FMO DATABASE

FMODB ID: 94MK2

Calculation Name: 4EMZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMZ

Chain ID: B

ChEMBL ID:

UniProt ID: P35585

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1342020.807456
FMO2-HF: Nuclear repulsion	1285257.699348
FMO2-HF: Total energy	-56763.108109
FMO2-MP2: Total energy	-56931.787455

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(B:5:TRP)

Summations of interaction energy for fragment #1(B:5:TRP)

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.
-10.995	-5.538	1.121	-2.212	-4.363	0.015

Interaction energy analysis for fragmet #1(B:5:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.007

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	B	7	LYS	1	0.975	0.987	3.828	-3.560	-1.421	0.017	-0.967	-1.187	0.007
4	B	8	SER	0	0.049	0.025	5.919	0.143	0.143	0.000	0.000	0.000	0.000
5	B	9	SER	0	0.041	0.012	3.937	-0.119	0.239	0.002	-0.092	-0.268	0.000
6	B	10	VAL	0	-0.035	-0.033	3.980	-0.623	-0.366	0.001	-0.072	-0.186	0.000
7	B	11	ILE	0	0.025	-0.003	6.412	-0.356	-0.356	0.000	0.000	0.000	0.000
8	B	12	GLY	0	0.016	0.015	9.213	-0.262	-0.262	0.000	0.000	0.000	0.000
9	B	13	TRP	0	0.017	-0.009	8.271	-0.230	-0.230	0.000	0.000	0.000	0.000
10	B	14	PRO	0	-0.039	-0.013	10.316	-0.146	-0.146	0.000	0.000	0.000	0.000
11	B	15	ALA	0	0.069	0.013	13.185	-0.113	-0.113	0.000	0.000	0.000	0.000
12	B	16	VAL	0	-0.001	0.010	12.250	-0.093	-0.093	0.000	0.000	0.000	0.000
13	B	17	ARG	1	0.897	0.984	11.612	-1.028	-1.028	0.000	0.000	0.000	0.000
14	B	18	GLU	-1	-0.879	-0.956	15.142	0.292	0.292	0.000	0.000	0.000	0.000
15	B	19	ARG	1	0.935	0.977	16.463	-0.240	-0.240	0.000	0.000	0.000	0.000
16	B	20	MET	0	-0.053	-0.019	15.443	-0.027	-0.027	0.000	0.000	0.000	0.000
17	B	21	ARG	1	0.860	0.926	17.052	-0.461	-0.461	0.000	0.000	0.000	0.000
18	B	22	ARG	1	0.961	0.997	20.655	-0.219	-0.219	0.000	0.000	0.000	0.000
19	B	23	ALA	0	-0.013	0.007	23.639	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	59	GLU	-1	-0.926	-0.975	25.077	0.103	0.103	0.000	0.000	0.000	0.000
21	B	60	ALA	0	0.026	0.006	26.179	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	61	GLN	0	-0.078	-0.064	28.132	-0.011	-0.011	0.000	0.000	0.000	0.000
23	B	62	GLU	-1	-0.971	-0.964	25.096	0.044	0.044	0.000	0.000	0.000	0.000
24	B	63	GLU	-1	-1.035	-1.014	24.912	0.004	0.004	0.000	0.000	0.000	0.000
25	B	64	GLU	-1	-1.029	-1.014	26.378	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	65	GLU	-1	-0.910	-0.937	27.595	0.002	0.002	0.000	0.000	0.000	0.000
27	B	66	VAL	0	-0.049	-0.020	28.059	-0.006	-0.006	0.000	0.000	0.000	0.000
28	B	67	GLY	0	0.001	-0.009	27.146	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	68	PHE	0	-0.014	-0.013	22.259	0.003	0.003	0.000	0.000	0.000	0.000
30	B	69	PRO	0	0.010	0.007	21.378	-0.018	-0.018	0.000	0.000	0.000	0.000
31	B	70	VAL	0	0.017	0.013	18.175	-0.026	-0.026	0.000	0.000	0.000	0.000
32	B	71	THR	0	-0.005	-0.019	15.278	0.032	0.032	0.000	0.000	0.000	0.000
33	B	72	PRO	0	-0.006	-0.002	17.636	-0.042	-0.042	0.000	0.000	0.000	0.000
34	B	73	GLN	0	0.028	-0.001	16.988	-0.019	-0.019	0.000	0.000	0.000	0.000
35	B	74	VAL	0	-0.058	0.000	11.733	-0.046	-0.046	0.000	0.000	0.000	0.000
36	B	75	PRO	0	0.014	0.008	11.879	0.033	0.033	0.000	0.000	0.000	0.000
37	B	76	LEU	0	-0.011	0.019	12.256	-0.136	-0.136	0.000	0.000	0.000	0.000
38	B	77	ARG	1	0.819	0.904	7.442	1.731	1.731	0.000	0.000	0.000	0.000
39	B	78	PRO	0	0.087	0.039	13.217	-0.046	-0.046	0.000	0.000	0.000	0.000
40	B	79	MET	0	-0.024	0.007	7.659	-0.113	-0.113	0.000	0.000	0.000	0.000
41	B	80	THR	0	-0.007	-0.006	8.452	0.121	0.121	0.000	0.000	0.000	0.000
42	B	81	TYR	0	0.007	-0.042	10.253	-0.022	-0.022	0.000	0.000	0.000	0.000
43	B	82	LYS	1	0.975	0.971	7.385	0.970	0.970	0.000	0.000	0.000	0.000
44	B	83	ALA	0	0.052	0.038	5.867	0.224	0.224	0.000	0.000	0.000	0.000
45	B	84	ALA	0	-0.001	0.005	6.633	0.029	0.029	0.000	0.000	0.000	0.000
46	B	85	VAL	0	0.061	0.045	8.091	0.178	0.178	0.000	0.000	0.000	0.000
47	B	86	ASP	-1	-0.917	-0.963	3.775	0.558	1.193	0.008	-0.093	-0.550	0.000
48	B	87	LEU	0	-0.066	-0.034	4.661	0.061	0.340	-0.001	-0.015	-0.262	0.000
49	B	88	SER	0	-0.024	-0.021	6.193	0.432	0.432	0.000	0.000	0.000	0.000
50	B	89	HIS	0	-0.001	0.002	6.004	0.052	0.052	0.000	0.000	0.000	0.000
51	B	90	PHE	0	0.014	0.029	2.724	-1.826	-0.181	1.096	-0.931	-1.810	0.008
52	B	91	LEU	0	-0.023	-0.028	4.822	0.050	0.075	-0.001	-0.010	-0.014	0.000
53	B	92	LYS	1	0.896	0.983	8.284	-0.527	-0.527	0.000	0.000	0.000	0.000
54	B	93	GLU	-1	-0.887	-0.959	5.445	0.701	0.701	0.000	0.000	0.000	0.000
55	B	94	LYS	1	0.834	0.932	4.835	-3.433	-3.433	0.000	0.000	0.000	0.000
56	B	95	GLY	0	0.086	0.048	9.047	-0.224	-0.224	0.000	0.000	0.000	0.000
57	B	96	GLY	0	-0.055	-0.050	11.851	0.080	0.080	0.000	0.000	0.000	0.000
58	B	97	LEU	0	0.023	0.003	12.848	-0.060	-0.060	0.000	0.000	0.000	0.000
59	B	98	GLU	-1	-0.788	-0.890	14.817	0.203	0.203	0.000	0.000	0.000	0.000
60	B	99	GLY	0	-0.077	-0.013	16.556	0.007	0.007	0.000	0.000	0.000	0.000
61	B	100	LEU	0	-0.014	-0.005	18.255	-0.034	-0.034	0.000	0.000	0.000	0.000
62	B	101	ILE	0	0.020	0.003	20.586	-0.016	-0.016	0.000	0.000	0.000	0.000
63	B	102	HIS	1	0.851	0.930	20.360	-0.058	-0.058	0.000	0.000	0.000	0.000
64	B	103	SER	0	0.014	0.007	22.456	-0.016	-0.016	0.000	0.000	0.000	0.000
65	B	104	GLN	0	0.042	0.002	22.108	0.019	0.019	0.000	0.000	0.000	0.000
66	B	105	ARG	1	1.026	1.016	21.799	-0.076	-0.076	0.000	0.000	0.000	0.000
67	B	106	ARG	1	0.931	0.954	19.403	-0.173	-0.173	0.000	0.000	0.000	0.000
68	B	107	GLN	0	0.008	-0.008	17.267	0.054	0.054	0.000	0.000	0.000	0.000
69	B	108	ASP	-1	-0.839	-0.909	16.631	-0.048	-0.048	0.000	0.000	0.000	0.000
70	B	109	ILE	0	-0.053	-0.002	15.865	-0.014	-0.014	0.000	0.000	0.000	0.000
71	B	110	LEU	0	-0.039	-0.026	10.822	0.009	0.009	0.000	0.000	0.000	0.000
72	B	111	ASP	-1	-0.811	-0.917	12.523	-0.180	-0.180	0.000	0.000	0.000	0.000
73	B	112	LEU	0	0.025	0.018	13.569	-0.097	-0.097	0.000	0.000	0.000	0.000
74	B	113	TRP	0	-0.027	0.005	7.140	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	114	ILE	0	-0.014	0.007	7.591	-0.069	-0.069	0.000	0.000	0.000	0.000
76	B	115	TYR	0	0.028	0.016	9.777	-0.250	-0.250	0.000	0.000	0.000	0.000
77	B	116	HIS	0	0.035	0.015	12.497	-0.109	-0.109	0.000	0.000	0.000	0.000
78	B	117	THR	0	-0.105	-0.082	8.315	-0.078	-0.078	0.000	0.000	0.000	0.000
79	B	118	GLN	0	-0.056	-0.035	3.894	-1.750	-1.631	-0.001	-0.032	-0.086	0.000
80	B	119	GLY	0	0.076	0.047	7.900	-0.252	-0.252	0.000	0.000	0.000	0.000
81	B	120	TYR	0	-0.052	-0.047	5.468	0.226	0.226	0.000	0.000	0.000	0.000
82	B	121	PHE	0	0.030	0.022	11.495	0.096	0.096	0.000	0.000	0.000	0.000
83	B	122	PRO	0	0.008	-0.004	14.893	-0.035	-0.035	0.000	0.000	0.000	0.000
84	B	123	ASP	-1	-0.903	-0.941	16.043	-0.296	-0.296	0.000	0.000	0.000	0.000
85	B	124	TRP	0	0.025	0.003	11.268	0.026	0.026	0.000	0.000	0.000	0.000
86	B	125	GLN	0	-0.024	0.003	14.294	0.088	0.088	0.000	0.000	0.000	0.000
87	B	126	ASN	0	0.032	0.018	16.500	0.035	0.035	0.000	0.000	0.000	0.000
88	B	127	TYR	0	-0.024	-0.030	17.095	0.004	0.004	0.000	0.000	0.000	0.000
89	B	128	THR	0	-0.008	0.004	22.277	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	129	PRO	0	-0.010	-0.009	25.648	0.012	0.012	0.000	0.000	0.000	0.000
91	B	130	GLY	0	-0.035	-0.020	28.777	0.004	0.004	0.000	0.000	0.000	0.000
92	B	131	PRO	0	0.002	-0.006	30.259	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	132	GLY	0	0.056	0.023	30.085	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	133	VAL	0	-0.032	-0.026	24.387	0.003	0.003	0.000	0.000	0.000	0.000
95	B	134	ARG	1	0.768	0.927	23.450	-0.024	-0.024	0.000	0.000	0.000	0.000
96	B	135	TYR	0	0.056	-0.002	21.880	0.016	0.016	0.000	0.000	0.000	0.000
97	B	136	PRO	0	0.028	0.015	17.224	-0.012	-0.012	0.000	0.000	0.000	0.000
98	B	137	LEU	0	0.023	0.011	19.351	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	138	THR	0	-0.038	-0.027	14.106	-0.033	-0.033	0.000	0.000	0.000	0.000
100	B	139	PHE	0	-0.018	-0.016	16.429	0.022	0.022	0.000	0.000	0.000	0.000
101	B	140	GLY	0	0.075	0.015	13.344	-0.062	-0.062	0.000	0.000	0.000	0.000
102	B	141	TRP	0	-0.047	-0.016	9.787	0.032	0.032	0.000	0.000	0.000	0.000
103	B	142	CYS	0	-0.043	-0.031	12.042	0.010	0.010	0.000	0.000	0.000	0.000
104	B	143	TYR	0	-0.019	-0.003	11.031	0.058	0.058	0.000	0.000	0.000	0.000
105	B	144	LYS	1	0.920	0.957	15.833	-0.116	-0.116	0.000	0.000	0.000	0.000
106	B	145	LEU	0	-0.034	-0.005	19.541	0.030	0.030	0.000	0.000	0.000	0.000
107	B	146	VAL	0	0.018	-0.011	22.179	-0.018	-0.018	0.000	0.000	0.000	0.000
108	B	147	PRO	0	-0.023	0.002	24.890	0.008	0.008	0.000	0.000	0.000	0.000
109	B	148	VAL	0	-0.035	-0.008	26.503	0.005	0.005	0.000	0.000	0.000	0.000
110	B	149	GLU	-1	-0.931	-0.961	29.317	0.071	0.071	0.000	0.000	0.000	0.000
111	B	150	PRO	0	-0.022	0.005	31.801	-0.002	-0.002	0.000	0.000	0.000	0.000
112	B	178	ARG	1	0.968	0.987	31.749	-0.024	-0.024	0.000	0.000	0.000	0.000
113	B	179	GLU	-1	-0.824	-0.917	30.732	0.033	0.033	0.000	0.000	0.000	0.000
114	B	180	VAL	0	0.017	0.002	27.891	-0.004	-0.004	0.000	0.000	0.000	0.000
115	B	181	LEU	0	-0.030	-0.028	25.309	-0.003	-0.003	0.000	0.000	0.000	0.000
116	B	182	GLU	-1	-0.778	-0.873	22.478	0.153	0.153	0.000	0.000	0.000	0.000
117	B	183	TRP	0	0.030	0.026	16.898	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	184	ARG	1	0.813	0.870	18.539	-0.157	-0.157	0.000	0.000	0.000	0.000
119	B	185	PHE	0	0.017	-0.008	11.039	-0.032	-0.032	0.000	0.000	0.000	0.000
120	B	186	ASP	-1	-0.812	-0.912	15.895	0.056	0.056	0.000	0.000	0.000	0.000
121	B	187	SER	0	0.085	0.021	13.913	-0.007	-0.007	0.000	0.000	0.000	0.000
122	B	188	ARG	1	0.872	0.937	15.745	-0.072	-0.072	0.000	0.000	0.000	0.000
123	B	189	LEU	0	0.005	0.026	16.481	-0.021	-0.021	0.000	0.000	0.000	0.000
124	B	190	ALA	0	-0.003	0.001	14.076	-0.030	-0.030	0.000	0.000	0.000	0.000
125	B	191	PHE	0	-0.033	0.011	15.590	-0.031	-0.031	0.000	0.000	0.000	0.000
126	B	192	HIS	0	-0.062	-0.031	18.977	-0.002	-0.002	0.000	0.000	0.000	0.000
127	B	193	HIS	0	-0.004	0.010	20.705	0.021	0.021	0.000	0.000	0.000	0.000
128	B	194	VAL	0	0.054	0.027	22.054	-0.003	-0.003	0.000	0.000	0.000	0.000
129	B	195	ALA	0	0.023	0.008	22.619	0.001	0.001	0.000	0.000	0.000	0.000
130	B	196	ARG	1	0.914	0.962	23.802	0.141	0.141	0.000	0.000	0.000	0.000
131	B	197	GLU	-1	-0.869	-0.921	25.722	-0.054	-0.054	0.000	0.000	0.000	0.000
132	B	198	LEU	0	-0.033	-0.028	27.084	0.003	0.003	0.000	0.000	0.000	0.000
133	B	199	HIS	1	0.835	0.911	27.689	0.061	0.061	0.000	0.000	0.000	0.000
134	B	200	PRO	0	0.038	0.028	28.138	-0.013	-0.013	0.000	0.000	0.000	0.000
135	B	201	GLU	-1	-0.839	-0.924	29.356	-0.081	-0.081	0.000	0.000	0.000	0.000
136	B	202	TYR	0	-0.045	-0.032	25.542	-0.002	-0.002	0.000	0.000	0.000	0.000
137	B	203	PHE	0	-0.061	-0.012	21.652	-0.016	-0.016	0.000	0.000	0.000	0.000
138	B	204	LYS	1	0.973	1.000	26.350	0.104	0.104	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:5:TRP)