FMO DATABASE

FMODB ID: YZN52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-968578.704795
FMO2-HF: Nuclear repulsion	921330.566213
FMO2-HF: Total energy	-47248.138582
FMO2-MP2: Total energy	-47381.394951

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.
-146.422	-140.112	19.542	-9.691	-16.161	-0.13

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 : 0.840 / q_NPA : 0.923

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	-0.905	-0.964	3.342	-45.474	-43.096	0.033	-1.077	-1.333	0.001
4	A	33	ILE	0	0.003	-0.010	5.417	4.484	4.484	0.000	0.000	0.000	0.000
5	A	34	ALA	0	-0.001	0.011	8.122	-0.949	-0.949	0.000	0.000	0.000	0.000
6	A	35	VAL	0	-0.008	-0.010	11.322	1.152	1.152	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.005	0.006	14.055	0.025	0.025	0.000	0.000	0.000	0.000
8	A	37	CYS	0	-0.001	-0.007	17.622	0.095	0.095	0.000	0.000	0.000	0.000
9	A	38	GLN	0	-0.028	-0.020	19.613	-0.071	-0.071	0.000	0.000	0.000	0.000
10	A	39	SER	0	-0.045	-0.050	22.737	0.446	0.446	0.000	0.000	0.000	0.000
11	A	40	GLU	-1	-0.830	-0.888	21.295	-14.968	-14.968	0.000	0.000	0.000	0.000
12	A	41	GLU	-1	-0.830	-0.944	20.558	-13.696	-13.696	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.031	-0.005	18.000	-0.576	-0.576	0.000	0.000	0.000	0.000
14	A	43	ARG	1	0.798	0.875	16.794	15.327	15.327	0.000	0.000	0.000	0.000
15	A	44	GLU	-1	-0.894	-0.940	15.778	-16.578	-16.578	0.000	0.000	0.000	0.000
16	A	45	ALA	0	0.015	0.025	16.052	-1.065	-1.065	0.000	0.000	0.000	0.000
17	A	46	VAL	0	0.004	-0.016	12.359	-1.301	-1.301	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.013	-0.007	11.773	-2.490	-2.490	0.000	0.000	0.000	0.000
19	A	48	THR	0	-0.036	-0.031	11.340	-1.601	-1.601	0.000	0.000	0.000	0.000
20	A	49	ALA	0	-0.017	-0.012	11.805	-1.023	-1.023	0.000	0.000	0.000	0.000
21	A	50	ALA	0	-0.032	-0.014	7.425	-2.207	-2.207	0.000	0.000	0.000	0.000
22	A	51	ILE	0	-0.037	-0.006	6.535	-5.644	-5.644	0.000	0.000	0.000	0.000
23	A	52	ASP	-1	-0.788	-0.875	8.625	-24.214	-24.214	0.000	0.000	0.000	0.000
24	A	53	ARG	1	0.936	0.957	7.917	17.033	17.033	0.000	0.000	0.000	0.000
25	A	54	ARG	1	0.841	0.905	7.979	19.214	19.214	0.000	0.000	0.000	0.000
26	A	55	MET	0	0.030	0.027	6.420	0.883	0.883	0.000	0.000	0.000	0.000
27	A	56	ALA	0	0.032	0.030	3.770	-9.865	-9.356	0.000	-0.194	-0.315	-0.001
28	A	57	ARG	1	0.883	0.932	1.880	-4.663	-4.082	6.998	-3.657	-3.922	-0.051
29	A	58	ALA	0	0.053	0.024	2.577	0.839	3.339	4.109	-2.208	-4.401	-0.034
30	A	59	THR	0	-0.013	-0.012	2.071	-27.819	-27.441	8.329	-2.700	-6.008	-0.045
31	A	60	VAL	0	0.010	0.019	3.292	7.637	7.601	0.073	0.145	-0.182	0.000
32	A	61	THR	0	-0.029	-0.009	7.010	0.608	0.608	0.000	0.000	0.000	0.000
33	A	62	VAL	0	0.004	0.001	9.684	1.209	1.209	0.000	0.000	0.000	0.000
34	A	63	LYS	1	0.889	0.949	12.837	22.469	22.469	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.043	0.021	16.213	0.169	0.169	0.000	0.000	0.000	0.000
36	A	65	GLY	0	-0.005	0.002	19.846	0.119	0.119	0.000	0.000	0.000	0.000
37	A	66	GLY	0	0.033	-0.002	21.364	-0.328	-0.328	0.000	0.000	0.000	0.000
38	A	67	MET	0	0.015	0.008	21.555	-0.375	-0.375	0.000	0.000	0.000	0.000
39	A	68	LYS	1	0.922	0.978	23.087	10.617	10.617	0.000	0.000	0.000	0.000
40	A	69	GLU	-1	-0.814	-0.906	21.260	-12.799	-12.799	0.000	0.000	0.000	0.000
41	A	70	ALA	0	0.002	0.005	18.614	-0.276	-0.276	0.000	0.000	0.000	0.000
42	A	71	THR	0	-0.004	-0.030	19.553	-0.287	-0.287	0.000	0.000	0.000	0.000
43	A	72	ALA	0	-0.010	0.004	22.307	0.127	0.127	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.056	-0.021	15.861	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	74	TYR	0	-0.014	-0.043	13.086	-0.658	-0.658	0.000	0.000	0.000	0.000
46	A	75	GLY	0	0.107	0.087	19.041	0.064	0.064	0.000	0.000	0.000	0.000
47	A	76	GLY	0	-0.086	-0.035	21.346	0.449	0.449	0.000	0.000	0.000	0.000
48	A	77	VAL	0	-0.089	-0.042	15.190	-0.200	-0.200	0.000	0.000	0.000	0.000
49	A	78	THR	0	0.036	0.015	12.855	0.279	0.279	0.000	0.000	0.000	0.000
50	A	79	SER	0	0.019	-0.001	14.072	-0.526	-0.526	0.000	0.000	0.000	0.000
51	A	80	PRO	0	-0.039	-0.003	8.828	-0.228	-0.228	0.000	0.000	0.000	0.000
52	A	81	ASN	0	-0.009	-0.008	6.350	-1.825	-1.825	0.000	0.000	0.000	0.000
53	A	82	LEU	0	-0.015	-0.009	9.514	1.622	1.622	0.000	0.000	0.000	0.000
54	A	83	VAL	0	0.027	0.026	10.852	-1.471	-1.471	0.000	0.000	0.000	0.000
55	A	84	VAL	0	0.001	-0.007	12.669	0.919	0.919	0.000	0.000	0.000	0.000
56	A	85	VAL	0	0.004	-0.007	15.331	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.712	-0.803	18.844	-13.681	-13.681	0.000	0.000	0.000	0.000
58	A	87	SER	0	-0.032	-0.029	21.498	0.493	0.493	0.000	0.000	0.000	0.000
59	A	88	ASP	-1	-0.803	-0.886	24.983	-11.724	-11.724	0.000	0.000	0.000	0.000
60	A	89	ASP	-1	-0.829	-0.885	28.234	-10.290	-10.290	0.000	0.000	0.000	0.000
61	A	90	GLY	0	0.006	0.001	30.163	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.803	-0.897	31.246	-9.464	-9.464	0.000	0.000	0.000	0.000
63	A	92	ALA	0	0.062	0.021	31.432	-0.179	-0.179	0.000	0.000	0.000	0.000
64	A	93	ARG	1	0.801	0.881	28.803	10.465	10.465	0.000	0.000	0.000	0.000
65	A	94	LEU	0	-0.003	0.000	25.061	-0.225	-0.225	0.000	0.000	0.000	0.000
66	A	95	MET	0	0.013	0.011	27.120	-0.404	-0.404	0.000	0.000	0.000	0.000
67	A	96	ALA	0	0.075	0.050	28.099	-0.231	-0.231	0.000	0.000	0.000	0.000
68	A	97	THR	0	-0.099	-0.070	26.074	-0.251	-0.251	0.000	0.000	0.000	0.000
69	A	98	LEU	0	0.014	0.006	22.233	-0.489	-0.489	0.000	0.000	0.000	0.000
70	A	99	GLU	-1	-0.937	-0.965	24.028	-10.434	-10.434	0.000	0.000	0.000	0.000
71	A	100	THR	0	-0.030	-0.027	25.888	0.024	0.024	0.000	0.000	0.000	0.000
72	A	101	LEU	0	0.003	0.003	18.987	-0.272	-0.272	0.000	0.000	0.000	0.000
73	A	102	ALA	0	-0.013	-0.011	21.015	-0.560	-0.560	0.000	0.000	0.000	0.000
74	A	103	MET	0	-0.080	-0.031	21.594	0.039	0.039	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.926	-0.957	21.049	-12.256	-12.256	0.000	0.000	0.000	0.000
76	A	105	CYS	0	-0.099	-0.045	17.150	-0.900	-0.900	0.000	0.000	0.000	0.000
77	A	106	VAL	0	0.022	0.026	14.803	0.644	0.644	0.000	0.000	0.000	0.000
78	A	107	THR	0	0.032	0.008	15.545	-0.667	-0.667	0.000	0.000	0.000	0.000
79	A	108	GLY	0	0.003	-0.001	13.085	-0.451	-0.451	0.000	0.000	0.000	0.000
80	A	109	THR	0	-0.026	-0.005	12.532	-1.556	-1.556	0.000	0.000	0.000	0.000
81	A	110	LYS	1	0.867	0.950	12.672	19.704	19.704	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.058	0.019	14.603	-0.823	-0.823	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.010	0.005	14.249	0.318	0.318	0.000	0.000	0.000	0.000
84	A	113	VAL	0	0.001	0.003	17.600	-0.114	-0.114	0.000	0.000	0.000	0.000
85	A	114	ILE	0	-0.007	-0.003	16.943	0.032	0.032	0.000	0.000	0.000	0.000
86	A	115	GLY	0	0.055	0.024	21.341	0.280	0.280	0.000	0.000	0.000	0.000
87	A	116	ARG	1	0.892	0.941	25.139	10.093	10.093	0.000	0.000	0.000	0.000
88	A	117	SER	0	-0.031	0.002	28.157	0.320	0.320	0.000	0.000	0.000	0.000
89	A	118	ASN	0	0.060	0.036	28.536	-0.670	-0.670	0.000	0.000	0.000	0.000
90	A	119	ASP	-1	-0.815	-0.915	30.211	-9.114	-9.114	0.000	0.000	0.000	0.000
91	A	120	VAL	0	0.012	0.001	30.416	-0.313	-0.313	0.000	0.000	0.000	0.000
92	A	121	GLY	0	-0.025	-0.014	30.972	-0.175	-0.175	0.000	0.000	0.000	0.000
93	A	122	LEU	0	0.011	-0.002	28.588	-0.037	-0.037	0.000	0.000	0.000	0.000
94	A	123	TYR	0	-0.046	-0.041	22.278	-0.050	-0.050	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.936	0.961	26.726	9.171	9.171	0.000	0.000	0.000	0.000
96	A	125	LYS	1	0.893	0.939	28.517	9.301	9.301	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.028	-0.007	24.665	-0.092	-0.092	0.000	0.000	0.000	0.000
98	A	127	LEU	0	-0.005	-0.007	22.564	-0.292	-0.292	0.000	0.000	0.000	0.000
99	A	128	ASP	-1	-0.971	-0.970	24.675	-10.402	-10.402	0.000	0.000	0.000	0.000
100	A	129	ALA	0	-0.065	-0.033	26.056	0.141	0.141	0.000	0.000	0.000	0.000
101	A	130	GLY	0	-0.004	0.008	22.303	-0.117	-0.117	0.000	0.000	0.000	0.000
102	A	131	VAL	0	-0.086	-0.030	20.338	-0.780	-0.780	0.000	0.000	0.000	0.000
103	A	132	SER	0	-0.039	-0.036	16.615	-0.086	-0.086	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.805	-0.910	18.217	-15.337	-15.337	0.000	0.000	0.000	0.000
105	A	134	TYR	0	-0.094	-0.056	19.927	-0.119	-0.119	0.000	0.000	0.000	0.000
106	A	135	LEU	0	0.008	0.002	16.776	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	136	VAL	0	-0.011	-0.004	21.407	0.160	0.160	0.000	0.000	0.000	0.000
108	A	137	LYS	1	0.786	0.880	23.035	12.344	12.344	0.000	0.000	0.000	0.000
109	A	138	PRO	0	-0.040	-0.031	24.566	0.525	0.525	0.000	0.000	0.000	0.000
110	A	139	LEU	0	0.014	0.001	16.906	-0.038	-0.038	0.000	0.000	0.000	0.000
111	A	140	GLU	-1	-0.835	-0.908	19.355	-16.194	-16.194	0.000	0.000	0.000	0.000
112	A	141	PRO	0	-0.026	-0.021	15.152	-0.818	-0.818	0.000	0.000	0.000	0.000
113	A	142	MET	0	-0.041	-0.040	14.998	-1.951	-1.951	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.816	-0.902	16.426	-15.638	-15.638	0.000	0.000	0.000	0.000
115	A	144	PHE	0	0.023	-0.001	10.086	-0.200	-0.200	0.000	0.000	0.000	0.000
116	A	145	VAL	0	-0.002	-0.006	11.145	-1.221	-1.221	0.000	0.000	0.000	0.000
117	A	146	ALA	0	-0.021	-0.003	12.720	-0.694	-0.694	0.000	0.000	0.000	0.000
118	A	147	ALA	0	0.050	0.026	15.450	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	148	VAL	0	0.006	0.010	8.791	0.028	0.028	0.000	0.000	0.000	0.000
120	A	149	HIS	0	-0.095	-0.066	10.237	-0.648	-0.648	0.000	0.000	0.000	0.000
121	A	150	ARG	1	0.855	0.940	12.524	15.552	15.552	0.000	0.000	0.000	0.000
122	A	151	CYS	0	-0.068	-0.021	12.463	0.954	0.954	0.000	0.000	0.000	0.000
123	A	152	PHE	0	-0.043	-0.003	9.277	0.436	0.436	0.000	0.000	0.000	0.000

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