FMO DATABASE

FMODB ID: MVYRZ

Calculation Name: 4X38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X38

Chain ID: A

ChEMBL ID:

UniProt ID: O73909

Base Structure: X-ray

Registration Date: 2023-09-19

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1560934.51359
FMO2-HF: Nuclear repulsion	1498438.708096
FMO2-HF: Total energy	-62495.805494
FMO2-MP2: Total energy	-62676.22499

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:ALA)

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

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.
-11.848	-6.249	1.988	-3.774	-3.812	-0.031

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.014

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	ARG	1	0.862	0.924	3.882	-1.805	-0.320	-0.018	-0.791	-0.677	0.001
4	A	6	TYR	0	-0.003	-0.013	6.523	-0.101	-0.101	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.102	-0.045	9.933	0.180	0.180	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.949	0.958	12.797	0.154	0.154	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.059	0.047	15.146	-0.067	-0.067	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.021	0.009	17.649	0.031	0.031	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.042	-0.016	20.504	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	12	PHE	0	-0.002	-0.013	19.869	0.013	0.013	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.857	-0.945	24.253	-0.107	-0.107	0.000	0.000	0.000	0.000
12	A	14	ILE	0	-0.001	-0.015	22.831	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	15	PHE	0	0.003	0.013	26.552	0.006	0.006	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.704	-0.856	27.484	-0.124	-0.124	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.004	-0.017	28.435	0.009	0.009	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.062	-0.024	30.369	0.007	0.007	0.000	0.000	0.000	0.000
17	A	19	GLN	0	-0.013	-0.017	32.363	0.004	0.004	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.812	0.942	31.174	0.115	0.115	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.038	-0.010	29.582	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	22	PHE	0	0.043	0.008	22.854	0.000	0.000	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.028	0.004	28.373	0.006	0.006	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.037	-0.008	25.684	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.883	-0.939	28.984	-0.098	-0.098	0.000	0.000	0.000	0.000
24	A	26	SER	0	0.028	0.009	29.629	0.005	0.005	0.000	0.000	0.000	0.000
25	A	27	PRO	0	-0.005	-0.015	26.386	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.022	0.013	25.043	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.063	-0.028	26.389	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.016	0.019	23.183	0.007	0.007	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.026	0.024	26.902	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.024	0.017	28.392	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.017	-0.025	30.189	0.007	0.007	0.000	0.000	0.000	0.000
32	A	34	HIS	0	0.019	0.025	33.645	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.016	-0.008	33.686	0.002	0.002	0.000	0.000	0.000	0.000
34	A	36	GLN	0	0.009	-0.009	37.377	0.004	0.004	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.020	0.017	41.085	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.023	0.019	44.189	0.001	0.001	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.030	-0.011	40.712	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.024	-0.023	40.537	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	SER	0	0.008	0.003	35.603	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	42	GLN	0	-0.010	-0.004	31.506	0.006	0.006	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.946	0.979	30.249	0.089	0.089	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.001	0.013	24.978	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.859	0.942	25.708	0.102	0.102	0.000	0.000	0.000	0.000
44	A	46	LEU	0	0.052	0.022	19.857	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.063	-0.053	19.818	0.021	0.021	0.000	0.000	0.000	0.000
46	A	48	ILE	0	0.026	0.025	15.864	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.002	0.009	13.249	0.045	0.045	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.024	-0.021	12.535	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.019	-0.015	7.206	0.043	0.043	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.920	0.960	8.118	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	53	PRO	0	0.067	0.047	4.472	-0.154	-0.103	-0.001	-0.071	0.022	0.000
52	A	54	ARG	1	0.932	0.944	4.156	-0.135	-0.013	-0.001	-0.015	-0.106	0.000
53	A	55	GLY	0	-0.009	-0.012	5.688	-0.228	-0.228	0.000	0.000	0.000	0.000
54	A	56	PRO	0	0.036	0.047	5.572	0.073	0.073	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.935	0.944	7.014	-0.781	-0.781	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.019	0.002	9.926	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.007	0.005	9.635	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.016	0.004	8.798	0.019	0.019	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.032	0.020	8.532	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	62	THR	0	0.001	0.001	9.059	0.039	0.039	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.027	-0.002	11.301	0.020	0.020	0.000	0.000	0.000	0.000
62	A	64	GLN	0	-0.054	-0.016	11.650	0.008	0.008	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.003	-0.001	11.847	0.006	0.006	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.001	0.025	7.330	0.033	0.033	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.034	-0.036	9.642	0.063	0.063	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.081	0.063	11.232	-0.082	-0.082	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.027	-0.024	12.667	0.083	0.083	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.073	0.046	16.371	0.001	0.001	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.024	0.014	18.693	0.023	0.023	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.916	0.941	22.320	0.127	0.127	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.036	-0.027	23.987	0.010	0.010	0.000	0.000	0.000	0.000
72	A	74	TYR	0	0.028	-0.002	24.716	0.011	0.011	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.875	0.952	21.456	0.123	0.123	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.088	0.068	20.316	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	77	TYR	0	-0.041	-0.019	15.189	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.029	-0.005	16.790	0.012	0.012	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.010	-0.028	14.119	-0.051	-0.051	0.000	0.000	0.000	0.000
78	A	80	CYS	0	-0.050	-0.004	13.866	0.068	0.068	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.016	-0.003	14.194	-0.062	-0.062	0.000	0.000	0.000	0.000
80	A	82	MET	0	-0.009	0.007	16.548	0.027	0.027	0.000	0.000	0.000	0.000
81	A	83	SER	0	-0.017	-0.008	18.987	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.038	0.030	22.409	0.012	0.012	0.000	0.000	0.000	0.000
83	A	85	THR	0	-0.042	-0.036	23.415	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.925	-0.972	22.794	-0.157	-0.157	0.000	0.000	0.000	0.000
85	A	87	PRO	0	-0.009	0.004	18.316	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.001	0.004	19.217	0.028	0.028	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.049	-0.014	17.866	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	90	GLN	0	0.017	-0.008	18.574	0.046	0.046	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.028	-0.017	18.700	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.746	-0.809	15.795	-0.409	-0.409	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.943	-0.982	18.777	-0.175	-0.175	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.039	-0.004	15.088	0.004	0.004	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.895	-0.950	15.060	-0.226	-0.226	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.054	-0.039	13.448	-0.057	-0.057	0.000	0.000	0.000	0.000
95	A	97	MET	0	0.026	0.037	9.219	0.038	0.038	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.961	0.977	9.657	-0.220	-0.220	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.816	-0.905	5.027	1.186	1.186	0.000	0.000	0.000	0.000
98	A	100	ILE	0	-0.001	0.005	3.691	-0.240	0.115	0.001	-0.082	-0.274	0.000
99	A	101	ASP	-1	-0.907	-0.965	2.373	-9.993	-6.484	1.996	-3.006	-2.499	-0.031
100	A	102	SER	0	0.054	0.031	3.305	0.970	1.009	0.012	0.191	-0.242	-0.001
101	A	103	VAL	0	0.047	0.009	5.594	-0.226	-0.226	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.861	-0.928	7.365	-0.610	-0.610	0.000	0.000	0.000	0.000
103	A	105	LEU	0	0.031	0.012	6.702	0.072	0.072	0.000	0.000	0.000	0.000
104	A	106	THR	0	-0.040	-0.035	5.116	-0.241	-0.203	-0.001	0.000	-0.036	0.000
105	A	107	ARG	1	0.761	0.845	6.965	0.668	0.668	0.000	0.000	0.000	0.000
106	A	108	PHE	0	-0.010	-0.008	9.874	0.109	0.109	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.068	-0.013	6.028	0.054	0.054	0.000	0.000	0.000	0.000
108	A	110	PHE	0	0.012	-0.006	9.340	0.081	0.081	0.000	0.000	0.000	0.000
109	A	111	TYR	0	0.002	-0.004	6.956	-0.122	-0.122	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.863	0.929	12.186	0.261	0.261	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.045	-0.023	14.497	0.015	0.015	0.000	0.000	0.000	0.000
112	A	114	ASP	-1	-0.772	-0.843	17.486	-0.169	-0.169	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.018	-0.005	20.564	0.011	0.011	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.013	0.003	23.306	0.003	0.003	0.000	0.000	0.000	0.000
115	A	117	THR	0	-0.007	-0.017	25.299	0.002	0.002	0.000	0.000	0.000	0.000
116	A	118	ALA	0	0.016	0.013	27.734	0.003	0.003	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.015	0.013	25.792	0.000	0.000	0.000	0.000	0.000	0.000
118	A	120	THR	0	-0.100	-0.043	25.443	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	121	THR	0	-0.005	-0.044	19.509	0.004	0.004	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.927	0.977	19.657	0.178	0.178	0.000	0.000	0.000	0.000
121	A	123	PHE	0	0.017	-0.008	15.966	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.810	-0.895	13.971	-0.304	-0.304	0.000	0.000	0.000	0.000
123	A	125	SER	0	0.012	0.007	12.912	-0.079	-0.079	0.000	0.000	0.000	0.000
124	A	126	ALA	0	-0.023	-0.027	7.377	0.027	0.027	0.000	0.000	0.000	0.000
125	A	127	ALA	0	-0.001	0.010	9.310	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.043	-0.022	10.529	0.063	0.063	0.000	0.000	0.000	0.000
127	A	129	PRO	0	0.043	0.015	11.083	0.038	0.038	0.000	0.000	0.000	0.000
128	A	130	GLY	0	-0.006	-0.010	13.664	0.034	0.034	0.000	0.000	0.000	0.000
129	A	131	TRP	0	-0.022	-0.008	16.175	0.031	0.031	0.000	0.000	0.000	0.000
130	A	132	PHE	0	-0.030	-0.028	16.534	-0.037	-0.037	0.000	0.000	0.000	0.000
131	A	133	ILE	0	0.014	0.012	17.061	0.016	0.016	0.000	0.000	0.000	0.000
132	A	134	CYS	0	-0.040	-0.011	20.364	0.013	0.013	0.000	0.000	0.000	0.000
133	A	135	THR	0	0.004	-0.010	24.103	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	136	SER	0	0.083	0.046	27.546	0.005	0.005	0.000	0.000	0.000	0.000
135	A	137	LEU	0	0.021	0.002	30.790	0.001	0.001	0.000	0.000	0.000	0.000
136	A	138	GLN	0	-0.025	-0.006	33.558	0.006	0.006	0.000	0.000	0.000	0.000
137	A	139	PRO	0	0.005	-0.009	33.695	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.930	0.941	33.980	0.082	0.082	0.000	0.000	0.000	0.000
139	A	141	GLN	0	-0.029	0.012	31.548	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	142	PRO	0	0.049	0.014	27.742	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	143	VAL	0	-0.073	-0.031	23.041	0.002	0.002	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.019	0.010	23.353	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	145	ILE	0	-0.009	-0.010	18.094	-0.014	-0.014	0.000	0.000	0.000	0.000
144	A	146	THR	0	-0.011	-0.004	21.255	0.016	0.016	0.000	0.000	0.000	0.000
145	A	147	ASN	0	0.074	0.038	20.945	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	148	GLN	0	-0.021	-0.002	21.997	0.016	0.016	0.000	0.000	0.000	0.000
147	A	149	PRO	0	-0.005	-0.007	21.660	0.006	0.006	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.823	-0.922	24.290	-0.133	-0.133	0.000	0.000	0.000	0.000
149	A	151	GLN	0	-0.022	0.006	27.515	0.008	0.008	0.000	0.000	0.000	0.000
150	A	152	VAL	0	-0.018	-0.024	29.594	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	153	ASN	0	-0.030	-0.015	26.548	-0.008	-0.008	0.000	0.000	0.000	0.000
152	A	154	ILE	0	-0.024	0.001	27.304	0.005	0.005	0.000	0.000	0.000	0.000
153	A	155	ALA	0	0.008	0.008	22.541	-0.010	-0.010	0.000	0.000	0.000	0.000
154	A	156	THR	0	-0.033	-0.019	22.896	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	157	TYR	0	-0.066	-0.058	22.159	0.013	0.013	0.000	0.000	0.000	0.000
156	A	158	LYS	1	0.926	0.966	25.353	0.099	0.099	0.000	0.000	0.000	0.000
157	A	159	LEU	0	0.011	0.012	20.684	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	160	SER	0	0.025	0.013	25.166	0.011	0.011	0.000	0.000	0.000	0.000
159	A	161	GLY	0	-0.020	0.008	25.357	0.000	0.000	0.000	0.000	0.000	0.000

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