FMO DATABASE

FMODB ID: 52N7Z

Calculation Name: 4MYR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MYR

Chain ID: A

ChEMBL ID:

UniProt ID: Q92YL8

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	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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-967291.19115
FMO2-HF: Nuclear repulsion	920043.622466
FMO2-HF: Total energy	-47247.568683
FMO2-MP2: Total energy	-47380.779252

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:30:LYS)

Summations of interaction energy for fragment #1(A:30: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.
-110.3	-101.814	7.054	-5.596	-9.943	-0.062

Interaction energy analysis for fragmet #1(A:30:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.932

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	32	ASP	-1	-0.889	-0.953	3.470	-44.072	-42.296	0.009	-0.737	-1.048	-0.001
4	A	33	ILE	0	-0.013	-0.016	5.804	4.355	4.355	0.000	0.000	0.000	0.000
5	A	34	ALA	0	-0.009	0.007	8.307	-0.887	-0.887	0.000	0.000	0.000	0.000
6	A	35	VAL	0	-0.001	-0.008	11.617	1.074	1.074	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.010	-0.001	14.287	-0.065	-0.065	0.000	0.000	0.000	0.000
8	A	37	CYS	0	-0.026	-0.015	17.928	0.219	0.219	0.000	0.000	0.000	0.000
9	A	38	GLN	0	-0.021	-0.019	20.171	-0.054	-0.054	0.000	0.000	0.000	0.000
10	A	39	SER	0	-0.024	-0.009	23.453	0.372	0.372	0.000	0.000	0.000	0.000
11	A	40	GLU	-1	-0.946	-0.978	22.037	-13.650	-13.650	0.000	0.000	0.000	0.000
12	A	41	GLU	-1	-0.836	-0.938	21.404	-12.806	-12.806	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.024	-0.001	18.578	-0.513	-0.513	0.000	0.000	0.000	0.000
14	A	43	ARG	1	0.931	0.963	17.476	15.087	15.087	0.000	0.000	0.000	0.000
15	A	44	GLU	-1	-0.931	-0.962	16.622	-15.325	-15.325	0.000	0.000	0.000	0.000
16	A	45	ALA	0	0.013	0.018	17.034	-0.942	-0.942	0.000	0.000	0.000	0.000
17	A	46	VAL	0	0.002	-0.019	13.053	-1.109	-1.109	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.008	-0.005	12.522	-2.037	-2.037	0.000	0.000	0.000	0.000
19	A	48	THR	0	-0.030	-0.020	12.466	-1.431	-1.431	0.000	0.000	0.000	0.000
20	A	49	ALA	0	-0.016	-0.011	12.603	-0.845	-0.845	0.000	0.000	0.000	0.000
21	A	50	ALA	0	-0.028	-0.013	8.254	-1.691	-1.691	0.000	0.000	0.000	0.000
22	A	51	ILE	0	-0.039	-0.007	7.612	-4.225	-4.225	0.000	0.000	0.000	0.000
23	A	52	ASP	-1	-0.797	-0.894	9.918	-22.433	-22.433	0.000	0.000	0.000	0.000
24	A	53	ARG	1	0.927	0.947	8.795	16.770	16.770	0.000	0.000	0.000	0.000
25	A	54	ARG	1	0.849	0.922	8.731	18.075	18.075	0.000	0.000	0.000	0.000
26	A	55	MET	0	0.041	0.032	7.135	0.572	0.572	0.000	0.000	0.000	0.000
27	A	56	ALA	0	0.018	0.024	4.806	-5.891	-5.891	0.000	0.000	0.000	0.000
28	A	57	ARG	1	0.865	0.920	2.499	8.905	11.222	2.361	-1.756	-2.923	-0.021
29	A	58	ALA	0	0.032	0.013	2.722	0.083	2.686	1.656	-1.685	-2.573	-0.018
30	A	59	THR	0	-0.032	-0.011	2.186	-15.345	-13.655	3.028	-1.388	-3.329	-0.022
31	A	60	VAL	0	0.022	0.016	4.270	5.087	5.187	0.000	-0.030	-0.070	0.000
32	A	61	THR	0	-0.026	-0.008	7.857	0.060	0.060	0.000	0.000	0.000	0.000
33	A	62	VAL	0	-0.001	0.003	10.727	1.200	1.200	0.000	0.000	0.000	0.000
34	A	63	LYS	1	0.896	0.948	13.368	21.175	21.175	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.039	0.019	17.107	0.196	0.196	0.000	0.000	0.000	0.000
36	A	65	GLY	0	0.005	0.007	20.755	0.069	0.069	0.000	0.000	0.000	0.000
37	A	66	GLY	0	0.035	-0.002	21.591	-0.279	-0.279	0.000	0.000	0.000	0.000
38	A	67	MET	0	0.017	0.012	21.863	-0.370	-0.370	0.000	0.000	0.000	0.000
39	A	68	LYS	1	0.924	0.983	23.318	10.186	10.186	0.000	0.000	0.000	0.000
40	A	69	GLU	-1	-0.821	-0.905	21.560	-12.374	-12.374	0.000	0.000	0.000	0.000
41	A	70	ALA	0	0.000	0.007	19.011	-0.304	-0.304	0.000	0.000	0.000	0.000
42	A	71	THR	0	-0.025	-0.048	19.980	-0.296	-0.296	0.000	0.000	0.000	0.000
43	A	72	ALA	0	0.004	0.012	22.722	0.093	0.093	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.058	-0.023	15.948	-0.096	-0.096	0.000	0.000	0.000	0.000
45	A	74	TYR	0	-0.009	-0.039	13.618	-0.683	-0.683	0.000	0.000	0.000	0.000
46	A	75	GLY	0	0.101	0.084	19.090	0.050	0.050	0.000	0.000	0.000	0.000
47	A	76	GLY	0	-0.078	-0.033	21.218	0.413	0.413	0.000	0.000	0.000	0.000
48	A	77	VAL	0	-0.089	-0.041	15.042	-0.270	-0.270	0.000	0.000	0.000	0.000
49	A	78	THR	0	0.027	0.007	12.620	0.318	0.318	0.000	0.000	0.000	0.000
50	A	79	SER	0	0.035	0.021	13.782	-0.493	-0.493	0.000	0.000	0.000	0.000
51	A	80	PRO	0	-0.050	-0.010	9.217	-0.387	-0.387	0.000	0.000	0.000	0.000
52	A	81	ASN	0	0.010	0.003	6.283	-1.302	-1.302	0.000	0.000	0.000	0.000
53	A	82	LEU	0	-0.015	-0.007	9.387	1.594	1.594	0.000	0.000	0.000	0.000
54	A	83	VAL	0	0.020	0.022	11.059	-1.347	-1.347	0.000	0.000	0.000	0.000
55	A	84	VAL	0	0.001	-0.009	12.698	0.855	0.855	0.000	0.000	0.000	0.000
56	A	85	VAL	0	0.004	-0.004	15.405	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.729	-0.841	18.968	-12.884	-12.884	0.000	0.000	0.000	0.000
58	A	87	SER	0	-0.037	-0.029	21.605	0.425	0.425	0.000	0.000	0.000	0.000
59	A	88	ASP	-1	-0.832	-0.899	25.070	-11.230	-11.230	0.000	0.000	0.000	0.000
60	A	89	ASP	-1	-0.897	-0.936	28.340	-10.039	-10.039	0.000	0.000	0.000	0.000
61	A	90	GLY	0	-0.004	-0.004	30.252	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.872	-0.950	31.283	-9.052	-9.052	0.000	0.000	0.000	0.000
63	A	92	ALA	0	0.054	0.016	31.511	-0.178	-0.178	0.000	0.000	0.000	0.000
64	A	93	ARG	1	0.857	0.917	29.309	10.001	10.001	0.000	0.000	0.000	0.000
65	A	94	LEU	0	0.006	0.003	25.071	-0.215	-0.215	0.000	0.000	0.000	0.000
66	A	95	MET	0	0.013	0.009	27.264	-0.339	-0.339	0.000	0.000	0.000	0.000
67	A	96	ALA	0	0.071	0.044	28.322	-0.212	-0.212	0.000	0.000	0.000	0.000
68	A	97	THR	0	-0.098	-0.068	26.382	-0.249	-0.249	0.000	0.000	0.000	0.000
69	A	98	LEU	0	0.025	0.011	22.414	-0.448	-0.448	0.000	0.000	0.000	0.000
70	A	99	GLU	-1	-0.957	-0.970	24.258	-10.027	-10.027	0.000	0.000	0.000	0.000
71	A	100	THR	0	-0.023	-0.020	25.747	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	101	LEU	0	0.002	0.003	19.103	-0.258	-0.258	0.000	0.000	0.000	0.000
73	A	102	ALA	0	-0.020	-0.020	20.826	-0.533	-0.533	0.000	0.000	0.000	0.000
74	A	103	MET	0	-0.079	-0.033	21.362	0.017	0.017	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.929	-0.959	21.070	-12.009	-12.009	0.000	0.000	0.000	0.000
76	A	105	CYS	0	-0.082	-0.037	16.837	-0.886	-0.886	0.000	0.000	0.000	0.000
77	A	106	VAL	0	0.018	0.023	14.262	0.564	0.564	0.000	0.000	0.000	0.000
78	A	107	THR	0	0.026	0.005	15.302	-0.586	-0.586	0.000	0.000	0.000	0.000
79	A	108	GLY	0	-0.007	-0.005	13.084	-0.442	-0.442	0.000	0.000	0.000	0.000
80	A	109	THR	0	-0.037	-0.023	12.628	-1.330	-1.330	0.000	0.000	0.000	0.000
81	A	110	LYS	1	0.894	0.961	12.706	17.754	17.754	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.067	0.026	14.723	-0.754	-0.754	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.005	0.001	14.034	0.306	0.306	0.000	0.000	0.000	0.000
84	A	113	VAL	0	-0.004	0.003	17.554	-0.120	-0.120	0.000	0.000	0.000	0.000
85	A	114	ILE	0	-0.008	-0.003	17.290	0.033	0.033	0.000	0.000	0.000	0.000
86	A	115	GLY	0	0.062	0.031	21.526	0.231	0.231	0.000	0.000	0.000	0.000
87	A	116	ARG	1	0.947	0.977	25.355	9.655	9.655	0.000	0.000	0.000	0.000
88	A	117	SER	0	-0.028	0.002	28.551	0.298	0.298	0.000	0.000	0.000	0.000
89	A	118	ASN	0	0.062	0.037	28.761	-0.547	-0.547	0.000	0.000	0.000	0.000
90	A	119	ASP	-1	-0.843	-0.916	30.404	-8.688	-8.688	0.000	0.000	0.000	0.000
91	A	120	VAL	0	0.026	-0.004	30.411	-0.269	-0.269	0.000	0.000	0.000	0.000
92	A	121	GLY	0	-0.007	-0.004	30.983	-0.160	-0.160	0.000	0.000	0.000	0.000
93	A	122	LEU	0	0.033	0.010	28.428	-0.050	-0.050	0.000	0.000	0.000	0.000
94	A	123	TYR	0	-0.074	-0.036	22.329	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.940	0.964	26.739	8.797	8.797	0.000	0.000	0.000	0.000
96	A	125	LYS	1	0.957	0.986	28.536	9.196	9.196	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.031	-0.011	24.577	-0.094	-0.094	0.000	0.000	0.000	0.000
98	A	127	LEU	0	-0.010	-0.006	22.344	-0.276	-0.276	0.000	0.000	0.000	0.000
99	A	128	ASP	-1	-0.971	-0.972	24.700	-9.987	-9.987	0.000	0.000	0.000	0.000
100	A	129	ALA	0	-0.075	-0.036	25.958	0.131	0.131	0.000	0.000	0.000	0.000
101	A	130	GLY	0	-0.010	0.004	22.530	-0.124	-0.124	0.000	0.000	0.000	0.000
102	A	131	VAL	0	-0.084	-0.030	20.303	-0.697	-0.697	0.000	0.000	0.000	0.000
103	A	132	SER	0	-0.033	-0.032	16.676	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.830	-0.937	18.230	-14.451	-14.451	0.000	0.000	0.000	0.000
105	A	134	TYR	0	-0.090	-0.063	19.929	-0.117	-0.117	0.000	0.000	0.000	0.000
106	A	135	LEU	0	0.001	-0.001	17.055	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	136	VAL	0	-0.010	-0.006	21.713	0.148	0.148	0.000	0.000	0.000	0.000
108	A	137	LYS	1	0.799	0.882	23.853	11.759	11.759	0.000	0.000	0.000	0.000
109	A	138	PRO	0	-0.034	-0.028	25.351	0.461	0.461	0.000	0.000	0.000	0.000
110	A	139	LEU	0	0.017	0.004	17.705	-0.032	-0.032	0.000	0.000	0.000	0.000
111	A	140	GLU	-1	-0.881	-0.918	20.441	-14.071	-14.071	0.000	0.000	0.000	0.000
112	A	141	PRO	0	-0.019	-0.023	16.036	-0.727	-0.727	0.000	0.000	0.000	0.000
113	A	142	MET	0	-0.023	-0.030	15.729	-1.565	-1.565	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.825	-0.913	17.290	-14.551	-14.551	0.000	0.000	0.000	0.000
115	A	144	PHE	0	0.031	0.005	11.054	-0.218	-0.218	0.000	0.000	0.000	0.000
116	A	145	VAL	0	0.004	-0.001	11.806	-1.001	-1.001	0.000	0.000	0.000	0.000
117	A	146	ALA	0	-0.024	-0.001	13.410	-0.610	-0.610	0.000	0.000	0.000	0.000
118	A	147	ALA	0	0.041	0.024	15.664	-0.038	-0.038	0.000	0.000	0.000	0.000
119	A	148	VAL	0	-0.001	0.000	9.063	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	149	HIS	0	-0.090	-0.069	10.720	-0.837	-0.837	0.000	0.000	0.000	0.000
121	A	150	ARG	1	0.909	0.963	12.532	14.496	14.496	0.000	0.000	0.000	0.000
122	A	151	CYS	0	-0.051	-0.008	12.549	0.802	0.802	0.000	0.000	0.000	0.000
123	A	152	PHE	0	-0.044	-0.003	9.160	0.363	0.363	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:LYS)