FMO DATABASE

FMODB ID: MV53Z

Calculation Name: 3WMD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WMD

Chain ID: A

ChEMBL ID:

UniProt ID: Q846W7

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	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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1292400.523147
FMO2-HF: Nuclear repulsion	1237398.479657
FMO2-HF: Total energy	-55002.043489
FMO2-MP2: Total energy	-55163.554844

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.
-23.92	-16.221	19.586	-7.62	-19.662	-0.07

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 : 0.017 / q_NPA : 0.025

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	GLU	-1	-0.770	-0.899	2.896	-1.547	1.285	0.301	-1.491	-1.642	-0.004
4	A	4	PHE	0	0.095	0.038	5.561	0.631	0.631	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.030	0.000	2.373	-0.147	-1.492	4.365	-0.894	-2.125	0.004
6	A	6	ARG	1	0.850	0.912	2.235	0.607	2.082	3.541	-1.398	-3.618	-0.001
7	A	7	LYS	1	0.901	0.956	4.371	-1.714	-1.639	0.010	0.011	-0.095	0.000
8	A	8	LYS	1	0.824	0.910	6.841	-2.128	-2.128	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.889	0.939	3.386	-1.476	-0.869	0.050	-0.111	-0.546	0.000
10	A	10	ALA	0	0.030	0.014	6.623	-0.494	-0.494	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.019	0.007	9.530	-0.216	-0.216	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.830	-0.886	8.484	0.108	0.108	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.064	0.054	10.558	-0.180	-0.180	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.013	0.011	12.215	-0.082	-0.082	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.843	0.922	10.183	-0.566	-0.566	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.760	0.839	9.627	0.041	0.041	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.031	0.024	15.344	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.088	-0.061	17.984	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.063	-0.030	17.908	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.021	0.019	19.727	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.906	-0.947	18.176	-0.084	-0.084	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.019	0.006	17.964	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.825	-0.904	17.401	-0.136	-0.136	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.009	0.005	14.340	-0.038	-0.038	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.002	-0.001	12.961	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.015	-0.010	13.114	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.869	-0.913	10.294	-0.480	-0.480	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.082	-0.031	8.163	-0.091	-0.091	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.041	-0.044	8.855	0.028	0.028	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.017	0.000	10.379	-0.094	-0.094	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.007	-0.024	11.732	0.084	0.084	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.860	-0.913	13.551	-0.573	-0.573	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.026	0.009	13.298	0.016	0.016	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.013	-0.001	14.839	0.048	0.048	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.018	0.007	15.700	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.800	-0.873	17.984	-0.124	-0.124	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.758	-0.837	19.906	0.044	0.044	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.031	0.028	21.991	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.041	-0.044	19.822	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.003	0.004	22.637	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.037	-0.005	25.572	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.025	-0.023	25.127	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.026	0.000	21.293	0.005	0.005	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.030	0.027	20.811	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.062	-0.055	18.663	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.056	0.037	18.906	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	HIS	0	-0.014	-0.030	18.263	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.842	-0.921	19.468	-0.150	-0.150	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.007	0.010	22.472	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.019	-0.016	16.055	0.018	0.018	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.783	0.884	19.909	0.138	0.138	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.035	0.016	21.504	0.017	0.017	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.075	-0.034	20.860	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	TYR	0	0.008	-0.019	16.507	0.027	0.027	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.816	-0.912	21.820	-0.070	-0.070	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.027	-0.013	24.573	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.003	-0.006	22.315	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.013	-0.012	20.425	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.018	-0.002	24.492	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.034	0.004	27.659	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	HIS	0	-0.044	-0.032	26.297	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.052	-0.014	21.450	0.008	0.008	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.853	0.932	22.396	-0.088	-0.088	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.852	-0.962	18.130	0.146	0.146	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.889	-0.893	20.616	0.138	0.138	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.013	-0.004	16.191	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.015	-0.001	18.286	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.936	-0.979	15.395	0.404	0.404	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.043	-0.008	11.028	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.001	-0.007	11.928	0.028	0.028	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.023	-0.037	7.192	0.121	0.121	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.030	0.047	8.395	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	GLN	0	-0.023	-0.010	7.938	-0.243	-0.243	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.748	-0.876	7.369	-0.778	-0.778	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.042	-0.029	2.899	-0.305	0.181	0.061	-0.165	-0.382	0.000
76	A	76	THR	0	-0.020	-0.006	2.430	-8.505	-5.770	0.999	-1.947	-1.787	-0.026
77	A	77	HIS	0	0.004	-0.005	5.112	0.608	0.710	-0.001	-0.002	-0.098	0.000
78	A	78	ALA	0	-0.031	-0.020	7.008	0.104	0.104	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.012	0.004	8.770	-0.098	-0.098	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.001	-0.001	12.594	0.071	0.071	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.010	0.017	14.842	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.016	-0.015	15.632	0.039	0.039	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.021	-0.011	19.819	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.008	-0.010	22.105	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.004	-0.015	24.049	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.009	0.017	26.097	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.797	-0.882	28.302	0.024	0.024	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.019	-0.023	31.281	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.031	-0.002	33.653	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.053	0.013	30.224	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.029	0.008	27.789	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.065	0.019	31.159	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.035	-0.030	33.651	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.019	0.022	30.563	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.030	0.000	26.988	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.027	-0.014	33.637	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.898	-0.938	35.624	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.823	0.916	30.237	0.026	0.026	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.008	0.006	36.581	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.043	-0.034	29.073	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.007	0.000	33.266	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.816	0.910	36.774	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.061	0.023	39.154	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.008	0.008	37.925	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.849	-0.925	41.034	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.015	0.006	41.235	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	PRO	0	-0.008	-0.006	38.901	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.001	-0.020	38.482	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.013	-0.005	38.211	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.010	0.015	37.295	0.003	0.003	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.863	0.911	28.346	-0.042	-0.042	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.039	-0.008	29.706	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	HIS	0	-0.040	-0.023	26.920	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.911	0.950	21.143	-0.068	-0.068	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.014	0.010	24.435	0.017	0.017	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.030	0.010	20.967	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.045	-0.025	18.208	0.021	0.021	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.018	0.024	14.426	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.014	-0.008	13.075	0.048	0.048	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.022	0.008	9.024	-0.039	-0.039	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.848	0.908	7.903	0.468	0.468	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.046	-0.015	4.620	0.685	1.121	0.014	-0.093	-0.357	0.000
123	A	123	ASP	-1	-0.731	-0.830	5.078	-3.739	-3.563	-0.001	-0.021	-0.154	0.000
124	A	124	ALA	0	-0.001	-0.019	2.022	-4.930	-2.340	2.556	-2.436	-2.710	-0.012
125	A	125	SER	0	-0.027	-0.033	2.697	-4.427	-2.512	1.862	-1.062	-2.715	-0.023
126	A	126	GLY	0	-0.024	-0.023	2.486	-0.621	-0.557	5.648	-2.790	-2.922	-0.004
127	A	127	LEU	0	-0.002	0.013	3.207	4.726	0.277	0.181	4.779	-0.511	-0.004
128	A	128	ILE	0	-0.012	-0.012	6.783	-0.092	-0.092	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.823	0.874	8.867	0.962	0.962	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.040	-0.024	11.018	0.002	0.002	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.020	-0.003	11.780	0.046	0.046	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.837	0.901	14.191	0.098	0.098	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.018	-0.010	16.919	0.040	0.040	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.004	-0.020	17.565	-0.028	-0.028	0.000	0.000	0.000	0.000
135	A	135	TRP	0	-0.015	-0.026	21.221	0.017	0.017	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.018	0.002	24.602	-0.012	-0.012	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.020	-0.021	28.273	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.048	-0.035	29.692	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.825	-0.876	26.912	0.040	0.040	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.030	0.002	28.244	0.007	0.007	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.028	-0.027	30.429	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.013	0.005	32.746	0.002	0.002	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.004	-0.001	33.127	0.001	0.001	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.030	0.013	36.253	-0.003	-0.003	0.000	0.000	0.000	0.000

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