FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: MZGNZ

Calculation Name: 1VCA-A-Xray549

Preferred Name: Vascular cell adhesion protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VCA

Chain ID: A

ChEMBL ID: CHEMBL3735

UniProt ID: P19320

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1961450.108148
FMO2-HF: Nuclear repulsion 1882726.892649
FMO2-HF: Total energy -78723.215499
FMO2-MP2: Total energy -78949.339103


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


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


Summations of interaction energy for fragment #1(A:1:PHE)
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.
-191.905-169.79926.823-17.739-31.195-0.124
Interaction energy analysis for fragmet #1(A:1:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.766 / q_NPA : 0.877
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   
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].
3A3ILE00.0210.0123.532-4.532-1.8210.030-1.000-1.7400.000
4A4GLU-1-0.950-0.9695.091-28.236-28.187-0.001-0.007-0.0420.000
25A25THR0-0.019-0.0172.217-4.901-4.3261.565-0.474-1.667-0.005
26A26THR00.0540.0343.980-0.632-0.247-0.001-0.121-0.2640.000
27A27GLY0-0.003-0.0122.228-29.509-27.3446.161-4.668-3.658-0.047
28A28CYS0-0.051-0.0321.943-39.548-33.86413.210-7.077-11.818-0.052
29A29GLU-1-0.897-0.9304.311-23.800-23.7190.001-0.056-0.0260.000
31A31PRO0-0.049-0.0023.959-0.1590.0750.000-0.030-0.2040.000
72A73ALA00.0240.0202.8790.1720.9190.228-0.277-0.698-0.002
73A74THR0-0.029-0.0232.601-6.041-3.9360.782-1.290-1.597-0.020
74A76GLU-1-0.815-0.9074.369-37.427-37.0930.007-0.018-0.3240.001
76A78ARG10.8520.9262.62947.11849.6080.980-0.875-2.596-0.001
77A79LYS10.9360.9463.14022.36923.7270.288-0.412-1.233-0.004
78A80LEU0-0.030-0.0012.536-3.736-0.7273.573-1.435-5.1470.006
79A81GLU-1-0.832-0.9153.973-21.011-20.8320.0000.001-0.1810.000
5A5THR00.011-0.0118.481-0.478-0.4780.0000.0000.0000.000
6A6THR00.0000.04611.2510.4470.4470.0000.0000.0000.000
7A7PRO00.0310.01114.8030.2510.2510.0000.0000.0000.000
8A8GLU-1-0.836-0.90714.518-21.324-21.3240.0000.0000.0000.000
9A9SER0-0.001-0.02314.641-0.686-0.6860.0000.0000.0000.000
10A10ARG10.7590.84217.02811.65311.6530.0000.0000.0000.000
11A11TYR00.009-0.00820.115-0.390-0.3900.0000.0000.0000.000
12A12LEU00.0590.03821.9890.1490.1490.0000.0000.0000.000
13A13ALA0-0.061-0.03924.2110.0090.0090.0000.0000.0000.000
14A14GLN00.0170.00526.2610.4200.4200.0000.0000.0000.000
15A15ILE0-0.029-0.02829.299-0.152-0.1520.0000.0000.0000.000
16A16GLY0-0.038-0.01930.6790.2470.2470.0000.0000.0000.000
17A17ASP-1-0.846-0.90228.533-9.447-9.4470.0000.0000.0000.000
18A18SER0-0.063-0.03625.782-0.319-0.3190.0000.0000.0000.000
19A19VAL00.0320.01721.319-0.109-0.1090.0000.0000.0000.000
20A20SER0-0.032-0.02118.387-0.055-0.0550.0000.0000.0000.000
21A21LEU00.0130.03315.061-0.091-0.0910.0000.0000.0000.000
22A22THR0-0.026-0.03212.867-0.567-0.5670.0000.0000.0000.000
23A23CYS0-0.0340.0107.729-1.451-1.4510.0000.0000.0000.000
24A24SER00.0430.0327.4960.7100.7100.0000.0000.0000.000
30A30SER0-0.005-0.0177.4093.9523.9520.0000.0000.0000.000
32A32PHE00.0020.0035.6092.8552.8550.0000.0000.0000.000
33A33PHE00.010-0.0065.553-2.414-2.4140.0000.0000.0000.000
34A34SER0-0.031-0.0117.9722.2302.2300.0000.0000.0000.000
35A35TRP00.039-0.0019.808-1.123-1.1230.0000.0000.0000.000
36A36ARG10.8460.92510.47318.80118.8010.0000.0000.0000.000
37A37THR00.0480.01414.980-0.423-0.4230.0000.0000.0000.000
38A38GLN0-0.001-0.02117.436-0.173-0.1730.0000.0000.0000.000
39A39ILE0-0.047-0.01318.5940.2300.2300.0000.0000.0000.000
40A40ASP-1-0.918-0.95217.024-13.543-13.5430.0000.0000.0000.000
41A41SER00.0020.02119.6090.3500.3500.0000.0000.0000.000
42A42PRO0-0.020-0.01920.444-0.454-0.4540.0000.0000.0000.000
43A43LEU00.0280.01216.3370.0920.0920.0000.0000.0000.000
44A44ASN0-0.055-0.02120.4520.0980.0980.0000.0000.0000.000
45A45GLY00.0760.04120.9680.1590.1590.0000.0000.0000.000
46A46LYS10.8870.95919.89012.36312.3630.0000.0000.0000.000
47A47VAL00.0600.02914.067-0.254-0.2540.0000.0000.0000.000
48A48THR0-0.085-0.05415.3490.9300.9300.0000.0000.0000.000
49A49ASN0-0.0020.01711.111-0.614-0.6140.0000.0000.0000.000
50A50GLU-1-0.911-0.95712.055-15.078-15.0780.0000.0000.0000.000
51A51GLY00.0180.01611.852-0.859-0.8590.0000.0000.0000.000
52A52THR0-0.036-0.0247.342-0.152-0.1520.0000.0000.0000.000
53A53THR0-0.005-0.0257.592-2.114-2.1140.0000.0000.0000.000
54A54SER00.013-0.0019.5451.3211.3210.0000.0000.0000.000
55A55THR00.0150.00111.029-0.190-0.1900.0000.0000.0000.000
56A56LEU0-0.0140.00314.3670.3410.3410.0000.0000.0000.000
57A57THR0-0.007-0.01516.5160.0660.0660.0000.0000.0000.000
58A58MET0-0.037-0.01120.1390.2240.2240.0000.0000.0000.000
59A59ASN00.0000.01022.9660.3040.3040.0000.0000.0000.000
60A60PRO00.0010.00926.2880.0570.0570.0000.0000.0000.000
61A61VAL0-0.007-0.00524.852-0.168-0.1680.0000.0000.0000.000
62A62SER00.003-0.00927.2990.4750.4750.0000.0000.0000.000
63A63PHE00.0810.01128.084-0.265-0.2650.0000.0000.0000.000
64A64GLY0-0.0330.00127.286-0.081-0.0810.0000.0000.0000.000
65A65ASN0-0.007-0.02522.8460.0470.0470.0000.0000.0000.000
66A66GLU-1-0.806-0.86723.536-10.109-10.1090.0000.0000.0000.000
67A67HIS0-0.0010.00220.217-0.154-0.1540.0000.0000.0000.000
68A68SER0-0.0050.00418.157-0.526-0.5260.0000.0000.0000.000
69A69TYR00.016-0.01515.6680.0780.0780.0000.0000.0000.000
70A70LEU0-0.013-0.01111.990-0.604-0.6040.0000.0000.0000.000
71A72THR00.001-0.0226.015-0.391-0.3910.0000.0000.0000.000
75A77SER0-0.010-0.0037.2220.5830.5830.0000.0000.0000.000
80A82LYS10.8190.9046.96322.08122.0810.0000.0000.0000.000
81A83GLY00.0210.0209.9330.4240.4240.0000.0000.0000.000
82A84ILE0-0.027-0.02113.004-0.350-0.3500.0000.0000.0000.000
83A85GLN0-0.017-0.01016.1090.7420.7420.0000.0000.0000.000
84A86VAL0-0.019-0.01519.557-0.058-0.0580.0000.0000.0000.000
85A87GLU-1-0.770-0.83922.007-10.972-10.9720.0000.0000.0000.000
86A88ILE0-0.050-0.02025.573-0.065-0.0650.0000.0000.0000.000
87A89TYR00.0220.00528.1890.3480.3480.0000.0000.0000.000
88A90SER0-0.042-0.04131.608-0.153-0.1530.0000.0000.0000.000
89A91PHE00.0270.01134.3560.2450.2450.0000.0000.0000.000
90A92PRO00.0580.04236.120-0.018-0.0180.0000.0000.0000.000
91A93LYS10.8320.90337.1727.1667.1660.0000.0000.0000.000
92A94ASP-1-0.842-0.90440.768-7.378-7.3780.0000.0000.0000.000
93A95PRO0-0.040-0.02443.2970.0800.0800.0000.0000.0000.000
94A96GLU-1-0.931-0.95446.270-6.171-6.1710.0000.0000.0000.000
95A97ILE0-0.041-0.03249.4010.0480.0480.0000.0000.0000.000
96A98HIS0-0.029-0.01651.3090.1760.1760.0000.0000.0000.000
97A99LEU0-0.008-0.01655.803-0.001-0.0010.0000.0000.0000.000
98A100SER00.0140.00959.4450.0010.0010.0000.0000.0000.000
99A101GLY00.0070.00662.6080.0860.0860.0000.0000.0000.000
100A102PRO00.0020.00563.281-0.088-0.0880.0000.0000.0000.000
101A103LEU00.0330.01061.3830.0290.0290.0000.0000.0000.000
102A104GLU-1-0.811-0.87765.679-4.337-4.3370.0000.0000.0000.000
103A105ALA0-0.006-0.01069.299-0.023-0.0230.0000.0000.0000.000
104A106GLY0-0.034-0.01770.5460.0660.0660.0000.0000.0000.000
105A107LYS10.8130.89970.3554.3444.3440.0000.0000.0000.000
106A108PRO0-0.015-0.00767.216-0.058-0.0580.0000.0000.0000.000
107A109ILE0-0.022-0.00762.2370.0100.0100.0000.0000.0000.000
108A110THR0-0.015-0.02659.776-0.016-0.0160.0000.0000.0000.000
109A111VAL0-0.016-0.01555.631-0.009-0.0090.0000.0000.0000.000
110A112LYS10.8990.93953.1965.6195.6190.0000.0000.0000.000
111A113CYS0-0.084-0.01249.285-0.013-0.0130.0000.0000.0000.000
112A114SER00.002-0.00948.7710.0480.0480.0000.0000.0000.000
113A115VAL00.0370.01642.297-0.024-0.0240.0000.0000.0000.000
114A116ALA00.0250.00843.5300.0420.0420.0000.0000.0000.000
115A117ASP-1-0.863-0.92338.695-7.410-7.4100.0000.0000.0000.000
116A118VAL00.0280.01938.074-0.242-0.2420.0000.0000.0000.000
117A119TYR0-0.0040.01531.7320.1790.1790.0000.0000.0000.000
118A120PRO00.0340.01933.345-0.176-0.1760.0000.0000.0000.000
119A121PHE00.058-0.00936.2540.0340.0340.0000.0000.0000.000
120A122ASP-1-0.849-0.92037.766-7.814-7.8140.0000.0000.0000.000
121A123ARG10.8600.93035.5188.1188.1180.0000.0000.0000.000
122A124LEU0-0.0360.00038.936-0.034-0.0340.0000.0000.0000.000
123A125GLU-1-0.795-0.89241.493-6.810-6.8100.0000.0000.0000.000
124A126ILE0-0.053-0.02844.240-0.063-0.0630.0000.0000.0000.000
125A127ASP-1-0.754-0.85146.864-6.456-6.4560.0000.0000.0000.000
126A128LEU0-0.005-0.01949.311-0.021-0.0210.0000.0000.0000.000
127A129LEU0-0.023-0.01150.1490.0700.0700.0000.0000.0000.000
128A130LYS10.8470.91454.1835.1265.1260.0000.0000.0000.000
129A131GLY0-0.017-0.00856.8420.0870.0870.0000.0000.0000.000
130A132ASP-1-0.932-0.96953.761-5.929-5.9290.0000.0000.0000.000
131A133HIS0-0.035-0.01554.656-0.038-0.0380.0000.0000.0000.000
132A134LEU0-0.014-0.00851.4260.0160.0160.0000.0000.0000.000
133A135MET0-0.043-0.01754.8510.1280.1280.0000.0000.0000.000
134A136LYS10.8750.93353.7945.6935.6930.0000.0000.0000.000
135A137SER00.004-0.01248.756-0.082-0.0820.0000.0000.0000.000
136A138GLN0-0.073-0.03749.2520.2500.2500.0000.0000.0000.000
137A139GLU-1-0.870-0.91945.416-6.887-6.8870.0000.0000.0000.000
138A140PHE0-0.028-0.04544.2070.2080.2080.0000.0000.0000.000
139A141LEU00.0150.01743.481-0.068-0.0680.0000.0000.0000.000
140A142GLU-1-0.981-0.98644.423-6.524-6.5240.0000.0000.0000.000
141A143ASP-1-0.916-0.96540.663-7.285-7.2850.0000.0000.0000.000
142A144ALA0-0.025-0.00538.6120.1030.1030.0000.0000.0000.000
143A145ASP-1-0.920-0.95539.350-7.120-7.1200.0000.0000.0000.000
144A146ARG10.8830.93236.9197.3937.3930.0000.0000.0000.000
145A147LYS10.8100.88930.6999.1069.1060.0000.0000.0000.000
146A148SER0-0.032-0.04535.782-0.068-0.0680.0000.0000.0000.000
147A149LEU0-0.030-0.01535.067-0.098-0.0980.0000.0000.0000.000
148A150GLU-1-0.851-0.89238.801-6.788-6.7880.0000.0000.0000.000
149A151THR0-0.047-0.02542.098-0.051-0.0510.0000.0000.0000.000
150A152LYS10.8880.97344.1016.7716.7710.0000.0000.0000.000
151A153SER00.004-0.01146.619-0.006-0.0060.0000.0000.0000.000
152A154LEU0-0.0140.01449.5940.0480.0480.0000.0000.0000.000
153A155GLU-1-0.837-0.91251.985-5.403-5.4030.0000.0000.0000.000
154A156VAL0-0.017-0.01455.7450.0000.0000.0000.0000.0000.000
155A157THR00.0090.01658.5250.0290.0290.0000.0000.0000.000
156A158PHE00.0070.00560.555-0.001-0.0010.0000.0000.0000.000
157A159THR00.0040.01163.9110.0630.0630.0000.0000.0000.000
158A160PRO0-0.0090.01064.957-0.031-0.0310.0000.0000.0000.000
159A161VAL00.0210.01366.6380.0910.0910.0000.0000.0000.000
160A162ILE00.0630.02767.845-0.049-0.0490.0000.0000.0000.000
161A163GLU-1-0.885-0.95067.616-4.589-4.5890.0000.0000.0000.000
162A164ASP-1-0.819-0.92363.580-5.076-5.0760.0000.0000.0000.000
163A165ILE0-0.0200.00063.170-0.090-0.0900.0000.0000.0000.000
164A166GLY0-0.013-0.00461.8250.0000.0000.0000.0000.0000.000
165A167LYS10.8440.94059.4664.9614.9610.0000.0000.0000.000
166A168VAL00.0320.01453.8960.0200.0200.0000.0000.0000.000
167A169LEU0-0.005-0.00355.2720.0200.0200.0000.0000.0000.000
168A170VAL00.005-0.00750.163-0.065-0.0650.0000.0000.0000.000
169A172ARG10.8980.92544.9546.5486.5480.0000.0000.0000.000
170A173ALA00.0040.01242.8900.0700.0700.0000.0000.0000.000
171A174LYS10.8290.90940.5616.7686.7680.0000.0000.0000.000
172A175LEU00.0160.00935.1480.1260.1260.0000.0000.0000.000
173A176HIS0-0.026-0.02536.210-0.400-0.4000.0000.0000.0000.000
174A177ILE0-0.019-0.01431.152-0.018-0.0180.0000.0000.0000.000
175A178ASP-1-0.877-0.93929.013-9.864-9.8640.0000.0000.0000.000
176A179GLU-1-0.838-0.86729.507-9.169-9.1690.0000.0000.0000.000
177A180MET0-0.036-0.02324.673-0.630-0.6300.0000.0000.0000.000
178A181ASP-1-0.911-0.95127.984-9.583-9.5830.0000.0000.0000.000
179A182SER0-0.057-0.04028.006-0.407-0.4070.0000.0000.0000.000
180A183VAL0-0.0390.00328.7450.2110.2110.0000.0000.0000.000
181A184PRO0-0.030-0.01731.372-0.029-0.0290.0000.0000.0000.000
182A185THR00.033-0.01134.8270.0500.0500.0000.0000.0000.000
183A186VAL0-0.060-0.03136.4080.2360.2360.0000.0000.0000.000
184A187ARG10.8360.92236.8827.7967.7960.0000.0000.0000.000
185A188GLN0-0.033-0.03541.5620.1340.1340.0000.0000.0000.000
186A189ALA00.0090.02945.295-0.039-0.0390.0000.0000.0000.000
187A190VAL00.016-0.00948.2660.0660.0660.0000.0000.0000.000
188A191LYS10.9070.95751.5045.6555.6550.0000.0000.0000.000
189A192GLU-1-0.901-0.94355.181-5.543-5.5430.0000.0000.0000.000
190A193LEU0-0.044-0.02457.8670.0570.0570.0000.0000.0000.000
191A194GLN00.0220.01261.0820.0850.0850.0000.0000.0000.000
192A195VAL0-0.045-0.02364.113-0.014-0.0140.0000.0000.0000.000
193A196TYR0-0.014-0.00866.0950.0580.0580.0000.0000.0000.000
194A197ILE00.012-0.00370.137-0.005-0.0050.0000.0000.0000.000
195A198SER0-0.016-0.03173.6530.0060.0060.0000.0000.0000.000
196A199PRO-1-0.970-0.96476.006-3.942-3.9420.0000.0000.0000.000