.000	0.000
44	A	66	PRO	0	0.016	0.007	18.838	-0.044	-0.044	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.809	-0.891	20.629	-14.187	-14.187	0.000	0.000	0.000	0.000
46	A	68	ASP	-1	-0.776	-0.872	16.056	-18.233	-18.233	0.000	0.000	0.000	0.000
47	A	69	GLN	0	-0.038	-0.026	19.009	0.491	0.491	0.000	0.000	0.000	0.000
48	A	70	GLU	-1	-0.959	-0.968	21.120	-11.713	-11.713	0.000	0.000	0.000	0.000
49	A	71	TRP	0	-0.079	-0.036	15.405	0.431	0.431	0.000	0.000	0.000	0.000
50	A	72	VAL	0	0.005	0.007	15.503	0.072	0.072	0.000	0.000	0.000	0.000
51	A	73	VAL	0	0.031	0.005	18.523	-0.092	-0.092	0.000	0.000	0.000	0.000
52	A	74	ASN	0	-0.035	-0.022	20.717	0.388	0.388	0.000	0.000	0.000	0.000
53	A	75	PHE	0	-0.015	-0.007	17.033	0.521	0.521	0.000	0.000	0.000	0.000
54	A	76	CYS	0	0.020	0.011	16.138	0.052	0.052	0.000	0.000	0.000	0.000
55	A	77	VAL	0	0.036	0.050	19.470	0.194	0.194	0.000	0.000	0.000	0.000
56	A	78	LYS	1	0.818	0.908	22.883	11.820	11.820	0.000	0.000	0.000	0.000
57	A	79	GLN	0	0.021	0.013	20.149	0.733	0.733	0.000	0.000	0.000	0.000
58	A	80	SER	0	0.010	-0.019	20.746	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	81	GLU	-1	-0.859	-0.923	22.686	-10.962	-10.962	0.000	0.000	0.000	0.000
60	A	82	CYS	0	-0.129	-0.061	25.396	0.596	0.596	0.000	0.000	0.000	0.000
61	A	83	GLY	0	0.044	0.011	23.802	0.238	0.238	0.000	0.000	0.000	0.000
62	A	84	VAL	0	-0.069	-0.020	21.137	0.102	0.102	0.000	0.000	0.000	0.000
63	A	85	ASP	-1	-0.763	-0.858	16.873	-17.071	-17.071	0.000	0.000	0.000	0.000
64	A	86	HIS	0	-0.102	-0.062	16.422	0.054	0.054	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.909	-0.963	11.359	-28.704	-28.704	0.000	0.000	0.000	0.000
66	A	88	ALA	0	0.004	-0.003	11.999	1.753	1.753	0.000	0.000	0.000	0.000
67	A	89	ASP	-1	-0.803	-0.875	10.209	-31.217	-31.217	0.000	0.000	0.000	0.000
68	A	90	TYR	0	-0.055	-0.065	10.858	1.962	1.962	0.000	0.000	0.000	0.000
69	A	91	ARG	1	0.716	0.822	11.303	14.679	14.679	0.000	0.000	0.000	0.000
70	A	92	ALA	0	0.056	0.036	11.018	1.520	1.520	0.000	0.000	0.000	0.000
71	A	93	LEU	0	-0.016	-0.007	13.063	0.077	0.077	0.000	0.000	0.000	0.000
72	A	94	HIS	0	0.037	0.029	11.683	0.421	0.421	0.000	0.000	0.000	0.000
73	A	95	ARG	1	0.929	0.981	14.688	15.838	15.838	0.000	0.000	0.000	0.000
74	A	96	ASP	-1	-0.935	-0.956	16.300	-16.364	-16.364	0.000	0.000	0.000	0.000
75	A	97	GLY	0	0.025	0.020	18.255	0.809	0.809	0.000	0.000	0.000	0.000
76	A	98	HIS	1	0.778	0.871	12.139	20.122	20.122	0.000	0.000	0.000	0.000
77	A	99	TYR	0	0.047	0.013	14.780	-0.338	-0.338	0.000	0.000	0.000	0.000
78	A	100	VAL	0	-0.047	-0.031	8.346	0.012	0.012	0.000	0.000	0.000	0.000
79	A	101	TRP	0	0.015	0.008	9.356	0.863	0.863	0.000	0.000	0.000	0.000
80	A	102	ILE	0	0.019	-0.003	6.630	-4.622	-4.622	0.000	0.000	0.000	0.000
81	A	103	ARG	1	0.795	0.865	6.004	38.359	38.359	0.000	0.000	0.000	0.000
82	A	104	ASP	-1	-0.766	-0.881	6.959	-29.627	-29.627	0.000	0.000	0.000	0.000
83	A	105	VAL	0	0.010	0.000	8.469	1.639	1.639	0.000	0.000	0.000	0.000
84	A	106	VAL	0	-0.013	-0.005	11.095	-0.451	-0.451	0.000	0.000	0.000	0.000
85	A	107	HIS	0	-0.068	-0.055	14.345	0.928	0.928	0.000	0.000	0.000	0.000
86	A	108	VAL	0	-0.025	-0.019	16.758	0.075	0.075	0.000	0.000	0.000	0.000
87	A	109	VAL	0	0.003	0.011	19.597	0.457	0.457	0.000	0.000	0.000	0.000
88	A	110	ARG	1	0.819	0.904	22.147	12.222	12.222	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.785	-0.865	25.942	-10.477	-10.477	0.000	0.000	0.000	0.000
90	A	112	ASP	-1	-0.942	-0.981	28.911	-10.026	-10.026	0.000	0.000	0.000	0.000
91	A	113	SER	0	-0.112	-0.075	31.887	0.363	0.363	0.000	0.000	0.000	0.000
92	A	114	GLY	0	-0.057	-0.020	30.046	0.195	0.195	0.000	0.000	0.000	0.000
93	A	115	GLU	-1	-0.969	-0.978	29.616	-9.910	-9.910	0.000	0.000	0.000	0.000
94	A	116	VAL	0	-0.013	-0.009	23.955	-0.299	-0.299	0.000	0.000	0.000	0.000
95	A	117	GLU	-1	-0.860	-0.919	23.897	-12.628	-12.628	0.000	0.000	0.000	0.000
96	A	118	ALA	0	-0.049	-0.049	20.809	-0.026	-0.026	0.000	0.000	0.000	0.000
97	A	119	LEU	0	0.013	0.025	17.654	-0.095	-0.095	0.000	0.000	0.000	0.000
98	A	120	ILE	0	0.008	-0.003	15.438	-0.137	-0.137	0.000	0.000	0.000	0.000
99	A	121	GLY	0	0.058	0.023	12.265	0.133	0.133	0.000	0.000	0.000	0.000
100	A	122	PHE	0	-0.059	-0.031	6.686	-0.591	-0.591	0.000	0.000	0.000	0.000
101	A	123	MET	0	0.023	0.047	7.215	-0.187	-0.187	0.000	0.000	0.000	0.000
102	A	124	PHE	0	-0.041	-0.041	2.223	-13.896	-12.051	1.370	-0.992	-2.224	-0.008
103	A	125	ASP	-1	-0.810	-0.886	2.597	-42.158	-40.488	0.440	-0.595	-1.515	-0.006
104	A	126	ILE	0	-0.012	0.001	2.375	-23.074	-20.448	2.101	-2.274	-2.453	-0.031
105	A	127	SER	0	-0.014	-0.043	5.132	7.589	7.610	-0.001	-0.001	-0.019	0.000
106	A	128	LEU	0	-0.051	-0.032	4.845	3.631	3.631	0.000	0.000	0.000	0.000
107	A	129	GLU	-1	-0.872	-0.905	6.165	-38.946	-38.946	0.000	0.000	0.000	0.000
108	A	130	HIS	1	0.808	0.908	9.275	28.758	28.758	0.000	0.000	0.000	0.000
109	A	131	HIS	0	-0.018	0.020	9.866	3.022	3.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:LYS)