FMO DATABASE

FMODB ID: 4NM3N

Calculation Name: 3G8L-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G8L

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JIP9

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	154
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1636637.190419
FMO2-HF: Nuclear repulsion	1570332.692992
FMO2-HF: Total energy	-66304.497427
FMO2-MP2: Total energy	-66493.487292

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:108:ACE )

Summations of interaction energy for fragment #1(A:108:ACE )

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.
-1.292	-0.386	0.004	-0.627	-0.283	0

Interaction energy analysis for fragmet #1(A:108:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.016

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].
3	A	110	GLY	0	-0.145	-0.090	3.803	1.384	2.473	0.004	-0.566	-0.527
4	A	111	ASN	0	-0.062	-0.045	5.817	0.657	0.657	0.000	0.000	0.000
5	A	112	ASP	-1	-0.697	-0.725	4.644	-4.185	-4.368	0.000	-0.061	0.244
6	A	113	LEU	0	-0.041	0.002	7.840	0.469	0.469	0.000	0.000	0.000
7	A	114	LEU	0	0.004	-0.007	10.397	0.224	0.224	0.000	0.000	0.000
8	A	115	GLU	-1	-0.925	-0.961	7.466	-1.096	-1.096	0.000	0.000	0.000
9	A	116	SER	0	-0.042	-0.026	11.533	0.170	0.170	0.000	0.000	0.000
10	A	117	LEU	0	0.009	-0.022	13.219	0.092	0.092	0.000	0.000	0.000
11	A	118	HIS	0	-0.035	-0.012	14.541	0.099	0.099	0.000	0.000	0.000
12	A	119	LYS	1	0.970	0.982	15.646	0.345	0.345	0.000	0.000	0.000
13	A	120	GLU	-1	-0.916	-0.948	17.444	-0.220	-0.220	0.000	0.000	0.000
14	A	121	GLN	0	0.009	0.026	19.603	0.050	0.050	0.000	0.000	0.000
15	A	122	ASN	0	-0.050	-0.038	20.832	0.002	0.002	0.000	0.000	0.000
16	A	123	ARG	1	0.890	0.957	18.554	0.241	0.241	0.000	0.000	0.000
17	A	124	TRP	0	0.085	0.031	20.365	0.010	0.010	0.000	0.000	0.000
18	A	125	TYR	0	-0.042	0.016	25.711	0.019	0.019	0.000	0.000	0.000
19	A	126	SER	0	-0.060	-0.030	27.390	0.011	0.011	0.000	0.000	0.000
20	A	127	GLU	-1	-0.914	-0.957	25.842	-0.144	-0.144	0.000	0.000	0.000
21	A	128	THR	0	-0.023	-0.051	29.256	0.008	0.008	0.000	0.000	0.000
22	A	129	LYS	1	0.838	0.929	31.493	0.089	0.089	0.000	0.000	0.000
23	A	130	THR	0	-0.035	-0.025	33.353	0.007	0.007	0.000	0.000	0.000
24	A	131	PHE	0	-0.009	0.031	36.926	-0.001	-0.001	0.000	0.000	0.000
25	A	132	SER	0	-0.056	-0.047	40.055	0.001	0.001	0.000	0.000	0.000
26	A	133	ASP	-1	-0.796	-0.904	42.277	-0.051	-0.051	0.000	0.000	0.000
27	A	134	SER	0	-0.022	0.010	43.554	-0.001	-0.001	0.000	0.000	0.000
28	A	135	SER	0	0.044	0.028	45.358	0.001	0.001	0.000	0.000	0.000
29	A	136	GLN	0	-0.077	-0.075	47.394	0.002	0.002	0.000	0.000	0.000
30	A	137	HIS	0	-0.051	-0.024	47.422	-0.002	-0.002	0.000	0.000	0.000
31	A	138	THR	0	0.097	0.014	49.401	0.000	0.000	0.000	0.000	0.000
32	A	139	GLY	0	-0.008	0.038	48.906	-0.001	-0.001	0.000	0.000	0.000
33	A	140	ARG	1	0.788	0.895	44.218	0.055	0.055	0.000	0.000	0.000
34	A	141	GLY	0	0.041	0.020	44.703	-0.002	-0.002	0.000	0.000	0.000
35	A	142	PHE	0	-0.115	-0.065	38.449	-0.001	-0.001	0.000	0.000	0.000
36	A	143	GLU	-1	-0.757	-0.890	35.770	-0.079	-0.079	0.000	0.000	0.000
37	A	144	LYS	1	0.853	0.907	34.918	0.073	0.073	0.000	0.000	0.000
38	A	145	TYR	0	0.000	-0.015	25.897	0.005	0.005	0.000	0.000	0.000
39	A	146	TRP	0	0.004	0.012	29.563	0.000	0.000	0.000	0.000	0.000
40	A	147	PHE	0	0.046	0.021	23.846	-0.007	-0.007	0.000	0.000	0.000
41	A	153	CYS	0	-0.057	-0.009	25.976	-0.001	-0.001	0.000	0.000	0.000
42	A	149	TYR	0	0.060	0.004	17.527	-0.020	-0.020	0.000	0.000	0.000
43	A	150	GLY	0	-0.013	0.011	23.306	0.007	0.007	0.000	0.000	0.000
44	A	151	ILE	0	0.064	0.035	24.106	0.008	0.008	0.000	0.000	0.000
45	A	152	LYS	1	0.773	0.877	26.847	0.134	0.134	0.000	0.000	0.000
46	A	154	TYR	0	-0.046	-0.027	25.414	0.006	0.006	0.000	0.000	0.000
47	A	155	TYR	0	0.047	0.022	29.867	-0.001	-0.001	0.000	0.000	0.000
48	A	156	PHE	0	0.031	0.000	27.155	0.004	0.004	0.000	0.000	0.000
49	A	157	VAL	0	-0.014	0.000	32.912	0.003	0.003	0.000	0.000	0.000
50	A	158	MET	0	-0.007	-0.023	32.253	-0.001	-0.001	0.000	0.000	0.000
51	A	159	ASP	-1	-0.891	-0.891	36.071	-0.060	-0.060	0.000	0.000	0.000
52	A	160	ARG	1	0.952	0.962	37.046	0.073	0.073	0.000	0.000	0.000
53	A	161	LYS	1	0.978	1.029	39.071	0.068	0.068	0.000	0.000	0.000
54	A	162	THR	0	0.036	0.022	40.219	-0.003	-0.003	0.000	0.000	0.000
55	A	163	TRP	0	0.027	0.038	37.907	0.002	0.002	0.000	0.000	0.000
56	A	164	SER	0	0.031	-0.034	41.114	0.000	0.000	0.000	0.000	0.000
57	A	165	GLY	0	0.032	-0.003	43.621	0.001	0.001	0.000	0.000	0.000
58	A	254	CYS	0	-0.021	0.001	34.650	0.000	0.000	0.000	0.000	0.000
59	A	167	LYS	1	0.914	0.982	40.346	0.054	0.054	0.000	0.000	0.000
60	A	168	GLN	0	0.074	0.006	41.557	0.000	0.000	0.000	0.000	0.000
61	A	169	THR	0	0.031	0.013	40.101	0.001	0.001	0.000	0.000	0.000
62	A	256	CYS	0	-0.082	0.008	32.976	0.003	0.003	0.000	0.000	0.000
63	A	171	GLN	0	0.002	-0.003	40.116	0.000	0.000	0.000	0.000	0.000
64	A	172	ILE	0	0.018	0.009	43.081	0.001	0.001	0.000	0.000	0.000
65	A	173	SER	0	-0.043	-0.017	40.062	0.001	0.001	0.000	0.000	0.000
66	A	174	SER	0	-0.054	-0.015	40.873	-0.001	-0.001	0.000	0.000	0.000
67	A	175	LEU	0	-0.057	-0.026	35.818	-0.004	-0.004	0.000	0.000	0.000
68	A	176	SER	0	-0.032	-0.033	37.313	0.003	0.003	0.000	0.000	0.000
69	A	177	LEU	0	0.031	0.007	35.185	-0.004	-0.004	0.000	0.000	0.000
70	A	178	LEU	0	-0.047	-0.034	28.347	0.004	0.004	0.000	0.000	0.000
71	A	179	LYS	1	0.906	0.956	32.070	0.086	0.086	0.000	0.000	0.000
72	A	180	ILE	0	-0.005	-0.016	26.820	-0.004	-0.004	0.000	0.000	0.000
73	A	181	ASP	-1	-0.781	-0.900	27.808	-0.095	-0.095	0.000	0.000	0.000
74	A	182	ASN	0	-0.037	0.020	23.912	-0.004	-0.004	0.000	0.000	0.000
75	A	183	GLU	-1	-0.850	-0.961	20.293	-0.154	-0.154	0.000	0.000	0.000
76	A	184	ASP	-1	-0.863	-0.908	19.751	-0.194	-0.194	0.000	0.000	0.000
77	A	185	GLU	-1	-0.763	-0.882	20.682	-0.154	-0.154	0.000	0.000	0.000
78	A	186	LEU	0	-0.062	-0.019	22.775	-0.010	-0.010	0.000	0.000	0.000
79	A	187	LYS	1	0.924	0.934	18.074	0.200	0.200	0.000	0.000	0.000
80	A	188	PHE	0	0.015	0.010	14.796	-0.018	-0.018	0.000	0.000	0.000
81	A	189	LEU	0	-0.005	-0.009	19.484	-0.011	-0.011	0.000	0.000	0.000
82	A	190	LYS	1	0.906	0.972	20.620	0.179	0.179	0.000	0.000	0.000
83	A	191	LEU	0	0.006	-0.020	15.907	0.003	0.003	0.000	0.000	0.000
84	A	192	LEU	0	0.015	0.026	18.648	-0.004	-0.004	0.000	0.000	0.000
85	A	193	VAL	0	-0.023	0.009	20.327	0.019	0.019	0.000	0.000	0.000
86	A	194	PRO	0	0.038	0.006	23.011	-0.013	-0.013	0.000	0.000	0.000
87	A	195	SER	0	-0.024	-0.007	24.702	0.002	0.002	0.000	0.000	0.000
88	A	196	ASP	-1	-0.870	-0.928	25.818	-0.100	-0.100	0.000	0.000	0.000
89	A	197	SER	0	-0.074	-0.031	29.121	-0.001	-0.001	0.000	0.000	0.000
90	A	198	TYR	0	0.019	-0.020	27.230	0.006	0.006	0.000	0.000	0.000
91	A	199	TRP	0	0.002	0.024	32.556	-0.002	-0.002	0.000	0.000	0.000
92	A	200	ILE	0	0.000	-0.006	30.744	-0.003	-0.003	0.000	0.000	0.000
93	A	201	GLY	0	-0.005	-0.011	34.266	0.005	0.005	0.000	0.000	0.000
94	A	202	LEU	0	-0.016	0.013	34.011	0.003	0.003	0.000	0.000	0.000
95	A	203	SER	0	0.011	-0.034	36.409	-0.001	-0.001	0.000	0.000	0.000
96	A	204	TYR	0	0.033	0.039	39.748	0.002	0.002	0.000	0.000	0.000
97	A	205	ASP	-1	-0.785	-0.877	42.807	-0.041	-0.041	0.000	0.000	0.000
98	A	206	ASN	0	-0.040	-0.045	46.053	0.001	0.001	0.000	0.000	0.000
99	A	207	LYS	1	0.910	0.959	49.072	0.034	0.034	0.000	0.000	0.000
100	A	208	LYS	1	0.859	0.908	45.142	0.037	0.037	0.000	0.000	0.000
101	A	209	LYS	1	0.959	0.994	46.309	0.032	0.032	0.000	0.000	0.000
102	A	210	ASP	-1	-0.822	-0.926	40.770	-0.047	-0.047	0.000	0.000	0.000
103	A	211	TRP	0	-0.067	0.002	38.039	-0.001	-0.001	0.000	0.000	0.000
104	A	212	ALA	0	0.009	0.015	39.373	0.001	0.001	0.000	0.000	0.000
105	A	213	TRP	0	0.042	0.022	31.427	-0.004	-0.004	0.000	0.000	0.000
106	A	214	ILE	0	-0.051	-0.060	37.748	0.003	0.003	0.000	0.000	0.000
107	A	215	ASN	0	-0.073	-0.034	39.614	0.003	0.003	0.000	0.000	0.000
108	A	216	ASN	0	0.060	0.055	40.852	0.001	0.001	0.000	0.000	0.000
109	A	217	GLY	0	-0.039	-0.006	38.046	0.002	0.002	0.000	0.000	0.000
110	A	218	PRO	0	-0.024	-0.023	35.328	0.000	0.000	0.000	0.000	0.000
111	A	219	SER	0	0.001	0.010	30.403	-0.003	-0.003	0.000	0.000	0.000
112	A	220	LYS	1	0.931	0.957	27.988	0.094	0.094	0.000	0.000	0.000
113	A	221	LEU	0	-0.018	-0.018	26.441	-0.006	-0.006	0.000	0.000	0.000
114	A	222	ALA	0	0.017	0.029	27.898	0.005	0.005	0.000	0.000	0.000
115	A	223	LEU	0	0.014	0.021	29.055	0.006	0.006	0.000	0.000	0.000
116	A	224	ASN	0	0.019	-0.009	30.781	0.003	0.003	0.000	0.000	0.000
117	A	225	THR	0	0.056	0.014	33.356	-0.002	-0.002	0.000	0.000	0.000
118	A	226	MET	0	0.020	0.027	36.546	-0.001	-0.001	0.000	0.000	0.000
119	A	227	LYS	1	0.889	0.955	28.064	0.091	0.091	0.000	0.000	0.000
120	A	228	TYR	0	-0.059	-0.049	31.020	-0.003	-0.003	0.000	0.000	0.000
121	A	229	ASN	0	-0.029	-0.007	36.971	0.006	0.006	0.000	0.000	0.000
122	A	230	ILE	0	0.108	0.030	40.236	-0.001	-0.001	0.000	0.000	0.000
123	A	231	ARG	1	0.818	0.927	42.399	0.039	0.039	0.000	0.000	0.000
124	A	232	ASP	-1	-0.897	-0.921	39.217	-0.054	-0.054	0.000	0.000	0.000
125	A	233	GLY	0	0.051	-0.007	40.527	-0.002	-0.002	0.000	0.000	0.000
126	A	234	GLY	0	-0.012	0.004	41.441	0.001	0.001	0.000	0.000	0.000
127	A	248	CYS	0	-0.146	-0.063	38.973	-0.001	-0.001	0.000	0.000	0.000
128	A	236	MET	0	-0.001	-0.007	32.007	0.000	0.000	0.000	0.000	0.000
129	A	237	LEU	0	0.031	0.045	32.404	-0.002	-0.002	0.000	0.000	0.000
130	A	238	LEU	0	-0.043	-0.047	26.296	-0.003	-0.003	0.000	0.000	0.000
131	A	239	SER	0	0.035	0.034	26.973	-0.001	-0.001	0.000	0.000	0.000
132	A	240	LYS	1	0.843	0.924	20.236	0.246	0.246	0.000	0.000	0.000
133	A	241	THR	0	-0.046	-0.014	22.146	-0.012	-0.012	0.000	0.000	0.000
134	A	242	ARG	1	0.870	0.919	24.073	0.102	0.102	0.000	0.000	0.000
135	A	243	LEU	0	0.002	0.005	26.014	-0.001	-0.001	0.000	0.000	0.000
136	A	244	ASP	-1	-0.898	-0.960	29.248	-0.080	-0.080	0.000	0.000	0.000
137	A	245	ASN	0	-0.011	-0.007	32.531	0.002	0.002	0.000	0.000	0.000
138	A	246	ASP	-1	-0.654	-0.838	36.302	-0.068	-0.068	0.000	0.000	0.000
139	A	247	ASN	0	0.026	0.054	38.851	0.002	0.002	0.000	0.000	0.000
140	A	249	ASP	-1	-0.975	-1.047	42.587	-0.050	-0.050	0.000	0.000	0.000
141	A	250	LYS	1	0.988	1.035	39.040	0.064	0.064	0.000	0.000	0.000
142	A	251	SER	0	-0.067	-0.099	40.547	-0.001	-0.001	0.000	0.000	0.000
143	A	252	PHE	0	-0.027	-0.018	35.290	-0.002	-0.002	0.000	0.000	0.000
144	A	253	ILE	0	0.073	0.054	31.990	0.003	0.003	0.000	0.000	0.000
145	A	255	ILE	0	-0.028	0.001	28.877	-0.002	-0.002	0.000	0.000	0.000
146	A	257	GLY	0	0.085	0.013	32.083	-0.010	-0.010	0.000	0.000	0.000
147	A	258	LYS	1	0.951	0.985	32.267	0.081	0.081	0.000	0.000	0.000
148	A	259	ARG	1	0.923	0.956	31.743	0.072	0.072	0.000	0.000	0.000
149	A	260	LEU	0	-0.007	-0.016	29.407	0.007	0.007	0.000	0.000	0.000
150	A	261	ASP	-1	-0.934	-0.987	33.003	-0.061	-0.061	0.000	0.000	0.000
151	A	262	LYS	1	0.913	0.986	34.716	0.055	0.055	0.000	0.000	0.000
152	A	263	PHE	0	-0.043	0.010	28.298	-0.006	-0.006	0.000	0.000	0.000
153	A	264	PRO	0	-0.008	-0.032	31.253	0.004	0.004	0.000	0.000	0.000
154	A	265	HIS	-1	-0.897	-0.940	33.651	-0.063	-0.063	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:108:ACE )