FMO DATABASE

FMODB ID: 1764Z

Calculation Name: 3H3M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H3M

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSideSolv
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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-564781.256062
FMO2-HF: Nuclear repulsion	529800.581564
FMO2-HF: Total energy	-34980.674498
FMO2-MP2: Total energy	-35082.551822

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:18:ALA)

Summations of interaction energy for fragment #1(A:18: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.
-2.082	2.201	0.17	-1.726	-2.727	0.002

Interaction energy analysis for fragmet #1(A:18:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.026

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	20	VAL	0	0.042	0.023	3.431	-1.744	0.877	-0.003	-1.359	-1.260	0.003
4	A	21	LEU	0	-0.017	-0.014	2.726	-0.070	0.893	0.171	-0.269	-0.866	-0.001
5	A	22	GLU	-1	-0.919	-0.948	5.039	-2.311	-2.141	-0.001	-0.016	-0.152	0.000
6	A	23	ILE	0	0.004	-0.001	7.172	0.593	0.593	0.000	0.000	0.000	0.000
7	A	24	TYR	0	-0.024	-0.038	7.352	0.336	0.336	0.000	0.000	0.000	0.000
8	A	25	GLN	0	-0.011	-0.007	8.975	0.230	0.230	0.000	0.000	0.000	0.000
9	A	26	ASP	-1	-0.851	-0.933	10.750	-0.780	-0.780	0.000	0.000	0.000	0.000
10	A	27	ILE	0	-0.004	0.001	12.888	0.152	0.152	0.000	0.000	0.000	0.000
11	A	28	ALA	0	0.047	0.037	13.805	0.116	0.116	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.030	-0.001	13.328	0.126	0.126	0.000	0.000	0.000	0.000
13	A	30	LEU	0	-0.057	-0.018	16.702	0.076	0.076	0.000	0.000	0.000	0.000
14	A	31	THR	0	0.014	-0.006	17.942	0.057	0.057	0.000	0.000	0.000	0.000
15	A	32	SER	0	-0.007	-0.008	18.582	0.051	0.051	0.000	0.000	0.000	0.000
16	A	33	ARG	1	0.755	0.853	17.944	0.475	0.475	0.000	0.000	0.000	0.000
17	A	34	MET	0	-0.057	-0.024	21.932	0.033	0.033	0.000	0.000	0.000	0.000
18	A	35	LEU	0	0.031	0.013	24.034	0.026	0.026	0.000	0.000	0.000	0.000
19	A	36	ALA	0	-0.003	0.000	25.374	0.021	0.021	0.000	0.000	0.000	0.000
20	A	37	ALA	0	-0.019	-0.015	27.306	0.017	0.017	0.000	0.000	0.000	0.000
21	A	38	ALA	0	0.038	0.017	28.719	0.015	0.015	0.000	0.000	0.000	0.000
22	A	39	ASN	0	-0.041	-0.013	29.731	0.019	0.019	0.000	0.000	0.000	0.000
23	A	40	ALA	0	-0.073	-0.020	31.511	0.011	0.011	0.000	0.000	0.000	0.000
24	A	41	SER	0	-0.019	-0.020	33.596	0.008	0.008	0.000	0.000	0.000	0.000
25	A	42	ASN	0	-0.030	-0.007	32.091	0.005	0.005	0.000	0.000	0.000	0.000
26	A	43	TRP	0	0.072	0.013	31.885	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	44	ASP	-1	-0.855	-0.932	31.913	-0.141	-0.141	0.000	0.000	0.000	0.000
28	A	45	LEU	0	-0.045	-0.008	28.011	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	46	VAL	0	-0.028	-0.013	27.152	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	47	LEU	0	0.018	-0.007	27.052	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	48	ASN	0	-0.033	-0.005	27.801	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	49	HIS	0	0.004	-0.010	23.660	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	50	GLY	0	0.060	0.024	23.067	-0.029	-0.029	0.000	0.000	0.000	0.000
34	A	51	GLN	0	-0.059	-0.031	23.617	0.000	0.000	0.000	0.000	0.000	0.000
35	A	52	GLU	-1	-0.757	-0.845	18.836	-0.454	-0.454	0.000	0.000	0.000	0.000
36	A	53	TYR	0	-0.037	-0.036	19.129	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	54	VAL	0	0.005	-0.001	18.747	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	55	CYS	0	-0.061	-0.026	19.040	0.008	0.008	0.000	0.000	0.000	0.000
39	A	56	LEU	0	0.018	0.007	14.617	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.021	0.011	14.315	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	58	GLU	-1	-0.825	-0.887	15.391	-0.258	-0.258	0.000	0.000	0.000	0.000
42	A	59	ARG	1	0.849	0.935	10.836	0.508	0.508	0.000	0.000	0.000	0.000
43	A	60	LEU	0	-0.010	-0.024	9.995	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	61	ARG	1	0.814	0.873	11.279	0.287	0.287	0.000	0.000	0.000	0.000
45	A	62	GLU	-1	-0.929	-0.948	12.754	-0.305	-0.305	0.000	0.000	0.000	0.000
46	A	63	LEU	0	-0.097	-0.047	6.728	0.023	0.023	0.000	0.000	0.000	0.000
47	A	64	GLU	-1	-0.782	-0.812	8.179	-0.398	-0.398	0.000	0.000	0.000	0.000
48	A	65	PRO	0	-0.050	-0.054	10.276	0.025	0.025	0.000	0.000	0.000	0.000
49	A	66	GLY	0	-0.035	0.006	9.176	0.027	0.027	0.000	0.000	0.000	0.000
50	A	67	GLU	-1	-0.872	-0.954	6.522	0.266	0.266	0.000	0.000	0.000	0.000
51	A	68	PRO	0	-0.079	-0.048	7.328	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	69	LEU	0	0.041	0.014	3.731	-0.137	0.070	0.004	-0.033	-0.178	0.000
53	A	70	ASP	-1	-0.869	-0.954	4.134	2.117	2.369	0.000	-0.041	-0.210	0.000
54	A	71	GLU	-1	-0.937	-0.948	7.265	0.180	0.180	0.000	0.000	0.000	0.000
55	A	72	ALA	0	0.016	0.005	8.197	-0.128	-0.128	0.000	0.000	0.000	0.000
56	A	73	ALA	0	0.025	0.001	4.254	-0.308	-0.238	-0.001	-0.008	-0.061	0.000
57	A	74	ARG	1	0.819	0.906	6.380	-0.571	-0.571	0.000	0.000	0.000	0.000
58	A	75	GLY	0	0.046	0.019	8.888	-0.111	-0.111	0.000	0.000	0.000	0.000
59	A	76	MET	0	0.038	0.034	6.494	-0.236	-0.236	0.000	0.000	0.000	0.000
60	A	77	LYS	1	0.860	0.929	7.234	0.403	0.403	0.000	0.000	0.000	0.000
61	A	78	PHE	0	-0.046	-0.024	9.133	0.042	0.042	0.000	0.000	0.000	0.000
62	A	79	ASP	-1	-0.860	-0.931	12.554	-0.263	-0.263	0.000	0.000	0.000	0.000
63	A	80	LEU	0	-0.033	-0.014	8.855	0.023	0.023	0.000	0.000	0.000	0.000
64	A	81	LEU	0	-0.009	-0.009	12.213	0.046	0.046	0.000	0.000	0.000	0.000
65	A	82	VAL	0	-0.002	0.011	14.503	0.040	0.040	0.000	0.000	0.000	0.000
66	A	83	ARG	1	0.853	0.914	15.926	0.330	0.330	0.000	0.000	0.000	0.000
67	A	84	ILE	0	-0.024	-0.004	13.497	0.025	0.025	0.000	0.000	0.000	0.000
68	A	85	LEU	0	0.000	-0.010	17.700	0.039	0.039	0.000	0.000	0.000	0.000
69	A	86	GLU	-1	-0.865	-0.913	20.165	-0.211	-0.211	0.000	0.000	0.000	0.000
70	A	87	ASN	0	-0.056	-0.038	19.370	0.049	0.049	0.000	0.000	0.000	0.000
71	A	88	ASP	-1	-0.827	-0.908	21.293	-0.276	-0.276	0.000	0.000	0.000	0.000
72	A	89	ALA	0	-0.073	-0.046	23.533	0.022	0.022	0.000	0.000	0.000	0.000
73	A	90	ALA	0	0.056	0.035	25.577	0.015	0.015	0.000	0.000	0.000	0.000
74	A	91	VAL	0	0.007	-0.002	25.605	0.014	0.014	0.000	0.000	0.000	0.000
75	A	92	ARG	1	0.896	0.955	26.111	0.174	0.174	0.000	0.000	0.000	0.000
76	A	93	ASP	-1	-0.913	-0.964	29.902	-0.124	-0.124	0.000	0.000	0.000	0.000
77	A	94	LEU	0	-0.037	-0.006	29.711	0.009	0.009	0.000	0.000	0.000	0.000
78	A	95	ALA	0	0.006	0.006	32.511	0.009	0.009	0.000	0.000	0.000	0.000
79	A	96	LEU	0	-0.009	-0.007	32.896	0.009	0.009	0.000	0.000	0.000	0.000
80	A	97	PRO	0	-0.021	-0.003	35.144	0.008	0.008	0.000	0.000	0.000	0.000
81	A	98	GLN	0	-0.019	-0.019	36.364	0.009	0.009	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.023	0.021	36.759	0.004	0.004	0.000	0.000	0.000	0.000
83	A	100	ALA	0	0.009	0.011	39.424	0.005	0.005	0.000	0.000	0.000	0.000
84	A	101	ARG	1	0.892	0.946	41.318	0.070	0.070	0.000	0.000	0.000	0.000
85	A	102	LEU	0	0.003	-0.004	41.649	0.004	0.004	0.000	0.000	0.000	0.000
86	A	103	SER	0	-0.065	-0.054	42.177	0.002	0.002	0.000	0.000	0.000	0.000
87	A	104	ASP	-1	-0.931	-0.966	44.802	-0.059	-0.059	0.000	0.000	0.000	0.000
88	A	105	LEU	0	-0.085	-0.019	47.365	0.003	0.003	0.000	0.000	0.000	0.000
89	A	106	LEU	0	-0.027	0.003	46.765	0.003	0.003	0.000	0.000	0.000	0.000
90	B	127	HOH	0	-0.017	-0.016	25.804	0.007	0.007	0.000	0.000	0.000	0.000

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Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ALA)