FMO DATABASE

FMODB ID: V5K31

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	OptAll
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	-972975.959457
FMO2-HF: Nuclear repulsion	925727.571117
FMO2-HF: Total energy	-47248.388341
FMO2-MP2: Total energy	-47381.65984

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.
-175.682	-170.282	26.113	-13.705	-17.807	-0.162

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 : 0.816 / q_NPA : 0.906

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	-0.846	-0.938	2.979	-51.872	-48.645	0.163	-1.692	-1.697	-0.006
4	A	33	ILE	0	-0.001	-0.009	5.620	4.549	4.549	0.000	0.000	0.000	0.000
5	A	34	ALA	0	0.002	0.017	8.512	-0.529	-0.529	0.000	0.000	0.000	0.000
6	A	35	VAL	0	-0.015	-0.017	11.140	0.767	0.767	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.009	0.009	13.699	0.153	0.153	0.000	0.000	0.000	0.000
8	A	37	CYS	0	0.013	-0.005	17.243	0.015	0.015	0.000	0.000	0.000	0.000
9	A	38	GLN	0	-0.035	-0.023	19.317	0.043	0.043	0.000	0.000	0.000	0.000
10	A	39	SER	0	-0.049	-0.051	22.454	0.616	0.616	0.000	0.000	0.000	0.000
11	A	40	GLU	-1	-0.831	-0.895	21.122	-15.050	-15.050	0.000	0.000	0.000	0.000
12	A	41	GLU	-1	-0.855	-0.953	20.468	-13.818	-13.818	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.027	-0.002	17.925	-0.725	-0.725	0.000	0.000	0.000	0.000
14	A	43	ARG	1	0.799	0.876	16.571	15.058	15.058	0.000	0.000	0.000	0.000
15	A	44	GLU	-1	-0.863	-0.918	15.521	-16.983	-16.983	0.000	0.000	0.000	0.000
16	A	45	ALA	0	0.011	0.020	15.875	-1.015	-1.015	0.000	0.000	0.000	0.000
17	A	46	VAL	0	0.010	-0.005	12.023	-1.372	-1.372	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.017	-0.010	11.412	-2.579	-2.579	0.000	0.000	0.000	0.000
19	A	48	THR	0	-0.032	-0.040	11.125	-1.820	-1.820	0.000	0.000	0.000	0.000
20	A	49	ALA	0	-0.020	-0.005	11.492	-0.752	-0.752	0.000	0.000	0.000	0.000
21	A	50	ALA	0	-0.038	-0.021	7.286	-2.329	-2.329	0.000	0.000	0.000	0.000
22	A	51	ILE	0	-0.027	-0.001	6.273	-6.283	-6.283	0.000	0.000	0.000	0.000
23	A	52	ASP	-1	-0.800	-0.883	8.470	-24.745	-24.745	0.000	0.000	0.000	0.000
24	A	53	ARG	1	0.926	0.950	7.710	17.173	17.173	0.000	0.000	0.000	0.000
25	A	54	ARG	1	0.839	0.906	8.104	20.004	20.004	0.000	0.000	0.000	0.000
26	A	55	MET	0	0.032	0.029	5.989	-0.088	-0.088	0.000	0.000	0.000	0.000
27	A	56	ALA	0	0.038	0.037	3.615	-12.099	-11.626	0.005	-0.193	-0.285	-0.001
28	A	57	ARG	1	0.886	0.931	1.941	-0.248	-0.286	7.204	-3.291	-3.875	-0.043
29	A	58	ALA	0	0.014	0.012	2.465	0.747	3.643	3.726	-2.882	-3.740	-0.030
30	A	59	THR	0	-0.015	-0.011	1.879	-51.515	-52.701	14.945	-5.768	-7.991	-0.082
31	A	60	VAL	0	0.016	0.010	3.206	7.961	7.989	0.070	0.121	-0.219	0.000
32	A	61	THR	0	-0.035	-0.005	6.987	1.655	1.655	0.000	0.000	0.000	0.000
33	A	62	VAL	0	0.023	0.002	9.541	1.937	1.937	0.000	0.000	0.000	0.000
34	A	63	LYS	1	0.882	0.950	12.815	22.525	22.525	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.043	0.032	16.082	0.238	0.238	0.000	0.000	0.000	0.000
36	A	65	GLY	0	-0.014	-0.011	19.798	0.077	0.077	0.000	0.000	0.000	0.000
37	A	66	GLY	0	0.032	-0.002	21.071	-0.320	-0.320	0.000	0.000	0.000	0.000
38	A	67	MET	0	0.012	0.010	21.734	-0.335	-0.335	0.000	0.000	0.000	0.000
39	A	68	LYS	1	0.911	0.977	23.450	10.852	10.852	0.000	0.000	0.000	0.000
40	A	69	GLU	-1	-0.805	-0.910	21.343	-12.904	-12.904	0.000	0.000	0.000	0.000
41	A	70	ALA	0	0.003	0.005	18.980	-0.393	-0.393	0.000	0.000	0.000	0.000
42	A	71	THR	0	-0.006	-0.024	19.985	-0.253	-0.253	0.000	0.000	0.000	0.000
43	A	72	ALA	0	-0.025	-0.019	22.680	0.059	0.059	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.058	-0.013	15.977	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	74	TYR	0	0.004	-0.029	13.604	-0.503	-0.503	0.000	0.000	0.000	0.000
46	A	75	GLY	0	0.094	0.071	19.582	0.058	0.058	0.000	0.000	0.000	0.000
47	A	76	GLY	0	-0.080	-0.033	21.740	0.559	0.559	0.000	0.000	0.000	0.000
48	A	77	VAL	0	-0.090	-0.040	15.815	-0.284	-0.284	0.000	0.000	0.000	0.000
49	A	78	THR	0	0.008	0.005	13.200	0.219	0.219	0.000	0.000	0.000	0.000
50	A	79	SER	0	0.035	0.012	14.375	-0.579	-0.579	0.000	0.000	0.000	0.000
51	A	80	PRO	0	-0.041	-0.002	9.030	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	81	ASN	0	-0.001	-0.010	6.566	-1.805	-1.805	0.000	0.000	0.000	0.000
53	A	82	LEU	0	-0.025	-0.011	9.661	1.739	1.739	0.000	0.000	0.000	0.000
54	A	83	VAL	0	0.017	0.012	11.223	-1.458	-1.458	0.000	0.000	0.000	0.000
55	A	84	VAL	0	0.007	0.001	12.798	1.165	1.165	0.000	0.000	0.000	0.000
56	A	85	VAL	0	-0.018	-0.017	15.456	-0.054	-0.054	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.703	-0.804	18.794	-13.952	-13.952	0.000	0.000	0.000	0.000
58	A	87	SER	0	-0.058	-0.051	21.247	0.479	0.479	0.000	0.000	0.000	0.000
59	A	88	ASP	-1	-0.755	-0.855	24.940	-11.973	-11.973	0.000	0.000	0.000	0.000
60	A	89	ASP	-1	-0.810	-0.865	28.240	-10.472	-10.472	0.000	0.000	0.000	0.000
61	A	90	GLY	0	0.002	0.006	30.262	0.042	0.042	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.794	-0.894	31.230	-9.581	-9.581	0.000	0.000	0.000	0.000
63	A	92	ALA	0	0.066	0.029	31.353	-0.217	-0.217	0.000	0.000	0.000	0.000
64	A	93	ARG	1	0.820	0.883	28.764	10.610	10.610	0.000	0.000	0.000	0.000
65	A	94	LEU	0	0.006	0.017	25.290	-0.247	-0.247	0.000	0.000	0.000	0.000
66	A	95	MET	0	-0.008	0.008	27.278	-0.427	-0.427	0.000	0.000	0.000	0.000
67	A	96	ALA	0	0.095	0.056	28.210	-0.258	-0.258	0.000	0.000	0.000	0.000
68	A	97	THR	0	-0.102	-0.066	26.477	-0.247	-0.247	0.000	0.000	0.000	0.000
69	A	98	LEU	0	0.013	0.008	22.336	-0.510	-0.510	0.000	0.000	0.000	0.000
70	A	99	GLU	-1	-0.931	-0.974	24.264	-10.556	-10.556	0.000	0.000	0.000	0.000
71	A	100	THR	0	-0.034	-0.036	26.318	0.039	0.039	0.000	0.000	0.000	0.000
72	A	101	LEU	0	-0.016	-0.011	19.322	-0.269	-0.269	0.000	0.000	0.000	0.000
73	A	102	ALA	0	-0.011	-0.011	21.562	-0.615	-0.615	0.000	0.000	0.000	0.000
74	A	103	MET	0	-0.080	-0.025	22.374	0.142	0.142	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.903	-0.956	21.439	-12.448	-12.448	0.000	0.000	0.000	0.000
76	A	105	CYS	0	-0.112	-0.045	17.692	-0.996	-0.996	0.000	0.000	0.000	0.000
77	A	106	VAL	0	0.036	0.025	15.243	0.612	0.612	0.000	0.000	0.000	0.000
78	A	107	THR	0	0.016	0.001	15.885	-0.804	-0.804	0.000	0.000	0.000	0.000
79	A	108	GLY	0	0.015	0.008	13.274	-0.252	-0.252	0.000	0.000	0.000	0.000
80	A	109	THR	0	-0.034	-0.013	12.824	-1.389	-1.389	0.000	0.000	0.000	0.000
81	A	110	LYS	1	0.845	0.936	12.531	20.079	20.079	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.067	0.027	14.752	-0.703	-0.703	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.002	0.003	14.230	0.278	0.278	0.000	0.000	0.000	0.000
84	A	113	VAL	0	0.016	0.015	17.668	-0.212	-0.212	0.000	0.000	0.000	0.000
85	A	114	ILE	0	0.005	0.003	16.952	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	115	GLY	0	0.062	0.020	21.434	0.250	0.250	0.000	0.000	0.000	0.000
87	A	116	ARG	1	0.868	0.921	25.205	10.230	10.230	0.000	0.000	0.000	0.000
88	A	117	SER	0	-0.050	0.002	28.391	0.410	0.410	0.000	0.000	0.000	0.000
89	A	118	ASN	0	0.062	0.024	28.549	-0.714	-0.714	0.000	0.000	0.000	0.000
90	A	119	ASP	-1	-0.807	-0.896	30.459	-9.224	-9.224	0.000	0.000	0.000	0.000
91	A	120	VAL	0	0.016	0.006	30.394	-0.350	-0.350	0.000	0.000	0.000	0.000
92	A	121	GLY	0	-0.029	-0.015	31.182	-0.120	-0.120	0.000	0.000	0.000	0.000
93	A	122	LEU	0	0.003	-0.010	28.436	-0.056	-0.056	0.000	0.000	0.000	0.000
94	A	123	TYR	0	-0.050	-0.042	22.268	-0.074	-0.074	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.924	0.965	26.774	9.257	9.257	0.000	0.000	0.000	0.000
96	A	125	LYS	1	0.898	0.931	28.103	9.311	9.311	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.016	-0.002	24.517	-0.114	-0.114	0.000	0.000	0.000	0.000
98	A	127	LEU	0	-0.002	0.002	22.592	-0.298	-0.298	0.000	0.000	0.000	0.000
99	A	128	ASP	-1	-0.962	-0.980	24.691	-10.522	-10.522	0.000	0.000	0.000	0.000
100	A	129	ALA	0	-0.056	-0.024	26.280	0.171	0.171	0.000	0.000	0.000	0.000
101	A	130	GLY	0	-0.013	-0.003	22.372	-0.207	-0.207	0.000	0.000	0.000	0.000
102	A	131	VAL	0	-0.082	-0.036	20.410	-0.841	-0.841	0.000	0.000	0.000	0.000
103	A	132	SER	0	-0.021	-0.026	16.475	-0.085	-0.085	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.800	-0.899	18.219	-15.672	-15.672	0.000	0.000	0.000	0.000
105	A	134	TYR	0	-0.100	-0.067	19.911	-0.041	-0.041	0.000	0.000	0.000	0.000
106	A	135	LEU	0	-0.003	0.002	16.995	0.155	0.155	0.000	0.000	0.000	0.000
107	A	136	VAL	0	0.005	-0.003	21.669	0.097	0.097	0.000	0.000	0.000	0.000
108	A	137	LYS	1	0.761	0.890	23.001	12.383	12.383	0.000	0.000	0.000	0.000
109	A	138	PRO	0	-0.033	-0.035	24.395	0.546	0.546	0.000	0.000	0.000	0.000
110	A	139	LEU	0	0.007	0.002	17.112	-0.032	-0.032	0.000	0.000	0.000	0.000
111	A	140	GLU	-1	-0.825	-0.901	18.382	-16.759	-16.759	0.000	0.000	0.000	0.000
112	A	141	PRO	0	-0.016	-0.013	14.603	-0.798	-0.798	0.000	0.000	0.000	0.000
113	A	142	MET	0	-0.050	-0.050	14.636	-1.937	-1.937	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.814	-0.898	16.149	-15.955	-15.955	0.000	0.000	0.000	0.000
115	A	144	PHE	0	0.028	0.009	9.909	-0.412	-0.412	0.000	0.000	0.000	0.000
116	A	145	VAL	0	-0.010	-0.012	10.796	-1.325	-1.325	0.000	0.000	0.000	0.000
117	A	146	ALA	0	-0.018	-0.003	12.536	-0.847	-0.847	0.000	0.000	0.000	0.000
118	A	147	ALA	0	0.041	0.020	15.480	0.085	0.085	0.000	0.000	0.000	0.000
119	A	148	VAL	0	0.015	0.005	9.061	-0.195	-0.195	0.000	0.000	0.000	0.000
120	A	149	HIS	0	-0.094	-0.065	10.048	-0.716	-0.716	0.000	0.000	0.000	0.000
121	A	150	ARG	1	0.857	0.941	12.292	15.945	15.945	0.000	0.000	0.000	0.000
122	A	151	CYS	0	-0.053	-0.010	12.239	1.208	1.208	0.000	0.000	0.000	0.000
123	A	152	PHE	0	-0.065	-0.018	9.421	0.163	0.163	0.000	0.000	0.000	0.000

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