FMO DATABASE

FMODB ID: MNN3Z

Calculation Name: 3UPS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UPS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NLX3

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-794364.717122
FMO2-HF: Nuclear repulsion	752514.185953
FMO2-HF: Total energy	-41850.531169
FMO2-MP2: Total energy	-41972.106226

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:14:PHE)

Summations of interaction energy for fragment #1(A:14:PHE)

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.
-18.035	-5.664	8.734	-5.762	-15.345	0.001

Interaction energy analysis for fragmet #1(A:14:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.005

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	16	PRO	0	0.087	0.036	2.724	-4.052	-0.461	0.657	-1.911	-2.338	-0.007
4	A	17	GLU	-1	-0.809	-0.884	4.962	-1.391	-1.241	-0.001	-0.006	-0.143	0.000
5	A	18	MET	0	-0.084	-0.039	2.687	-2.095	0.120	1.911	-1.064	-3.063	0.011
6	A	19	LEU	0	-0.006	0.002	2.240	-3.514	-1.129	2.260	-1.355	-3.289	-0.005
7	A	20	LEU	0	0.000	-0.008	3.076	1.711	1.333	0.083	0.567	-0.273	0.000
8	A	21	LYS	1	0.825	0.897	5.764	0.592	0.592	0.000	0.000	0.000	0.000
9	A	22	LEU	0	-0.038	-0.006	3.529	-0.104	0.399	0.015	-0.095	-0.424	0.000
10	A	23	VAL	0	0.017	-0.003	5.768	0.336	0.336	0.000	0.000	0.000	0.000
11	A	24	THR	0	0.008	-0.006	8.415	0.109	0.109	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.830	-0.899	9.024	-0.140	-0.140	0.000	0.000	0.000	0.000
13	A	26	SER	0	-0.006	0.001	9.769	0.112	0.112	0.000	0.000	0.000	0.000
14	A	27	LEU	0	-0.037	-0.027	11.432	0.043	0.043	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.919	-0.952	13.810	-0.089	-0.089	0.000	0.000	0.000	0.000
16	A	29	ASP	-1	-0.813	-0.870	14.157	0.098	0.098	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.825	-0.905	15.637	0.065	0.065	0.000	0.000	0.000	0.000
18	A	31	GLN	0	-0.050	-0.021	17.745	0.000	0.000	0.000	0.000	0.000	0.000
19	A	32	ALA	0	-0.005	-0.005	17.273	0.003	0.003	0.000	0.000	0.000	0.000
20	A	33	LEU	0	-0.020	-0.012	19.267	0.000	0.000	0.000	0.000	0.000	0.000
21	A	34	GLU	-1	-0.905	-0.959	20.019	-0.170	-0.170	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.014	0.010	14.231	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	36	ALA	0	-0.002	0.020	16.688	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	37	THR	0	0.014	-0.008	12.680	-0.049	-0.049	0.000	0.000	0.000	0.000
25	A	38	ILE	0	-0.036	-0.019	15.219	0.043	0.043	0.000	0.000	0.000	0.000
26	A	39	PRO	0	0.060	0.035	13.930	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.021	-0.009	14.173	0.128	0.128	0.000	0.000	0.000	0.000
28	A	41	ALA	0	0.098	0.050	14.185	0.059	0.059	0.000	0.000	0.000	0.000
29	A	42	GLY	0	-0.030	-0.016	15.956	0.079	0.079	0.000	0.000	0.000	0.000
30	A	43	LYS	1	0.772	0.877	18.242	0.595	0.595	0.000	0.000	0.000	0.000
31	A	44	SER	0	-0.011	-0.009	17.825	0.041	0.041	0.000	0.000	0.000	0.000
32	A	45	SER	0	-0.002	-0.010	15.709	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	46	ILE	0	-0.061	-0.018	15.099	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	47	ALA	0	0.050	0.039	11.292	0.001	0.001	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.881	-0.929	9.166	-1.826	-1.826	0.000	0.000	0.000	0.000
36	A	49	TYR	0	-0.111	-0.091	9.015	0.356	0.356	0.000	0.000	0.000	0.000
37	A	50	MET	0	-0.036	-0.005	11.894	0.029	0.029	0.000	0.000	0.000	0.000
38	A	51	VAL	0	0.003	0.001	10.983	0.015	0.015	0.000	0.000	0.000	0.000
39	A	52	ILE	0	-0.026	-0.019	14.259	0.044	0.044	0.000	0.000	0.000	0.000
40	A	53	ALA	0	0.028	0.028	16.734	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	54	SER	0	-0.021	-0.021	18.654	0.015	0.015	0.000	0.000	0.000	0.000
42	A	55	GLY	0	0.036	0.008	21.226	0.005	0.005	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.892	0.943	23.030	0.030	0.030	0.000	0.000	0.000	0.000
44	A	57	SER	0	-0.009	-0.017	25.562	0.012	0.012	0.000	0.000	0.000	0.000
45	A	58	SER	0	0.104	0.062	25.041	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	59	ARG	1	0.947	0.987	24.131	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	60	GLN	0	-0.070	-0.052	21.229	0.008	0.008	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.075	0.041	20.472	0.003	0.003	0.000	0.000	0.000	0.000
49	A	62	THR	0	-0.003	-0.020	19.567	0.000	0.000	0.000	0.000	0.000	0.000
50	A	63	ALA	0	-0.054	-0.020	19.342	0.017	0.017	0.000	0.000	0.000	0.000
51	A	64	MET	0	-0.013	0.015	16.277	0.015	0.015	0.000	0.000	0.000	0.000
52	A	65	ALA	0	0.029	0.017	14.885	0.010	0.010	0.000	0.000	0.000	0.000
53	A	66	GLN	0	-0.068	-0.043	14.894	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	67	LYS	1	0.797	0.875	14.036	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	68	LEU	0	0.012	0.020	8.944	0.068	0.068	0.000	0.000	0.000	0.000
56	A	69	ALA	0	0.025	0.012	10.183	0.104	0.104	0.000	0.000	0.000	0.000
57	A	70	ASP	-1	-0.893	-0.933	11.301	0.498	0.498	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.757	0.852	7.952	0.005	0.005	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.052	0.027	6.440	0.378	0.378	0.000	0.000	0.000	0.000
60	A	73	LYS	1	0.955	1.003	6.784	0.175	0.175	0.000	0.000	0.000	0.000
61	A	74	ALA	0	-0.062	-0.038	8.260	0.232	0.232	0.000	0.000	0.000	0.000
62	A	75	ALA	0	-0.028	-0.006	3.060	-0.828	-0.130	0.167	-0.271	-0.593	0.002
63	A	76	THR	0	-0.038	-0.034	2.703	-3.951	-1.077	3.640	-1.571	-4.944	0.000
64	A	77	GLY	0	-0.025	-0.005	4.322	-0.484	-0.243	0.003	-0.047	-0.197	0.000
65	A	78	TYR	0	-0.070	-0.043	5.962	-0.446	-0.446	0.000	0.000	0.000	0.000
66	A	79	VAL	0	-0.050	-0.039	7.693	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	80	SER	0	0.024	-0.014	10.646	-0.062	-0.062	0.000	0.000	0.000	0.000
68	A	81	LYS	1	0.783	0.895	12.050	0.086	0.086	0.000	0.000	0.000	0.000
69	A	82	ILE	0	0.020	-0.004	15.294	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.827	-0.891	17.827	-0.075	-0.075	0.000	0.000	0.000	0.000
71	A	84	GLY	0	0.021	0.007	21.050	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.006	0.015	19.485	0.009	0.009	0.000	0.000	0.000	0.000
73	A	86	PRO	0	-0.012	-0.019	23.669	0.001	0.001	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.005	0.003	25.982	0.001	0.001	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.025	0.024	23.206	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.815	-0.916	24.914	-0.049	-0.049	0.000	0.000	0.000	0.000
77	A	90	TRP	0	-0.072	-0.047	22.587	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.005	-0.003	17.774	0.020	0.020	0.000	0.000	0.000	0.000
79	A	92	LEU	0	-0.034	0.008	16.782	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	93	LEU	0	0.000	-0.015	11.650	0.049	0.049	0.000	0.000	0.000	0.000
81	A	94	ASP	-1	-0.795	-0.887	12.168	-0.584	-0.584	0.000	0.000	0.000	0.000
82	A	95	ALA	0	-0.011	-0.008	7.515	0.205	0.205	0.000	0.000	0.000	0.000
83	A	96	GLY	0	0.022	0.030	7.190	-0.289	-0.289	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.888	-0.940	4.520	-4.533	-4.441	-0.001	-0.009	-0.081	0.000
85	A	98	ILE	0	-0.052	-0.028	6.552	0.215	0.215	0.000	0.000	0.000	0.000
86	A	99	ILE	0	-0.001	0.010	9.420	0.176	0.176	0.000	0.000	0.000	0.000
87	A	100	ILE	0	-0.011	-0.007	9.754	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	101	HIS	0	-0.016	-0.012	14.014	0.095	0.095	0.000	0.000	0.000	0.000
89	A	102	LEU	0	0.011	0.003	15.829	0.000	0.000	0.000	0.000	0.000	0.000
90	A	103	PHE	0	-0.032	-0.024	19.405	0.017	0.017	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.858	0.927	23.202	0.048	0.048	0.000	0.000	0.000	0.000
92	A	105	PRO	0	0.021	0.006	25.497	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	106	GLU	-1	-0.766	-0.870	28.088	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	107	VAL	0	-0.012	0.000	29.563	0.001	0.001	0.000	0.000	0.000	0.000
95	A	108	ARG	1	0.949	0.982	25.785	0.152	0.152	0.000	0.000	0.000	0.000
96	A	109	SER	0	-0.039	-0.035	29.477	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	110	PHE	0	-0.016	-0.001	32.487	0.000	0.000	0.000	0.000	0.000	0.000
98	A	111	TYR	0	0.001	-0.030	30.276	0.000	0.000	0.000	0.000	0.000	0.000
99	A	112	ASN	0	-0.034	-0.017	29.763	0.000	0.000	0.000	0.000	0.000	0.000
100	A	113	LEU	0	-0.017	0.004	33.899	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	114	GLU	-1	-0.845	-0.936	36.877	-0.050	-0.050	0.000	0.000	0.000	0.000
102	A	115	ARG	1	0.895	0.943	30.204	0.091	0.091	0.000	0.000	0.000	0.000
103	A	116	MET	0	-0.057	-0.017	36.971	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	117	TRP	0	-0.068	-0.032	38.947	0.002	0.002	0.000	0.000	0.000	0.000
105	A	118	GLY	0	0.009	0.014	40.325	0.004	0.004	0.000	0.000	0.000	0.000
106	A	119	PHE	0	-0.059	-0.035	39.462	0.004	0.004	0.000	0.000	0.000	0.000
107	A	120	GLY	0	-0.013	0.007	38.397	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	121	ASP	-1	-0.996	-0.999	38.545	-0.057	-0.057	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:PHE)