FMO DATABASE

FMODB ID: 5N26Z

Calculation Name: 5K35-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5K35

Chain ID: A

ChEMBL ID:

UniProt ID: P63208

Base Structure: X-ray

Registration Date: 2023-09-26

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	OptH
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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1542398.705664
FMO2-HF: Nuclear repulsion	1476395.900728
FMO2-HF: Total energy	-66002.804936
FMO2-MP2: Total energy	-66198.687188

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
48.631	50.958	-0.028	-1.259	-1.039	0.001

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.001 / q_NPA : 0.997

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	4	ASN	0	-0.023	-0.024	3.840	2.579	4.906	-0.028	-1.259	-1.039	0.001
4	A	5	PHE	0	0.074	0.047	7.252	-0.063	-0.063	0.000	0.000	0.000	0.000
5	A	6	PHE	0	0.077	0.023	8.055	0.431	0.431	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.041	-0.015	9.371	0.791	0.791	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.932	-0.944	9.634	-22.113	-22.113	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.017	-0.005	12.497	0.845	0.845	0.000	0.000	0.000	0.000
9	A	10	PRO	0	0.041	0.024	14.963	0.339	0.339	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.753	-0.903	18.713	-12.884	-12.884	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.935	-0.961	20.192	-10.892	-10.892	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.010	-0.019	18.759	0.092	0.092	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.011	0.001	15.603	-0.105	-0.105	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.028	0.009	18.644	0.121	0.121	0.000	0.000	0.000	0.000
15	A	16	ASN	0	0.056	0.035	21.943	0.555	0.555	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.012	0.070	17.038	0.153	0.153	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.042	-0.034	18.563	0.161	0.161	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.124	-0.120	21.531	0.277	0.277	0.000	0.000	0.000	0.000
19	A	20	PHE	0	0.003	0.010	22.565	0.434	0.434	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.072	-0.023	19.322	0.100	0.100	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.991	0.992	23.874	9.275	9.275	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.008	-0.003	25.478	-0.319	-0.319	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.017	-0.004	25.861	-0.494	-0.494	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.027	-0.001	20.498	-0.275	-0.275	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.003	0.006	21.298	-0.460	-0.460	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.014	-0.008	22.019	-0.302	-0.302	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.966	0.980	19.723	11.186	11.186	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.015	0.018	15.021	-0.369	-0.369	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.009	0.011	18.242	-0.455	-0.455	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.061	-0.026	20.086	0.375	0.375	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.014	-0.019	14.423	-0.383	-0.383	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.041	0.007	15.290	-0.792	-0.792	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.076	0.025	17.349	-0.108	-0.108	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.019	0.000	15.164	0.631	0.631	0.000	0.000	0.000	0.000
35	A	36	PHE	0	0.105	0.005	13.379	0.514	0.514	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.019	0.011	18.632	0.687	0.687	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.820	0.922	21.150	12.991	12.991	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.006	0.003	19.913	0.463	0.463	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.042	0.035	21.205	0.258	0.258	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.171	-0.101	23.027	0.727	0.727	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.814	-0.908	25.545	-9.851	-9.851	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.931	0.966	27.323	9.052	9.052	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.020	-0.017	29.419	0.547	0.547	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.023	0.019	24.386	0.097	0.097	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.802	-0.925	28.698	-8.839	-8.839	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.027	0.001	25.154	0.276	0.276	0.000	0.000	0.000	0.000
47	A	48	HIS	0	0.010	0.011	28.718	0.276	0.276	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.037	0.006	30.766	0.365	0.365	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.033	-0.014	31.967	0.294	0.294	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.982	0.991	27.846	9.661	9.661	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.006	0.011	33.694	0.390	0.390	0.000	0.000	0.000	0.000
52	A	53	GLN	0	-0.037	-0.023	36.776	0.181	0.181	0.000	0.000	0.000	0.000
53	A	54	HIS	0	0.002	0.006	35.836	0.204	0.204	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.050	0.024	35.286	0.149	0.149	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.957	0.972	38.915	6.843	6.843	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.893	0.947	39.636	7.293	7.293	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.905	-0.927	39.723	-7.090	-7.090	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.009	-0.007	42.703	0.171	0.171	0.000	0.000	0.000	0.000
59	A	60	TRP	0	-0.057	-0.026	44.948	0.133	0.133	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.013	0.006	46.109	0.153	0.153	0.000	0.000	0.000	0.000
61	A	62	ASN	0	0.047	0.015	45.015	0.176	0.176	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.015	-0.006	48.657	0.149	0.149	0.000	0.000	0.000	0.000
63	A	64	MET	0	-0.036	-0.015	50.733	0.134	0.134	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.025	0.009	51.134	0.136	0.136	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.003	0.015	52.847	0.107	0.107	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.016	-0.023	54.557	0.111	0.111	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.846	0.917	53.960	5.490	5.490	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.033	-0.022	56.520	0.097	0.097	0.000	0.000	0.000	0.000
69	A	70	ASN	0	0.031	0.005	59.122	0.035	0.035	0.000	0.000	0.000	0.000
70	A	71	ASN	0	0.074	0.066	55.748	0.068	0.068	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.033	0.007	56.814	-0.103	-0.103	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.916	-0.977	56.884	-5.181	-5.181	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.907	-0.952	50.281	-6.017	-6.017	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.004	-0.001	52.442	-0.113	-0.113	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.893	0.944	53.147	5.053	5.053	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.925	0.972	50.121	5.690	5.690	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.011	0.011	47.712	-0.104	-0.104	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.004	-0.006	48.584	-0.074	-0.074	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.906	0.946	50.107	5.560	5.560	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.885	0.960	42.724	6.738	6.738	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.022	0.025	45.279	-0.124	-0.124	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.028	-0.010	45.152	-0.115	-0.115	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.774	-0.886	47.965	-5.626	-5.626	0.000	0.000	0.000	0.000
84	A	85	PRO	0	-0.059	-0.027	50.372	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	86	THR	0	-0.033	-0.039	52.618	0.055	0.055	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.047	-0.012	48.135	-0.079	-0.079	0.000	0.000	0.000	0.000
87	A	88	THR	0	-0.012	-0.021	49.980	-0.126	-0.126	0.000	0.000	0.000	0.000
88	A	89	ASN	0	0.000	-0.009	45.631	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	90	SER	0	0.117	0.034	48.273	0.074	0.074	0.000	0.000	0.000	0.000
90	A	91	TYR	0	-0.020	0.012	41.573	0.035	0.035	0.000	0.000	0.000	0.000
91	A	92	HIS	1	0.848	0.931	45.285	6.272	6.272	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.017	0.014	49.049	0.103	0.103	0.000	0.000	0.000	0.000
93	A	94	ASN	0	0.041	0.013	51.579	0.038	0.038	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.873	0.938	53.085	5.367	5.367	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.050	0.030	53.350	-0.078	-0.078	0.000	0.000	0.000	0.000
96	A	97	PRO	0	0.036	-0.002	52.950	0.070	0.070	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.016	0.009	55.538	0.060	0.060	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.025	0.008	58.188	0.072	0.072	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.016	-0.002	56.005	0.041	0.041	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.030	0.005	58.058	0.053	0.053	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.049	-0.011	60.452	0.072	0.072	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.765	-0.849	58.125	-5.082	-5.082	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.033	-0.010	61.370	0.037	0.037	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.811	0.900	62.244	4.480	4.480	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.026	0.047	61.870	0.054	0.054	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.011	-0.061	63.596	-0.039	-0.039	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.011	0.005	64.791	0.022	0.022	0.000	0.000	0.000	0.000
108	A	109	THR	0	0.017	-0.006	58.969	-0.042	-0.042	0.000	0.000	0.000	0.000
109	A	110	ALA	0	0.033	0.010	61.306	-0.055	-0.055	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.000	-0.002	62.905	0.003	0.003	0.000	0.000	0.000	0.000
111	A	112	TYR	0	-0.069	-0.026	57.441	0.015	0.015	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.019	-0.023	56.483	-0.027	-0.027	0.000	0.000	0.000	0.000
113	A	114	TRP	0	0.029	0.012	60.156	-0.084	-0.084	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.997	1.009	62.906	4.772	4.772	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.807	0.911	58.945	5.032	5.032	0.000	0.000	0.000	0.000
116	A	117	TYR	0	0.024	0.005	54.311	-0.110	-0.110	0.000	0.000	0.000	0.000
117	A	118	THR	0	0.043	0.027	58.368	0.091	0.091	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.005	-0.018	56.555	-0.106	-0.106	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.803	-0.906	59.801	-4.782	-4.782	0.000	0.000	0.000	0.000
120	A	121	PRO	0	-0.020	-0.016	61.648	-0.038	-0.038	0.000	0.000	0.000	0.000
121	A	122	ASN	0	0.008	-0.019	64.175	0.079	0.079	0.000	0.000	0.000	0.000
122	A	123	PHE	0	-0.043	0.000	55.400	0.007	0.007	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.904	0.940	60.649	4.609	4.609	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.730	-0.864	56.371	-5.178	-5.178	0.000	0.000	0.000	0.000
125	A	126	ASN	0	-0.063	-0.043	52.459	0.078	0.078	0.000	0.000	0.000	0.000
126	A	127	TYR	0	-0.057	-0.032	54.032	-0.047	-0.047	0.000	0.000	0.000	0.000
127	A	128	GLY	0	-0.008	0.015	58.949	0.080	0.080	0.000	0.000	0.000	0.000
128	A	129	ASP	-1	-0.880	-0.962	60.671	-4.627	-4.627	0.000	0.000	0.000	0.000
129	A	130	SER	0	-0.041	-0.003	61.021	-0.046	-0.046	0.000	0.000	0.000	0.000
130	A	131	PRO	0	0.013	-0.006	61.386	0.049	0.049	0.000	0.000	0.000	0.000
131	A	132	ILE	0	0.057	0.030	64.048	0.058	0.058	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.067	-0.029	65.794	0.036	0.036	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.034	0.032	62.575	0.063	0.063	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.014	-0.005	66.526	0.055	0.055	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.943	0.965	68.711	4.232	4.232	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.972	0.992	66.948	4.557	4.557	0.000	0.000	0.000	0.000
137	A	138	GLN	0	0.006	0.017	66.189	0.063	0.063	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.024	-0.009	70.786	0.047	0.047	0.000	0.000	0.000	0.000
139	A	140	ALA	0	0.007	0.005	74.122	0.058	0.058	0.000	0.000	0.000	0.000
140	A	141	ASN	0	0.011	0.012	71.142	0.066	0.066	0.000	0.000	0.000	0.000
141	A	142	PRO	0	0.031	0.007	74.599	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	143	ALA	0	0.006	0.016	72.846	0.020	0.020	0.000	0.000	0.000	0.000
143	A	144	PHE	0	-0.064	-0.020	68.224	-0.054	-0.054	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.993	0.988	71.679	4.296	4.296	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.796	-0.900	75.901	-3.865	-3.865	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.912	0.937	73.014	4.186	4.186	0.000	0.000	0.000	0.000
147	A	148	GLU	-1	-0.793	-0.886	71.012	-4.344	-4.344	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.867	0.938	72.985	4.010	4.010	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.923	0.971	75.090	3.960	3.960	0.000	0.000	0.000	0.000
150	A	151	GLN	0	-0.037	-0.040	69.817	0.003	0.003	0.000	0.000	0.000	0.000
151	A	152	ILE	0	0.039	0.038	70.272	-0.025	-0.025	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.990	1.004	71.970	3.899	3.899	0.000	0.000	0.000	0.000
153	A	154	ALA	0	-0.054	-0.021	73.003	0.012	0.012	0.000	0.000	0.000	0.000
154	A	155	LEU	0	0.047	0.022	66.698	-0.018	-0.018	0.000	0.000	0.000	0.000
155	A	156	ILE	0	-0.042	-0.014	70.063	-0.021	-0.021	0.000	0.000	0.000	0.000
156	A	157	ARG	1	0.983	0.982	71.590	3.984	3.984	0.000	0.000	0.000	0.000
157	A	158	GLY	0	0.036	0.031	70.553	0.011	0.011	0.000	0.000	0.000	0.000
158	A	159	MET	0	-0.067	-0.053	64.480	-0.029	-0.029	0.000	0.000	0.000	0.000
159	A	160	GLN	0	-0.074	-0.040	68.980	-0.037	-0.037	0.000	0.000	0.000	0.000
160	A	161	GLU	-1	-0.946	-0.979	71.827	-3.973	-3.973	0.000	0.000	0.000	0.000
161	A	162	GLU	-1	-0.951	-0.948	69.600	-4.356	-4.356	0.000	0.000	0.000	0.000
162	A	163	LYS	1	0.946	0.967	69.899	4.306	4.306	0.000	0.000	0.000	0.000
163	A	164	ILE	0	0.036	0.022	65.578	-0.051	-0.051	0.000	0.000	0.000	0.000
164	A	165	ALA	0	-0.027	-0.007	63.614	0.039	0.039	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)