FMO DATABASE

FMODB ID: Y97L2

Calculation Name: 1GCV-B-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

PDB ID: 1GCV

Chain ID: B

ChEMBL ID:

UniProt ID: Q9YGW2

Base Structure: X-ray

Registration Date: 2025-09-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1305861.338482
FMO2-HF: Nuclear repulsion	1249992.779042
FMO2-HF: Total energy	-55868.55944
FMO2-MP2: Total energy	-56031.799321

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:VAL)

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

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.
-45.285	-37.682	5.091	-3.453	-9.241	-0.033

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.829 / q_NPA : 0.913

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	TRP	0	0.016	-0.004	2.725	-6.135	-0.586	2.594	-2.526	-5.616	-0.027
4	A	4	THR	0	0.038	0.009	4.555	3.090	3.134	-0.001	-0.011	-0.033	0.000
69	A	69	ASP	-1	-0.822	-0.875	3.731	-52.789	-52.389	0.007	-0.121	-0.286	0.000
70	A	70	ASP	-1	-0.898	-0.955	4.813	-33.957	-33.918	-0.001	-0.002	-0.036	0.000
72	A	72	LYS	1	0.824	0.879	4.506	49.497	49.610	-0.001	-0.004	-0.108	0.000
122	A	122	LYS	1	0.877	0.926	2.668	42.232	42.797	0.670	-0.204	-1.031	-0.001
123	A	123	PHE	0	-0.040	-0.027	4.680	-4.774	-4.645	-0.001	-0.007	-0.120	0.000
126	A	126	VAL	0	-0.025	-0.020	2.324	-3.261	-2.519	1.825	-0.577	-1.991	-0.005
127	A	127	VAL	0	-0.011	0.001	5.303	1.623	1.645	-0.001	-0.001	-0.020	0.000
5	A	5	GLN	0	-0.013	-0.025	8.118	-1.620	-1.620	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.832	-0.904	11.027	-19.563	-19.563	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.780	-0.871	5.633	-36.666	-36.666	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.846	0.897	6.173	35.344	35.344	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.871	-0.901	9.733	-17.642	-17.642	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.736	-0.836	12.003	-16.424	-16.424	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.001	0.016	7.797	1.110	1.110	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.025	-0.050	12.035	1.685	1.685	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.870	0.921	14.205	18.276	18.276	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.009	-0.005	15.258	1.170	1.170	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.035	-0.041	13.331	0.690	0.690	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.052	-0.013	17.144	0.181	0.181	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.008	0.011	19.753	0.701	0.701	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.034	-0.016	19.771	0.410	0.410	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.799	-0.874	21.242	-11.903	-11.903	0.000	0.000	0.000	0.000
20	A	20	MET	0	0.037	0.006	15.894	0.287	0.287	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.907	0.969	20.365	10.926	10.926	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.008	-0.013	22.875	0.207	0.207	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.015	0.015	19.244	0.110	0.110	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.027	0.002	18.118	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.063	-0.052	21.134	0.271	0.271	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.048	-0.034	24.494	0.449	0.449	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.018	0.013	20.187	0.160	0.160	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.025	-0.009	21.779	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.832	-0.892	23.955	-10.100	-10.100	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.795	0.887	23.026	11.746	11.746	0.000	0.000	0.000	0.000
31	A	31	MET	0	0.029	0.018	21.945	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.040	-0.021	24.286	0.144	0.144	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.909	0.954	27.688	9.588	9.588	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.007	-0.010	25.018	0.280	0.280	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.018	0.016	21.559	-0.094	-0.094	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.029	0.029	26.225	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.077	0.036	24.080	0.429	0.429	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.007	-0.021	23.378	0.051	0.051	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.011	-0.022	26.234	-0.068	-0.068	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.940	0.996	26.959	11.112	11.112	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.030	-0.015	24.542	0.233	0.233	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.011	-0.016	23.488	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.022	0.009	29.604	0.129	0.129	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.891	0.961	28.991	10.510	10.510	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.896	0.956	27.317	10.619	10.619	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.031	0.006	33.092	-0.147	-0.147	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.898	-0.937	33.765	-8.916	-8.916	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.027	-0.008	26.140	-0.232	-0.232	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.949	0.965	29.969	9.657	9.657	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.014	-0.026	26.729	-0.244	-0.244	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.035	0.016	25.719	-0.277	-0.277	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.049	-0.018	26.559	-0.164	-0.164	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.054	0.023	21.358	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.048	0.022	21.581	-0.609	-0.609	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.021	-0.008	20.894	-0.498	-0.498	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.004	0.006	20.528	-0.405	-0.405	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.004	-0.003	16.519	-0.664	-0.664	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.005	0.000	16.356	-1.024	-1.024	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.020	0.009	16.731	-0.589	-0.589	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.005	0.001	14.818	-0.558	-0.558	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.000	-0.005	11.672	-1.366	-1.366	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.004	0.003	12.063	-0.628	-0.628	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.851	-0.943	13.793	-19.124	-19.124	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.007	0.004	8.604	-1.036	-1.036	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.010	-0.012	8.684	-2.257	-2.257	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.895	0.949	10.377	16.281	16.281	0.000	0.000	0.000	0.000
67	A	67	HIS	1	0.829	0.921	9.566	22.770	22.770	0.000	0.000	0.000	0.000
68	A	68	MET	0	0.032	0.029	5.364	-0.742	-0.742	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.012	0.012	5.268	3.239	3.239	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.079	-0.038	8.032	2.302	2.302	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.009	0.008	10.091	1.994	1.994	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.003	-0.011	10.546	1.685	1.685	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.955	0.992	12.582	21.984	21.984	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.828	-0.931	14.263	-15.337	-15.337	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.023	-0.002	13.946	0.908	0.908	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.028	-0.018	13.992	0.650	0.650	0.000	0.000	0.000	0.000
80	A	80	LYS	1	1.004	1.000	16.103	15.961	15.961	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.892	0.966	19.330	13.043	13.043	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.064	-0.066	17.841	1.092	1.092	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.012	0.022	19.475	0.498	0.498	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.886	-0.945	21.356	-13.038	-13.038	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.955	-0.978	23.847	-10.998	-10.998	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.106	-0.062	21.928	0.577	0.577	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.044	-0.007	24.688	0.280	0.280	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.040	-0.032	20.513	0.400	0.400	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.847	-0.913	21.365	-14.255	-14.255	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.044	0.021	16.480	-0.139	-0.139	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.022	0.011	16.929	-0.869	-0.869	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.059	-0.058	18.791	0.309	0.309	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.001	0.017	15.046	0.269	0.269	0.000	0.000	0.000	0.000
94	A	94	HIS	1	0.894	0.931	14.328	16.696	16.696	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.020	0.016	15.691	0.283	0.283	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.049	0.016	17.610	0.575	0.575	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.023	0.007	12.514	0.089	0.089	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.832	-0.899	15.145	-17.098	-17.098	0.000	0.000	0.000	0.000
99	A	99	CYS	0	-0.071	-0.026	16.811	0.752	0.752	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.002	-0.006	15.745	0.520	0.520	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.015	0.016	12.322	0.285	0.285	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.012	-0.005	16.424	0.550	0.550	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.802	-0.880	20.173	-11.123	-11.123	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.016	-0.004	15.334	0.478	0.478	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.025	0.017	19.241	0.350	0.350	0.000	0.000	0.000	0.000
106	A	106	TYR	0	-0.047	-0.022	20.567	0.683	0.683	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.007	-0.002	21.374	0.532	0.532	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.826	0.884	15.908	16.028	16.028	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.853	0.932	22.980	10.810	10.810	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.883	-0.936	22.760	-11.325	-11.325	0.000	0.000	0.000	0.000
111	A	111	CYS	0	-0.022	-0.013	21.880	-0.260	-0.260	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.042	-0.022	14.915	-0.818	-0.818	0.000	0.000	0.000	0.000
113	A	113	THR	0	0.048	0.022	18.293	-0.270	-0.270	0.000	0.000	0.000	0.000
114	A	114	PRO	0	0.039	-0.005	16.850	-0.670	-0.670	0.000	0.000	0.000	0.000
115	A	115	HIS	0	-0.049	-0.018	12.348	-0.909	-0.909	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.016	0.014	12.702	-1.419	-1.419	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.016	-0.006	12.729	-0.454	-0.454	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.037	0.019	10.923	-0.846	-0.846	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.014	-0.004	8.285	-2.608	-2.608	0.000	0.000	0.000	0.000
120	A	120	TRP	0	-0.077	-0.062	7.930	-2.560	-2.560	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.953	-0.966	9.431	-23.459	-23.459	0.000	0.000	0.000	0.000
124	A	124	PHE	0	0.010	-0.022	6.363	-0.643	-0.643	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.924	-0.949	5.911	-35.076	-35.076	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.011	0.000	8.308	2.002	2.002	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.785	-0.867	6.796	-38.116	-38.116	0.000	0.000	0.000	0.000
130	A	130	ALA	0	-0.037	-0.017	7.301	1.795	1.795	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.023	-0.015	9.183	1.891	1.891	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.007	-0.003	12.187	2.432	2.432	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.875	0.948	8.541	30.495	30.495	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.106	-0.065	12.938	0.973	0.973	0.000	0.000	0.000	0.000
135	A	135	TYR	0	-0.009	-0.015	16.417	0.887	0.887	0.000	0.000	0.000	0.000
136	A	136	HIS	-1	-0.938	-0.947	17.023	-14.577	-14.577	0.000	0.000	0.000	0.000

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