FMO DATABASE

FMODB ID: 1NY4Z

Calculation Name: 3O7X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O7X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TC59

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptHSide
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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-918684.407826
FMO2-HF: Nuclear repulsion	870040.283235
FMO2-HF: Total energy	-48644.124591
FMO2-MP2: Total energy	-48783.522689

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:386:SER)

Summations of interaction energy for fragment #1(A:386:SER)

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.
-5.605	-4.353	-0.009	-0.43	-0.814	0.002

Interaction energy analysis for fragmet #1(A:386:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.037

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	388	ASP	-1	-0.805	-0.910	3.814	-5.158	-3.906	-0.009	-0.430	-0.814	0.002
4	A	389	CYS	0	-0.132	-0.030	6.128	0.586	0.586	0.000	0.000	0.000	0.000
5	A	390	VAL	0	0.069	0.011	7.397	-0.172	-0.172	0.000	0.000	0.000	0.000
6	A	391	LEU	0	-0.006	-0.004	8.853	-0.066	-0.066	0.000	0.000	0.000	0.000
7	A	392	ASP	-1	-0.790	-0.911	9.931	-1.122	-1.122	0.000	0.000	0.000	0.000
8	A	393	VAL	0	0.005	0.006	5.639	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	394	MET	0	-0.083	-0.050	8.710	0.234	0.234	0.000	0.000	0.000	0.000
10	A	395	HIS	0	0.004	0.015	11.992	0.175	0.175	0.000	0.000	0.000	0.000
11	A	396	ALA	0	-0.008	0.001	10.183	0.118	0.118	0.000	0.000	0.000	0.000
12	A	397	ILE	0	0.014	0.000	9.026	0.152	0.152	0.000	0.000	0.000	0.000
13	A	398	TYR	0	0.030	0.031	12.782	0.169	0.169	0.000	0.000	0.000	0.000
14	A	399	GLN	0	-0.052	-0.027	15.886	0.082	0.082	0.000	0.000	0.000	0.000
15	A	400	GLN	0	0.014	-0.004	11.304	0.087	0.087	0.000	0.000	0.000	0.000
16	A	401	ASN	0	-0.063	-0.030	15.901	0.129	0.129	0.000	0.000	0.000	0.000
17	A	402	LYS	1	0.938	0.970	18.880	0.465	0.465	0.000	0.000	0.000	0.000
18	A	403	GLU	-1	-0.872	-0.935	19.564	-0.538	-0.538	0.000	0.000	0.000	0.000
19	A	404	HIS	0	-0.020	-0.005	21.186	0.016	0.016	0.000	0.000	0.000	0.000
20	A	405	PHE	0	-0.009	-0.012	22.844	0.041	0.041	0.000	0.000	0.000	0.000
21	A	406	GLN	0	0.007	-0.008	25.094	0.022	0.022	0.000	0.000	0.000	0.000
22	A	407	ASP	-1	-0.875	-0.938	25.467	-0.306	-0.306	0.000	0.000	0.000	0.000
23	A	408	GLU	-1	-0.989	-0.978	27.069	-0.215	-0.215	0.000	0.000	0.000	0.000
24	A	409	CYS	0	-0.017	0.002	28.826	0.025	0.025	0.000	0.000	0.000	0.000
25	A	410	THR	0	0.042	0.014	30.310	0.018	0.018	0.000	0.000	0.000	0.000
26	A	411	LYS	1	0.862	0.923	27.721	0.264	0.264	0.000	0.000	0.000	0.000
27	A	412	LEU	0	-0.011	-0.002	32.855	0.012	0.012	0.000	0.000	0.000	0.000
28	A	413	LEU	0	-0.033	-0.015	35.064	0.013	0.013	0.000	0.000	0.000	0.000
29	A	414	VAL	0	-0.035	-0.007	35.175	0.011	0.011	0.000	0.000	0.000	0.000
30	A	415	GLY	0	-0.030	-0.013	37.623	0.001	0.001	0.000	0.000	0.000	0.000
31	A	416	ASN	0	-0.083	-0.038	39.514	0.015	0.015	0.000	0.000	0.000	0.000
32	A	417	ILE	0	-0.018	-0.019	42.387	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	418	VAL	0	0.006	0.005	41.950	0.001	0.001	0.000	0.000	0.000	0.000
34	A	419	ILE	0	-0.017	-0.024	45.205	0.004	0.004	0.000	0.000	0.000	0.000
35	A	420	THR	0	0.032	0.014	46.267	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	421	ARG	1	0.962	0.981	48.019	0.087	0.087	0.000	0.000	0.000	0.000
37	A	422	TYR	0	0.007	0.014	46.940	0.003	0.003	0.000	0.000	0.000	0.000
38	A	423	ASN	0	0.019	-0.003	51.200	0.001	0.001	0.000	0.000	0.000	0.000
39	A	424	ASN	0	-0.040	-0.014	53.198	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	425	ARG	1	0.928	1.002	51.248	0.088	0.088	0.000	0.000	0.000	0.000
41	A	426	THR	0	-0.029	-0.025	49.148	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	427	TYR	0	-0.011	-0.005	45.777	0.002	0.002	0.000	0.000	0.000	0.000
43	A	428	ARG	1	0.843	0.901	43.475	0.121	0.121	0.000	0.000	0.000	0.000
44	A	429	ILE	0	-0.001	0.009	38.157	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	430	ASP	-1	-0.788	-0.862	39.798	-0.133	-0.133	0.000	0.000	0.000	0.000
46	A	431	ASP	-1	-0.764	-0.889	34.337	-0.210	-0.210	0.000	0.000	0.000	0.000
47	A	432	VAL	0	-0.040	-0.013	32.909	0.012	0.012	0.000	0.000	0.000	0.000
48	A	433	ASP	-1	-0.847	-0.926	33.065	-0.232	-0.232	0.000	0.000	0.000	0.000
49	A	434	TRP	0	0.006	-0.026	28.732	0.004	0.004	0.000	0.000	0.000	0.000
50	A	435	ASN	0	-0.090	-0.038	28.804	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	436	LYS	1	0.959	0.998	30.997	0.179	0.179	0.000	0.000	0.000	0.000
52	A	437	THR	0	0.020	0.005	33.688	0.001	0.001	0.000	0.000	0.000	0.000
53	A	438	PRO	0	-0.049	-0.020	35.712	0.007	0.007	0.000	0.000	0.000	0.000
54	A	439	LYS	1	0.875	0.931	33.327	0.193	0.193	0.000	0.000	0.000	0.000
55	A	440	ASP	-1	-0.835	-0.901	35.965	-0.186	-0.186	0.000	0.000	0.000	0.000
56	A	441	SER	0	-0.051	-0.058	38.929	0.006	0.006	0.000	0.000	0.000	0.000
57	A	442	PHE	0	-0.073	-0.032	41.925	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	443	THR	0	0.023	0.013	44.531	0.002	0.002	0.000	0.000	0.000	0.000
59	A	444	MET	0	-0.054	-0.021	47.509	0.002	0.002	0.000	0.000	0.000	0.000
60	A	445	SER	0	0.004	-0.011	50.941	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	446	ASP	-1	-0.925	-0.967	53.920	-0.086	-0.086	0.000	0.000	0.000	0.000
62	A	447	GLY	0	0.014	0.012	50.779	0.001	0.001	0.000	0.000	0.000	0.000
63	A	448	LYS	1	0.916	0.969	49.774	0.081	0.081	0.000	0.000	0.000	0.000
64	A	449	GLU	-1	-0.864	-0.919	43.924	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	450	ILE	0	-0.094	-0.045	46.574	0.006	0.006	0.000	0.000	0.000	0.000
66	A	451	THR	0	0.055	0.013	42.416	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	452	PHE	0	0.006	-0.008	40.235	0.008	0.008	0.000	0.000	0.000	0.000
68	A	453	LEU	0	0.026	0.025	40.576	0.006	0.006	0.000	0.000	0.000	0.000
69	A	454	GLU	-1	-0.815	-0.882	44.373	-0.096	-0.096	0.000	0.000	0.000	0.000
70	A	455	TYR	0	-0.004	-0.003	46.858	0.007	0.007	0.000	0.000	0.000	0.000
71	A	456	TYR	0	0.026	-0.007	44.469	0.003	0.003	0.000	0.000	0.000	0.000
72	A	457	SER	0	-0.020	-0.002	48.348	0.005	0.005	0.000	0.000	0.000	0.000
73	A	458	LYS	1	0.813	0.901	50.259	0.095	0.095	0.000	0.000	0.000	0.000
74	A	459	ASN	0	-0.034	-0.015	52.111	0.003	0.003	0.000	0.000	0.000	0.000
75	A	460	TYR	0	-0.039	-0.027	50.522	0.003	0.003	0.000	0.000	0.000	0.000
76	A	461	GLY	0	0.003	0.026	53.093	0.002	0.002	0.000	0.000	0.000	0.000
77	A	462	ILE	0	-0.070	-0.043	47.106	0.001	0.001	0.000	0.000	0.000	0.000
78	A	463	THR	0	0.004	-0.007	45.627	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	464	VAL	0	-0.033	-0.015	40.939	0.002	0.002	0.000	0.000	0.000	0.000
80	A	465	LYS	1	0.859	0.928	40.847	0.095	0.095	0.000	0.000	0.000	0.000
81	A	466	GLU	-1	-0.885	-0.941	35.038	-0.155	-0.155	0.000	0.000	0.000	0.000
82	A	467	GLU	-1	-0.941	-0.970	36.995	-0.137	-0.137	0.000	0.000	0.000	0.000
83	A	468	ASP	-1	-0.876	-0.952	30.557	-0.223	-0.223	0.000	0.000	0.000	0.000
84	A	469	GLN	0	-0.072	-0.027	32.416	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	470	PRO	0	0.072	0.024	31.533	0.002	0.002	0.000	0.000	0.000	0.000
86	A	471	LEU	0	-0.023	-0.006	34.112	0.015	0.015	0.000	0.000	0.000	0.000
87	A	472	LEU	0	-0.029	-0.011	36.468	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	473	ILE	0	0.035	0.019	36.723	0.008	0.008	0.000	0.000	0.000	0.000
89	A	474	HIS	0	-0.017	-0.005	39.995	0.003	0.003	0.000	0.000	0.000	0.000
90	A	475	ARG	1	0.780	0.854	36.947	0.175	0.175	0.000	0.000	0.000	0.000
91	A	476	PRO	0	-0.007	-0.017	44.487	0.004	0.004	0.000	0.000	0.000	0.000
92	A	477	SER	0	-0.007	-0.023	47.441	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	478	GLU	-1	-0.854	-0.899	49.977	-0.088	-0.088	0.000	0.000	0.000	0.000
94	A	479	ARG	1	0.959	0.990	42.473	0.134	0.134	0.000	0.000	0.000	0.000
95	A	480	GLN	0	0.028	0.020	42.863	0.002	0.002	0.000	0.000	0.000	0.000
96	A	481	ASP	-1	-0.902	-0.965	47.316	-0.092	-0.092	0.000	0.000	0.000	0.000
97	A	482	ASN	0	0.033	0.003	49.876	0.001	0.001	0.000	0.000	0.000	0.000
98	A	483	HIS	0	-0.012	-0.002	48.535	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	484	GLY	0	-0.015	0.004	45.204	0.000	0.000	0.000	0.000	0.000	0.000
100	A	485	MET	0	-0.037	-0.010	45.608	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	486	LEU	0	-0.008	0.009	43.393	0.001	0.001	0.000	0.000	0.000	0.000
102	A	487	LEU	0	-0.002	-0.019	47.176	0.004	0.004	0.000	0.000	0.000	0.000
103	A	488	LYS	1	0.750	0.861	49.569	0.093	0.093	0.000	0.000	0.000	0.000
104	A	489	GLY	0	0.018	0.014	46.604	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	490	GLU	-1	-0.867	-0.947	40.289	-0.161	-0.161	0.000	0.000	0.000	0.000
106	A	491	ILE	0	-0.051	-0.011	44.690	0.002	0.002	0.000	0.000	0.000	0.000
107	A	492	LEU	0	0.023	0.015	39.573	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	493	LEU	0	-0.038	-0.010	41.779	0.007	0.007	0.000	0.000	0.000	0.000
109	A	494	LEU	0	0.054	0.026	39.952	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	495	PRO	0	0.047	0.018	36.402	0.009	0.009	0.000	0.000	0.000	0.000
111	A	496	GLU	-1	-0.831	-0.899	39.472	-0.112	-0.112	0.000	0.000	0.000	0.000
112	A	497	LEU	0	-0.069	-0.036	40.986	0.008	0.008	0.000	0.000	0.000	0.000
113	A	498	SER	0	-0.053	-0.026	41.847	0.006	0.006	0.000	0.000	0.000	0.000
114	A	499	PHE	0	-0.013	-0.009	42.841	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	500	MET	0	0.040	0.019	39.545	0.000	0.000	0.000	0.000	0.000	0.000
116	A	501	THR	0	-0.015	0.002	43.845	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:386:SER)