FMO DATABASE

FMODB ID: 82ZRY

Calculation Name: 5B7W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B7W

Chain ID: A

ChEMBL ID:

UniProt ID: Q4UQD0

Base Structure: X-ray

Registration Date: 2023-06-20

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1499134.357045
FMO2-HF: Nuclear repulsion	1435848.242904
FMO2-HF: Total energy	-63286.114142
FMO2-MP2: Total energy	-63472.778249

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-10.501	-8.491	5.744	-1.061	-6.694	0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.022

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	A	3	SER	0	-0.024	-0.019	3.810	-1.878	-0.480	-0.011	-0.610	-0.777	0.003
4	A	4	PHE	0	-0.039	-0.011	6.206	0.612	0.612	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.832	-0.917	9.904	-1.530	-1.530	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.051	-0.040	12.764	0.169	0.169	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.020	0.003	15.225	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.017	-0.023	18.537	0.048	0.048	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.908	-0.950	21.367	-0.434	-0.434	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.026	0.004	24.334	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.830	-0.905	27.782	-0.186	-0.186	0.000	0.000	0.000	0.000
12	A	12	LYS	1	1.016	0.990	29.121	0.197	0.197	0.000	0.000	0.000	0.000
13	A	13	HIS	0	-0.026	0.000	31.768	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.796	-0.895	31.722	-0.101	-0.101	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.022	-0.004	32.570	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.035	-0.027	34.607	0.005	0.005	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.027	0.012	37.120	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.032	-0.012	36.871	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.008	0.000	38.478	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.884	-0.939	40.853	-0.098	-0.098	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.080	-0.059	40.068	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.006	0.015	42.401	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.010	-0.009	44.294	0.006	0.006	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.969	0.984	46.632	0.067	0.067	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.920	-0.965	45.774	-0.061	-0.061	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.009	-0.008	48.262	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.896	-0.934	50.445	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.139	-0.067	51.362	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.885	0.957	50.194	0.059	0.059	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.017	-0.006	54.017	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.870	-0.953	54.149	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.007	-0.016	50.956	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.943	0.989	55.781	0.048	0.048	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.012	-0.016	59.005	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.077	-0.020	54.932	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.940	-0.966	55.460	-0.067	-0.067	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.011	-0.022	50.875	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.929	0.978	48.527	0.094	0.094	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.002	-0.008	43.072	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.938	-0.966	43.556	-0.117	-0.117	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.033	-0.006	36.237	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.869	-0.937	39.158	-0.148	-0.148	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.885	-0.952	35.868	-0.186	-0.186	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.076	-0.039	34.242	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.902	0.940	29.903	0.248	0.248	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.030	0.025	34.144	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.029	0.021	36.882	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.045	-0.018	39.701	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.002	-0.013	42.883	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.051	-0.025	45.410	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.054	0.016	49.146	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	PRO	0	0.041	0.031	52.074	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.022	-0.016	54.166	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.842	-0.939	49.582	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.013	-0.010	50.008	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	GLN	0	0.069	0.028	50.730	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.073	0.039	46.162	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.958	0.987	46.225	0.064	0.064	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.019	-0.017	46.182	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	MET	0	-0.028	0.003	45.967	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	THR	0	0.027	0.022	41.038	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.944	-0.970	41.696	-0.077	-0.077	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.037	-0.012	42.594	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.013	0.009	38.906	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.924	0.956	37.357	0.098	0.098	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.012	0.010	37.677	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.899	0.956	39.059	0.072	0.072	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.030	0.005	34.436	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.024	-0.008	33.247	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.057	-0.013	34.630	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.765	0.873	34.636	0.097	0.097	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.001	0.007	31.124	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.023	-0.007	29.587	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.802	-0.901	27.688	-0.145	-0.145	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.046	0.014	29.919	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.862	0.916	25.721	0.173	0.173	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.091	-0.038	28.464	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.036	-0.004	29.895	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.965	-0.978	32.740	-0.200	-0.200	0.000	0.000	0.000	0.000
80	A	80	PHE	0	-0.060	-0.036	34.556	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.049	0.032	38.316	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.888	-0.942	40.276	-0.111	-0.111	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.076	-0.036	43.701	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.921	-0.951	45.850	-0.111	-0.111	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.032	-0.023	48.904	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.003	-0.011	52.581	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.009	-0.017	55.377	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.051	-0.019	55.485	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.010	0.017	54.843	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.034	-0.014	50.522	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.943	0.950	47.601	0.093	0.093	0.000	0.000	0.000	0.000
92	A	92	GLN	0	0.014	0.005	42.406	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.999	1.026	37.699	0.170	0.170	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.022	-0.014	36.688	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.012	0.005	32.515	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.014	-0.004	30.887	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.920	0.978	28.241	0.209	0.209	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.092	-0.068	26.103	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.016	0.016	22.460	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.090	-0.057	17.876	0.031	0.031	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.831	-0.910	20.647	-0.379	-0.379	0.000	0.000	0.000	0.000
102	A	102	GLN	0	0.026	-0.015	20.023	0.008	0.008	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.919	0.976	20.813	0.270	0.270	0.000	0.000	0.000	0.000
104	A	104	GLN	0	0.064	0.016	21.876	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.065	0.034	16.884	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.951	0.969	16.891	0.456	0.456	0.000	0.000	0.000	0.000
107	A	107	GLN	0	-0.026	-0.015	18.075	0.023	0.023	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.004	0.003	15.924	0.020	0.020	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.024	-0.016	12.384	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.012	0.002	14.425	0.020	0.020	0.000	0.000	0.000	0.000
111	A	111	LYS	1	1.047	1.018	17.087	0.295	0.295	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.003	0.020	11.082	0.051	0.051	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.954	0.968	12.738	0.565	0.565	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.970	-0.996	13.860	-0.131	-0.131	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.093	-0.028	15.111	0.057	0.057	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.890	0.938	13.293	0.071	0.071	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.053	0.043	9.796	0.127	0.127	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.873	0.942	7.104	-1.249	-1.249	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.025	-0.026	5.785	0.355	0.355	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.947	-0.968	4.631	-3.831	-3.667	-0.001	-0.007	-0.156	0.000
121	A	121	ALA	0	-0.019	-0.011	6.329	-0.302	-0.302	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.005	0.000	9.149	-0.178	-0.178	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.014	-0.008	10.734	0.056	0.056	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.042	-0.037	11.916	-0.206	-0.206	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.011	0.012	15.318	0.045	0.045	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.893	-0.933	19.015	-0.552	-0.552	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.988	1.012	15.866	0.684	0.684	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.031	-0.019	12.246	-0.056	-0.056	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.941	0.991	7.656	1.869	1.869	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.037	-0.017	7.846	-0.147	-0.147	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.009	-0.013	3.075	-1.540	-0.779	0.079	-0.221	-0.620	0.000
132	A	132	GLY	0	0.091	0.042	3.471	-0.776	-0.080	0.017	-0.209	-0.504	0.000
133	A	133	LYS	1	0.919	0.961	2.769	-4.287	-2.201	5.717	-3.985	-3.818	0.003
134	A	134	LYS	1	0.904	0.939	3.671	-1.004	-4.342	-0.056	3.992	-0.598	0.000
135	A	135	ARG	1	0.993	0.985	5.982	-0.915	-0.915	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.879	-0.945	8.007	0.626	0.626	0.000	0.000	0.000	0.000
137	A	137	ASP	-1	-0.806	-0.905	7.699	1.844	1.844	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.021	-0.005	5.826	-0.218	-0.218	0.000	0.000	0.000	0.000
139	A	139	GLN	0	0.004	0.000	9.627	-0.203	-0.203	0.000	0.000	0.000	0.000
140	A	140	ASP	-1	-0.866	-0.915	12.517	0.338	0.338	0.000	0.000	0.000	0.000
141	A	141	ALA	0	0.000	-0.004	11.050	-0.076	-0.076	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.044	-0.018	12.651	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.044	-0.026	14.986	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	144	VAL	0	-0.027	-0.018	15.993	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	145	LEU	0	-0.029	-0.022	13.984	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	146	LYS	1	0.909	0.961	18.065	0.130	0.130	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.877	0.954	20.838	0.023	0.023	0.000	0.000	0.000	0.000
148	A	148	ALA	0	0.016	0.016	20.590	0.012	0.012	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.951	-0.967	22.716	-0.130	-0.130	0.000	0.000	0.000	0.000
150	A	150	PHE	0	-0.038	-0.027	20.984	-0.020	-0.020	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.941	-0.968	24.633	-0.239	-0.239	0.000	0.000	0.000	0.000
152	A	152	LEU	0	0.008	-0.014	23.106	0.001	0.001	0.000	0.000	0.000	0.000
153	A	153	PRO	0	-0.027	-0.002	24.096	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.008	0.008	18.420	-0.034	-0.034	0.000	0.000	0.000	0.000
155	A	155	GLN	0	0.023	0.018	19.742	0.029	0.029	0.000	0.000	0.000	0.000
156	A	156	PHE	0	0.008	-0.017	14.598	-0.034	-0.034	0.000	0.000	0.000	0.000
157	A	157	ASP	-1	-0.853	-0.928	15.108	-0.487	-0.487	0.000	0.000	0.000	0.000
158	A	158	ASN	0	0.007	0.008	12.800	-0.270	-0.270	0.000	0.000	0.000	0.000
159	A	159	PHE	0	-0.024	-0.017	10.316	-0.233	-0.233	0.000	0.000	0.000	0.000
160	A	160	ARG	1	0.927	0.975	7.447	2.333	2.333	0.000	0.000	0.000	0.000
161	A	161	ASP	-1	-0.926	-0.956	4.764	-0.096	0.147	-0.001	-0.021	-0.221	0.000

Top

Graph

Manual

About

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