FMO DATABASE

FMODB ID: VYVG1

Calculation Name: 2GC7-D-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c | 2-amino-3-(6,7-dioxo-6,7-dihydro-1h-indol-3-yl)-propionic acid

Ligand 3-letter code: HEC | TRQ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GC7

Chain ID: D

ChEMBL ID:

UniProt ID: P22364

Base Structure: X-ray

Registration Date: 2025-10-05

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
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1362022.394681
FMO2-HF: Nuclear repulsion	1303614.87455
FMO2-HF: Total energy	-58407.520131
FMO2-MP2: Total energy	-58573.858193

3D Structure Molmil

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:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-326.584	-320.031	4.866	-6.498	-4.921	-0.06

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.914

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	GLN	0	-0.066	-0.027	3.503	2.972	4.197	0.015	-0.570	-0.669	0.000
4	A	4	PHE	0	0.034	0.027	4.453	2.688	2.773	-0.001	-0.008	-0.076	0.000
33	A	33	GLU	-1	-0.983	-0.982	3.300	-56.813	-54.952	0.069	-0.976	-0.954	-0.008
34	A	34	THR	0	-0.055	-0.064	2.199	-32.546	-29.114	4.784	-4.936	-3.281	-0.052
35	A	35	GLY	0	-0.027	-0.025	4.479	-1.164	-1.214	-0.001	-0.008	0.059	0.000
5	A	5	PHE	0	-0.016	-0.010	8.265	0.781	0.781	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.068	0.027	11.680	0.517	0.517	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.008	-0.007	15.208	0.105	0.105	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.090	-0.029	17.182	0.813	0.813	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.853	-0.908	18.079	-15.622	-15.622	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.006	0.004	15.482	0.131	0.131	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.094	-0.068	14.476	-1.252	-1.252	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.046	-0.039	10.397	-0.761	-0.761	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.006	0.015	10.658	1.555	1.555	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.024	-0.018	10.969	-2.286	-2.286	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.013	0.000	8.136	0.301	0.301	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.948	-0.970	12.463	-18.035	-18.035	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.927	-0.953	15.618	-14.843	-14.843	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.071	-0.023	14.983	0.585	0.585	0.000	0.000	0.000	0.000
19	A	19	MET	0	-0.020	-0.006	17.027	0.292	0.292	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.962	-0.980	17.975	-14.435	-14.435	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.914	-0.967	18.495	-13.700	-13.700	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.059	0.020	18.460	-0.265	-0.265	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.905	0.950	13.851	16.337	16.337	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.931	-0.965	13.461	-17.811	-17.811	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.012	-0.016	15.290	-0.843	-0.843	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.844	-0.937	13.430	-21.676	-21.676	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.032	0.033	12.033	-1.942	-1.942	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.004	0.007	11.006	-2.194	-2.194	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.791	0.891	9.178	17.881	17.881	0.000	0.000	0.000	0.000
30	A	30	HIS	0	0.006	-0.007	7.427	-4.754	-4.754	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.009	0.017	6.609	-6.008	-6.008	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.011	-0.012	5.565	-4.928	-4.928	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.917	-0.940	6.382	-22.413	-22.413	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.011	-0.017	9.485	-0.498	-0.498	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.008	-0.004	11.944	1.314	1.314	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.034	-0.045	14.323	1.163	1.163	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.048	-0.041	15.004	1.591	1.591	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.852	-0.920	18.063	-13.282	-13.282	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.820	-0.896	19.924	-13.939	-13.939	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.039	-0.051	21.850	0.325	0.325	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-1.001	-0.989	23.662	-12.002	-12.002	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.043	-0.015	20.264	0.260	0.260	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.015	-0.002	23.090	0.210	0.210	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.005	0.000	24.986	0.141	0.141	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.812	-0.886	23.989	-12.453	-12.453	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.017	-0.009	22.545	-0.064	-0.064	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.953	-0.968	24.111	-10.259	-10.259	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.949	-0.981	27.412	-9.960	-9.960	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.007	-0.004	22.229	0.212	0.212	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.018	-0.025	24.562	-0.055	-0.055	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.015	-0.011	26.268	0.266	0.266	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.009	0.008	29.456	0.275	0.275	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.010	-0.004	25.520	0.125	0.125	0.000	0.000	0.000	0.000
57	A	57	CYS	0	-0.083	-0.032	24.748	-0.319	-0.319	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.015	-0.010	27.439	0.321	0.321	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.018	0.003	30.504	0.287	0.287	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.019	-0.022	29.428	0.289	0.289	0.000	0.000	0.000	0.000
61	A	61	HIS	1	0.891	0.919	25.936	11.970	11.970	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.002	0.033	29.720	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.043	-0.028	30.866	-0.348	-0.348	0.000	0.000	0.000	0.000
64	A	64	TYR	0	0.045	0.007	30.381	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.016	0.028	26.689	-0.202	-0.202	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.776	-0.888	28.703	-9.871	-9.871	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.010	0.003	30.958	0.119	0.119	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.775	0.870	31.890	9.539	9.539	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.049	-0.009	33.577	0.201	0.201	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.017	0.007	30.068	-0.078	-0.078	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.003	-0.006	27.184	0.244	0.244	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.060	0.035	28.448	-0.134	-0.134	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.099	-0.061	23.134	-0.319	-0.319	0.000	0.000	0.000	0.000
74	A	74	ASN	0	0.073	0.046	24.089	-0.518	-0.518	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.858	-0.913	26.228	-11.257	-11.257	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.017	-0.002	23.980	-0.518	-0.518	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.086	-0.035	23.979	-0.380	-0.380	0.000	0.000	0.000	0.000
78	A	78	TRP	0	0.044	0.017	21.059	-0.281	-0.281	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.053	-0.029	23.093	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.018	0.004	19.292	0.259	0.259	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.032	0.013	19.233	-0.529	-0.529	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.072	0.029	15.380	-0.228	-0.228	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.016	0.008	14.698	-2.256	-2.256	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.926	-0.950	16.060	-17.668	-17.668	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.019	-0.021	11.517	-1.318	-1.318	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.700	-0.852	11.501	-20.339	-20.339	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.016	0.006	7.169	-0.114	-0.114	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.000	0.021	9.844	0.713	0.713	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.035	0.009	13.282	1.098	1.098	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.059	0.017	10.730	0.884	0.884	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.046	-0.042	11.118	0.436	0.436	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.038	-0.013	13.309	1.473	1.473	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.036	-0.009	16.576	1.080	1.080	0.000	0.000	0.000	0.000
94	A	94	TYR	0	0.011	-0.022	13.826	0.789	0.789	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.006	-0.012	15.690	0.601	0.601	0.000	0.000	0.000	0.000
96	A	96	GLY	0	-0.011	0.013	16.828	0.892	0.892	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.017	-0.027	19.428	-0.510	-0.510	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.026	-0.014	22.119	0.442	0.442	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.014	-0.012	25.825	0.120	0.120	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.023	-0.030	28.210	0.033	0.033	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.008	0.023	21.876	0.247	0.247	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.030	0.015	23.629	-0.373	-0.373	0.000	0.000	0.000	0.000
103	A	103	PRO	0	-0.004	0.005	19.536	-0.131	-0.131	0.000	0.000	0.000	0.000
104	A	104	MET	0	0.020	-0.004	19.264	0.738	0.738	0.000	0.000	0.000	0.000
105	A	105	TRP	0	0.021	0.011	17.031	0.589	0.589	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.005	0.007	18.956	0.105	0.105	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.138	-0.086	22.021	0.775	0.775	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.003	0.015	20.105	0.311	0.311	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.015	-0.023	18.537	-0.771	-0.771	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.016	-0.013	11.553	-0.247	-0.247	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.735	-0.816	15.243	-17.820	-17.820	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.767	-0.857	16.678	-13.470	-13.470	0.000	0.000	0.000	0.000
113	A	113	MET	0	-0.073	-0.003	15.742	-0.063	-0.063	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.030	0.011	11.596	0.198	0.198	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.824	0.897	15.674	14.790	14.790	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.002	-0.026	19.301	0.702	0.702	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.098	-0.029	12.601	0.311	0.311	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.036	0.032	18.215	0.265	0.265	0.000	0.000	0.000	0.000
119	A	119	TRP	0	0.029	0.018	19.325	0.361	0.361	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.045	-0.028	20.473	0.424	0.424	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.733	0.855	15.165	18.714	18.714	0.000	0.000	0.000	0.000
122	A	122	HIS	1	0.866	0.915	20.912	12.676	12.676	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.010	-0.005	23.960	0.579	0.579	0.000	0.000	0.000	0.000
124	A	124	TYR	0	-0.069	-0.013	23.377	0.409	0.409	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.022	-0.024	25.495	0.324	0.324	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.024	-0.005	27.027	0.395	0.395	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.876	-0.957	27.197	-11.464	-11.464	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.057	0.013	24.851	-0.516	-0.516	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.769	0.871	23.229	11.725	11.725	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.884	-0.921	22.168	-13.239	-13.239	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.032	0.033	20.674	-0.467	-0.467	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.037	-0.034	16.213	-0.481	-0.481	0.000	0.000	0.000	0.000
133	A	133	TRP	0	-0.020	-0.003	14.617	-1.157	-1.157	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.006	0.014	15.544	-0.319	-0.319	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.004	-0.019	15.103	-0.031	-0.031	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.861	-0.936	17.365	-15.319	-15.319	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.914	-0.950	19.531	-15.110	-15.110	0.000	0.000	0.000	0.000
138	A	138	GLN	0	0.050	0.033	16.871	0.267	0.267	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.814	0.896	18.013	17.172	17.172	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.065	-0.028	23.015	0.585	0.585	0.000	0.000	0.000	0.000
141	A	141	GLY	0	-0.041	-0.014	25.068	0.545	0.545	0.000	0.000	0.000	0.000
142	A	142	PHE	0	-0.028	0.000	23.855	0.278	0.278	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.061	-0.032	25.984	0.347	0.347	0.000	0.000	0.000	0.000
144	A	144	PRO	0	-0.027	-0.011	28.094	-0.082	-0.082	0.000	0.000	0.000	0.000
145	A	145	PHE	0	0.004	0.004	28.193	0.425	0.425	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.086	-0.055	30.084	0.373	0.373	0.000	0.000	0.000	0.000
147	A	147	PRO	-1	-0.947	-0.954	33.793	-8.695	-8.695	0.000	0.000	0.000	0.000

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