FMO DATABASE

FMODB ID: ZY8MN

Calculation Name: 3K1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1H

Chain ID: A

ChEMBL ID:

UniProt ID: O25709

Base Structure: X-ray

Registration Date: 2023-06-20

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-919787.088145
FMO2-HF: Nuclear repulsion	873735.423093
FMO2-HF: Total energy	-46051.665052
FMO2-MP2: Total energy	-46184.583973

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:33:PHE)

Summations of interaction energy for fragment #1(A:33: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.
-16.51	-6.964	2.771	-5.172	-7.147	-0.032

Interaction energy analysis for fragmet #1(A:33:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	35	ARG	1	0.799	0.892	3.048	-2.113	2.276	0.120	-2.278	-2.231	-0.002
4	A	36	ASP	-1	-0.848	-0.903	5.307	-0.987	-0.941	-0.001	-0.002	-0.043	0.000
5	A	37	MET	0	-0.082	-0.029	8.267	0.229	0.229	0.000	0.000	0.000	0.000
6	A	38	LYS	1	0.869	0.922	11.237	0.203	0.203	0.000	0.000	0.000	0.000
7	A	39	ASN	0	0.016	-0.010	13.679	0.020	0.020	0.000	0.000	0.000	0.000
8	A	40	ILE	0	0.096	0.054	15.981	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	41	ASN	0	-0.008	-0.007	18.147	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	42	GLU	-1	-0.845	-0.905	12.142	-0.284	-0.284	0.000	0.000	0.000	0.000
11	A	43	SER	0	0.023	0.008	13.559	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	44	VAL	0	0.042	0.022	14.603	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	45	GLY	0	-0.032	-0.012	15.986	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	46	ALA	0	0.010	-0.001	10.660	0.017	0.017	0.000	0.000	0.000	0.000
15	A	47	LEU	0	0.038	0.019	12.618	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	48	GLN	0	0.006	0.009	14.515	0.008	0.008	0.000	0.000	0.000	0.000
17	A	49	VAL	0	-0.019	-0.011	13.510	0.029	0.029	0.000	0.000	0.000	0.000
18	A	50	LEU	0	0.048	0.023	10.310	0.051	0.051	0.000	0.000	0.000	0.000
19	A	51	GLN	0	0.033	0.019	13.626	0.031	0.031	0.000	0.000	0.000	0.000
20	A	52	ILE	0	-0.057	-0.036	17.104	0.046	0.046	0.000	0.000	0.000	0.000
21	A	53	ALA	0	0.008	0.007	14.593	0.044	0.044	0.000	0.000	0.000	0.000
22	A	54	CYS	0	0.021	0.008	14.552	0.006	0.006	0.000	0.000	0.000	0.000
23	A	55	LYS	1	0.943	0.972	16.970	0.389	0.389	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.887	0.955	19.467	0.238	0.238	0.000	0.000	0.000	0.000
25	A	57	LEU	0	0.003	0.007	14.992	0.035	0.035	0.000	0.000	0.000	0.000
26	A	58	PHE	0	0.028	0.026	19.558	0.031	0.031	0.000	0.000	0.000	0.000
27	A	59	ASN	0	0.008	-0.010	21.648	0.024	0.024	0.000	0.000	0.000	0.000
28	A	60	LYS	1	0.770	0.873	22.330	0.153	0.153	0.000	0.000	0.000	0.000
29	A	61	SER	0	-0.035	-0.016	22.230	0.018	0.018	0.000	0.000	0.000	0.000
30	A	62	MET	0	0.005	0.012	24.360	0.006	0.006	0.000	0.000	0.000	0.000
31	A	63	GLY	0	0.057	0.020	27.526	0.015	0.015	0.000	0.000	0.000	0.000
32	A	64	LEU	0	-0.082	-0.038	24.150	0.015	0.015	0.000	0.000	0.000	0.000
33	A	65	GLU	-1	-0.863	-0.944	28.112	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	66	ASP	-1	-0.923	-0.949	29.666	-0.103	-0.103	0.000	0.000	0.000	0.000
35	A	67	LYS	1	0.750	0.895	28.484	0.142	0.142	0.000	0.000	0.000	0.000
36	A	68	ASP	-1	-0.806	-0.901	32.154	-0.055	-0.055	0.000	0.000	0.000	0.000
37	A	69	ALA	0	0.034	-0.009	31.453	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.022	0.007	30.680	0.002	0.002	0.000	0.000	0.000	0.000
39	A	71	GLN	0	0.019	0.000	30.361	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	72	ALA	0	0.026	0.018	27.812	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	73	SER	0	-0.085	-0.051	26.134	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	74	ILE	0	0.009	-0.003	25.475	0.002	0.002	0.000	0.000	0.000	0.000
43	A	75	ILE	0	0.036	0.015	24.091	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	76	LYS	1	0.946	0.970	21.929	0.119	0.119	0.000	0.000	0.000	0.000
45	A	77	GLN	0	-0.025	-0.025	20.200	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	78	GLU	-1	-0.808	-0.886	20.367	-0.101	-0.101	0.000	0.000	0.000	0.000
47	A	79	LEU	0	-0.046	-0.024	18.672	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	80	ARG	1	0.808	0.876	16.000	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	81	GLU	-1	-0.840	-0.894	15.297	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	82	ILE	0	-0.069	-0.031	15.957	0.011	0.011	0.000	0.000	0.000	0.000
51	A	83	VAL	0	-0.010	-0.006	10.982	-0.037	-0.037	0.000	0.000	0.000	0.000
52	A	84	GLU	-1	-0.828	-0.893	11.351	0.056	0.056	0.000	0.000	0.000	0.000
53	A	85	ASN	0	-0.091	-0.051	12.098	0.139	0.139	0.000	0.000	0.000	0.000
54	A	86	CYS	0	-0.087	-0.010	11.131	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	87	GLN	0	-0.006	-0.007	9.868	0.033	0.033	0.000	0.000	0.000	0.000
56	A	88	PHE	0	0.014	0.001	9.824	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	89	LEU	0	-0.018	-0.015	9.662	0.038	0.038	0.000	0.000	0.000	0.000
58	A	90	ALA	0	0.002	0.012	9.778	0.077	0.077	0.000	0.000	0.000	0.000
59	A	91	SER	0	0.005	0.010	4.787	-0.171	-0.056	-0.001	-0.007	-0.107	0.000
60	A	92	PRO	0	0.071	0.029	3.839	-0.783	-0.345	0.003	-0.044	-0.398	0.000
61	A	93	LEU	0	-0.021	-0.015	5.521	-0.418	-0.418	0.000	0.000	0.000	0.000
62	A	94	PHE	0	0.065	0.024	7.129	-0.360	-0.360	0.000	0.000	0.000	0.000
63	A	95	ASP	-1	-0.845	-0.913	4.122	-2.073	-1.816	-0.001	-0.041	-0.215	0.000
64	A	96	THR	0	-0.076	-0.043	2.297	-10.918	-7.181	2.648	-2.647	-3.738	-0.030
65	A	97	GLN	0	-0.054	-0.033	3.755	1.870	2.434	0.003	-0.153	-0.415	0.000
66	A	98	LEU	0	-0.024	-0.021	5.792	0.053	0.053	0.000	0.000	0.000	0.000
67	A	99	ASN	0	0.007	0.010	7.949	0.136	0.136	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.030	-0.005	10.500	0.124	0.124	0.000	0.000	0.000	0.000
69	A	101	ALA	0	-0.004	0.016	13.681	0.025	0.025	0.000	0.000	0.000	0.000
70	A	102	ILE	0	-0.014	-0.023	16.994	0.019	0.019	0.000	0.000	0.000	0.000
71	A	103	ASN	0	-0.016	-0.020	20.121	0.013	0.013	0.000	0.000	0.000	0.000
72	A	104	ASP	-1	-0.936	-0.955	21.846	-0.233	-0.233	0.000	0.000	0.000	0.000
73	A	105	GLU	-1	-0.940	-0.948	20.379	-0.371	-0.371	0.000	0.000	0.000	0.000
74	A	106	ILE	0	-0.055	-0.043	13.792	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	107	PHE	0	0.017	0.015	15.551	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	108	SER	0	-0.011	-0.032	10.646	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	109	MET	0	-0.037	0.008	10.763	0.170	0.170	0.000	0.000	0.000	0.000
78	A	110	ILE	0	-0.007	-0.005	5.063	-0.391	-0.391	0.000	0.000	0.000	0.000
79	A	111	VAL	0	0.001	0.007	8.380	0.417	0.417	0.000	0.000	0.000	0.000
80	A	112	VAL	0	0.019	0.005	7.576	-0.351	-0.351	0.000	0.000	0.000	0.000
81	A	113	ASN	0	0.051	-0.009	8.208	0.293	0.293	0.000	0.000	0.000	0.000
82	A	114	PRO	0	-0.010	0.002	10.116	0.082	0.082	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.048	-0.032	13.569	0.090	0.090	0.000	0.000	0.000	0.000
84	A	116	ASP	-1	-0.898	-0.947	13.067	-0.273	-0.273	0.000	0.000	0.000	0.000
85	A	117	LEU	0	0.010	0.004	15.518	0.037	0.037	0.000	0.000	0.000	0.000
86	A	118	LEU	0	-0.069	-0.032	18.116	0.033	0.033	0.000	0.000	0.000	0.000
87	A	119	GLU	-1	-1.032	-1.007	20.323	-0.123	-0.123	0.000	0.000	0.000	0.000
88	A	120	ASN	0	-0.005	-0.004	22.009	0.026	0.026	0.000	0.000	0.000	0.000
89	A	121	VAL	0	0.027	0.001	22.427	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	122	GLY	0	0.054	0.026	23.278	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	123	GLU	-1	-0.875	-0.926	20.421	-0.303	-0.303	0.000	0.000	0.000	0.000
92	A	124	PHE	0	-0.035	-0.019	17.089	-0.054	-0.054	0.000	0.000	0.000	0.000
93	A	125	GLN	0	-0.033	-0.026	18.967	-0.046	-0.046	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.037	0.020	21.190	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	127	TYR	0	0.042	0.032	11.644	-0.110	-0.110	0.000	0.000	0.000	0.000
96	A	128	LEU	0	-0.022	-0.021	15.560	-0.069	-0.069	0.000	0.000	0.000	0.000
97	A	129	GLU	-1	-0.957	-0.973	17.733	-0.345	-0.345	0.000	0.000	0.000	0.000
98	A	130	GLU	-1	-0.913	-0.953	18.141	-0.542	-0.542	0.000	0.000	0.000	0.000
99	A	131	LYS	1	0.803	0.880	12.434	1.030	1.030	0.000	0.000	0.000	0.000
100	A	132	LEU	0	-0.050	-0.036	16.292	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	133	ASN	0	-0.061	-0.036	18.721	0.045	0.045	0.000	0.000	0.000	0.000
102	A	134	GLU	-1	-0.788	-0.869	14.792	-0.933	-0.933	0.000	0.000	0.000	0.000
103	A	135	ILE	0	0.010	-0.007	14.155	0.012	0.012	0.000	0.000	0.000	0.000
104	A	136	LYS	1	0.855	0.927	17.362	0.394	0.394	0.000	0.000	0.000	0.000
105	A	137	GLU	-1	-0.852	-0.914	20.629	-0.341	-0.341	0.000	0.000	0.000	0.000
106	A	138	LEU	0	0.019	0.014	14.936	0.019	0.019	0.000	0.000	0.000	0.000
107	A	139	LEU	0	-0.040	-0.028	18.186	0.043	0.043	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.009	0.017	20.267	0.044	0.044	0.000	0.000	0.000	0.000
109	A	141	TYR	0	0.026	-0.004	20.690	0.018	0.018	0.000	0.000	0.000	0.000
110	A	142	LEU	0	-0.004	-0.004	16.895	0.028	0.028	0.000	0.000	0.000	0.000
111	A	143	SER	0	-0.041	-0.047	21.603	0.039	0.039	0.000	0.000	0.000	0.000
112	A	144	GLU	-1	-0.934	-0.955	24.625	-0.238	-0.238	0.000	0.000	0.000	0.000
113	A	145	SER	0	-0.043	-0.021	23.336	0.012	0.012	0.000	0.000	0.000	0.000
114	A	146	LEU	0	-0.103	-0.044	22.691	0.018	0.018	0.000	0.000	0.000	0.000
115	A	147	SER	0	-0.119	-0.041	26.029	0.039	0.039	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:PHE)