FMO DATABASE

FMODB ID: 943G2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1291040.931953
FMO2-HF: Nuclear repulsion	1236039.271708
FMO2-HF: Total energy	-55001.660245
FMO2-MP2: Total energy	-55163.177683

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.
-19.549	-13.745	14.754	-4.15	-16.406	-0.039

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 : 0.012 / 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	3.143	-1.631	1.310	0.092	-1.519	-1.513	0.003
4	A	4	PHE	0	0.094	0.028	5.807	0.598	0.598	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.024	-0.017	2.720	-0.954	-0.920	2.061	-0.508	-1.586	0.003
6	A	6	ARG	1	0.872	0.930	2.046	0.716	1.676	3.643	-1.385	-3.218	-0.002
7	A	7	LYS	1	0.894	0.948	4.107	-1.828	-1.739	0.010	0.025	-0.125	0.000
8	A	8	LYS	1	0.847	0.933	6.612	-2.213	-2.213	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.904	0.951	3.048	-2.390	-1.471	0.266	-0.202	-0.983	0.000
10	A	10	ALA	0	0.042	0.025	6.194	-0.578	-0.578	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.023	0.004	9.196	-0.250	-0.250	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.862	-0.916	8.037	0.175	0.175	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.054	0.049	10.108	-0.211	-0.211	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.001	0.004	11.683	-0.106	-0.106	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.864	0.933	10.075	-0.659	-0.659	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.782	0.861	9.586	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.022	0.021	14.910	-0.044	-0.044	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.098	-0.068	17.497	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.070	-0.036	17.556	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.024	0.018	19.310	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.893	-0.940	18.076	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.004	-0.004	17.892	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.849	-0.935	17.545	-0.114	-0.114	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.002	0.003	14.300	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.007	0.004	12.790	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.008	0.002	12.958	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.877	-0.921	10.840	-0.400	-0.400	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.104	-0.037	7.846	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.073	-0.069	9.033	0.019	0.019	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.012	0.002	9.826	-0.100	-0.100	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.006	-0.016	11.409	0.092	0.092	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.886	-0.921	13.286	-0.617	-0.617	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.027	0.001	12.994	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.031	-0.017	14.299	0.047	0.047	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.015	0.006	15.530	0.014	0.014	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.817	-0.884	17.709	-0.130	-0.130	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.779	-0.831	19.833	0.075	0.075	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.042	0.016	21.739	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.003	-0.033	19.995	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.015	-0.001	22.807	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.047	-0.017	25.308	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.042	-0.027	25.022	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.015	-0.003	21.188	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.019	0.023	20.938	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.047	-0.038	18.433	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.063	0.038	18.809	0.013	0.013	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.000	-0.027	18.009	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.857	-0.930	19.427	-0.150	-0.150	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.007	0.005	22.724	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.020	-0.011	16.330	0.020	0.020	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.865	0.936	20.279	0.126	0.126	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.023	0.014	21.682	0.017	0.017	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.084	-0.039	20.858	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	TYR	0	0.001	-0.027	16.397	0.029	0.029	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.853	-0.927	21.866	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.031	-0.013	24.705	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.008	-0.002	22.066	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.009	-0.003	20.258	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.018	0.007	24.320	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.032	-0.002	27.286	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	HIS	0	-0.064	-0.038	25.913	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.057	-0.022	21.219	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.881	0.952	22.077	-0.129	-0.129	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.871	-0.963	17.541	0.213	0.213	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.908	-0.913	20.059	0.182	0.182	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.000	-0.009	15.843	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.003	0.005	17.962	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.954	-0.987	15.500	0.493	0.493	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.027	-0.013	10.876	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.018	-0.004	12.006	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.030	-0.033	7.414	0.123	0.123	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.039	0.045	8.826	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	73	GLN	0	-0.012	-0.010	8.533	-0.153	-0.153	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.757	-0.878	8.025	-0.649	-0.649	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.064	-0.037	3.674	-0.197	-0.023	0.000	-0.029	-0.146	0.000
76	A	76	THR	0	-0.025	-0.009	3.580	-3.077	-2.308	0.016	-0.419	-0.365	-0.003
77	A	77	HIS	0	-0.022	-0.027	5.322	0.468	0.564	-0.001	0.000	-0.095	0.000
78	A	78	ALA	0	-0.021	-0.009	7.128	0.159	0.159	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.009	0.008	8.942	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.007	-0.004	12.443	0.095	0.095	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.003	0.013	14.628	-0.072	-0.072	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.014	-0.020	15.355	0.038	0.038	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.013	0.004	19.583	-0.037	-0.037	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.023	-0.002	22.119	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.000	-0.009	23.995	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.007	0.012	25.838	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.780	-0.861	28.152	0.044	0.044	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.007	-0.017	31.011	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.033	0.003	33.217	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.043	0.009	30.036	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.049	0.011	27.716	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.056	0.013	31.162	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.051	-0.033	33.556	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.023	0.025	30.370	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.019	-0.011	26.600	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.026	-0.029	33.268	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.982	-0.965	36.638	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.893	0.953	29.342	0.018	0.018	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.001	0.022	36.199	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.056	-0.045	28.669	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.012	0.008	32.739	0.005	0.005	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.931	0.966	36.255	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.030	0.009	39.158	0.003	0.003	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.022	-0.002	38.264	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.918	-0.956	41.205	0.014	0.014	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.016	0.001	40.553	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	PRO	0	-0.029	-0.019	38.272	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.024	-0.007	37.698	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	THR	0	0.002	0.002	37.688	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.002	0.022	37.000	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.866	0.902	28.781	-0.065	-0.065	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.035	0.000	29.342	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	113	HIS	0	-0.033	-0.015	26.763	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.928	0.963	21.639	-0.097	-0.097	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.013	0.009	24.164	0.020	0.020	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.036	0.015	20.755	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.042	-0.013	18.599	0.028	0.028	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.018	0.014	14.394	-0.035	-0.035	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.027	-0.021	12.679	0.048	0.048	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.015	0.006	8.953	-0.058	-0.058	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.878	0.940	8.062	0.518	0.518	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.047	-0.030	4.359	0.541	0.993	0.014	-0.089	-0.376	0.000
123	A	123	ASP	-1	-0.732	-0.858	4.980	-3.971	-3.796	-0.001	-0.023	-0.151	0.000
124	A	124	ALA	0	-0.004	-0.019	2.517	-5.768	-2.779	0.935	-1.671	-2.253	-0.016
125	A	125	SER	0	-0.023	-0.009	2.992	-4.374	-1.812	0.658	-1.337	-1.883	-0.013
126	A	126	GLY	0	-0.048	-0.038	2.492	-0.599	-0.618	6.899	-3.754	-3.126	-0.006
127	A	127	LEU	0	0.019	0.028	3.011	6.534	0.197	0.162	6.761	-0.586	-0.005
128	A	128	ILE	0	-0.014	-0.002	6.592	-0.117	-0.117	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.818	0.874	8.562	1.007	1.007	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.010	-0.009	10.668	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.007	0.008	11.878	0.062	0.062	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.842	0.915	14.235	0.090	0.090	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.020	-0.014	16.805	0.055	0.055	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.003	-0.016	17.746	-0.036	-0.036	0.000	0.000	0.000	0.000
135	A	135	TRP	0	-0.012	-0.030	21.515	0.017	0.017	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.004	0.003	24.765	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.013	-0.025	28.361	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.022	-0.010	30.324	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.855	-0.900	26.826	0.064	0.064	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.049	-0.016	28.219	0.009	0.009	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.001	-0.004	30.369	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.013	-0.005	32.532	0.003	0.003	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.010	-0.015	32.950	0.000	0.000	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.023	0.016	35.891	-0.004	-0.004	0.000	0.000	0.000	0.000

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