FMO DATABASE

FMODB ID: N925Q

Calculation Name: 4P6Z-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P6Z

Chain ID: S

ChEMBL ID:

UniProt ID: Q10567

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1532045.26443
FMO2-HF: Nuclear repulsion	1469122.686911
FMO2-HF: Total energy	-62922.577519
FMO2-MP2: Total energy	-63100.911936

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(S:1:MET)

Summations of interaction energy for fragment #1(S:1:MET)

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.
-34.803	-32.235	29.151	-10.522	-21.196	-0.077

Interaction energy analysis for fragmet #1(S:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.040

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	S	3	ARG	1	0.887	0.916	2.346	-11.713	-9.237	8.280	-3.970	-6.787	0.013
4	S	4	PHE	0	-0.049	-0.032	3.414	-0.643	-3.240	-0.016	3.123	-0.510	0.000
5	S	5	MET	0	0.040	0.027	6.250	-0.205	-0.205	0.000	0.000	0.000	0.000
6	S	6	LEU	0	-0.065	-0.027	9.469	0.024	0.024	0.000	0.000	0.000	0.000
7	S	7	LEU	0	0.059	0.044	13.052	-0.057	-0.057	0.000	0.000	0.000	0.000
8	S	8	PHE	0	0.042	-0.008	15.692	0.028	0.028	0.000	0.000	0.000	0.000
9	S	9	SER	0	0.053	0.037	19.534	-0.012	-0.012	0.000	0.000	0.000	0.000
10	S	10	ARG	1	0.859	0.909	23.187	0.015	0.015	0.000	0.000	0.000	0.000
11	S	11	ARG	1	0.939	0.969	25.315	0.023	0.023	0.000	0.000	0.000	0.000
12	S	12	GLY	0	0.046	0.029	22.622	0.008	0.008	0.000	0.000	0.000	0.000
13	S	13	LYS	1	0.818	0.890	22.704	-0.034	-0.034	0.000	0.000	0.000	0.000
14	S	14	LEU	0	0.043	0.016	15.679	-0.013	-0.013	0.000	0.000	0.000	0.000
15	S	15	ARG	1	0.778	0.881	18.499	0.029	0.029	0.000	0.000	0.000	0.000
16	S	16	LEU	0	0.087	0.060	14.003	-0.008	-0.008	0.000	0.000	0.000	0.000
17	S	17	GLN	0	-0.036	-0.007	12.349	0.095	0.095	0.000	0.000	0.000	0.000
18	S	18	LYS	1	0.880	0.943	7.897	0.562	0.562	0.000	0.000	0.000	0.000
19	S	19	TRP	0	-0.036	-0.042	6.402	0.170	0.170	0.000	0.000	0.000	0.000
20	S	20	TYR	0	0.006	-0.003	2.574	-0.713	-0.340	1.135	-0.374	-1.135	0.001
21	S	21	LEU	0	0.027	0.026	2.855	-2.077	-0.958	0.769	-0.536	-1.352	-0.005
22	S	22	ALA	0	0.019	0.015	4.256	-0.190	-0.132	0.000	-0.016	-0.042	0.000
23	S	23	THR	0	-0.032	-0.035	8.041	0.333	0.333	0.000	0.000	0.000	0.000
24	S	24	SER	0	0.038	0.025	10.245	-0.114	-0.114	0.000	0.000	0.000	0.000
25	S	25	ASP	-1	-0.751	-0.867	13.654	0.228	0.228	0.000	0.000	0.000	0.000
26	S	26	LYS	1	0.991	0.994	15.592	-0.261	-0.261	0.000	0.000	0.000	0.000
27	S	27	GLU	-1	-0.779	-0.872	13.439	0.533	0.533	0.000	0.000	0.000	0.000
28	S	28	ARG	1	0.942	0.987	7.918	-0.371	-0.371	0.000	0.000	0.000	0.000
29	S	29	LYS	1	0.875	0.914	12.937	-0.182	-0.182	0.000	0.000	0.000	0.000
30	S	30	LYS	1	0.777	0.885	16.440	-0.513	-0.513	0.000	0.000	0.000	0.000
31	S	31	MET	0	0.013	0.000	10.226	-0.007	-0.007	0.000	0.000	0.000	0.000
32	S	32	VAL	0	0.043	0.029	13.638	-0.031	-0.031	0.000	0.000	0.000	0.000
33	S	33	ARG	1	0.920	0.955	15.420	-0.244	-0.244	0.000	0.000	0.000	0.000
34	S	34	GLU	-1	-0.837	-0.897	16.144	0.497	0.497	0.000	0.000	0.000	0.000
35	S	35	LEU	0	0.044	0.025	12.756	-0.052	-0.052	0.000	0.000	0.000	0.000
36	S	36	MET	0	-0.012	0.019	16.550	-0.071	-0.071	0.000	0.000	0.000	0.000
37	S	37	GLN	0	-0.058	-0.027	18.731	-0.041	-0.041	0.000	0.000	0.000	0.000
38	S	38	VAL	0	0.015	0.007	18.424	-0.031	-0.031	0.000	0.000	0.000	0.000
39	S	39	VAL	0	-0.001	-0.007	16.849	-0.035	-0.035	0.000	0.000	0.000	0.000
40	S	40	LEU	0	-0.059	-0.020	19.967	-0.033	-0.033	0.000	0.000	0.000	0.000
41	S	41	ALA	0	-0.004	0.010	23.345	-0.016	-0.016	0.000	0.000	0.000	0.000
42	S	42	ARG	1	0.840	0.928	18.186	-0.001	-0.001	0.000	0.000	0.000	0.000
43	S	43	LYS	1	0.999	0.987	23.877	-0.001	-0.001	0.000	0.000	0.000	0.000
44	S	44	PRO	0	0.011	-0.009	24.654	-0.009	-0.009	0.000	0.000	0.000	0.000
45	S	45	LYS	1	0.922	0.960	25.092	0.089	0.089	0.000	0.000	0.000	0.000
46	S	46	MET	0	-0.017	0.010	21.670	0.000	0.000	0.000	0.000	0.000	0.000
47	S	47	CYS	0	0.021	0.026	17.733	-0.025	-0.025	0.000	0.000	0.000	0.000
48	S	48	SER	0	0.014	-0.003	15.671	0.033	0.033	0.000	0.000	0.000	0.000
49	S	49	PHE	0	0.030	0.008	13.181	-0.037	-0.037	0.000	0.000	0.000	0.000
50	S	50	LEU	0	-0.089	-0.045	13.468	0.044	0.044	0.000	0.000	0.000	0.000
51	S	51	GLU	-1	-0.861	-0.914	12.742	0.112	0.112	0.000	0.000	0.000	0.000
52	S	52	TRP	0	-0.064	-0.069	10.195	-0.007	-0.007	0.000	0.000	0.000	0.000
53	S	53	ARG	1	0.792	0.874	12.676	-0.656	-0.656	0.000	0.000	0.000	0.000
54	S	54	ASP	-1	-0.879	-0.935	12.001	0.931	0.931	0.000	0.000	0.000	0.000
55	S	55	LEU	0	-0.046	-0.013	6.431	0.432	0.432	0.000	0.000	0.000	0.000
56	S	56	LYS	1	0.809	0.911	7.149	0.641	0.641	0.000	0.000	0.000	0.000
57	S	57	VAL	0	-0.022	-0.022	8.583	0.105	0.105	0.000	0.000	0.000	0.000
58	S	58	VAL	0	0.009	0.015	9.586	-0.019	-0.019	0.000	0.000	0.000	0.000
59	S	59	TYR	0	0.008	0.008	11.951	0.047	0.047	0.000	0.000	0.000	0.000
60	S	60	LYS	1	0.955	0.987	15.139	0.264	0.264	0.000	0.000	0.000	0.000
61	S	61	ARG	1	0.836	0.918	17.685	0.088	0.088	0.000	0.000	0.000	0.000
62	S	62	TYR	0	0.023	-0.003	18.102	-0.013	-0.013	0.000	0.000	0.000	0.000
63	S	63	ALA	0	0.079	0.037	23.065	0.013	0.013	0.000	0.000	0.000	0.000
64	S	64	SER	0	-0.054	-0.042	26.035	0.007	0.007	0.000	0.000	0.000	0.000
65	S	65	LEU	0	0.023	0.018	19.934	0.025	0.025	0.000	0.000	0.000	0.000
66	S	66	TYR	0	-0.035	-0.025	18.970	-0.018	-0.018	0.000	0.000	0.000	0.000
67	S	67	PHE	0	0.079	0.044	15.497	0.033	0.033	0.000	0.000	0.000	0.000
68	S	68	CYS	0	-0.034	-0.030	13.034	-0.016	-0.016	0.000	0.000	0.000	0.000
69	S	69	CYS	0	-0.001	0.005	8.587	0.053	0.053	0.000	0.000	0.000	0.000
70	S	70	ALA	0	-0.014	-0.005	7.743	-0.176	-0.176	0.000	0.000	0.000	0.000
71	S	71	ILE	0	-0.018	-0.008	3.521	0.855	1.304	0.004	-0.133	-0.320	0.000
72	S	72	GLU	-1	-0.730	-0.841	2.530	5.772	8.244	0.621	-0.866	-2.226	-0.001
73	S	73	GLY	0	-0.002	-0.017	4.322	-0.649	-0.590	-0.001	-0.003	-0.054	0.000
74	S	74	GLN	0	-0.038	-0.031	4.030	-0.690	-0.507	-0.001	-0.019	-0.163	0.000
75	S	75	ASP	-1	-0.780	-0.876	2.050	-17.349	-21.792	14.016	-5.307	-4.267	-0.062
76	S	76	ASN	0	0.011	0.004	4.888	0.893	0.925	-0.001	-0.007	-0.023	0.000
77	S	77	GLU	-1	-0.769	-0.889	7.960	-0.879	-0.879	0.000	0.000	0.000	0.000
78	S	78	LEU	0	-0.023	-0.004	9.890	0.017	0.017	0.000	0.000	0.000	0.000
79	S	79	ILE	0	0.045	0.019	7.880	0.064	0.064	0.000	0.000	0.000	0.000
80	S	80	THR	0	0.006	-0.003	5.965	0.015	0.015	0.000	0.000	0.000	0.000
81	S	81	LEU	0	-0.025	-0.024	8.819	0.177	0.177	0.000	0.000	0.000	0.000
82	S	82	GLU	-1	-0.852	-0.926	12.536	-0.400	-0.400	0.000	0.000	0.000	0.000
83	S	83	LEU	0	0.001	0.021	7.296	0.079	0.079	0.000	0.000	0.000	0.000
84	S	84	ILE	0	-0.008	-0.018	11.269	0.103	0.103	0.000	0.000	0.000	0.000
85	S	85	HIS	0	-0.002	0.013	13.395	0.083	0.083	0.000	0.000	0.000	0.000
86	S	86	ARG	1	0.836	0.899	14.380	0.549	0.549	0.000	0.000	0.000	0.000
87	S	87	TYR	0	0.029	-0.005	13.877	0.055	0.055	0.000	0.000	0.000	0.000
88	S	88	VAL	0	-0.016	-0.015	15.911	0.054	0.054	0.000	0.000	0.000	0.000
89	S	89	GLU	-1	-0.844	-0.912	19.084	-0.315	-0.315	0.000	0.000	0.000	0.000
90	S	90	LEU	0	-0.029	0.003	15.950	0.030	0.030	0.000	0.000	0.000	0.000
91	S	91	LEU	0	0.002	0.002	17.863	0.032	0.032	0.000	0.000	0.000	0.000
92	S	92	ASP	-1	-0.894	-0.949	21.146	-0.169	-0.169	0.000	0.000	0.000	0.000
93	S	93	LYS	1	0.843	0.908	23.583	0.210	0.210	0.000	0.000	0.000	0.000
94	S	94	TYR	0	-0.058	-0.042	22.738	0.012	0.012	0.000	0.000	0.000	0.000
95	S	95	PHE	0	-0.006	-0.010	21.815	0.012	0.012	0.000	0.000	0.000	0.000
96	S	96	GLY	0	-0.012	0.005	26.686	0.013	0.013	0.000	0.000	0.000	0.000
97	S	97	SER	0	-0.067	-0.042	28.483	0.013	0.013	0.000	0.000	0.000	0.000
98	S	98	VAL	0	-0.034	0.014	23.258	0.010	0.010	0.000	0.000	0.000	0.000
99	S	99	CYS	0	-0.085	-0.049	26.345	0.007	0.007	0.000	0.000	0.000	0.000
100	S	100	GLU	-1	-0.793	-0.889	23.416	-0.057	-0.057	0.000	0.000	0.000	0.000
101	S	101	LEU	0	0.015	-0.007	24.646	0.004	0.004	0.000	0.000	0.000	0.000
102	S	102	ASP	-1	-0.734	-0.848	25.121	-0.121	-0.121	0.000	0.000	0.000	0.000
103	S	103	ILE	0	0.012	0.001	19.553	-0.001	-0.001	0.000	0.000	0.000	0.000
104	S	104	ILE	0	-0.128	-0.071	22.393	0.009	0.009	0.000	0.000	0.000	0.000
105	S	105	PHE	0	-0.015	-0.014	24.532	0.010	0.010	0.000	0.000	0.000	0.000
106	S	106	ASN	0	-0.002	0.023	23.696	0.002	0.002	0.000	0.000	0.000	0.000
107	S	107	PHE	0	0.027	0.015	19.203	-0.020	-0.020	0.000	0.000	0.000	0.000
108	S	108	GLU	-1	-0.813	-0.884	18.422	-0.161	-0.161	0.000	0.000	0.000	0.000
109	S	109	LYS	1	0.940	0.951	18.757	0.109	0.109	0.000	0.000	0.000	0.000
110	S	110	ALA	0	-0.012	-0.007	17.941	-0.031	-0.031	0.000	0.000	0.000	0.000
111	S	111	TYR	0	-0.050	-0.054	12.530	-0.025	-0.025	0.000	0.000	0.000	0.000
112	S	112	PHE	0	0.037	0.028	14.500	-0.062	-0.062	0.000	0.000	0.000	0.000
113	S	113	ILE	0	0.028	0.008	15.949	-0.051	-0.051	0.000	0.000	0.000	0.000
114	S	114	LEU	0	-0.071	-0.034	10.662	-0.039	-0.039	0.000	0.000	0.000	0.000
115	S	115	ASP	-1	-0.805	-0.890	11.116	-0.648	-0.648	0.000	0.000	0.000	0.000
116	S	116	GLU	-1	-0.885	-0.933	12.206	-0.538	-0.538	0.000	0.000	0.000	0.000
117	S	117	PHE	0	-0.077	-0.045	12.260	-0.014	-0.014	0.000	0.000	0.000	0.000
118	S	118	LEU	0	-0.026	-0.021	7.200	-0.114	-0.114	0.000	0.000	0.000	0.000
119	S	119	MET	0	0.065	0.032	7.675	0.190	0.190	0.000	0.000	0.000	0.000
120	S	120	GLY	0	-0.013	-0.014	4.705	-0.234	-0.087	-0.001	-0.036	-0.109	0.000
121	S	121	GLY	0	-0.019	-0.010	2.167	-4.199	-3.622	4.167	-2.212	-2.532	-0.011
122	S	122	ASP	-1	-0.918	-0.948	3.053	-4.324	-2.692	0.180	-0.165	-1.648	-0.012
123	S	123	VAL	0	-0.026	-0.020	5.141	0.293	0.324	-0.001	-0.001	-0.028	0.000
124	S	124	GLN	0	-0.018	0.001	8.813	-0.065	-0.065	0.000	0.000	0.000	0.000
125	S	125	ASP	-1	-0.792	-0.885	11.616	-0.347	-0.347	0.000	0.000	0.000	0.000
126	S	126	THR	0	0.002	-0.003	12.752	-0.036	-0.036	0.000	0.000	0.000	0.000
127	S	127	SER	0	-0.091	-0.042	14.923	0.047	0.047	0.000	0.000	0.000	0.000
128	S	128	LYS	1	0.907	0.934	18.573	0.317	0.317	0.000	0.000	0.000	0.000
129	S	129	LYS	1	0.948	0.966	19.613	0.229	0.229	0.000	0.000	0.000	0.000
130	S	130	SER	0	-0.040	-0.028	19.230	0.035	0.035	0.000	0.000	0.000	0.000
131	S	131	VAL	0	0.072	0.037	15.882	0.021	0.021	0.000	0.000	0.000	0.000
132	S	132	LEU	0	-0.036	-0.022	19.108	0.020	0.020	0.000	0.000	0.000	0.000
133	S	133	LYS	1	0.789	0.873	22.330	0.213	0.213	0.000	0.000	0.000	0.000
134	S	134	ALA	0	0.001	0.015	19.889	0.019	0.019	0.000	0.000	0.000	0.000
135	S	135	ILE	0	0.001	-0.002	18.090	0.014	0.014	0.000	0.000	0.000	0.000
136	S	136	GLU	-1	-0.854	-0.906	21.935	-0.170	-0.170	0.000	0.000	0.000	0.000
137	S	137	GLN	0	0.023	0.008	25.117	0.019	0.019	0.000	0.000	0.000	0.000
138	S	138	ALA	0	-0.012	0.007	22.069	0.011	0.011	0.000	0.000	0.000	0.000
139	S	139	ASP	-1	-0.817	-0.893	24.113	-0.184	-0.184	0.000	0.000	0.000	0.000
140	S	140	LEU	0	-0.022	-0.015	26.154	0.013	0.013	0.000	0.000	0.000	0.000
141	S	141	LEU	0	-0.044	-0.011	25.488	0.009	0.009	0.000	0.000	0.000	0.000
142	S	142	GLN	0	-0.024	-0.018	24.176	0.004	0.004	0.000	0.000	0.000	0.000
143	S	143	GLU	-1	-0.981	-0.993	27.957	-0.106	-0.106	0.000	0.000	0.000	0.000
144	S	144	GLU	-1	-0.918	-0.929	31.274	-0.091	-0.091	0.000	0.000	0.000	0.000
145	S	145	ASP	-1	-0.977	-0.987	28.593	-0.115	-0.115	0.000	0.000	0.000	0.000
146	S	146	GLU	-1	-1.033	-1.001	32.076	-0.070	-0.070	0.000	0.000	0.000	0.000
147	S	147	SER	0	-0.163	-0.105	34.185	0.011	0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(S:1:MET)