FMO DATABASE

FMODB ID: YZM52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1148023.686024
FMO2-HF: Nuclear repulsion	1096021.453826
FMO2-HF: Total energy	-52002.232198
FMO2-MP2: Total energy	-52152.816199

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.
-9.858	-6.408	12.63	-4.458	-11.617	-0.018

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 : 0.020 / q_NPA : 0.006

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	-0.006	0.008	3.890	0.511	2.047	-0.004	-0.641	-0.890	0.002
4	B	3	GLN	0	-0.020	0.006	6.356	-0.040	-0.040	0.000	0.000	0.000	0.000
5	B	4	LEU	0	-0.035	-0.019	8.116	0.274	0.274	0.000	0.000	0.000	0.000
6	B	5	VAL	0	0.024	0.003	10.828	0.038	0.038	0.000	0.000	0.000	0.000
7	B	6	GLU	-1	-0.743	-0.861	14.593	-0.828	-0.828	0.000	0.000	0.000	0.000
8	B	7	SER	0	-0.039	-0.024	17.219	0.026	0.026	0.000	0.000	0.000	0.000
9	B	8	GLY	0	0.041	0.031	20.871	0.006	0.006	0.000	0.000	0.000	0.000
10	B	9	GLY	0	0.007	0.018	23.557	-0.020	-0.020	0.000	0.000	0.000	0.000
11	B	10	ARG	1	0.845	0.898	25.108	0.223	0.223	0.000	0.000	0.000	0.000
12	B	11	LEU	0	-0.009	0.008	28.818	0.003	0.003	0.000	0.000	0.000	0.000
13	B	12	VAL	0	-0.043	-0.022	30.195	0.002	0.002	0.000	0.000	0.000	0.000
14	B	13	GLN	0	-0.004	-0.009	33.104	0.001	0.001	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.021	0.003	35.254	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	15	GLY	0	-0.008	-0.004	35.640	0.007	0.007	0.000	0.000	0.000	0.000
17	B	16	ASP	-1	-0.793	-0.872	34.511	-0.194	-0.194	0.000	0.000	0.000	0.000
18	B	17	SER	0	-0.028	-0.053	31.274	0.002	0.002	0.000	0.000	0.000	0.000
19	B	18	LEU	0	-0.045	-0.030	26.856	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	19	ARG	1	0.831	0.925	23.978	0.332	0.332	0.000	0.000	0.000	0.000
21	B	20	LEU	0	0.009	0.017	20.788	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	21	SER	0	-0.003	-0.020	19.805	0.031	0.031	0.000	0.000	0.000	0.000
23	B	22	CYS	0	-0.084	-0.045	13.515	-0.023	-0.023	0.000	0.000	0.000	0.000
24	B	23	ALA	0	0.046	0.048	15.336	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	24	ALA	0	0.010	-0.009	10.081	-0.128	-0.128	0.000	0.000	0.000	0.000
26	B	25	SER	0	0.011	0.007	10.514	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	26	GLY	0	0.044	0.018	8.228	0.221	0.221	0.000	0.000	0.000	0.000
28	B	27	ARG	1	0.866	0.952	8.552	0.949	0.949	0.000	0.000	0.000	0.000
29	B	28	THR	0	-0.004	-0.023	9.508	0.308	0.308	0.000	0.000	0.000	0.000
30	B	29	PHE	0	0.002	0.000	6.984	0.160	0.160	0.000	0.000	0.000	0.000
31	B	30	THR	0	0.028	0.022	4.699	0.165	0.282	-0.001	-0.005	-0.110	0.000
32	B	31	THR	0	-0.019	-0.011	6.283	0.125	0.125	0.000	0.000	0.000	0.000
33	B	32	TYR	0	0.043	0.032	6.751	0.174	0.174	0.000	0.000	0.000	0.000
34	B	33	LEU	0	-0.069	-0.035	9.509	0.183	0.183	0.000	0.000	0.000	0.000
35	B	34	MET	0	0.005	0.022	9.844	-0.276	-0.276	0.000	0.000	0.000	0.000
36	B	35	GLY	0	0.013	-0.004	12.262	0.141	0.141	0.000	0.000	0.000	0.000
37	B	36	TRP	0	-0.016	-0.004	14.188	-0.108	-0.108	0.000	0.000	0.000	0.000
38	B	37	PHE	0	0.004	0.004	13.798	0.063	0.063	0.000	0.000	0.000	0.000
39	B	38	ARG	1	0.779	0.878	17.598	0.173	0.173	0.000	0.000	0.000	0.000
40	B	39	GLN	0	-0.026	-0.015	19.733	0.002	0.002	0.000	0.000	0.000	0.000
41	B	40	ALA	0	0.041	0.021	21.769	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	41	PRO	0	0.041	0.021	25.021	0.004	0.004	0.000	0.000	0.000	0.000
43	B	42	GLY	0	-0.022	-0.016	27.492	0.002	0.002	0.000	0.000	0.000	0.000
44	B	43	LYS	1	0.804	0.882	25.289	0.144	0.144	0.000	0.000	0.000	0.000
45	B	44	GLU	-1	-0.815	-0.894	21.473	-0.141	-0.141	0.000	0.000	0.000	0.000
46	B	45	ARG	1	0.973	0.988	16.668	0.103	0.103	0.000	0.000	0.000	0.000
47	B	46	GLU	-1	-0.792	-0.867	19.072	-0.161	-0.161	0.000	0.000	0.000	0.000
48	B	47	PHE	0	0.021	-0.001	16.791	-0.035	-0.035	0.000	0.000	0.000	0.000
49	B	48	VAL	0	-0.023	0.001	19.188	0.021	0.021	0.000	0.000	0.000	0.000
50	B	49	ALA	0	0.007	-0.011	19.057	0.032	0.032	0.000	0.000	0.000	0.000
51	B	50	ALA	0	0.023	0.007	15.587	-0.056	-0.056	0.000	0.000	0.000	0.000
52	B	51	ILE	0	-0.018	0.005	15.583	0.049	0.049	0.000	0.000	0.000	0.000
53	B	52	ARG	1	0.923	0.960	12.688	0.187	0.187	0.000	0.000	0.000	0.000
54	B	53	TRP	0	0.020	0.003	10.951	0.102	0.102	0.000	0.000	0.000	0.000
55	B	54	SER	0	0.015	0.003	15.844	0.043	0.043	0.000	0.000	0.000	0.000
56	B	55	GLY	0	0.028	0.013	17.889	0.002	0.002	0.000	0.000	0.000	0.000
57	B	56	GLY	0	-0.006	-0.002	19.311	0.013	0.013	0.000	0.000	0.000	0.000
58	B	57	SER	0	-0.026	-0.008	19.063	0.010	0.010	0.000	0.000	0.000	0.000
59	B	58	THR	0	-0.011	-0.012	19.332	-0.027	-0.027	0.000	0.000	0.000	0.000
60	B	59	TYR	0	-0.011	-0.007	16.621	0.028	0.028	0.000	0.000	0.000	0.000
61	B	60	TYR	0	0.034	0.013	20.799	-0.041	-0.041	0.000	0.000	0.000	0.000
62	B	61	ALA	0	0.048	0.038	22.666	0.025	0.025	0.000	0.000	0.000	0.000
63	B	62	ASP	-1	-0.805	-0.922	24.130	-0.110	-0.110	0.000	0.000	0.000	0.000
64	B	63	SER	0	0.007	0.004	27.076	0.003	0.003	0.000	0.000	0.000	0.000
65	B	64	VAL	0	-0.014	-0.003	24.171	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	65	LYS	1	0.832	0.927	26.832	0.103	0.103	0.000	0.000	0.000	0.000
67	B	66	GLY	0	0.001	0.013	28.509	0.009	0.009	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.765	0.851	29.491	0.169	0.169	0.000	0.000	0.000	0.000
69	B	68	PHE	0	0.022	0.000	24.184	-0.013	-0.013	0.000	0.000	0.000	0.000
70	B	69	THR	0	-0.041	-0.027	25.426	0.017	0.017	0.000	0.000	0.000	0.000
71	B	70	ILE	0	-0.021	0.013	17.199	-0.020	-0.020	0.000	0.000	0.000	0.000
72	B	71	SER	0	-0.009	-0.017	20.822	0.026	0.026	0.000	0.000	0.000	0.000
73	B	72	ARG	1	0.857	0.920	17.025	0.329	0.329	0.000	0.000	0.000	0.000
74	B	73	ASP	-1	-0.793	-0.888	19.347	-0.387	-0.387	0.000	0.000	0.000	0.000
75	B	74	ASN	0	-0.014	-0.022	16.855	-0.076	-0.076	0.000	0.000	0.000	0.000
76	B	75	ALA	0	0.006	0.021	17.390	-0.053	-0.053	0.000	0.000	0.000	0.000
77	B	76	LYS	1	0.890	0.931	19.000	0.487	0.487	0.000	0.000	0.000	0.000
78	B	77	ASN	0	-0.014	0.013	12.999	0.076	0.076	0.000	0.000	0.000	0.000
79	B	78	THR	0	0.019	0.001	15.008	-0.113	-0.113	0.000	0.000	0.000	0.000
80	B	79	VAL	0	-0.011	-0.003	14.297	0.085	0.085	0.000	0.000	0.000	0.000
81	B	80	TYR	0	-0.004	-0.022	17.219	-0.012	-0.012	0.000	0.000	0.000	0.000
82	B	81	LEU	0	0.008	0.002	20.329	0.010	0.010	0.000	0.000	0.000	0.000
83	B	82	GLN	0	0.025	0.027	22.140	-0.014	-0.014	0.000	0.000	0.000	0.000
84	B	83	MET	0	-0.017	-0.003	24.823	0.003	0.003	0.000	0.000	0.000	0.000
85	B	84	ASN	0	0.090	0.055	27.662	-0.005	-0.005	0.000	0.000	0.000	0.000
86	B	85	SER	0	-0.001	0.007	31.459	0.007	0.007	0.000	0.000	0.000	0.000
87	B	86	LEU	0	-0.014	0.009	28.194	0.002	0.002	0.000	0.000	0.000	0.000
88	B	87	LYS	1	0.872	0.906	31.664	0.136	0.136	0.000	0.000	0.000	0.000
89	B	88	LEU	0	0.035	0.026	31.963	-0.009	-0.009	0.000	0.000	0.000	0.000
90	B	89	GLU	-1	-0.756	-0.870	31.011	-0.138	-0.138	0.000	0.000	0.000	0.000
91	B	90	ASP	-1	-0.749	-0.825	27.864	-0.196	-0.196	0.000	0.000	0.000	0.000
92	B	91	THR	0	-0.037	-0.014	26.817	-0.027	-0.027	0.000	0.000	0.000	0.000
93	B	92	ALA	0	-0.025	-0.008	23.391	0.013	0.013	0.000	0.000	0.000	0.000
94	B	93	VAL	0	0.006	0.019	19.579	-0.011	-0.011	0.000	0.000	0.000	0.000
95	B	94	TYR	0	-0.033	-0.044	19.789	0.007	0.007	0.000	0.000	0.000	0.000
96	B	95	TYR	0	0.032	0.010	14.449	-0.008	-0.008	0.000	0.000	0.000	0.000
97	B	97	ALA	0	0.033	0.016	9.906	-0.106	-0.106	0.000	0.000	0.000	0.000
98	B	98	ALA	0	-0.007	-0.026	6.844	0.129	0.129	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.013	0.011	5.765	-0.242	-0.242	0.000	0.000	0.000	0.000
100	B	100	ALA	0	-0.044	-0.039	2.482	-0.364	-0.089	0.559	-0.188	-0.646	0.000
101	B	101	ARG	1	0.879	0.941	2.356	-7.267	-8.010	6.719	-1.449	-4.527	0.002
102	B	102	PRO	0	0.046	0.029	4.916	-0.379	-0.355	-0.001	-0.004	-0.018	0.000
103	B	103	SER	0	-0.003	-0.028	6.664	0.709	0.709	0.000	0.000	0.000	0.000
104	B	104	TYR	0	0.017	0.028	9.089	-0.240	-0.240	0.000	0.000	0.000	0.000
105	B	105	SER	0	0.010	-0.003	12.867	-0.058	-0.058	0.000	0.000	0.000	0.000
106	B	106	GLY	0	-0.022	-0.004	15.553	0.008	0.008	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.858	-0.926	13.197	0.363	0.363	0.000	0.000	0.000	0.000
108	B	108	TYR	0	-0.018	-0.012	11.622	-0.079	-0.079	0.000	0.000	0.000	0.000
109	B	109	GLY	0	0.058	0.033	13.464	-0.006	-0.006	0.000	0.000	0.000	0.000
110	B	110	TYR	0	-0.049	-0.038	14.081	-0.041	-0.041	0.000	0.000	0.000	0.000
111	B	111	THR	0	0.034	0.014	15.389	-0.049	-0.049	0.000	0.000	0.000	0.000
112	B	112	GLU	-1	-0.894	-0.937	14.368	-0.037	-0.037	0.000	0.000	0.000	0.000
113	B	113	ALA	0	0.005	-0.001	12.979	-0.028	-0.028	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.001	-0.013	11.142	-0.090	-0.090	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.781	0.892	9.114	0.004	0.004	0.000	0.000	0.000	0.000
116	B	116	TYR	0	-0.065	-0.032	7.524	-0.013	-0.013	0.000	0.000	0.000	0.000
117	B	117	ASP	-1	-0.734	-0.862	2.420	-0.895	-0.196	1.334	-0.522	-1.511	-0.004
118	B	118	TYR	0	-0.016	-0.017	2.176	-4.610	-3.068	4.024	-1.649	-3.915	-0.018
119	B	119	TRP	0	0.018	0.002	5.525	0.486	0.486	0.000	0.000	0.000	0.000
120	B	120	GLY	0	0.010	0.019	9.258	-0.257	-0.257	0.000	0.000	0.000	0.000
121	B	121	GLN	0	-0.049	-0.028	12.153	0.023	0.023	0.000	0.000	0.000	0.000
122	B	122	GLY	0	0.000	-0.003	15.005	0.087	0.087	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.054	-0.040	17.513	0.016	0.016	0.000	0.000	0.000	0.000
124	B	124	GLN	0	-0.036	-0.011	21.075	0.004	0.004	0.000	0.000	0.000	0.000
125	B	125	VAL	0	0.012	0.013	24.115	0.003	0.003	0.000	0.000	0.000	0.000
126	B	126	THR	0	-0.044	-0.040	26.476	0.010	0.010	0.000	0.000	0.000	0.000
127	B	127	VAL	0	0.021	0.023	29.935	0.000	0.000	0.000	0.000	0.000	0.000
128	B	128	SER	0	-0.016	-0.026	32.496	0.010	0.010	0.000	0.000	0.000	0.000
129	B	129	SER	0	-0.003	-0.016	35.848	0.003	0.003	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.030	0.034	38.456	0.006	0.006	0.000	0.000	0.000	0.000
131	B	131	HIS	0	0.026	0.035	39.494	-0.010	-0.010	0.000	0.000	0.000	0.000

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