FMO DATABASE

FMODB ID: YVM72

Calculation Name: 1XSR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XSR

Chain ID: A

ChEMBL ID:

UniProt ID: P63487

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1583092.977691
FMO2-HF: Nuclear repulsion	1519519.51167
FMO2-HF: Total energy	-63573.466021
FMO2-MP2: Total energy	-63760.43145

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.
-20.799	-12.88	6.797	-6.335	-8.382	-0.068

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 : -0.019 / q_NPA : -0.004

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	LEU	0	0.015	0.009	2.469	-7.601	-4.723	2.346	-2.166	-3.058	-0.022
4	A	4	GLN	0	0.011	-0.008	4.644	1.098	1.245	-0.001	-0.016	-0.129	0.000
5	A	5	VAL	0	-0.037	-0.009	7.352	-0.215	-0.215	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.037	-0.012	10.415	0.233	0.233	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.008	-0.006	13.048	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.006	0.015	16.754	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.004	-0.001	18.496	0.070	0.070	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.098	0.012	20.256	-0.075	-0.075	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.939	-0.965	20.633	-0.427	-0.427	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.038	-0.013	15.829	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.013	-0.012	16.818	-0.111	-0.111	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.024	0.016	18.806	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.034	-0.013	18.109	0.030	0.030	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.073	-0.054	13.105	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.063	0.003	19.222	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.813	-0.884	22.338	-0.413	-0.413	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.011	-0.011	21.857	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.035	-0.003	24.473	0.035	0.035	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.852	-0.932	25.837	-0.379	-0.379	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.024	0.011	28.929	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.008	-0.004	28.048	0.016	0.016	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.008	-0.007	29.229	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.854	0.957	26.778	0.327	0.327	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.880	-0.940	32.860	-0.194	-0.194	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.029	-0.030	36.315	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.050	-0.019	39.016	0.008	0.008	0.000	0.000	0.000	0.000
29	A	29	HIS	0	0.041	0.023	42.742	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.020	-0.013	44.693	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.019	-0.001	47.307	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.048	-0.037	50.362	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.051	0.030	47.777	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.105	-0.052	46.769	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.002	0.010	42.841	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.873	-0.919	39.967	-0.153	-0.153	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.911	0.941	39.809	0.178	0.178	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.026	0.015	34.915	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.055	-0.036	35.789	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.978	-0.998	33.385	-0.281	-0.281	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.008	0.020	30.121	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.024	-0.022	28.499	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.015	0.023	28.321	0.025	0.025	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.034	-0.010	29.290	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.876	-0.953	29.908	-0.319	-0.319	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.023	-0.017	30.391	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.007	0.019	30.941	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.946	-0.966	33.374	-0.259	-0.259	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.066	-0.060	34.085	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.941	-0.976	37.003	-0.182	-0.182	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.911	0.995	37.958	0.187	0.187	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.060	0.030	33.472	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.012	-0.013	33.238	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.004	0.012	32.993	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.035	-0.013	30.769	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.015	-0.003	30.970	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.029	-0.017	25.978	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.910	0.957	27.276	0.192	0.192	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.022	0.020	22.159	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.011	-0.014	22.459	0.030	0.030	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.028	0.003	20.555	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.032	0.019	15.190	0.014	0.014	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.025	-0.021	15.590	0.009	0.009	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.028	0.010	14.109	-0.063	-0.063	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.018	-0.015	10.454	0.053	0.053	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.039	0.004	10.711	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.040	-0.019	6.803	-0.398	-0.398	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.006	0.016	7.779	0.283	0.283	0.000	0.000	0.000	0.000
69	A	69	HIS	1	0.920	0.943	6.877	0.541	0.541	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.874	-0.932	8.705	-0.992	-0.992	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.006	-0.019	10.459	-0.170	-0.170	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.839	-0.920	13.596	-0.532	-0.532	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.894	0.980	17.283	0.543	0.543	0.000	0.000	0.000	0.000
74	A	74	HIS	1	0.877	0.937	19.649	0.597	0.597	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.075	0.031	23.209	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.018	-0.004	25.097	0.017	0.017	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.050	-0.028	26.824	0.031	0.031	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.017	0.031	25.684	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.035	-0.029	23.389	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.007	0.018	24.332	-0.039	-0.039	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.014	-0.022	22.139	0.019	0.019	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.006	0.001	25.316	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	83	PRO	0	-0.016	0.006	24.926	0.021	0.021	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.015	-0.011	27.585	0.016	0.016	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.839	0.896	30.098	0.213	0.213	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.060	0.058	28.919	0.012	0.012	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.880	-0.932	25.591	-0.261	-0.261	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.013	-0.014	20.361	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.072	-0.044	19.640	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.007	-0.009	13.448	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.004	0.020	15.302	0.016	0.016	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.011	-0.015	9.428	-0.124	-0.124	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.009	-0.008	12.091	0.151	0.151	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.022	0.003	11.097	-0.326	-0.326	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.045	0.029	13.027	0.155	0.155	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.009	0.007	14.707	-0.097	-0.097	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.921	-0.960	16.555	-0.554	-0.554	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.935	-0.966	18.920	-0.432	-0.432	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.893	0.947	14.549	0.616	0.616	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.018	0.017	11.377	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.805	-0.877	11.657	-1.297	-1.297	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.001	-0.019	6.408	-0.138	-0.138	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.073	-0.030	7.344	-0.484	-0.484	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.043	-0.039	9.082	0.023	0.023	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.001	0.014	5.652	0.172	0.172	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.867	0.940	8.513	1.525	1.525	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.025	0.022	9.163	0.074	0.074	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.009	-0.009	10.829	0.061	0.061	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.015	0.004	14.306	0.015	0.015	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.041	0.027	16.744	0.038	0.038	0.000	0.000	0.000	0.000
111	A	111	ASN	0	0.003	-0.015	20.414	0.019	0.019	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.022	-0.033	23.171	0.033	0.033	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.927	-0.940	25.315	-0.223	-0.223	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.061	-0.039	22.046	-0.029	-0.029	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.007	-0.022	24.460	-0.016	-0.016	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.052	-0.033	19.816	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.010	-0.019	23.236	0.031	0.031	0.000	0.000	0.000	0.000
118	A	118	TYR	0	0.021	0.020	17.591	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	119	HIS	0	0.066	0.047	21.892	0.055	0.055	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.879	0.930	22.439	0.338	0.338	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.063	-0.055	21.776	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.024	0.022	17.433	-0.053	-0.053	0.000	0.000	0.000	0.000
123	A	123	TRP	0	-0.028	-0.020	14.250	0.002	0.002	0.000	0.000	0.000	0.000
124	A	124	HIS	0	0.029	-0.001	14.667	-0.088	-0.088	0.000	0.000	0.000	0.000
125	A	125	HIS	1	0.809	0.927	12.168	1.156	1.156	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.023	0.013	14.495	0.062	0.062	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.045	0.011	17.060	-0.046	-0.046	0.000	0.000	0.000	0.000
128	A	128	PHE	0	-0.052	-0.027	14.258	0.019	0.019	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.022	0.035	19.148	-0.025	-0.025	0.000	0.000	0.000	0.000
130	A	130	TRP	0	0.054	0.013	15.095	-0.042	-0.042	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.003	0.010	19.824	0.047	0.047	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.899	0.924	21.794	0.215	0.215	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.009	-0.003	24.380	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	134	THR	0	0.011	0.015	24.655	0.004	0.004	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.888	-0.932	26.578	-0.236	-0.236	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.018	0.001	22.554	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.010	0.005	27.845	0.010	0.010	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.039	-0.016	26.554	-0.025	-0.025	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.000	-0.011	28.666	0.030	0.030	0.000	0.000	0.000	0.000
140	A	140	ASP	-1	-0.828	-0.910	27.154	-0.390	-0.390	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.847	0.930	29.239	0.302	0.302	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.039	0.008	28.343	0.018	0.018	0.000	0.000	0.000	0.000
143	A	143	GLY	0	-0.033	-0.016	29.409	0.017	0.017	0.000	0.000	0.000	0.000
144	A	144	SER	0	-0.087	-0.040	29.128	-0.009	-0.009	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.822	-0.919	27.215	-0.288	-0.288	0.000	0.000	0.000	0.000
146	A	146	ASN	0	-0.028	-0.024	25.779	-0.035	-0.035	0.000	0.000	0.000	0.000
147	A	147	CYS	0	-0.096	-0.035	22.291	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.839	-0.902	20.456	-0.455	-0.455	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.045	-0.029	17.428	-0.071	-0.071	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.885	-0.951	14.457	-0.622	-0.622	0.000	0.000	0.000	0.000
151	A	151	SER	0	-0.067	-0.037	11.600	-0.187	-0.187	0.000	0.000	0.000	0.000
152	A	152	ILE	0	0.013	0.004	6.925	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	153	PRO	0	-0.046	-0.020	4.506	0.116	0.250	-0.001	-0.012	-0.121	0.000
154	A	154	GLU	-1	-0.906	-0.960	4.167	-1.326	-1.031	-0.001	-0.100	-0.195	0.000
155	A	155	GLN	0	-0.012	-0.009	2.164	-14.088	-10.338	4.454	-3.840	-4.365	-0.046
156	A	156	GLU	-1	-0.884	-0.939	3.549	3.673	4.388	0.000	-0.201	-0.514	0.000
157	A	157	LEU	0	-0.031	-0.024	5.453	-0.328	-0.328	0.000	0.000	0.000	0.000
158	A	158	CYS	0	-0.056	-0.012	7.755	0.929	0.929	0.000	0.000	0.000	0.000
159	A	159	PHE	0	0.055	0.022	9.575	-0.241	-0.241	0.000	0.000	0.000	0.000
160	A	160	ALA	0	-0.003	0.007	10.758	0.160	0.160	0.000	0.000	0.000	0.000

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