FMO DATABASE

FMODB ID: G6LQ1

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	OptH
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	-927907.568728
FMO2-HF: Nuclear repulsion	882580.360238
FMO2-HF: Total energy	-45327.208489
FMO2-MP2: Total energy	-45458.747097

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.
-149.456	-148.357	6.884	-2.837	-5.144	-0.027

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 : 0.953 / q_NPA : 0.969

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	0.008	0.005	3.459	6.424	8.204	0.047	-0.627	-1.199	0.000
4	A	26	PRO	0	-0.018	0.009	6.078	0.978	0.978	0.000	0.000	0.000	0.000
5	A	27	TRP	0	0.033	0.010	8.925	2.597	2.597	0.000	0.000	0.000	0.000
6	A	28	LYS	1	0.948	0.982	12.472	15.501	15.501	0.000	0.000	0.000	0.000
7	A	29	ILE	0	-0.002	0.005	15.739	0.372	0.372	0.000	0.000	0.000	0.000
8	A	30	ASN	0	0.006	0.015	18.730	0.446	0.446	0.000	0.000	0.000	0.000
9	A	31	TRP	0	0.066	0.015	22.185	-0.179	-0.179	0.000	0.000	0.000	0.000
10	A	32	GLN	0	0.017	0.019	23.726	0.226	0.226	0.000	0.000	0.000	0.000
11	A	33	THR	0	-0.052	-0.043	25.423	0.154	0.154	0.000	0.000	0.000	0.000
12	A	34	MET	0	0.016	0.017	22.308	-0.157	-0.157	0.000	0.000	0.000	0.000
13	A	35	ALA	0	0.012	0.005	22.362	-0.377	-0.377	0.000	0.000	0.000	0.000
14	A	36	PHE	0	-0.027	-0.023	14.658	-0.380	-0.380	0.000	0.000	0.000	0.000
15	A	37	GLU	-1	-0.946	-0.971	17.877	-13.742	-13.742	0.000	0.000	0.000	0.000
16	A	38	TYR	0	-0.061	-0.047	12.049	-0.118	-0.118	0.000	0.000	0.000	0.000
17	A	39	ILE	0	0.045	0.022	10.899	-0.744	-0.744	0.000	0.000	0.000	0.000
18	A	40	GLY	0	-0.012	0.009	7.920	1.101	1.101	0.000	0.000	0.000	0.000
19	A	41	PRO	0	0.040	0.006	7.815	-0.092	-0.092	0.000	0.000	0.000	0.000
20	A	42	GLN	0	0.012	-0.003	2.959	4.440	4.937	0.019	-0.126	-0.390	0.000
21	A	43	ILE	0	0.041	0.025	6.093	-1.186	-1.186	0.000	0.000	0.000	0.000
22	A	44	GLU	-1	-0.886	-0.919	8.515	-16.789	-16.789	0.000	0.000	0.000	0.000
23	A	45	ALA	0	-0.063	-0.027	6.698	0.879	0.879	0.000	0.000	0.000	0.000
24	A	46	LEU	0	-0.022	0.000	5.887	0.530	0.530	0.000	0.000	0.000	0.000
25	A	47	LEU	0	0.015	-0.013	8.075	1.383	1.383	0.000	0.000	0.000	0.000
26	A	48	GLY	0	-0.002	-0.005	11.394	1.754	1.754	0.000	0.000	0.000	0.000
27	A	49	TRP	0	-0.053	-0.048	13.463	1.625	1.625	0.000	0.000	0.000	0.000
28	A	50	PRO	0	0.028	0.019	13.926	-0.782	-0.782	0.000	0.000	0.000	0.000
29	A	51	GLN	0	0.041	0.022	11.921	0.692	0.692	0.000	0.000	0.000	0.000
30	A	52	GLY	0	-0.042	-0.027	14.049	0.032	0.032	0.000	0.000	0.000	0.000
31	A	53	SER	0	-0.109	-0.081	16.587	0.637	0.637	0.000	0.000	0.000	0.000
32	A	54	TRP	0	0.028	0.013	13.451	0.262	0.262	0.000	0.000	0.000	0.000
33	A	55	LYS	1	0.931	0.974	17.226	13.108	13.108	0.000	0.000	0.000	0.000
34	A	56	SER	0	0.006	0.004	20.519	0.181	0.181	0.000	0.000	0.000	0.000
35	A	57	VAL	0	0.074	0.029	19.515	-0.568	-0.568	0.000	0.000	0.000	0.000
36	A	58	GLU	-1	-0.920	-0.949	20.499	-12.152	-12.152	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.847	-0.925	19.065	-14.252	-14.252	0.000	0.000	0.000	0.000
38	A	60	TRP	0	-0.051	-0.044	14.000	0.434	0.434	0.000	0.000	0.000	0.000
39	A	61	ALA	0	0.004	0.006	17.612	-0.379	-0.379	0.000	0.000	0.000	0.000
40	A	62	THR	0	-0.011	-0.004	20.185	0.393	0.393	0.000	0.000	0.000	0.000
41	A	63	ARG	1	0.826	0.924	16.354	16.514	16.514	0.000	0.000	0.000	0.000
42	A	64	MET	0	-0.012	-0.002	16.087	-1.173	-1.173	0.000	0.000	0.000	0.000
43	A	65	HIS	0	0.019	0.012	17.805	0.812	0.812	0.000	0.000	0.000	0.000
44	A	66	PRO	0	0.025	0.008	19.745	-0.047	-0.047	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.910	-0.962	22.469	-12.574	-12.574	0.000	0.000	0.000	0.000
46	A	68	ASP	-1	-0.788	-0.892	17.717	-17.409	-17.409	0.000	0.000	0.000	0.000
47	A	69	GLN	0	-0.046	-0.033	20.405	0.394	0.394	0.000	0.000	0.000	0.000
48	A	70	GLU	-1	-0.981	-0.986	21.941	-11.497	-11.497	0.000	0.000	0.000	0.000
49	A	71	TRP	0	-0.095	-0.042	16.997	0.410	0.410	0.000	0.000	0.000	0.000
50	A	72	VAL	0	0.000	0.009	16.825	0.011	0.011	0.000	0.000	0.000	0.000
51	A	73	VAL	0	0.055	0.024	19.836	-0.205	-0.205	0.000	0.000	0.000	0.000
52	A	74	ASN	0	0.010	-0.004	21.653	0.212	0.212	0.000	0.000	0.000	0.000
53	A	75	PHE	0	-0.033	-0.006	17.294	0.454	0.454	0.000	0.000	0.000	0.000
54	A	76	CYS	0	0.035	0.007	17.322	-0.246	-0.246	0.000	0.000	0.000	0.000
55	A	77	VAL	0	0.012	0.031	19.778	0.060	0.060	0.000	0.000	0.000	0.000
56	A	78	LYS	1	0.940	0.962	23.038	11.862	11.862	0.000	0.000	0.000	0.000
57	A	79	GLN	0	-0.048	-0.033	20.121	0.329	0.329	0.000	0.000	0.000	0.000
58	A	80	SER	0	0.032	0.010	20.009	-0.166	-0.166	0.000	0.000	0.000	0.000
59	A	81	GLU	-1	-0.933	-0.961	21.733	-11.169	-11.169	0.000	0.000	0.000	0.000
60	A	82	CYS	0	-0.131	-0.048	24.755	0.656	0.656	0.000	0.000	0.000	0.000
61	A	83	GLY	0	-0.028	-0.018	22.854	0.239	0.239	0.000	0.000	0.000	0.000
62	A	84	VAL	0	-0.068	-0.021	20.464	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	85	ASP	-1	-0.770	-0.869	15.902	-18.431	-18.431	0.000	0.000	0.000	0.000
64	A	86	HIS	0	-0.104	-0.066	15.747	0.365	0.365	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.924	-0.970	11.599	-27.569	-27.569	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.017	-0.005	12.641	1.786	1.786	0.000	0.000	0.000	0.000
67	A	89	ASP	-1	-0.803	-0.865	11.427	-28.578	-28.578	0.000	0.000	0.000	0.000
68	A	90	TYR	0	0.020	-0.004	12.410	1.645	1.645	0.000	0.000	0.000	0.000
69	A	91	ARG	1	0.804	0.900	12.823	14.397	14.397	0.000	0.000	0.000	0.000
70	A	92	ALA	0	0.045	0.023	12.147	1.188	1.188	0.000	0.000	0.000	0.000
71	A	93	LEU	0	-0.010	0.000	14.115	0.071	0.071	0.000	0.000	0.000	0.000
72	A	94	HIS	0	0.048	0.051	12.375	0.364	0.364	0.000	0.000	0.000	0.000
73	A	95	ARG	1	0.949	0.989	15.334	15.653	15.653	0.000	0.000	0.000	0.000
74	A	96	ASP	-1	-0.966	-0.974	16.920	-15.658	-15.658	0.000	0.000	0.000	0.000
75	A	97	GLY	0	0.021	0.010	18.820	0.642	0.642	0.000	0.000	0.000	0.000
76	A	98	HIS	1	0.790	0.881	12.975	18.765	18.765	0.000	0.000	0.000	0.000
77	A	99	TYR	0	0.045	0.005	15.837	-0.328	-0.328	0.000	0.000	0.000	0.000
78	A	100	VAL	0	-0.031	-0.020	9.142	0.077	0.077	0.000	0.000	0.000	0.000
79	A	101	TRP	0	-0.002	0.008	10.858	0.319	0.319	0.000	0.000	0.000	0.000
80	A	102	ILE	0	0.012	-0.005	7.793	-3.372	-3.372	0.000	0.000	0.000	0.000
81	A	103	ARG	1	0.771	0.865	7.134	34.390	34.390	0.000	0.000	0.000	0.000
82	A	104	ASP	-1	-0.873	-0.956	7.809	-30.301	-30.301	0.000	0.000	0.000	0.000
83	A	105	VAL	0	0.002	-0.011	8.000	1.235	1.235	0.000	0.000	0.000	0.000
84	A	106	VAL	0	-0.003	-0.011	10.319	-0.744	-0.744	0.000	0.000	0.000	0.000
85	A	107	HIS	0	-0.047	-0.024	13.378	0.991	0.991	0.000	0.000	0.000	0.000
86	A	108	VAL	0	-0.022	-0.023	15.404	0.136	0.136	0.000	0.000	0.000	0.000
87	A	109	VAL	0	-0.016	-0.004	18.451	0.173	0.173	0.000	0.000	0.000	0.000
88	A	110	ARG	1	0.905	0.946	20.954	12.482	12.482	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.712	-0.817	24.758	-10.924	-10.924	0.000	0.000	0.000	0.000
90	A	112	ASP	-1	-0.927	-0.980	27.381	-10.474	-10.474	0.000	0.000	0.000	0.000
91	A	113	SER	0	-0.190	-0.111	30.382	0.386	0.386	0.000	0.000	0.000	0.000
92	A	114	GLY	0	-0.062	-0.036	29.036	0.217	0.217	0.000	0.000	0.000	0.000
93	A	115	GLU	-1	-0.967	-0.978	28.897	-10.052	-10.052	0.000	0.000	0.000	0.000
94	A	116	VAL	0	-0.055	-0.021	22.994	-0.379	-0.379	0.000	0.000	0.000	0.000
95	A	117	GLU	-1	-0.907	-0.955	24.018	-12.084	-12.084	0.000	0.000	0.000	0.000
96	A	118	ALA	0	-0.067	-0.062	19.932	-0.083	-0.083	0.000	0.000	0.000	0.000
97	A	119	LEU	0	-0.002	0.028	16.842	-0.119	-0.119	0.000	0.000	0.000	0.000
98	A	120	ILE	0	-0.020	-0.009	14.236	-0.108	-0.108	0.000	0.000	0.000	0.000
99	A	121	GLY	0	0.062	0.030	10.842	0.243	0.243	0.000	0.000	0.000	0.000
100	A	122	PHE	0	-0.052	-0.028	5.486	-1.874	-1.874	0.000	0.000	0.000	0.000
101	A	123	MET	0	-0.016	0.020	7.221	1.397	1.397	0.000	0.000	0.000	0.000
102	A	124	PHE	0	-0.043	-0.040	1.681	-21.864	-23.804	6.811	-1.982	-2.890	-0.027
103	A	125	ASP	-1	-0.808	-0.873	3.350	-30.208	-29.689	0.008	-0.079	-0.447	0.000
104	A	126	ILE	0	-0.007	-0.015	4.504	-6.493	-6.250	-0.001	-0.023	-0.218	0.000
105	A	127	SER	0	-0.008	-0.048	6.767	5.531	5.531	0.000	0.000	0.000	0.000
106	A	128	LEU	0	-0.049	-0.030	6.115	2.584	2.584	0.000	0.000	0.000	0.000
107	A	129	GLU	-1	-0.870	-0.914	7.598	-31.129	-31.129	0.000	0.000	0.000	0.000
108	A	130	HIS	1	0.830	0.925	10.481	24.638	24.638	0.000	0.000	0.000	0.000
109	A	131	HIS	0	0.012	0.027	10.818	1.974	1.974	0.000	0.000	0.000	0.000

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