FMO DATABASE

FMODB ID: RY118

Calculation Name: 1A62-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A62

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG30

Base Structure: X-ray

Registration Date: 2023-09-26

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1044146.427837
FMO2-HF: Nuclear repulsion	995188.159291
FMO2-HF: Total energy	-48958.268547
FMO2-MP2: Total energy	-49102.023219

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.
-23.331	-9.366	10.474	-7.44	-16.998	-0.031

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 : 0.017 / q_NPA : 0.022

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

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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	LEU	0	0.046	0.013	3.868	-1.603	0.758	-0.020	-1.231	-1.109	0.002
4	A	4	THR	0	-0.022	-0.038	5.892	0.227	0.227	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.855	-0.928	2.546	-6.265	-3.154	1.232	-2.160	-2.183	-0.024
6	A	6	LEU	0	0.015	0.012	2.664	-1.160	-0.639	2.816	-0.628	-2.709	0.003
7	A	7	LYS	1	0.839	0.890	5.852	-0.273	-0.273	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.004	0.007	9.027	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.024	-0.002	7.035	-0.092	-0.092	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.009	0.013	9.353	0.132	0.132	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.030	0.002	11.183	0.070	0.070	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.041	0.022	12.457	0.069	0.069	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.874	-0.934	9.328	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.011	-0.002	6.687	0.023	0.023	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.014	-0.010	8.078	0.109	0.109	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.010	-0.002	9.888	-0.046	-0.046	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.007	0.003	2.695	-1.107	-0.415	1.240	-0.277	-1.655	0.001
18	A	18	GLY	0	0.038	-0.003	5.746	-0.253	-0.253	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.943	-0.974	7.071	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.100	-0.061	7.695	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.044	0.014	2.250	-0.021	0.118	1.128	-0.214	-1.054	-0.001
22	A	22	GLY	0	0.000	0.004	7.278	0.149	0.149	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.071	-0.024	7.747	0.112	0.112	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.854	-0.936	11.060	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.037	-0.033	14.086	0.059	0.059	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.050	0.029	9.579	0.015	0.015	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.017	0.005	13.860	0.023	0.023	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.841	0.925	16.537	-0.164	-0.164	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.039	0.001	13.481	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.952	0.974	16.253	-0.258	-0.258	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.845	0.912	10.545	-0.372	-0.372	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.025	0.008	11.336	0.142	0.142	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.803	-0.910	11.516	0.558	0.558	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.027	-0.006	8.937	0.096	0.096	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.021	0.018	6.250	0.295	0.295	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.019	-0.020	6.998	0.512	0.512	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.027	-0.008	9.048	0.049	0.049	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.051	0.015	3.189	-0.705	-0.323	0.957	-0.258	-1.081	0.001
39	A	39	LEU	0	0.029	0.014	2.996	-1.072	-0.057	0.630	-0.335	-1.309	0.001
40	A	40	LYS	1	0.790	0.865	5.397	-1.317	-1.301	-0.001	-0.005	-0.010	0.000
41	A	41	GLN	0	-0.026	-0.009	6.610	-0.240	-0.240	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.008	-0.014	2.802	-3.553	-0.962	2.132	-1.164	-3.559	-0.012
43	A	43	ALA	0	0.024	0.010	5.458	-0.601	-0.601	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.803	0.890	7.893	-0.304	-0.304	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.051	-0.020	7.484	-0.055	-0.055	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.049	-0.016	9.587	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.900	-0.926	5.248	-3.185	-3.185	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.809	-0.891	5.304	0.112	0.112	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.041	-0.011	2.604	-3.493	-1.622	0.258	-0.731	-1.398	-0.004
50	A	50	PHE	0	-0.018	-0.023	2.876	-0.149	1.117	0.102	-0.437	-0.931	0.002
51	A	51	GLY	0	0.000	-0.012	5.823	-0.383	-0.383	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.873	-0.913	8.744	0.267	0.267	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.042	0.020	12.013	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.017	-0.003	15.212	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.033	-0.013	19.023	0.005	0.005	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.833	-0.922	20.521	0.118	0.118	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.047	-0.025	22.852	0.006	0.006	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.008	0.005	24.398	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.004	-0.019	27.489	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.922	-0.953	27.993	0.089	0.089	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.030	-0.009	28.703	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.065	-0.037	22.984	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.045	0.009	22.458	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.034	-0.014	17.878	0.005	0.005	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.001	0.015	14.002	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.791	0.875	15.750	-0.141	-0.141	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.062	0.035	14.959	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.025	0.036	15.802	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.878	-0.951	16.382	0.175	0.175	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.031	-0.034	18.445	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.037	-0.016	20.213	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	72	TYR	0	-0.018	-0.005	21.992	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.049	-0.010	22.014	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.012	0.004	20.327	0.011	0.011	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.012	0.004	17.667	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.076	-0.046	15.395	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.858	-0.947	11.434	0.392	0.392	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.768	-0.853	12.791	0.197	0.197	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.038	-0.009	10.656	0.012	0.012	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.008	-0.004	14.252	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.026	0.011	16.731	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.026	0.010	19.146	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.084	0.023	21.884	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.067	-0.028	23.423	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.001	-0.004	16.656	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.068	0.036	21.319	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.936	0.967	23.468	-0.072	-0.072	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.884	0.948	21.992	-0.081	-0.081	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.009	-0.013	19.065	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.028	0.001	23.361	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.024	0.025	20.080	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.813	0.888	24.428	-0.097	-0.097	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.022	0.002	24.372	0.008	0.008	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.017	0.001	23.742	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.784	-0.861	21.730	0.110	0.110	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.005	-0.004	16.858	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.053	-0.025	15.005	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	SER	0	0.004	-0.020	11.357	0.013	0.013	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.032	-0.005	10.479	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.812	0.907	7.788	0.122	0.122	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.014	-0.007	6.887	0.046	0.046	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.829	0.884	9.087	-0.246	-0.246	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.070	0.030	9.379	0.033	0.033	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.048	-0.002	11.598	-0.097	-0.097	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.899	0.924	15.063	-0.113	-0.113	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.825	-0.908	17.325	0.244	0.244	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.027	0.022	19.908	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.827	-0.854	17.866	0.166	0.166	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.929	0.946	18.219	-0.178	-0.178	0.000	0.000	0.000	0.000
110	A	110	TYR	0	0.038	0.031	15.383	0.005	0.005	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.026	0.024	8.347	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.028	-0.008	12.743	-0.040	-0.040	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.044	0.022	12.293	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.069	-0.025	10.478	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.824	0.882	12.287	-0.190	-0.190	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.030	0.039	12.475	0.030	0.030	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.027	-0.019	9.641	-0.104	-0.104	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.839	-0.884	13.710	0.347	0.347	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.008	-0.023	15.972	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.035	-0.035	19.174	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.003	-0.005	15.990	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.746	-0.832	18.509	0.120	0.120	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.842	0.913	17.930	-0.091	-0.091	0.000	0.000	0.000	0.000
124	A	124	PRO	0	-0.059	-0.030	17.317	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.980	-0.995	20.120	0.091	0.091	0.000	0.000	0.000	0.000

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