FMO DATABASE

FMODB ID: MV3GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-942550.307719
FMO2-HF: Nuclear repulsion	894075.193788
FMO2-HF: Total energy	-48475.113931
FMO2-MP2: Total energy	-48616.517516

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.
-2.888	0.508	-0.04	-1.731	-1.625	-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 : -0.021 / q_NPA : -0.025

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	-0.910	-0.929	3.817	-2.270	1.126	-0.040	-1.731	-1.625	-0.002
4	A	80	LYS	1	0.927	0.963	6.054	-0.441	-0.441	0.000	0.000	0.000	0.000
5	A	81	SER	0	0.043	0.031	6.983	0.027	0.027	0.000	0.000	0.000	0.000
6	A	82	LEU	0	-0.020	-0.022	9.310	-0.135	-0.135	0.000	0.000	0.000	0.000
7	A	83	ASN	0	-0.001	-0.006	11.137	0.007	0.007	0.000	0.000	0.000	0.000
8	A	84	LYS	1	0.924	0.958	13.317	-0.128	-0.128	0.000	0.000	0.000	0.000
9	A	85	ILE	0	-0.002	0.009	17.017	0.001	0.001	0.000	0.000	0.000	0.000
10	A	86	MET	0	-0.001	-0.008	19.770	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	87	LEU	0	-0.010	0.000	23.415	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	88	ILE	0	0.044	0.018	26.268	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	89	GLY	0	-0.002	0.003	30.022	0.000	0.000	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.836	0.911	31.775	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	91	VAL	0	0.014	0.017	31.568	0.000	0.000	0.000	0.000	0.000	0.000
16	A	92	GLY	0	0.035	-0.003	32.498	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	93	CYS	0	-0.118	-0.057	32.490	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	94	GLU	-1	-0.765	-0.898	34.551	0.020	0.020	0.000	0.000	0.000	0.000
19	A	95	PRO	0	-0.034	-0.011	31.351	0.000	0.000	0.000	0.000	0.000	0.000
20	A	96	ASP	-1	-0.845	-0.885	29.586	0.024	0.024	0.000	0.000	0.000	0.000
21	A	97	ILE	0	0.013	0.000	29.704	0.003	0.003	0.000	0.000	0.000	0.000
22	A	98	LYS	1	0.835	0.893	27.417	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	99	ILE	0	0.011	0.004	28.665	0.001	0.001	0.000	0.000	0.000	0.000
24	A	100	LEU	0	-0.019	-0.002	23.109	0.000	0.000	0.000	0.000	0.000	0.000
25	A	101	ASN	0	0.025	-0.010	26.354	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	102	GLY	0	-0.008	-0.001	26.731	0.002	0.002	0.000	0.000	0.000	0.000
27	A	103	GLY	0	-0.022	-0.011	28.872	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	104	ASP	-1	-0.905	-0.930	24.422	0.031	0.031	0.000	0.000	0.000	0.000
29	A	105	LYS	1	0.831	0.893	26.988	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	106	VAL	0	-0.023	-0.003	23.058	0.002	0.002	0.000	0.000	0.000	0.000
31	A	107	ALA	0	0.020	0.032	25.806	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	108	THR	0	-0.080	-0.038	24.624	0.003	0.003	0.000	0.000	0.000	0.000
33	A	109	PHE	0	0.055	0.019	27.031	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	110	SER	0	0.026	0.016	27.331	0.002	0.002	0.000	0.000	0.000	0.000
35	A	111	LEU	0	0.016	-0.003	27.172	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	112	ALA	0	0.027	0.020	28.568	0.001	0.001	0.000	0.000	0.000	0.000
37	A	113	THR	0	0.015	0.002	27.990	0.001	0.001	0.000	0.000	0.000	0.000
38	A	114	ASN	0	-0.063	-0.041	30.599	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	115	GLU	-1	-0.868	-0.905	29.202	0.042	0.042	0.000	0.000	0.000	0.000
40	A	116	PHE	0	-0.008	-0.029	32.698	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	117	TRP	0	-0.021	-0.004	33.344	0.002	0.002	0.000	0.000	0.000	0.000
42	A	118	ARG	1	0.943	0.962	36.552	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	119	ASP	-1	-0.845	-0.911	37.491	0.014	0.014	0.000	0.000	0.000	0.000
44	A	120	ARG	1	0.951	0.975	35.910	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	121	ASN	0	-0.015	-0.014	38.023	0.001	0.001	0.000	0.000	0.000	0.000
46	A	122	THR	0	0.021	0.005	41.023	0.000	0.000	0.000	0.000	0.000	0.000
47	A	123	ASN	0	-0.025	-0.004	41.857	0.001	0.001	0.000	0.000	0.000	0.000
48	A	124	GLU	-1	-0.807	-0.880	41.189	0.011	0.011	0.000	0.000	0.000	0.000
49	A	125	LEU	0	-0.034	-0.023	40.125	0.001	0.001	0.000	0.000	0.000	0.000
50	A	126	LYS	1	0.815	0.895	36.749	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	127	SER	0	0.005	-0.003	35.781	0.001	0.001	0.000	0.000	0.000	0.000
52	A	128	LYS	1	0.846	0.909	27.683	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	129	THR	0	0.012	0.008	32.417	0.002	0.002	0.000	0.000	0.000	0.000
54	A	130	ASP	-1	-0.863	-0.905	26.902	0.026	0.026	0.000	0.000	0.000	0.000
55	A	131	TRP	0	0.020	0.017	28.356	0.002	0.002	0.000	0.000	0.000	0.000
56	A	132	HIS	1	0.847	0.913	23.767	-0.040	-0.040	0.000	0.000	0.000	0.000
57	A	133	ARG	1	0.898	0.934	22.472	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	134	ILE	0	-0.002	0.008	22.551	0.005	0.005	0.000	0.000	0.000	0.000
59	A	135	VAL	0	-0.004	-0.005	20.741	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	136	VAL	0	-0.019	-0.006	21.668	0.004	0.004	0.000	0.000	0.000	0.000
61	A	137	TYR	0	0.053	0.002	18.825	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	138	ASP	-1	-0.844	-0.918	22.340	0.034	0.034	0.000	0.000	0.000	0.000
63	A	139	GLN	0	0.076	0.024	23.911	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	140	ASN	0	0.025	0.020	27.058	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	141	ILE	0	-0.021	-0.016	25.002	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	142	VAL	0	-0.005	-0.003	26.385	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	143	ASP	-1	-0.769	-0.865	29.091	0.021	0.021	0.000	0.000	0.000	0.000
68	A	144	LEU	0	-0.010	-0.005	31.254	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	145	ILE	0	-0.043	-0.027	28.267	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	146	ASP	-1	-0.865	-0.924	32.648	0.021	0.021	0.000	0.000	0.000	0.000
71	A	147	LYS	1	0.882	0.935	34.574	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	148	TYR	0	-0.022	-0.021	36.188	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	149	LEU	0	-0.104	-0.016	31.439	0.000	0.000	0.000	0.000	0.000	0.000
74	A	150	ARG	1	0.874	0.928	35.506	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	151	LYS	1	0.943	0.966	36.548	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	152	GLY	0	0.001	0.006	36.717	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	153	ARG	1	0.887	0.949	36.211	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	154	ARG	1	0.860	0.918	34.342	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	155	VAL	0	-0.007	0.002	30.133	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	156	TYR	0	0.017	0.008	25.654	0.002	0.002	0.000	0.000	0.000	0.000
81	A	157	VAL	0	-0.003	0.000	23.772	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	158	GLN	0	-0.024	-0.008	20.550	0.010	0.010	0.000	0.000	0.000	0.000
83	A	159	GLY	0	0.031	0.009	19.488	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.029	-0.002	13.935	0.005	0.005	0.000	0.000	0.000	0.000
85	A	161	LEU	0	-0.017	-0.007	14.866	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	162	HIS	0	0.004	0.002	10.772	0.012	0.012	0.000	0.000	0.000	0.000
87	A	163	THR	0	0.004	-0.006	11.919	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	164	ARG	1	0.917	0.940	12.355	-0.039	-0.039	0.000	0.000	0.000	0.000
89	A	165	LYS	1	0.955	0.966	9.762	0.082	0.082	0.000	0.000	0.000	0.000
90	A	166	TRP	0	-0.046	-0.032	14.732	0.018	0.018	0.000	0.000	0.000	0.000
91	A	167	HIS	0	0.058	0.030	16.049	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	168	THR	0	0.033	0.016	20.661	0.007	0.007	0.000	0.000	0.000	0.000
93	A	169	ASN	0	-0.027	-0.005	23.555	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	170	ASP	-1	-0.748	-0.872	23.445	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	171	MET	0	0.020	0.031	25.599	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	172	ASN	0	0.009	0.002	26.214	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	173	SER	0	-0.049	-0.037	20.642	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	174	GLN	0	-0.023	-0.002	21.446	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	175	PRO	0	-0.012	-0.011	16.695	0.006	0.006	0.000	0.000	0.000	0.000
100	A	176	LYS	1	0.873	0.934	18.747	0.003	0.003	0.000	0.000	0.000	0.000
101	A	177	GLN	0	-0.025	-0.005	13.822	0.003	0.003	0.000	0.000	0.000	0.000
102	A	178	ILE	0	-0.039	-0.005	16.960	0.000	0.000	0.000	0.000	0.000	0.000
103	A	179	THR	0	-0.001	-0.007	16.813	0.004	0.004	0.000	0.000	0.000	0.000
104	A	180	GLU	-1	-0.779	-0.864	17.652	0.047	0.047	0.000	0.000	0.000	0.000
105	A	181	ILE	0	0.007	-0.002	17.758	0.007	0.007	0.000	0.000	0.000	0.000
106	A	182	ILE	0	-0.019	-0.006	16.065	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	183	LEU	0	0.029	0.014	18.316	0.005	0.005	0.000	0.000	0.000	0.000
108	A	184	SER	0	0.006	-0.008	17.100	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	185	TYR	0	0.051	-0.004	19.402	0.001	0.001	0.000	0.000	0.000	0.000
110	A	186	ASN	0	-0.044	-0.013	19.878	0.000	0.000	0.000	0.000	0.000	0.000
111	A	187	LYS	1	0.930	0.975	13.380	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	188	GLY	0	-0.007	0.003	19.324	0.008	0.008	0.000	0.000	0.000	0.000
113	A	189	ASP	-1	-0.852	-0.927	21.637	0.044	0.044	0.000	0.000	0.000	0.000
114	A	190	LEU	0	-0.018	-0.019	25.284	0.001	0.001	0.000	0.000	0.000	0.000
115	A	191	ILE	0	0.018	0.020	28.172	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	192	PHE	0	-0.008	-0.014	31.496	0.000	0.000	0.000	0.000	0.000	0.000
117	A	193	LEU	0	0.016	0.011	32.730	0.000	0.000	0.000	0.000	0.000	0.000
118	A	194	ASP	-1	-0.807	-0.882	36.418	0.025	0.025	0.000	0.000	0.000	0.000

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