FMO DATABASE

FMODB ID: 531ZZ

Calculation Name: 3MAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MAY

Chain ID: A

ChEMBL ID:

UniProt ID: I6X8R5

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	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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-468217.195677
FMO2-HF: Nuclear repulsion	436508.381564
FMO2-HF: Total energy	-31708.814113
FMO2-MP2: Total energy	-31799.422991

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:40:CYS)

Summations of interaction energy for fragment #1(A:40:CYS)

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.
-33.981	-24.838	13.996	-9.2	-13.94	-0.064

Interaction energy analysis for fragmet #1(A:40:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.110 / q_NPA : -0.056

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	42	ALA	0	0.053	0.016	3.744	-2.263	-1.021	-0.006	-0.486	-0.751	0.004
4	A	43	SER	0	-0.016	-0.036	6.090	-0.036	-0.036	0.000	0.000	0.000	0.000
5	A	44	GLU	-1	-0.793	-0.876	2.617	0.889	1.589	0.170	-0.225	-0.645	-0.001
6	A	45	VAL	0	-0.021	0.000	3.526	-0.549	-0.131	0.012	-0.079	-0.351	0.000
7	A	46	ALA	0	0.039	0.010	5.662	-0.084	-0.084	0.000	0.000	0.000	0.000
8	A	47	ARG	1	0.867	0.933	7.643	-0.999	-0.999	0.000	0.000	0.000	0.000
9	A	48	THR	0	0.000	-0.002	6.800	0.031	0.031	0.000	0.000	0.000	0.000
10	A	49	VAL	0	-0.015	0.003	9.273	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	50	GLY	0	0.038	0.022	11.367	0.067	0.067	0.000	0.000	0.000	0.000
12	A	51	SER	0	-0.049	-0.028	11.941	0.051	0.051	0.000	0.000	0.000	0.000
13	A	52	VAL	0	0.019	0.004	12.174	0.018	0.018	0.000	0.000	0.000	0.000
14	A	53	ALA	0	-0.015	0.006	14.971	0.073	0.073	0.000	0.000	0.000	0.000
15	A	54	LYS	1	0.820	0.899	17.029	0.388	0.388	0.000	0.000	0.000	0.000
16	A	55	SER	0	-0.032	-0.014	17.364	0.017	0.017	0.000	0.000	0.000	0.000
17	A	56	MET	0	0.013	-0.005	16.372	0.038	0.038	0.000	0.000	0.000	0.000
18	A	57	GLY	0	0.017	-0.003	20.479	0.047	0.047	0.000	0.000	0.000	0.000
19	A	58	ASP	-1	-0.765	-0.860	22.502	-0.319	-0.319	0.000	0.000	0.000	0.000
20	A	59	TYR	0	-0.048	-0.063	23.357	0.038	0.038	0.000	0.000	0.000	0.000
21	A	60	LEU	0	-0.009	-0.016	23.349	0.028	0.028	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.954	-0.956	26.529	-0.282	-0.282	0.000	0.000	0.000	0.000
23	A	62	SER	0	-0.041	-0.025	27.929	0.023	0.023	0.000	0.000	0.000	0.000
24	A	63	HIS	1	0.803	0.913	27.951	0.442	0.442	0.000	0.000	0.000	0.000
25	A	64	PRO	0	0.078	0.024	30.233	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	65	GLU	-1	-0.875	-0.922	32.683	-0.402	-0.402	0.000	0.000	0.000	0.000
27	A	66	THR	0	0.060	-0.014	26.344	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	67	ASN	0	-0.029	-0.003	28.129	-0.059	-0.059	0.000	0.000	0.000	0.000
29	A	68	GLN	0	0.004	0.015	29.204	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	69	VAL	0	-0.005	-0.002	29.009	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	70	MET	0	-0.018	-0.005	23.234	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	71	THR	0	-0.010	-0.017	27.190	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	72	ALA	0	-0.042	-0.020	29.254	0.000	0.000	0.000	0.000	0.000	0.000
34	A	73	VAL	0	0.030	-0.006	25.331	0.003	0.003	0.000	0.000	0.000	0.000
35	A	74	LEU	0	-0.010	0.006	23.315	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	75	GLN	0	-0.027	-0.003	27.242	0.017	0.017	0.000	0.000	0.000	0.000
37	A	76	GLN	0	-0.047	-0.024	30.491	0.014	0.014	0.000	0.000	0.000	0.000
38	A	77	GLN	0	-0.031	-0.013	27.574	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	78	VAL	0	-0.016	-0.009	23.293	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	79	GLY	0	0.049	0.036	26.637	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	80	PRO	0	-0.004	-0.032	29.723	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	81	GLY	0	0.009	0.007	31.333	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	82	SER	0	-0.003	0.010	29.500	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	83	VAL	0	0.043	0.007	26.113	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	84	ALA	0	-0.057	-0.029	28.494	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	85	SER	0	0.048	0.026	31.063	0.015	0.015	0.000	0.000	0.000	0.000
47	A	86	LEU	0	-0.005	0.001	24.441	0.007	0.007	0.000	0.000	0.000	0.000
48	A	87	LYS	1	0.895	0.955	26.811	0.620	0.620	0.000	0.000	0.000	0.000
49	A	88	ALA	0	0.085	0.043	28.108	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	89	HIS	0	-0.035	0.007	27.849	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	90	PHE	0	0.007	-0.020	22.465	0.003	0.003	0.000	0.000	0.000	0.000
52	A	91	GLU	-1	-0.932	-0.964	27.675	-0.563	-0.563	0.000	0.000	0.000	0.000
53	A	92	ALA	0	-0.041	-0.014	29.937	0.022	0.022	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.044	-0.010	29.470	0.047	0.047	0.000	0.000	0.000	0.000
55	A	94	PRO	0	0.072	0.032	27.011	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	95	LYS	1	0.840	0.915	25.652	0.414	0.414	0.000	0.000	0.000	0.000
57	A	96	VAL	0	0.028	0.023	25.083	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.000	0.016	23.205	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	98	SER	0	-0.024	-0.027	21.079	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	99	ASP	-1	-0.758	-0.842	20.229	-0.588	-0.588	0.000	0.000	0.000	0.000
61	A	100	LEU	0	-0.007	-0.011	20.078	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	101	HIS	0	-0.025	-0.009	14.412	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	102	ALA	0	-0.004	-0.014	15.780	-0.182	-0.182	0.000	0.000	0.000	0.000
64	A	103	LEU	0	-0.019	-0.009	15.507	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	104	SER	0	-0.050	-0.031	13.841	-0.122	-0.122	0.000	0.000	0.000	0.000
66	A	105	GLN	0	0.020	0.011	10.354	-0.210	-0.210	0.000	0.000	0.000	0.000
67	A	106	PRO	0	0.030	0.037	9.353	-0.623	-0.623	0.000	0.000	0.000	0.000
68	A	107	LEU	0	-0.018	-0.011	7.708	-0.839	-0.839	0.000	0.000	0.000	0.000
69	A	108	THR	0	0.020	0.000	7.093	-0.966	-0.966	0.000	0.000	0.000	0.000
70	A	109	ASP	-1	-0.901	-0.961	5.857	-4.490	-4.490	0.000	0.000	0.000	0.000
71	A	110	LEU	0	0.025	0.002	3.038	-7.195	-5.336	1.721	-1.161	-2.419	-0.004
72	A	111	SER	0	0.001	0.003	1.834	-17.987	-20.154	9.866	-4.034	-3.665	-0.057
73	A	112	THR	0	-0.054	-0.013	2.328	0.830	4.862	0.515	-1.907	-2.640	-0.005
76	A	116	LEU	0	0.039	0.014	2.498	0.309	3.242	1.720	-1.305	-3.348	-0.001
77	A	117	PRO	0	-0.043	0.000	5.336	1.247	1.373	-0.002	-0.003	-0.121	0.000
78	A	118	ILE	0	0.063	0.034	7.513	-0.567	-0.567	0.000	0.000	0.000	0.000
79	A	119	SER	0	0.008	-0.005	8.072	-0.468	-0.468	0.000	0.000	0.000	0.000
80	A	120	GLY	0	0.011	-0.008	9.057	0.355	0.355	0.000	0.000	0.000	0.000
81	A	121	LEU	0	0.082	0.039	12.070	0.053	0.053	0.000	0.000	0.000	0.000
82	A	122	GLN	0	-0.008	0.001	7.712	-0.071	-0.071	0.000	0.000	0.000	0.000
83	A	123	ALA	0	-0.027	-0.024	10.686	0.168	0.168	0.000	0.000	0.000	0.000
84	A	124	ILE	0	-0.083	-0.029	13.131	0.144	0.144	0.000	0.000	0.000	0.000
85	A	125	GLY	0	-0.020	-0.001	13.560	0.071	0.071	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:40:CYS)