FMO DATABASE

FMODB ID: K9YM3

Calculation Name: 5CWD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CWD

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1613930.271335
FMO2-HF: Nuclear repulsion	1548167.263924
FMO2-HF: Total energy	-65763.007411
FMO2-MP2: Total energy	-65946.716696

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-42.168	-43.427	27.01	-14.918	-10.836	-0.054

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.053

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	5	GLU	-1	-0.809	-0.901	3.088	-1.582	1.502	0.173	-1.443	-1.815	0.008
4	A	6	ASP	-1	-0.824	-0.870	1.591	-40.368	-46.480	26.497	-12.839	-7.546	-0.068
5	A	7	ALA	0	0.020	0.023	3.699	-0.093	0.335	0.010	-0.135	-0.304	0.000
6	A	8	ARG	1	0.830	0.896	6.009	-1.656	-1.656	0.000	0.000	0.000	0.000
7	A	9	SER	0	-0.021	0.005	6.738	-0.163	-0.163	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.015	-0.027	7.142	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	11	CYS	0	-0.113	-0.051	9.536	0.090	0.090	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.737	-0.863	11.528	0.115	0.115	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.945	0.972	11.983	0.834	0.834	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.022	-0.006	13.417	0.017	0.017	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.012	0.007	15.302	0.026	0.026	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.753	0.837	16.841	0.044	0.044	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.960	0.977	16.812	0.417	0.417	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.037	-0.014	19.303	0.010	0.010	0.000	0.000	0.000	0.000
17	A	19	ALA	0	-0.046	-0.024	21.150	0.016	0.016	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.942	-0.977	20.904	-0.189	-0.189	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.068	-0.016	23.891	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.027	-0.020	25.764	0.007	0.007	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.828	-0.916	26.809	-0.080	-0.080	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.782	-0.884	25.843	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.862	-0.905	24.250	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.010	0.016	21.479	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.044	0.022	20.502	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.765	0.867	19.714	0.031	0.031	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.086	-0.045	16.789	0.052	0.052	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.052	0.035	16.311	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.017	-0.008	14.938	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.908	0.948	14.718	0.077	0.077	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.815	-0.892	12.653	-0.314	-0.314	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.028	-0.028	9.998	0.111	0.111	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.930	-0.951	10.622	-0.096	-0.096	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.059	0.022	5.403	0.182	0.182	0.000	0.000	0.000	0.000
35	A	38	ALA	0	-0.001	-0.002	5.777	0.488	0.488	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.902	0.956	7.614	0.250	0.250	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.083	-0.037	6.040	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	41	ALA	0	-0.041	-0.016	3.145	-0.400	0.815	0.330	-0.608	-0.937	0.005
39	A	42	GLY	0	-0.018	0.004	3.999	0.421	0.547	0.000	0.107	-0.234	0.001
40	A	43	MET	0	-0.117	-0.055	6.443	-0.358	-0.358	0.000	0.000	0.000	0.000
41	A	44	PRO	0	-0.025	-0.013	7.994	-0.284	-0.284	0.000	0.000	0.000	0.000
42	A	45	THR	0	0.053	0.012	11.788	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.943	0.973	13.620	-0.415	-0.415	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.772	-0.867	10.545	1.217	1.217	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.062	0.026	10.724	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.030	0.004	12.220	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.835	0.907	15.728	-0.448	-0.448	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.028	0.008	12.464	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.008	-0.004	14.352	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	53	CYS	0	-0.088	-0.022	15.791	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.873	-0.940	17.190	0.294	0.294	0.000	0.000	0.000	0.000
52	A	55	ALA	0	-0.004	0.007	15.255	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	56	ALA	0	-0.010	-0.001	17.409	-0.034	-0.034	0.000	0.000	0.000	0.000
54	A	57	ALA	0	-0.035	-0.014	20.264	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.892	0.931	15.570	-0.196	-0.196	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.000	0.013	20.164	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	60	ALA	0	0.025	-0.006	22.032	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	61	ALA	0	-0.053	-0.014	24.813	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.807	-0.892	21.264	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.097	-0.044	25.674	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	64	ASN	0	-0.024	-0.025	27.080	0.001	0.001	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.787	-0.887	29.808	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.819	-0.897	30.723	0.017	0.017	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.838	-0.915	31.934	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.020	0.015	25.753	0.004	0.004	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.011	0.015	26.848	0.008	0.008	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.794	0.878	27.979	0.009	0.009	0.000	0.000	0.000	0.000
68	A	71	ILE	0	-0.004	0.019	24.979	0.011	0.011	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.035	0.020	23.664	0.004	0.004	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.034	-0.014	23.724	0.018	0.018	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.839	0.902	25.131	0.010	0.010	0.000	0.000	0.000	0.000
72	A	75	ALA	0	0.063	0.035	21.213	0.008	0.008	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.005	-0.026	21.318	0.027	0.027	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.924	-0.962	21.754	0.043	0.043	0.000	0.000	0.000	0.000
75	A	79	VAL	0	0.044	0.014	15.746	0.017	0.017	0.000	0.000	0.000	0.000
76	A	80	ALA	0	-0.036	-0.015	18.583	0.040	0.040	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.946	0.959	20.614	-0.057	-0.057	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.071	-0.022	18.040	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	ALA	0	-0.032	-0.018	16.540	0.022	0.022	0.000	0.000	0.000	0.000
80	A	84	GLY	0	-0.005	0.009	17.809	0.047	0.047	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.092	-0.038	19.033	0.040	0.040	0.000	0.000	0.000	0.000
82	A	86	PRO	0	-0.008	-0.010	21.105	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	87	THR	0	0.060	0.022	23.922	0.013	0.013	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.857	0.909	26.035	-0.142	-0.142	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.830	-0.888	21.711	0.294	0.294	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.029	0.018	22.023	0.005	0.005	0.000	0.000	0.000	0.000
87	A	91	ALA	0	0.052	0.023	23.037	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	92	ARG	1	0.865	0.929	25.648	-0.183	-0.183	0.000	0.000	0.000	0.000
89	A	93	SER	0	-0.027	-0.017	20.768	0.001	0.001	0.000	0.000	0.000	0.000
90	A	94	PHE	0	0.050	0.018	22.708	0.000	0.000	0.000	0.000	0.000	0.000
91	A	95	CYS	0	-0.086	-0.033	23.619	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.881	-0.937	24.151	0.218	0.218	0.000	0.000	0.000	0.000
93	A	97	ALA	0	-0.025	-0.008	21.055	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	98	ALA	0	0.011	0.009	22.859	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.031	-0.019	25.549	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	100	ARG	1	0.837	0.899	20.936	-0.243	-0.243	0.000	0.000	0.000	0.000
97	A	101	ALA	0	0.042	0.029	23.217	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	102	ALA	0	0.008	-0.004	24.897	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	103	ALA	0	-0.090	-0.050	28.107	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	104	GLU	-1	-0.957	-0.979	23.915	0.106	0.106	0.000	0.000	0.000	0.000
101	A	105	SER	0	-0.021	-0.015	27.164	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	106	ASN	0	-0.066	-0.028	28.738	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	107	ASP	-1	-0.810	-0.916	32.192	0.006	0.006	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.864	-0.933	33.512	0.036	0.036	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.920	-0.934	34.830	0.001	0.001	0.000	0.000	0.000	0.000
106	A	110	VAL	0	0.072	0.038	28.701	0.003	0.003	0.000	0.000	0.000	0.000
107	A	111	ALA	0	-0.017	-0.003	31.155	0.008	0.008	0.000	0.000	0.000	0.000
108	A	112	LYS	1	0.813	0.894	32.973	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	113	ILE	0	-0.007	0.008	29.745	0.005	0.005	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.018	0.009	28.997	0.004	0.004	0.000	0.000	0.000	0.000
111	A	115	ALA	0	-0.038	-0.019	30.130	0.008	0.008	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.772	0.856	32.958	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	117	ALA	0	0.060	0.034	28.335	0.002	0.002	0.000	0.000	0.000	0.000
114	A	119	LEU	0	-0.025	-0.031	29.821	0.005	0.005	0.000	0.000	0.000	0.000
115	A	120	GLU	-1	-0.781	-0.853	31.512	0.038	0.038	0.000	0.000	0.000	0.000
116	A	121	VAL	0	0.026	0.014	26.123	0.001	0.001	0.000	0.000	0.000	0.000
117	A	122	ALA	0	-0.008	-0.018	29.379	0.006	0.006	0.000	0.000	0.000	0.000
118	A	123	LYS	1	0.809	0.893	31.523	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	124	GLN	0	-0.078	-0.055	29.943	0.001	0.001	0.000	0.000	0.000	0.000
120	A	125	ALA	0	-0.048	-0.010	28.528	0.003	0.003	0.000	0.000	0.000	0.000
121	A	126	GLY	0	0.001	0.001	29.989	0.006	0.006	0.000	0.000	0.000	0.000
122	A	127	MET	0	-0.107	-0.044	29.056	0.009	0.009	0.000	0.000	0.000	0.000
123	A	128	PRO	0	0.017	0.003	32.990	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	129	THR	0	0.105	0.038	35.190	0.006	0.006	0.000	0.000	0.000	0.000
125	A	130	LYS	1	0.975	0.994	36.402	-0.080	-0.080	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.773	-0.878	32.853	0.135	0.135	0.000	0.000	0.000	0.000
127	A	132	ALA	0	0.019	0.036	31.758	0.008	0.008	0.000	0.000	0.000	0.000
128	A	133	ALA	0	0.060	0.025	32.252	0.004	0.004	0.000	0.000	0.000	0.000
129	A	134	ARG	1	0.809	0.895	34.350	-0.118	-0.118	0.000	0.000	0.000	0.000
130	A	135	SER	0	-0.014	-0.024	29.359	0.008	0.008	0.000	0.000	0.000	0.000
131	A	136	PHE	0	0.039	0.024	29.334	0.008	0.008	0.000	0.000	0.000	0.000
132	A	137	CYS	0	-0.079	-0.032	30.974	0.003	0.003	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.853	-0.930	32.000	0.122	0.122	0.000	0.000	0.000	0.000
134	A	139	ALA	0	0.002	0.009	27.242	0.006	0.006	0.000	0.000	0.000	0.000
135	A	140	ALA	0	0.046	0.028	28.955	0.004	0.004	0.000	0.000	0.000	0.000
136	A	141	LYS	1	0.859	0.905	30.737	-0.087	-0.087	0.000	0.000	0.000	0.000
137	A	142	ARG	1	0.803	0.892	27.847	-0.189	-0.189	0.000	0.000	0.000	0.000
138	A	143	ALA	0	0.064	0.031	27.193	0.004	0.004	0.000	0.000	0.000	0.000
139	A	144	ALA	0	0.019	0.010	28.459	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	145	LYS	1	0.838	0.891	31.803	-0.099	-0.099	0.000	0.000	0.000	0.000
141	A	146	GLU	-1	-0.875	-0.913	25.900	0.212	0.212	0.000	0.000	0.000	0.000
142	A	147	SER	0	-0.029	-0.019	28.904	0.002	0.002	0.000	0.000	0.000	0.000
143	A	148	ASN	0	-0.104	-0.043	29.829	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	149	ASP	-1	-0.800	-0.908	32.969	0.063	0.063	0.000	0.000	0.000	0.000
145	A	150	GLU	-1	-0.947	-0.977	34.726	0.063	0.063	0.000	0.000	0.000	0.000
146	A	151	GLU	-1	-0.842	-0.895	35.453	0.041	0.041	0.000	0.000	0.000	0.000
147	A	152	VAL	0	0.070	0.036	30.437	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	153	GLU	-1	-0.827	-0.904	33.629	0.083	0.083	0.000	0.000	0.000	0.000
149	A	154	LYS	1	0.753	0.861	35.931	-0.045	-0.045	0.000	0.000	0.000	0.000
150	A	155	ILE	0	0.049	0.042	32.507	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	156	ALA	0	0.039	0.026	33.100	0.001	0.001	0.000	0.000	0.000	0.000
152	A	157	LYS	1	0.832	0.904	34.360	-0.068	-0.068	0.000	0.000	0.000	0.000
153	A	158	LYS	1	0.826	0.907	37.082	-0.037	-0.037	0.000	0.000	0.000	0.000
154	A	159	ALA	0	0.070	0.040	33.243	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	161	LYS	1	0.892	0.935	37.004	-0.056	-0.056	0.000	0.000	0.000	0.000
156	A	162	GLU	-1	-0.767	-0.864	36.977	0.032	0.032	0.000	0.000	0.000	0.000
157	A	163	VAL	0	0.014	0.010	34.096	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	164	ALA	0	-0.063	-0.029	37.157	0.000	0.000	0.000	0.000	0.000	0.000
159	A	165	LYS	1	0.855	0.913	40.548	-0.038	-0.038	0.000	0.000	0.000	0.000
160	A	166	GLN	0	-0.037	-0.008	36.910	-0.006	-0.006	0.000	0.000	0.000	0.000
161	A	167	ALA	0	-0.019	-0.013	38.233	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	168	GLY	0	0.032	0.032	40.088	0.000	0.000	0.000	0.000	0.000	0.000
163	A	169	MET	0	-0.075	-0.037	40.881	0.003	0.003	0.000	0.000	0.000	0.000
164	A	170	PRO	0	0.047	-0.002	42.954	0.004	0.004	0.000	0.000	0.000	0.000
165	A	171	TRP	0	-0.032	-0.013	44.387	0.001	0.001	0.000	0.000	0.000	0.000
166	A	172	LEU	0	-0.079	-0.015	37.788	0.004	0.004	0.000	0.000	0.000	0.000
167	A	173	GLU	-1	-0.741	-0.858	39.779	0.070	0.070	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)