FMO DATABASE

FMODB ID: 94GJ2

Calculation Name: 3ULP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ULP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8I415

Base Structure: X-ray

Registration Date: 2023-06-21

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-940992.004656
FMO2-HF: Nuclear repulsion	892517.769893
FMO2-HF: Total energy	-48474.234762
FMO2-MP2: Total energy	-48615.703656

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:77:MET)

Summations of interaction energy for fragment #1(A:77: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.
-2.872	0.497	-0.042	-1.721	-1.605	-0.002

Interaction energy analysis for fragmet #1(A:77:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.018

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	79	GLU	-1	-0.911	-0.931	3.817	-2.293	1.076	-0.042	-1.721	-1.605	-0.002
4	A	80	LYS	1	0.930	0.963	6.054	-0.410	-0.410	0.000	0.000	0.000	0.000
5	A	81	SER	0	0.045	0.033	7.298	0.032	0.032	0.000	0.000	0.000	0.000
6	A	82	LEU	0	-0.013	-0.019	9.332	-0.141	-0.141	0.000	0.000	0.000	0.000
7	A	83	ASN	0	-0.020	-0.012	11.101	0.005	0.005	0.000	0.000	0.000	0.000
8	A	84	LYS	1	0.963	0.975	13.323	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	85	ILE	0	0.006	0.017	17.022	0.002	0.002	0.000	0.000	0.000	0.000
10	A	86	MET	0	-0.015	-0.015	19.771	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	87	LEU	0	-0.009	-0.001	23.417	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	88	ILE	0	0.055	0.028	26.267	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	89	GLY	0	-0.009	-0.003	30.020	0.000	0.000	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.868	0.928	31.770	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	91	VAL	0	0.007	0.012	31.751	0.000	0.000	0.000	0.000	0.000	0.000
16	A	92	GLY	0	0.020	-0.001	32.482	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	93	CYS	0	-0.127	-0.066	32.460	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	94	GLU	-1	-0.791	-0.912	34.530	0.021	0.021	0.000	0.000	0.000	0.000
19	A	95	PRO	0	-0.038	-0.015	31.522	0.000	0.000	0.000	0.000	0.000	0.000
20	A	96	ASP	-1	-0.872	-0.922	29.892	0.023	0.023	0.000	0.000	0.000	0.000
21	A	97	ILE	0	0.004	-0.002	29.697	0.003	0.003	0.000	0.000	0.000	0.000
22	A	98	LYS	1	0.910	0.955	27.615	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	99	ILE	0	-0.004	-0.005	28.640	0.001	0.001	0.000	0.000	0.000	0.000
24	A	100	LEU	0	-0.029	-0.007	23.033	0.000	0.000	0.000	0.000	0.000	0.000
25	A	101	ASN	0	0.038	-0.001	26.362	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	102	GLY	0	-0.021	-0.009	26.682	0.002	0.002	0.000	0.000	0.000	0.000
27	A	103	GLY	0	-0.020	-0.011	28.838	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	104	ASP	-1	-0.892	-0.922	23.972	0.033	0.033	0.000	0.000	0.000	0.000
29	A	105	LYS	1	0.923	0.948	26.943	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	106	VAL	0	-0.021	-0.002	23.091	0.003	0.003	0.000	0.000	0.000	0.000
31	A	107	ALA	0	0.026	0.039	25.784	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	108	THR	0	-0.091	-0.047	24.625	0.003	0.003	0.000	0.000	0.000	0.000
33	A	109	PHE	0	0.056	0.012	27.033	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	110	SER	0	0.015	0.015	27.311	0.002	0.002	0.000	0.000	0.000	0.000
35	A	111	LEU	0	0.028	0.003	27.422	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	112	ALA	0	0.022	0.017	28.558	0.001	0.001	0.000	0.000	0.000	0.000
37	A	113	THR	0	0.020	0.012	27.960	0.002	0.002	0.000	0.000	0.000	0.000
38	A	114	ASN	0	-0.075	-0.043	30.596	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	115	GLU	-1	-0.857	-0.903	29.547	0.045	0.045	0.000	0.000	0.000	0.000
40	A	116	PHE	0	-0.013	-0.030	32.702	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	117	TRP	0	-0.024	-0.008	33.385	0.002	0.002	0.000	0.000	0.000	0.000
42	A	118	ARG	1	0.924	0.951	36.563	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	119	ASP	-1	-0.857	-0.945	37.489	0.017	0.017	0.000	0.000	0.000	0.000
44	A	120	ARG	1	0.936	0.973	35.393	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	121	ASN	0	-0.005	-0.006	38.039	0.001	0.001	0.000	0.000	0.000	0.000
46	A	122	THR	0	0.049	0.024	41.039	0.000	0.000	0.000	0.000	0.000	0.000
47	A	123	ASN	0	-0.010	0.003	41.876	0.001	0.001	0.000	0.000	0.000	0.000
48	A	124	GLU	-1	-0.941	-0.950	41.284	0.013	0.013	0.000	0.000	0.000	0.000
49	A	125	LEU	0	-0.037	-0.022	40.505	0.001	0.001	0.000	0.000	0.000	0.000
50	A	126	LYS	1	0.948	0.982	36.880	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	127	SER	0	0.004	-0.005	35.798	0.002	0.002	0.000	0.000	0.000	0.000
52	A	128	LYS	1	0.891	0.945	27.749	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	129	THR	0	0.016	0.014	32.457	0.003	0.003	0.000	0.000	0.000	0.000
54	A	130	ASP	-1	-0.905	-0.946	26.903	0.029	0.029	0.000	0.000	0.000	0.000
55	A	131	TRP	0	0.019	0.009	28.344	0.002	0.002	0.000	0.000	0.000	0.000
56	A	132	HIS	1	0.848	0.910	23.534	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	133	ARG	1	0.910	0.941	21.956	-0.039	-0.039	0.000	0.000	0.000	0.000
58	A	134	ILE	0	-0.002	0.007	22.533	0.005	0.005	0.000	0.000	0.000	0.000
59	A	135	VAL	0	-0.009	-0.006	20.721	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	136	VAL	0	-0.009	0.001	21.646	0.005	0.005	0.000	0.000	0.000	0.000
61	A	137	TYR	0	0.045	-0.002	18.844	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	138	ASP	-1	-0.847	-0.920	22.313	0.037	0.037	0.000	0.000	0.000	0.000
63	A	139	GLN	0	0.077	0.023	23.878	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	140	ASN	0	0.026	0.024	27.019	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	141	ILE	0	-0.010	-0.009	25.145	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	142	VAL	0	-0.018	-0.014	26.351	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	143	ASP	-1	-0.852	-0.922	29.067	0.023	0.023	0.000	0.000	0.000	0.000
68	A	144	LEU	0	-0.007	-0.008	31.682	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	145	ILE	0	-0.057	-0.033	28.257	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	146	ASP	-1	-0.921	-0.962	32.628	0.021	0.021	0.000	0.000	0.000	0.000
71	A	147	LYS	1	0.925	0.968	34.555	-0.024	-0.024	0.000	0.000	0.000	0.000
72	A	148	TYR	0	-0.044	-0.035	36.211	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	149	LEU	0	-0.110	-0.018	31.464	0.000	0.000	0.000	0.000	0.000	0.000
74	A	150	ARG	1	0.909	0.960	35.488	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	151	LYS	1	0.977	0.983	36.539	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	152	GLY	0	0.004	0.008	36.711	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	153	ARG	1	0.903	0.965	35.983	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	154	ARG	1	0.896	0.955	34.575	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	155	VAL	0	0.008	0.017	30.000	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	156	TYR	0	0.053	0.017	25.543	0.001	0.001	0.000	0.000	0.000	0.000
81	A	157	VAL	0	0.003	0.002	23.724	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	158	GLN	0	-0.043	-0.025	19.529	0.002	0.002	0.000	0.000	0.000	0.000
83	A	159	GLY	0	0.018	0.005	19.485	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.031	-0.003	14.087	0.007	0.007	0.000	0.000	0.000	0.000
85	A	161	LEU	0	-0.021	-0.007	14.880	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	162	HIS	0	0.018	0.005	10.985	0.013	0.013	0.000	0.000	0.000	0.000
87	A	163	THR	0	0.007	0.006	11.922	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	164	ARG	1	0.937	0.967	12.316	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	165	LYS	1	0.961	0.966	10.161	0.121	0.121	0.000	0.000	0.000	0.000
90	A	166	TRP	0	-0.049	-0.030	14.669	0.017	0.017	0.000	0.000	0.000	0.000
91	A	167	HIS	0	0.049	0.028	16.071	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	168	THR	0	0.029	0.020	20.590	0.007	0.007	0.000	0.000	0.000	0.000
93	A	169	ASN	0	0.033	0.003	23.259	0.001	0.001	0.000	0.000	0.000	0.000
94	A	170	ASP	-1	-0.823	-0.910	23.974	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	171	MET	0	0.032	0.041	25.731	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	172	ASN	0	0.016	0.008	26.130	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	173	SER	0	-0.041	-0.029	21.054	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	174	GLN	0	-0.038	-0.018	21.478	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	175	PRO	0	-0.011	-0.010	16.623	0.006	0.006	0.000	0.000	0.000	0.000
100	A	176	LYS	1	0.874	0.935	18.723	0.005	0.005	0.000	0.000	0.000	0.000
101	A	177	GLN	0	-0.029	-0.009	14.138	0.001	0.001	0.000	0.000	0.000	0.000
102	A	178	ILE	0	-0.028	-0.007	16.921	0.001	0.001	0.000	0.000	0.000	0.000
103	A	179	THR	0	-0.011	-0.008	16.858	0.005	0.005	0.000	0.000	0.000	0.000
104	A	180	GLU	-1	-0.800	-0.888	17.698	0.048	0.048	0.000	0.000	0.000	0.000
105	A	181	ILE	0	0.010	-0.004	17.741	0.008	0.008	0.000	0.000	0.000	0.000
106	A	182	ILE	0	-0.017	-0.001	15.943	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	183	LEU	0	0.015	0.003	18.301	0.006	0.006	0.000	0.000	0.000	0.000
108	A	184	SER	0	0.000	-0.011	17.035	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	185	TYR	0	0.072	0.003	19.374	0.001	0.001	0.000	0.000	0.000	0.000
110	A	186	ASN	0	-0.046	-0.016	19.844	0.000	0.000	0.000	0.000	0.000	0.000
111	A	187	LYS	1	0.916	0.965	13.957	-0.030	-0.030	0.000	0.000	0.000	0.000
112	A	188	GLY	0	-0.003	0.016	19.316	0.008	0.008	0.000	0.000	0.000	0.000
113	A	189	ASP	-1	-0.873	-0.927	21.628	0.047	0.047	0.000	0.000	0.000	0.000
114	A	190	LEU	0	-0.023	-0.024	25.276	0.002	0.002	0.000	0.000	0.000	0.000
115	A	191	ILE	0	0.016	0.022	28.163	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	192	PHE	0	-0.013	-0.022	31.489	0.000	0.000	0.000	0.000	0.000	0.000
117	A	193	LEU	0	0.000	0.005	32.562	0.000	0.000	0.000	0.000	0.000	0.000
118	A	194	ASP	-1	-0.893	-0.956	36.412	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:77:MET)