FMO DATABASE

FMODB ID: 988G2

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	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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-792581.788067
FMO2-HF: Nuclear repulsion	750731.624787
FMO2-HF: Total energy	-41850.163281
FMO2-MP2: Total energy	-41971.867349

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.
-18.337	-6.215	9.037	-5.434	-15.725	0.012

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 : -0.016 / q_NPA : -0.020

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	0.110	0.052	2.941	-3.887	-0.639	0.236	-1.531	-1.952	-0.002
4	A	17	GLU	-1	-0.815	-0.884	5.047	-1.323	-1.176	-0.001	-0.006	-0.140	0.000
5	A	18	MET	0	-0.090	-0.037	2.767	-2.439	0.070	1.935	-1.122	-3.322	0.012
6	A	19	LEU	0	-0.008	-0.002	2.419	-3.752	-1.270	2.183	-1.469	-3.196	-0.006
7	A	20	LEU	0	0.001	-0.009	3.013	2.169	1.499	0.070	0.872	-0.271	-0.001
8	A	21	LYS	1	0.842	0.901	5.600	0.569	0.569	0.000	0.000	0.000	0.000
9	A	22	LEU	0	-0.019	0.003	3.289	-0.169	0.452	0.034	-0.131	-0.525	0.000
10	A	23	VAL	0	0.024	0.000	5.581	0.381	0.381	0.000	0.000	0.000	0.000
11	A	24	THR	0	0.021	-0.004	8.052	0.143	0.143	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.855	-0.894	8.845	-0.109	-0.109	0.000	0.000	0.000	0.000
13	A	26	SER	0	-0.012	0.007	9.632	0.121	0.121	0.000	0.000	0.000	0.000
14	A	27	LEU	0	-0.042	-0.037	11.281	0.047	0.047	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.915	-0.954	13.500	-0.103	-0.103	0.000	0.000	0.000	0.000
16	A	29	ASP	-1	-0.866	-0.910	13.760	0.083	0.083	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.868	-0.907	15.375	0.040	0.040	0.000	0.000	0.000	0.000
18	A	31	GLN	0	-0.065	-0.041	17.461	0.000	0.000	0.000	0.000	0.000	0.000
19	A	32	ALA	0	0.001	-0.009	17.019	0.003	0.003	0.000	0.000	0.000	0.000
20	A	33	LEU	0	-0.026	-0.013	19.006	0.005	0.005	0.000	0.000	0.000	0.000
21	A	34	GLU	-1	-0.977	-1.003	20.136	-0.211	-0.211	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.035	0.019	14.075	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	36	ALA	0	-0.020	-0.001	17.194	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	37	THR	0	0.032	0.006	12.640	-0.065	-0.065	0.000	0.000	0.000	0.000
25	A	38	ILE	0	-0.043	-0.024	15.007	0.055	0.055	0.000	0.000	0.000	0.000
26	A	39	PRO	0	0.058	0.036	14.212	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.008	-0.010	14.354	0.148	0.148	0.000	0.000	0.000	0.000
28	A	41	ALA	0	0.095	0.055	14.908	0.051	0.051	0.000	0.000	0.000	0.000
29	A	42	GLY	0	-0.046	-0.032	16.464	0.077	0.077	0.000	0.000	0.000	0.000
30	A	43	LYS	1	0.784	0.899	18.672	0.606	0.606	0.000	0.000	0.000	0.000
31	A	44	SER	0	-0.006	-0.018	18.156	0.042	0.042	0.000	0.000	0.000	0.000
32	A	45	SER	0	0.018	0.008	16.286	-0.030	-0.030	0.000	0.000	0.000	0.000
33	A	46	ILE	0	-0.081	-0.030	15.249	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	47	ALA	0	0.047	0.032	11.624	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.869	-0.932	9.092	-1.995	-1.995	0.000	0.000	0.000	0.000
36	A	49	TYR	0	-0.104	-0.094	9.057	0.407	0.407	0.000	0.000	0.000	0.000
37	A	50	MET	0	-0.038	-0.004	11.974	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	51	VAL	0	0.011	0.003	10.846	0.039	0.039	0.000	0.000	0.000	0.000
39	A	52	ILE	0	-0.021	-0.009	14.063	0.039	0.039	0.000	0.000	0.000	0.000
40	A	53	ALA	0	0.028	0.027	16.495	0.003	0.003	0.000	0.000	0.000	0.000
41	A	54	SER	0	0.010	0.012	18.427	0.017	0.017	0.000	0.000	0.000	0.000
42	A	55	GLY	0	0.054	0.012	20.755	0.005	0.005	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.919	0.946	22.493	0.048	0.048	0.000	0.000	0.000	0.000
44	A	57	SER	0	-0.027	-0.018	25.245	0.013	0.013	0.000	0.000	0.000	0.000
45	A	58	SER	0	0.118	0.056	24.939	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	59	ARG	1	0.950	0.991	24.122	0.017	0.017	0.000	0.000	0.000	0.000
47	A	60	GLN	0	-0.083	-0.048	20.984	0.005	0.005	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.096	0.054	20.427	0.002	0.002	0.000	0.000	0.000	0.000
49	A	62	THR	0	0.013	-0.005	19.463	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	63	ALA	0	-0.051	-0.027	19.320	0.011	0.011	0.000	0.000	0.000	0.000
51	A	64	MET	0	-0.032	0.015	16.383	0.012	0.012	0.000	0.000	0.000	0.000
52	A	65	ALA	0	0.038	0.019	14.853	0.002	0.002	0.000	0.000	0.000	0.000
53	A	66	GLN	0	-0.060	-0.034	14.655	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	67	LYS	1	0.847	0.900	13.841	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	68	LEU	0	0.011	0.021	8.614	0.078	0.078	0.000	0.000	0.000	0.000
56	A	69	ALA	0	0.029	0.012	10.008	0.083	0.083	0.000	0.000	0.000	0.000
57	A	70	ASP	-1	-0.899	-0.943	11.208	0.367	0.367	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.751	0.844	7.859	0.033	0.033	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.059	0.034	6.166	0.420	0.420	0.000	0.000	0.000	0.000
60	A	73	LYS	1	0.961	1.011	6.744	0.304	0.304	0.000	0.000	0.000	0.000
61	A	74	ALA	0	-0.074	-0.042	8.142	0.233	0.233	0.000	0.000	0.000	0.000
62	A	75	ALA	0	-0.043	-0.015	3.040	-0.798	-0.077	0.193	-0.287	-0.628	0.003
63	A	76	THR	0	-0.030	-0.032	2.677	-4.257	-1.459	4.381	-1.711	-5.468	0.005
64	A	77	GLY	0	-0.024	-0.006	4.226	-0.872	-0.606	0.006	-0.049	-0.223	0.001
65	A	78	TYR	0	-0.029	-0.010	5.747	-0.405	-0.405	0.000	0.000	0.000	0.000
66	A	79	VAL	0	-0.046	-0.035	7.715	0.099	0.099	0.000	0.000	0.000	0.000
67	A	80	SER	0	0.046	0.017	10.082	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	81	LYS	1	0.810	0.909	11.994	0.242	0.242	0.000	0.000	0.000	0.000
69	A	82	ILE	0	0.005	-0.005	15.403	-0.046	-0.046	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.830	-0.900	17.823	-0.166	-0.166	0.000	0.000	0.000	0.000
71	A	84	GLY	0	0.016	-0.009	20.870	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.014	0.034	19.650	0.009	0.009	0.000	0.000	0.000	0.000
73	A	86	PRO	0	-0.025	-0.028	23.801	0.000	0.000	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.021	-0.023	26.084	0.002	0.002	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.037	0.034	23.405	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.864	-0.926	25.179	-0.086	-0.086	0.000	0.000	0.000	0.000
77	A	90	TRP	0	-0.082	-0.050	22.137	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.013	0.005	17.781	0.021	0.021	0.000	0.000	0.000	0.000
79	A	92	LEU	0	-0.039	0.005	16.762	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	93	LEU	0	-0.017	-0.012	11.259	0.046	0.046	0.000	0.000	0.000	0.000
81	A	94	ASP	-1	-0.858	-0.930	12.767	-0.777	-0.777	0.000	0.000	0.000	0.000
82	A	95	ALA	0	-0.037	-0.048	7.917	0.162	0.162	0.000	0.000	0.000	0.000
83	A	96	GLY	0	0.014	0.021	7.786	-0.338	-0.338	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.875	-0.932	5.491	-4.108	-4.108	0.000	0.000	0.000	0.000
85	A	98	ILE	0	-0.036	-0.014	6.875	0.215	0.215	0.000	0.000	0.000	0.000
86	A	99	ILE	0	0.009	0.020	9.540	0.167	0.167	0.000	0.000	0.000	0.000
87	A	100	ILE	0	-0.030	-0.024	9.765	0.013	0.013	0.000	0.000	0.000	0.000
88	A	101	HIS	0	-0.001	0.000	14.020	0.098	0.098	0.000	0.000	0.000	0.000
89	A	102	LEU	0	0.011	-0.002	15.625	0.005	0.005	0.000	0.000	0.000	0.000
90	A	103	PHE	0	-0.016	-0.020	19.110	0.021	0.021	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.914	0.964	22.868	0.085	0.085	0.000	0.000	0.000	0.000
92	A	105	PRO	0	0.046	0.022	25.140	0.002	0.002	0.000	0.000	0.000	0.000
93	A	106	GLU	-1	-0.788	-0.892	27.775	-0.091	-0.091	0.000	0.000	0.000	0.000
94	A	107	VAL	0	-0.020	-0.005	28.974	0.003	0.003	0.000	0.000	0.000	0.000
95	A	108	ARG	1	0.963	0.990	25.987	0.190	0.190	0.000	0.000	0.000	0.000
96	A	109	SER	0	-0.039	-0.036	29.534	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	110	PHE	0	-0.007	0.006	32.463	0.002	0.002	0.000	0.000	0.000	0.000
98	A	111	TYR	0	-0.006	-0.038	30.158	0.001	0.001	0.000	0.000	0.000	0.000
99	A	112	ASN	0	-0.054	-0.038	29.755	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	113	LEU	0	-0.014	0.001	33.766	0.000	0.000	0.000	0.000	0.000	0.000
101	A	114	GLU	-1	-0.857	-0.931	36.843	-0.075	-0.075	0.000	0.000	0.000	0.000
102	A	115	ARG	1	0.915	0.957	30.086	0.126	0.126	0.000	0.000	0.000	0.000
103	A	116	MET	0	-0.066	-0.022	37.065	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	117	TRP	0	-0.065	-0.030	38.790	0.003	0.003	0.000	0.000	0.000	0.000
105	A	118	GLY	0	0.002	0.012	40.402	0.005	0.005	0.000	0.000	0.000	0.000
106	A	119	PHE	0	-0.058	-0.037	39.568	0.004	0.004	0.000	0.000	0.000	0.000
107	A	120	GLY	0	-0.037	-0.019	38.629	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	121	ASP	-1	-0.975	-0.972	38.695	-0.081	-0.081	0.000	0.000	0.000	0.000

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