FMO DATABASE

FMODB ID: 1N3VZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1585095.937929
FMO2-HF: Nuclear repulsion	1521520.963407
FMO2-HF: Total energy	-63574.974522
FMO2-MP2: Total energy	-63761.851358

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.
-24.194	-17.695	10.873	-7.751	-9.624	-0.073

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 : 0.001 / q_NPA : 0.013

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	0.010	0.004	2.481	-7.014	-3.154	1.620	-2.445	-3.035	-0.016
4	A	4	GLN	0	-0.008	-0.012	4.740	0.889	0.999	-0.001	-0.012	-0.098	0.000
5	A	5	VAL	0	-0.025	0.002	7.528	-0.143	-0.143	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.032	-0.012	10.070	0.215	0.215	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.011	-0.011	13.523	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.011	0.013	17.385	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.007	-0.004	18.817	0.075	0.075	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.090	0.031	20.498	-0.062	-0.062	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.939	-0.963	21.169	-0.422	-0.422	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.022	-0.006	16.046	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.009	-0.004	16.822	-0.101	-0.101	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.026	0.009	18.945	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.050	-0.018	18.093	0.029	0.029	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.078	-0.061	13.128	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.043	-0.010	19.295	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.816	-0.879	22.250	-0.400	-0.400	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.005	-0.006	22.152	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.040	-0.004	24.817	0.040	0.040	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.795	-0.896	25.719	-0.440	-0.440	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.038	0.012	29.296	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.023	-0.017	27.269	0.028	0.028	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.011	-0.008	29.395	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.801	0.903	27.247	0.356	0.356	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.883	-0.944	32.730	-0.209	-0.209	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.013	-0.017	36.255	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.043	-0.014	39.088	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	HIS	0	0.046	0.024	42.877	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.012	-0.004	44.758	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.006	-0.015	47.468	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.042	-0.025	50.786	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.018	47.608	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.072	-0.029	47.106	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.007	-0.005	42.780	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.840	-0.886	39.696	-0.182	-0.182	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.912	0.947	40.202	0.183	0.183	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.015	-0.020	35.012	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.095	-0.046	36.586	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.944	-0.981	34.347	-0.266	-0.266	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.032	-0.009	30.477	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.009	-0.013	28.362	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.006	0.024	28.972	0.023	0.023	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.021	-0.012	29.297	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.828	-0.907	30.391	-0.269	-0.269	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.023	-0.020	30.704	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.006	0.019	30.977	0.019	0.019	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.896	-0.958	33.460	-0.222	-0.222	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.072	-0.053	34.000	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.854	-0.904	36.902	-0.175	-0.175	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.818	0.907	38.482	0.173	0.173	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.053	0.022	33.278	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.030	-0.006	33.112	0.016	0.016	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.010	-0.001	33.196	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.026	-0.009	31.058	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.011	-0.012	30.884	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.005	0.005	25.821	0.012	0.012	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.855	0.911	27.022	0.252	0.252	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.019	0.028	22.357	0.009	0.009	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.040	-0.002	22.444	0.020	0.020	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.031	0.001	20.604	-0.047	-0.047	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.026	0.020	15.258	0.018	0.018	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.035	-0.026	15.055	0.038	0.038	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.009	0.010	13.562	-0.130	-0.130	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.002	-0.011	9.637	0.144	0.144	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.001	0.009	10.574	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.064	-0.048	6.859	-0.747	-0.747	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.016	-0.002	7.047	0.573	0.573	0.000	0.000	0.000	0.000
69	A	69	HIS	1	0.910	0.929	6.577	0.560	0.560	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.814	-0.883	8.542	-0.988	-0.988	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.032	-0.015	10.863	-0.225	-0.225	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.821	-0.910	13.586	-0.514	-0.514	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.838	0.908	17.366	0.391	0.391	0.000	0.000	0.000	0.000
74	A	74	HIS	1	0.877	0.914	19.816	0.555	0.555	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.077	0.046	23.450	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.020	-0.003	25.475	0.017	0.017	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.024	-0.027	27.358	0.026	0.026	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.021	0.035	26.098	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.063	-0.060	23.134	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.012	0.026	24.425	-0.043	-0.043	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.030	-0.019	22.225	0.022	0.022	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.007	-0.006	25.313	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	83	PRO	0	-0.009	0.010	24.985	0.020	0.020	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.037	-0.015	27.676	0.021	0.021	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.797	0.880	30.238	0.307	0.307	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.046	0.050	29.070	0.012	0.012	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.879	-0.947	26.085	-0.367	-0.367	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.003	-0.012	20.788	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.053	-0.031	19.947	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.002	-0.003	13.808	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.011	0.020	15.331	0.036	0.036	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.018	-0.025	9.540	-0.167	-0.167	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.004	0.011	12.164	0.160	0.160	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.007	-0.006	11.432	-0.264	-0.264	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.043	0.019	13.347	0.140	0.140	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.033	0.022	14.809	-0.065	-0.065	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.915	-0.945	16.875	-0.392	-0.392	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.888	-0.947	19.534	-0.279	-0.279	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.782	0.872	14.778	0.341	0.341	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.020	0.022	11.598	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.817	-0.892	11.699	-0.870	-0.870	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.007	-0.007	6.358	-0.173	-0.173	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.063	-0.037	7.544	-0.450	-0.450	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.015	-0.015	9.329	-0.051	-0.051	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.023	0.034	5.895	0.069	0.069	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.822	0.907	8.504	1.426	1.426	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.032	0.013	9.282	0.067	0.067	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.004	-0.001	10.939	0.067	0.067	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.010	-0.006	14.388	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.019	0.018	17.005	0.043	0.043	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.004	-0.022	20.734	0.010	0.010	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.019	-0.002	23.600	0.035	0.035	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.960	-0.973	25.737	-0.289	-0.289	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.024	-0.020	22.437	-0.027	-0.027	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.001	-0.007	24.907	-0.022	-0.022	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.048	-0.018	20.147	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.002	-0.031	23.602	0.023	0.023	0.000	0.000	0.000	0.000
118	A	118	TYR	0	0.022	0.015	17.976	-0.061	-0.061	0.000	0.000	0.000	0.000
119	A	119	HIS	0	0.045	0.024	22.270	0.052	0.052	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.806	0.880	22.830	0.279	0.279	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.082	-0.059	22.412	0.014	0.014	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.037	0.014	17.767	-0.031	-0.031	0.000	0.000	0.000	0.000
123	A	123	TRP	0	-0.022	-0.018	14.652	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	124	HIS	0	0.010	-0.013	14.945	-0.048	-0.048	0.000	0.000	0.000	0.000
125	A	125	HIS	1	0.811	0.893	11.918	1.301	1.301	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.053	0.040	14.697	0.070	0.070	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.006	0.007	17.041	-0.084	-0.084	0.000	0.000	0.000	0.000
128	A	128	PHE	0	-0.056	-0.026	14.332	0.001	0.001	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.022	0.025	19.164	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	TRP	0	0.045	0.005	14.879	-0.082	-0.082	0.000	0.000	0.000	0.000
131	A	131	GLN	0	0.018	0.002	19.470	0.036	0.036	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.879	0.938	21.907	0.371	0.371	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.001	-0.001	23.829	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	134	THR	0	0.016	0.014	24.654	0.002	0.002	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.833	-0.890	26.597	-0.294	-0.294	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.044	0.010	22.366	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.002	0.005	27.753	0.013	0.013	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.025	-0.008	27.248	-0.035	-0.035	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.009	-0.008	28.926	0.031	0.031	0.000	0.000	0.000	0.000
140	A	140	ASP	-1	-0.785	-0.884	27.766	-0.384	-0.384	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.879	0.955	29.215	0.278	0.278	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.023	0.014	29.365	0.023	0.023	0.000	0.000	0.000	0.000
143	A	143	GLY	0	-0.049	-0.028	30.324	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	SER	0	-0.057	-0.027	29.507	-0.017	-0.017	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.902	-0.953	27.284	-0.241	-0.241	0.000	0.000	0.000	0.000
146	A	146	ASN	0	-0.038	-0.044	25.586	-0.035	-0.035	0.000	0.000	0.000	0.000
147	A	147	CYS	0	-0.063	0.004	22.770	-0.009	-0.009	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.787	-0.869	20.794	-0.384	-0.384	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.017	-0.007	17.574	-0.065	-0.065	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.824	-0.894	14.365	-0.337	-0.337	0.000	0.000	0.000	0.000
151	A	151	SER	0	-0.050	-0.025	11.604	-0.174	-0.174	0.000	0.000	0.000	0.000
152	A	152	ILE	0	0.016	0.005	7.440	0.031	0.031	0.000	0.000	0.000	0.000
153	A	153	PRO	0	-0.021	-0.012	4.408	-0.008	0.120	-0.001	-0.012	-0.115	0.000
154	A	154	GLU	-1	-0.889	-0.922	4.138	-2.825	-2.437	-0.001	-0.171	-0.216	0.000
155	A	155	GLN	0	-0.019	-0.015	1.934	-14.298	-13.046	9.256	-4.866	-5.643	-0.057
156	A	156	GLU	-1	-0.808	-0.887	3.777	0.693	1.454	0.000	-0.245	-0.517	0.000
157	A	157	LEU	0	0.010	0.003	5.604	-0.072	-0.072	0.000	0.000	0.000	0.000
158	A	158	CYS	0	-0.073	-0.028	7.346	0.862	0.862	0.000	0.000	0.000	0.000
159	A	159	PHE	0	0.039	0.003	9.424	-0.071	-0.071	0.000	0.000	0.000	0.000
160	A	160	ALA	0	-0.003	0.009	11.185	0.150	0.150	0.000	0.000	0.000	0.000

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