FMO DATABASE

FMODB ID: 6NYGZ

Calculation Name: 1BD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BD8

Chain ID: A

ChEMBL ID:

UniProt ID: P55273

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1363685.855746
FMO2-HF: Nuclear repulsion	1305796.155744
FMO2-HF: Total energy	-57889.700003
FMO2-MP2: Total energy	-58060.318868

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-17.692	-9.581	2.28	-3.677	-6.713	-0.023

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.024 / q_NPA : 1.003

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	9	GLY	0	0.122	0.069	3.840	-0.137	1.136	-0.002	-0.523	-0.748	0.001
4	A	10	ASP	-1	-0.823	-0.910	2.687	-55.683	-51.823	1.511	-2.298	-3.072	-0.024
5	A	11	ARG	1	0.731	0.829	2.221	46.537	49.230	0.771	-0.816	-2.648	0.000
6	A	12	LEU	0	0.055	0.038	5.413	3.817	3.817	0.000	0.000	0.000	0.000
7	A	13	SER	0	0.034	0.013	7.749	3.774	3.774	0.000	0.000	0.000	0.000
8	A	14	GLY	0	-0.004	0.001	7.092	2.205	2.205	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.049	-0.030	8.126	1.892	1.892	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.049	0.021	10.241	2.111	2.111	0.000	0.000	0.000	0.000
11	A	17	ALA	0	-0.003	0.010	11.174	1.663	1.663	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.780	0.875	8.949	28.550	28.550	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.066	0.041	13.352	0.969	0.969	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.815	-0.890	12.035	-22.445	-22.445	0.000	0.000	0.000	0.000
15	A	21	VAL	0	0.044	-0.009	14.043	-0.913	-0.913	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.052	-0.013	15.458	0.700	0.700	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.849	-0.915	8.242	-32.239	-32.239	0.000	0.000	0.000	0.000
18	A	24	VAL	0	0.021	0.003	11.858	-0.948	-0.948	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.870	0.929	13.367	15.049	15.049	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.853	0.924	11.080	24.934	24.934	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.005	-0.020	6.864	-0.261	-0.261	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.001	0.009	10.675	0.406	0.406	0.000	0.000	0.000	0.000
23	A	29	HIS	0	-0.031	-0.021	13.649	0.694	0.694	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.883	0.945	14.010	18.782	18.782	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.830	-0.870	6.519	-34.659	-34.659	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.027	0.002	11.322	0.144	0.144	0.000	0.000	0.000	0.000
27	A	33	VAL	0	-0.037	-0.016	7.616	-0.096	-0.096	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.062	0.036	10.106	-0.138	-0.138	0.000	0.000	0.000	0.000
29	A	35	PRO	0	0.025	-0.001	10.374	-1.892	-1.892	0.000	0.000	0.000	0.000
30	A	36	ASP	-1	-0.845	-0.921	12.089	-17.294	-17.294	0.000	0.000	0.000	0.000
31	A	37	ALA	0	-0.064	-0.038	6.477	-0.451	-0.451	0.000	0.000	0.000	0.000
32	A	38	LEU	0	-0.001	0.007	7.914	-1.660	-1.660	0.000	0.000	0.000	0.000
33	A	39	ASN	0	-0.049	-0.029	4.985	-3.292	-3.292	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.847	0.891	3.838	47.505	47.790	0.000	-0.040	-0.245	0.000
35	A	41	PHE	0	-0.046	-0.022	6.819	1.256	1.256	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.002	0.013	9.299	1.664	1.664	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.889	0.950	10.227	17.989	17.989	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.035	0.020	9.768	-2.186	-2.186	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.039	0.006	10.514	0.128	0.128	0.000	0.000	0.000	0.000
40	A	46	LEU	0	0.019	0.003	11.866	0.406	0.406	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.023	0.016	14.353	0.030	0.030	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.057	-0.029	11.228	0.026	0.026	0.000	0.000	0.000	0.000
43	A	49	MET	0	-0.015	0.010	14.681	-0.850	-0.850	0.000	0.000	0.000	0.000
44	A	50	MET	0	-0.030	-0.012	15.924	1.080	1.080	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.050	0.029	18.079	0.323	0.323	0.000	0.000	0.000	0.000
46	A	52	GLY	0	0.052	0.047	21.389	0.544	0.544	0.000	0.000	0.000	0.000
47	A	53	SER	0	-0.046	-0.028	18.953	0.184	0.184	0.000	0.000	0.000	0.000
48	A	54	THR	0	0.017	-0.007	20.678	-0.483	-0.483	0.000	0.000	0.000	0.000
49	A	55	ALA	0	-0.014	-0.011	21.441	-0.056	-0.056	0.000	0.000	0.000	0.000
50	A	56	ILE	0	-0.016	-0.004	15.377	-0.259	-0.259	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.055	0.030	18.280	-0.444	-0.444	0.000	0.000	0.000	0.000
52	A	58	LEU	0	0.064	0.038	20.004	-0.068	-0.068	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.834	-0.905	17.922	-14.435	-14.435	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.011	-0.014	13.508	-0.318	-0.318	0.000	0.000	0.000	0.000
55	A	61	LEU	0	0.001	0.003	17.147	0.005	0.005	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.862	0.934	20.302	13.882	13.882	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.072	-0.032	16.242	0.907	0.907	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.014	-0.006	17.121	-0.357	-0.357	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.055	-0.026	16.224	-0.168	-0.168	0.000	0.000	0.000	0.000
60	A	66	SER	0	0.013	-0.005	16.947	0.992	0.992	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.003	-0.004	18.969	-0.479	-0.479	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.023	-0.015	21.491	0.164	0.164	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.033	0.002	15.845	0.097	0.097	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.002	0.002	19.122	0.185	0.185	0.000	0.000	0.000	0.000
65	A	71	ASP	-1	-0.806	-0.867	17.802	-14.938	-14.938	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.025	-0.006	19.513	0.363	0.363	0.000	0.000	0.000	0.000
67	A	73	SER	0	-0.087	-0.046	21.830	0.559	0.559	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.050	0.021	23.349	0.472	0.472	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.021	-0.010	21.817	0.361	0.361	0.000	0.000	0.000	0.000
70	A	76	SER	0	0.017	-0.018	21.042	-0.385	-0.385	0.000	0.000	0.000	0.000
71	A	77	PRO	0	-0.032	-0.029	18.623	0.192	0.192	0.000	0.000	0.000	0.000
72	A	78	VAL	0	0.041	0.028	21.313	0.031	0.031	0.000	0.000	0.000	0.000
73	A	79	HIS	0	0.058	0.023	24.761	-0.086	-0.086	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.796	-0.888	21.456	-13.047	-13.047	0.000	0.000	0.000	0.000
75	A	81	ALA	0	-0.038	-0.001	24.024	0.115	0.115	0.000	0.000	0.000	0.000
76	A	82	ALA	0	-0.007	0.006	25.297	0.267	0.267	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.873	0.920	23.636	12.413	12.413	0.000	0.000	0.000	0.000
78	A	84	THR	0	-0.073	-0.068	24.055	0.037	0.037	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.033	0.029	27.364	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	86	PHE	0	-0.015	0.002	23.892	0.181	0.181	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.034	0.005	27.570	-0.239	-0.239	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.826	-0.910	28.826	-9.981	-9.981	0.000	0.000	0.000	0.000
83	A	89	THR	0	-0.022	-0.029	22.572	-0.111	-0.111	0.000	0.000	0.000	0.000
84	A	90	LEU	0	0.008	0.012	25.322	-0.210	-0.210	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.829	0.914	27.373	9.688	9.688	0.000	0.000	0.000	0.000
86	A	92	VAL	0	0.004	0.010	24.146	0.006	0.006	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.019	-0.018	21.133	-0.193	-0.193	0.000	0.000	0.000	0.000
88	A	94	VAL	0	0.016	0.015	24.999	-0.068	-0.068	0.000	0.000	0.000	0.000
89	A	95	GLU	-1	-0.950	-0.968	28.387	-10.349	-10.349	0.000	0.000	0.000	0.000
90	A	96	HIS	0	-0.103	-0.058	24.219	-0.086	-0.086	0.000	0.000	0.000	0.000
91	A	97	GLY	0	0.006	0.004	25.366	-0.237	-0.237	0.000	0.000	0.000	0.000
92	A	98	ALA	0	-0.063	-0.027	24.655	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	99	ASP	-1	-0.803	-0.912	26.231	-9.046	-9.046	0.000	0.000	0.000	0.000
94	A	100	VAL	0	-0.016	-0.019	28.209	-0.373	-0.373	0.000	0.000	0.000	0.000
95	A	101	ASN	0	-0.026	-0.021	30.776	0.319	0.319	0.000	0.000	0.000	0.000
96	A	102	VAL	0	-0.005	0.008	26.709	0.176	0.176	0.000	0.000	0.000	0.000
97	A	103	PRO	0	-0.027	-0.006	29.396	-0.159	-0.159	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.796	-0.867	26.756	-10.486	-10.486	0.000	0.000	0.000	0.000
99	A	105	GLY	0	0.011	-0.012	27.284	0.356	0.356	0.000	0.000	0.000	0.000
100	A	106	THR	0	-0.128	-0.090	28.915	0.355	0.355	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.010	-0.011	31.526	0.346	0.346	0.000	0.000	0.000	0.000
102	A	108	ALA	0	-0.042	-0.014	31.356	0.223	0.223	0.000	0.000	0.000	0.000
103	A	109	LEU	0	0.033	0.026	31.060	-0.265	-0.265	0.000	0.000	0.000	0.000
104	A	110	PRO	0	0.019	-0.006	28.198	0.012	0.012	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.050	0.028	30.458	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	112	HIS	0	-0.002	0.006	33.906	-0.047	-0.047	0.000	0.000	0.000	0.000
107	A	113	LEU	0	-0.011	-0.002	28.082	0.054	0.054	0.000	0.000	0.000	0.000
108	A	114	ALA	0	-0.008	0.003	32.219	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	115	VAL	0	-0.013	-0.010	33.488	0.098	0.098	0.000	0.000	0.000	0.000
110	A	116	GLN	0	-0.066	-0.028	33.760	0.409	0.409	0.000	0.000	0.000	0.000
111	A	117	GLU	-1	-0.902	-0.942	31.126	-9.711	-9.711	0.000	0.000	0.000	0.000
112	A	118	GLY	0	-0.040	-0.024	34.557	0.206	0.206	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.006	0.011	30.632	0.328	0.328	0.000	0.000	0.000	0.000
114	A	120	THR	0	0.041	-0.001	35.162	-0.038	-0.038	0.000	0.000	0.000	0.000
115	A	121	ALA	0	-0.003	0.003	35.479	0.088	0.088	0.000	0.000	0.000	0.000
116	A	122	VAL	0	0.003	0.003	31.393	0.001	0.001	0.000	0.000	0.000	0.000
117	A	123	VAL	0	0.003	0.000	34.365	0.024	0.024	0.000	0.000	0.000	0.000
118	A	124	SER	0	-0.025	-0.018	37.085	0.150	0.150	0.000	0.000	0.000	0.000
119	A	125	PHE	0	-0.043	-0.020	32.276	0.117	0.117	0.000	0.000	0.000	0.000
120	A	126	LEU	0	0.039	0.016	31.581	0.035	0.035	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.016	-0.003	35.743	0.070	0.070	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.035	-0.001	39.274	0.168	0.168	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.917	-0.965	33.364	-9.034	-9.034	0.000	0.000	0.000	0.000
124	A	130	SER	0	-0.010	-0.017	35.332	-0.254	-0.254	0.000	0.000	0.000	0.000
125	A	131	ASP	-1	-0.824	-0.897	36.804	-7.591	-7.591	0.000	0.000	0.000	0.000
126	A	132	LEU	0	-0.025	-0.018	38.797	-0.086	-0.086	0.000	0.000	0.000	0.000
127	A	133	HIS	0	0.007	-0.003	40.810	0.071	0.071	0.000	0.000	0.000	0.000
128	A	134	ARG	1	0.805	0.890	36.267	8.044	8.044	0.000	0.000	0.000	0.000
129	A	135	ARG	1	0.764	0.848	38.980	6.956	6.956	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.791	-0.879	35.565	-8.161	-8.161	0.000	0.000	0.000	0.000
131	A	137	ALA	0	0.005	0.000	35.307	0.223	0.223	0.000	0.000	0.000	0.000
132	A	138	ARG	1	0.851	0.919	37.248	7.833	7.833	0.000	0.000	0.000	0.000
133	A	139	GLY	0	0.002	0.018	39.795	0.209	0.209	0.000	0.000	0.000	0.000
134	A	140	LEU	0	-0.056	-0.027	40.347	0.236	0.236	0.000	0.000	0.000	0.000
135	A	141	THR	0	0.027	-0.017	39.772	-0.203	-0.203	0.000	0.000	0.000	0.000
136	A	142	PRO	0	0.019	-0.002	37.727	0.018	0.018	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.025	0.004	39.964	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.791	-0.845	43.132	-6.698	-6.698	0.000	0.000	0.000	0.000
139	A	145	LEU	0	-0.018	0.007	37.129	0.001	0.001	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.021	0.006	41.319	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	147	LEU	0	0.022	0.018	43.244	0.105	0.105	0.000	0.000	0.000	0.000
142	A	148	GLN	0	-0.066	-0.027	43.344	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	149	ARG	1	0.831	0.907	37.738	8.291	8.291	0.000	0.000	0.000	0.000
144	A	150	GLY	0	-0.023	-0.006	43.541	-0.026	-0.026	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.013	-0.011	42.548	0.092	0.092	0.000	0.000	0.000	0.000
146	A	152	GLN	0	0.025	-0.006	44.513	-0.073	-0.073	0.000	0.000	0.000	0.000
147	A	153	ASP	-1	-0.891	-0.932	43.493	-7.045	-7.045	0.000	0.000	0.000	0.000
148	A	154	LEU	0	-0.029	-0.018	39.441	-0.083	-0.083	0.000	0.000	0.000	0.000
149	A	155	VAL	0	-0.042	-0.015	42.974	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	156	ASP	-1	-0.881	-0.944	45.987	-6.375	-6.375	0.000	0.000	0.000	0.000
151	A	157	ILE	0	-0.032	-0.017	41.575	0.044	0.044	0.000	0.000	0.000	0.000
152	A	158	LEU	0	-0.025	-0.022	40.258	0.001	0.001	0.000	0.000	0.000	0.000
153	A	159	GLN	0	-0.023	-0.010	44.334	0.134	0.134	0.000	0.000	0.000	0.000
154	A	160	GLY	0	-0.039	-0.004	47.342	0.107	0.107	0.000	0.000	0.000	0.000
155	A	161	HIS	0	-0.024	-0.009	43.121	0.064	0.064	0.000	0.000	0.000	0.000
156	A	162	MET	0	-0.054	-0.020	45.704	0.051	0.051	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)