FMO DATABASE

FMODB ID: 52K1Z

Calculation Name: 3N77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N77

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZNF5

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1314955.188793
FMO2-HF: Nuclear repulsion	1257464.082281
FMO2-HF: Total energy	-57491.106512
FMO2-MP2: Total energy	-57655.464275

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.
-13.842	-8.839	7.129	-5.709	-6.422	-0.036

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 : -0.002 / q_NPA : 0.005

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	GLN	0	0.036	0.004	3.871	-1.153	1.062	-0.022	-1.219	-0.975	0.006
4	A	4	ARG	1	0.898	0.947	6.850	1.321	1.321	0.000	0.000	0.000	0.000
5	A	5	THR	0	0.033	0.022	10.218	0.099	0.099	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.036	-0.015	13.264	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.027	0.003	16.077	0.042	0.042	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.008	-0.007	19.811	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.003	0.010	21.843	0.020	0.020	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.008	-0.016	25.556	0.004	0.004	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.010	-0.006	27.297	0.014	0.014	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.018	-0.014	30.556	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ASN	0	0.024	0.001	33.856	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.909	-0.941	37.484	-0.061	-0.061	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.023	0.014	38.446	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.118	-0.051	36.310	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.037	-0.003	30.854	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.005	0.023	29.930	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.045	-0.020	27.006	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	CYS	0	0.044	0.012	26.818	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.844	0.935	26.643	0.113	0.113	0.000	0.000	0.000	0.000
22	A	22	MET	0	0.048	0.006	19.329	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.045	0.031	25.075	0.018	0.018	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.883	-0.953	24.717	-0.148	-0.148	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.102	-0.065	23.519	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.822	0.910	20.487	0.236	0.236	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.047	0.027	17.886	0.015	0.015	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.081	-0.053	14.666	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.011	-0.003	17.680	0.029	0.029	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.014	0.025	21.320	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.056	0.034	23.730	0.016	0.016	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.044	-0.022	21.205	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.018	-0.011	24.786	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.034	-0.024	22.163	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.027	-0.009	23.211	0.018	0.018	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.043	0.026	22.997	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.020	-0.038	21.023	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.021	0.029	18.808	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.034	-0.013	17.065	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.026	-0.029	17.580	0.057	0.057	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.906	-0.950	18.303	-0.548	-0.548	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.056	-0.043	18.142	0.029	0.029	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.035	-0.021	20.672	0.028	0.028	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.797	-0.839	22.639	-0.308	-0.308	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.869	0.904	22.862	0.164	0.164	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.025	-0.003	20.229	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.812	-0.886	22.680	-0.165	-0.165	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.854	-0.913	26.125	-0.201	-0.201	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.027	0.028	22.166	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.003	0.001	23.575	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.832	0.879	25.027	0.160	0.160	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.641	0.780	21.887	0.348	0.348	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.773	-0.869	21.175	-0.372	-0.372	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.014	0.001	25.274	0.012	0.012	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.893	0.963	28.202	0.201	0.201	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.869	-0.927	25.800	-0.259	-0.259	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.812	-0.908	24.054	-0.268	-0.268	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.046	-0.034	27.403	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.065	0.047	30.856	0.014	0.014	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.939	-0.999	33.533	-0.154	-0.154	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.055	-0.022	35.719	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.037	0.041	32.331	0.008	0.008	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.009	-0.007	35.524	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.005	-0.015	31.335	0.005	0.005	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.045	-0.024	35.522	0.005	0.005	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.901	-0.954	34.608	-0.107	-0.107	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.046	-0.031	28.463	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.018	-0.011	29.853	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.015	-0.010	24.931	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	TRP	0	0.003	0.008	23.950	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.016	-0.020	21.499	0.015	0.015	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.029	-0.006	16.439	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.800	0.889	15.263	0.297	0.297	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.829	-0.891	11.127	-0.258	-0.258	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.783	-0.877	11.068	-0.181	-0.181	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.010	0.007	5.991	-0.282	-0.282	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.908	0.967	8.004	0.766	0.766	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.037	0.011	6.502	-0.225	-0.225	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.783	0.892	6.519	1.327	1.327	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.025	0.004	8.034	0.273	0.273	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.035	-0.031	7.520	-0.079	-0.079	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.017	-0.006	12.465	0.055	0.055	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.835	-0.900	13.838	0.037	0.037	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.004	0.009	14.431	0.036	0.036	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.867	0.924	10.049	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.019	-0.027	7.709	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.820	-0.884	3.267	-2.322	-1.783	0.044	-0.148	-0.434	0.000
88	A	88	GLU	-1	-0.886	-0.933	2.550	-2.563	-0.162	1.227	-1.248	-2.380	0.002
89	A	89	ILE	0	-0.062	-0.054	2.022	-9.900	-10.215	5.881	-3.080	-2.486	-0.044
90	A	90	TYR	0	-0.043	-0.041	4.591	0.691	0.854	-0.001	-0.014	-0.147	0.000
91	A	91	MET	0	-0.037	-0.008	6.256	-0.249	-0.249	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.025	0.006	9.937	0.145	0.145	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.008	-0.003	12.557	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.021	0.003	16.046	0.059	0.059	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.017	-0.010	19.002	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.032	0.007	21.775	0.020	0.020	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.763	-0.841	25.683	-0.115	-0.115	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.048	-0.018	28.194	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.017	0.018	30.980	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.010	0.007	34.631	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.008	-0.005	36.450	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.090	-0.062	39.045	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.867	0.914	37.599	0.076	0.076	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.867	-0.906	37.619	-0.095	-0.095	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.008	-0.001	32.386	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	106	CYS	0	-0.074	-0.048	34.165	0.010	0.010	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.015	0.011	29.889	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.014	-0.004	24.965	0.015	0.015	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.815	-0.899	25.745	-0.243	-0.243	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.928	-0.948	21.114	-0.337	-0.337	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.045	-0.026	23.860	0.001	0.001	0.000	0.000	0.000	0.000
112	A	112	GLN	0	-0.110	-0.080	27.312	0.014	0.014	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.872	-0.941	30.462	-0.098	-0.098	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.043	-0.023	30.664	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.009	0.002	32.414	0.010	0.010	0.000	0.000	0.000	0.000
116	A	116	TRP	0	0.021	0.008	33.168	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.033	-0.015	32.717	0.009	0.009	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.060	0.024	34.915	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.043	-0.003	33.787	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.001	0.001	33.600	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.003	0.006	35.051	0.003	0.003	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.009	0.010	29.736	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.008	-0.008	29.314	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.028	-0.021	29.843	0.002	0.002	0.000	0.000	0.000	0.000
125	A	125	TYR	0	0.033	0.035	29.004	0.003	0.003	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.832	-0.897	25.840	-0.105	-0.105	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.045	-0.019	24.233	-0.016	-0.016	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.059	0.041	19.458	0.007	0.007	0.000	0.000	0.000	0.000
129	A	129	VAL	0	0.012	-0.006	16.694	0.001	0.001	0.000	0.000	0.000	0.000
130	A	130	ALA	0	0.020	0.020	15.931	0.014	0.014	0.000	0.000	0.000	0.000
131	A	131	THR	0	0.056	0.016	17.775	0.005	0.005	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.837	0.919	21.463	0.105	0.105	0.000	0.000	0.000	0.000
133	A	133	HIS	0	-0.051	-0.042	16.162	0.046	0.046	0.000	0.000	0.000	0.000
134	A	134	THR	0	0.017	0.015	19.893	0.012	0.012	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.041	0.014	21.517	0.013	0.013	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.020	-0.010	23.223	0.013	0.013	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.027	-0.003	20.356	0.012	0.012	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.780	0.878	23.964	0.109	0.109	0.000	0.000	0.000	0.000
139	A	139	GLY	0	-0.019	-0.003	27.015	0.006	0.006	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.046	-0.021	28.597	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.061	-0.013	25.763	0.003	0.003	0.000	0.000	0.000	0.000

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