FMO DATABASE

FMODB ID: N1Z6Q

Calculation Name: 1AMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AMX

Chain ID: A

ChEMBL ID:

UniProt ID: Q53654

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptH
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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1465561.621165
FMO2-HF: Nuclear repulsion	1406251.125379
FMO2-HF: Total energy	-59310.495786
FMO2-MP2: Total energy	-59486.868239

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:169:THR)

Summations of interaction energy for fragment #1(A:169:THR)

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.
-3.731	-2.047	-0.007	-0.824	-0.854	0

Interaction energy analysis for fragmet #1(A:169:THR)

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 : -0.032

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	171	SER	0	-0.017	-0.017	3.527	-3.465	-1.781	-0.007	-0.824	-0.854
4	A	172	VAL	0	0.022	0.021	6.168	0.259	0.259	0.000	0.000	0.000
5	A	173	PHE	0	0.021	0.033	9.903	0.020	0.020	0.000	0.000	0.000
6	A	174	TYR	0	0.003	-0.036	11.987	0.011	0.011	0.000	0.000	0.000
7	A	175	TYR	0	-0.045	-0.020	12.112	0.037	0.037	0.000	0.000	0.000
8	A	176	LYN	0	0.002	0.041	16.073	-0.014	-0.014	0.000	0.000	0.000
9	A	177	THR	0	-0.029	-0.021	17.809	0.021	0.021	0.000	0.000	0.000
10	A	178	GLY	0	0.058	0.018	19.878	-0.026	-0.026	0.000	0.000	0.000
11	A	179	ASP	-1	-0.871	-0.917	22.796	0.186	0.186	0.000	0.000	0.000
12	A	180	MET	0	0.046	0.020	24.847	-0.015	-0.015	0.000	0.000	0.000
13	A	181	LEU	0	-0.008	0.005	26.002	0.008	0.008	0.000	0.000	0.000
14	A	182	PRO	0	-0.004	0.001	28.107	-0.007	-0.007	0.000	0.000	0.000
15	A	183	GLU	-1	-0.941	-0.980	29.635	0.106	0.106	0.000	0.000	0.000
16	A	184	ASP	-1	-0.872	-0.952	32.136	0.071	0.071	0.000	0.000	0.000
17	A	185	THR	0	0.002	0.000	32.848	0.003	0.003	0.000	0.000	0.000
18	A	186	THR	0	-0.044	-0.011	34.715	-0.003	-0.003	0.000	0.000	0.000
19	A	187	HIS	0	-0.036	-0.025	31.900	-0.008	-0.008	0.000	0.000	0.000
20	A	188	VAL	0	-0.002	0.018	27.603	0.007	0.007	0.000	0.000	0.000
21	A	189	ARG	1	0.796	0.893	23.558	-0.154	-0.154	0.000	0.000	0.000
22	A	190	TRP	0	0.061	0.020	24.061	0.017	0.017	0.000	0.000	0.000
23	A	191	PHE	0	-0.033	-0.015	19.495	-0.008	-0.008	0.000	0.000	0.000
24	A	192	LEU	0	0.019	0.021	19.799	0.015	0.015	0.000	0.000	0.000
25	A	193	ASN	0	-0.007	-0.001	14.710	-0.034	-0.034	0.000	0.000	0.000
26	A	194	ILE	0	0.039	-0.001	15.370	-0.004	-0.004	0.000	0.000	0.000
27	A	195	ASN	0	-0.013	0.005	12.822	-0.056	-0.056	0.000	0.000	0.000
28	A	196	ASN	0	-0.047	-0.052	9.962	0.014	0.014	0.000	0.000	0.000
29	A	197	GLU	-1	-0.924	-0.955	5.454	-0.827	-0.827	0.000	0.000	0.000
30	A	198	LYS	1	0.805	0.922	8.779	0.064	0.064	0.000	0.000	0.000
31	A	199	SER	0	0.017	0.001	10.796	-0.050	-0.050	0.000	0.000	0.000
32	A	200	TYR	0	0.029	0.014	12.437	0.071	0.071	0.000	0.000	0.000
33	A	201	VAL	0	-0.020	-0.009	15.470	-0.026	-0.026	0.000	0.000	0.000
34	A	202	SER	0	0.001	0.003	17.890	0.011	0.011	0.000	0.000	0.000
35	A	203	LYS	1	0.811	0.943	20.760	0.071	0.071	0.000	0.000	0.000
36	A	204	ASP	-1	-0.816	-0.915	21.593	-0.071	-0.071	0.000	0.000	0.000
37	A	205	ILE	0	-0.043	-0.015	18.463	-0.002	-0.002	0.000	0.000	0.000
38	A	206	THR	0	-0.028	-0.015	21.929	0.008	0.008	0.000	0.000	0.000
39	A	207	ILE	0	-0.032	-0.024	20.026	0.001	0.001	0.000	0.000	0.000
40	A	208	LYS	1	0.924	0.973	24.002	-0.013	-0.013	0.000	0.000	0.000
41	A	209	ASP	-1	-0.778	-0.887	25.481	0.076	0.076	0.000	0.000	0.000
42	A	210	GLN	0	-0.037	-0.015	27.452	-0.002	-0.002	0.000	0.000	0.000
43	A	211	ILE	0	0.065	0.054	29.508	0.007	0.007	0.000	0.000	0.000
44	A	212	GLN	0	-0.071	-0.036	30.516	-0.007	-0.007	0.000	0.000	0.000
45	A	213	GLY	0	-0.007	-0.021	32.894	0.000	0.000	0.000	0.000	0.000
46	A	214	GLY	0	0.035	0.027	35.228	0.005	0.005	0.000	0.000	0.000
47	A	215	GLN	0	0.035	0.034	30.615	0.006	0.006	0.000	0.000	0.000
48	A	216	GLN	0	-0.073	-0.036	35.661	-0.003	-0.003	0.000	0.000	0.000
49	A	217	LEU	0	-0.004	0.014	30.840	0.003	0.003	0.000	0.000	0.000
50	A	218	ASP	-1	-0.854	-0.906	33.193	0.043	0.043	0.000	0.000	0.000
51	A	219	LEU	0	0.007	0.003	32.434	0.002	0.002	0.000	0.000	0.000
52	A	220	SER	0	-0.064	-0.034	33.298	-0.001	-0.001	0.000	0.000	0.000
53	A	221	THR	0	-0.049	-0.044	30.470	0.003	0.003	0.000	0.000	0.000
54	A	222	LEU	0	-0.063	-0.019	27.345	0.006	0.006	0.000	0.000	0.000
55	A	223	ASN	0	-0.062	-0.027	24.835	-0.003	-0.003	0.000	0.000	0.000
56	A	224	ILE	0	0.013	0.006	22.958	0.005	0.005	0.000	0.000	0.000
57	A	225	ASN	0	0.011	0.008	19.269	-0.016	-0.016	0.000	0.000	0.000
58	A	226	VAL	0	0.009	0.009	19.548	0.001	0.001	0.000	0.000	0.000
59	A	227	THR	0	-0.020	-0.015	15.672	0.005	0.005	0.000	0.000	0.000
60	A	228	GLY	0	0.042	0.007	16.020	-0.022	-0.022	0.000	0.000	0.000
61	A	229	THR	0	-0.043	-0.008	16.829	0.004	0.004	0.000	0.000	0.000
62	A	230	HIS	0	-0.035	-0.024	19.631	0.013	0.013	0.000	0.000	0.000
63	A	231	SER	0	0.016	-0.007	19.464	0.007	0.007	0.000	0.000	0.000
64	A	232	ASN	0	-0.026	-0.011	21.558	0.008	0.008	0.000	0.000	0.000
65	A	233	TYR	0	-0.010	0.013	23.277	0.002	0.002	0.000	0.000	0.000
66	A	234	TYR	0	0.007	0.004	24.967	-0.005	-0.005	0.000	0.000	0.000
67	A	235	SER	0	0.052	0.005	27.519	0.007	0.007	0.000	0.000	0.000
68	A	236	GLY	0	0.009	0.015	30.090	-0.005	-0.005	0.000	0.000	0.000
69	A	237	GLN	0	0.035	-0.004	33.570	0.002	0.002	0.000	0.000	0.000
70	A	238	SER	0	-0.039	-0.016	35.076	0.000	0.000	0.000	0.000	0.000
71	A	239	ALA	0	0.020	0.024	29.707	-0.004	-0.004	0.000	0.000	0.000
72	A	240	ILE	0	0.071	0.033	30.327	-0.004	-0.004	0.000	0.000	0.000
73	A	241	THR	0	0.016	0.003	31.335	-0.004	-0.004	0.000	0.000	0.000
74	A	242	ASP	-1	-0.892	-0.957	31.626	0.003	0.003	0.000	0.000	0.000
75	A	243	PHE	0	0.001	0.005	23.914	-0.004	-0.004	0.000	0.000	0.000
76	A	244	GLU	-1	-0.831	-0.947	28.754	-0.008	-0.008	0.000	0.000	0.000
77	A	245	LYS	1	0.864	0.949	30.757	0.001	0.001	0.000	0.000	0.000
78	A	246	ALA	0	-0.020	-0.011	28.231	-0.004	-0.004	0.000	0.000	0.000
79	A	247	PHE	0	-0.059	-0.003	23.456	-0.009	-0.009	0.000	0.000	0.000
80	A	248	PRO	0	0.052	0.038	27.935	0.001	0.001	0.000	0.000	0.000
81	A	249	GLY	0	0.010	-0.007	29.463	-0.006	-0.006	0.000	0.000	0.000
82	A	250	SER	0	-0.061	-0.059	26.711	-0.001	-0.001	0.000	0.000	0.000
83	A	251	LYS	1	0.823	0.927	28.223	0.010	0.010	0.000	0.000	0.000
84	A	252	ILE	0	-0.008	-0.001	26.547	0.000	0.000	0.000	0.000	0.000
85	A	253	THR	0	-0.018	-0.005	29.815	-0.001	-0.001	0.000	0.000	0.000
86	A	254	VAL	0	0.021	0.010	31.399	0.003	0.003	0.000	0.000	0.000
87	A	255	ASP	-1	-0.855	-0.931	33.586	0.021	0.021	0.000	0.000	0.000
88	A	256	ASN	0	0.011	-0.021	36.175	0.001	0.001	0.000	0.000	0.000
89	A	257	THR	0	-0.010	0.020	37.605	0.003	0.003	0.000	0.000	0.000
90	A	258	LYS	1	0.911	0.952	36.920	-0.024	-0.024	0.000	0.000	0.000
91	A	259	ASN	0	0.029	0.031	33.994	0.003	0.003	0.000	0.000	0.000
92	A	260	THR	0	0.025	0.010	31.742	0.004	0.004	0.000	0.000	0.000
93	A	261	ILE	0	-0.034	-0.027	27.789	-0.003	-0.003	0.000	0.000	0.000
94	A	262	ASP	-1	-0.886	-0.936	28.249	0.022	0.022	0.000	0.000	0.000
95	A	263	VAL	0	-0.011	-0.009	23.770	-0.002	-0.002	0.000	0.000	0.000
96	A	264	THR	0	-0.011	-0.011	25.636	-0.003	-0.003	0.000	0.000	0.000
97	A	265	ILE	0	-0.013	0.001	20.963	0.003	0.003	0.000	0.000	0.000
98	A	266	PRO	0	0.039	0.039	23.701	-0.008	-0.008	0.000	0.000	0.000
99	A	267	GLN	0	0.022	-0.038	21.674	0.001	0.001	0.000	0.000	0.000
100	A	268	GLY	0	-0.013	0.004	21.343	-0.016	-0.016	0.000	0.000	0.000
101	A	269	TYR	0	-0.011	-0.013	22.315	-0.008	-0.008	0.000	0.000	0.000
102	A	270	GLY	0	-0.003	-0.005	19.813	0.000	0.000	0.000	0.000	0.000
103	A	271	SER	0	-0.049	-0.035	17.240	-0.027	-0.027	0.000	0.000	0.000
104	A	272	TYR	0	-0.032	-0.013	14.638	0.009	0.009	0.000	0.000	0.000
105	A	273	ASN	0	0.001	0.007	15.849	0.018	0.018	0.000	0.000	0.000
106	A	274	SER	0	0.001	0.012	13.038	-0.010	-0.010	0.000	0.000	0.000
107	A	275	PHE	0	-0.026	-0.014	15.347	0.016	0.016	0.000	0.000	0.000
108	A	276	SER	0	-0.028	-0.003	17.498	0.009	0.009	0.000	0.000	0.000
109	A	277	ILE	0	0.021	0.008	19.044	-0.006	-0.006	0.000	0.000	0.000
110	A	278	ASN	0	-0.034	-0.039	22.345	0.009	0.009	0.000	0.000	0.000
111	A	279	TYR	0	0.030	0.015	24.217	-0.010	-0.010	0.000	0.000	0.000
112	A	280	LYS	1	0.957	0.983	27.307	-0.076	-0.076	0.000	0.000	0.000
113	A	281	THR	0	-0.034	-0.032	29.959	-0.006	-0.006	0.000	0.000	0.000
114	A	282	LYS	1	0.976	0.998	32.440	-0.050	-0.050	0.000	0.000	0.000
115	A	283	ILE	0	0.028	0.009	33.437	-0.002	-0.002	0.000	0.000	0.000
116	A	284	THR	0	-0.070	-0.047	36.559	-0.002	-0.002	0.000	0.000	0.000
117	A	285	ASN	0	-0.011	-0.007	38.933	-0.003	-0.003	0.000	0.000	0.000
118	A	286	GLU	-1	-0.900	-0.958	38.793	0.062	0.062	0.000	0.000	0.000
119	A	287	GLN	0	-0.034	-0.018	39.666	0.003	0.003	0.000	0.000	0.000
120	A	288	GLN	0	-0.106	-0.046	34.183	-0.003	-0.003	0.000	0.000	0.000
121	A	289	LYS	1	0.912	0.944	33.541	-0.080	-0.080	0.000	0.000	0.000
122	A	290	GLU	-1	-0.887	-0.941	29.653	0.117	0.117	0.000	0.000	0.000
123	A	291	PHE	0	0.016	0.018	29.994	-0.009	-0.009	0.000	0.000	0.000
124	A	292	VAL	0	-0.015	-0.002	27.905	0.010	0.010	0.000	0.000	0.000
125	A	293	ASN	0	-0.032	-0.041	24.923	-0.015	-0.015	0.000	0.000	0.000
126	A	294	ASN	0	0.018	-0.003	25.656	0.019	0.019	0.000	0.000	0.000
127	A	295	SER	0	0.050	0.010	22.538	-0.006	-0.006	0.000	0.000	0.000
128	A	296	GLN	0	-0.062	-0.044	23.755	-0.001	-0.001	0.000	0.000	0.000
129	A	297	ALA	0	-0.001	0.000	20.031	-0.006	-0.006	0.000	0.000	0.000
130	A	298	TRP	0	-0.037	-0.006	22.018	0.003	0.003	0.000	0.000	0.000
131	A	299	TYR	0	0.036	0.008	15.150	0.012	0.012	0.000	0.000	0.000
132	A	300	GLN	0	0.037	-0.005	18.057	0.018	0.018	0.000	0.000	0.000
133	A	301	GLU	-1	-0.855	-0.908	11.118	-0.458	-0.458	0.000	0.000	0.000
134	A	302	HIS	0	0.000	-0.013	15.011	0.037	0.037	0.000	0.000	0.000
135	A	303	GLY	0	-0.003	0.005	14.631	-0.050	-0.050	0.000	0.000	0.000
136	A	304	LYS	1	0.921	0.977	8.519	0.627	0.627	0.000	0.000	0.000
137	A	305	GLU	-1	-0.926	-0.960	15.456	-0.052	-0.052	0.000	0.000	0.000
138	A	306	GLU	-1	-0.895	-0.957	17.463	-0.065	-0.065	0.000	0.000	0.000
139	A	307	VAL	0	-0.042	-0.010	16.951	0.018	0.018	0.000	0.000	0.000
140	A	308	ASN	0	0.031	-0.026	20.108	-0.006	-0.006	0.000	0.000	0.000
141	A	309	GLY	0	0.004	0.006	23.667	0.006	0.006	0.000	0.000	0.000
142	A	310	LYS	1	0.920	0.984	17.317	-0.104	-0.104	0.000	0.000	0.000
143	A	311	SER	0	0.004	-0.005	22.396	-0.004	-0.004	0.000	0.000	0.000
144	A	312	PHE	0	-0.031	-0.022	16.180	0.014	0.014	0.000	0.000	0.000
145	A	313	ASN	0	0.080	0.053	20.905	-0.015	-0.015	0.000	0.000	0.000
146	A	314	HIS	0	-0.030	-0.009	20.189	0.006	0.006	0.000	0.000	0.000
147	A	315	THR	0	0.039	0.013	23.311	-0.022	-0.022	0.000	0.000	0.000
148	A	316	VAL	0	-0.007	0.018	24.718	0.016	0.016	0.000	0.000	0.000
149	A	317	HIS	0	-0.045	-0.030	24.977	-0.002	-0.002	0.000	0.000	0.000
150	A	318	ASN	0	0.023	0.015	28.328	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:169:THR)