FMO DATABASE

FMODB ID: YVMN2

Calculation Name: 1RCU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RCU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0E5

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1709070.84364
FMO2-HF: Nuclear repulsion	1645387.752542
FMO2-HF: Total energy	-63683.091097
FMO2-MP2: Total energy	-63870.843332

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:1:MET)

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

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.
-8.416	-4.733	1.931	-2.361	-3.253	-0.024

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.015

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	3	LYS	1	0.893	0.949	3.674	0.349	1.565	0.001	-0.436	-0.781	0.002
4	A	4	VAL	0	0.007	0.004	6.307	0.712	0.712	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.009	0.000	9.112	-0.015	-0.015	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.021	-0.007	12.372	0.102	0.102	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.006	-0.009	14.929	0.003	0.003	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.073	0.015	18.717	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.040	-0.007	22.036	0.002	0.002	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.019	0.026	24.126	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.009	-0.011	25.849	0.019	0.019	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.002	-0.013	27.458	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.089	0.048	24.345	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.036	-0.027	27.343	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.942	0.975	30.600	0.158	0.158	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.043	0.018	30.636	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.084	-0.034	29.183	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.023	-0.007	24.908	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.064	-0.053	26.381	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.768	-0.858	27.944	-0.168	-0.168	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.010	-0.004	23.776	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.886	0.959	23.064	0.201	0.201	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.893	-0.940	21.975	-0.231	-0.231	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.083	0.040	20.506	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.064	-0.027	18.619	-0.039	-0.039	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.001	-0.008	17.186	-0.058	-0.058	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.890	-0.959	16.682	-0.273	-0.273	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.028	0.021	13.571	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.001	-0.001	12.806	-0.087	-0.087	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.842	0.885	11.862	0.208	0.208	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.030	-0.031	12.104	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.014	-0.012	8.599	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.001	0.006	7.192	-0.303	-0.303	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.905	0.951	7.679	0.266	0.266	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.798	0.897	7.557	0.153	0.153	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.001	0.014	4.209	0.528	0.639	-0.001	-0.040	-0.069	0.000
37	A	37	TYR	0	-0.037	-0.028	2.251	-8.069	-6.175	1.918	-1.794	-2.019	-0.026
38	A	38	LEU	0	-0.017	-0.001	3.420	0.181	0.645	0.014	-0.088	-0.390	0.000
39	A	39	VAL	0	0.030	0.012	5.219	0.411	0.409	-0.001	-0.003	0.006	0.000
40	A	40	PHE	0	0.022	0.005	7.168	0.120	0.120	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.034	0.008	11.268	0.145	0.145	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.032	0.005	15.063	0.006	0.006	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.040	0.007	17.580	0.049	0.049	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.738	0.814	18.911	0.316	0.316	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.718	-0.847	21.286	-0.304	-0.304	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.023	0.006	22.800	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.030	-0.005	19.283	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.056	0.007	18.240	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.873	-0.917	18.063	-0.360	-0.360	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.010	-0.010	19.348	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.007	0.005	13.951	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.001	-0.028	14.796	-0.098	-0.098	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.033	-0.017	15.614	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.010	0.010	16.157	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.043	-0.011	10.417	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.819	0.893	12.825	0.543	0.543	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.806	-0.874	15.094	-0.303	-0.303	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.097	-0.040	12.572	0.055	0.055	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.009	0.008	12.691	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.003	0.007	9.275	-0.070	-0.070	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.054	-0.040	7.289	0.218	0.218	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.002	-0.004	8.638	-0.270	-0.270	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.011	-0.006	9.495	0.157	0.157	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.031	0.011	12.153	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.035	-0.022	13.640	0.035	0.035	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.024	0.001	17.075	0.021	0.021	0.000	0.000	0.000	0.000
67	A	67	PRO	0	-0.016	0.015	20.771	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.877	-0.936	24.063	-0.211	-0.211	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.860	-0.959	25.118	-0.250	-0.250	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.832	-0.887	24.535	-0.273	-0.273	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.032	-0.013	24.086	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.043	0.008	21.176	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.032	-0.013	18.180	0.016	0.016	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.006	-0.005	20.512	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.033	-0.022	17.813	0.008	0.008	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.002	0.027	15.488	-0.078	-0.078	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.012	0.006	11.870	0.024	0.024	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.019	-0.010	12.359	0.048	0.048	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.024	0.021	14.650	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.027	-0.018	14.706	0.033	0.033	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.876	0.950	17.991	0.275	0.275	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.038	-0.050	20.254	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.002	0.016	22.760	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.032	-0.009	23.117	0.017	0.017	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.744	-0.869	26.090	-0.242	-0.242	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.039	0.008	25.014	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.016	-0.005	24.105	-0.032	-0.032	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.016	-0.019	23.950	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.820	0.926	20.032	0.362	0.362	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.018	-0.038	19.796	-0.044	-0.044	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.023	-0.013	19.192	-0.044	-0.044	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.022	-0.003	17.899	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.009	0.004	14.211	-0.082	-0.082	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.018	0.004	14.317	-0.121	-0.121	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.882	0.949	13.945	0.374	0.374	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.058	-0.017	10.480	-0.190	-0.190	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.034	0.028	10.077	-0.233	-0.233	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.858	-0.927	5.628	-2.251	-2.251	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.032	-0.015	9.228	0.244	0.244	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.013	-0.008	11.955	-0.169	-0.169	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.004	0.003	13.045	0.082	0.082	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.024	-0.032	15.848	-0.037	-0.037	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.034	0.012	18.408	0.027	0.027	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.052	0.029	21.533	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.017	0.018	24.915	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.775	-0.879	25.673	-0.149	-0.149	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.002	-0.002	27.383	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.055	0.030	26.177	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	109	THR	0	0.051	0.024	22.043	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.002	0.005	23.781	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.013	-0.005	24.899	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.827	-0.897	20.344	-0.394	-0.394	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.015	0.012	20.881	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.001	-0.013	22.113	0.006	0.006	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.001	0.000	22.009	0.013	0.013	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.009	-0.015	17.821	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.001	-0.031	18.379	0.008	0.008	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.024	-0.017	20.658	0.017	0.017	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.097	-0.044	16.835	0.011	0.011	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.007	0.008	16.365	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.812	0.913	10.879	0.687	0.687	0.000	0.000	0.000	0.000
122	A	122	PRO	0	0.046	0.028	13.361	0.013	0.013	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.014	-0.015	15.383	-0.077	-0.077	0.000	0.000	0.000	0.000
124	A	124	ILE	0	-0.007	0.000	14.058	0.048	0.048	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.048	-0.024	18.037	-0.037	-0.037	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.016	0.012	18.680	0.023	0.023	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.821	0.892	21.099	0.124	0.124	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.013	0.006	24.887	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	THR	0	-0.010	-0.018	22.904	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.000	-0.007	26.269	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.023	0.006	27.468	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	132	TRP	0	-0.028	-0.036	27.028	0.015	0.015	0.000	0.000	0.000	0.000
133	A	133	THR	0	0.016	0.020	22.604	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.742	-0.846	25.062	-0.146	-0.146	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.775	0.883	27.982	0.166	0.166	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.008	-0.005	25.421	0.011	0.011	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.018	-0.028	27.436	0.013	0.013	0.000	0.000	0.000	0.000
138	A	138	GLN	0	-0.081	-0.043	28.740	0.017	0.017	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.029	-0.011	30.680	0.007	0.007	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.028	0.009	26.399	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.020	0.016	29.730	0.012	0.012	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.822	-0.909	29.144	-0.044	-0.044	0.000	0.000	0.000	0.000
143	A	143	GLY	0	-0.012	0.000	29.448	0.007	0.007	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.853	0.929	24.737	0.031	0.031	0.000	0.000	0.000	0.000
145	A	145	TYR	0	0.009	0.009	23.235	-0.008	-0.008	0.000	0.000	0.000	0.000
146	A	146	LEU	0	0.041	0.015	24.564	0.001	0.001	0.000	0.000	0.000	0.000
147	A	147	ASP	-1	-0.775	-0.860	26.944	-0.106	-0.106	0.000	0.000	0.000	0.000
148	A	148	ASN	0	0.037	0.004	28.393	0.007	0.007	0.000	0.000	0.000	0.000
149	A	149	ARG	1	0.876	0.934	26.478	0.106	0.106	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.758	0.878	25.387	0.055	0.055	0.000	0.000	0.000	0.000
151	A	151	ILE	0	-0.038	0.001	20.269	0.009	0.009	0.000	0.000	0.000	0.000
152	A	152	VAL	0	0.003	0.016	16.804	0.005	0.005	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.871	-0.941	19.575	-0.043	-0.043	0.000	0.000	0.000	0.000
154	A	154	ILE	0	-0.047	-0.026	19.583	-0.034	-0.034	0.000	0.000	0.000	0.000
155	A	155	HIS	0	0.006	-0.007	17.107	0.008	0.008	0.000	0.000	0.000	0.000
156	A	156	GLN	0	-0.006	-0.005	21.022	-0.027	-0.027	0.000	0.000	0.000	0.000
157	A	157	ALA	0	0.019	0.024	19.619	0.016	0.016	0.000	0.000	0.000	0.000
158	A	158	TRP	0	-0.014	-0.017	21.588	-0.020	-0.020	0.000	0.000	0.000	0.000
159	A	159	THR	0	-0.006	-0.002	20.213	0.003	0.003	0.000	0.000	0.000	0.000
160	A	160	VAL	0	-0.001	0.014	15.328	-0.008	-0.008	0.000	0.000	0.000	0.000
161	A	161	GLU	-1	-0.917	-0.957	15.955	-0.088	-0.088	0.000	0.000	0.000	0.000
162	A	162	GLU	-1	-0.790	-0.900	16.244	-0.081	-0.081	0.000	0.000	0.000	0.000
163	A	163	ALA	0	0.007	-0.012	16.175	0.015	0.015	0.000	0.000	0.000	0.000
164	A	164	VAL	0	-0.028	-0.028	10.753	-0.034	-0.034	0.000	0.000	0.000	0.000
165	A	165	GLN	0	-0.003	0.001	12.285	0.049	0.049	0.000	0.000	0.000	0.000
166	A	166	ILE	0	0.007	0.002	14.554	0.066	0.066	0.000	0.000	0.000	0.000
167	A	167	ILE	0	-0.034	-0.007	8.763	0.011	0.011	0.000	0.000	0.000	0.000
168	A	168	GLU	-1	-0.805	-0.890	9.961	0.269	0.269	0.000	0.000	0.000	0.000
169	A	169	GLN	0	-0.032	0.001	11.457	0.108	0.108	0.000	0.000	0.000	0.000
170	A	170	ILE	0	-0.073	-0.032	9.130	-0.114	-0.114	0.000	0.000	0.000	0.000

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