FMO DATABASE

FMODB ID: 52Q7Z

Calculation Name: 5GXB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GXB

Chain ID: B

ChEMBL ID:

UniProt ID: P02920

Base Structure: X-ray

Registration Date: 2023-06-26

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1147351.087651
FMO2-HF: Nuclear repulsion	1095350.348725
FMO2-HF: Total energy	-52000.738926
FMO2-MP2: Total energy	-52151.333316

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:0:MET)

Summations of interaction energy for fragment #1(B:0: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.
-13.9	-11.923	19.204	-6.333	-14.848	-0.02

Interaction energy analysis for fragmet #1(B:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.013

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	2	VAL	0	-0.009	0.027	3.705	-0.829	1.722	-0.008	-1.173	-1.371	0.002
4	B	3	GLN	0	-0.016	-0.015	5.631	-0.392	-0.392	0.000	0.000	0.000	0.000
5	B	4	LEU	0	-0.048	-0.034	7.895	0.187	0.187	0.000	0.000	0.000	0.000
6	B	5	VAL	0	0.038	0.011	10.749	0.046	0.046	0.000	0.000	0.000	0.000
7	B	6	GLU	-1	-0.785	-0.890	14.114	-0.632	-0.632	0.000	0.000	0.000	0.000
8	B	7	SER	0	-0.052	-0.022	16.936	0.006	0.006	0.000	0.000	0.000	0.000
9	B	8	GLY	0	0.046	0.012	20.578	0.005	0.005	0.000	0.000	0.000	0.000
10	B	9	GLY	0	-0.017	-0.002	23.425	-0.006	-0.006	0.000	0.000	0.000	0.000
11	B	10	ARG	1	0.886	0.936	25.063	0.166	0.166	0.000	0.000	0.000	0.000
12	B	11	LEU	0	-0.009	0.004	28.447	0.004	0.004	0.000	0.000	0.000	0.000
13	B	12	VAL	0	-0.040	-0.026	29.779	-0.004	-0.004	0.000	0.000	0.000	0.000
14	B	13	GLN	0	0.010	-0.004	32.662	0.001	0.001	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.024	0.005	35.044	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	15	GLY	0	-0.006	0.001	34.812	0.004	0.004	0.000	0.000	0.000	0.000
17	B	16	ASP	-1	-0.831	-0.889	34.324	-0.145	-0.145	0.000	0.000	0.000	0.000
18	B	17	SER	0	-0.024	-0.046	30.890	0.003	0.003	0.000	0.000	0.000	0.000
19	B	18	LEU	0	-0.041	-0.024	26.425	-0.007	-0.007	0.000	0.000	0.000	0.000
20	B	19	ARG	1	0.843	0.927	23.837	0.251	0.251	0.000	0.000	0.000	0.000
21	B	20	LEU	0	0.012	0.020	20.273	-0.013	-0.013	0.000	0.000	0.000	0.000
22	B	21	SER	0	0.028	0.006	19.354	0.025	0.025	0.000	0.000	0.000	0.000
23	B	22	CYS	0	-0.093	-0.043	12.872	-0.022	-0.022	0.000	0.000	0.000	0.000
24	B	23	ALA	0	0.046	0.032	14.978	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	24	ALA	0	-0.024	-0.020	9.963	-0.107	-0.107	0.000	0.000	0.000	0.000
26	B	25	SER	0	0.017	0.004	10.633	-0.040	-0.040	0.000	0.000	0.000	0.000
27	B	26	GLY	0	0.018	0.011	7.946	0.085	0.085	0.000	0.000	0.000	0.000
28	B	27	ARG	1	0.895	0.933	7.938	1.069	1.069	0.000	0.000	0.000	0.000
29	B	28	THR	0	0.000	-0.009	8.837	0.240	0.240	0.000	0.000	0.000	0.000
30	B	29	PHE	0	0.024	0.005	7.027	0.112	0.112	0.000	0.000	0.000	0.000
31	B	30	THR	0	0.006	0.017	4.680	0.003	0.118	-0.001	-0.005	-0.108	0.000
32	B	31	THR	0	0.090	0.061	5.683	0.163	0.163	0.000	0.000	0.000	0.000
33	B	32	TYR	0	-0.058	-0.034	6.802	0.053	0.053	0.000	0.000	0.000	0.000
34	B	33	LEU	0	-0.123	-0.069	9.175	0.098	0.098	0.000	0.000	0.000	0.000
35	B	34	MET	0	0.034	0.027	9.853	-0.165	-0.165	0.000	0.000	0.000	0.000
36	B	35	GLY	0	0.021	0.008	12.115	0.108	0.108	0.000	0.000	0.000	0.000
37	B	36	TRP	0	-0.020	-0.003	13.572	-0.085	-0.085	0.000	0.000	0.000	0.000
38	B	37	PHE	0	0.023	0.000	13.967	0.066	0.066	0.000	0.000	0.000	0.000
39	B	38	ARG	1	0.828	0.905	16.911	0.060	0.060	0.000	0.000	0.000	0.000
40	B	39	GLN	0	0.011	0.001	19.154	0.024	0.024	0.000	0.000	0.000	0.000
41	B	40	ALA	0	0.028	0.006	21.306	-0.021	-0.021	0.000	0.000	0.000	0.000
42	B	41	PRO	0	-0.008	0.008	24.274	0.001	0.001	0.000	0.000	0.000	0.000
43	B	42	GLY	0	0.042	0.016	26.664	0.004	0.004	0.000	0.000	0.000	0.000
44	B	43	LYS	1	0.763	0.888	25.299	0.030	0.030	0.000	0.000	0.000	0.000
45	B	44	GLU	-1	-0.840	-0.927	21.359	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	45	ARG	1	0.928	0.979	16.384	-0.113	-0.113	0.000	0.000	0.000	0.000
47	B	46	GLU	-1	-0.774	-0.870	19.413	-0.025	-0.025	0.000	0.000	0.000	0.000
48	B	47	PHE	0	0.011	-0.008	16.620	-0.031	-0.031	0.000	0.000	0.000	0.000
49	B	48	VAL	0	-0.009	0.003	18.476	0.006	0.006	0.000	0.000	0.000	0.000
50	B	49	ALA	0	-0.010	-0.013	18.474	0.018	0.018	0.000	0.000	0.000	0.000
51	B	50	ALA	0	0.018	0.006	15.361	-0.034	-0.034	0.000	0.000	0.000	0.000
52	B	51	ILE	0	-0.037	-0.017	15.234	0.025	0.025	0.000	0.000	0.000	0.000
53	B	52	ARG	1	0.996	1.004	12.743	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	53	TRP	0	-0.010	-0.017	10.488	0.082	0.082	0.000	0.000	0.000	0.000
55	B	54	SER	0	0.018	0.005	15.412	0.022	0.022	0.000	0.000	0.000	0.000
56	B	55	GLY	0	0.048	0.026	17.459	0.025	0.025	0.000	0.000	0.000	0.000
57	B	56	GLY	0	-0.019	-0.007	18.889	0.006	0.006	0.000	0.000	0.000	0.000
58	B	57	SER	0	-0.013	0.000	18.553	0.010	0.010	0.000	0.000	0.000	0.000
59	B	58	THR	0	0.003	-0.003	18.925	-0.016	-0.016	0.000	0.000	0.000	0.000
60	B	59	TYR	0	0.007	-0.006	16.396	0.023	0.023	0.000	0.000	0.000	0.000
61	B	60	TYR	0	0.037	0.013	20.420	-0.030	-0.030	0.000	0.000	0.000	0.000
62	B	61	ALA	0	0.016	0.034	22.157	0.017	0.017	0.000	0.000	0.000	0.000
63	B	62	ASP	-1	-0.811	-0.934	23.650	-0.017	-0.017	0.000	0.000	0.000	0.000
64	B	63	SER	0	0.000	0.011	26.765	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	64	VAL	0	-0.036	-0.017	24.327	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	65	LYS	1	0.982	0.986	26.897	0.012	0.012	0.000	0.000	0.000	0.000
67	B	66	GLY	0	-0.027	0.013	28.225	0.001	0.001	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.702	0.809	29.147	0.092	0.092	0.000	0.000	0.000	0.000
69	B	68	PHE	0	0.014	-0.004	23.307	-0.014	-0.014	0.000	0.000	0.000	0.000
70	B	69	THR	0	-0.031	-0.012	24.823	0.011	0.011	0.000	0.000	0.000	0.000
71	B	70	ILE	0	-0.012	0.017	16.681	-0.020	-0.020	0.000	0.000	0.000	0.000
72	B	71	SER	0	-0.008	-0.007	20.586	0.016	0.016	0.000	0.000	0.000	0.000
73	B	72	ARG	1	0.828	0.910	17.151	0.218	0.218	0.000	0.000	0.000	0.000
74	B	73	ASP	-1	-0.856	-0.929	18.352	-0.316	-0.316	0.000	0.000	0.000	0.000
75	B	74	ASN	0	-0.018	-0.022	16.450	-0.038	-0.038	0.000	0.000	0.000	0.000
76	B	75	ALA	0	0.030	0.015	17.421	-0.055	-0.055	0.000	0.000	0.000	0.000
77	B	76	LYS	1	0.935	0.979	18.412	0.471	0.471	0.000	0.000	0.000	0.000
78	B	77	ASN	0	-0.013	0.025	12.782	0.097	0.097	0.000	0.000	0.000	0.000
79	B	78	THR	0	0.043	0.007	15.301	-0.067	-0.067	0.000	0.000	0.000	0.000
80	B	79	VAL	0	-0.028	-0.007	14.273	0.057	0.057	0.000	0.000	0.000	0.000
81	B	80	TYR	0	-0.005	-0.021	16.937	-0.019	-0.019	0.000	0.000	0.000	0.000
82	B	81	LEU	0	0.009	0.000	20.015	0.019	0.019	0.000	0.000	0.000	0.000
83	B	82	GLN	0	-0.007	-0.003	21.732	-0.016	-0.016	0.000	0.000	0.000	0.000
84	B	83	MET	0	-0.007	0.007	24.304	0.014	0.014	0.000	0.000	0.000	0.000
85	B	84	ASN	0	0.080	0.046	27.034	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	85	SER	0	0.012	0.005	30.714	0.006	0.006	0.000	0.000	0.000	0.000
87	B	86	LEU	0	0.005	0.023	27.774	0.006	0.006	0.000	0.000	0.000	0.000
88	B	87	LYS	1	0.867	0.914	31.383	0.071	0.071	0.000	0.000	0.000	0.000
89	B	88	LEU	0	0.034	0.017	32.643	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	89	GLU	-1	-0.794	-0.899	30.497	-0.069	-0.069	0.000	0.000	0.000	0.000
91	B	90	ASP	-1	-0.790	-0.848	27.750	-0.106	-0.106	0.000	0.000	0.000	0.000
92	B	91	THR	0	0.024	0.012	26.784	-0.021	-0.021	0.000	0.000	0.000	0.000
93	B	92	ALA	0	-0.017	-0.014	23.114	0.015	0.015	0.000	0.000	0.000	0.000
94	B	93	VAL	0	-0.023	-0.003	18.973	-0.018	-0.018	0.000	0.000	0.000	0.000
95	B	94	TYR	0	-0.015	-0.017	19.197	0.017	0.017	0.000	0.000	0.000	0.000
96	B	95	TYR	0	-0.008	-0.002	13.820	-0.007	-0.007	0.000	0.000	0.000	0.000
97	B	97	ALA	0	0.043	0.018	9.229	-0.082	-0.082	0.000	0.000	0.000	0.000
98	B	98	ALA	0	-0.014	-0.025	6.557	0.115	0.115	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.026	-0.002	5.594	-0.193	-0.193	0.000	0.000	0.000	0.000
100	B	100	ALA	0	-0.007	-0.005	2.360	-0.614	-0.433	0.833	-0.257	-0.758	-0.001
101	B	101	ARG	1	0.884	0.956	2.230	-9.812	-12.344	10.239	-2.101	-5.605	0.008
102	B	102	PRO	0	0.019	0.017	4.545	-0.389	-0.341	-0.001	-0.006	-0.041	0.000
103	B	103	SER	0	0.062	-0.007	6.621	0.595	0.595	0.000	0.000	0.000	0.000
104	B	104	TYR	0	-0.044	-0.007	9.165	-0.278	-0.278	0.000	0.000	0.000	0.000
105	B	105	SER	0	0.029	0.008	13.017	-0.052	-0.052	0.000	0.000	0.000	0.000
106	B	106	GLY	0	-0.034	-0.006	15.875	-0.022	-0.022	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.904	-0.952	12.985	0.649	0.649	0.000	0.000	0.000	0.000
108	B	108	TYR	0	0.015	0.021	11.635	-0.048	-0.048	0.000	0.000	0.000	0.000
109	B	109	GLY	0	0.071	0.037	13.247	0.014	0.014	0.000	0.000	0.000	0.000
110	B	110	TYR	0	-0.058	-0.041	13.779	-0.018	-0.018	0.000	0.000	0.000	0.000
111	B	111	THR	0	0.056	0.014	15.256	-0.053	-0.053	0.000	0.000	0.000	0.000
112	B	112	GLU	-1	-0.882	-0.932	14.338	0.176	0.176	0.000	0.000	0.000	0.000
113	B	113	ALA	0	0.014	0.003	12.984	0.011	0.011	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.045	-0.028	11.019	-0.053	-0.053	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.804	0.916	9.233	-0.329	-0.329	0.000	0.000	0.000	0.000
116	B	116	TYR	0	-0.070	-0.036	7.241	0.103	0.103	0.000	0.000	0.000	0.000
117	B	117	ASP	-1	-0.776	-0.895	2.316	0.203	0.677	2.059	-0.756	-1.777	-0.007
118	B	118	TYR	0	0.011	-0.015	2.084	-4.611	-3.539	6.084	-2.034	-5.122	-0.022
119	B	119	TRP	0	0.006	-0.004	5.217	0.256	0.324	-0.001	-0.001	-0.066	0.000
120	B	120	GLY	0	0.022	0.030	8.902	-0.251	-0.251	0.000	0.000	0.000	0.000
121	B	121	GLN	0	-0.047	-0.013	11.763	0.063	0.063	0.000	0.000	0.000	0.000
122	B	122	GLY	0	0.067	0.016	14.732	0.077	0.077	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.052	-0.028	17.526	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	124	GLN	0	-0.011	0.004	20.896	0.012	0.012	0.000	0.000	0.000	0.000
125	B	125	VAL	0	0.002	0.010	23.576	-0.003	-0.003	0.000	0.000	0.000	0.000
126	B	126	THR	0	-0.031	-0.016	25.994	0.016	0.016	0.000	0.000	0.000	0.000
127	B	127	VAL	0	0.004	0.000	29.333	-0.004	-0.004	0.000	0.000	0.000	0.000
128	B	128	SER	0	-0.011	-0.009	31.940	0.008	0.008	0.000	0.000	0.000	0.000
129	B	129	SER	0	0.014	0.003	35.525	0.003	0.003	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.031	0.019	37.992	0.003	0.003	0.000	0.000	0.000	0.000
131	B	131	HIS	0	0.016	0.027	38.900	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:MET)