FMO DATABASE

FMODB ID: 534VZ

Calculation Name: 3IX0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IX0

Chain ID: A

ChEMBL ID:

UniProt ID: P08118

Base Structure: X-ray

Registration Date: 2023-06-19

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-555334.779892
FMO2-HF: Nuclear repulsion	517482.871781
FMO2-HF: Total energy	-37851.908111
FMO2-MP2: Total energy	-37953.367583

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:SER)

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

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.
-14.936	-19.956	19.994	-8.593	-6.384	0.023

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.035

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	TYR	0	-0.034	0.004	3.794	0.607	3.367	-0.027	-1.477	-1.257	0.003
4	A	4	PHE	0	0.016	-0.001	6.286	-0.327	-0.327	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.022	-0.011	9.825	0.047	0.047	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.056	0.031	13.151	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.047	-0.023	16.791	-0.059	-0.059	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.919	-0.960	18.830	-0.094	-0.094	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.081	-0.028	21.792	0.010	0.010	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.930	0.957	23.335	0.155	0.155	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.035	0.011	13.295	0.002	0.002	0.000	0.000	0.000	0.000
12	A	19	MET	0	-0.033	-0.018	20.226	0.009	0.009	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.724	-0.837	16.230	-0.445	-0.445	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.045	0.001	13.748	0.043	0.043	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.794	0.897	17.084	0.503	0.503	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.018	0.018	20.069	0.028	0.028	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.057	-0.027	19.641	0.053	0.053	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.949	0.968	21.213	0.162	0.162	0.000	0.000	0.000	0.000
19	A	26	HIS	1	0.829	0.885	18.319	0.382	0.382	0.000	0.000	0.000	0.000
20	A	27	PRO	0	-0.011	-0.001	21.083	0.014	0.014	0.000	0.000	0.000	0.000
21	A	28	ILE	0	0.065	0.030	20.160	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	29	ASN	0	-0.047	-0.031	18.275	0.012	0.012	0.000	0.000	0.000	0.000
23	A	30	SER	0	-0.051	-0.004	18.202	0.010	0.010	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.843	-0.895	12.425	-0.652	-0.652	0.000	0.000	0.000	0.000
25	A	32	TRP	0	-0.039	-0.034	13.815	0.069	0.069	0.000	0.000	0.000	0.000
26	A	33	GLN	0	0.072	0.042	11.841	-0.089	-0.089	0.000	0.000	0.000	0.000
27	A	34	THR	0	-0.024	-0.011	11.236	0.125	0.125	0.000	0.000	0.000	0.000
28	A	35	ASP	-1	-0.856	-0.925	13.773	-0.516	-0.516	0.000	0.000	0.000	0.000
29	A	36	ASN	0	-0.104	-0.087	10.294	0.228	0.228	0.000	0.000	0.000	0.000
30	A	37	CYS	0	-0.079	-0.013	9.570	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.831	-0.913	6.907	-1.850	-1.850	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.055	-0.050	7.177	0.403	0.403	0.000	0.000	0.000	0.000
33	A	40	CYS	0	-0.023	-0.005	8.261	-0.265	-0.265	0.000	0.000	0.000	0.000
34	A	41	THR	0	-0.003	-0.005	11.078	0.132	0.132	0.000	0.000	0.000	0.000
35	A	43	TYR	0	0.062	0.036	11.810	0.054	0.054	0.000	0.000	0.000	0.000
36	A	44	GLU	-1	-0.929	-0.986	17.473	-0.104	-0.104	0.000	0.000	0.000	0.000
37	A	45	THR	0	0.016	0.005	17.358	0.000	0.000	0.000	0.000	0.000	0.000
38	A	46	GLU	-1	-0.933	-0.964	13.439	0.032	0.032	0.000	0.000	0.000	0.000
39	A	47	ILE	0	-0.023	-0.028	13.030	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	48	SER	0	0.009	0.016	8.565	-0.078	-0.078	0.000	0.000	0.000	0.000
41	A	51	THR	0	0.000	0.005	1.880	1.970	1.678	2.876	-1.112	-1.472	0.002
42	A	52	LEU	0	0.034	0.010	4.126	-0.341	-0.169	-0.001	-0.044	-0.128	0.000
43	A	53	VAL	0	-0.047	-0.021	5.946	0.580	0.580	0.000	0.000	0.000	0.000
44	A	54	SER	0	0.010	0.015	5.808	0.560	0.560	0.000	0.000	0.000	0.000
45	A	55	THR	0	-0.027	-0.034	7.372	-0.501	-0.501	0.000	0.000	0.000	0.000
46	A	56	PRO	0	-0.022	0.025	9.458	0.168	0.168	0.000	0.000	0.000	0.000
47	A	57	VAL	0	0.014	-0.018	10.878	-0.121	-0.121	0.000	0.000	0.000	0.000
48	A	58	GLY	0	0.043	0.040	13.886	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	59	TYR	0	-0.008	-0.014	15.907	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	60	ASP	-1	-0.759	-0.860	19.906	0.072	0.072	0.000	0.000	0.000	0.000
51	A	61	LYS	1	0.909	0.942	16.422	-0.184	-0.184	0.000	0.000	0.000	0.000
52	A	62	ASP	-1	-0.864	-0.908	22.490	0.029	0.029	0.000	0.000	0.000	0.000
53	A	63	ASN	0	-0.063	-0.049	26.120	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	64	CYS	0	-0.083	-0.028	22.207	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	65	GLN	0	-0.004	-0.012	20.659	0.000	0.000	0.000	0.000	0.000	0.000
56	A	66	ARG	1	0.895	0.960	12.924	-0.068	-0.068	0.000	0.000	0.000	0.000
57	A	67	ILE	0	-0.030	-0.022	17.713	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	68	PHE	0	0.007	0.000	11.191	0.016	0.016	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.960	0.979	15.123	0.074	0.074	0.000	0.000	0.000	0.000
60	A	70	LYS	1	0.950	0.966	14.305	0.466	0.466	0.000	0.000	0.000	0.000
61	A	71	GLU	-1	-0.919	-0.960	14.886	-0.243	-0.243	0.000	0.000	0.000	0.000
62	A	72	ASP	-1	-0.845	-0.926	15.955	-0.135	-0.135	0.000	0.000	0.000	0.000
63	A	74	LYS	1	0.873	0.950	11.186	0.117	0.117	0.000	0.000	0.000	0.000
64	A	75	TYR	0	0.008	-0.002	10.083	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	76	ILE	0	-0.034	-0.003	14.313	0.031	0.031	0.000	0.000	0.000	0.000
66	A	77	VAL	0	0.034	0.000	16.707	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	78	VAL	0	-0.039	-0.004	19.193	0.007	0.007	0.000	0.000	0.000	0.000
68	A	79	GLU	-1	-0.779	-0.882	22.898	0.039	0.039	0.000	0.000	0.000	0.000
69	A	80	LYS	1	0.788	0.877	24.194	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.864	0.917	26.883	-0.037	-0.037	0.000	0.000	0.000	0.000
71	A	82	ASP	-1	-0.811	-0.902	28.754	0.000	0.000	0.000	0.000	0.000	0.000
72	A	83	PRO	0	0.025	0.015	24.855	0.006	0.006	0.000	0.000	0.000	0.000
73	A	84	LYS	1	0.913	0.953	25.187	0.019	0.019	0.000	0.000	0.000	0.000
74	A	85	LYS	1	0.843	0.925	27.335	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	86	THR	0	0.012	0.004	22.478	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	88	SER	0	0.009	0.011	21.438	0.004	0.004	0.000	0.000	0.000	0.000
77	A	89	VAL	0	-0.073	-0.044	15.449	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	90	SER	0	0.008	-0.008	18.258	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.932	-0.965	12.434	0.644	0.644	0.000	0.000	0.000	0.000
80	A	92	TRP	0	0.011	-0.018	10.649	-0.121	-0.121	0.000	0.000	0.000	0.000
81	A	93	ILE	0	0.031	0.019	5.757	0.098	0.098	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.001	-0.017	1.852	-16.284	-23.944	17.146	-5.960	-3.527	0.018

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