FMO DATABASE

FMODB ID: R5238

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:

Apendix: None

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-924231.453749
FMO2-HF: Nuclear repulsion	878179.659311
FMO2-HF: Total energy	-46051.794438
FMO2-MP2: Total energy	-46184.678823

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.
-19.022	-11.788	9.11	-7.558	-8.785	-0.055

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 : 0.024 / q_NPA : 0.009

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	0.788	0.885	2.694	-2.263	2.486	0.745	-2.686	-2.808	-0.007
4	A	36	ASP	-1	-0.844	-0.902	5.062	-1.043	-1.012	-0.001	-0.005	-0.025	0.000
5	A	37	MET	0	-0.068	-0.023	7.841	0.219	0.219	0.000	0.000	0.000	0.000
6	A	38	LYS	1	0.842	0.913	11.258	0.375	0.375	0.000	0.000	0.000	0.000
7	A	39	ASN	0	-0.031	-0.024	13.887	0.045	0.045	0.000	0.000	0.000	0.000
8	A	40	ILE	0	0.120	0.070	15.788	-0.071	-0.071	0.000	0.000	0.000	0.000
9	A	41	ASN	0	0.000	0.002	17.848	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	42	GLU	-1	-0.822	-0.911	12.418	-0.402	-0.402	0.000	0.000	0.000	0.000
11	A	43	SER	0	0.016	0.000	13.301	-0.109	-0.109	0.000	0.000	0.000	0.000
12	A	44	VAL	0	0.039	0.019	14.497	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	45	GLY	0	-0.019	-0.011	15.597	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	46	ALA	0	0.018	-0.001	10.565	0.013	0.013	0.000	0.000	0.000	0.000
15	A	47	LEU	0	0.031	0.019	12.480	-0.054	-0.054	0.000	0.000	0.000	0.000
16	A	48	GLN	0	0.022	0.022	14.296	0.016	0.016	0.000	0.000	0.000	0.000
17	A	49	VAL	0	-0.028	-0.016	13.477	0.043	0.043	0.000	0.000	0.000	0.000
18	A	50	LEU	0	0.054	0.032	9.900	0.069	0.069	0.000	0.000	0.000	0.000
19	A	51	GLN	0	0.035	0.019	13.365	0.050	0.050	0.000	0.000	0.000	0.000
20	A	52	ILE	0	-0.061	-0.040	16.945	0.060	0.060	0.000	0.000	0.000	0.000
21	A	53	ALA	0	-0.002	-0.003	14.193	0.054	0.054	0.000	0.000	0.000	0.000
22	A	54	CYS	0	0.030	0.009	14.213	0.026	0.026	0.000	0.000	0.000	0.000
23	A	55	LYS	1	0.931	0.966	16.846	0.427	0.427	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.886	0.952	19.273	0.289	0.289	0.000	0.000	0.000	0.000
25	A	57	LEU	0	0.003	0.008	14.749	0.039	0.039	0.000	0.000	0.000	0.000
26	A	58	PHE	0	0.029	0.026	19.394	0.039	0.039	0.000	0.000	0.000	0.000
27	A	59	ASN	0	0.000	-0.011	21.450	0.027	0.027	0.000	0.000	0.000	0.000
28	A	60	LYS	1	0.766	0.875	22.454	0.172	0.172	0.000	0.000	0.000	0.000
29	A	61	SER	0	-0.035	-0.029	21.735	0.016	0.016	0.000	0.000	0.000	0.000
30	A	62	MET	0	0.024	0.025	23.852	0.012	0.012	0.000	0.000	0.000	0.000
31	A	63	GLY	0	0.065	0.035	27.064	0.015	0.015	0.000	0.000	0.000	0.000
32	A	64	LEU	0	-0.122	-0.055	23.629	0.015	0.015	0.000	0.000	0.000	0.000
33	A	65	GLU	-1	-0.824	-0.928	27.670	-0.159	-0.159	0.000	0.000	0.000	0.000
34	A	66	ASP	-1	-0.925	-0.952	29.209	-0.103	-0.103	0.000	0.000	0.000	0.000
35	A	67	LYS	1	0.771	0.900	28.088	0.147	0.147	0.000	0.000	0.000	0.000
36	A	68	ASP	-1	-0.814	-0.909	31.652	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	69	ALA	0	0.034	-0.002	30.893	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.031	0.009	30.132	0.002	0.002	0.000	0.000	0.000	0.000
39	A	71	GLN	0	0.023	0.000	29.844	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	72	ALA	0	0.036	0.018	27.515	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	73	SER	0	-0.084	-0.049	25.831	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	74	ILE	0	0.007	-0.005	25.004	0.000	0.000	0.000	0.000	0.000	0.000
43	A	75	ILE	0	0.036	0.021	23.969	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	76	LYS	1	0.930	0.966	21.686	0.107	0.107	0.000	0.000	0.000	0.000
45	A	77	GLN	0	-0.009	-0.003	19.972	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	78	GLU	-1	-0.809	-0.894	20.004	-0.122	-0.122	0.000	0.000	0.000	0.000
47	A	79	LEU	0	-0.039	-0.018	18.548	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	80	ARG	1	0.784	0.858	15.959	-0.081	-0.081	0.000	0.000	0.000	0.000
49	A	81	GLU	-1	-0.848	-0.901	15.222	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	82	ILE	0	-0.067	-0.035	16.074	0.001	0.001	0.000	0.000	0.000	0.000
51	A	83	VAL	0	0.008	0.002	10.821	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	84	GLU	-1	-0.827	-0.893	11.396	0.042	0.042	0.000	0.000	0.000	0.000
53	A	85	ASN	0	-0.095	-0.051	12.187	0.121	0.121	0.000	0.000	0.000	0.000
54	A	86	CYS	0	-0.075	-0.012	10.698	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	87	GLN	0	-0.018	-0.008	9.595	-0.055	-0.055	0.000	0.000	0.000	0.000
56	A	88	PHE	0	0.030	0.007	9.739	0.023	0.023	0.000	0.000	0.000	0.000
57	A	89	LEU	0	-0.029	-0.017	9.570	-0.036	-0.036	0.000	0.000	0.000	0.000
58	A	90	ALA	0	0.006	0.008	9.237	0.017	0.017	0.000	0.000	0.000	0.000
59	A	91	SER	0	0.015	0.019	4.379	-0.192	-0.072	-0.001	-0.010	-0.109	0.000
60	A	92	PRO	0	0.048	0.018	3.838	-0.649	-0.245	0.002	-0.039	-0.366	0.000
61	A	93	LEU	0	-0.026	-0.014	6.017	-0.414	-0.414	0.000	0.000	0.000	0.000
62	A	94	PHE	0	0.082	0.036	7.073	-0.248	-0.248	0.000	0.000	0.000	0.000
63	A	95	ASP	-1	-0.838	-0.906	3.816	-2.323	-1.874	0.000	-0.157	-0.293	0.000
64	A	96	THR	0	-0.065	-0.040	1.900	-12.971	-12.130	8.354	-4.495	-4.700	-0.048
65	A	97	GLN	0	-0.038	-0.029	3.584	1.793	2.433	0.011	-0.166	-0.484	0.000
66	A	98	LEU	0	-0.021	-0.020	5.944	0.086	0.086	0.000	0.000	0.000	0.000
67	A	99	ASN	0	0.016	0.020	8.115	0.207	0.207	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.004	-0.017	10.535	0.079	0.079	0.000	0.000	0.000	0.000
69	A	101	ALA	0	0.012	0.020	13.607	0.034	0.034	0.000	0.000	0.000	0.000
70	A	102	ILE	0	-0.028	-0.025	16.763	0.011	0.011	0.000	0.000	0.000	0.000
71	A	103	ASN	0	0.004	0.002	20.050	0.015	0.015	0.000	0.000	0.000	0.000
72	A	104	ASP	-1	-0.926	-0.956	21.846	-0.241	-0.241	0.000	0.000	0.000	0.000
73	A	105	GLU	-1	-0.952	-0.950	20.722	-0.373	-0.373	0.000	0.000	0.000	0.000
74	A	106	ILE	0	-0.062	-0.049	14.141	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	107	PHE	0	0.020	0.019	15.744	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	108	SER	0	-0.007	-0.034	10.349	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	109	MET	0	-0.035	0.015	10.934	0.124	0.124	0.000	0.000	0.000	0.000
78	A	110	ILE	0	-0.003	-0.012	4.944	-0.449	-0.449	0.000	0.000	0.000	0.000
79	A	111	VAL	0	-0.016	-0.002	7.863	0.467	0.467	0.000	0.000	0.000	0.000
80	A	112	VAL	0	0.025	0.008	7.106	-0.422	-0.422	0.000	0.000	0.000	0.000
81	A	113	ASN	0	0.026	-0.028	7.893	0.218	0.218	0.000	0.000	0.000	0.000
82	A	114	PRO	0	-0.001	0.009	9.809	0.107	0.107	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.064	-0.033	13.228	0.095	0.095	0.000	0.000	0.000	0.000
84	A	116	ASP	-1	-0.875	-0.924	12.309	-0.171	-0.171	0.000	0.000	0.000	0.000
85	A	117	LEU	0	-0.001	0.000	15.021	0.031	0.031	0.000	0.000	0.000	0.000
86	A	118	LEU	0	-0.100	-0.035	17.481	0.028	0.028	0.000	0.000	0.000	0.000
87	A	119	GLU	-1	-0.998	-0.998	19.677	-0.090	-0.090	0.000	0.000	0.000	0.000
88	A	120	ASN	0	0.025	-0.004	21.867	0.016	0.016	0.000	0.000	0.000	0.000
89	A	121	VAL	0	0.007	-0.012	22.047	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	122	GLY	0	0.061	0.037	22.953	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	123	GLU	-1	-0.890	-0.936	19.758	-0.278	-0.278	0.000	0.000	0.000	0.000
92	A	124	PHE	0	-0.036	-0.023	16.729	-0.057	-0.057	0.000	0.000	0.000	0.000
93	A	125	GLN	0	-0.054	-0.034	18.788	-0.049	-0.049	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.047	0.020	20.762	-0.030	-0.030	0.000	0.000	0.000	0.000
95	A	127	TYR	0	0.044	0.029	11.219	-0.126	-0.126	0.000	0.000	0.000	0.000
96	A	128	LEU	0	-0.026	-0.020	15.267	-0.087	-0.087	0.000	0.000	0.000	0.000
97	A	129	GLU	-1	-0.952	-0.971	17.521	-0.350	-0.350	0.000	0.000	0.000	0.000
98	A	130	GLU	-1	-0.913	-0.959	17.603	-0.542	-0.542	0.000	0.000	0.000	0.000
99	A	131	LYS	1	0.806	0.885	11.977	1.075	1.075	0.000	0.000	0.000	0.000
100	A	132	LEU	0	-0.032	-0.022	15.856	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	133	ASN	0	-0.035	-0.019	18.403	0.050	0.050	0.000	0.000	0.000	0.000
102	A	134	GLU	-1	-0.794	-0.876	14.238	-0.981	-0.981	0.000	0.000	0.000	0.000
103	A	135	ILE	0	0.005	-0.013	13.723	0.005	0.005	0.000	0.000	0.000	0.000
104	A	136	LYS	1	0.804	0.896	16.907	0.426	0.426	0.000	0.000	0.000	0.000
105	A	137	GLU	-1	-0.829	-0.882	20.357	-0.361	-0.361	0.000	0.000	0.000	0.000
106	A	138	LEU	0	0.015	0.011	14.844	0.020	0.020	0.000	0.000	0.000	0.000
107	A	139	LEU	0	-0.030	-0.023	18.001	0.038	0.038	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.003	0.022	20.176	0.047	0.047	0.000	0.000	0.000	0.000
109	A	141	TYR	0	0.005	-0.025	21.017	0.020	0.020	0.000	0.000	0.000	0.000
110	A	142	LEU	0	-0.008	-0.005	16.983	0.023	0.023	0.000	0.000	0.000	0.000
111	A	143	SER	0	-0.031	-0.035	21.639	0.038	0.038	0.000	0.000	0.000	0.000
112	A	144	GLU	-1	-0.935	-0.953	24.774	-0.260	-0.260	0.000	0.000	0.000	0.000
113	A	145	SER	0	-0.048	-0.028	22.966	0.014	0.014	0.000	0.000	0.000	0.000
114	A	146	LEU	0	-0.091	-0.041	22.525	0.016	0.016	0.000	0.000	0.000	0.000
115	A	147	SER	0	-0.136	-0.065	25.612	0.044	0.044	0.000	0.000	0.000	0.000

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